Glossary

A Hyperfine interactions between the electron spin and nuclear spin. A DNA A conformation adopted by dehydrated right-handed double-helical DNA. The molecule is shorter and wider than a B DNA of an equivalent number of base pairs, and the base pairs are tilted relative to a line perpendicular to the helical axis. A site The acceptor (A) site on a ribosome at which the incoming aminoacyl-tRNA binds and is decoded. The site involves both the small and large subunits and binds a complex of elongation factor (EF-Tu in bacteria; EF-1 in archaea and eukaryotes), GTP and the aminoacyl-tRNA. abaxial Facing away from the main growth axis. For example, the underside of a leaf is the abaxial surface, as it faces away from the direction of growth of the stem. ABC proteins Proteins containing the ATP-binding cassette motif. They include several types of transporters. abiotic Of or pertaining to the nonliving. abiotic factors The chemical and physical environmental factors in ecosystems. absorbance optics Optical method for measuring the concentration of a substance by measuring the loss of light due to absorbance of photons by molecules. absorptive endocytosis Internalization of a protein by a cell after the protein has bound weakly and nonspecifically to charged groups at the cell surface. acaricide A chemical treatment applied to animals to kill ticks and prevent transmission of tick-borne pathogens. accelerated run The propulsive run a large bird or a poor flier needs to make during take-off in order to achieve the minimum flight speed. acceptor The larger of two reactants that interact reversibly to form a complex. acceptor arm The end of a tRNA molecule to which an amino acid becomes bound. It contains both the 50 and 30 ends of the tRNA. The 30 -terminal sequence of cytidine-cytidine-adenosine (CCA) overhangs the end, and the terminal A is the site of ‘acceptance’ of the amino acid. acceptor end Four nucleotides at the 30 end of tRNA, which form the site at which the amino acid becomes bound. The last three nucleotides are cytidine-cytidine-adenosine (CCA) and the ribose of the terminal adenosine forms a bond with the amino acid. acceptor stem That part of the acceptor arm of a tRNA molecule in which nucleotide sequences from the 50 and 30 ends are paired to form duplex RNA. accommodation An increase in the threshold for an action potential that occurs in some neurons during a slowly developing or prolonged depolarization. The result is that only a few action potentials are generated during prolonged depolarization above the normal threshold level. Ac/Ds Activator and Dissociation, the two mutable loci originally identified by Barbara McClintock that were able to move in the genome. acetylcholine A chemical neurotransmitter that is released from the ends of certain types of nerve fibre when they are stimulated. It transmits a signal to an adjacent nerve or muscle cell by binding to receptors on the target cell surface. acetylcholine receptor channel A type of receptor for the neurotransmitter acetylcholine, found on skeletal muscle cells and some nerve cells. Also known as the nicotinic acetylcholine receptor, it is made up of a number of protein subunits which form an ion channel through the cell membrane. The channel is opened by the binding of acetylcholine to extracellular sites on the protein. Achaete-scute complex (AS-C) A set of four closely linked genes in Drosophila that are important for the formation of the nervous system. They encode transcription factors of the basic helix-loophelix (bHLH) type. achene A single-seeded dry fruit that does not split open. Acheulian Stone tool industry dominated by handaxes. aciclovir Nucleoside analogue inhibitor of human herpesvirus 1. acid A substance that donates protons (H 1 ions) to water (forming H3O 1 ) or to another acceptor. An acid can also be considered as a compound that dissociates to produce H 1 and its conjugate base. acid–base catalysis Enzymatic catalysis that involves a general acid (a molecular species that can donate a proton, e.g. histidine) and a general base (a molecular species that can accept a proton, e.g. aspartic acid) at the enzyme active site. acid hydrolases Hydrolytic enzymes that have maximum activity at acid pH. In animal cells they are found mainly in lysosomes. acquired immunity See adaptive immunity. acquisition Uptake of virus by a vector. acquisition period Time required for a vector feeding on the host to acquire the virus. acrocentric A chromosome with the centromere near one end and thus having one very short arm and one long arm. acron The most anterior portion of the crustacean body, generally thought not to be homologous to the other segments and usually including the protocerebrum and eyes. acropetal Refers to leaves, flowers, or other structures developing successively along an axis so that the youngest are at the tip. acrosome A cap-like structure covering the anterior part of the sperm head, containing enzymes important for fertilization. actin The protein monomer (G-actin) that polymerizes to form the microfilaments (F-actin) of the eukaryotic cell cytoskeleton and the thin filaments of muscle and other contractile structures in eukaryotic cells. actin-binding proteins Proteins that interact with actin, either to modulate its polymerization and depolymerization, or to link actin microfilaments to each other, to membranes or to other proteins. actin cycle The polymerization/depolymerization of actin filaments, which is coupled to nucleotide hydrolysis and exchange. actinosporean phase The alternate phase of development in myxozoan parasites, which occurs in annelid worms and culminates in the formation of actinosporean spores. actinotroch, actinotrocha The larval form in the Phoronida, a phylum of marine worm-like animals. action potential An electrical impulse that propagates along neurons, and other electrically excitable cells such as muscle, in response to stimulation above a certain threshold. It consists of a self-propagating depolarization of 0.1 V in the cell membrane and carries an informational signal from the cell body to the nerve terminals, where it activates synaptic transmission.

143

Glossary

activating regions Sites on transcription-activating proteins that make direct contact with RNA polymerase during the initiation of transcription at gene promoters. activation Stimulation of a cell, protein or gene to carry out its function. A gene, for example, is said to be activated when it is being transcribed; an ion channel is said to be activated when it is open. activation energy Difference in free energy between the groundstate energy of a substrate and the transition state for the conversion of substrate into product. activator A regulatory molecule, usually a protein, that increases gene expression. active site The part of an enzyme to which substrate binds and where conversion to product is catalysed. active transport Transport of molecules or ions across a membrane against a concentration or electrochemical gradient and which thus requires energy. active zone Region within an axon terminal where synaptic vesicles fuse with the plasma membrane to release neurotransmitter into the synaptic cleft. Proteins involved in the docking and fusion of synaptic vesicles are concentrated at this site. activism Confronting and attempting to improve problematic situations. activity coefficient Ratio of the activity of a solute to its actual molar concentration. It is the fraction of the actual concentration that appears to be present as measured by some physical process. acylenzyme Enzyme to which an acyl group is covalently bonded by the reaction between a nucleophile on the enzyme and an acylating agent. ADA See adenine deaminase deficiency. adaptation (1) A feature of an organism whose presence can be explained by the fact that it served some fitness-enhancing function in the organism’s ancestors, allowing those organisms that possessed the trait in question to out-reproduce those that did not. (2) Changes in the function or behaviour of an organism made in response to changes in the external environment. adaptive Describes a feature or behaviour of an organism that serves to enhance that organism’s fitness. adaptive immunity The antigen-specific immune responses mounted by B and T lymphocytes, which give rise to antibodies, effector T cells and immunological memory specific for the antigen that evoked them. This type of immune response can be mounted against an almost infinite variety of antigens and is found only in vertebrates. Subsequent re-exposure to the antigen produces a more rapid and stronger immune response, due to the presence of immunological memory. adaptive landscape A graphical representation of all possible frequencies of a given set of alleles in a population, which confer different degrees of fitness. ‘Peaks’ and ‘valleys’ in the landscape represent combinations of allele frequencies of high and low fitness, respectively. adaptive radiation Rapid evolutionary divergence of a single phyletic line, e.g. the mammals, into different ecological niches or adaptive zones, with the formation of many different groups. The different groups arise almost synchronously, so that in the fossil record they are perceived as originating at about the same time. adaxial Facing towards the main growth axis. For example, the upper surface of a leaf is the adaxial surface, as it faces towards the direction of growth of the stem.

additive distance The distance between two operational taxonomic units in a phylogenetic tree, which should be equal to the sum of the connecting branch lengths. This assumes a constant rate of substitutions since the time of divergence from the ancestral sequence. addressins Proteins on the surface of endothelial cells which act as ligands for lymphocyte homing receptors, guiding the lymphocyte into the appropriate tissue. adduct (1) A type of DNA damage in which a foreign chemical group is inappropriately attached to the DNA molecule. (2) A product of a chemical addition reaction. adenine (A) Purine base that is one of the four types of bases in RNA and DNA. adenosine deaminase deficiency (ADA) A deficiency of the purine salvage enzyme adenosine deaminase, which results in severe combined immunodeficiency (SCID) due to toxic effects on lymphocyte development. adenosinetriphosphatase See ATPase. adenosine triphosphate (ATP) A small, water-soluble nucleotide that is the principal carrier of energy in cellular metabolism. It is formed by the phosphorylation of adenosine diphosphate (ADP) during the light reaction of photosynthesis and during respiration. adhesins Proteins on the surface of bacteria that mediate adhesion to host cells by binding to receptors on the host cell. adhesion molecules (1) Cell-surface proteins of various types through which cells bind to other cells or to the extracellular matrix. (2) Proteins produced by granulocytes in some invertebrates. They are released by exocytosis and may act as opsonins for infecting antigens. Adhesion molecules are also located on the plasma membrane. adhesion receptor A cell-surface protein that confers mechanical stability on cell–cell or cell–matrix interactions by binding to particular ligands. Also known as adhesion molecule. adipohaemocyte A rarely seen type of haemocyte in invertebrates, characterized by refringent intracytoplasmic lipid droplets. adjuvant Any substance that when mixed with an antigen nonspecifically enhances the immune response to that antigen. admixed population A population originating from the mixing of individuals from two or more ancestral populations, but having an identity of its own distinguishable from the parental populations. adoptive transfer The transfer of immune system cells or cell derivatives into an animal or human to initiate or augment an immune response. adrenal cortex The outer layers of the adrenal gland, which are responsible for synthesis and secretion of corticosteroid hormones (e.g. cortisol, aldosterone). adrenaline (epinephrine) The main catecholamine hormone released by the adrenal medulla. adrenal medulla The inner core of the adrenal gland. It is made up of chromaffin cells, which are developmentally related to adrenergic neurons. They synthesize and secrete the catecholamine hormones – noradrenaline and adrenaline. adventitia External connective tissue layer of a blood vessel wall. adventitious root Root formed on tissue other than young root tissue (apart from the embryonic root). AER See apical ectodermal ridge.

144

Glossary

aerobic metabolism The biochemical processes that occur when an organism is breaking down glucose in the presence of oxygen (aerobic respiration). aerobic respiration The breakdown of glucose by cells in the presence of molecular oxygen. aeropyles External openings in the chambered chorion of tardigrade eggs and in many insect eggs, which permit gas exchange with minimal water loss. aetiological Causative. aetiological mutation Allelic variants directly predisposing to a disease. aetiology The underlying cause of a disease or other pathological condition. afebrile Without fever. afferent Carrying towards. afferent fibre A nerve fibre that is derived from a sensory neuron and connects a peripheral sensory structure to the brain. afferent nerve fibres Nerve fibres that conduct from the periphery to the central nervous system. The term broadly corresponds to sensory fibres. afferent projection The axons that project from a structure to its target, providing input to the target. affinity The binding strength of one molecule for another, considered as the strength of binding of a single binding site to a monovalent ligand, e.g. ligand to receptor, substrate to enzyme or a single antigen-binding site on an antibody to its corresponding antigenic determinant. cf. Avidity afimbrial adhesins Bacterial adhesins that are not associated with fimbrial structures. afterhyperpolarizing potential A brief membrane potential more negative than the resting potential that occurs after an action potential. It is due to the conductances through voltagedependent potassium channels (and calcium-activated potassium channels in some neurons) that open as a result of the action potential. agammaglobulinaemia The absence of immunoglobulins, and hence of antibodies. aganglionosis The absence of parasympathetic ganglion cells in the colon. agar A sulphated polysaccharide rich in galactose- and 3,6anhydrogalactose that is found in the walls of some red algae and used in the food, medicinal and dental industries. agarose gel electrophoresis Electrophoresis carried out in an agarose gel, which is used to separate DNA fragments between 100 bp and 50 kb in length. age rank In a clade of N taxa, each taxon has an age rank from 1 to N reflecting the order of first appearances, with the oldest given the rank of 1 and the youngest a rank of N. agonist A drug or natural ligand that binds to and activates a receptor. AIDS Acquired immune deficiency syndrome. A severe immunodeficiency due to the depletion of T lymphocytes caused by infection with the human immunodeficiency virus (HIV). airway hyperresponsiveness An exaggerated bronchoconstrictor response to various stimuli, which results in bronchospasm and increased obstruction of the airways. algae General name for several taxonomic groups of single-celled or simple multicellular photosynthetic eukaryotic organisms, including the seaweeds.

algaean An outer cell wall component of some chlorococcalean green algae that consists of long polymethylenic chains associated with amide groups and minor amounts of N-alkyl-substituted pyrroles. alginate A polysaccharide composed of D-mannuronic acid and L-glucuronic acid residues in irregular sequences, found primarily in some brown algae. Alginate is used as a thickener and stabilizing agent in the food and pharmaceutical industries. algorithm A set of rules for solving a problem in a finite number of steps. alkaline enzymes Enzymes whose activities are optimal at alkaline pH (410). Alkaliphilic microorganisms produce various extracellular alkaline enzymes, e.g. cellulases, amylases and proteases. alkaliphiles Microorganisms that grow optimally or very well at pH 4 9, often between pH 10 and 12, but which cannot grow, or grow only slowly, at neutral pH. alkaptonuria A mild recessive genetic disorder of humans in which the metabolic breakdown of tyrosine is abnormal because the enzyme homogentisate oxidase is missing. Affected individuals accumulate homogentisic acid, which causes their urine and cartilaginous parts of their bodies to blacken. alkylating agents Reactive chemicals that can transfer alkyl groups to cellular macromolecules, including DNA, RNA and proteins. allele One of two or more alternative forms of a gene that can occupy the same position, or gene locus, on the chromosome. For some genes, one allele is present in the great majority of the population and is considered the normal or ‘wild-type’ form. For other genes, there are numerous different alleles within the population, none of which clearly predominates. allele frequency For a given gene in a given population, the frequency of occurrence of a particular allele, expressed as a fraction of all the alleles. allelic heterogeneity Phenotypic differences or similarities produced by different mutations at a single gene locus. allergen An environmental protein antigen or small-molecule hapten that provokes an allergic reaction in a sensitized individual. On initial encounter (sensitization) the allergen induces the production of allergen-specific IgE antibodies. Subsequent encounter with the allergen induces allergic reactions mediated by these antibodies. Common allergens are the proteins in pollens and other substances that provoke hay fever and asthma. allergy An adverse immune reaction against a common environmental antigen (the allergen). It occurs only in certain individuals. alloantigen An antigen found only in some members of a species. allocation of carbon The flow of assimilated carbon into various compartments or biochemical pathways. allogeneic Describes tissues, cells or molecules from one individual that provoke an immune reaction in another individual of the same species. Allogeneic reactions are due to the genetic differences between individuals, which are reflected in antigenic differences in some of the proteins and other macromolecules they make. allogeneic mouse strains Strains of mice that possess different major histocompatibility genes, and thus produce different major histocompatibility antigens. allograft A graft of tissue to a genetically nonidentical individual of the same species. Allografts are usually rejected, due to the differences in major and minor histocompatibility antigens between unrelated individuals. Also known as a homograft. alloimmune Describes the immune response to a genetically nonidentical graft from an individual of the same species.

145

Glossary

alloimmunization An immune response mounted by an individual to ‘foreign’ antigens from another member of the same species. Examples of antigens that produce alloimmunization are MHC molecules and blood group antigens. allometry (1) Effects of differences in size on the structure and function of organs and organisms. (2) The study of the relationship between size or mass, and the shape, structure and function of an organism or part of an organism. allomorph One of the crystalline forms of a chemical compound. alloparapatric species A species that is thought to have arisen by a two-stage model of speciation in which allopatric speciation is followed by completion of speciation by parapatric hybridization. allopatric Occupying separate geographic areas. allopatric speciation Origin of new species through geographic isolation of two distinct populations. allopatry Geographic isolation of two species or populations. allopolyploid A polyploid that originated by the doubling of the chromosomes of a zygote with two unlike chromosome sets, usually as a result of the hybridization of two species. allosteric Describes an enzyme or other protein that can adopt at least two different tertiary structures that differ in their activity. allosteric effect Change in protein activity produced by the binding of another molecule to a site outside the active site. allosteric effector A molecule that can activate (or inhibit) an enzyme or other protein by binding to a site (the allosteric site) distinct from the active site, and inducing a change in the protein’s conformation. Such effectors can be structurally quite different from the substrate of the enzyme. allosteric proteins See allosteric. allostery The long-range interaction that can occur between spatially distant ligand-binding sites on certain protein molecules, which is due to a change in protein conformation induced by binding of ligand at one of the sites. alopecia Hair loss. alpha-satellite Repetitive DNA sequences present in great abundance in and around the centromeres of all the human chromosomes. alternation of generations (1) Life history characterized by the presence of two phases, one haploid (the gametophyte) and one diploid (the sporophyte). (2) Sequential development of sexual medusoid stages from asexual polyp in jellyfish. alternative splicing The process whereby different proteins can be generated from a single gene by the choice of different splicing sites during the processing of the RNA transcript of the gene. altricial Describes young that are relatively underdeveloped and helpless at birth, with limited sensory abilities and movement. Some features needed for survival may be more advanced. alvarezsaurids Group of flightless, stout-forelimbed birds from the Late Cretaceous that includes the Asian Mononykus olecranus, Shuvuuia deserti and Parvicursor remotus, and the South American Patagonykus puertai and Alvarezsaurus calvoi. alveoli (1) Flattened fluid-filled vesicles typically forming a layer beneath the surface membrane of some protozoa. They form an integral part of the complex outer layer of cells in ciliates. (2) Plural of alveolus. alveolus Individual terminal air sac in the lung. The human lung contains approximately 300 Â 106 alveoli. Alzheimer disease A human degenerative disorder characterized by progressive dementia. amantadine An inhibitor of the Influenza A virus.

amastigote The form of the parasitic protozoan Leishmania in the mammalian stage of infection. amber Fossilized resin, usually from coniferous trees. ambisexuality Occurrence of male and female function in a single individual, either as simultaneous or sequential hermaphroditism. amino acid Organic acid of the general formula RCH(NH2)COOH (a amino acid), where R is a distinctive side chain. They are the building blocks of proteins and precursors of many other organic molecules. The 20 amino acids specified by the genetic code are all L isomers. aminoacyl-adenylate Mixed anhydride formed between the acarboxylate of an amino acid and the a-phosphate of adenylic acid (AMP). aminoacylation Reaction by which an amino acid is attached to the 31 end of its appropriate tRNA. Also known as charging of the tRNA. aminoacyl-tRNA Transfer RNA (tRNA) carrying the appropriate 0 amino acid esterified to the 3-OH of the 3 -terminal adenosine residue of the tRNA. aminoacyl-tRNA synthetases Enzymes that specifically attach amino acids to their appropriate tRNAs (aminoacylation). aminoglycosides A family of antibiotics (mostly naturally occurring products of Streptomyces or Micromonospora species) that inhibit bacterial protein synthesis. Members of the group include streptomycin, gentamicin, tobramycin and amikacin. ammonite Member of an extinct group of the molluscan class Cephalopoda, having a chambered shell. amniocentesis Aspiration of the amniotic fluid that surrounds the fetus, in order to diagnose abnormalities. amniote Vertebrate with an embryo that is surrounded by an amnion. Reptiles, birds and mammals are amniotes amniotic egg An enclosed egg with a shell and amniotic membranes that protect and nourish the developing embryo. Laid by reptiles, birds and egg-laying mammals. Also called a cleidoic egg. amoebal-plasmodial transition Differentiation of the CL strain of amoebae into a multinucleate plasmodium without mating. amoebocyte An immunocyte (haemocyte) of some invertebrates, synonymous with the archaeocyte of Porifera and coelenterates and the granulocyte of Annelida, Mollusca, some Arthropoda and Echinodermata. AMPA receptors A group of receptors that respond to the excitatory neurotransmitter glutamate and are distinguished from other glutamate receptors by their selective response to a-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid (AMPA). amphimixis Type of sexual reproduction in which eggs and sperm come from separate individuals. amphipathic Describes a molecule in which one end is hydrophobic and the other is hydrophilic. amphiphile Surface-active molecule with a hydrophilic group at one end and a hydrophobic chain at the other. amphiphilic Having both water-soluble and water-insoluble regions. amphisbaenians A group of long-bodied, generally limbless squamate reptiles. Their body scales are arranged into rings (annuli) and they superficially resemble stout earthworms. One genus retains front limbs.

146

Glossary

amphotericin B A member of the polyene class of antifungal drugs. It has been used for over 30 years to treat a variety of serious invasive fungal infections. ampullae of Lorenzini Electroreceptor organs located on the heads of sharks. amyloid A proteinaceous deposit arising from incorrectly folded, protease-resistant peptides. It is present in pathologies such as neurofilament tangles in Alzheimer disease. amyloidosis Extracellular deposition of an insoluble protein complex, usually derived from serum proteins, with a fibrillar structure and a characteristic twisted b-pleated sheet conformation. amylolytic Describes starch degradation by hydrolytic enzymes, that is, by amylases. amyloplast A form of mature plastid filled with starch grains and found in plant storage tissues. anabolism Constructive metabolic reactions in which complex molecules are synthesized from simpler ones and tissues built up. anaemia Abnormal condition in which there is a reduced number of red blood cells per unit volume of blood. This reduction may also be expressed as decreased concentration of haemoglobin in the blood, or decreased packed cell volume (haematocrit). anaerobic Occurring in the absence of oxygen. anaerobic glycolysis Metabolic pathway for the breakdown of glucose in the absence of oxygen. anaerobic metabolism The biochemical processes that occur when an organism is breaking down glucose or other respiratory substrate in the absence of oxygen (anaerobic respiration). anaerobic polypeptides (ANPs) A small set of proteins that are synthesized in roots and shoots of young seedlings in an anaerobic environment. anaerobic respiration The breakdown of glucose or other respiratory substrate by cells in the absence of molecular oxygen. analogous Describes features, including proteins, that are similar by convergent evolution. analogy Similarity between characters or character states that is not due to a common origin but is generally explained through independent adaptation. anamorph An asexual, usually haploid yeast culture, of a single mating type. anaphylatoxins Complement peptides C3a, C4a and C5a, which are powerful systemic triggers of inflammation and can thus induce systemic anaphylactic shock. anaphylaxis A rapid life-threatening systemic allergic reaction that can result when a sensitized individual encounters an allergen. It is characterized by tracheal swelling and systemic shock resulting in complete circulatory system shutdown. anaplerotic Associated with biosynthetic biochemical pathways. anaplerotic reaction A reaction which replaces a component that has been removed, usually from a cyclic reaction sequence, for use in biosynthesis. anapsid The primitive condition of the vertebrate skull in which there are no temporal openings. andesite Volcanic lava of intermediate composition in the calcalkaline volcanic suite of rocks. androgen Class of steroid hormones, including the male sex hormone testosterone, produced by the gonads and adrenal glands. anergy (1) A state of nonresponsiveness to antigen. Lymphocytes are said to be anergic when they cannot respond to their specific antigen under optimal conditions of stimulation. (2) A lack of delayed-type hypersensitivity response to antigens to which there is universal exposure.

aneuploid, aneuploidy Having too many or too few chromosomes, or chromosome segments, compared to the normal genotype. Usually refers to the presence of an extra copy of a single chromosome (trisomy) or the absence of a single chromosome (monosomy). aneurogenic limbs Limbs of larval Ambystoma that develop in the absence of innervation. aneurysmal Abnormally enlarged or dilated. anf Gene designation for the iron-only nitrogenase system. angiogenesis Formation of new blood vessels. angioplasty A process whereby restenosis of an artery following surgery is prevented by insertion of a balloon device within the artery. angiosperm A plant with seeds that are produced in an ovary. Angiosperms are also known as the flowering plants. 3,6-anhydro ring An internal, cyclic ether formed by formally eliminating HOH between the hydroxyl groups at positions C3 and C6. animal cap In amphibian embryos, the area of smaller, more rapidly dividing cells around the non-yolky animal pole. animal venom Complex mixture of substances produced by an animal in which one or more components are toxins. anlage (plural anlagen) The primordial undifferentiated stage of a structure in an embryo or larva. Annelida, annelids The ringed or segmented worms. A large grouping of mainly marine animals that also contains terrestrial groups such as earthworms and leeches. anomer One of the two isomers (a or b) of a monosaccharide as determined by the stereochemistry at the carbonyl carbon atom. Anopheles A genus of mosquitoes that includes species capable of transmitting malaria parasites to mammals. anorexia Diminished appetite or aversion to food. anoxia The complete absence of oxygen. anoxygenic photosynthesis Type of photosynthesis in which oxygen is not generated. ANPs See anaerobic polypeptides. antagonistic interaction (1) An interaction between two species that results in one of the species increasing its fitness while the fitness of the other is reduced. (2) An interaction of a drug with a receptor that inhibits the usual function of the receptor. antennae The complexes of light-harvesting molecules in photosynthetic systems. anterior Towards the ‘head’ end of an animal. anthelmintic A drug used to eradicate intestinal parasites. anther The organ in a flower in which the pollen, which contains the male gametophytes, is formed. anthocyanidin Red, blue or purple pigments with the basic structure 2-phenylbenzopyrylium (or flavylium) ion, consisting of two benzene rings (A and B) joined by an O-heterocyclic ring. An anthocyanidin combined with one or more sugars forms an anthocyanin. anthropogenic Caused by human activities. anthropoid A general term of primate classification that includes only monkeys, apes and humans. antibiogram The spectrum of susceptibility or resistance of a bacterial strain to multiple different antibiotics. antibiotic peptides Small 2–7 kDa peptides that kill certain microorganisms. In most cases, they bind to phospholipids in the cell membrane, associating and forming pores in the lipid bilayer.

147

Glossary

antibodies Proteins secreted by the immune system in response to an infection or to immunization with a foreign antigen. Antibodies, or immunoglobulins, are highly variable proteins, specific to the antigen that evoked them. They bind to that antigen and aid its destruction and clearance from the body. They are made only by the B lymphocytes of the immune system. An immunoglobulin molecule consists of two heavy (H) and two light (L) chains each containing one variable (V) region, which forms the antigen-binding site, and one (L chains) or two to three (H chains) constant (C) regions. antibody-dependent cell-mediated cytotoxicity (ADCC) Cell killing by natural killer (NK) cells of cells coated with antibodies specific for antigens on the cell surface. anticholinesterase Enzyme that breaks down acetylcholine at synapses, thus limiting its effect after a nerve impulse is passed on. This prevents the target nerve or muscle cell from being continually stimulated. anticipation In genetics, a phenomenon characterized by the earlier onset of an inherited disease in each succeeding generation. The disease is also usually more aggressive in the newest generation. anticipatory immunity See adaptive immunity. anticodon The three consecutive ribonucleotides in a transfer RNA (tRNA) molecule that base pair directly with a complementary codon of three nucleotides in the messenger RNA (mRNA), thus enabling the genetic code to be translated into a sequence of amino acids. antidromic Describes the passage of nerve impulses from the axon terminal of a neuron to its cell body. rather than in the more usual (orthodromic) direction – cell body to axon terminal. antifolate drug Substance that interferes with the synthesis of folate and its derivatives, thereby blocking replication of DNA. antigen Any substance that can be specifically recognized by T and B lymphocytes and elicit an adaptive immune response. Most antigens are proteins, but carbohydrates and nucleic acids can be antigenic. Small molecules can act as antigens if attached to a protein carrier. If an antigen is capable of inducing an immune response on its own, it is also called an immunogen. antigen-binding site The part of an immunoglobulin molecule that binds antigen. An antigen-binding site is formed by the paired variable (V) regions of a heavy and a light chain. Each immunoglobulin monomer thus contains two identical antigenbinding sites. antigen presentation The display of antigenic peptides, derived from processed protein antigens, complexed with major histocompatibility complex (MHC) molecules on the surface of a cell. The complex of peptide and MHC molecule is the form of antigen recognized by T cells. antigenic determinant See epitope. antigenic drift Stepwise changes in the antigenic properties of a protein caused by successive point mutations in the gene for the protein. antigenic shift A major change in the antigenic properties of certain viral protein antigens (e.g. haemagglutinin and neuraminidase in influenza virus) that occurs when the RNA segments of a human strain of the virus reassort or exchange with those from an animal strain of the virus. antigenic site See antigenic determinant. antigenic variation The ability of certain pathogenic microorganisms, such as trypanosomes and some bacteria, to vary their surface antigens from generation to generation and thus evade the immune defences of the host.

antigenicity (1) Degree to which an antigen stimulates an immune response. In this sense the term is synonymous with immunogenicity. (2) Degree to which an antigen reacts with a particular antigen receptor. antigen-presenting cell (APC) A cell displaying antigenic peptide on its surface in a complex with MHC class I or class II molecules, the form of antigen that can be recognized by T cells. The term usually refers to macrophages, dendritic cells and B cells, which also produce co-stimulatory molecules such as the B7 molecules, and are thus able to activate naive T cells specific for the antigen presented. antigen-specific cells T lymphocytes and B lymphocytes that have receptors specific for a particular antigen on their surface. antiglobulin test A means of detecting antibody or complement fragments on red blood cells taken directly from the patient (direct antiglobulin test), or antibody to red blood cells in plasma (indirect antiglobulin test). antihypertensive Able to reduce high blood pressure, applied to drugs. anti-idiotope A binding site within the antigen-binding site of an immunoglobulin or T-cell receptor that is specific for a particular idiotope on a particular immunoglobulin. anti-idiotypic antibody An antibody that is directed specifically against the idiotype unique to another antibody molecule. anti-inflammatory agents Drugs that block or inhibit all or part of the inflammatory reaction. antioxidant Any substance that significantly delays or prevents oxidation of an oxidizable substrate when present at a low concentration compared with that of the substrate. anti-peptide antibodies In biotechnology, antibodies elicited against synthetic peptides. anti-phase Describes two oscillatory systems in which the time between some measured event in each of them is exactly half a cycle. anti-phosphoprotein antibodies Antibodies generated against particular phosphorylation sites of a phosphoprotein that can be used to distinguish between phosphorylated and non-phosphorylated forms of the protein. antiporter A transmembrane protein that couples the transport of two solutes across a membrane in opposite directions. antisense RNA (1) Any RNA complementary to an mRNA and which is able to base pair with the mRNA and block its function. (2) In bacteria, a naturally occurring short, untranslated RNA transcript, often acting as a repressor of plasmid replication. The antisense RNA exerts its effect by binding to a complementary transcript, and modifying its secondary structure or preventing its translation. antisense RNA injection Technique for analysing gene function in Caenorhabditis elegans in which antisense RNA for a particular gene is injected into the gonad of a hermaphrodite worm, and the progeny studied for abnormal phenotypes. antisperm antibodies Immunoglobulins that react with sperm. antitermination Mechanism that suppresses intrinsic transcription termination signals through modification of RNA polymerase activity. antivenin A substance that can block, neutralize or reverse the toxic effects of a venom. antivenom See antivenin. aperture In regard to computed tomography, the hole in the gantry through which the patient is moved as the examination progresses. Ideally, this should be as large as possible, thereby diminishing any sense of claustrophobia.

148

Glossary

apical complex Organelles (rhoptries, micronemes) at the apical end of the invasive stages (merozoite, sporozoite, ookinete) of the malaria parasite. apical ectodermal cap Epidermis covering the distal end of a developing limb in amphibian embryos. It is homologous to the apical ectodermal ridge of chick embryos. apical ectodermal ridge (AER) Thickened ridge of ectoderm at the distal tip of the limb buds in avian and mammalian embryos that is necessary for proximo-distal growth of the limb. It produces fibroblast growth factor signals. apicomplexans Protozoan parasites of the phylum Apicomplexa which are characterized by a set of subcellular organelles located at the apical end of the parasite that have important roles in hostcell invasion. apiculate Describes a lemon-shaped yeast cell. aplacental yolk sac viviparity A form of uterine incubation of a yolk-dependent embryo in which the uterus does not augment yolk stores to provide additional nutrients. apodemes Downward-projecting knobs on the underside of the arthropod exoskeleton, for the attachment of ligaments or muscles, and limb bases. apolipoprotein The protein component of the complexes of lipid and protein carried in blood plasma. apomorphic Describes an evolutionarily novel character that has appeared in the phylogenetic group in question (a derived character), as opposed to primitive or plesiomorphous characters, which are characters inherited by that group. apomorphy See apomorphic. apomixis Asexual reproduction without meiosis and fertilization in plants, which can involve cells other than the ovule. apoplasm Cell walls and other compartments outside the cell membranes. apoptosis A type of physiological cell death in multicellular animals, also known as programmed cell death, in which an internal death programme is activated in the cell. This leads to DNA fragmentation, nuclear condensation and surface changes that result in the dying cell being rapidly phagocytosed by macrophages. Apoptosis is essential in both embryonic and adult tissues to eliminate unwanted or potentially harmful cells and maintain cellular homeostasis. It contrasts with necrosis, which is a lytic form of cell death induced by toxic agents. aposymbiotic host A host whose symbionts have been removed. appetitive conditioning A classical conditioning protocol based on pairing a neutral conditioning stimulus (CS) with a rewarding unconditioned stimulus (US) such as food. AQP See aquaporin. aquaporins Family of water-channel proteins present in the plasma membrane (plasma membrane intrinsic protein, PIP) and tonoplast (tonoplast intrinsic protein, TIP). They are identified by their permeability to water and by the signature Asn-Pro-Ala sequence present in both the amino- and carboxyterminal halves of the molecule. Aquifex pyrophilus Hyperthermophilic rod-shaped bacterium that forms water during growth on hydrogen and oxygen. arabinogalactan A polysaccharide composed primarily of Larabinosyl and D-galactosyl units. In every case, the galactosyl units form the backbone structure, which may be branched or unbranched, with the L-arabinosyl units present as single side units or in short oligomeric chains.

arabinoxylan A polysaccharide composed primarily of L-arabinosyl and D-xylosyl units. In every case, the xylosyl units form the backbone structure, which may be branched or unbranched, with the L-arabinosyl units present as single side units or in short oligomeric chains. arachidonic acid An unsaturated 20-carbon fatty acid that is the major precursor for prostaglandin and leukotriene (eicosanoids) biosynthesis. arachnoid villi Microscopically visible outpouchings of the arachnoid through the dura mater, protruding into the lumen of venous sinuses. arboreal (1) Living in trees. (2) Adapted for life in the trees. arborescent (1) Describes a plant architecture resembling that of a tree but in which the trunk is not constructed primarily of secondary wood. (2) Branched like a tree, applied e.g. to dendrites of neurons. arboviruses Arthropod-borne viruses, viruses transmitted by insects and other arthropod vectors. arbuscule The much branched ‘tree-like’ hyphal structure produced inside plant cells by certain mycorrhizal fungi (arbuscular mucorrhizal fungi). The major processes of nutrient exchange between the partners are thought to occur across the membranes investing these branches. Archaea A kingdom of prokaryotic organisms that forms one of the two major divisions of the prokaryotic world. Archaea differ as much from other prokaryotes (the Bacteria or eubacteria) as both do from eukaryotes. Many live in extreme conditions. archaeal virus, archaeal phage Virus that infects an archaeal host. Also known as an archaeophage. archaeocyte A motile amoeboid cell found in the mesopyl of sponges. It is nucleolate, capable of phagocytosis and able to develop into any other sponge cell type. Archaeopterygids The most primitive group of birds, including the Late Jurassic Archaeopteryx lithographica from Germany and the Late Cretaceous Rahonavis ostromi from Madagascar. archetype An idealized image of the most fundamental ‘ground plan’ upon which the structure of the group of animals or plants is based. Archosauria A group of amniote (laying shelled eggs) animals that includes not only the living crocodiles and birds, but also dinosaurs, flying reptiles (pterosaurs) and a range of more obscure Permian and Triassic amniotes. Ardipithecus A genus of primitive hominins established in 1995 by Tim White and colleagues. At present it contains only one species, A. ramidus. areoles Spaces between the grooves that pass over the epicuticle of arthropods. aromatase Enzyme that catalyses the conversion of testosterone to oestradiol (also androstenedione to oestrone). ARP complex A complex of proteins, including two actin-related proteins, that is implicated in controlling actin polymerization. arthroconidium A conidium that results from fragmentation of a septate hypha. Also called an arthrospore. Arthus reaction, Arthus response Typical type III hypersensitivity reaction that is induced a few hours after injecting a soluble antigen into the skin of a sensitized animal. The formation of immune complexes causes an inflammatory reaction at the site of antigen injection that is characterized by local oedema, haemorrhage and necrosis. artiodactyl mammals Hoofed mammals with an even number of functional toes on each foot, such as camels, bison and cattle.

149

Glossary

AS-C See Achaete-scute complex. ascites Collection of fluid in the peritoneal cavity. In the context of haemolytic disease of the newborn, ascites is due to congestive cardiac failure. ascocarp A complex fruiting body containing sac-like asci produced by ascomycete fungi. ascomycete A member of the ‘sac’ or ‘cup fungi’, phylum Ascomycotina. They are characterized by the production of sexual spores within a sac-like structure, the ascus, the sacs sometimes being borne in cup-shaped fruiting bodies. ascus The sexual spore-bearing structure in ascomycete fungi, which carries the meiotic products (ascospores). aseptic necrosis Tissue death occurring in the absence of infection. aseptic technique A set of working practices designed to minimize the risk of biological contamination of the work. asexual proliferation Division of a cell without the exchange of genetic material. asexual reproduction Reproduction that does not involve meiosis and fusion of gametes, and which produces progeny genetically identical to the parent. aspergillosis Disease caused by invasive infection by fungi of the genus Aspergillus. asplenia The total absence of a spleen. assembly The stage of viral replication during which all the structural components of the virus come together at one site in the cell to form the basic virus particle. association by colonization The acquisition of a parasite from another host that is not itself ancestral to the present host. association by descent The inheritance of a parasite from a host that is ancestral to the present host. assortative mating A tendency for the characteristics of mating partners to be correlated. For example, large males may tend to mate with large females (positive assortative mating) or palecoloured males with dark-coloured females (negative assortative mating). astragalus The bone in the ankle which has a joint with the tibia (shin bone) proximally and the navicular and cuboid (other ankle bones) distally. astrocyte Non-nervous support cell type that constitutes the ‘connective tissue’ of the central nervous system. ataxia telangiectasia Complex multisystem disorder characterized by neurological impairment, variable immunodeficiency and dilation of ocular and cutaneous capillaries. atomic force microscope A microscope that scans a fine tip (radius 1–20 nm) over a surface and provides images of solids, including biological structures, with atomic accuracy (lateral resolution of 1 nm, vertical resolution 0.1 nm). The image is formed by the continuous measurement of forces between the tip and sample. ATP See adenosine triphosphate. ATPase Adenosinetriphosphatase. Enzyme activity that hydrolyses ATP to give ADP and inorganic phosphate. ATP-dependent H1 pump See H1 ATPase. ATP synthase A membrane-bound protein complex that synthesizes ATP from ADP. It uses the energy stored in the proton electrochemical gradients across the thylakoid membrane of chloroplasts or the inner mitochondrial membrane. atresia A congenital complete closure of a normal body orifice or organ, such as the oesophagus.

atrium (1) Concave ventral side of a zooid, surrounded by the tentacles. (2) Upper thin-walled chamber of the vertebrate heart. atrophy A wasting away or diminution in the size of a cell, tissue, organ or part. attachment In a viral infection, the binding of a virus particle to a specific receptor on the surface of a host cell. attenuated strain A non-pathogenic form of a normally pathogenic microorganism. It retains the capacity to evoke an immune response but lacks the capacity to do harm within the host. Such strains can arise naturally or be produced by prolonged culture in the laboratory. attenuated vaccine A vaccine consisting of a living attenuated strain of the relevant microorganism. Such strains are unable to cause disease but can still cause a limited infection in the host and induce immunity. attenuation (1) Regulated arrest or termination of transcription due to structural alterations of transcriptional pausing or termination sites. (2) See attenuated strain. attractor An object in phase space to which the trajectory ultimately comes (and stays) arbitrarily close. auditory bulla The bony capsule surrounding the sensory structures of the ear. aufwuchs community All the sessile microorganisms living on any animate or inanimate substrate. The term is mostly used in the context of aquatic microorganisms. AUG Adenine-uracil-guanine, the methionine codon used as the start signal for translation. augmentation In short-term synaptic plasticity, an Intermediate phase of enhanced transmission lasting several seconds. aura Warning symptoms that occur before the headache in about 25% of migraine sufferers. It is most often visual, but weakness or numbness of one side of the body and speech disturbance may occur. AURE Adenosine uridine-rich element. A sequence motif conferring instability on mRNA. It is located in the 30 -untranslated region of some mRNAs in mammalian cells. Different AUREbinding proteins (AUBPs) have been identified. australopithecine Informal name describing the species included in the hominin subfamily Australopithecinae. The subfamily includes the genera Ardipithecus, Australopithecus and Paranthropus. Australopithecus The genus name introduced by Raymond Dart in 1925 for the first discoveries of early hominins in Africa. autacoids Substances produced in physiological or pathophysiological responses to injury. They have a brief lifetime and generally act locally, near the site of synthesis. Examples are histamine, bradykinin, and 5-hydroxytryptamine. autapomorphy A derived character, a unique character possessed by a taxon. auto A prefix denoting derived from self or acting on self. See autoantigen, autoantibody, autoimmune disease. autoantibodies Antibodies produced by an individual to constituents of their own tissue. autoantigen A constituent of an individual’s own tissues to which the immune system mounts an immune response. autoclave A pressure vessel used to sterilize materials by use of compressed steam, typically at 0.1 to 0.2 MPa (15 to 30 psig) and a high temperature. autocrine Describes the action of a hormone, cytokine or other secreted factor when it acts on the cell that has produced it.

150

Glossary

autocrine growth factor A secreted polypeptide that acts on the same cell that produced it, stimulating proliferation or differentiation. autograft A transplant of tissue from one site to another in the same individual. autoimmune disease Any disease in which the immune system attacks the body’s own cells. Disorders in this category include acquired haemolytic anaemia, rheumatic fever, insulin-dependent diabetes and myasthenia gravis. autoimmune haemolytic anaemia A condition in which a person produces antibodies to antigens on their own red blood cells, leading to destruction of red cells. autoimmune uveitis A degenerative eye disease characterized by inflammation of the uvea (iris, ciliary body and choroid) which is caused by the generation of antibodies against antigens in these tissues. autoimmunity Immune responses to components of the body’s own tissues, which can result in tissue damage and inflammation leading to autoimmune disease. autolysis Cell lysis catalysed by the cell’s own enzymes. autonomic nervous system The parasympathetic and sympathetic nervous systems, which are responsible for largely unconscious regulation of visceral functions such as heartbeat, smooth muscle contraction and relaxation, and glandular secretion. autonomy The capacity to be self-determining. Autonomous agents are able to direct their lives by making choices in accordance with some underlying value structure that the individual has. autophagic vacuoles Membrane-bounded cellular organelles that contain cytoplasmic contents but no lysosomal hydrolases. autophagosomes Membrane-bounded cellular organelles resulting from fusion of lysosomes and autophagic vacuoles, in which the digestion of contents occurs. autopolyploid A species in which the genome consists of multiple identical copies of a basic set of chromosomes, arising from the doubling of an original chromosome set. autoradiography Photographic process that captures the location of a radioisotope-labelled substance that has been used to probe an in vivo or in vitro system. The radiation emitted by the labelled molecule or structure is recorded on a photographic plate (light microscopy) or on thin, self-supporting film (electron microscopy) autoregulation (1) Situation in which an enzyme acts to activate or inhibit its own activity. (2) Process by which a protein inhibits further synthesis of itself. (3) Of blood flow, the ability of blood vessels to respond to chemical and physical signals in their local environment, i.e. non-neuronal signals, and adjust blood flow to capillary beds to meet the local demand. autosomal dominant A mutation or allele of an autosomal gene (a gene on any chromosome other than the X and Y sex chromosomes) that determines the phenotype when only one copy is present in the diploid genome (the heterozygous state). autosomal recessive A mutation or allele of an autosomal gene (a gene on any chromosome other than the X and Y sex chromosomes) that only determines the phenotype when two copies are present in the diploid genome (the homozygous state). autosomal recessive inheritance The pattern of inheritance of a trait that is determined by an autosomal recessive allele. Parents heterozygous for the allele do not show the trait, but for each of their offspring there is a 1 in 4 chance that they will be homozygous for the allele and thus display the trait.

autosomal set One copy of each type of non-sex chromosome in an organism. A normal diploid female mammal, for example, is 2X:2A, meaning that her cells contain two X chromosomes and two autosomal sets (two copies of each autosome). autosome Any chromosome other than the X and Y sex chromosomes. autotoky Type of reproduction characterized by the production of progeny by a single parent. It includes hermaphroditism and parthenogenesis. autotroph, autotrophic organism An organism that uses carbon dioxide as the sole carbon source and can use inorganic sources for the other essential elements such as nitrogen. Autotrophs include the plants and photosynthetic bacteria, which use sunlight as the energy source, and chemoautotrophic bacteria, which use inorganic chemicals as energy sources. Directly or indirectly, autotrophs support all the other organisms in an ecosystem. autotrophic See autotroph. auxotroph A genetic variant, usually of a microorganism, that has nutritional requirements in addition to those of the wild type. In this context the latter is known as a prototroph. auxotrophy Having nutritional requirements in addition to those of the wild type. aversive conditioning A classical conditioning protocol based on pairing a neutral conditional stimulus (CS) with an aversive unconditional stimulus (US) such as an electric shock. avidity The summation of the individual binding strengths, or affinities, when molecules with multiple binding sites bind to each other. An example would be the overall strength of binding when an antibody with multiple binding sites (e.g. IgM) binds to an antigen with multiple identical epitopes. avifauna In palaeontology, an assemblage of fossil birds from a single deposit. avirulence factor (Avr factor) In plant pathology, a product of a pathogen that specifically elicits expression of a dominant resistance gene on a gene-for-gene basis. avirulence gene (Avr gene) In a plant pathogenic microbe, a gene that specifies an avirulence factor. avirulent A form of an infectious agent that does not cause significant disease. avulsion Tearing away or forcefully extruding a segment of bone or other tissue. axillary Pertaining to, or situated near, the axilla, or armpit. axis formation Formation of the main body axis, which occurs early in development. In vertebrate embryos, it refers to the establishment of the prechordal plate and the notochord, the main components of the axial mesoderm. axolemma The membrane surrounding an individual neuron. axon A long thin process (0.5–2.0 mm in diameter) originating from the cell body of a nerve cell (neuron) and specialized to transmit information. It conveys electrical impulses from the cell body to the axon terminals, where the signal is passed on via synapses to other neurons or target cells. axonal transport The active transport of cytoplasmic constituents within the axon. Transport occurs in both directions within the axon. axoneme The core of any cell appendage based on microtubules, such as cilia, axopodia or suctorian tentacles. axon guidance During the development of nervous systems, the response of the highly mobile growth cone of migrating axons to environmental cues that guide them to their targets.

151

Glossary

axopodia Long, stiff, tapering cytoplasmic projections from the surface of certain protozoa. azole Type of antifungal agent introduced over the past 20 years, which is used to treat a range of fungal infections. azygospore A spore that is morphologically similar to a zygospore, but is of asexual origin.

B cell Type of antigen-specific lymphocyte that produces immunoglobulins (antibodies) and is responsible for humoral immunity. It is produced in the bone marrow (or in the bursa of Fabricius in birds) and develops independently of the thymus. After encounter with antigen, B cells differentiate into antibodysecreting plasma cells. B DNA The most common form of double-stranded DNA helix in biological systems. The helix is right-handed and the bases lie at roughly 901 to the helix axis. The helix has distinct major and minor grooves. B lymphocyte See B cell. B1 cells A subpopulation of B cells found in sites such as the peritoneal cavity. Unlike the majority of B cells they are selfrenewing and carry (in humans and mice) the cell-surface marker protein CD5. B2 (or conventional) B cells The vast majority of the B cells found in peripheral lymphoid organs. B800 Bulk bacteriochlorophyll a molecules with absorption maximum at 800 nm. B850 Bulk bacteriochlorophyll a molecules with absorption maximum at 850 nm. BAC Bacterial artificial chromosome. A large-insert cloning system that utilizes a small cloning vector based on the Escherichia coli F factor. It incorporates an antibiotic-resistance marker, cloning sites and rare-cutter restriction sites for mapping. back focal plane The focal plane of a lens that lies behind it when viewed in the direction of illumination. This term is usually used when referring to the objective lens, where the phase ring, carried on the phase plate, is properly found. backprojection Method used to generate a three-dimensional structure from several different two-dimensional images of the object. Bacteria One of the two domains of prokaryotes (the other is the Archaea), comprising most common microbes. bacterial artificial chromosome See BAC. bacterial photosynthesis Type of photosynthesis found in some bacteria, in which light harvesting by photosynthetic pigments is linked, via electron transport, to the generation of an electrochemical proton gradient or reducing equivalent, but without the production of oxygen. bactericidal permeability-increasing protein (BPI) A cationic protein that binds and inactivates lipopolysaccharide in the outer membrane of Gram-negative bacteria, thus killing them. bactericidal Able to kill bacteria. bacteriochlorophylls The bacterial equivalents of plant chlorophylls. bacteriocin A plasmid-encoded protein that is toxic to other bacteria. bacteriocyte Fat-body cells of aphids containing intracellular bacteria as symbionts.

bacteriolytic Able to cause sufficient damage to the bacterial cell wall to cause lysis of the bacterial cell. Lysozyme and penicillin are examples of bacteriolytic molecules. bacteriophage k cI protein A transcription factor encoded by the bacteriophage l genome that regulates phage gene expression during lysogeny. bacteriophage A virus that infects bacteria. Also known as phage. bacteriostatic Able to stop bacterial growth, but not to kill, leaving the bacteria able to resume growth and replication on removal of the bacteriostatic agent bacterium (plural bacteria) A member of the domain Bacteria. baculovirus vector A DNA virus that infects insects and is often used as a vector to express foreign proteins in cultured cells. baculum A bone within the penis. balanced genotype Having the normal number of each gene. A cell with a reciprocal translocation has an abnormal karyotype but retains a balanced genotype. ballistoconidium Any spore that is forcibly discharged. Also called a ballistospore, barbed end The fast-growing end of an actin microfilament. basal lamina A thin sheet of extracellular matrix, composed of proteoglycans and glycoproteins, particularly laminins, that lies immediately underneath an epithelium, or around muscle cells and Schwann cells, separating them from connective tissue. The basal lamina has important functions in controlling cell differentiation, cell polarity and cell division. Also known as basement membrane. basal metabolic rate See basal rate of metabolism. basal plasma membrane Region of the plasma membrane of an epithelial cell on the face of the cell away from the lumen. basal rate of metabolism The rate of metabolism in adult endotherms when they are at rest in a thermally neutral environment after a short period of fasting. It represents the rate of energy expenditure for self-maintenance (homeostatic regulation) measured as oxygen consumption or production of heat or carbon dioxide by resting animals. base (1) A substance that accepts protons from water or another donor. A strong inorganic base is a compound that dissociates, producing hydroxyl (OHÀ) ions. (2) Any of the nitrogen-containing ring compounds (purines or pyrimidines) that are constituents of nucleotides. They are referred to as bases because they can combine with H 1 in acidic solutions. Also called a heterocycle. base modification A change in the chemical structure and/or composition of the purine and pyrimidine bases in RNA or DNA. base pair A pair of complementary nucleotides held together by hydrogen bonding in a double-stranded DNA molecule. In DNA, adenine pairs with thymine and cytosine with guanine. base-exchange reaction An enzymatic reaction in which one class of glycerophospholipids is converted into another by exchange of the polar head group. basement membrane See basal lamina. basic replicon The smallest piece of a plasmid which will replicate to give the normal number of copies. basidiomycete Any fungus of the phylum Basidiomycotina. They are characterized by production of sexual spores (basidiospores) externally on cells known as basidia. The spores are often produced in complex fruit bodies commonly known as mushrooms and toadstools. basidiospore A sexual spore in fungi of the phylum Basidiomycotina. It is borne on the outside of a basidium.

152

Glossary
b-glycosolic linkage Bond between C10 of the sugar ring and the base in a nucleoside or nucleotide, which is b because the base lies above the plane of the sugar. b-lactam antibiotics Naturally occurring or semisynthetic antibacterial compounds characterized by a b-lactam ring that is essential for biological activity. Examples are penicillins, cephalosporins, carbapenems and monobactams. b-lactamases A family of bacterial enzymes that are able to inactivate penicillins, cephalosporins or other b-lactam antibiotics by hydrolysis of the b-lactam ring. b-pleated sheet A regular element of secondary structure in proteins, in which two or more extended strands of the polypeptide chain lie side by side (running either parallel or antiparallel), held together by a regular array of hydrogen bonds between backbone NH and C5O groups, to form a ridged planar surface. The amino-acid side chains alternately face to opposite sides of the sheet. b-sheet structure See b-pleated sheet. bilateral infiltrates Appearance of a localized, ill-defined opacity on both lungs in a chest radiograph, indicating airspace disease. Bilateria, bilaterians Animals with bilaterally symmetrical bodies, or which are descended from phyla of bilaterally symmetrical animals. All present-day bilaterians are triploblasts. bilayer A membrane or biomolecular leaflet consisting of two monolayers of amphiphilic molecules. bilayer defect A disruption in the regular bilayered structure of a biological membrane that must occur for membrane fusion to proceed. biliary contrast agents In radiography, contrast agents that are taken up by the liver. biliary Pertaining to the liver or bile system. binary specification A decision between only two alternative states. binding constant Equilibrium constant for an interaction written as an association reaction. binding function Concentration of ligand bound divided by the total acceptor concentration. binding isotherm Mathematical expression of the relationship between ligand concentration bound to a macromolecule and the free form of the ligand at equilibrium. binding pocket Putative region of a receptor where the ligand is recognized and bound. binding site Site on a macromolecule at which another molecule binds specifically. binomial nomenclature The system of naming organisms created by Swedish naturalist Carolus Linnaeus, in which two Latin names are used, e.g. Homo sapiens. The first name is that of the genus, and the second is the specific name, which distinguishes that species from other species in the genus. biochemical threshold The level at which the mutated DNA load in a cell type causes an apparent biochemical defect. bioconversion The conversion of biomass (organic matter, mostly from plants) into food, feed, biogas or biofertilizer through the activity of living organisms, generally fungi. biodiversity See biological diversity. bioethics The study of ethical issues within biology and the other life sciences, healthcare and medicine. biofacies A rock unit that contains an assemblage of fossils characteristic of a particular environment. biofilm Layers of bacteria, often forming individual consortia, that attach to fluid interfaces or, more frequently solid surfaces, forming microbial communities.

basidium (plural basidia) A cell in fungi of the phylum Basidiomycotina in which karyogamy and meiosis occur and which develops a definite number of basidiospores on its surface following meiosis. basilar impression, basilar invagination Developmental process in which the floor of the posterior fossa of the skull is pushed superiorly by the bony elements of the upper portion of the cervical spine. basolateral membrane The plasma membrane on the nonluminal face of an epithelial cell. Nutrients are transported across the basolateral membrane of absorptive cells to the blood or intercellular space. basophil A type of polymorphonuclear white blood cell. It has receptors for IgE antibodies and is involved in allergic reactions. It contains granules that stain with basic dyes. batholith Large magma chamber that formed at the base of a volcanic chain and later cooled. bauplan The basic body plan or body organization of an animal. Only about 30–40 different bauplans exist, and virtually all were established by the early Cambrian period, 500–600 million years ago. BBP Branch site-binding protein. See splicing factor 1. B-cell antigen receptor (BCR) See B-cell receptor B-cell receptor (BCR) The antigen-specific receptor on B cells. It consists of membrane-bound antigen-specific immunoglobulin complexed with signal-transducing non-immunoglobulin Iga and Igb chains. Individual B cells carry B-cell receptors of a single antigen-specificity. B-cell tolerance The fact that the mature B cells present in an individual do not normally respond to that individual’s own antigens. It arises mainly from the inactivation or death of immature potentially self-reactive B cells when they encounter their specific antigen. Bchla Bacteriochlorophyll a. Bence-Jones protein Light chains of immunoglobulins produced in excess by a malignant monoclonal B-cell line (e.g. in multiple myeloma). benign paroxysmal positional vertigo Common form of vertigo due to canalolithiasis (free-floating heavy debris from otoconia) of the posterior semicircular canal. benthic Living primarily on the sea or lake floor, at the bottom of the water column. benzene ring The ring system composed of six carbon atoms. benzynes A group of intermediates, unstable under most conditions, that result from the removal of two hydrogen atoms from an aromatic hydrocarbon. Berlese–Tullgren funnel See Tullgren funnel. berry Fleshy fruit that does not split open. Bertrand lens A supplementary lens in the optical path of the microscope, between the objective and eyepiece(s), that allows the front focal plane of the condenser and back focal plane of the objective to be viewed by the eyepiece(s). bet-hedging Life-history traits that act to reduce variance in fitness induced by environmental variation. b-glucan A polysaccharide composed of b-D-glucopyranosyl units. The term is used primarily with those polysaccharides in which the b-D-glucopyranosyl units are linked (1-6) and/ or (1-3) and not with cellulose in which the units are linked (1-4).

153

Glossary

bioimmuration Fossilization of soft organisms as moulds in calcareous matter secreted by cemented bivalves or tube-building polychaetes. biolistic transformation Introduction of DNA into cells by highvelocity bombardment with small metallic particles coated with DNA. The term ‘biolistics’ is short for biological ballistics. Also called microprojectile bombardment. biological community A group of one or more populations of plants, animals and other organisms, living in a common space (region). biological diversity The complete range of species, genetic variation, biological communities, and ecosystem processes on Earth, or in a particular designated area. biological species concept The idea that species are groups of interbreeding natural populations that are reproductively isolated from other such groups. bioluminescence Production of light by living organisms. biomimetic matrix An artificial material able to duplicate the biological properties of normal tissue extracellular matrix. bioreactor A device designed to support the growth of mammalian, plant, or microbial cells. Such a device typically provides contact between cells, growth medium and oxygen/air. It may support the growth of either attached cells or cells in suspension. bioremediation The use of organisms or biological products to decontaminate polluted ecosystems. biosurfactant An amphiphilic molecule of biological origin. Such a molecule has the surface-active properties of being able to reduce surface and interfacial tensions. Microorganisms very often make them to emulsify and solubilize n-alkanes. biosynthesis The formation of a natural product in a living system. biotic Of or pertaining to living organisms. biotic factors The effects of living organisms on other living things in ecosystems. biotin–streptavidin A detection system that utilizes the high affinity of streptavidin for biotin. For example, the binding of enzyme-conjugated streptavidin to biotinylated antibodies constitutes a convenient detection system in ELISA. biozone A stratigraphic unit characterized by a fossil species or association. bipedal Describes animals for which a gait using the two hindlimbs only is a significant part of their repertoire of movement. bipedalism The ability to walk on the hindlimbs only. Many extant primates can walk for short periods on their hindlimbs, but only modern humans are well adapted to do so. biramous limbs Arthropod limbs having two rami or branches, i.e. both endopod and exopod. bivalent A pair of synapsed homologous chromosomes, each having two sister chromatids, that appear during prophase and metaphase I of meiosis. bivalves A class of molluscs (phylum Mollusca, class Bivalvia (or Pelecypoda)) including clams, scallops and oysters, which have bivalved, hinged shells, typically with left and right valves showing mirror image symmetry, present from the Cambrian to the present. BLAST Basic Local Alignment Search Tool, a sequence-based search tool developed at the National Center for Biotechnological Information, that compares a given sequence with a database of sequences and produces an optimal local alignment. blastema Mass of proliferating mesenchymal cells that forms at the site of an amputated limb in some animals and can regenerate the severed limb.

blastic development Formation of a conidium by the enlargement of a conidial initial that is distinct from the conidiogenous cell and enlarges before a septa separates the conidium from the conidiogenous cell. blastoconidium A budding cell borne on a pseudomycelium. Also called a blastospore, blastomere identity In some organisms, the descendants of a given blastomere show a complex invariant differentiation pattern with many different cell fates characteristic of that blastomere. blastomeres Cells formed by the first few embryonic cleavages. blastopore In sea urchins and amphibians, the site of movement of cells from the outside to the inside of the embryo during gastrulation. blastula The hollow sphere of cells that results from the cleavage divisions in many animal embryos. It precedes the formation of germ layers. blastulation The development of a blastula. bleaching Loss of symbiotic algae, and hence pigmentation, in corals and other symbiotic reef organisms in response to stress. blepharoplast Basal body of flagellates, typically associated with a flagellum and sometimes additional structures. it is identical to the basal body or kinetosome. blood–brain barrier A selective mechanism that hinders the passage of cells and large molecules, including many antimicrobial agents, from the bloodstream to the cerebrospinal fluid. Bloom syndrome (BS) Disorder characterized by growth retardation, facial erythema and proneness to respiratory tract infections. blot A nitrocellulose or nylon sheet that contains spots of immobilized macromolecules (protein, DNA or RNA) or their fragments. A molecular probe is applied to identify specific components of the spots. blotting General term for the transfer of protein, RNA or DNA molecules from a relatively thick acrylamide or agarose gel to a thin membrane (usually nylon or nitrocellulose) by capillarity or an electric field. blue-light photoreceptor A protein that senses a blue-light signal and transduces this signal to downstream proteins that elicit the biological responses to blue light. body fossil A fossil that preserves part, or all, of the body of an ancient animal or plant. bolide A general term used for an extraterrestrial object that strikes the Earth and explodes, without specifying if the object is a comet, meteor or asteroid. bone marrow Highly vascular cellular substance in the central portion of many bones that synthesizes all the blood cells (erythrocytes, leukocytes and platelets). bone marrow transplantation The correction of a lack (as in immunodeficiencies) or abnormality (as in leukaemia) of blood cells by extracting bone marrow cells from a healthy donor and transfusing them into the patient to replace the defective bone marrow. Unless the patient is immunodeficient, the bone marrow must be matched for tissue type to avoid being rejected. bone-lining cells The primary cell in the periosteal and endosteal surfaces of adult bone, which are, in essence, inactive osteoblasts. book gills Gills of horseshoe crabs and some extinct chelicerates formed by a series of closely spaced cuticular plates (lamellae) and located on appendages of the opisthosoma.

154

Glossary

book lungs Respiratory organs of certain terrestrial chelicerates (scorpions, spiders, whipscorpions) formed by a series of closely spaced cuticular plates (lamellae). The lungs are contained within an air-filled chamber that opens to the outside through a hole. Boolean operators When searching a database with two or more terms, the terms are combined by the operators AND, OR, NOT. The default Boolean operator is AND. borders Well-defined sequences at the extremities of T-DNAs that are cut by the T-DNA processing enzymes. boutons Small synaptic contacts on hair cells. BPA Brooks’ parsimony analysis, a technique for comparing host and parasite cladograms. BPI See bactericidal permeability-increasing protein. brachials The generally smaller, dorsal valve of a brachiopod shell, which supports a lophophore (a tentacle-bearing feeding organ). brachiation Swinging along branches by the arms. bradycardia Severe slowing of the heart rate. brain death A widely accepted standard for the declaration of death based on the death of the whole brain. brain plasticity Change in the output of the brain that depends on experience, and reflects changes in synaptic connections. brainstem That part of the brain located above the spinal cord and comprising the medulla, pons and midbrain. branch migration In general genetic recombination, a step during homologous DNA pairing and strand exchange in which the length of the initial DNA joint is extended. branch site The location within an intron at which a 20 ,50 phosphodiester bond is formed during the first step of splicing. brassinosteroids Plant steroid hormones that are involved in stem elongation and photomorphogenesis. An example is brassinolide. bronchoalveolar lavage fluid Fluid recovered from washings of the lower respiratory tract. bronchodilators Drugs that relax airway smooth muscle, usually resulting in enlargement of the airway lumen, and improved bronchial air flow. bronchospasm Constriction of airway smooth muscles, resulting in narrowed airway lumen size, which reduces the amount of air that can flow through the airways. browser Computer program used for navigation and for viewing information on the World Wide Web. The interface is based on highlighted hypertext links, active words, phrases and graphics that can be clicked on to jump to different information. brush border Microscopic projections of the luminal membrane of intestinal cells. bryozoan ‘Moss animals’ (phylum Bryozoa), marine and freshwater colonial organisms whose colonies are made up of numerous tiny animals, each of which normally bears a lophophore, a crown of ciliated tentacles for filter feeding. Present from the Ordovician to the present. bubble contrast agent A preparation of gas bubbles used to increase ultrasound scatter, and therefore echogenicity in the body. buccal Associated with the foregut (pharynx region). budding compartment The cellular location of virus assembly and budding. buffer Something that resists change. A pH buffer resists a change in the pH of its solution when small quantities of H1 are added (or produced therein) or consumed.

buffer capacity A measure of the degree to which a buffer can resist a pH change. ‘Practical buffer capacity’ is the concentration of H1 that must be added or removed to change the pH by one unit. bulges/bulged-out nucleotides Nucleotides within a stem region that are not base paired, i.e. are located between two helical segments. bulla The bony covering of the middle ear space in mammals. bunodont The condition where cusps of the molar teeth are bulbous, as in humans. buoyancy The upward force of any fluid upon an object immersed in it. byssus Solid mass or threads secreted by a bivalve mollusc to attach itself to a substrate. Sometimes the byssus is calcified, and in most cases it can be renewed if destroyed.

C period The time for a round of DNA replication, from initiation at the origin to completion at the terminus. In Escherichia coli the C period, for cells growing between 20 and 60 min doubling times, is a constant of approximately 40 min. C3 convertase Bimolecular proteolytic enzyme from the classical and alternative complement pathways. It cleaves complement protein C3 into fragments C3a and C3b. C3 pathway Photosynthetic pathway of carbon dioxide reduction and incorporation into carbohydrate in which the first product is the three-carbon compound phosphoglycerate. Most plants use the C3 pathway. C3 photosynthetic carbon reduction cycle See C3 pathway. C4 pathway Photosynthetic pathway in certain types of plant (C4 plants) in which carbon dioxide is preconcentrated in a process involving four-carbon compounds such as malate and aspartate before fixation by the C3 reactions. C5 pathway A pathway for the synthesis of 5-aminolaevulinic acid, a common precursor for tetrapyrroles, from glutamic acid using tRNAGlu. C24 An ecotype of Arabidopsis thaliana. Ca21-ATPase A transmembrane transport protein that hydrolyses ATP and uses the energy released to transport Ca2 1 across a membrane. cachexia General weight loss and wasting occurring in the course of a chronic disease. cadastral gene Any member of a class of floral homeotic genes that repress the activity of other floral homeotic genes. They do not have a positive function in specifying organ identity on their own. cadherins Family of proteins that mediate calcium-dependent cell–cell interactions in animal tissues. caecilians A group (order Gymnophiona) of living amphibians characterized by very elongated limbless bodies and large copulatory organs in the tail region. They are tailless or nearly so. caecum Blind-ended pouch in ruminants formed at the junction between the small and large intestine (equivalent to the rudimentary human appendix), which has the specific function of housing microbes and semidigested food in order to augment assimilation of metabolites. calcite A common mineral constituent of some animal skeletons (e.g. brachiopods, bryozoans, many extinct corals, some clams). It is composed of calcium carbonate (CaCO3), has a rhombohedral or hexagonal crystal symmetry and is more stable than the other polymorph of calcium carbonate, aragonite. It is the main constituent of limestone.

155

Glossary
calcium inhibition Inhibitory effect of Ca21 on actin–myosin interaction, which causes cytoplasmic streaming of plasmodia and amoeboid movement of amoebae. This action of Ca21 is ubiquitous in plants and lower eukaryotes but not in animals. calix The Latin word meaning ‘cup’ from which the name calicivirus was derived. It refers to cup-like structures on the surface of the virus particle that are characteristic of calicivirus morphology. callase An enzyme that degrades the wall of the pollen tetrad and releases the pollen grains. callus Unorganized mass of cells that forms on the surface of a wound in plants, or when a piece of plant tissue is cultured. calnexin Protein found in the endoplasmic reticulum that acts as a molecular chaperone for glycoproteins and assists in proteinfolding pathways. calorimetry Measurement of the amount of energy (heat) liberated by metabolism. calotte (1) The anterior or head region of dicyemid mesozoan parasites, by which they attach to the cephalopod kidney. (2) In vertebrate anatomy, the brain case, that is the cranium minus the face and the cranial base. calreticulin Protein found in the endoplasmic reticulum that acts as a molecular chaperone for glycoproteins and assists in proteinfolding pathways. calvaria In anatomy, the cranium minus the face. calyx (1) The outermost part of a flower, consisting of the sepals. (2) Contacts of sensory neurons that wrap around the entire hair cells. CAM See crassulacean acid metabolism. cancer A general term for any malignant growth. The word derives from the Latin for ‘crab’, as many tumours resemble a crab, with the body represented by the main tumour mass and the claws by the invasive tumour margins. candidiasis Invasive infection caused by species of the fungus Candida. canonical structure A small repertoire of main-chain conformations observed in the antigen-binding sites of antibodies. Most known variations in the amino-acid sequences of antigen-binding sites modify the surface by altering side-chains on these mainchain structures. cap A methyl guanosine found at the 50 end of some RNAs and joined to it by an unusual 50 ,50 triphosphate linkage. All RNAs transcribed by RNA polymerase II (including pre-mRNA), most spliceosomal snRNAs and several other snRNAs are capped. capping (1) The formation of a methylated GTP on the 50 end of eukaryotic mRNA and some other RNAs during their maturation. (2) Binding of a protein to the end of a microfilament of microtubule. capsid The protein coat surrounding the nucleic acid core of a virus. The proteins are virus encoded. capsid protein A protein component of the coat or outer shell of the virus particle. capsule (1) Multiple-seeded fruit of a syncarpous ovary that breaks open by splits or pores. (2) Highly hydrated amorphous material, chiefly polysaccharide, which forms a thick outer coat, outside the cell wall, on some bacteria. captive breeding The breeding of plants or animals in captivity, usually with the aim of reintroducing populations into the wild. carapace Outgrowth of head ectodermal tissue in arthropods, covering and often fusing to the thoracic segments.

carbenes A group of chemical intermediates, unstable in most instances, that contain a divalent carbon atom. carbocations A group of chemical intermediates, unstable under most conditions, that result from the departure of an anion from an organic molecule, or from its protonation. carbon cycle The cycle of carbon on Earth through atmosphere, living organisms, oceans and rock. Carboniferous period The penultimate major division of the Palaeozoic era. carboxylation In plants that photosynthesize via the C4 pathway, the addition of a carbon dioxide molecule to phosphoenolpyruvate to form four-carbon acids in mesophyll cells. carboxysomes Primitive carbon dioxide-fixing organelles present in some bacteria. carcinogenesis The generation of a cancer. The process by which a normal cell is converted into a cancer (tumour) cell. carcinization The evolution of a crab-like form. carcinogen Any chemical or physical agent that can cause cancer. Most carcinogens act by producing mutations in a cell’s DNA, eventually leading to the transformation of this cell into a tumour cell. carcinoma A malignant tumour of epithelial cells. This is the most common type of cancer. cardenolides Derivatives of the plant steroid calotropagenin, which has the lactone ring at position 17, a characteristic of cardiac poisons. cardiac arrhythmias A group of cardiac disorders characterized by irregular cardiac rhythm. There are two types of arrhythmias: tachycardia (the heart beats too rapidly) and bradycardia (the heart rate is too slow). cardiac pacemaker A region of the heart where specialized cardiac cells spontaneously depolarize and set the rhythm and frequency of the heartbeat. carinate Applied to birds having a keel on the sternum (breastbone). carnivore An animal that eats other animals. carotenoids Orange, red and yellow terpenoid pigments in living organisms, that have a photoprotective and structural role. carpel The female reproductive structure in angiosperm flowers that encloses the ovule(s). Carpels can occur either separately or fused with other carpels. carrageenan A sulfated galactose and anhydrogalactose-rich polysaccharide in the walls of red algae, especially the order Gigartinales. It is extracted and used as a gelling agent and stabilizer in the food and pharmaceutical industries. cartilage Tough but flexible skeletal tissue composed of an organic matrix of chondrin. caruncle A fleshy protuberance. cascade Organization of multiple enyzmes in succession within a signalling pathway, each activating the next enzyme in the pathway. case–control study A study in which it is determined whether an exposure to some factor (e.g. increased plasma cholesterol concentration) is different between cases (e.g. individuals with myocardial infarction) compared with controls (individuals without disease). case-fatality The proportion of all cases of a disease who die. Casparian band Modifications (containing suberin and lignin) in the radial cell walls of the root endodermis. caspases A family of aspartate-specific cysteine proteases that mediate the execution phase of cell apoptosis. Caspases are related to mammalian interleukin 1b-converting enzyme (ICE/ caspase-1) and to the nematode apoptotic gene product Ced-3.

156

Glossary

catabolic Degradative. catabolism Metabolic reactions in which substrates are broken down, liberating energy. catalase Enzyme that removes potentially toxic hydrogen peroxide (H2O2) from cells by degrading it to water and molecular oxygen. In animal cells, catalase is found mainly in peroxisomes, and is frequently used as a marker for the peroxisomal compartment. The ‘catalase test’ is used widely in microbiology as a diagnostic test. catalysis Increase in the rate of a chemical reaction achieved by a substance, the catalyst, that remains unchanged after the reaction. In catalysis, the rate of reaction is increased without altering the position of the overall chemical equilibrium. catalysis of elementary steps An increase in reaction rate that results from an interaction of the enzyme and substrate that selectively stabilizes the transition state of the chemical catalytic step. catalyst Any substance that speeds up a chemical reaction while remaining unchanged at the end of the reaction. Enzymes are catalysts. catalytic power The effectiveness of a catalyst, as measured by the rate enhancement that it causes. catalytic RNAs RNAs that are able to catalyse, in the absence of proteins, specific chemical reactions. For natural RNAs, these reactions are usually transesterifications affecting the catalytic RNA itself. catalytic triad A constellation of functional groups at the active site of an enzyme that can work in cooperation to make a reaction proceed more quickly than is possible with any single function acting alone. catarrhine A general term of primate classification that refers to the Old World monkeys, apes and humans. catecholamine A compound consisting of a catechol nucleus (an aromatic structure with two adjacent hydroxyl groups on the benzene ring) and hydrocarbon tail ending in an amine group. The body’s endogenous catecholamines are noradrenaline, adrenaline and dopamine. category A level such as the genus in a formal classification system. catenane Interlinked double-stranded DNA circles, as in the links in a chain. caudal Towards the tail. caveolae Bulb-shaped invaginations at the plasma membrane of ~50 to ~100 nm diameter, distinguished by the presence of oligomers of the protein caveolin and enriched in cholesterol and sphingolipids. They are involved in the transport of small molecules into the cell. cavitary lesions An abnormality on a chest radiograph showing a localized infiltrate with a central lucency (hole) in an otherwise dense infiltrate. CD marker See CD nomenclature. CD molecule See CD nomenclature. CD nomenclature The CD (cluster differentiation) nomenclature system is used to identify specific antigenic structures on blood leukocytes and tissue cells. A cell-surface protein that can be identified uniquely by a set of monoclonal antibodies is designated CD followed by a number, e.g. CD4. CD molecules are often used as markers to distinguish different cell types and stages in differentiation. CD3 A component of the T-cell receptor complex.

CD34 A cell-surface protein present on a small population of haematopoietic cells that includes stem cells and multipotential progenitors. CD4 Cell-surface protein that distinguishes a major subset of T cells. It acts as a co-receptor in conjunction with the T-cell antigen receptor by binding to MHC class II molecules. CD4 T lymphocytes, CD4 T cells One of the two major subsets of T lymphocytes, distinguished by the presence of the co-receptor molecule CD4 on the cell surface. CD4 T cells include cells that activate infected macrophages and the ‘helper’ T cells that provide antigen-specific ‘help’ to activate B cells and other T cells. CD46 Decay-accelerating factor, a cell-surface protein that protects cells from lysis by complement, and also serves as the receptor for measles virus. CD8 Cell-surface protein that distinguishes a major subset of T cells. It acts as a co-receptor in conjunction with the T-cell antigen receptor by binding to MHC class I molecules. CD8 T lymphocytes, CD8 T cells One of the two major subsets of T lymphocytes, distinguished by the presence of CD8 on the cell surface. CD8 T cells are mostly cytotoxic cells responsible for the antigen-specific killing of infected or foreign cells; they may also be involved in inhibiting the activity of other T cells. Also called cytolytic T lymphocytes (CTLs), or cytotoxic or killer T cells. CD26P See P-selectin. CDK See cyclin-dependent kinases. cDNA A DNA of sequence complementary to an RNA. It can refer either to a single-stranded DNA copy of the RNA, or to the double-stranded form of this DNA. Synthesis of cDNA on the RNA template is catalysed by reverse transcriptase. cell banking Preservation of cells in a frozen state. cell body The part of a neuron containing the nucleus, ribosomes and other cytoplasmic components required for cell survival and maintenance. cell cycle stages The intervals between one mitosis (M) and the next are known as gap 1 (G1), DNA synthesis stage (S) and gap 2 (G2). cell cycle The sequence of stages that an actively growing cell passes through between the time it is formed and the time it divides to give two new cells. During this time it doubles its cytoplasmic constituents, replicates its DNA, and finally divides to give two daughter cells. The stages are distinguished by the state of the nuclear DNA within the cell. The cell cycle’s four phases are G1 (first stage of interphase), S phase (period of DNA synthesis), G2 (postsynthetic interphase) and M (mitosis). Also called the cell division cycle. cell envelope All structures outside the cytoplasm in bacteria. It consists of the inner (cell) membrane, the peptidoglycan cell wall, the outer membrane (in Gram-negative bacteria), and the capsule, when present. cell extract The soluble constituents of cells, obtained by breaking cells open and separating out the insoluble material. cell fate specification The point in a cell lineage at which a cell becomes fixed, or determined, in the type or types of cells and tissues its descendants can produce. cell homogenate Buffered suspension containing all cell organelles and subcellular components after the mechanical destruction of tissues or cells. cell invasion Penetration of cells through basement membranes and extracellular matrix.

157

Glossary

cell junctions Structures that hold the faces of neighbouring cells together, especially in an epithelium. Epithelial cell junctions include tight junctions and desmosomes. Other types of cell junction are gap junctions, by which cells can communicate with each other, and septate junctions in insect cells. cell lineage A pedigree of cells produced from an ancestral cell by mitotic divisions. Cells may adopt specific developmental fates because of their unique lineages. cell membrane In bacteria, usually refers to the lipid bilayer membrane immediately surrounding the cytoplasm and under the peptidoglycan cell wall. It is analogous with the plasma membrane of eukaryotic cells. Some types of bacteria have an additional outer bilayer membrane containing lipopolysaccharide, outside the peptidoglycan layer. cell migration Movement of cells over a surface. cell models Cells that have been permeabilized by mild detergents and subsequently incubated in experimental solutions, usually in order to reactivate a living process, e.g. motility. cell signalling Communication between components of an individual cell or between cells through the generation and release of bioactive compounds. cell transformation A change to a state of unrestricted growth in culture, resembling the tumorigenic condition. cell wall In plants, algae, fungi, bacteria, and archaea, the semirigid layer of material lying immediately above the plasma membrane. In plants and some protists, the wall is composed mainly of cellulose. Fungal cell walls are composed mainly of chitin. In bacteria, the cell wall consists chiefly of peptidoglycan. Walls of Gram-positive bacteria consist of a thick layer of peptidoglycan plus secondary polymers such as teichoic acid. Gram-negative walls consist of a thin layer of peptidoglycan, over which is an outer lipid bilayer membrane containing lipopolysaccharide. In archaea, the cell wall can be a simple S-layer, a multi-S-layered complex, or an amorphous matrix of pseudomurein or methanochondroitin. cell-mediated cytotoxicity The direct killing of one cell by another. cell-mediated immunity Immunity mediated by the T lymphocytes of the immune system. It can be transferred to naive individuals by transferring cells from an immunized individual but not by plasma or serum. cell–substratum contacts Sites on a cultured cell at which it is attached to a solid substratum. These sites are distinguished by the formation of specialized cytoskeletal structures. cellular immunity See cell-mediated immunity. cellular oncogene In a eukaryotic cell, a gene that, if activated by a virus or mutation, can cause the cell to become a tumour cell and develop into a tumour. cellular P450 system Membrane-bound enzymes present in the endoplasmic reticulum that convert nonpolar chemicals to watersoluble, excretable forms. cellular responses See cell-mediate immunity. cellulolytic Able to digest cellulose molecules into simpler carbohydrates. cellulose A linear polysaccharide polymer of b-D-glucose, which is deposited in the form of crystalline microfibrils and forms the main component of plant cell walls. cement gland An ectodermal derivative found in amphibian embryos just anterior to the neural plate. It arises as a result of neural induction. The gland secretes a sticky mucous substance that allows embryos to anchor themselves to aquatic plants.

Cenozoic Geological era from 65 million years ago to the present. central cell Cell in the embryo sac of an angiosperm that fuses with one sperm to give rise to the endosperm, a nutritive tissue for the developing embryo. central dogma The information for the amino-acid sequence of a protein resides in the nucleotide sequence of the RNA, which is in turn encoded by the nucleotide sequence of the genes in DNA; in short, ‘DNA makes RNA makes protein’. central nervous system (CNS) The brain and spinal cord. central pattern generator An oscillatory neural network that produces a stereotypical rhythmic motor output. centric fission Reverse process of centric fusion. centric fusion A genetic process whereby two acrocentric chromosomes (in which the centromere is located near the end of the chromosome) are joined in the region of their centromere. centrifugal Away from the axis or centre. centring telescope A telescopic eyepiece that can be inserted in place of an eyepiece to permit alignment of the phase-contrast microscope. An alternative to the Bertrand lens. centriole A specialized, self-replicating microtubule-organizing centre. In animal cells, the mitotic spindle microtubules form between a pair of centrioles. centripetal Towards the axis or centre. centromere Specialized constricted region of a chromosome at which the pair of chromatids in a metaphase chromosome are held together. The centromere divides the chromosome into two arms. It contains the kinetochores, which attach the chromosome to the spindle and ensure correct segregation of chromatids during mitosis and meiosis. cephalic version The turning of the baby in utero by external manipulation so as to change the position (usually from breech) in order to have the head of the baby as the presenting part for delivery. cephalon The head of a trilobite, often semicircular in form, and usually with compound eyes. ceramide A basic building block of all the complex glycosphingolipids. It consists of a sphingosine base in which the amino group is N-acylated with a long-chain fatty acid. cerci Abdominal appendages of insects. cerebellum An upward hemispherical outgrowth from the hindbrain which plays an essential role in motor coordination. cerebral cortex Outer layer of grey matter covering the cerebral hemispheres. cerebrum The most anterior part of the brain, also called the telencephalon. cerophyl A form of dry, highly refined, powdered grass leaves available commercially. It stimulates the growth of bacteria, which can then be used as food by ciliates or other protists. CFTR Cystic fibrosis transmembrane protein. Chagas disease Disease caused by Trypanosoma cruzi, restricted to the New World. chancre The primary infectious syphilis lesion which occurs at the site of inoculation of infection in a person with no previous infection. It is always associated with dependent lymphadenopathy. channels Transmembrane proteins that function as selective pores in the membrane to allow the passage of ions and other solutes. Channels are usually gated, opening as a result of a particular stimulus to let an unlimited number of ions or other solutes through, and then closing again.

158

Glossary

chaperone A protein that interacts with unfolded, often newly synthesized proteins, and assists in their folding to the native state. Chaperones promote folding mainly by suppressing the aggregation of unfolded proteins with one another. Chaperone proteins include GroE, Hsp70 and Hsp90. They are essential for life and are abundant in all cells. chaperonin Any of a class of chaperone proteins that participate in protein folding. chaperone/usher pathway A process in the assembly of bacterial fimbriae that requires a periplasmic protein (the chaperone) that helps fold pilin protein molecules and an outer-membrane protein (the usher) that directs the ordered assembly of pilins. characterization The process of obtaining data on organisms. charging See aminoacylation. ´diak–Higashi syndrome (CHS) A disease characterized by Che decreased pigmentation, abnormal susceptibility to pyogenic infections and neurologic disorders. checkpoint A point in the cell cycle where progression through the cycle is stopped while errors are corrected. chelation The formation of a coordination compound between a metal cation and an anionic ligand. chelicera (plural chelicerae) The first appendage in chelicerates (spiders and their allies). It is typically composed of two or three segments and is specialized for capturing and manipulating food. cheliped In arthropods, a walking leg equipped with a claw. chemical potential (ll) The rate of change of the Gibbs energy (G) of a system with respect to the amount of species i at constant temperature (T), pressure (P) and the amounts of other species present. It is used in derivations, but is replaced by DfGI in calculations. chemoattractant A chemical that attracts bacteria (or other cells or organisms) to move towards it. chemocline The zone between two stable and long-term water layers of different chemistry and specific gravity. chemoheterotrophic growth Growth of an organism on organic compounds, without the use of light as a source of energy. chemokines A superfamily of small secreted proteins that attract, guide and activate white blood cells during immune reactions. chemokinesis An increase in the random motion of a cell in response to a chemical stimulus. chemolithoautotroph Microorganism that obtains energy through chemical oxidation, using inorganic compounds as electron donors, and obtains its cellular carbon from the reduction of carbon dioxide. chemolithoautotrophic Growing on inorganic carbon and energy sources. chemo-organotrophic Using organic material as the source of both energy and carbon for growth. chemorepellant A stimulant that causes bacteria (or other cells or organisms) to move away from it. chemosensation Sensory mechanism whereby an organism recognizes chemicals (water or airborne) in its environment. chemotactic factors Molecules that induce chemotaxis or chemokinesis. chemotactic receptors A subfamily of seven-span G-proteincoupled receptors which bind chemokines and transmit the chemotactic signal to the cells. They are found mainly on leukocytes. chemotaxis Orientation of an organism or cell towards the source of a chemical and its directional movement up a concentration gradient of the chemical.

chemotherapy-induced neutropenia A deficiency of blood neutrophils due to cancer chemotherapy drugs that suppress production of neutrophils in the bone marrow. chert Rock made of extremely fine-grained quartz silicon dioxide. Different colour varieties are known as flint or jasper. chi Crossover hotspot instigator, the DNA recognition sequence (50 GCTGGTGG30 ) for the bacterial RecBCD enzyme. Chi modulates RecBCD activity into a recombination mode, and from double-strand exonuclease mode, which results in elevated recombination at and near Chi sites. chimaera (1) Embryo derived from a composite of two or more zygotes. (2) Any organism that is a composite of cells of two or more genotypes, for example, experimental mouse bone marrow chimaeras are produced by killing the bone marrow and replacing it with bone marrow of a different genotype. chimaeras Cartilaginous fishes related to sharks and rays. chimaeric (1) Describes any organism that is composed of cells of two or more different genotypes. (2) Describes a DNA molecule containing DNA from two or more different sources, e.g. a recombinant DNA. chimaeric chromosomes Chromosomes made by joining together DNA from two or more different chromosomes. chimaeric mice Mice composed of cells of two different genotypes. Such mice may be produced by transgenesis or by the fusion of very early embryos from two different sources. chimaerism The situation in which cells from genetically different individuals coexist in one body. chirality The ‘handedness’ of a molecule, so that it is not superimposable on its mirror-image. chitin A high relative molecular mass polymer of 1:4 linked Nacetyl glucosamine residues. chitinous Containing the polysaccharide chitin (poly-N-acetylglucosamine). chitinozoans Extinct tiny flask or bottle-shaped organisms believed to have been single-celled protistans, and which were an important element of the Devonian zooplankton. chlamydospore A thick-walled asexual spore that develops from a transformed hyphal cell. chloride equilibrium Unequal distribution of chloride on the intracellular and extracellular sides of a cell membrane at which, because of the presence of other nonpermeable ion species and the resting potential, no chloride flux occurs. chloroplast Subcellular chlorophyll-containing organelle in higher plants and algae in which light capture and the fundamental energy transformation processes of photosynthesis occur. It contains a DNA genome which is transcribed in situ and encodes some of the proteins essential for photosynthesis. chlorosis The yellowing of photosynthetic tissues associated with a loss of chlorophyll. chlorosome The nonmembranous light-harvesting structure in green bacteria. choanocyte A cell type in sponges. It has a collar of cytoplasmic tentacles and an apical flagellum and is responsible for generating the water current through the sponge. Choanocytes are typically arranged in groups, making up a choanocyte chamber. choanoderm The inner, or feeding, layer of the body wall of a sponge, composed of choanocytes. cholera Acute gastrointestinal illness resulting from infection with the bacterium Vibrio cholerae. It is characterized by profuse, watery diarrhoea and vomiting, resulting in severe, life-threatening dehydration.

159

Glossary

cholestasis A stoppage in the flow of bile through the biliary tree, before its excretion into the duodenum. cholinergic synapse A synapse at which acetylcholine (ACh) is the neurotransmitter. chondrite A type of stony meteorite that contains numerous small spherules of silicate mineral. A subset, the carbonaceous chondrites, contain several per cent organic carbon. chondroblast Specialized cell that secretes cartilage. Also known as a chondrocyte. chordate A member of the phylum Chordata, which includes vertebrates and a few marine invertebrate groups such as tunicates and amphioxus. chorion The proteinaceous outer shell of many arthropod eggs. chorionic villus sampling Biopsy of the placenta. chromatid One of the two identical copies of a chromosome after replication, while the two copies are still held together at the centromere. chromatin Originally defined by Flemming in 1880 as the deeply staining material present in the interphase nuclei of eukaryotic cells and corresponding to the chromosomes. The term is now used more specifically to refer to the complex of DNA (and small amounts of transcribed RNA) and proteins (histones and nonhistone proteins) of which chromosomes are composed. chromatin diminution Chromosomal fragmentation, followed by the elimination of part of the chromosome during mitosis. chromatin elimination Originally defined by Seiler in 1914 as the elimination of chromatin during the meiotic divisions. This unfortunate term should be replaced by ribonucleoprotein shedding. The term is now used to denote the loss of chromatin in chromatin diminution. chromatin marking system A system of enzymatic machinery in the cell that blocks expression of certain segments of DNA by attaching additional chemical groups to some base pairs in those segments. Chromatin marks are transmitted in cell lineages to create differential gene expression patterns in different cells. chromatography The separation of molecules of different sorts by dissolving them in an appropriate solvent and passing them over a solid support of various types (e.g. paper or a column of packed resin beads). Molecules will be differentially retained on the support on the basis of their size, charge or binding properties, depending on the type of chromatography used. chromophore A chemical group that can absorb light and undergo a conformational change. Such groups mediate biological responses to light. A chemical group that becomes lightabsorbing in the course of a chemical or enzymatic reaction is called a chromogenic group. chromosomal polymorphism The presence of more than one type of chromosomal morphology in a population. chromosomal rearrangement General term for any chromosomal abnormality in which part of the chromosome has been deleted, duplicated, inverted, transposed to another position on the chromosome, or translocated to another chromosome. chromosomal speciation Speciation as a result of chromosomal rearrangements that cause post-mating reproductive isolation. chromosomal translocation Relocation of a chromosomal segment within the chromosomal complement of any cell, usually involving a reciprocal exchange of material between two or more chromosomes.

chromosome A thread-like structure that carries the genetic information in eukaryotic cells. Chromosomes are contained in the nucleus, and each chromosome is composed of a single long DNA molecule complexed with protein. Chromosomes only become visible under the light microscope during mitosis and meiosis, when they become highly compacted. chromosome elimination Elimination of whole chromosomes during mitosis, meiosis or interphase. chromosome inversion Type of chromosomal rearrangement in which a segment of chromosome is inverted and the order of the genes on it reversed. chronic condition A long, continued illness. chronic granulomatous disease (CGD) Immunodeficiency disease resulting from a defect in phagocytosis in neutrophils, macrophages and other myeloid cells. chronostratigraphy The geological time scale as defined by absolute time rather than the relative time scales of lithological and biostratigraphical units. chylomicron Droplet of fat present in the blood or lymph after absorption from the intestine. chylous ascites Ascitic fluid which contains milk-white lymph (i.e. chyle). chyme Pulpy acidic fluid consisting of gastric juices and partly digested food that passes from the stomach into the intestine. cilia (singular cilium) Tiny motile hair-like structures present on a variety of eukaryotic cells, including some sensory receptor cells, and microorganisms. They are microtubule-based, containing a core of microtubules in a stereotypical arrangement. In different cell types, cilia are involved in cell movement, sensory transduction, or the movement of fluid over the cell surface. circadian clock A self-sustaining oscillator system within an organism with a period of about 24 hours, and occurring independently of external synchronizing signals. It organizes various cellular and physiological processes with the day–night cycle. circadian rhythm Any rhythmic biological process within an organism with a period of about 24 hours and occurring independently of external synchronizing signals. Circe A sorceress who lured Ulysses and his men into her palace and turned them into pigs. circular permutation The variable location of DNA termini in a virus population. circularization End-to-end joining of linear DNA molecules to form a circular DNA. circularizing oligonucleotide probes Oligonucleotides that when successfully hybridized can be converted to closed molecules ligated to the target sequences. Also known as ‘padlock probes’. circularly permuted DNA A collection of DNA molecules whose sequences could all be derived from the same circular DNA molecule by cutting it (once) at different points. circulative transmission Persistent transmission of a pathogen during which the pathogen does not replicate in the vector, but is passed through both the digestive and circulatory systems of the vector. circumventricular organs Epithelial organs that line the ventricle of the central nervous system. They are typically composed of neuronal and nonneuronal elements. cirri (singular cirrus) Clusters of individual cilia acting as a unit in locomotion. cis On or affecting the same molecule.

160

Glossary

cis-acting Describes a gene or regulatory element that affects genes located on the same chromosome. cis-acting determinant Describes a component of a DNA/RNA sequence that influences the activity or level of the same sequence. For example, the 30 stem–loop structure that protects an mRNA against exoribonucleases is a cis-acting determinant. cis-acting element A site in the regulatory region of a gene that usually delineates a site of interaction with a gene-regulatory protein. cisternae (singular cisterna) Membrane-bounded disc-shaped sacs that stack to form each individual Golgi body or cisternal stack. cistron A DNA sequence encoding a single polypeptide chain or a single functional RNA molecule. clade A group of species that derives from a single ancestor (monophyletic) and includes all descendants of that ancestor. clade rank In a clade of N taxa, each taxon has an age rank from 1 to N, reflecting the order of first appearances (with the oldest given the rank of 1 and the youngest given a rank of N ). cladistic Phylogenetic ordering of organisms based on the evaluation of individual characters. cladistics A method of working out the phylogeny of organisms by building phylogenetic trees, or cladograms, that group organisms strictly on the relative recency of common ancestry. cladogenesis The generation of new lineages (clades) by speciation. cladogram In phylogenetic systematics (cladistics), a tree-like representation of a phylogenetic hypothesis based on shared apomorphies (synapomorphies) of the taxa included. It depicts basic (i.e. sister taxon) relationships among taxa but lacks information about more specific (i.e. ancestor–descendant) relationships. Clark electrode Electrochemical cell used for the determination of oxygen concentration. classification Ordering of organisms based on a given theory and philosophy. class switch See isotype switch. clastogen A chemical capable of breaking chromosomes. clathrin-coated pits Regions of plasma membrane that are susceptible to sequestration, or endocytosis, due to cytoplasmic-side association with clathrin. claudication Occlusion of blood vessel flow, usually caused by atheromatous plaque formation, leading to ischaemia of tissues. cleidoic egg An enclosed egg incorporating much yolk to nourish the developing embryo. Also called an amniotic egg. climbing fibre Axon of an inferior olivary neuron forming multiple synaptic junctions with a Purkinje cell; each Purkinje cell receives one climbing fibre. cline Variation in a trait along an environmental gradient or across ecotones. clionid A group of marine sponges (phylum Porifera) that perforate (bore into) skeletons of other organisms, making a gallery of holes in which they reside. cloaca In some animals, a common chamber connected to the exterior that receives products from the digestive, urinary and reproductive tracts. clonal expansion The multiplication of a single cell through several divisions to produce a number of identical daughter cells.

clonal rearrangement The case where a large number of lymphocytes contain an identical rearrangement of the immunoglobulin or T-cell receptor genes, usually as a result of proliferation of the cell containing the original rearrangement. clonal selection theory The theory underpinning our present understanding of the adaptive immune response. It requires that individual lymphocytes each have a single unique antigen specificity, and that only those lymphocytes whose receptors match epitopes on the antigen will be activated to proliferate and achieve effector status. Originally formulated as a theory of antibody formation by F. Macfarlane Burnet. clonal selection The activation and proliferation of small preexisting clones of antigen-specific lymphocytes during the course of an adaptive immune response. clonal tumour Malignancy in which all cells share a single common genetic ancestor. clonality The evolution and spread of a single gene, a single group of genes or a single strain of a bacterium locally or worldwide in response to environmental changes. clone (1) A group of cells that are all descended from the same progenitor cell and thus have the same genetic make-up. (2) A group of individuals, derived by asexual reproduction, that are genetically identical to the parent and each other. (3) A fragment of DNA isolated from the genome and produced in multiple copies by introducing it, via a specific vector, into a living cell where it will reproduce itself. (4) To isolate and replicate an individual gene. clone contig A set of overlapping DNA clones. closed circular DNA Double-helical DNA in which both strands are closed circles; i.e. there are no free ends. cluster headache A disorder, mainly of men, characterized by agonizing, daily, one-sided, intense pain lasting for 30–120 min, accompanied by a running eye, blocked nostril and intense restlessness. The cluster of daily attacks ceases after 4–12 weeks. Cluster of differentiation (CD) markers See CD nomenclature. cmc See critical micelle concentration. C–N glycosidic bond Covalent link between C1 of the ribose ring and N3 of pyrimidine or N9 of purine heterocyclic rings. cnidocyst A stinging organelle in cnidaria. It is a capsule-bearing inverted tubule, sometimes capped by an operculum. Pressure on a fine-hair-like cnidocil triggers its eversion, which in some cases is accompanied by the release of toxins. CNS stimulant A substance that stimulates activity in the central nervous system (i.e. the spinal cord and the brain). CNS See central nervous system coagonist Chemical that is required for receptor activation in addition to the principal neurotransmitter. coagulation A defensive immunological and haemostatic process in which the blood solidifies locally, immobilizing the foreign antigen and preventing excessive bleeding following injury. It involves a cascade of activity of protein coagulation factors. This results in the formation of an insoluble fibrin meshwork which, together with blood platelets, forms a clot. coagulocyte A synonym for granulocyte in arthropods. coalescence The genealogy of a sample of homologous DNA sequences from a population. Looking forward from the ancestral sequence they form a tree of descent, while looking backward from the presence they undergo coalescence events. coat protein Protein that encases the nucleic acid core of a virus particle.

161

Glossary

coatomer Complex of proteins forming a coat around COPI vesicles which are involved in retrograde transport across the Golgi stack and to the endoplasmic reticulum. cobalamin Vitamin B12. coccidioidomycosis Invasive infection caused by the fungus Coccidioides immitis. coccolith A scale-like structure on the surface of prymnesiophycean golden algae. it consists of an organic plate surrounded by a rim of calcium carbonate crystals. coccolithophores, coccolithophorids A group of microscopic photosynthetic planktonic algae that produce calcareous coccoliths on their surface. Coccolithophores first appear in the fossil record in the Late Triassic but they did not become an abundant component of the world’s plankton until the Cretaceous. cocultivation The culturing together of a mixture of cells of different origins or from different individuals, generally for the purpose of transferring and propagating viral infection. code for To specify the amino-acid sequence of a protein by the sequence of nucleotides comprising the gene for that protein. codominant Describes different alleles that, when both are present at a locus, result in a phenotype different from that produced if only one type is present. codon A sequence of three consecutive bases in mRNA that encodes a particular amino acid. coelenteron Digestive and distribution cavity of coelenterates. It acts as a hydrostatic skeleton and sometimes as a brood chamber for planula larvae. coelom In certain animals, a fluid-filled cavity that lies between the gut and outer muscle layers (the body wall) and is lined with mesodermally derived tissue. coelomocyte The haemocyte (immunocyte) of annelids. coenocyte A multinucleated cell. The plasmodium of slime moulds is a coenocyte. coenzyme, cofactor A small organic molecule (often a vitamin) that assists the enzyme catalysis of certain classes of reaction (e.g. reduction of a ketone to an alcohol). coevolutionary hotspots Local communities where an interaction between two or more species is under reciprocal selection (i.e. the species affect the Darwinian fitness of each other). coevolution Reciprocal evolution of interacting species that is driven by natural selection such that the interacting species shape the evolution of each other. cofactor An organic molecule or inorganic ion that is needed for the catalytic activity of an enzyme. cognate Describes an aminoacyl-tRNA synthetase and its corresponding set of tRNAs that are specific for the same amino acid. cohesion species concept The idea that species are the most inclusive populations of individuals that have the potential for phenotypic cohesion through intrinsic cohesion mechanisms. cohesion–tension theory A widely accepted mechanism for the ascent of water in plants. Using energy from transpiration, water is pulled from above, creating a negative pressure which is transmitted all the way to the soil by the cohesion of water molecules. cohesive ends ‘Sticky ends’, complementary single-stranded ends of a double-stranded nucleic acid that has been digested with certain restriction enzymes. cohort study See observational study. cold-reactive autoantibody Antibody to red blood cells that binds to the cells most efficiently at temperatures below 371C. It is principally IgM.

coleoptile A long, cylindrical, modified leaf acting as a sheath to protect the young shoot of a grass seedling. Col The Columbia ecotype of Arabidopsis thaliana. collagen Strong, triple-helical fibrous protein that is the major extracellular structural component of most connective tissues including bone and cartilage. collaterals Output connections made from a neuron that act in parallel with, and secondary to, the main output connections. collectins Family of proteins that contain a collagen-like segment attached to a lectin-like domain that binds carbohydrate. Several collectins play an important part in innate immunity. collenchyma Peripheral supporting tissue in plants with thickwalled cells. colloid A stable mixed phase in which one substance (e.g. a solid) is nonhomogeneously distributed within another (e.g. a liquid). colonocyte Cell of the epithelial lining of the gut wall. colony-stimulating factor 1 (CSF-1) Also known as M-CSF, this was the first haematopoietic growth factor to be purified and named. It predominantly stimulates the growth of macrophage (M) colonies. columella An extension of the sporangiophore which occurs within a sporangium. combinatorial biosynthesis The biosynthesis of ‘unnatural’ natural products by genetic engineering, e.g. by the introduction of a gene for a particular pathway from one species into a different species. combinatorial specification The idea that a combination of signals or lack of signals specifies the fate of a cell. commensal An organism that benefits from its relationship with a host organism but without either benefiting or harming the host. commensalistic interaction Interaction in which one of the interacting species increases its fitness while the other species is not harmed or benefited as a result. comminution The conversion of leaf litter to organic topsoil by decomposers. commissural axons Axons that cross from one side of the body to the other. commissure Axon bundle connecting the right and left halves of the brain. commitment A point in a developmental programme in which developmental options become restricted. community A group of organisms from different species that occur in the same area and interact with each other. comparison matrix A matrix specifying the context-independent score between any two amino acids or nucleotides in two different sequences. compartments Regions of a tissue in which cells do not mix across a common boundary, usually because the cells have differential adhesive properties. compatible Describes fungal sexual partners that are able to produce a fertile cross. compatible solute or osmolyte Organic compound synthesized or taken up by halophilic and halotolerant organisms to balance the osmotic strength of the medium. competence (1) The ability of cells to respond to an environmental cue in a specific manner. For example head ectoderm (but not trunk ectoderm) is competent to form lens in response to a neuralplate-derived signal. The competence of cells is usually restricted to specific time windows during development. (2) The natural development in Bacillus subtilis of the ability to take up and internalize exogenous DNA from the medium.

162

Glossary

complement, complement system A group of 20 or more plasma proteins (and their associated receptors and regulatory proteins) that are involved in the elimination of extracellular pathogens in both innate and adaptive immunity in vertebrates (and also reported from some invertebrates). When activated by an infection, they can opsonize the infecting microorganism, facilitating its phagocytosis, cause inflammation, and attack cell membranes, causing cell lysis. complementarity-determining regions (CDRs) The hypervariable regions of an immunoglobulin molecule, consisting of three regions (loops) from the heavy chain and three from the light chain, that come together to form the antigen-binding site. complementary base pairing Specific hydrogen bonding between complementary purine and pyrimidine bases that holds the antiparallel strands of the DNA double-helical structure together, and enables single-stranded RNA of complementary sequence to be transcribed from DNA. Guanine pairs with cytosine, and adenine pairs with thymine (in DNA) or uracil (in RNA). Base-pairing has been exploited in the techniques of nucleic acid hybridization, PCR and sequencing methods. complementation Restoration of a missing function in a mutant cell or organism, usually by introduction of a functional gene from another cell or organism of the same type. complementation studies Experiments that enable the identification of genes with similar or redundant function, by testing the ability of one gene to fulfil the function of another that is absent or deficient. complementation test (1) Genetic cross between a parent heterozygous for mutation A and a parent heterozygous for mutation B in order to test whether mutations A and B are affecting the same gene. (2) A test in which two different nuclei or genomes bearing recessive mutations are associated in single cells (heterozygotes or heterokaryons) to determine if together they will impart a normal phenotype. If so, they are said to complement each other, and therefore the mutations lie in different genes. complement-like factors Circulating proteins found in some invertebrates that appear to be similar to the complement proteins of vertebrates. complete remission Total absence of symptomatic, physical and laboratory evidence of a given disease. complex spike Action potential with a complex configuration, induced in a Purkinje cell by activation via a climbing fibre. complicated migraine Persisting neurological deficits that start in the aura or during the headache phase, but continue for 24 hours or more. compression A shortening of a structure that results from an applied force (negative linear strain). computed tomography (CT) An imaging technique in which multiple X-ray beams are used to obtain numerous projections through the body. Images of slices through the body (tomograms) are generated by computer. Also known as CAT (computerassisted tomography) and sometimes as CAT scanning. However, scan is a confusing word and is best avoided in the context of imaging. computer-assisted tomography (CAT) See computed tomography. concatemer (1) DNA molecule that contains multiple tandem head-to-tail repeats of a particular sequence. (2) Giant molecule consisting of multiple copies of covalently joined units.

concealed antigens Antigens that are not normally seen by the host immune system because the host is never exposed to them. For example, antigens which are part of the tick’s midgut and are therefore not introduced with the salivary antigens. concentration gradient The difference in concentration of an ion or solute on the two sides of a membrane. If the membrane is permeable to the solute, it tends to diffuse from the side of high concentration to the one of lower concentration until the concentrations on both sides are equal. conceptus All products of the fertilized egg, both embryonic and extraembryonic. conchicolous habit Of molluscs, the habit of living in shells. concurrent asynchronous lactation Simultaneous production of two very different types of milk from adjacent mammary glands for two young of different ages. conditional gene knockout Inactivation of a gene in particular cells and/or at a particular time through gene targeting techniques. conditional lethal mutation A mutation in a gene essential to growth, in which the growth blockade can be bypassed under one condition but not another. An example is a temperature-sensitive mutation, which restricts growth at one temperature but not at a slightly lower temperature. configuration The spatial variation that is possible in organic molecules, as the result of the tetravalency and the tetrahedral nature of carbon atoms. Different configurations can be interconverted only by breaking and remaking bonds. D and L isomers and cis and trans isomers represent different configurations. confinement Limitation of, for instance, motion to a specific part of space. confocal microscope A microscope in which the illumination and the image detection are confined to the same spot in the specimen using a spatial filter. conformation Different three-dimensional arrangements of a molecule that can be interconverted by a simple rotation about a single bond, without breaking any covalent bonds. Confuciusornithids Primitive flying birds from the Late Jurassic– earliest Cretaceous of China, including Confuciusornis sanctus and Changchengornis hengdaoziensis. congenic Describes strains of animals that are identical at all but one chromosomal region. congenic mouse strains Inbred strains of mice which are identical except for a short chromosomal segment encoding a different histocompatibility antigen. congenital heart defects (CHD) Structural heart abnormalities that are present at birth. congestive heart failure (CHF) A cardiac disorder in which the normal function of the heart is impaired so that blood ejection is decreased and blood return from the venous system is impeded. conidiogenous cell A cell that directly produces a conidium. It is often a specialized structure, the conidiophore. conidiophore A specialized hypha that bears one or more conidiogenous cells. conidium (plural conidia) A thin-walled nonmotile deciduous asexual fungal spore that is produced at the tip of a specialized hypha or by fragmentation of a hypha. conjugate base The deprotonated species remaining after an acid donates a proton. The original acid and its base are known as a conjugate acid-conjugate base pair. conjugate planes Those planes that are equivalent in an optical system. An object placed in one plane will be imaged sharply in each subsequent plane of that series.

163

Glossary

conjugation (1) Close joining between two unicellular organisms during which genetic material may be exchanged. (2) The sexual transfer of plasmid or chromosomal DNA between bacteria that requires direct contact between the donor and the recipient cell. The delivery system is encoded by sex plasmids in the donor cell. (3) The temporary fusion of two cells of ciliate protozoans to allow exchange of gametic nuclei. it typically results in fertilization and the formation of zygote nuclei in both participating ciliates. conjugative plasmid A self-transmissible plasmid that encodes all the functions needed for its own intercellular transmission by conjugation. connective Tissue that keeps an anther together and connects it to the filament. conodonts Tiny, tooth-like fossils of calcium phosphate from the Cambrian to the Triassic. They are thought to represent a complex, tooth-like bony jaw apparatus that belonged to small, eel-like animals that were probably primitive vertebrates. The whole conodont animal is rarely found fossilized because of its soft body, but conodonts themselves are common. consensus sequence A theoretical sequence that is derived by comparing a group of related sequences and designating the most commonly occurring residue that is found at each aligned position. conservation biology An academic discipline that studies biological diversity and develops methods to protect it. conserved protein sequences Amino acid-sequences that share at least 70% identity. conserved sequences Nucleic acid or amino-acid sequences are said to be conserved when they are similar in different organisms. Conservation is considered evidence for some type of function. Sequences without function usually diverge rapidly in the course of evolution, ¨ Conservitat Lagerstatten Exceptionally well-preserved biotas consisting of organisms that do not normally form part of the rock record, principally those that have an unmineralized or poorly mineralized skeleton. consortia Assemblages of different species of organisms in which all species derive benefit from each other (See also biofilm). constitutive Unregulated production. constitutive activity of a protein State in which a protein is in the activated state in the absence of the ligand that is generally needed to induce its activation. constitutive heterochromatin Regions of highly repetitive sequences of DNA that contain no genes. consumer An organism that obtains nutrition by eating other organisms. contact hypersensitivity T cell-mediated hypersensitivity reaction produced in the skin of a sensitized individual on contact with certain chemicals. contig A contiguous segment of DNA sequence assembled from partially overlapping DNA clones. continuous cell line A culture that can be passaged indefinitely without becoming senescent. These cultures are often referred to as ‘immortalized’ cells. contractile vacuole A clear vacuole within a cell which swells by accumulation of fluid from the cytoplasm and contracts to expel the fluid out of the cell. contralateral On the opposite side of the brain. contrast A relative difference in brightness (or in colour) between two objects or between two areas in an object or image.

convection Heat transfer between the air and an object of different temperature. convolution A mathematical operation that extracts particular features from a function or an image. cooperativity (1) In a protein with multiple binding sites, the influence of bound ligands on the affinity of the molecule for binding subsequent ligands. (2) A change in enzyme activity that comes from interactions between the protein subunits that help to stabilize a new conformation. coordinate bond A metal–ligand bond resulting from the interaction of a Lewis base (the ligand) and a Lewis acid (the metal ion). coproantibodies Secretory antibodies that can be detected in intestinal contents and in fresh faecal substrate. coproantigen Antigen detectable in stool. coprolite A fossilized faecal pellet. Literally ‘dung stone’. Occasionally the term is used also to describe the fossilized intestinal contents of some creatures (notably fish). coprological examination A method of detection of infective stages of parasites in the faeces of animals or humans. coprophagy Ingestion of faeces. It is nutritionally important for some animals because it allows recovery of otherwise lost protein, vitamins, and other fermentation products. co-protease A specific activity of the RecA nucleoprotein filament which allows it to bind to a protein and cause that protein to cleave itself. copulatrix See bursa. copy number The number of identical plasmid copies per cell or per chromosome. co-receptor In immunology, the term often refers to the CD4 and CD8 molecules, which aid the binding of T-cell receptors to class II and class I MHC molecules, respectively. coronal the plane of the body which bisects it from side to side, and which runs at right angles to the anteroposterior, or sagittal, plane. corrinoid A compound resembling vitamin B12 and containing a porphyrin-like corrin ring displaying a central atom of cobalt. cortex (1) Generally, the outer layer of an organ. (2) The outer layer of the brain, in which the neuronal cell bodies are organized in a layered manner. (3) The layer of cytoplasm immediately below the plasma membrane in cells. (4) The thick peptidoglycan shell surrounding the core of a bacterial endospore. cortical alveoli Membrane-bounded flattened vesicles or sacs in the cortex or pellicle of various protozoan protists, specifically found in dinoflagellates, ciliates and sporozoan apicomplexans. cortical blindness Rare form of blindness arising from dysfunction in the visual cortex rather than in the retina and optic nerve. cortical death A proposed standard for declaration of death based on the permanent loss of brain cortical function. cortical map The spatially orderly projection of a receptor organ on to the cerebral cortex. cortical plasticity Reversible modification of the functional organization of a cortical region associated with sensory experience or sensory learning. cospeciation Speciation in two or more interacting evolutionary lineages, such as host and parasite, where each speciation event in one lineage results in a matched speciation event in the other lineage. The process may or may not involve coevolution.

164

Glossary

costa Slender rib-like structure subtending the undulating membrane of typanosomatids. cosuppression See post-transcriptional gene silencing. Cot The initial concentration of DNA (in mole nucleotides per litre) in a hybridization reaction multiplied by the duration (in seconds) of the incubation. cotranslational Describes any process that acts upon a polypeptide chain while it is being synthesized. cotranslational modification A modification to a polypeptide chain that occurs while it is being synthesized. cotransmitter Many neurons use more than one neurotransmitter for communication with target cells, for example an amino acid such as glutamate and a neuropeptide. In this situation each of the neurotransmitters is referred to as a cotransmitter. cotransport Transmembrane transport of a substrate coupled to that of another substrate in the same direction. cotransporters Integral membrane proteins that mediate the coupled transport of ions and other substrates across a cellular membrane. These proteins often use the energy gained by moving an ion down its electrochemical gradient to move the other ion or substrate up its gradient. Coulomb force Force between two charges. countertranscript An RNA that is encoded by the opposite strand of DNA to that encoding the mRNA for a particular gene. Not all countertranscripts are antisense RNAs that regulate target function. countertransport Transport of a substrate coupled to that of another substrate in the opposite direction. coupling The process whereby osteoclast activity is linked to osteoblast activity, coordinating bone resorption with bone deposition. covalent bond The sharing of a pair of electrons between two atoms. coxa The most proximal segment in the arthropod walking leg. Coxsackie and adenovirus receptor The cell-surface receptor for most adenovirus serotypes. CpG island Stretches of DNA (500–1000 nucleotides) rich in guanine plus cytosine, usually flanking housekeeping genes and most tissue-specific genes. cranial fenestration In vertebrate evolution, upper and lower temporal windows first (fenestrae) developed just behind the orbit (diapsid condition), and later a window just in front of the orbit also appeared (archosaur condition). These cavities then increased in size, making the skull much lighter. cranial kinesis (1) The mobility of the upper jaw, or parts of it, in relation to the braincase. All birds that have been studied adequately have some degree of cranial kinesis. (2) The capacity for movement (usually due to movable joints) between bones of the normally rigid skull roof. This occurs notably in bony fish, many lizards, snakes and birds. It has also been recognized in some dinosaurs. cranium The vertebrate skull minus the mandible. CREB Cyclic adenosine monophosphate (cAMP) responsive element-binding protein. A transcription factor regulated by cAMP. Crenarchaeota A kingdom of the Archaea that contains primarily hyperthermophiles. cresta Fibrillar, noncontractile structure located below the basal portion of the trailing flagellum of devescovinid flagellates. Cretaceous period The last period of the Mesozoic era. cribriform plate A thin bone separating the olfactory epithelium from the frontal brain area.

crinoid ‘Sea lilies’, a class of echinoderms (phylum Echinodermata, class Crinoidea) typically bearing an elongate stem or column that elevates a flower-like crown with feathery arms used for suspension feeding. They were both abundant and diverse for several hundred million years from the Ordovician onwards. They are relatively rare today and generally confined to deep waters. crista The sensory organ of the semicircular canal, containing hair cells. It is situated in an ampullary enlargement and covered with a cupula. cristae Invaginations of the inner mitochondrial membrane that form a series of projections of various shapes. criterion A combination of incubation temperature and solvent composition chosen to dissociate DNA duplexes having more than a specified amount of base mismatch. As the criterion increases, the amount of base mismatch that the duplexes can have decreases. critical micelle concentration (cmc) The concentration of detergent at which micelles begin to form. critical region The minimal region of a chromosome which, when altered, results in a specific phenotype or syndrome. cross transmission Transmission of an infectious agent from one vertebrate group to another, e.g. from reptiles to mammals. crossing-over Exchange of chromosomal segments between homologous chromosomes during meiosis, producing new combinations of alleles. cross-linker Chemical that conjugates different parts of proteins such as amino, carboxy or thiol groups, and thereby generates protein complexes. cross-reaction Reaction of an antiserum with a molecule not present in the immunizing preparation. It usually reflects structural similarity with the immunizing antigen. crown gall Galls caused by the pathogenic bacterium Agrobacterium tumefaciens on dicotyledonous plants. crural Pertaining to the leg. cryoelectron microscopy A technique that allows macromolecules to be visualized in their native state in a thin (~50–80 nm) layer of vitreous ice. cryopreservation Preservation in a frozen state, for example in a deep-freeze or a liquid-nitrogen refrigerator. cryoultramicrotome An apparatus for cutting, at low temperature, ultrathin sections of frozen material for cryoelectron microscopy. cryptic plasmid A plasmid for which there is no known phenotypic function but which replicates and spreads to other cells. cryptobiosis Ability of an organism to form a resting stage in order to survive unfavourable (e.g. drought) conditions. cryptococcosis Invasive infection caused by the fungus Cryptococcus neoformans. cryptozoic Refers to the fauna that lives hidden beneath the soil/ leaf litter surface or beneath bark and other similar surfaces. crystal cell Haemocyte comparable to prohaemocyte of some invertebrates. crystal lattice The three-dimensional distribution of points defining the origin of each copy of the unit cell in a crystal. crystal unit cell The repeating unit of a crystal, which periodically reproduced in three dimensions yields the crystal. crystallins Major soluble proteins of the lens of the eye, which fill the cytoplasmic space of mature lens cells. Crystallins are thought to maintain the transparency and reflective index of the lens.

165

Glossary

crystallized song See stereotyped song. crystallography The study of protein structure by means of X-ray diffraction through crystals of the protein. ctenidium Molluscan ‘gill’, which originally only created the water current, but which is also involved in respiration in larger animals. CTL Cytotoxic T lymphocyte, the CD8 T cell type with cell-killing capacity. Their T-cell receptors recognize peptides presented by major histocompatibility complex (MHC) class I molecules. C-type lectins Lectins that bind their carbohydrate ligands in a calcium-dependent fashion. Seven separate families of C-type lectins have been described and all share a characteristic carbohydrate recognition domain (CRD). current Flow of charged particles. Current is measured in amperes and is defined in terms of the number of elementary charges moving per second. current-to-voltage converter An electronic device consisting of an operational amplifier and a resistor that measures current and converts it to a voltage that is easily displayed and recorded. curve fitting An analysis method in which the correlation of data points is expressed in terms of the parameters in a mathematical function. For example, pairs of x, y points may be fit to the mathematical function describing a straight line, in which case the parameters determined will be the slope and y intercept. In sedimentation, the functions are derived from hydrodynamic and thermodynamic theory, and the parameters are those sought by the experimenter (e.g. s, D, Mb, etc.) cushingoid Resembling the signs and symptoms of Cushing disease: buffalo hump obesity, striations, hypertension and osteoporosis. cut and paste transposition Type of transposition in which the transposable element is disconnected from the flanking DNA in the donor site by double-strand breaks and is then joined to the target DNA. CVHD See graft-versus-host disease. C-value The amount of DNA in the nonreplicated haploid genome, given in picograms or base pairs. C-value paradox The fact that C-values for closely related species can differ enormously and there is no close relationship between C-value and the degree of complexity of various multicellular organisms. It arises from the presence of different amounts of repetitive or ‘junk’ DNA in different species. cyanobacteria (singular cyanobacterium) Ubiquitous oxygenic photosynthetic prokaryotes that are evolutionarily ancient and that have maintained a significant presence on Earth in essentially all habitats. Previously called blue-green algae. cyanocyte Haemocyanin-containing haemocyte found in Porifera, Mollusca and some Arthropoda. cycle The period of an oscillation. cyclic AMP (cAMP) The intracellular signalling molecule cyclic adenosine monophosphate, which is generated by the hydrolysis of adenosine triphosphate (ATP) by G-protein-dependent adenylyl cyclase. cyclic AMP receptor protein (CRP) This transcription factor, which is triggered by cyclic AMP, activates scores of promoters and plays a major role in bacterial responses to the availability of different sugars. At some promoters it functions to repress transcription initiation. cyclic GMP (cGMP) The intracellular signalling molecule cyclic guanosine monophosphate. It is generated by the hydrolysis of guanosine triphosphate (GTP) by G-protein-dependent guanylyl cyclase.

cyclin-dependent kinase inhibitor Regulatory protein of the eukaryotic cell cycle that inhibits the activity of cyclin-dependent kinases. cyclin-dependent kinases (CDKs) Regulatory proteins of the eukaryotic cell cycle which become activated when complexed with the appropriate cyclin. cyclins Regulatory proteins of the eukaryotic cell cycle whose level in the cell rises and falls during a single cycle. They are involved in the progression from one stage of the cycle to the next and there are several different types, acting at different stages in the cycle. cyclol A structure in which polypeptide chains fold into a planar hexagonal array. cyclosis Movement of subcellular components, also known as cytoplasmic streaming. cyclostomes The most primitive class of vertebrates. CYP21 genes Cytochrome P450 or steroid 21-hydroxylase genes. cyst A nonmotile reproductive or resting form of a cell, especially a protozoon, that is enclosed in a rigid secreted envelope, external to the plasma membrane, that limits free movement of the cell. In this form it is resistant to unfavourable environmental conditions. cystic Describes an arrested development of the ear that shows only one largely undivided central lumen much like an otocyst. cystocyte A misnomer for coagulocyte (granulocyte). cytochrome bf complex A membrane-bound electron transfer protein complex found in all oxygenic photosynthetic organisms that oxidizes reduced plastoquinone and reduces plastocyanin (or cytochrome c). cytochrome c A mobile haem-containing electron transport protein in the mitochondrial respiratory chain. cytochrome oxidase The terminal protein complex of the electron transport chain, which reduces molecular oxygen to water. cytochrome P450 A family of haem-containing enzymes that serve as monooxygenases by activation of dioxygen. One oxygen atom is inserted into the substrate, while the second atom is released as water. They are membrane-bound enzymes found in the endoplasmic reticulum and convert non-polar chemicals to water-soluble, excretable forms. cytochromes Family of haem-containing electron transport proteins present in the respiratory and photosynthetic electron transport chains of mitochondria, chloroplasts and bacteria. cytocidal Causing lysis or dissolution of a cell. cytogenetics The study of cellular genetics at the level of the chromosome. cytokeratins Intermediate filament proteins characteristic of epithelial cells. cytokines The general term for a large group of small soluble proteins that are secreted by cells and affect the behaviour of other cells, for example cell proliferation, differentiation and migration. They include, for example, the leukocyte interleukins and numerous growth factors and differentiation factors. Cytokines act by binding to specific receptors on target cell surfaces. Many cytokines are secreted by immune system cells during an immune response, and act locally and distantly to modify the response to infection. cytokinesis The last step of cell division, in which the cytoplasms of both daughter cells become separated. It should be distinguished from karyokinesis, the nuclear separation during cell division. cytolytic The phase in the viral life cycle in which virions are produced and released, destroying the host cell. cytomegalovirus A species-specific herpesvirus.

166

Glossary

cytomorphology The form or structure of individual cells, usually discerned by microscopic examination. cytopathic effect, cytopathicity Characteristic deleterious morphological changes in host cells, including cell killing, following viral infection. cytophilic antibody Antibody molecules that bind to a cell, sometimes rather weakly but sometimes strongly, by regions of the molecule other than the antigen-binding site. Thus the binding is nonspecific, i.e. not related to the presence of the specific antigen that evoked production of the antibody. cytoplasm The collective name for all the components of a cell that are not associated with either the cell wall or the genome. In a eukaryotic cell, it comprises all organelles and material outside the nucleus. It consists of a continuous aqueous phase (the cytosol) and the organelles and inclusions suspended in it and is the site of most of the chemical activities of the cell. cytoplasmic determinant An mRNA or protein which is segregated into only one of the daughters of a mother cell and causes this cell to execute a fate different from that of its sister. cytosine Commonly occurring pyrimidine base, one of the four types of bases in RNA and DNA. cytoskeleton A network of proteinaceous filaments within eukaryotic cells, which gives a cell its shape, is involved in motility, and organizes the position of internal organelles. It is composed primarily of actin microfilaments (diameter 5 nm), intermediate filaments (diameter 10 nm), and microtubules (diameter 25 nm), which are associated with motor proteins such as myosin, dynein and kinesin. The cytoskeleton is anchored to the plasma membrane. cytosol The fluid constituents of the cytoplasm. cytostome The cell ‘mouth’ in certain protozoa, the site at which food particles are ingested and food vacuoles are formed. cytotoxic lymphocyte antigen 4 (CTLA4) Cell-surface molecule on activated lymphocytes, which tends to inhibit activation. cytotoxic T cells, cytotoxic T lymphocytes (CTLs) T lymphocytes that can kill virus-infected cells displaying viral antigens or cells bearing other foreign antigens. Most cytotoxic T cells carry the CD8 co-receptor and act against target cells that present the specific peptide antigen in association with a major histocompatibility complex (MHC) class I molecule. cytotoxicity The property of being able to kill cells.

D6S45 See RD gene. 3D reconstruction Construction of a three-dimensional model of an object from several two-dimensional views of it. D period The time between termination of DNA replication and cell division. In Escherichia coli the D period, for cells growing between 20 and 60 min doubling times, is a constant of approximately 20 min. Dam methyltransferase Enzyme that transfers methyl groups to the adenine of GATC sites. dauer larva Alternative third larval stage of Caenorhabditis elegans, induced by starvation in early larval development, with many morphological differences to the normal L3 larva. It is long-lived and resistant to stress. From the German dauer, enduring.

days postcoitum (dpc) The number of days elapsed since conception. It is often used as an approximate guide to stage mouse conceptuses. DDT Dichlorodiphenyltrichloroethane, a synthetic chemical pesticide. de novo biosynthesis The synthesis of molecules from the simplest precursors. de novo synthetic pathway Synthesis of complex nucleotide molecules from simple precursors such as ammonia or amino acids. deactivation The suppression of an activity, e.g. the return of open ionic channels to the closed state. dead space A volume in the respiratory tract that is renewed at each respiratory cycle but that does not contribute to gas exchange. In mammals, the upper airways are filled with inspired air which never reaches the alveolar space and thus constitutes a dead space. deadenylation The enzymatic removal of the poly(A) tract from the 30 region of an mRNA. death receptors A family of transmembrane receptors which deliver intracellular signals that culminate in proapoptotic and antiapoptotic responses. death-receptor-mediated apoptosis A highly regulated form of transmembrane signalling where the outcome may be cell death. decapping The enzymatic removal of the cap from the 50 end of an mRNA. decarboxylation In C4 plants, the removal of carbon dioxide from four-carbon acids in bundle sheath cells. decubitus ulcers Ulceration caused by prolonged pressure caused by lying in bed for long periods. dedifferentiation The loss of specific characteristics from a terminally differentiated cell. DEFC24 An ecotype of Arabidopsis thaliana. defective interfering (DI) particles Virus particles that contain less than a complete genome. They are dependent on the presence of homologous undeleted helper genomes for their replication, and interfere with the replication of infectious virus. defence An organism’s mechanism of reducing potential damage by another organism. defensins A family of cationic proteins that lyse pathogens by pore formation. defensive membranes Immunologically protective membranes secreted by some insect parasites to avoid recognition by the insect’s immune system. deficiency a lack or defect. definitive haematopoiesis The formation of blood cells in the fetus or adult. Erythrocytes in the adult stage express different globin chains from those expressed during embryogenesis. definitive host The host in which sexual recombination of a parasite takes place. degree of esterification (DE) The percentage of carboxyl groups of a pectin preparation in the methyl ester form. degree of polymerization The number of monomeric units in a molecule of a polymer. DE See degree of esterification. dehiscence The natural release of a seed or fruit from the plant. dehiscent Describes a fruit that opens by splits or pores. dehydroascorbic acid A reversibly oxidized form of ascorbic acid. dehydrogenase An enzyme that catalyses oxidation/reduction reactions, usually involving NADH or NADPH.

167

Glossary

delavirdine Non-nucleoside analogue inhibitors of human immunodeficiency virus 1 (HIV1). delayed hypersensitivity, delayed-type hypersensitivity (DTH) T cell-mediated type IV hypersensitivity. An immune response to subcutaneous injection of the relevant antigen that results in oedema and inflammation, which reaches a maximum after 24–48 hours. It involves T cells and macrophages. deme A small group of randomly mating individuals that is more or less isolated from other such groups. In some models, mating within demes occurs between genetic relatives and is not random. demographic stochasticity The temporal variation in birth and death rates due to chance sampling of individuals, even though the environment remains the same. dendrite A long, branching outgrowth or extension from a neuron or nerve cell, which carries electrical signals from synapses to the cell body (unlike an axon which carries electrical signals away from the cell body). A typical vertebrate neuron extends many dendrites but only a single axon. dendritic Describes a cell with many long thin processes extending from it. dendritic cell The professional antigen-presenting cell that takes up proteins and presents peptide antigens to T cells in conjunction with accessory molecules that stimulate T-cell activation. dendritic spine Wine glass- or mushroom-shaped protrusion from a dendrite that represents the principal site of termination of axons from excitatory neurons on interneurons, especially in the cortical regions. dendritic transport The active transport of cytoplasmic constituents within a dendrite. dendrogram In phenetic (numeric) systematics, a tree-like representation of shared similarities between taxonomic units. denervation Removal of nerves that innervate a muscle or other tissue. densitometry Technique by which the intensity of a particular chemical species is quantified using a relative measure of the light absorbed. deoxyribonucleic acid (DNA) See DNA. depletion force The force that drives macromolecules together. It is due to entropy effects associated with the presence of other macromolecules. depolarization Cells have a transmembrane electrical potential of the order of –70 mV (inside negative). A change in the membrane potential towards zero is termed a depolarization. deposit feeding Obtaining nutrients from sediments. depotentiation A decrease in synaptic strength produced by an activity-dependent process, when this occurs after long-term potentiation has previously been induced. depression See synaptic depression. depth of field In microscopy, the axial depth within a specimen that appears acceptably sharp in an image. derivative chromosome Any structurally abnormal chromosome resulting from deletions, duplications or translocations. The identity of the derivative is determined by the origin of the centromere. dermal bone Bone produced by the ossification of connective tissue of the dermis. See also endochondral bone. dermatomyositis Progressive condition characterized by muscular inflammation and weakness. dermatophytosis Superficial infection caused by dermatophytes (fungi parasitic upon the skin).

dermopterans An order of placental mammals having exceptional adaptations for gliding, also known as flying lemurs or colugos. desaturase Enzyme that inserts a carbon–carbon double or triple bond into a molecule. desmotubule The central membranous component of plasmodesmata, structures that connect the cytoplasms of plant cells. It is believed to be derived from endoplasmic reticulum. desoxyanthocyanidin, deoxyanthocyanidin Anthocyanidins lacking a hydroxyl group in the 3-position. desulfurylation The enzymatic removal of sulfur from sulfurcontaining compounds. detectors In computed tomography (CT), an array of individual measuring devices that capture the photons that have passed through the patient. Scintillation crystals and gas-filled ionization chambers are both used. detergents Amphiphilic molecules that lyse cell membranes and solubilize lipids and hydrophobic proteins. Examples are Nonidet P-40 and Triton X-100. determinant See antigenic determinant. determination In development, a stable change in cell fate. detritivore An organism that feeds on dead plant and animal matter. deuterostomes Animals (e.g. Echinodermata, Tunicata and Chordata) in which the oral and anal openings are derived from two different openings during development. developmental host A host in which the parasite can complete its development. Sometimes called the final host. diacylglycerophospholipids The most abundant class of membrane lipids in all organisms (except archaea), forming the bulk of the lipid bilayer. They are amphipathic phospholipids containing two fatty-acyl chains (the hydrophobic portion) esterified to a glycerol backbone, and a phosphate group linked via a phosphodiester linkage to both the glycerol backbone and a polar alcohol (the hydrophilic headgroup). Examples are phosphatidylcholine, phosphatidylethanolamine and phosphatidylinositol. diagenesis The physical and chemical modifications that occur in rocks, and fossils, after burial. diapause (1) A regulated transient delay in embryonic development, usually at the blastocyst stage. (2) A state of arrested development in insects that is characterized by a strong suppression of metabolic rate. diapedesis The movement of leukocytes through the intact walls of blood vessels. diaspore Any part of an organism that is adapted for dispersal, e.g. a seed. diastole Period of relaxation of the ventricles of the heart. diatoms Group of single-celled, photosynthetic organisms that secrete outer coverings (tests) made of silica. diauxy, diauxic growth The using up by bacteria of one carbohydrate growth substrate before using another when growing on medium containing a mixture of substrates. diazotrophic Capable of meeting all needs for nitrogen nutrition by fixing elemental dinitrogen. dicentric A chromosome with two distinct centromeres. DIC See differential interference contrast. DIC See disseminated intravascular coagulation. DICOM Digital Imaging and Communications in Medicine. This is the industry standard for transfer of radiological images and other medical information between computers.

168

Glossary

dicotyledonous Belonging to the Dicotyledons, those angiosperm plants whose seedlings have two cotyledons. dictyosome A name sometimes used for a Golgi stack in plant cells. See Golgi apparatus. didanosine Nucleoside analogue inhibitor of human immunodeficiency virus (HIV) reverse transcriptase. Used as an anti-HIV drug. diencephalon The part of the brain located immediately behind the cerebrum. diether lipid A membrane lipid with two acyl (phytanyl) analogues of fatty acids attached to the polar head group by ether linkage. differential binding Differential binding arises from an enzymatic interaction that stabilizes one of successive stable internal states more than the other. differential centrifugation Centrifugation procedure by which subcellular particles are separated by virtue of their differences in speed of sedimentation. differential interference contrast A special contrast method in light microscopy by which live unstained cells can be viewed. differentiation The structural and functional specialization of cells and tissues during development. It occurs by the gradual maturation of cells with specialized structure and function from unspecialized precursors as a result of changes in gene expression. Differentiation is usually accompanied by a restriction in potential for further development. diffusion The movement of molecules from a region of high concentration (high chemical potential energy) to that of low concentration (low chemical potential energy). The movement itself is random and driven by thermal fluctuations. diffusion constant Proportionality constant for the distance moved in a given time due to diffusion. DiGeorge syndrome (DGS) Genetic disorder with a broad spectrum of symptoms such as cardiac defects, facial dysmorphia, and absence of thymus (leading to immunodeficiency) and parathyroid glands. Also called DiGeorge anomaly. digestive caeca Pockets of the midgut which in some malacostracans may fuse to form a digestive gland. digital Describes processes that deal with discrete numerical values, often as an approximation of an analogue signal. digital mask A numerical array that is applied to an image pixelby-pixel, resulting in a processed image. Digital masks are most often used for noise reduction, contrast enhancement and feature extraction. digitigrade A foot posture in which the animal stands with the digits flat on the ground and the sole or palm of the foot off the ground. digitonin-permeabilized cells Cells whose membranes have been made permeable to macromolecules by the detergent digitonin, which tends to solubilize cholesterol in membranes and creates membrane pores. dihedral angle Angle between the two planes containing the first and last three of four contiguously bonded atoms. dihydropteridine reductase (DHPR) The enzyme responsible for the conversion of the inactive, oxidized pterin cosubstrate quinonoid dihydrobiopterin (q-BH2) to the active, reduced form, tetrahydrobiopterin (BH4). dikaryon A cell with two nuclei or a tissue composed of such cells, especially a fungal mycelium consisting of cells that each contain two nuclei, usually of unlike mating types. dikaryotic Describes a cell with two nuclei.

dilambdodont Describes a molar tooth cusp pattern with Wshaped ridges. dimer A complex consisting of two similar or identical components. dimerization The physical association of two (often identical) proteins. dinitrogenase Bacterial enzyme that catalyses the essential reaction of nitrogen fixation, the reduction of N2. It is the product of the nifDK genes. Also known as the MoFe protein. dinitrogenase reductase Homodimeric protein that serves as the unique electron donor to dinitrogenase and is also involved in the insertion of the iron–molybdenum cofactor into dinitrogenase. It is encoded by the nifH gene. Also known as the Fe protein. dipicolonic acid (DPA) Pyridine-2,6-dicarboxylic acid, a major component of most bacterial endospores, where it is located in the core. diplegia See paraplegia. diploid An individual or cell having two full sets (2n) of homologous chromosomes (with the exception of the sex chromosomes). Somatic cells of sexually reproducing multicellular organisms usually contain a diploid number of chromosomes (in humans this is 46). Diploid cells thus have two copies of each genetic locus. diplospory Type of apomixis in which a diploid megaspore gives rise directly to the embryo. dipole magnet See bending magnet. directed transport Any type of transport that results in a linear increase of the distance moved as a function of time. directional mutation pressure Misincorporation of a particular nucleotide(s) during DNA replication. After a number of generations, the genome exhibits a highly biased AT or GC bias in nucleotide composition. Directional mutation pressure is one of the driving forces for genetic code change. directional selection Selection acting against individuals at one extreme of a phenotypic distribution. directive interactions Morphogenetic interactions that lead to a new developmental pathway of the responding cells and restriction of their developmental options. disaggregatase An enzyme in the bacterium Methanosarcina which solubilizes the cell wall so that the typical aggregated clusters of cells are liberated as single cells. disinfectant An agent, usually chemical, that is used to kill microorganisms. disinfection The killing of harmful organisms. dismutation The conversion of two moles of aldehyde into an equimolar mixture of alcohol and carboxylate. disomy The presence in a cell or organism of two copies of a chromosome or chromosomal segment. disparity A measure of the morphological distance between taxa. displacement reactions Reactions of organic compounds in which a leaving group is displaced by a nucleophilic reagent, with inversion of configuration. disruptive selection Selection that acts against individuals exhibiting intermediate values of some phenotype. It results in two or more adaptive forms and eliminates intermediate forms. disseminated intravascular coagulation (DIC) Abnormal overactivity of the blood coagulation system that results in widespread formation of microscopic clots throughout the circulatory system, which may cause organ damage and failure. The circulating blood is rapidly depleted of essential clotting factors so that it becomes unable to clot.

169

Glossary

dissociation constant (Kd) A measure of the rate at which two molecules dissociate from each other, and therefore a measure of their strength of binding. For protein–DNA interactions, Kd is usually expressed as the protein concentration at which there is half-maximal binding to the DNA target. dissociation profile The fraction of duplexes remaining in a population of DNA molecules, plotted against the temperature as the temperature is progressively increased. distance matrix A display that shows pair-wise quantitative measures of genetic distance between DNA sequences, usually as numbers of substitutions. distance methods Methods of determining the evolutionary relatedness of two homologous DNA sequences. They measure the number of nucleotide substitutions per nucleotide site that have accumulated in the two sequences since they diverged. disulfide A chemical structure involving covalent bond formation between two sulfur atoms. disulfide bridge The covalent linkage of the sulfur atoms in two cysteine residues in a protein. This bond can tie two different portions of a protein together. diterpenoid A lipid molecule with 20 carbon atoms that is formed enzymatically by the condensation of isoprenyl units. diuretic A substance that increases the elimination of urine. diurnal Having a daily rhythm with most activity during daylight hours. diurnal tides A sequence of tides consisting of one high and one low tide over approximately 24 hours and 50 minutes. diversity The number of taxa, such as species, that are present in the biota under consideration. divided circulation A circulation pattern in which blood is pumped twice, once by the right side of the heart and once by the left side of the heart, before it completes a full circuit of the body, i.e. through the respiratory circulation and through the peripheral circulation. dizygotic twins Twins that are derived from two different eggs and are thus not genetically identical. DNA Deoxyribonucleic acid. The biological macromolecule that carries the permanent store of genetic information in a cell. It is a polymer of the nucleotides guanine, adenine, cytosine and thymine, and the genetic information is carried in the form of the sequence of nucleotides, which corresponds to a sequence of amino acids in protein. DNA is transcribed to make messenger RNA, which is used to direct the synthesis of proteins. DNA adduct A DNA base that has been covalently modified by reaction with a mutagen or carcinogen. DNA base composition The proportion of the total bases in a DNA that are guanine (G) and cytosine (C), or thymine (T) and adenine (A), expressed as (G 1 C) content. Bacterial genomes range between ~25% and 75% G 1 C. DNA damage A change in the structure of DNA (such as chemical modification of bases, or formation of a base adduct or a strand break) resulting from exposure to physical or chemical agents. In some cases, DNA damage may cause mutations or cell death. DNA double-strand break repair Repair of DNA double-strand breaks either by homologous recombination or by nonhomologous end-joining. DNA–DNA hybridization In molecular systematics, a technique whereby single-stranded DNA from two species is associated (hybridized) into double-stranded hybrid duplex molecules. Melting temperatures of DNA hybrids are used to estimate genealogical distances between species is being compared.

DNA helicase Protein that unwinds double-stranded DNA processively. In Escherichia coli, it is the product of the dnaB gene. DNA labelling Attachment of a radioactive or other marker to a DNA molecule so that it can be traced during subsequent experiments, for example if it is being used as a hybridization probe. DNA polymerase III holoenzyme Dimeric multisubunit DNA replication enzyme consisting of two DNA polymerase III core enzymes and their b and g subunits, in which the leading and lagging strand polymerases are linked together by the t dimer. The holoenzyme carries out coordinated synthesis of the leading and lagging strands. DNA polymerase DNA replication enzyme that joins deoxyribonucleotides together in a template-dependent reaction to form a new DNA strand. It joins nucleotides together in the 50 -to-30 direction only. DNA primase Enzyme that synthesizes short RNA primers for DNA replication. DNA repair The cellular processes that result in the removal of damaged or mismatched nucleotides from DNA and the restoration of the DNA to its previous sequence or to an intact structure. DNA replication The cellular processes that result in the copying of both strands (template strands) of a parental, double-stranded DNA molecule into two daughter double-stranded DNA molecules each containing one parental strand and a complementary, newly synthesized strand. DNA strand exchange A process whereby single strands of DNA are exchanged between two homologous double-stranded DNA molecules. DNA strand exchange protein A protein that, upon binding to a single-stranded DNA, catalyses the transfer of that strand to a homologous region of a double-stranded DNA molecule, disrupting the original duplex to produce a new heteroduplex. DNA transposable element Transposable element that moves via a DNA intermediate. doctrine of double effect A doctrine for those committed to the inviolability of specific moral laws. When the unintended effect of an action meets the doctrine’s four conditions it is morally permissible. dolichol A polyisoprenoid lipid that acts as a carbohydrate carrier and donor in glycosylation reactions. dolipore A septal pore complex in certain basidiomycete yeasts in which the pore wall is swollen into a barrel-like morphology. domain (1) A discrete, compactly folded, structural unit in a protein, which often also has a discrete function. A protein may consist of a single domain or of multiple similar or different domains. (2) A region of DNA with a level of supercoiling different from that of the bulk DNA. (3) In taxonomy, the highest level of biological classification. The three domains of living organisms are Bacteria, Archaea and Eukarya. domestication The breeding of plants or animals for human use. dominance The situation in which an allele determines the phenotype when it is present in only one copy. dominant allele An allele that determines the phenotype when it is present with another allele (the recessive allele) in a heterozygote. dominant mutation A mutation that results in a phenotypic effect when in the heterozygous state. The mutant allele prevails over the normal allele. The phenotype of individuals heterozygous or homozygous for the mutation is similar.

170

Glossary

dominant-negative mutation A mutation that gives rise to an abnormal gene product that interferes with the function of the product of the normal allele when the mutant and normal allele are present together. do-not-resuscitate A medical order that tells the healthcare team that a particular patient should not receive certain procedures such as cardiopulmonary resuscitation in the event that their heartbeat or respiration stops. DOPA Dihydroxyphenylalanine, the catechol amino acid precursor of catecholamines. dopamine The catecholamine precursor of noradrenaline and adrenaline. It is also an important neurotransmitter in its own right. dormancy In spores and seeds, a period of minimal metabolic activity during which no further development occurs. dorsal Towards the back of an animal. dorsoventral The axis between the back and underside of an animal, or the upper and lower surfaces of a leaf. dosage compensation The process by which the expression of genes on the X chromosome is adjusted in cells that contain more than one X chromosome, so that levels of expression of Xchromosome genes are equalized in males and females. double-stranded RNA-binding motif (dsRBD) An RNA-binding domain in proteins that consists of 65–70 amino acids and interacts with double-stranded RNA only. Dounce homogenization Breaking open cells by shearing forces generated in a Dounce homogenizer, a glass tube with a tightfitting ball that acts as a teflon or glass pestle. downstream A way of referring to relative positions on nucleic acids. As DNA and RNA chains are synthesized in the 50 to 30 direction, downstream means ‘toward the 30 end’. drift Differential survival and reproduction of organisms that is not due to environmental interaction. drug resistance Ability of microorganisms to grow in the presence of a usually effective antibiotic. dry deposition The adsorption of gaseous or particular material from the atmosphere on land, water or plant surfaces. DTH See delayed-type hypersensitivity. duplex DNA Double-stranded DNA. duplex Double, usually refers to the double helix of DNA. duration The actual ‘lifetime’ of a taxon, from origination to extinction. This is usually unknown. dwarf mutants Plants with an altered gene or genes that result in a short stature. dysmetria Failure of precise reaching, as is revealed when a person tries to touch the tip of the nose with their fingertip with the eyes closed. dyspnoea Shortness of breath.

EAE See experimental autoimmune encephalomyelitis. E box The specific DNA sequence to which basic helix-loop-helix (bHLH) factors bind. E site Exit (E) site, the site on the ribosome where tRNA that has discharged its amino acid is bound before it exits the ribosome. early genes The first viral genes transcribed, enabling nucleic acid replication and other viral functions. ecdysis The shedding or moulting of an old arthropod exoskeleton to reveal a new, larger one underneath.

ecdysozoan An animal belonging to the clade containing arthropods, onychophorans, tardigrades, nematodes, nematomorphs, chaetognaths and cephalorhynchs. ecdysteroids Invertebrate steroid hormones involved in signalling ecdysis or moulting. echogenicity The degree to which ultrasound is returned, by reflection or scattering, from the region (usually of the body) being scanned. It is indicated in the display by the level of brightness in the greyscale image. eclampsia Convulsions associated with the syndrome of preeclampsia. eclipse period The interval early after phage infection during which no infectious particles can be recovered from infected cells. ecological integrity The condition of an ecosystem that is largely free from human interference and possesses a species composition and functional organization comparable to natural ecosystems in the region. ecological niche The role of an organism in a biological community, including where it lives, what environmental conditions it requires, and how it interacts with other organisms. ecological species concept The idea of a species as a lineage that occupies an adaptive zone minimally different from that of any other lineage in its range, and that evolves separately from all lineages outside its range. ecomorph A morphological body design that fits a specific set of ecological features. economic development Projects that contribute financial benefits to people. ecosystem A community of organisms and the physical environment with which they interact. ecosystem goods and services The set of all economic goods (e.g. timber, fish) and services (e.g. pollination, flood control, climate regulation) that are provided by functioning ecosystems and that sustain and enrich human lives and societies. economic threshold The economic limit above which it becomes advantageous to use a chemical such as a fertilizer, herbicide or pesticide. For a herbicide, for example, the threshold might be expressed as the number of weed seedlings per square metre. ecotype A genetically specialized population living in a particular type of habitat, for example, populations of plants living in alpine environments. An ecotype is a subset of a more broadly distributed species. ectoderm (1) One of the three germ layers of a tribloblastic animal embryo. It consists of the outer tissue layer and gives rise to the nervous system and the epidermis. (2) Epithelium covering the outer surface of cnidarians. ectopic Out of normal context and/or location. ectopic exchange Recombination between two related sequences (e.g. transposable elements) at nonhomologous positions in the genome. ectopic expression Misexpression of a gene with respect to space or time. ectotherm Animal in which body temperature principally reflects environmental temperature and is determined mainly by the heat content of the immediate environment. See also exothermy.

171

Glossary

ectothermy ‘Cold-bloodedness’; the condition in which an animal does not generate the heat to warm its body by internal means. edentulous Lacking teeth. editing In the context of translation, the ability of aminoacyltRNA synthetases to prevent or correct mistakes in the aminoacylation of tRNA. editosome A complex of proteins and/or RNAs that is assembled for the purpose of editing RNA. efavirenz Non-nucleoside analogue inhibitors of human immunodeficiency virus 1 (HIV1). effective population size The number of breeding individuals (Ne) in a randomly mating population that has the same effect on genetic variability (i.e. gene diversity) as observed in the population under investigation. It reflects the strength of random genetic drift. effector gene A gene that encodes a regulatory protein, either an activator or a repressor, that can affect the expression of a reporter gene in a co-transfection assay. effector lymphocytes Lymphocytes that can carry out their functions without further differentiation and proliferation, for example mature cytotoxic T cells. efferent Carrying away from. Efferent fibres carry signals away from the central nervous system; efferent lymphatics carry lymph away from lymph nodes and other lymphoid organs. efferent nerve fibres Nerve fibres that conduct from the centre (e.g. the spinal cord) to the periphery. The term broadly corresponds to motor fibres. efferent lymphatic vessel A lymphatic vessel that carries lymph from a lymph node. efferent projection The axons that project to a structure from a source – the output. egg activation A sequence of biochemical and cellular changes that occurs after fertilization, leading to the release from meiotic arrest, division of the fertilized egg and further embryonic development. egg chamber Cluster of oocyte and associated nurse cells surrounded by somatically derived follicle cells, in polytrophic ovaries of insects. eicosanoids A class of lipid signalling molecules including the prostaglandins, thromboxanes and leukotrienes. EJP See excitatory junctional potential. elasmobranchs The sharks and rays. elasticity The tendency of a material to return to its original shape after an applied load is removed. elastin Protein component of elastic connective tissue, present in artery walls, skin and intestinal walls. The elastin protein chain is particularly flexible and will return to its original shape after being stretched. electrical field The pattern of the electrical influence derived from the presence of an electrical potential and current. electrocardiogram A recording of the waves of electrical activity associated with contractions of the heart. electrochemical gradient The combination of the concentration gradient and the electrical gradient (voltage difference) of an ion distributed unequally across a biological membrane. electrogenicity A property of a coupled transport process which results in an increase in net charge on one side of the membrane. The mammalian sodium pump is electrogenic.

electrolytes Charged particles, or ions, that carry an electrical current when dissolved in solution. electromagnetic radiation The energy emitted by an electrical or magnetic source, and which obeys Maxwell equations. electromagnetic waves Travelling disturbance comprising an electric field and a magnetic field at right angles to each other. electron carrier A protein or other organic molecule that can either accept or donate electrons in oxidation–reduction reactions. electron transfer A set of serial redox reactions that results in transport of electrons or reducing equivalents from one molecule to another. electron transport Transport of electrons via redox proteins such as cytochromes. electron transport chain Sequence of membrane-bound electron carriers, which carry electrons from an electronegative electron donor to a more electropositive acceptor. In the electron transport chains of bacterial cell membranes, mitochondria and chloroplasts this transport is coupled to the movement of protons across the membrane, forming an electrochemical gradient that powers ATP synthesis. electron paramagnetic resonance (EPR) A magnetic resonance technique used to study the chemical nature and environment of paramagnetic chemical species (those with unpaired electrons) such as organic radicals and certain oxidation states of transition metals. electropherotype The migration pattern of RNA segments subjected to gel electrophoresis. electrophile An electron-deficient atom (e.g. a carbon atom with a partial positive charge, C/d1 ) or compound that tends to react with electron-containing nucleophiles. electrophilic Involving an electron-deficient centre. electrophoresis A procedure that separates a heterogeneous population of similar molecules (e.g. DNA fragments of different sizes) on the basis of their movement in an electric field. Separation is on the basis of the size and electrical charge of the molecules. In gel electrophoresis, the mixture is applied to a gel and an electric current passed through it. electroporation Subjection of cells to a high-voltage electric field to make them temporarily permeable to macromolecules such as DNA. electroreceptors Sensory receptors for detection of weak electrical discharges. electrostatic effects The use of complementary electrical charges by enzymes to stabilize the binding of substrate at an active site and to stabilize polar transition states in reactions. electrotonic decay Passive decay of a voltage change, as a function of distance from the point of origin, as it travels through a membrane. electrotonic propagation The passive transfer of electrical potentials from one location to another in a neuron whose membrane contains no voltage-dependent conductances. The strength of the signal gradually decays with distance from its source. elicitor Pathogen-encoded molecule that induces a plant defence response such as phytoalexin accumulation, programmed cell death or synthesis of PR (pathogenesis-related) proteins. Elicitors can be abiotic (e.g. ultraviolet light, low temperature) or biotic (e.g. microbial cell wall polymers).

172

Glossary

elicitor active site A domain of an avirulence factor of a plant pathogenic microbe that is recognized by the protein product of the corresponding resistance gene in the plant. Mutations in elicitor active sites result in a loss of recognition and induction of resistance. ELISA Enzyme-linked immunosorbent assay. A sensitive test for the presence of an antigen or an antibody in a sample, which makes use of enzyme-labelled antibodies as detectors. ELISPOT An adaptation of ELISA which is used, for example, to detect the frequency of T cells secreting a particular cytokine. Individual cells are placed on a plastic surface coated with cytokine-specific antibody and incubated. After removal of the cells, cytokines secreted by a cell and bound to the immobilized antibody can be detected as coloured spots by a second enzymelabelled anti-cytokine antibody. elongation The successive addition of amino acids to the growing protein chain during translation of mRNA. At each round of elongation, one amino acid is added to the chain in a reaction involving the ribosome, mRNA, the aminoacyl-tRNA, elongation factors and GTP. elongation factors Proteins that participate in the elongation reaction of translation. ELSI Abbreviation for ethical, legal and social issues. emargination Reduction (of the skull roof in this case) by reduction of bone from the edges. Embden-Meyerhof-Parnas pathway A pathway that degrades glucose to pyruvate through the conversion of glucose to fructose-1,6-bisphosphate. Adenosine triphosphate (ATP) is generated during the process. embedding medium A matrix for encapsulating or infiltrating a specimen. When solidified, this matrix acts as a support to facilitate slicing of the specimen into thin sections. embryo (1) Generally, the stage in the development of a multicellular organism from the zygote when it is not yet fully formed and capable of independent life. (2) In mammalian development, the portion of the conceptus that will eventually give rise to the fetus, when in the gastrulation and presomite stages. embryogenesis The development of the embryo from the fertilized egg. embryonic (1) Generally, pertaining to an embryo. (2) Refers to those tissues in the mammalian conceptus that will form the fetus. embryonic induction Interaction between two cell lineages required for the control of normal cytodifferentiation and organogenesis. embryonic root Root structure formed during embryogenesis in plants. embryo sac Female gametophyte in angiosperms. It contains an egg cell, a central cell, and accessory cells (synergids and antipodals). embryonic stem cell (ES cell) An undifferentiated cell type isolated from the inner cell mass of blastocyst-stage mammalian embryos. Embryonic stem cells can be maintained indefinitely in culture. With the appropriate induction signals, they can potentially differentiate into any somatic cell type of the body. embryonic suspensor A product of the early zygotic divisions in angiosperm plants. This structure provides positional and nutritional support for the developing embryo within the embryo sac.

embryophytes Collective term for bryophytes (hornworts, liverworts and mosses) and vascular plants (ferns, fern allies, gymnosperms and angiosperms). They have sexual reproduction involving antheridia and archegonia (or their derivatives in the case of gymnosperms and angiosperms). emission spectrum The wavelength distribution of the light emitted by a light source. enantiornithomorphs Diverse group of flying Cretaceous birds of worldwide distribution. encapsidation The enveloping of the viral nucleic acid in a protein coat during virus replication in an infected cell. encephalitis Inflammation of the brain. endemic (1) A species whose habitat is restricted to a particular region or specific locality. (2) The continuous presence of disease, at a low level, in a population. end-joining repair Repair of double-strand breaks in DNA by rejoining the broken ends without the involvement of unbroken homologous strands or extensive homologous sequences on either side of the break. Addition or deletion of one or a few bases may occur. endochondral bone Bone produced by ossification of a cartilage model, also called cartilage replacement bone. endochondral ossification Bone development and repair achieved through the intermediate step of formation of a cartilage scaffold. endocommensal A symbiont that lives inside its host without harming it. It derives nutrition from this association while the host is neither harmed nor benefited. endocrine gland A ductless gland that produces a secretion that spreads or is transported in the circulating body fluids. endocytosis The uptake of extracellular molecules by animal cells through the formation of membrane-bound vesicles. In receptor-mediated endocytosis specialized receptors bind specific ligands and the complex is then internalized. In pinocytosis, small amounts of liquid and small particles are taken up nonspecifically. endoderm (1) One of the three germ layers of a tribloblastic animal embryo. Endodermal cells move from the surface of the embryo into the interior at gastrulation, and develop into the gut and associated organs. (2) Epithelium lining the coelenteron of cnidarians. Also called the gastrodermis. endodermis Single layer of cells separating the root cortex from the stele characterized by a Casparian band. endogenous Originating within the body. endogenous retrovirus Retrovirus integrated into chromosomal DNA and transmitted in this form through the germline of a species. endogenous stages The stages of the life-cycle of a parasite that occur inside the host. endolymph A modified extracellular fluid filling the inner ear. Endolymph has an ionic composition similar to that of intracellular fluid (rich in potassium ions). endonuclease Enzyme that breaks down a nucleic acid strand into fragments by cleaving it at internal phosphodiester bonds. endopeptidase Enzyme that cleaves a protein chain at specific amino acid(s). endophyte A microorganism living within the tissues of a plant, usually in a symbiotic or commensal relationship.

173

Glossary

endoplasmic reticulum (ER) A specialized membrane-bounded compartment that extends throughout much of the cytoplasm of eukaryotic cells. It is involved in the maturation, modification and transport of newly synthesized secretory and plasma membrane proteins which are delivered into it from ribosomes on its cytosolic face. It is also a site of steroid synthesis and calcium storage. endoprotease Enzyme that hydrolyses internal peptide bonds in proteins. endoproteolytic Refers to the cleavage of internal peptide bonds within a protein chain. endoreduplication Replication of DNA without nuclear division. endoribonuclease An enzyme that degrades RNA by cleaving at internal phosphodiester bonds. endosialidase An enzyme that releases polysialic acid from glycolipids and proteins. endosomal latency The ratio between membrane-associated horseradish peroxidase activity and activity released due to disruption of endosomal membranes. endosomes Membrane-bounded cytoplasmic vesicles, deriving initially from the plasma membrane, that are formed when extracellular material is internalized by endocytosis in animal cells. They carry the endocytosed material to lysosomes for degradation. endosperm The storage tissue in angiosperm seeds. It derives from a cell with two female polar nuclei, with which one male gamete nucleus has fused. endospore (1) A spore formed within a cell. (2) A dormant cell formed by Bacillus subtilis in response to nutrient limitation, and which is resistant to heat, desiccation and ultraviolet light. endosternite A horizontal sheet of cartilage-like connective tissue in the prosoma of most chelicerates that serves as an internal skeleton for the attachment of muscles. endosteum A single layer of bone cells that covers the internal surface of bone and physically separates the bone surface from the bone marrow within. endosymbiont A microorganism that lives within the cells of another organism to their mutual advantage. endosymbiosis A mutually beneficial symbiotic relationship in which one organism, the endosymbiont, lives inside the cells of another, the host. endosymbiotic relationship See endosymbiosis. endothecium Cell layer comprising the anther wall. endothelium The inner lining of blood and lymph vessels, formed of a single epithelial layer of flattened cells. It separates the blood from the outer layers of the vessel wall, or subendothelium. endotherm Animal whose body temperature is independent of environmental temperature and remains fairly constant, and is determined mainly by the balance of heat generated by metabolism and heat lost through thermal conductance. endothermy Regulation of body temperature by the generation of heat inside the body as the result of metabolic processes. endplate A specialized synapse connecting motor nerve endings and striated muscle cells. Also called a neuromuscular junction or motor endplate. energized membrane A membrane across which an electrical potential exists.

enhancer A regulatory DNA sequence at which binding of gene regulatory proteins increases the expression of a linked gene. enhancer of PEV (E(var)) A second-site mutation that leads to enhancement of the position-effect variegation (PEV) phenotype, i.e. a mutation that results in less expression (more silencing) of a euchromatic gene subject to PEV. enteroblastic A type of repeated budding at the same location of the cell surface in basidiomycete yeasts. enterocyte Absorptive cell of the intestinal wall. enterogenous Describes the condition in which the outer wall of a conidium is formed by the ruptured conidiogenous cell and a new wall is laid down within the conidium. enterohepatic circulation Situation in which drugs or their metabolites are taken up by, or produced in, the liver, and excreted by the liver in the bile which carries them into the gut. From the gut they are absorbed into the portal vein and carried back to the liver. enterotoxin A toxin that affects the physiological function of the intestine. entoparasitic Describes a parasite that lives within the body of the host. entropy A measure of the randomness in a system. The change in entropy for a system is given by the ratio of the heat absorbed by the system in a reversible isothermal process divided by the absolute temperature. envelope The envelope of lipid and protein that surrounds some virus particles. It is acquired as the virus buds from the cell through the plasma membrane. The envelope proteins are encoded by the virus and inserted into the cell plasma membrane before budding. envenoming, envenomation The effects of entry of venoms into the living organisms. environmental ethics A set of beliefs, exemplified by Aldo Leopold’s ‘and ethic’, which holds that all life has intrinsic value and therefore the destruction of other species is immoral. environmetrics The application of statistical theory to environmental data. enzyme A protein that catalyses a specific biochemical reaction. enzyme covalent intermediate A chemical entity that is directly on the pathway leading to the observed product(s) of an enzymecatalysed reaction and that involves a covalent bond between a nucleophile provided by the enzyme and at least a portion of one of the substrates. enzyme crystal structure The atomic structure of an enzyme molecule deduced from the pattern of diffracted X-rays when an X-ray beam is passed through a crystal of the enzyme protein. enzyme inhibitor Any substance that decreases the catalytic activity of an enzyme, usually by binding to it. enzyme-linked immunosorbent assay See ELISA. enzyme repression Inhibition of the synthesis of an enzyme by a specific repressor substance, often the end product of the pathway. enzyme substrate A reactant that binds to an enzyme and, while bound, participates in the reaction catalysed by the enzyme. enzyme–substrate complex See Michaelis complex. epidermis The outermost layer of cells on the body of an animal or plant. In vertebrate skin, it is the outer layer of keratinocytes, separated by a basal layer from the dermis.

174

Glossary

Eph receptors Receptor tyrosine kinases that are activated by ephrins. They fall into two classes: EphA receptors bind ephrin-A ligands; EphB receptors bind ephrin-B ligands. ephrins Cell-surface adhesion molecules involved in axon guidance and other aspects of neural development. They fall into two classes: the ephrin-A family are tethered to the plasma membrane by glycosylphosphatidylinositol anchors; the ephrin-B family are transmembrane proteins. epibiont Organism using another organism as a substrate to live on. epicuticle (1) The outermost waxy covering of the arthropod cuticle. (2) The outermost body layer of horse-hair worms (nematomorphs), often sculptured and containing bristles and warts. epidemic Large-scale outbreak of an infectious disease that spreads rapidly through the population. epidermal basal cells The proliferating undifferentiated stem cells in the basal layer of the epidermis, from which the keratinocytes of the skin are derived. epifluorescence Microscopical technique that uses an ultraviolet filter to detect autofluorescence. epigenetic development Those aspects of development that are not directly programmed by gene action. epigenetic inheritance The transmission of a stable pattern of gene expression that is due to reversible modifications of DNA or chromatin, such as DNA methylation or histone acetylation. epigenetic regulation Process by which stable modifications of gene function occur (heritable through mitosis) that are not due to changes in the base sequence of the DNA, but reflect other changes in the chromatin. X-chromosome inactivation in female mammals is an example. epimastigote A developmental stage of trypanosomatids in which the kinetoplast is located in the anterior region of the cell, in front of the nucleus. In this form the flagellum emerges laterally, forming a short flagellar pocket. epimerase An enzyme that will racemize a single chiral centre in a molecule that contains more than one such centre. epimorphic regeneration Regrowth of amputated structures from an anatomically complex stump. This may involve either replacement of parts of appendages or regeneration of fractions of organisms into new complete individuals after their bisection. epiphyte An organism growing on the surface of a plant. epipod A lateral process from the base (protopod) of the arthropod limb. episome A plasmid that can exist either as a circular extrachromosomal DNA or integrated into the cell chromosome. The terms ‘plasmid’ and ‘episome’ are sometimes used interchangeably. epistasis Alteration of the expression of one gene by effects at another gene locus. This is how different genes interact in the development of behaviour, physiology, and morphology. epistatic fitness interactions The fitness of a genotype is determined by allele combinations at multiple loci in a nonadditive manner. epistome Lip along the inner tentacle row in bryozoans, covering the mouth from the dorsal side. epithelial cell (1) Cell that forms part of an epithelium. (2) Large myoepithelial cell of either ectodermal or endodermal origin in hydrozoans. Epithelial cells differentiate progressively as they migrate towards the extremities, thus becoming head- or footspecific.

epithelial–mesenchymal interactions Morphogenetic or inductive interactions between an epithelium and its mesenchymal stroma, e.g. in parenchymal organs. epithelium Sheet of cells that forms the linings of body cavities and the glandular structures of organs. Epithelia are formed of cells tightly bound together and polarized, with distinct apical and basal faces. The small portion of an antigen that provides the actual binding site for an antibody or (after processing of the antigen) a T-cell receptor. A single antigen may have more than one epitope. Also known as an antigenic determinant. epitope The small portion of an antigen that provides the actual binding site for an antibody or (after processing of the antigen) a T-cell receptor. A single antigen may have more than one epitope. Also known as an antigenic determinant. epitope tagging The addition of a well-characterized epitope from a known antigen (such as influenza virus haemagglutinin) to another protein to make it readily detectable by antibodies specific for the epitope. epizootic A large-scale outbreak of an infectious disease in animals, originating from a common source. EPR See electron paramagnetic resonance. EPS (1) Extracellular polymeric substances. (2) See exopolysaccharide. EPSP See excitatory postsynaptic potential. Epstein–Barr virus A virus of the herpesvirus family that infects B lymphocytes and causes infectious mononucleosis and is also implicated in the development of certain cancers. equatorial and axial bonds A bond to a tetrahedral atom in a sixmembered ring system, as in glucopyranose, is said to be equatorial if it makes a small angle to the plane of the ring and axial if it makes a large angle to the plane of the ring. equilibrium (1) The condition that prevails when a forward and a reverse reaction proceed with equal rates. (2) A state of a macromolecule–ligand system in which concentrations of all reactants remain constant (time change of any concentration C is dC/d, t 5 0). Generally, such a state is achieved in an infinite time. equilibrium centrifugation Technique by which particles are separated by centrifugation by virtue of their different densities in a density gradient. equivalent Cot (Ecot) The Cot value with a correction applied for salt concentration if the solvent is other than 0.12 mole per litre sodium phosphate buffer. ER See endoplasmic reticulum. erectile tissue Tissue that becomes firm or rigid due to increased blood flow, usually during sexual arousal. ergosterol A fungal-specific membrane lipid targeted by all three classes of current antifungal therapies. erratics Glacially transported boulders, deposited far from their geologic source, often with a mineral composition different from that of their resting place. erythroblastosis The flooding of the circulation with erythroblasts (nucleated red cells), which occurs when haemolysis is so severe that blood production is stimulated in sites other than the bone marrow. erythrocyte Red blood cell. erythropoiesis The generation of red blood cells from undifferentiated precursors in bone marrow. EST See expressed sequence tag. electrospray ionization mass spectrometry See ESI-MS. espundia Mucocutaneous leishmaniasis.

175

Glossary

essentialism Belief in essences, or timeless and unchanging patterns, often associated with thinking in stereotypes and deemphasis of diversity. Also known as typology. estuarine Pertaining to an estuary where tidal water meets a river current. E-tests A commercial system for estimating minimum inhibitory concentrations of antimicrobial agents. ethylene Gaseous plant hormone involved in regulating plant responses to stress, including mechanical damage. euchromatin Whole chromosomes or chromosomal segments that show normal staining properties, the normal cycle of chromosome condensation and decondensation and DNA replication, and may be genetically active. eugenics Practices that attempt to control human biological heredity. eukaryotes Organisms of the Domain Eukarya: protists, animals and plants. They may be multicellular or unicellular and have cells with a complex organization, distinguished from the cells of prokaryotes by a distinct nucleus containing the DNA in the form of chromosomes, and a cytoplasm containing membranebounded organelles of different functions such as mitochondria, endoplasmic reticulum, Golgi bodies and (in plants) chloroplasts. eukaryotic Pertaining to eukaryotes or their cells. eukaryotic cell A cell of a eukaryote, distinguished from prokaryotic cells by their generally larger size and complex organization, with the genetic material enclosed in a membrane-bounded nucleus, and a cytoplasm containing many different types of membrane-bounded organelles. euploid Having the normal number of each chromosome. Europa A moon of Jupiter which may harbour a water ocean beneath its icy carapace. Euryarchaeota A kingdom of Archaea consisting of methanogens, extreme halophiles, hyperthermophilic sulfate reducers, Thermoplasma and the Thermococcus–Pyrococcus group. eurytopic Adapted to a broad range of environments and so having a broad ecological range. eustatic sea level An estimate of average global sea level after correcting for local variations in land surface subsidence and/or emergence. eutely A constancy of cell number in particular tissues or organ systems. It is common when structures are secondarily simplified (e.g. through miniaturization). eutherian mammals, Eutheria Subclass of mammals in which the embryo is nourished through the placental circulation (cf. marsupial mammals). euthermy Regulation of body temperature in the range 30–451C, generally by endothermic processes. eutrophic Describes a nutrient-rich aqueous environment. E(var) See enhancer of PEV. evaporite mineral A mineral deposited from a saline solution as a result of concentration through evaporative water loss. e-vector orientation Sunlight is linearly polarized, i.e. it oscillates in a preferred orientation perpendicular to the direction of propagation. Many animals can sense this orientation. evolutionary species concept A lineage evolving separately and temporally from others and with its own unitary evolutionary role and tendencies. EXAFS See extended X-ray absorption fine structure spectroscopy. excess mortality An increase in the death rate that occurs during influenza pandemics and many epidemics.

excision repair A type of DNA-repair process in which a singlestranded tract of DNA containing damaged or mismatched bases is excised from the DNA helix and replaced with new bases. excitable media Materials that actively respond to their environments by virtue of intrinsic chemical or electrical properties. All living tissue and cell aggregates fall into this category, and some nonliving excitable media have also been described. excitation (1) Of a neuron or other excitable cell such as muscle, the induction of an action potential by stimuli that produce a sufficiently large depolarization of the cell membrane. (2) The mechanism by which the initial signal from the chemotactic receptor is transduced to the bacterial flagellar motor and affects the direction of flagellar rotation. excitatory signal See excitation. excitation–contraction coupling The process by which the electrical events associated with cell membrane depolarization in muscle cells are coupled to the activation of contractile proteins to initiate muscle contraction. excitatory Describes an influence tending to depolarize the membrane potential of a neuron towards its action potential threshold. excitatory junctional potential (EJP) The postsynaptic response of a muscle cell to activity in an excitatory motor neuron. excitatory neurotransmitter A chemical released from nerve terminals that produces excitation of the target neuron. excitatory postsynaptic potential (EPSP) The depolarization of the membrane of a postsynaptic cell which brings membrane potential nearer the threshold at which an action potential will be generated. It occurs in response to an excitatory stimulus (neurotransmitter) from the presynaptic cell. excitotoxicity Neuronal toxicity induced by overstimulation by glutamate or related amino acids. It is due to overstimulation of the ionotropic receptors for these molecules and the resultant ion movements across the neuronal membrane. excluded volume The volume around a three-dimensional object that is inaccessible to other three-dimensional objects. excrescences DNA extensions or protuberances of the bacterial nucleoid that reach far into the cytoplasm towards the ribosomes. excretory antigen Antigens excreted by an organism. exfoliation The constant shedding of cells from the uppermost layers of squamous epithelium. exobiology Study of the origins, early evolution and distribution of life in the Universe. exocrine gland A gland that has a duct and produces a secretion that passes out of the gland onto a body surface (external or internal), e.g. salivary gland. exocytosis The fusion of an intracellular vesicle with the cell membrane and discharge of its contents to the exterior of the cell. exodermis Hypodermal cells of plant roots having a Casparian band. exogenous stage The stage in the life-cycle of a parasite that is released outside the host to the environment. exon A sequence within a gene or primary RNA transcript that is retained following the splicing reaction and thus represented in the final mature RNA product. Exons usually, but not always, represent protein-coding sequences. exon splicing Processing of a primary RNA transcript that removes intervening (intron) sequences and joins the remaining exon sequences together to form the functional RNA. exonuclease Enzyme that degrades a nucleic acid from the ends, cleaving off one nucleotide at a time.

176

Glossary

exopeptidase Enzyme that hydrolyses one or two amino acids from either end of a peptide. exoplanet A planet beyond the Solar System. exopolysaccharide (EPS) Polysaccharide found outside the microbial cell wall. exoribonuclease An enzyme that degrades an RNA molecule by removal of successive nucleotides from either the 50 or 30 end. exoskeleton The hard external supporting skeleton of insects and other arthropods. It is secreted by epidermal cells. exosporium The loosely fitting envelope of complex chemical composition surrounding the outer coat of a bacterial endospore. exothermy Regulation of body temperature by variation in the flow of heat into the body from outside, generally by behavioural adjustments. expansin An enzyme whose activity is to break hydrogen bonds. It is thought to act primarily to break hydrogen bonds between cellulose and molecules bound to the surface of cellulose in plant cell walls. experimental autoimmune encephalomyelitis (EAE) An autoimmune disorder of the central nervous system experimentally induced in mice by injection of myelin components. It serves as a model for human multiple sclerosis. explant Tissue removed from an organism and transferred to an artificial nutrient medium for growth. expressed sequence tag (EST) A clone from a cDNA library for which a partial sequence has been generated. expression system A cell culture system into which a foreign DNA can be introduced as part of a specialized vector that enables it to be expressed as protein. expression vector In recombinant DNA work, a type of vector that contains promoters and other regulatory sequences that enable a protein-coding DNA inserted into the vector to be transcribed and translated if introduced into the appropriate cells. extant Living, not extinct. extender unit See starter and extender units. extended X-ray absorption fine structure spectroscopy (EXAFS) An X-ray spectroscopic technique that can reveal shortrange distances (less than approximately 0.4 nm) between a metal atom and neighbouring metal and ligand atoms. Unlike X-ray diffraction methods, EXAFS can be performed on non-crystalline preparations. extensibility A quantitative strain of a cell wall as a result of the stress induced by the osmotic pressure above the yield threshold. external sense organ Sensory structures that originate in the periphery, with axons that project into the central nervous system. They serve mechano- and chemoreceptor functions. external state Free enzyme plus free ligand. extinction The disappearance of a species, or other larger group of plants or animals. extracellular matrix A material composed mainly of protein and proteoglycan that is secreted by cells and fills the extracellular spaces in tissues. extracellular pathogens Microorganisms that replicate and/or persist on surfaces or in the extracellular spaces of tissues. extracellular polymeric substances (EPS) Polysaccharide and proteinaceous material secreted outside of the diatom frustule that takes the shape of stalks, tubes, films and pads.

extracellular signals Molecules, including metabolic intermediates, proteins and peptides, that can be exchanged between cells as a means of communication. extracytoplasmic location Location of a parasite inside the cell but without contact with the cell cytoplasm. extraembryonic Refers to those tissues in the conceptus required for implantation and maintenance of the conceptus during gestation, but which will be shed at birth (e.g. placenta, yolk sac, amnion). extrarenal transplants Transplants other than kidney transplants, including heart, lungs, liver, pancreas and intestinal transplants. extrasporogonic forms Vegetative stages of a parasite that multiply in tissue locations different from the site of sporulation. extravasation Migration of white blood cells from the bloodstream into a tissue. extreme halophiles Archaea that can only live in the presence of high concentrations of sodium chloride (usually more than 10%). extremely thermophilic sulfur metabolizers Archaea that live between 601C and 1131C and gain energy by the oxidation or reduction of sulfur compounds or by anaerobic sulfate respiration. extremophile An organism that exists under extreme conditions of temperature, salt and/or pressure, e.g. in deep oceanic vents. extrinsic allergic alveolitis A type III immune complex disease produced by the inhalation of soluble antigens. exuviae The cast-off fragments of a moulted arthropod exoskeleton. ex vivo Describes a type of therapy in which cells extracted from a patient are subjected to treatment and then reintroduced into the patient. ex vivo gene transfer Gene transfer into cells preceding the cells’ implantation into the body.

F chlorosomes Chlorosomes found in the nonsulfur filamentous bacterial family Chloroflexiaceae. F factor See F plasmid. F pilus Protein filament on the bacterial surface through which DNA is passed from one bacterium (the ‘male’) to another (the ‘female’). F plasmid A sex plasmid of the bacterium Escherichia coli, which enables conjugation and its own transfer by encoding formation of the F pili. F0 F-prime, an F plasmid that carries a stretch of bacterial chromosomal DNA, and can thus transfer chromosomal genes from one cell to another. F1F0 ATPase The protein complex located in the inner mitochondrial membrane that synthesizes ATP from ADP and PI. The energy for the reaction comes from the flow of protons through the protein complex. Fab fragment A fragment of an antibody molecule that contains one of the antigen-binding sites. It consists of one entire light chain and the V and CH1 domains of the paired heavy chain and is obtained by papain digestion. facies A particular kind of sedimentary environment, e.g. black shale, shallow marine carbonate.

177

Glossary

facilitation The fastest phases of enhanced transmission in shortterm synaptic plasticity, consisting of two components with time constants of tens and hundreds of milliseconds. FACS See fluorescence-activated cell sorter. factor A general term for a molecule (almost always a protein) or complex of molecules, that carries out a particular function or is involved in a particular reaction. It is used especially when a molecule is identified only by its function and has not yet been chemically characterized. The names of many proteins, such as epidermal growth factor, factor VIII, elongation factor, initiation factor, nerve growth factor, arise historically from this usage. factor VIII Blood coagulation factor whose lack of activity in plasma causes haemophilia A. factor IX Blood coagulation factor whose lack of activity in plasma causes haemophilia B. facultative heterotrophs Organisms that are able to grow as chemolithoautotrophs as well as heterotrophs. falsifiability An indicator of the scientific status of a theory, in that it is in principle open to disproof. A good scientific hypothesis will make predictions about the world that expose it to refutation by empirical evidence. FAOS Fluorescence-assisted organelle sorting. A method of purification by which fluorescently-labelled organelles, such as phagosomes containing microorganisms that express the green fluorescent protein (GFP), can be isolated from other organelles using a fluorescence-activated cell sorter. Farenholz’s rule ‘Parasite phylogeny mirrors host phylogeny’. fasciculation The growth of nerve cell axons side-by-side to form a bundle. FASTA format A standard format for nucleic acid or protein sequences. The first line begins with a ‘greater than’ sign (4) followed by a short description of the sequence. The subsequent lines consist of strings of one-letter amino acid or nucleic acid codes. fate map A definition of regions in the early embryo that will normally give rise to a particular tissue in the adult. fat-soluble vitamins Vitamins A, D, E and K, a group of terpenoids composed of an activated five-carbon isopentenoid unit. fatty acid The carboxylic acid of a (sometimes modified) hydrocarbon chain. In cells, they are used as energy sources and as building blocks for more complex molecules such as membrane phospholipids, fats and oils. fauces The passage from the mouth to the pharynx. Fc receptor Cell-surface receptor on phagocytes and other cells that binds the constant part (Fc region) of an antibody when it is complexed with its antigen. There are different Fc receptors specific for the different classes of antibody. Fc That part of an antibody molecule comprising most of the constant region, including the binding sites for complement and for receptors (Fc receptors) on various types of white blood cell. It is responsible for antibody effector functions and has no antigenrecognition capability. Fc/epsilonRI High-affinity receptor for the Fc portion of IgE, present on mast cells and basophils. Fc/epsilonRII A C-type lectin which is a low-affinity receptor for IgE, present on B cells. febrile With an abnormally high body temperature.

febrile neutropenia A clinical condition with severe neutrophil deficiency (neutropenia) (usually less than 0.5 Â 109 neutrophils per litre) and fever (usually temperature greater than 38.51C). feral Describes an animal that is wild and untamed, not domesticated. fermentation A type of metabolism in which glucose (or other substrate) is partially oxidized using internal electron acceptors, e.g. pyruvate. ferredoxin A soluble FeS protein located in the stroma of chloroplasts that accepts electrons from photosystem I. Ferredoxin serves as a branch point in photosynthetic electron transport. fertility An individual’s ability to produce offspring, measured in population terms as the average number of offspring per parent. fertilization The fusion of the cells and nuclei of two gametes of opposite sex to form a zygote. fetoscopy Direct visualization of the fetus through an endoscope during pregnancy. fetus In mammalian development, the embryonic portion of the conceptus once the somites have formed and beyond. FGF, Fgf, fgf Gene symbols for fibroblast growth factor genes. FGF See fibroblast growth factors. FH Bacteriophage of the archaeon Halobacterium salinarium. fibrinogen Plasma protein that is converted to insoluble fibrin through the proteolytic action of thrombin during the blood clotting reaction. fibroblast Cell type present in the dermis and in the connective tissues of other organs. It produces most of the extracellular matrix proteins. fibroblast growth factors A family of signalling proteins, many of which are secreted and bind to extracellular matrix. They have a variety of roles in embryonic development and in the adult. fibrolamellar bone Bone tissue initially formed as a finely cancellous framework of woven bone, which is later compacted by lamellar bone that forms around blood vessels and results in primary osteons. fictive feeding A rhythmic neuronal firing pattern underlying the generation of rhythmic feeding movements. filopodia (singular filopodium) Fine actin-based finger-like protrusions that extend and retract at the leading edge of migrating cells. Also known as microspikes. fimbriae (singular fimbria) Nonflagellar filamentous structures on the surface of bacteria. Also called pili. final host The host in which the sexual stages of a parasite occur. Also called the definitive host. fine needle aspiration The sampling of tissue or cells from the body by insertion of a small hollow needle, such as that used to take a blood sample, and application of negative pressure via an attached syringe. finite cell line A cell culture that can be maintained by serial passage but has a characteristic finite limit on the number of population doublings it can achieve before entering a state of senescence. FIS A bacterial histone-like protein. Fisher runaway process The rapid coevolution of mating preferences and secondary sexual traits. FISH See fluorescence in situ hybridization. fistula An unnatural connection between an organ and the body surface or between organs.

178

Glossary

fitness In the Darwinian sense, the probability that an individual organism will survive and produce viable offspring, relative to the survival and reproductive success of other individuals in the population. It is thus a measure of the relative adaptive value of a given genotype in comparison to other genotypes in the population. It can give a quantitative assessment of an organism’s ability to pass on its own genes, in itself and its relatives (offspring, siblings, etc.), to future generations of the population of which it is a member. It is measured as the relative contribution of an individual’s genotype to the next generation relative to the contributions of other genotypes. fixation (1) In genetics, the case when one allele comes to predominate in a population such that all individuals possess that allele. (2) Stabilization of biological specimens for microscopic examination in a form that retains as much as possible of their natural structure. Chemical treatment converts macromolecules to insoluble derivatives. fixation index An index of genetic variation between populations, expressed in terms of gene frequency variability between populations, standardized in relation to the maximum possible variability. fixed lineage A stereotyped sequence of cell divisions that usually generates a defined array of cell types. flagellum (plural flagella) (1) A motile structure on the surface of some prokaryotes, whose rotation propels the microorganism through an aqueous milieu. It consists of a whip-like filament attached to a basal body embedded in the bacterial membrane. (2) A superficially similar motile structure on eukaryotic cells, which has a different microtubule-based, molecular structure and mechanism. flip-flop The movement of a phospholipid from one leaflet of a bilayer membrane to the other. flocculate A complex of organic and inorganic materials which settles out of the water column. flood basalt province Vast province of flat-lying lava flows that often contains up to several million cubic kilometres of lava. More than 10 such provinces are known and they constitute by far the most spectacular manifestation of volcanic activity on earth. floor plate The ventral midline region of the epithelium of the early vertebrate neural tube. floral meristem identity genes A group of genes that specify the identity of the floral meristem in Arabidopsis. floral organ identity genes Genes that determine the identity of individual floral organs such as sepals or petals in Arabidopsis. flow cytometry Photoelectronic technique for the counting and sorting of individual cells based on detection of granularity or fluorescent labelling. flow cytometry Photoelectronic technique for the counting and sorting of individual cells based on light scattering or the detection of fluorescence. The cells pass in front of a laser beam and both scattered light (a function of size) and fluorescence can be measured. FLT-3 ligand A growth factor for stem cells in vivo. It is a ligand for an FMS-like receptor tyrosine kinase. fluctuating asymmetry Morphological asymmetry in bilaterally symmetric organs which does not show a bias toward either side. fluidity The degree of motion within the lipid components of the bilayer membrane. It is enhanced by the presence of double bonds in the fatty acyl chains and by shortening of the acyl chain length.

fluorescence-activated cell sorter (FACS) An opto-electronic device used to detect and sort different types of cells from a mixture by detecting fluorescently labelled antibody bound to their surface antigens. Antibodies specific for different antigens are labelled with different fluorescent tags, enabling the detection and quantitation of particular cell types. fluorescence-assisted organelle sorting See FAOS. fluorescence in situ hybridization (FISH) A technique for identifying chromosomes or genes on chromosomes by the use of fluorescently labelled DNA probes. The probes are hybridized to chromosomes or nuclei immobilized on glass slides to determine visually the presence or absence of a particular DNA sequence. fluorescence resonance energy transfer (FRET) Technique for investigating molecular structure and function which depends on the fact that some molecular groups begin to fluoresce when they come sufficiently close together. fluorescent dyes Dyes that emit fluorescent light of various colours when viewed under specially equipped light microscopes with near-blue ultraviolet light and appropriate filters. They are used to stain cells and to label antibodies and DNA probes. fluorophore A chemical group that fluoresces strongly when suitably illuminated, and which can be observed using a fluorescence microscope. flush The appearance of mushrooms at intervals (rhythmic cycle) for harvesting. flux (1) The number of objects passing through a plane of known area in a unit of time. The usual units of flux are moles (or grams) per cm2 per second. (2) Reaction rate. fMet-tRNAfMet Initiator tRNA charged with formyl-methionine. FMO protein Protein responsible for the attachment of S chlorosomes to the plasma membrane. FNR An enzyme located in the chloroplast stroma that oxidizes ferredoxin and reduces NADP1 . FNR protein A homologue of the cyclic AMP receptor protein that is activated in the absence of oxygen. It is a bacterial transcriptional activator with an essential role in the induction of gene expression during adaptation to anaerobic growth conditions. focal adhesion sites Sites at which cultured eukaryotic cells make contact with their substratum. Focal adhesion sites contain clusters of integrins, with their extracellular parts bound to extracellular matrix proteins and their intracellular parts attached to actin filaments. folding of proteins The process by which a polypeptide chain adopts the precise three-dimensional structural conformation that is of lowest free energy. folding pattern The unique three-dimensional spatial arrangement of atoms in a protein molecule that has adopted its final conformation. follicle In botany, a single-cavity, multi-seeded fruit that opens by splitting. footprint Of a transposable element, the characteristic donor site sequence that is left after transposition. foramen magnum The opening in the base of the cranium of the skull that connects the posterior fossa and the cervical spinal canal. foraminifera Small benthic or planktonic marine protozoans (phylum Sarcodina, class Rhizopoda, order Foraminiferida) that secrete tubular, commonly chambered, tests of agglutinated sediment grains or, more commonly of calcite. They are common and important microfossils.

179

Glossary

force An influence on a body that causes it to accelerate (product of mass and acceleration). foregut The oesophagus and stomach. foreign antigen Any nonself tissue or substance whose presence triggers an immune reaction in the host. forespore Cell formed after asymmetric division early in sporulation that is destined to become the mature spore. fork arrest In DNA replication, the arrest (or pausing) of a replication fork at a defined location on the chromosome. formation In geology, a mappable rock unit with a common character. fossorial Adapted for burrowing or digging or for a subterranean life. founder cell (1) Cell from which a structure or tissue originates. (2) Early embryonic cell in Caenorhabditis elegans whose fate has been specified as to the division patterns it follows and the type of cells it produces. founder event The establishment of a new population by a relatively small number of individuals. fourfold degenerate site Any nucleotide can occupy this site in a codon and the codon will encode the same amino acid. four-helix bundles A protein folding pattern in which four segments of helical structure are packed together so that hydrophobic sides of the helices are inside. Fourier analysis A technique by which a complex mathematical function (e.g. a spectrum) is approximated as the sum of a series of sine waves. fovea A depressed region of the retina that, because of its high density of cone receptors, allows maximum visual acuity. foveate retina A retina with a circumscribed region of highest acuity, the fovea. frameshift A mutation that results in the loss of the correct reading frame. free energy The combination of energy, entropy, and work terms, the sign of which determines in which direction a given reaction will proceed. It is the energy available too do useful work. free radical An atom or group of atoms possessing an unpaired electron, which usually makes it highly reactive. free-flow electrophoresis Injection of a sample into a continuous flow of buffer between two electrodes. Deflection of material is dependent on charge and flow time (distance). freezing point Temperature of a solution at which an ice crystal placed in the solution begins to grow. frequency facilitation See facilitation. frequency-dependent selection Selection that increases or decreases depending on the relative frequency of an allele in a population. Fresnel reflection coefficient A number that expresses the fraction of the intensity of unpolarized light partially reflected at a surface boundary between two transparent substances with different refractive indices. FRET See fluorescence resonance energy transfer. friction Tangential force that resists motion between two objects in contact. frond The leaf of a fern plant, which is often the most conspicuous part of the plant. front focal plane The focal plane of a lens that lies in front of it when viewed in the direction of illumination. This term is usually employed when referring to the condenser lens, where the phase annulus is properly found.

fructan A polysaccharide composed primarily of D-fructosyl units in the furanose ring form. fruiting bodies (1) The sexual or asexual spore-bearing structures of fungi and similar organisms. They include the ‘mushrooms’ and ‘toadstools’ (basidiocarps) of basidiomycetes and the ascocarps of ascomycetes. (2) The multicellular spore-bearing structures of slime moulds and myxobacteria. fruiting body development The aggregation and coordination of hundreds of thousands of myxobacteria to form a compact multicellular structure that contains myxospores. frustule The silica-containing coat of diatoms which consists of two overlapping halves, the epivalve and hypovalve. FST The measure of the fraction of the total genetic variation at a locus that is among populations. It measures how genetically different one deme in a metapopulation is from another, when averaged across loci. fucoxanthin Accessory pigment (carotenoid) in many golden and brownish algae. functional food A food that provides health benefits beyond those of basic nutrition. functional genomics Determination of the function of genes that have been identified via genome sequencing programmes. functional imaging The formation of an image containing information relating to physiological function. functional mRNA half-life The length of time an mRNA remains sufficiently intact to allow the synthesis of a full-length protein. fusion partner A protein molecule that, when combined with another, will introduce a new property to that molecule such as affinity for a matrix or greater stability. fusion protein (1) A protein on the surface of a virus particle responsible for fusion of the virus envelope with cell membranes. (2) Novel protein that is encoded by two coding sequences from different proteins that have been joined together. futile cycle A set of enzyme-catalysed cyclic reactions that consumes energy (mostly adenosine triphosphate) in an apparently useless process. When its role in regulation is established, it is then known as a ‘substrate cycle’.

G 1 C content The mol% of the bases guanine and cytosine in the chromosomal DNA. The range in known genomes is between ~22–74 mol%. G proteins Guanine-nucleotide-binding proteins. A large family of proteins that act as molecular switches in intracellular signalling pathways. They exist in an active state when GTP is bound and in an inactive, conformationally altered, state when the bound GTP is hydrolysed to GDP by the G protein’s intrinsic GTPase activity. The term G protein itself is usually reserved for the heterotrimeric G proteins that transmit signals from the large class of seven-span receptors. The monomeric guanine-nucleotide-binding proteins that act in a wide range of intracellular signalling pathways are usually known as the ‘small GTPases’ or ‘small G proteins’. G0 phase A phase of the eukaryotic cell cycle in which the cell is temporarily or permanently arrested in its progression through the cycle and remains in a state resembling the G1 phase.

180

Glossary

G1 phase The ‘gap’ 1 phase of the eukaryotic cell cycle that succeeds cell division. It is the pre-DNA synthesis period of the cell cycle in which the cell is increasing in size and chromosomes are preparing for replication. G2 phase The ‘gap’ 2 phase of the eukaryotic cell cycle that often succeeds DNA replication (S phase) and precedes mitosis (M phase). GABA See g-Aminobutyric acid. gain of function mutation A mutation in the protein-coding region of a gene that confers an additional, deleterious, activity on the protein. Such mutations are generally dominant. galactomannan A polysaccharide composed of D-galactosyl and D-mannosyl. In every case, the mannosyl units form the backbone structure (a linear main chain) with the D-galactosyl as single side units. gametangium (plural gametangia) A differentiated cell that produces gametes or whose protoplast functions in place of a gamete. gamete The haploid germ cell produced by a sexually reproducing organism. A gamete is capable of fusing with another gamete of opposite sex to produce a zygote. The male gamete is usually called the sperm, and the female the ovum. gametic-phase disequilibrium An association (at greater than chance levels) between particular alleles at two or more loci that has arisen as a result of mating preferences, and thus as a result of selection acting on the gamete. gametogony Formation of gametes from haploid merozoites in parasitic protozoans. gametophyte The phase of a plant’s life cycle in which the gametes are formed. Male and female gametes fuse to form the sporophyte. c-Aminobutyric acid (GABA) One of two major inhibitory neurotransmitters in the mammalian nervous system, the other being glycine. cd T cells A subpopulation of T cells bearing a T-cell receptor consisting of g and d chains. They are found in locations such as the epidermis. gamone A soluble mating-inducing substance, also called mating pheromone. gamont The cell (or organism) that produces gametes, or, in the case of ciliate conjugation, which produces gametic nuclei (pronuclei). ganglion (plural ganglia) An anatomically discrete collection of nerve cell bodies within the central or peripheral nervous system, containing from a few to many thousands of cell bodies and associated structures. In invertebrates, a ganglion is usually a nodular mass surrounded by connective tissue. ganglion cells Neurons in the retina that carry visual signals to the optic nerve. ganglioside A type of sphingosine-based glycolipid found especially in the cell membranes of nervous system cells. Production of gangliosides is also associated with certain carcinomas. gantry In computed tomography, the housing for the tube and detectors. It contains all moving parts. There is a central aperture through which the patient passes. Garden of Eden hypothesis The hypothesis that modern humans arose by a speciation event or something similar from a small focal population. This is usually thought to have occurred in Africa. gas vesicles (1) Hollow, buoyancy-conferring, intracellular proteinaceous structures found in a large number of aquatic and photosynthetic prokaryotes. (2) Intracellular vesicles produced by accumulation of a gas, e.g. hydrogen, which is produced as a byproduct of metabolic reactions.

gastritis Inflammation of the stomach. gastrodermis See endoderm (2). gastropods Snails, slugs, sea hares and kin (class Gastropoda, phylum Mollusca), a class of molluscs typified (usually) by a twisted body and a helically coiled, nonchambered shell. A characteristic feature is a large flat muscular ‘foot’ on which they crawl about. Present from the Cambrian to the present day. gastrulation The period in animal embryonic development in which tissue reorganization leads to the formation of the definitive germ layers (ectoderm, mesoderm and endoderm), formation of the gut, and the emergence of the body plan of the larval or adult organism. gating currents Transient currents caused by charge displacements of voltage sensors within voltage-gated ion channels. gating The regulated opening and closing of the pore of an ion channel. gaussian Describes a generalized normal distribution, in reference to the discoverer, Karl Friedrich Gauss (1777–1855). gaze Direction of the line of sight in space. Gaze depends on eye position in the orbit and head position in space. G-banding Unique banding patterns that appear on chromosomes stained with Giemsa dye. G-CSF See granulocyte colony-stimulating factor. gel electrophoresis Procedure by which proteins or DNA or RNA fragments can be separated according to size under the influence of an applied electric field. The matrix through which the particles migrate is usually a polyacrylamide or agarose gel. gene Classically, the region of a chromosome that controls a single hereditary trait. The term gene is sometimes used as a synonym for allele (a particular version of a gene) and sometimes as a synonym for locus (the position on the chromosome occupied by the gene). At the molecular level, a gene is a sequence of DNA that encodes the information for a protein or an RNA, together with the regulatory sequences necessary for the gene’s expression. gene amplification Sudden increase in the number of copies of a gene on a chromosome by successive rounds of gene duplication that lead to a serial array of repeats of the gene. gene conversion (1) An unusual segregation of genetic markers in a single meiosis where three of the four gametes carry one allele and one carries the other, in contrast to the normal 2:2 segregation. It is due to a nonreciprocal DNA recombination event that has converted one copy of one of the alleles into the other type. (2) A type of nonreciprocal recombination in which a DNA sequence copied from a donor gene (or allele) displaces the equivalent sequence in a homologous acceptor gene (or allele). gene diversity The probability that two alleles chosen at random from a population are not identical. It is also equivalent to the proportion of heterozygous individuals in a randomly mating population. gene exchange Transfer of alleles between populations or species by hybridization followed by backcrossing to the parental forms. This process is equivalent to gene flow but the term gene exchange is usually used to refer to interchange between genetically distinct populations. gene expression The transcription and/or translation of a gene to form the RNA and/or protein product. Regulation of gene expression can be at the level of transcription or translation. gene flow Exchange of genes between populations caused by immigration and emigration of individuals across populations.

181

Glossary

gene-for-gene interaction In plant pathology, a specific recognition between an avirulence gene from the pathogen and a corresponding resistance gene from the host plant, resulting in resistance of the plant to that pathogen. gene-for-gene theory The principle that operates in some plant– pathogen interactions, in which an avirulence gene in the pathogen encodes, or results in the production of, a molecule that is recognized by the product of a specific resistance gene in the plant, which induces a resistance response in the plant. gene fusion The covalent joining of DNA sequences from two different genes, which may occur naturally or be constructed experimentally. gene gun A device used to accelerate and deliver DNA-coated microprojectiles into a target tissue. gene knockout The result of creating a germline mutation in a particular gene that completely disrupts the function of the protein encoded by that gene. In mammals, the gene is disrupted by a technique that involves homologous recombination in embryonic stem cells in culture followed by preparation of chimaeric mice by injection of these cells into a blastocyst. gene pool (1) All the alleles present in a population of sexually reproducing individuals. (2) All alleles at a given locus in such a population. gene rearrangement A site-specific somatic recombination event that rearranges the order of genes or DNA sequences on the same chromosome. gene switching The process of turning a gene on or off as a result of the binding of gene regulatory proteins to the regulatory elements of the gene. gene targeting See gene knockout. gene therapy Treatment of genetically based disease by the introduction of a functional gene into the patient’s cells. general circulation model A computer model capable of simulating global climatological processes over long time scales. general drift Changes in the genetic make-up of a population as a result of random processes. general recombinase Enzyme that catalyses the homologous DNA pairing and strand-exchange reaction in general genetic recombination. general-base catalysis Catalytic mechanism involving the removal of a proton from a chemical group, which makes it a stronger nucleophile. generalist An organism with a broad realized niche, i.e. it is able to live in a variety of different habitats or use a wide variety of resources. generalized recombination See homologous recombination. generative cells Cells within plasmodia that form sporoblasts and then spores. genetic Pertaining to or caused by genes. genetic balance The coordinated balance between the levels of gene products in a particular genotype. Failure to establish the correct balance usually results in severe defects and may be lethal. genetic code The code by which the nucleotide sequence of a DNA or RNA molecule specifies the amino-acid sequence of a polypeptide. It consists of three-nucleotide (triplet) codons that either specify a particular amino acid or a stop signal. genetic complexity The amount of genetic information carried by an organism. For viruses lacking redundant nucleotide sequences, complexity can be equated with genome size.

genetic co-optation The stabilization, reinforcement or consolidation by new or modified genetic circuitry of biological properties originally established by generic and epigenetic mechanisms during organism–environment or tissue–tissue interactions. genetic distance A measure of genetic or evolutionary closeness or remoteness between two taxa or sequences that originated from a common ancestor. For DNA sequences it is the number of nucleotide differences per position between the two sequences. genetic drift Random changes in allele frequencies in small isolated populations as a result of factors other than natural selection, such as sampling of only small numbers of gametes in each generation. genetic heterogeneity Similar phenotypes produced by defects in different genes. genetic map Linear arrangement of genes and DNA markers on a chromosome, determined on the basis of recombination frequencies. genetic marker A detectable gene, DNA sequence or phenotypic trait with a known chromosomal location. genetic polymorphism The presence of two or more alleles of a gene at appreciable frequencies in a population. genetic reassortment The generation of hybrid viruses possessing combinations of different genomic segments when a single cell is infected with two or more related viruses containing segmented genomes, such as influenza viruses. genetic screening The systematic search in a population for individuals of particular genotypes. genetic testing Testing performed to determine the genotype of an individual suspected of having a mutation. genetically engineered live vaccine A vaccine containing a microorganism whose genes have been deliberately manipulated such that the infectious agent can still infect the host and induce immunity but cannot cause disease. genic Of or pertaining to individual genes. genome (1) The total set of genes, and any additional non-coding DNA, carried by an individual organism, cell or virus particle. When the size of a genome is quoted, this usually refers to the haploid genome. (2) The total DNA content of a cell. genome co-linearity The situation when homologous regions of chromosomes derived from two different species show the same order of markers or genes. genome economization Reduction of genome size as observed in the genomes of animal mitochondria. Mitochondria are thought to have reduced their genome sizes by transferring some of their genes to host cell genomes during the evolution of their symbiosis with the host cell. genome replication The stage of viral replication at which the virus genome is copied to form new viral genomes. genome sequence The complete nucleotide sequence of an organism’s DNA. genomic RNA RNA that is the genetic material of certain viruses and encodes all their viral proteins. genomics The study of a genome or genomes as a whole. The genome-wide analysis of genes. genotoxic Able to cause damage to DNA. genotype The genetic make-up of an organism, as opposed to the phenotype, which is the outward appearance of the organism. A listing of a complete genotype would include all alleles and mutant sequences. In practice, genotypes are usually given in respect of a selected set of loci under consideration.

182

Glossary

genotype–phenotype correlation The relationship of specific mutations at a genetic locus or loci to their manifestations in the phenotype. geochronological age The absolute age of a stratigraphical unit, horizon or body. It is usually determined by radioisotopic methods and expressed in units of millions of years or millions of years ago (Ma). geognosy The study of the three-dimensional structure and relationships of rock masses, particularly as applied to mines and mining. geological record Rocks and fossils as found on the surface of the Earth, from which the history of the Earth is interpreted. geological time The period from the formation of the Earth to the beginning of written history. germ layers The three initial tissue types (ectoderm, mesoderm, endoderm) in an animal embryo, each of which gives rise to a particular set of organs and differentiated tissues. germinal centre An aggregation of rapidly proliferating activated B cells and a smaller number of CD4 helper T cells that forms in a lymphoid follicle of a secondary lymphoid organ (e.g. a lymph node) during an adaptive immune response. It is the site of B-cell differentiation to plasma or memory cells and of isotype switching and affinity maturation of the humoral immune response. germination The outgrowth of a dormant reproductive propagule, such as a spore or seed, into a new organism. germline A cell lineage in animals that gives rise to the reproductive (or germ) cells and is continuous through succeeding generations. It separates early and clearly from somatic cell lineages during development. The cells of the germline are potentially immortal. GFP See green fluorescent protein. ghost lineages, ghost taxa See range extensions. giardiasis Infection with Giardia lamblia, a pathogenic flagellate protozoan that can cause gastrointestinal symptoms in humans. Gibbs free energy A measure of energy that combines the enthalpy with the entropy of a system at constant pressure and temperature. gingival hyperplasia Growth of the gingiva or tissue of the gums. It is a frequent side-effect of therapy with dilantin or cyclosporin A. GISH See genomic in situ hybridization. glabella The upraised central part of the trilobite head. glacio-eustatic Global sea-level change caused by the growth or decay of ice caps. glia Non-neuronal cells of the central nervous system, comprising microglia, astrocytes and oligodendrocytes. They provide various support functions required for the proper development and function of neurons. glioma Central nervous system tumour composed of and derived from glial cells. global alignment In DNA sequence analysis, the alignment of two or more sequences along their whole length. This form of alignment is not well suited to sequences of disparate length, but is well suited to the alignment of a group of sequence homologues. global regulation Control of gene expression in a manner appropriate to the prevailing nutritional and environmental conditions.

globular and fibrillar appearance At the electron microscopic resolution limit achievable with thin sections, concentrated solutions of small macromolecules are not resolved in detail but produce distinct ‘fibrillar’ or ‘globular’ aspects of such plasms. globular protein A protein with a relatively compact, roughly spherical overall structure. Typically, hydrophobic amino acids are found in the center of globular proteins and hydrophilic amino acids on the surface. glucan A polysaccharide composed of glucose subunits. glucocerebroside A lipid that accumulates in Gaucher disease owing to a deficiency of the enzyme needed to degrade it. glucogenic Refers to metabolites that can be metabolized to generate extra glucose or glycogen. glucogenic amino acid An amino acid that can be metabolized to give glucose. glucomannan A polysaccharide composed of D-glucosyl and D-mannosyl units, generally with a preponderance of the latter. gluconeogenesis The synthesis of glucose from molecules such as amino acids. glucose homeostasis The maintenance of plasma glucose concentration within normal limits (4.4–6.1 mmol l–1) by the actions of regulatory mechanisms that compensate for changes in the supply of and/or demand for glucose. glucose–alanine cycle A metabolic pathway in which a product from glycolysis (pyruvic acid) in muscle is converted to alanine and transported to the liver, where it is converted to glucose, which returns to muscle. glutaminylglucan Polymer composed of glycosylated polyglutamine chains. glutathione (GSH) The tripeptide g-glutamylcysteinylglycine (gGluCysGly), which is present at high concentration in cells. It has numerous biological functions in detoxification, reduction and biosynthesis. glutathione disulfide (GSSG) The symmetrical disulfide of glutathione. glycan transferase An enzyme that transfers a specific sugar residue from a nucleotide sugar onto other molecules such as amino acids, lipids or sugars. glycocalyx The cell coat. In animal cells, a layer external to the plasma membrane that contains the carbohydrate moieties of glycoproteins and glycolipids embedded in the membrane, and secreted molecules such as proteoglycans. glycogen Polymer of glucose monomers linked by a-1,4-glucosidic bonds and branched through a-1,6-glucosidic bonds. It is the main glucose storage compound in animal cells. glycogen granules Intracellular deposits of glycogen, a storage polymer of glucose. glycogenolysis The breakdown of glycogen into glucose. glycolysis, glycolytic pathway The pathway by which glucose is converted to pyruvic acid with production of energy in the form of ATP, and reducing power in the form of NADH. It occurs in the cytosol and does not require oxygen. In aerobically respiring cells it is the first stage in the complete oxidative breakdown of glucose. In anaerobic cells, the term is often used for the complete pathway in which the pyruvate is subsequently converted to metabolites such as lactic acid. glycopeptide resistance Resistance to one or more of the glycopeptide antibiotics, e.g. vancomycin or teicoplanin.

183

Glossary

glycoprotein A protein to which short oligosaccharide side-chains (chains of a few sugar residues) are covalently attached to the protein backbone. The mass of sugar is normally a fairly small fraction of the mass of the whole molecule. glycosidase An enzyme that catalyses the hydrolysis of glycosidic bonds, for example the bonds that link sugar molecules together in polysaccharides. glycoside Molecules composed of a sugar linked to another molecule (either another sugar or a nonsugar molecule) through a hydroxy group. A nonsugar component of a glycoside is called an aglycone. glycosidic bond The covalent bond characteristic of sugar-tosugar linkages. glycosome Cytoplasmic organelle in trypanosomatids in which glycolysis takes place. glycosphingolipid Type of membrane lipid containing a ceramide moiety linked through its terminal hydroxyl group to a variety of either monosaccharide or oligosaccharide units. glycosylate To add a carbohydrate moiety to a protein biochemically. glycosylated shell components Polypeptides with attached carbohydrate moieties that surround carboxysomes. glycosylation The covalent addition of oligosaccharide to another molecule, usually a protein or lipid. glycosylenzyme An enzyme on which a glycosyl group has been covalently bonded to a nucleophilic group. glycosylphosphatidylinositol anchor (GPI anchor) A covalent linkage, by way of two fatty acids and an oligosaccharide chain, between a membrane phospholipid (phospatidylinositol) and the carboxyl terminus of an externally exposed protein. glycosyltransferase An enzyme that catalyses the transfer of monosaccharide from an activated donor to a protein, lipid or oligosaccharide acceptor. glyoxysomes A type of peroxisome found in plant cotyledons. Although deficient in many peroxisomal functions, they do contain enzymes of the glyoxylate cycle. GlyR Abbreviation for the glycine receptor on neurons. GMSF See granulocyte–macrophage colony-stimulating factor. gnathobases Spiny processes at the bases of the paired legs of arthropods, used in feeding. gnathopods Mouthpart structures in some arthropods. Golgi apparatus Organelle in eukaryotic cells that is responsible for polysaccharide synthesis, glycoprotein processing, lipid biosynthesis and packaging of material for secretion to the vacuole or cell surface. It receives proteins from the endoplasmic reticulum. The complete organelle consists of one or more stacks of flattened sacs of membrane (cisternae). Golgi body, Golgi stack Individual unit (stack of membrane sacs) of the Golgi apparatus. Sometimes termed a dictyosome. Golgi complex See Golgi apparatus gonad General name for organs in which gametes are formed (ovary and testis). Gondwana The southern continental landmass formed during the early Mesozoic. It included what were to become South America, Africa, Antarctica, Australia, India and New Zealand. Gondwanaland See Gondwana. gonochoristic See gonochorous. gonochorous Describes organisms in which there is separation of the sexes such that individuals are either male or female (as compared to hermaphrode, where individuals produce both types of gametes).

gonopods Specialized limbs of myriapods, usually located on or close to the reproductive segment (bearing the gonopore) and functioning in the handling of spermatophores and eggs. goosecoid A homeobox-containing gene in Xenopus that encodes a transcription factor involved in executing the functions of the Spemann organizer. GPI anchor See glycosylphosphatidylinositol anchor. GPI Glycosylphosphatidylinositol. See glycosylphosphatidylinositol anchor. G-protein-coupled receptors, G-protein-linked receptors A large class of transmembrane receptor proteins in which binding of the extracellular ligand activates intracellular heterotrimeric proteins named G proteins. Activated G proteins stimulate intracellular enzymatic pathways or, in some cases, act directly on nearby ion channels. grade A group of animals similar in level of organization and adaptation. A level of evolutionary advance. grading Formal scoring system for the cytological and architectural features of carcinomas. graft-versus-host disease (GVHD) Disease that occurs when mature immunocompetent T cells in a transplant react against the tissues of the host. It is particularly a feature of bone marrow transplants into immunodeficient patients which are unable to reject the transplanted cells. Gram staining An important method for classifying bacteria which depends on the differential retention of Gram stain (crystal violet) by the cell envelope. Bacteria that retain the stain are termed Gram-positive, and those that do not are termed Gramnegative. Gram-negative Refers to bacteria that do not retain Gram stain (crystal violet) (e.g. Escherichia, Pseudomonas). Gram-positive Refers to bacteria that retain Gram stain (crystal violet) (e.g. Clostridium, Streptococcus, Staphylococcus). Gram-type A phylogenetic term used in the classification of prokaryotes, which is independent of the results of the Gramstaining reaction and is based on the presence or absence of lipopolysaccharide in the cell envelope and on the 16S rDNA sequence analysis. Gram-type is defined as positive, negative or zero (i.e. the archaea). grana membranes Circular stacks of membrane formed by the thylakoid membranes in chloroplasts. granitic Describes rock composed of large crystals of potassium feldspar, sodium plagioclase, feldspar, quartz and biotite, formed from a magma rich in silicon, aluminium, potassium and sodium that cooled in a deep magma chamber. granulation tissue The tissue that first forms during the repair of a wound or lesion. It consists of newly formed blood vessels, activated fibroblasts and their products, and inflammatory cells. granule An intracellular particle composed of material packed within a membrane vesicle. granule-mediated apoptosis Cell death that is induced by perforin-mediated delivery of granzymes to the cytosol of the target cell. granules of phagocytes Intracellular storage vesicles containing microbicidal substances, present in phagocytic cells such as macrophages and neutrophils. They can be mobilized to deliver their contents to the exterior of the cell or into phagosomes.

184

Glossary

granulocyte (1) Type of white blood cell whose cytoplasm is rich in granules. In humans, there are three main types – eosinophils, basophils, and neutrophils (polymorphonuclear leucocytes) – the most abundant of which is the neutrophil. (2) Major haemocyte type found in all major arthropod taxa and characterized by the presence of numerous prominent intracytoplasmic membranebounded granules. granulocyte colony-stimulating factor (G-CSF) A cytokine that predominantly stimulates the growth of granulocytes from bone marrow cells. granulocyte–macrophage colony-stimulating factor (GMSF) A haematopoietic growth factor that stimulates growth of granulocytes (G) and macrophages (M) from bone marrow cells. granulomatous disorders Diseases characterized by the appearance of granulomas. granzymes A family of cytotoxic serine proteases that are present in the granules of cytotoxic cells. Graves disease An autoimmune disease caused by the production of antibodies that stimulate the thyroid-stimulating hormone receptor, resulting in an overproduction of thyroid hormones (thyrotoxicosis). green fluorescent protein (GFP) An autofluorescent protein from the jellyfish Aequorea victoria. It is commonly used, via recombinant DNA techniques, to mark a particular protein within living cells and/or whole organisms, so that it can be detected visually. greenstone Basalt that has cooled under the ocean, usually forming lava pillows, and then is later subjected to low-grade (greenschist-grade) metamorphism, forming the green mica chlorite that gives the characteristic colour. grey matter A generic term for a collection of nerve cell bodies in the central nervous system. grey-scale image An image in which the intensity of signal coming from, or the amount of sound or radiation absorbed by, each region of the body is represented on an image of the body by a shade of grey ranging from black to white. group selection Differential survival or reproduction of groups of organisms, such as a population of parasites on a host. growth cone A specialized region at the tip of a growing neurite (axon or dendrite) that is responsible for sensing the local environment and moving toward the neuron’s target cell. Growth cones are roughly hand shaped, and extend several actin-based processes, called filopodia, that navigate the axon tip over the substrate. growth factor receptors Transmembrane proteins in the plasma membrane that bind growth factors and mediate their biological effects. growth factors General term for cytokines that affect cell proliferation and differentiation. Gs G proteins that activate adenylyl cyclase. GSH See glutathione. GSK-3 Glycogen synthase kinase 3, a serine/threonine kinase with a role in early embryonic development. It is regulated by multiple signalling pathways, including Wnt signalling and insulin signalling. GSSG See glutathione disulfide. guanine Commonly occurring purine base, one of the four types of bases in RNA and DNA.

guard cells In plant cells, the paired cells comprising a stoma. Their expansion as a result of a change in turgor pressure opens the stomatal pore. guide fossils A fossil species that characterizes a particular interval of the rock record, which is termed the biozone of that species. They are essential tools in local and international biostratigraphic correlation. ´ Guillain–Barre syndrome Acute inflammation of peripheral nerves following an infectious disease of viral or bacterial origin. Gulf War syndrome A group of ailments reported by a number of soldiers who fought in the war to liberate Kuwait from its Iraqi invaders. The cause remains unknown and there is controversy over the syndrome’s existence. gumma The tertiary noninfectious syphilis lesion that occurs either at the site of inoculation in the sensitized host or following spread of Treponema pallidum through the blood stream. gustatory Relating to the sense of taste. gustducin The a subunit of a G protein that is found uniquely in a subset of taste receptor cells and in certain chemoreceptor cells in the gut. Gustducin is hypothesized to couple bitter receptors to intracellular signalling pathways inside taste receptor cells. guttation The excretion of water from specialized openings, the hydathodes, in plant leaves when the air is saturated. Gvp proteins Proteins associated with gas vesicle formation. gymnamoebae A group of amoebae that lack a definite enclosing shell or test, but sometimes have a thin glycocalyx coating the plasma membrane. gymnosperm A plant that produces seeds not enclosed in an ovary. Gymnosperms include the conifers. gynoecium All of the female reproductive structures in a flower.

H See enthalpy. HAART See highly active antiretroviral therapy. habitat Both the place occupied by an organism and the combination of physical and environmental conditions required for an organism to survive and reproduce. habituation A reduction in response following repeated presentations of a stimulus. haem The iron(II) complex of a porphyrin, a prosthetic group on many proteins haemagglutination The clumping of red blood cells, usually by specific antibody. haemagglutinin A protein that can bring about the agglutination of red blood cells. Influenza haemagglutinin is a glycoprotein on the surface of the influenza virus that is responsible for binding of the virus to receptors on host cells. haematite An iron oxide mineral, typically red in colour; Fe2O3. haematocrit The proportion of red cells in the circulating blood related to the plasma volume, often reported as the percentage of a centrifuged blood sample that contains the red cells. haematogenous dissemination Spread of a pathogen via the blood system.

185

Glossary

haematopoiesis The production of all the cellular elements of blood, including platelets, red blood cells and leucocytes. haematopoietic cell A cell from which blood cells derive. haemin The chloroiron(III) complex of a porphyrin. haemocoel (1) A blood-filled body cavity that bathes the internal organs. (2) The open blood system of arthropods and molluscs. It comprises a system of sinuses through which the haemolymph or ‘blood’ travels. haemoglobin A haem-containing protein, contained in red blood cells in vertebrates, that reversibly binds molecular oxygen and transports it from the lungs to tissues. haemolymph The multipurpose ‘blood’ of arthropods. It transports cells, nutrients, wastes and dissolved gases throughout the body. haemolysin A protein that causes the rupture of red blood cells. haemolysis The lysis of red blood cells. haemolytic Causing lysis of red blood cells. Many pathogenic bacteria, notably Streptococcus pyogenes and some other streptococci, possess this property. haemolytic anaemia Anaemia due to decreased survival of red blood cells in the circulation. Clinically, the disease is characterized by anaemia with a raised reticulocyte count in the absence of bleeding. haemolytic disease of the newborn More correctly, haemolytic disease of the fetus and newborn. A fetal and neonatal anaemia caused by the action of maternal antibodies against fetal red blood cells. haemophilia A hereditary bleeding disorder that affects almost exclusively male patients. It is caused by genetic defects that result in the absence of either of the clotting factors VIII or IX from the plasma. haemorrhagic fever A disease characterized by widespread bleeding as a result of blocking and permeabilization of capillaries throughout the body. haemostasis The physiological mechanisms that normally maintain the blood in a fluid state but immediately arrest of bleeding from a damaged vessel by blood clotting, vasoconstriction or other means. hairy root Aberrant root growth caused by the bacterium Agrobacterium rhizogenes on dicotyledonous plants. half-centre oscillator A reciprocally inhibitorily coupled pair of circuits that oscillate in anti-phase. half-life The time taken to reduce the amount or activity of a given substance by half. Used, for example, as an estimate of the time a drug remains in the body, or as a measure of the radioactivity of a substance. In transplantation medicine it refers to the time at which half of the patients have lost their grafts. halides The negatively charged monovalent anions FÀ, ClÀ, BrÀ, IÀ . hallucinogen A substance that causes mental disorientation (hallucinations). halocarbon A (usually manmade) organic compound containing halogen atoms, e.g. pentachlorophenol, a wood preservative. They are often highly resistant to biodegradation. halophile An organism that requires high concentrations of salt to survive. halotolerant Capable of growth in hypersaline conditions but not necessarily requiring them for growth. hammerhead structure A particular class of ribozyme present in one or both polarity strands of some viroid and viroid-like satellite RNAs.

haploid An individual or cell (e.g. a gamete) having a single set of chromosomes (n). The number of chromosomes is species specific. haploinsufficiency Insufficiency of gene product resulting from the presence of only one functional copy of the gene instead of the usual two. haplorrhine A cladistic term of primate classification that includes tarsiers and anthropoids, in order to better reflect their shared phylogenetic origin. haplotype The combination of the major histocompatibility complex (MHC) alleles carried on one chromosome of the homologous pair. hapten A compound, usually of low molecular weight, that is not itself immunogenic but that, after conjugation to a carrier protein or cell, becomes immunogenic and can induce specific antibodies. These antibodies can bind the hapten alone in the absence of the carrier. haptocyst Organelle in the suctorian tentacle that is extruded to make contact with a prey organism. haptotaxis The directional migration of cells towards the source of a chemical signal bound to a substrate. hard selection Selection based on the absolute fitness of individuals in a population. It is usually independent of the frequency of particular genotypes. hardening Acclimation of a chill-resistant plant to freezing temperatures by pretreatment at low, but not freezing, temperatures. haustorium (plural haustoria) A specialized branch of a fungus developed within the cell of another fungus or plant, which absorbs nutrients. H1 ATPase A transmembrane protein that uses the energy released by hydrolysis of ATP to transport H1 across a membrane. 1 H -dependent vesicular uptake Uptake of neurotransmitter into synaptic vesicles by transporter proteins that use the proton gradient between the cytosol and the lumen of the synaptic vesicles as an energy source. H1-pyrophosphatase (H1-PPase) Pyrophosphate-driven proton pump localized in the tonoplast of plant cells. HCG See human chorionic gonadotrophin. headful packaging A mechanism of encapsulation of DNA in a phage head in which a concatemeric DNA is cut after uptake of a length of DNA sufficient to fill the head. headgut Mouthparts and pharynx of the mammalian intestinal system. heart A valved, muscular pump in animals that propels fluid, usually blood or lymph, around the body. heat-shock protein Protein synthesized in response to raised temperature or other stress. Heat-shock proteins assist the correct folding of other proteins newly synthesized and denatured by stresses. heavy chain The larger of the two types of polypeptide chain in an immunoglobulin molecule. Hebb rule Synapses should be strengthened if there is both presynaptic activity and strong enough depolarization of the postsynaptic cell to cause spiking. helicase An enzyme that unwinds double-stranded DNA in an ATP-dependent reaction. helix-turn-helix A common protein fold associated with the ability to bind DNA.

186

Glossary

HELLP syndrome Complication of pre-eclampsia characterized by haemolysis, liver damage and disseminated intravascular coagulation. helper component A nonstructural protein encoded by the virus genome that is needed for a successful transmission of the virus by the insect. helper T cells A functional subset of T cells which carry the CD4 co-receptor and primarily function to help B cells produce antibody. hemizygous Describes the condition in which only a single copy of a set of genes is present in a diploid organism. Human males are hemizygous for the genes on the X chromosome because they possess only one X. heparin Sulfated glycosaminoglycan of varying molecular weight which is composed of polymers of repeating disaccharide units of glucosamine and D-glucuronic acid or L-iduronic acid. It is released by mast cells and basophils and has anticoagulant activity. hepatitis Any disease characterized by inflammation and damage to the liver. hepatocyte The main cell type in liver, which carries out most of the liver functions. hepatocyte growth factor (HGF) Secreted signalling molecule expressed in the vertebrate embryo in the lateral plate mesenchyme and required for the migration of prospective muscle cells into the limbs. hepatosplenomegaly Enlargement of the liver and spleen due to blood production in these organs and congestive cardiac failure. hepatotoxicity The property of being toxic to liver cells. herbivore An organism that consumes live plant tissues. hermaphrodite An animal that produces both male and female gametes. Self-fertile hermaphrodites can produce viable embryos by fertilizing their own eggs with their own sperm. hermaphroditism Being male and female at some stage in the life cycle. Often both male and female organs can be present at once, and this is termed simultaneous hermaphroditism. herpes simplex virus A herpesvirus producing a variety of infections involving mucocutaneous surfaces, the central nervous system and visceral organs. herpes An infectious disease caused by a herpesvirus. herpesviruses Viruses of the family Herpesviridae which typically cause cold sores and genital sores. hesperornithiforms Flightless, toothed birds from the Cretaceous of North America and Europe, including Hesperornis regalis, Parahesperornis alexi, and Baptornis advenus. heterochromatin Densely staining chromatin that remains relatively condensed throughout interphase, and is later replicating than euchromatin. It is found at centromeres and telomeres, is usually gene poor, and is thought to be genetically inactive. heterochronic Describes evolutionary change that occurs by modifying the timing of developmental events. heterochrony The slowing-down or speeding up of the relative rate of development of an organ (or whole organism) by comparison with its development in the ancestor. It is an important process in evolution. heterocyst A terminally differentiated nitrogen-fixing cell present in many cyanobacteria. heterodimer A protein molecule composed of two different subunits.

heteroduplex (1) Double-stranded DNA in which the two strands are not of identical complementary sequence. (2) A doublestranded nucleotide polymer in which one strand is DNA and one strand is RNA. heteroencapsidation The situation when some of the RNA of one virus (or virus strain) is coated with proteins of another virus (or strain). heterogametic Having different kinds of sex chromosomes, e.g. X and Y in mammals. In mammals, males are the heterogametic sex. heterogenesis See alternation of generations. heterograft See xenograft. heterokaryon A multinucleate cell or mycelium having genetically different nuclei. heterologous Pertaining to a gene or protein which is being expressed in an organism or cell in which it is not normally present. heterologous expression Expression of a foreign gene in a given expression system. An example is when a human gene is expressed in Escherichia coli. heteromeric A protein composed of two or more different polypeptide chains. heteroplasmy The presence of two or more subpopulations of mitochondrial DNA in the same organism or cell. heteropolysaccharide A polysaccharide composed of more than one type of monosaccharide. heterosaccharide A polysaccharide composed of a complex mixture of monosaccharides. heterosis The case when the heterozygous progeny is superior in fitness to its homozygous parents. heterospecific Between different species. heterosynaptic long-term depression (LTD) The weakening of inactive synapses as a result of activity in other synapses on the same cell. heterotaxia, heterotaxy (1) Randomized left–right distribution of organs. (2) A cardiac looping defect characterized by altered left–right asymmetry that can be expressed as randomization (situs ambiguus) or complete reversal (situs inversus) of normal organ positions (situs solitus). heterothallic Describes organisms in which matings are restricted to parents of different mating types. heterotrichous Having two (or more) forms of filament development in the same thallus. heterotrimeric G proteins G proteins that consist of three different subunits (a, b and g) and are activated by receptors of the seven-span class. Four major classes of G proteins are Gs, Gi, Gq and Go, which interact with distinct downstream effectors (enzymes and ion channels). heterotroph Organism that requires organic carbon (usually material derived from other organisms) for energy and growth. heterotrophic Requiring organic compounds as a source of carbon. heterotropic interactions Allosteric interactions between sites that bind different types of ligands (e.g. between O2 and H1 or 2,3-BPG in haemoglobin). heterotypic pairs Conjugating cells of different mating type. heterozygosity A measure of genetic variation within a population. For a given locus, the frequency of heterozygotes at that locus within the population. heterozygote A diploid organism that carries two different alleles at a given genetic locus.

187

Glossary

heterozygote advantage Situation in which a heterozygote has greater fitness than either of the homozygotes in a given environment. Also known as hybrid vigour and heterosis. heterozygous Possessing two different alleles at a given genetic locus. heuristic search In taxonomy, choosing a phylogenetic tree based on the examination of only a selected subset of all possible trees. The tree chosen may not be the optimal tree. HEV See high endothelial venule. hexagonal Describes a form of crystal symmetry characterized by three equal axes intersecting at 1201 and a fourth of unequal length perpendicular to the others. This type of symmetry is typical of quartz and calcite. Hfr A bacterium with a sex plasmid such as F incorporated into its chromosome and which transfers its chromosome at high frequency. HGF See hepatocyte growth factor. hiatus A gap within the time record represented by a stratigraphical succession. hibernaculum Small resting body of entoprocts (Entoprocta) consisting of an inner mass of cells, usually with much yolk, surrounded by a thick chitinous wall. hierarchy A system with levels, such as the familiar Linnaean hierarchy in biological classification. high endothelial venule (HEV) A specialized blood vessel through which lymphocytes leave the blood circulation and enter lymphoid tissue. higher-order repeats Tandem arrays in which basic repeating units are combined into composite units such as dimers. highly active antiretroviral therapy (HAART) Therapy usually involving a combination of at least three antiretroviral drugs, typically two reverse transcriptase inhibitors and a protease inhibitor. high-performance liquid chromatography (HPLC) Chromatography performed under high back pressure in steel columns using a matrix of silica particles of different sizes that enables separation of polypeptides according to their size, net charge or hydrophobicity. high-threshold channel A voltage-gated channel that opens when the membrane potential is depolarized close to 0 mV. hilum A small gap or hollow in an organ where vessels, nerves and ducts enter or leave it. hindbrain The posterior part of the brain, consisting of the pons, medulla and cerebellum. hindgut The large intestine in many species. hirsutism Presence of excessive body and facial hair. HIS See Hospital Information System. histidine protein kinase Enzyme with a conserved histidine residue which, when activated, can autophosphorylate at the histidine and then phosphorylate target proteins. histiocyte Tissue cell derived from the monocyte which can be activated to become a phagocyte. histoincompatibility The genetic difference between individuals that is responsible for the rejection of skin and organ grafts. histolysis Tissue breakdown due to remodelling of extracellular matrix by proteases. histones Small basic proteins that are a major component of chromatin. They form the cores of nucleosomes, in which DNA is wrapped around the protein core. histone-like proteins Bacterial proteins that can bend or package DNA.

histopathology The study of the structural alterations of cells and tissues caused by disease. HLA Human leucocyte antigen, the name given to the human major histocompatibility complex. hnRNA Heterogeneous nuclear RNA, an old name for pre-mRNA. hnRNP protein Heterogeneous nuclear RNA protein. A protein that binds pre-mRNA in the nucleus. Although a distinction is sometimes made between hnRNP proteins and splicing factors, there is considerable overlap due to incomplete knowledge and actual overlap in function. H-NS A bacterial histone-like protein. hodological Refers to axonal pathways and connections in the central nervous system. Derived from the Greek hodos, which means way or road. HO-endonuclease A restriction enzyme from the yeast Saccharomyces cerevisiae that recognizes a single site in the yeast genome. Holliday junction A four-way junction linking two DNA molecules which results from the reciprocal exchange of DNA strands between homologous DNA duplexes. It is a central intermediate in homologous recombination. Resolution of the Holliday junction by specialized nucleases can give rise to crossover recombinants. holobasidium A single-celled basidium, often club shaped. holocentric chromosome A chromosome that has a single and continuous (diffuse) centromere, extending along the whole, or a considerable part, of the chromatids and to which the spindle microtubules attach. holoenzyme For multisubunit enzymes, the complete enzyme containing all the components necessary for its regulated activity. hologenous The situation where the inner and outer walls of the conidiogenous cells and the developing conidium are continuous. HOM genes The name given to the Hox genes in Drosophila. home range Area used over extended periods by an individual or social group for feeding and other needs. homeologous Refers to nucleic acid sequences that are similar but not identical. homeostasis The intrinsic physiological process by which the internal systems of the body (e.g. ionic and osmotic concentrations, hydration, pH, resting body temperature) are maintained at equilibrium (autoregulated), despite variations in the external environment. homeothermic ‘Warm-blooded’, able to maintain a relatively constant body temperature under a range of environmental temperatures. homeothermy An old term used to refer to animals that are able to maintain stable, high body temperatures. This word has generally been replaced by the terms ‘endothermy’ and ‘exothermy’, which emphasize the functional nature of the regulation rather than its result. homeotic (1) Describes genes that specify the identity of parts of the body. (2) Describes mutations in such genes that transform one body part into another. homeotic transformation The replacement of an organ with an organ of different type during development. homing Targeted migration of lymphocytes to a given anatomical location. homing receptor An adhesion molecule on lymphocytes that is required for lymphocyte migration to a specific target organ.

188

Glossary

Homininae, hominins The name given to a tribe of higher primates that includes humans. There is only one living, monotypic genus, Homo sapiens, but the fossil record of the group includes species attributed to Australopithecus, Paranthropus and Ardipithecus. Hominoidea Superfamily of primates that includes all living and fossil apes. hominoid A general term of primate classification that refers to apes and humans. homoctenids The Cricoconarida, tiny, cone-shaped fossil organisms whose mode of life was similar to that of modern planktonic gastropods such as pteropods. homodimer A protein composed of two identical subunits. homogalacturonan A polysaccharide composed of 1,4-linked galactosyluronic acid residues. homogametic sex The sex with two of the same kind of sex chromosome (e.g., mammalian females, which are XX). homogeneity Consisting of identical entities. A substance or cell culture is homogeneous when exacting analytical tests show that it is pure. homogeneous RNA RNA of a single length and sequence. homograft See allograft. homoiohydric Describes organisms that are resistant to desiccation and maintain internal hydration, even in drought, by the use of waterproof cuticles, etc. homologous (1) Refers to DNA sequences, molecules or structures that are similar as a result of their derivation from a common ancestor. (2) Refers to the maternal and paternal copies of a given chromosome in a diploid organism, which carry the same genetic loci although they may carry different alleles. homologous DNA pairing and strand exchange The enzymatic process that pairs an initiating single-strand DNA substrate with a homologous duplex during homologous recombination. homologous recombination Reciprocal exchange of genetic information between two homologous chromosomes, or between DNA molecules sharing extensive homology. homologous sequences DNA or amino-acid sequences with a common origin. They result either from speciation or gene duplication. homology (1) Relationship between characters or character states in organisms that derive from the same feature in a common ancestor. (2) Significant sequence identity between genes or proteins at the nucleotide or amino acid level, respectively, as a result of their derivation from the same ancestral sequence. homology-dependent gene silencing A type of epigenetic gene silencing induced by the presence of several homologous copies of a gene. homomeric Describes a protein composed of two or more polypeptide chains of identical sequence. homonomous Having segments that are very much alike. homoplasmy The case where all mitochondrial DNA molecules in a population are identical. homoploid Possessing the same number of sets of chromosomes. homopolymers Nucleotide polymers composed of only one type of nucleotide. homopolysaccharide Polysaccharide consisting of one type of monosaccharide subunit. homosynaptic long-term depression (LTD) The situation when the long-term decrease (depression) in synaptic strength occurs at the same synapses that were stimulated.

homotetramer A tetrameric molecule composed of four identical subunits. homothallic Not sexually differentiated, applied to populations of e.g. yeasts of the same mating type. homotropic interactions Allosteric interactions between sites that bind the same type of ligand (e.g. O2 in haemoglobin). homotypic pairs Conjugating cells of the same mating type. homozygote A diploid organism that carries two identical alleles at a given genetic locus. homozygous Possessing two identical alleles at a given genetic locus. horizontal gene transfer (1) The transmission of genetic material between cells in a process not involving reproduction. (2) Transfer of genetic material between species. horizontal transport Concentration or dispersal of surface algae by small- to large-scale currents. host (1) The symbiotic partner that is the largest or most conspicuous member of the association. (2) Animal or plant infected by a virus, bacterium, fungus or other parasite. host factors In insect immunity, factors secreted by the immunocyte, that opsonize the foreign antigen and attract other immunocytes. host switch Transfer of a parasite from one host to another. Hox genes Family of homeobox-containing genes that are characteristic of animals and are involved in specifying positional identity along the anterior-posterior axis. HPLC See high-performance liquid chromatography. HTLV-I Human T-lymphotropic retrovirus type-I (HTLV-I). It causes leukaemia and lymphomas. HU A bacterial histone-like protein. human chorionic gonadotrophin (HCG) Polypeptide hormone that maintains the corpus luteum in humans. human genome All the genes possessed by a human individual. Human Genome Project International project to map and sequence the human genome. humification The biochemical reprocessing by microbes of organic matter in leaf litter, particularly the more resistant tannins and lignins, into complex aromatic compounds, collectively termed humic acids or humus. humoral (1) Relating to any clear fluid or semifluid translucent anatomical substance. (2) Relating to the B-cell or antibody response of adaptive immunity. humoral capsule See encapsulation. humoral factors All substances (e.g. attacins, cecropins, defensin, gallysin 1 and 2, haemolin and lysozyme) that are synthesized by the insect’s immune system and the fat body in arthropods in reaction to invasion by foreign antigens. humoral immunity Antibody-mediated immunity. humoral responses The immune response mediated by B cells. Huntington disease A heritable degenerative brain disease. HVRI One of the regions within the mitochondrial DNA that codes for proteins involved in cellular metabolism. hybrid (1) The offspring of a cross between two pure-breeding lines of different genotype. (2) The offspring of a cross between different species. hybrid zone A region where the geographic ranges of two genetically divergent groups of populations meet and produce at least some offspring of mixed ancestry. hybridization (1) A cross between individuals from genetically differentiated populations. (2) The pairing of two complementary nucleic acid strands from different sources.

189

Glossary

hybridization probing The use of a labelled nucleic acid molecule as a probe to identify complementary sequences to which the probe base pairs. hydration shell Water around a solute that is perturbed by the solute. hydration Solvation in water. hydrocephalus Accumulation of intracranial cerebrospinal fluid (CSF) resulting in ventricular enlargement, and, frequently, increased intracranial pressure. hydrodynamic Related to the force or pressure of moving water (or other fluids). hydrodynamics The motion of fluids. In sedimentation this refers to the motion of particles dissolved or suspended in a liquid. hydrogen bond Noncovalent interaction involving two electronegative atoms (in biochemistry mainly N, O and S), one acting as a donor and the other as an acceptor of a hydrogen atom. An important type of bond in biological macromolecules. hydrogenosome A membrane-bounded respiratory organelle, typically found in anaerobic protozoa, in which enzymes oxidize pyruvate to acetate and carbon dioxide. Under anaerobic conditions this reaction releases hydrogen. hydrolases Enzymes that cleave ester, amide, anhydride and glycosidic bonds by using the oxygen of water as the nucleophile in a substitution reaction. hydrophilic Easily dissolvable in and attracted to water, as a result of polar or ionic interactions. Hydrophilic chemical structures include hydrogen-bonding groups and charged groups, which can participate in the structure of water. hydrophilicity The property of having high solubility in water. hydrophobic Water-repelling. Nonpolar hydrophobic molecules or chemical groups tend to be oriented toward the interior of proteins or toward the interior of a lipid bilayer membrane, and are insoluble in water but soluble in lipids. Hydrophobic chemical structures, such as chains of methylene and methyl groups, cannot participate in the structure of water, and thus force an energetically unfavourable organization upon the water structure. hydrophobicity Low solubility in water. hydrophobicity plot Diagram showing the running average of the index of hydrophobicity of amino acids in a protein sequence. Hydrophobic stretches of amino acids tend to arrange in such a manner as to avoid contact with polar charges. hydrops fetalis A condition that arises in the fetus as a result of extreme anaemia. It results in lack of oxygen in the fetal tissues and congestive cardiac failure, leading to a bloated appearance with swelling of the tissues. hydrostatic equation dF/dp 5 – a, where F is the geopotential of an isobaric surface, p is pressure, and a is specific volume. hydrostatic skeleton A fluid-filled cavity in e.g. echinoderms which is constrained by the muscular body walls. hydrothermal system An ocean subsurface at which magmaheated water spews out at temperatures as high as 3501C. hydrothermal vents Hot springs found at depths up to 4000 m in areas along mid-ocean ridges in the Atlantic and Pacific Oceans and support a unique community of organisms. They are created by plate movements that occur on the crustal zones of the Earth. hydroxyapatite A naturally occurring calcium phosphate (Ca10(PO4)6(OH)2), which is the major inorganic constituent of the bone matrix. hyoid apparatus Bones in the neck of tetrapod animals that support the tongue and larynx. They are the remains of embryonic gill arches.

hyperacute rejection A rejection response against a transplanted organ that is initiated by pre-existing host antibodies to antigens on the transplant. Rejection occurs rapidly, within minutes to hours after transplantation, and is untreatable. hyperammonaemia Increased blood ammonia level that may have a potentially toxic effect on the brain. hyperbilirubinaemia Increased bilirubin concentration in the circulation due to haemolysis (breakdown of red blood cells), releasing haem from haemoglobin, which is broken down to bilirubin. hypercalcaemia A condition in which there are relatively large amounts of calcium ions in body fluids. hyperchromic shift, hyperchromicity Increase in absorption of ultraviolet light of 260 nm wavelength that occurs when a DNA duplex dissociates. hyperglycaemia Increased level of blood sugar. hyperlipidaemia Increased levels of blood lipids. hypermodified base Highly modified base in a nucleic acid. hyperosmolality Having a greater osmotic pressure than body fluids. hyperphenylalaninaemia An error in metabolism whereby dietary phenylalanine is not converted to tyrosine and so its concentrations build up to dangerous levels in the blood. hyperplasia Increase in the size of a tissue or organ resulting from an increase in the number of cells. hyperpolarization A change in membrane potential away from zero, making it more negative. hypersaline Having a salinity greater than that of sea water. hypersensitive response (1) A manifestation of plant disease resistance resulting from restriction of pathogen to a small zone around the infection site and accompanied by localized death and necrosis of host tissue. (2) An exaggerated inflammatory response to an antigen. hypersensitivity An exaggerated inflammatory response to the exposure of an antigen. hypertension Increase in blood pressure. hyperthermophile A microorganism with a temperature optimum for growth above 801C. hypertrophy Increase in the size of a tissue or organ resulting from an increase in the size of the cells present. hyperuricaemia Increased concentration of uric acid in peripheral blood plasma. hypervariable regions The parts of an immunoglobulin variable region having the highest degree of amino-acid sequence polymorphism and principally responsible for conferring specificity on the antigen-binding site. hypha (plural hyphae) The fungal vegetative growth form, which is a tubular branching filament that elongates by apical extension. hyphal body A segment of a hypha that becomes separated before reproducing by budding or fission. hyphosphere The zone immediately surrounding the external surface of the hypha. hypoblast See primitive endoderm. hypodermis Epidermis or skin of a nematode. hypodigm All the fossil specimens that have been attributed to an extinct species. hypoglossal nucleus Region of the medulla that controls the muscles of the tongue and syrinx (vocal organ of birds). hypoglossal Nerve that supplies the intrinsic muscles, and all but one of the extrinsic muscles, of the tongue. hypokalaemia Low level of potassium in the blood.

190

Glossary

hypoplasia Underdevelopment of a tissue. hypoproteinaemia Low plasma protein levels in the blood. hyposplenism Reduction in activity of spleen. hypostome Most apical region in hydra, surrounding the mouth opening. hypothalamus An area of the brain situated below the thalamus containing centres regulating many functions, including reproduction. hypotonic Refers to a fluid whose osmolarity is lower than the osmolarity of normal extracellular fluid. hypoxaemia Decreased oxygen tension (concentration) in the blood, measured by arterial oxygen partial pressure values. It is sometimes associated with decreased oxygen content. hypoxia Condition in which the concentration of oxygen is greater than 0% but less than 20%. In water this is a concentration of less than 2 mg O2 per litre.

in situ In the natural location. in vivo gene transfer Gene transfer directly into cells of the body. iatrogenic Induced by medical intervention or treatment. IC50 Inhibitory concentration 50. The drug concentration that inhibits viral activity by 50%. iccosomes Immune complex-coated bodies released by follicular dendritic cells in germinal centres. Iccosomes are endocytosed by antigen-specific B cells, processed and presented to T cells in the germinal centre. ichthyornithiforms Toothed flying birds from the Late Cretaceous of North America, including Ichthyornis dispar and Ichthyornis victor. ICM See inner cell mass. icosahedral Having 20 sides or faces. icosahedron A regular polyhedron with 20 faces, each an equilateral triangle, and 12 vertices, found as the morphological form of many viruses. icterus gravis neonatorum Yellow jaundice in the newborn due to haemolysis. identity elements A set of spatially organized chemical features of an RNA molecule specifically recognized by an enzyme or protein. idiomorphs The non-homologous regions of DNA, lying at the same positions on homologous chromosomes, that constitute the mating type genes A and a of Neurospora. idiopathic ventricular fibrillation (IVF) Ventricular fibrillation without structural heart disease. idiosyncratic drug-induced neutropenia Blood neutrophil deficiency occurring as an unpredictable response to a drug. idiotope Single site (epitope) on an immunoglobulin or T-cell receptor that is bound by a specific anti-idiotypic antibody or Tcell receptor. One immunoglobulin or T-cell receptor usually contains various idiotopes. idiotype Collection of the idiotopes of an individual immunoglobulin or T-cell receptor. idiotypic determinant Antigenic determinant characteristic of a particular variable domain of an immunoglobulin or T-cell receptor. Ig See immunoglobulin. IHF A bacterial histone-like protein. IL-1 See interleukin-1. IL-2 See interleukin-2. IL-4 See interleukin-4.

IL-5 See interleukin-5. IL-6 See interleukin-6. ileus Obstruction of the bowel. image artefact A component or aspect of an image that does not correspond to a real object or function. imaginal disc A single-layered pouch of undifferentiated cells in insect larval stages that gives rise to adult structures such as the wings, legs, antennae and eyes. imidazole An azole antifungal agent containing an azole ring with two nitrogen atoms. An example is ketoconazole. imino group A portion of a molecule with the formula 5C5NH. immediate early gene A member of a set of genes that is rapidly but transiently expressed in response to extracellular signals. immediate hypersensitivity Immunological hypersensitivity reaction that occurs in a sensitized individual within minutes to a few hours of re-exposure to antigen. Most immediate hypersensitivity reactions are mediated by IgE. immune activation Enhancement of the antimicrobial activities of macrophages by interferon-g produced by antigen-activated T cells. immune evasion Strategy by which microbial pathogens subvert host immune responses in order to establish an infection, e.g. by expression of virulence factors such as capsules, toxins, adhesins, siderophores, modulins, impedins. immune haemolytic anaemia Anaemia due to destruction of red blood cells mediated by an immune reaction, i.e. by antibody, with or without the involvement of complement. immune repertoire The totality of lymphocyte receptors. The repertoire consists of millions of precursors of mature lymphocytes, each bearing antigen receptors of a unique specificity. immunity Protection against a particular disease. Innate immunity is that nonspecific protection conferred by the body’s fixed defences such as the skin, antimicrobial proteins and phagocytes. Long-lasting adaptive immunity is generated by the immune system after a first exposure to the disease, and is specific for the pathogen or toxin. immunization Introduction of an immunogen into a host in order to initiate an immune response against the immunogen. immunoadsorbent A material carrying bacterial proteins A or G (from Staphylococcus aureus) or secondary antibodies that will bind the Fc portions of antibodies and thereby bring them out of solution. immunoaffinity chromatography Method of large-scale purification of an antigen (or antibody) by passing cell extracts over columns containing immobilized specific antibodies (or antigen) covalently linked to an inert matrix. immunocompetent Able to mount a normal adaptive immune response against an immunogen. immunocompetent host An individual with a fully functional immune system. immunocyte Arthropod granulocyte and/or plasmatocyte that mediates immunological defence reactions. immunocytochemistry Techniques by which cellular molecules can be visualized by binding of labelled specific antibodies to cells or tissues and the use of colour-based fluorescent or enzymatic systems to detect this binding. immunoelectron microscopy Localization of intracellular structures or of individual proteins within a macromolecular assembly by the binding of specific antibody bearing a label, such as gold particles, that can be detected using an electron microscope.

191

Glossary

immunoelectrophoresis Immunological characterization of electrophoretically separated proteins by reaction with specific antibodies. immunofluorescence A technique in which a fluorescently tagged antibody is used to mark the cellular location of its corresponding antigen (usually a protein). Fluorescently tagged antigen can also be used to detect the presence of its specific antibody. immunogen A substance that is able to elicit an immune response. immunogenicity The degree to which an antigen is capable of eliciting an immune response. immunoglobulin (Ig) The class of proteins to which antibodies and their membrane-bound equivalents, the B-cell antigen receptors, belong. Single immunoglobulin molecules consist of two identical k or l light chains and two identical a, d, e, g or m heavy chains. They are highly variable antigen-specific proteins made exclusively by B cells and occur as five classes – IgA, IgD, IgE, IgG, IgM – which are distinguished by their heavy-chain type. Invertebrates do not possess immunoglobulins. immunoglobulin E (IgE) One of the five classes of immunoglobulin. This class is usually responsible for fighting parasitic infections. In sensitized individuals, however, IgE is the immunoglobulin responsible for much allergic disease. immunoglobulin fold Characteristic tertiary structure found in the immunoglobulin domains of members of the immunoglobulin superfamily. It comprises two surfaces of antiparallel bpleated sheet linked through a disulfide bridge between conserved cysteine residues. immunoisolation The separation of transplanted tissue from the immune system of the host by an artificial barrier. immunolabelling See immunocytochemistry. immunological hypersensitivity An immune response to normally innocuous antigens by previously sensitized individuals. Examples are allergic responses. immunological memory A feature of the adaptive immune response, in which the immune system responds more rapidly, and often more strongly, to an antigen that it has previously encountered. immunological tolerance (1) The situation in which the immune system of an individual does not make an immune response to a particular antigen. This may result from natural exposure to that antigen during fetal development or experimental exposure to high doses later in life. (2) The acceptance of a transplanted organ without continuing immunosuppressive drug therapy. immunology The study of the immune system. immunomodulation An increase or decrease in the level of immune response brought about by various specific and nonspecific means. immunopathology Damaging effects caused by an immune response, such as tissue damage due to overly aggressive cytotoxic lymphocytes and autoreactive antibodies (autoimmunity) immunophenotype The pattern of gene expression manifested by any cell population with specific reference to proteins, or carbohydrates bound to proteins, which can be detected by antibodies. immunopotentiator A substance capable of raising an immune response. immunoprecipitation Precipitation of an antigen from a soluble cell extract by binding to a specific antibody.

immunoreceptor tyrosine-based activation motif (ITAM) Amino-acid sequence found in the cytoplasmic portions of various receptors on immune system cells. It comprises ...Y-x-x[I/V]yY-x-x-[I/V]... and is a site of tyrosine phosphorylation and association with protein tyrosine kinases that carry the activating signal onwards. immunoreceptor tyrosine-based inhibitory motif (ITIM) Amino-acid sequence found in the cytoplasmic portions of various receptors on immune system cells. It comprises [V/L]-xY-x-x-L, and binds protein phosphatases that inhibit the onward transmission of the signal. immunostaining See immunocytochemistry. immunosurveillance The constant monitoring of the body by the immune system in order to prevent primary tumour development. immunotherapy The attempt to augment or enhance the action of the immune system response against a disease. The term often refers to the attempt to activate the immune system to attack an existing tumour. immunotrophism A theory that postulates that cells of the reproductive tract use T-cell-secreted cytokines as some of their growth factors. imperforate Abnormally closed. importin Also called karyopherin. The generic term for a protein that recognizes a nuclear transport cargo and targets it to the nuclear pore complex. imprinting (1) In relation to genetics, the phenomenon that for some genes the paternal copy or the maternal copy only is expressed in the early embryo. (2) A developmental phenomena in which simple exposure to an object at a particular stage of development leads to a specific complex of behaviours being directed to that object at later stages of the life cycle. in situ carcinoma Noninvasive neoplastic epithelial proliferation in the breast, confined within the boundary of the basement membrane of the terminal duct lobular unit or duct system. in vitro Refers to a biological process made to occur in a laboratory vessel or other controlled experimental environment rather than within a living organism or natural setting. in vivo Refers to a biological process occurring or made to occur within a living organism or natural setting. inactivation Prevention of a cell, protein or gene from carrying out its function. A gene, for example, is said to be inactivated when it is altered so that it cannot be transcribed; an ion channel is said to be inactivated when it no longer conducts ions although it remains open. inbreeding Self-fertilization in hermaphrodite individuals or, in outcrossing species, mating among individuals that are genetically closely related, such as brother–sister matings. inclusion body (1) Granular proteinaceous body in cytoplasm. In bacteria genetically engineered to express a recombinant protein, they often contain a high content of the protein. (2) A localized accumulation of viral protein in infected cells. May have distinctive appearance, location or stain uptake properties. incoming solar radiation See insolation. incompatibility The impossibility of two different plasmids coexisting in the same cell. Incompatibility results from crossreaction between replication control systems and, to a lesser extent, partition mechanisms. incompatibility group A group of plasmids whose replication control systems are sufficiently closely related that they inhibit each other’s replication. Used as a convenient method of plasmid classification.

192

Glossary

incubation period The time from contracting an infectious agent to the first clinical symptoms of infection. incus Small bone in the mammalian middle ear that articulates with the stapes and the malleus. It is homologous with the quadrate of nonmammalian amniotes. In many Mesozoic forms it is a substantial bone directly articulated to the jaw. indehiscent Describes a fruit that does not open by splits or pores. indigenous Living naturally in the region. individual In ontology, a general term for any concrete, particular thing whatsoever, not just an organism. induced systemic resistance Disease resistance in plants due to a physiological change in the plant that is induced by nonpathogenic organisms. inducible enzyme An enzyme that can be induced in response to a stimulus. induction of differentiation The dependence of differentiation in one tissue on signals from other tissues. It serves to correlate differentiation with other developmental and functional events. induction (1) A cellular interaction in embryonic development in which signals from one cell (or group of cells) cause another cell (or group of cells) to change its developmental fate. (2) The production of a specific protein following activation of its gene in response to a particular signal, often environmental. inductive signals In development, signals delivered by extracellular molecules to bring about cell differentiation and migration. Cells release inductive signals to organize development. infection Invasion and replication within a host organism by microorganisms. infectious clone Complete complementary DNA (cDNA) copy of viral RNA that can be used to obtain infectious transcripts in vitro. The cDNA copy can also be incorporated in a plasmid, which upon entering the bacterial cell leads to phage infection. infective centre An entity in a phage-infected cell culture that is capable of forming a single plaque. It is either a phage particle or an infected cell that has not yet lysed when plated. inferior Towards the feet. infertility In humans, the inability to conceive after one year of unprotected intercourse. inflammation Infiltration of leucocytes and plasma fluid and proteins into extravascular tissues, causing swelling, pain, reddening and heat. It can be caused by infection or tissue damage and, in the case of infection, both initiates and is amplified by a subsequent immune response. inflorescence The shoot of a plant during the reproductive phase of the life cycle, bearing the flowers or other reproductive structures. infradian rhythm A rhythmic process within an organism with a phase longer than 24 hours. infundibulum A funnel-shaped structure lying in ctenophores immediately aboral to the stomodaeum, corresponding to the stomach or oesophagus of higher invertebrates. infusion A culture made by soaking leaves or grasses in water, with or without moderate heating, and then allowing the microbial community to grow. infusion-related adverse effect An acute response to intravenous infusion of an agent. inguinal Pertaining to the groin area. inhibitory neurotransmitter Chemical released from nerve terminals that produces inhibition of a target neuron.

inhibitory postsynaptic potential (IPSP) An alteration in membrane potential in a post-synaptic cell (neuron or muscle), as a result of a stimulus such as a neurotransmitter, which inhibits the cell from producing an action potential. inhibitory synapse A synapse that when activated inhibits the postsynaptic neuron from producing an action potential. initial lymphatic Microscopic lymph channels made up of endothelial walls without a smooth muscle coat. Previously called terminal lymphatics or lymphatic capillaries. initial segment That part of the axon closest to the cell body. It is unmyelinated and extends to the start of myelination. initial velocity Rate of unidirectional transport across a membrane measured before any back-flux of substrate occurs. initials Cells in plant meristems that remain undifferentiated and continue to divide. initiation The first step of translation and protein synthesis, where the initiator tRNA (Met-tRNAI) is correctly matched to the AUG start codon in the mRNA in the ribosomal P site. initiation codon A codon specifying the first amino acid of a polypeptide chain (e.g. AUG). initiation factor IF-2 Prokaryotic initiation factor that ensures correct ribosomal P-site binding of the initiator fMet-tRNAfMet. initiation factor IF-3 Prokaryotic initiation factor that carries out proofreading of the 30S ribosomal initiation complex. in-line attack Attack of an activated nucleophile (e.g. OHÀ) on phosphorus ‘in line’ with the phosphodiester bond to be cleaved. innate immunity Immediate antimicrobial responses due to preexisting components of the immune system whose intrinsic activity is unaffected by, and not specific for, a particular antigen. innate responses See innate immunity. inner cell mass (ICM) Portion of the mammalian blastocyst that will form primitive endoderm and the epiblast. innervate See innervation. innervation Establishing contact of a nerve with its target tissue. innovation See novelty. inoculum A small number of individual cells used to initiate a bacterial culture. iNOS See inducible nitric oxide synthase. inosine A purine base similar to adenine, but lacking one amino group. Present in RNA in small amounts, it base pairs with cytosine instead of uracil. inositol 1,4,5-trisphosphate (IP3) An intracellular signalling molecule that is generated by the hydrolysis of membrane phospholipids via activation of a G-protein-coupled phospholipase. IP3 triggers the release of calcium from intracellular stores. INR See International Normalized Ratio. insertion element A mobile DNA sequence in bacteria that carries only the genes needed to move it from one site to another in DNA. Its insertion into another site generally causes a mutation. insertion mutagenesis See insertional mutagenesis. insertional inactivation See insertional mutagenesis. insertional mutagenesis Disruption of gene function by the insertion of a foreign DNA sequence into a gene. inside-out signalling Signalling from within a cell that leads to changes in integrin-mediated cell adhesion. insolation The radiant energy received on Earth from the Sun. It is currently 1350 watts mÀ2 at the top of the atmosphere, at the Equator. Acronym for incoming solar radiation. insonation The exposure of a region of tissue to ultrasound. instar The period between two moults in arthropods.

193

Glossary

integral membrane protein Membrane protein that interacts strongly with the lipid bilayer and can be solubilized only by detergents. Such proteins have a portion of their mass buried in the lipid bilayer. integrase The transposase encoded by a retrovirus that mediates the integration of the DNA form of the virus into chromosomal DNA by site-specific recombination. integration host factor (IHF) Bacterial protein required for the integration of phage l into the host cell genome. integrins A superfamily of heterodimeric cell adhesion molecules that mediate cell–cell and cell–matrix interactions, and thereby control multiple cellular responses. They each consist of one a and one b subunit. integron A genetic cassette within which antibiotic-resistance genes are acquired, lost and reshuffled by site-specific recombination. integumentary structures Structures related to the epidermis (skin). integument Skin. intercalary regeneration A type of regeneration that fills space between the edges of a wound. interclavicle A midline T-shaped bone present in the ancestors of the mammals and in early mammals. It connects the right and left pectoral girdles. Among extant mammals it is present only in monotremes. interdigitating dendritic cell Large antigen-presenting cell with extensive and numerous processes found in T-cell areas of peripheral lymphoid organs. interfascicular Refers to the area between vascular bundles. interferons A family of proteins with antiviral activity. interfertile Able to exchange genes. intergenic recombination Recombination between closely linked homologous genes, following chromosomal misalignment at meiosis. The recombination event may be crossing-over or gene conversion, and results in a gene that represents a hybrid of the two misaligned genes. interleukin-1 (IL-1) A cytokine produced by macrophages and epithelial cells that synergizes with other factors to stimulate colony growth from bone marrow. interleukin-2 (IL-2) Cytokine secreted by activated T cells that stimulates the growth of T cells. interleukin-3 (IL-3) Cytokine produced by T cells and epithelial cells, also known as multi-colony-stimulating factor, this stimulates the growth of multiple types of colonies from bone marrow stem cells, i.e. blast cell, erythroid, megakaryocyte and mixed colonies. interleukin-4 (IL-4) Cytokine secreted by T cells and mast cells that stimulates B-cell activation and isotype switching. interleukin-5 (IL-5) Cytokine produced by T cells and mast cells that stimulates the growth of eosinophils. interleukin-6 (IL-6) Cytokine required for bone marrow stem cell growth in vivo. It stimulates the production of granulocyte and granulocyte–macrophage colonies from bone marrow cells in vitro and the final stages of B-cell differentiation. It also has effects on the liver and bone formation. interleukins Members of the cytokine family that were originally thought of as intercellular messengers between leukocytes but are now perceived as having wider immunological and inflammatory effects. intermediate filaments Protein filaments of the eukaryotic cell cytoskeleton intermediate in diameter between microtubules and microfilaments. They are constructed from a family of related intermediate filament proteins.

intermediate host A host in which no sexual reproduction of a parasite occurs. intermediates Short-lived chemical species hypothesized as occurring transiently on the way from reactants to products in chemical reactions. internal state Enzyme–ligand or enzyme–transition state complex. International Normalized Ratio (INR) Correction of the prothrombin ratio – the patient’s prothrombin time : control prothrombin time (PT) – by the International Sensitivity Index (ISI) assigned to a thromboplastin, calculated as follows: INR 5 (PT ratio) ISI. Internet Worldwide digital communications network, conceived and developed originally by the US Department of Defense and now transferred to international commercial enterprises. interneuron Neuron that is interposed between, and synaptically connected with, two other neurons. interphase The time a eukaryotic cell spends between successive mitoses. There is considerable variation in duration of interphase between individual cells within an actively dividing population. interspecies hydrogen transfer Production and consumption of hydrogen (H2) by different groups of microbes interacting closely during anaerobic catabolism. interspecific Between two or more species. interspersion pattern The pattern in which repeated sequences and single-copy sequences are intermingled in the genome. interstitial (1) Pertaining to or belonging to interstices or interspaces of a tissue or organ. (2) Pertaining to the spaces between mineral grains. interstitial cell Stem-cell population in cnidarians giving rise to nerve cells, gland cells, nematoblasts and nematocytes (stinging cells), and gametes (observed only when the animals follow the sexual cycle). interstitial organism Organism that inhabits the spaces between sand grains. intersubunit space Partially open space between the small and the large ribosomal subunits, whose shape is tailored to accommodate tRNAs. intertidal Describes the area covered by the sea at high tide and exposed at low tide. intervening sequence See intron. interventional radiology The use of an imaging procedure to control an interventional procedure, as distinct from making a diagnosis. intima An inner layer of cells in the pulmonary vascular wall, consisting of cells of endothelial or perhaps smooth muscle derivation. intracellular messenger Any intracellular ion or protein produced as a result of receptor stimulation and which directly modifies the activity of another protein. intracytoplasmic membrane The photosynthetic apparatus in purple phototrophic bacteria. intramembranous ossification Bone formation and repair achieved through the direct transformation of mesenchymal stem cells into osteoblasts, without requiring the intermediate step of a cartilage anlage. in trans On or affecting another molecule. intraspecific Within a species. intraspecific variation Variation, either morphological or genetic, that occurs within a species so that no two individuals are exactly alike unless they are clones.

194

Glossary

intrastrand exchange Recombination between copies of a tandem array of sequences on the same DNA strand. intrinsic rate of population growth The instantaneous rate of growth of a population not subject to density limitation. Usually symbolized as r. introgression The transfer of genes between genetically differentiated populations or species. intromittent organ The male copulatory organ. intron A noncoding region in an RNA (or a gene) that is removed from the initial RNA transcript by splicing during maturation to produce the functional RNA. Also known as an intervening sequence. intron phase The position of an intron within the reading frame of the coding sequence. intronless Describes a gene that is made up of a single long exon and thus lacks introns. invariant lineage Describes the developmental condition in which the corresponding cells in different individuals always have the same descent. Cell fates are thus invariantly specified. invasion The spread of tumour cells to surrounding tissues. invasive species A species introduced from its native range to a new area (also known as exotic or introduced species). Invasive species can compete with or prey on local species, at times causing extinctions and shifts in community composition and function. inversion Structural rearrangement within a chromosome resulting from two breaks in the chromosome with inversion of the intervening segment of chromosome before rejoining. invertebrate Any of the animals without vertebrae or backbones. All animals other than vertebrates. ion channel A transmembrane protein that forms a selective pore for the diffusion of ions through a cell membrane. Ion channels are usually specific for a certain type of ion and most are gated, in which case they open only in response to a particular stimulus such as a change in membrane potential or the binding of an extracellular ligand. ionic strength A measure of the total ionic concentration of a solution regardless of net charge. ionotropic receptor A ligand-activated ion channel. When ligand molecules (typically neurotransmitters) bind the extracellular portion of the receptor, the receptor channel opens and allows ions to flow through the channel and across the cell membrane. IP3 See inositol 1,4,5-trisphosphate. ipsilateral Belonging to or occurring on the same side of the body, as opposed to contralateral, which refers to the opposite side of the body. IPSP See inhibitory postsynaptic potential. iridium An element in the platinum group having the atomic number of 77. Iridium is enriched in some extraterrestrial asteroids, and is depleted in the Earth’s surficial rocks. iridocyclitis Inflammation of the iris and ciliary body. iron reduction A form of anaerobic bacterial decay in which iron hydroxides or oxides serve in the metabolism of organic matter. iron–molybdenum cofactor (FeMo-co) The active site cofactor of dinitrogenase: Fe7S9Mo:homocitrate. ischaemic heart disease A disease of the coronary artery wall characterized by atheromatous plaque formation reducing blood flow to the myocardium. ischial callosities Hard pads present on the ischial bones of monkeys and partially on gibbons, an adaptation for sitting on branches.

island model migration The random movement of individuals between populations. isoacceptor tRNA A member of a set of tRNAs that accept the same amino acid. isochromosome A structurally abnormal chromosome composed of either identical short or long arms, formed by the aberrant division of the centromere. isodiametric Of similar dimensions in all directions. isoenzymes Enzymes with identical substrate specificity but of different biochemical structure. isoforms Multiple forms of a molecule (e.g. a protein) that perform the same function (e.g. catalyse the same reaction in the case of isoenzymes) but differ in their composition (i.e. amino-acid sequence in the case of a protein). isogamontic ciliates Ciliate protozoans in which the co-conjugants do not differ from each other morphologically. isograft A tissue or organ transplant from one individual of an inbred strain to another. Such grafts not rejected. isomerase An enzyme that catalyses the interconversion of two isomers, i.e. two compounds comprising the same atoms. isomerization The process of interconverting isomers, i.e. different covalent arrangements of the same atoms. isometry The situation when there is a linear proportionality in respect to increase in size, e.g. a tenfold increase in mass and volume of heart, muscle, blood, and lung is associated with a tenfold increase in body mass. isomorphous replacement A technique in X-ray crystallography in which a heavy metal ion is introduced into a crystal without changing the crystal’s shape, in order to determine the signs (positive or negative amplitudes) of diffracted X-rays. isoschizomers Restriction enzymes from different bacterial species that recognize and cleave identical DNA sequences. isotope signature The evidence that organic molecules have been processed by living systems, which can be obtained by analysis of isotopes of e.g. carbon. isotopes Physically and chemically different atoms of the same element, resulting from differences in the number of neutrons in the atomic nuclei. isotopic tracer technique A method of investigating biosynthetic mechanisms by feeding an organism with a putative biosynthetic intermediate labelled with an isotope not naturally present in large amounts (e.g. 13C, 14C, 2H, 3H, 15N, 18O). isotopomer A molecule that has been labelled, in a known position, with an isotope (distinguishable by nuclear magnetic resonance) of the element normally found at that position. isotype The class of an antibody (e.g. IgG, IgA, IgM), which depends on the type of its heavy chain. isotype switch The change in a B cell or its progeny from the secretion of immunoglobulin (antibody) of one class to immunoglobulin with the same V regions but a different heavy-chain C region and, hence, a different isotype (or class). isoxazolylpenicillins A group of semisynthetic penicillins that are not inactivated by staphylococcal b-lactamase. They include oxacillin, cloxacillin, dicloxacillin and flucloxacillin. isozymic forms Physically distinct forms of an enzyme present in different cells. ITAM See immunoreceptor tyrosine-based activation motif. iteroparity Repeated episodes of reproduction within the life cycle. ITIM See immunoreceptor tyrosine-based inhibitory motif. IVF See idiopathic ventricular fibrillation.

195

Glossary

Janus kinase (JAK) A member of a family of tyrosine kinases that includes the interferon-associated enzymes Tyk2 (tyrosine kinase 2), JAK1 (Janus kinase 1) and JAK2 (Janus kinase 2). They act by activating STATs which then act as transcription factors. Jarisch–Herxheimer reaction A transient, short-term immunological reaction, commonly seen after antibiotic treatment of syphilis and sometimes other diseases, due to liberation of endotoxin or antigens from the killed microorganisms. It is marked by fever, chills, headache, muscular and cutaneous lesions. jasmonic acid Plant hormone, a structural analogue of animal prostaglandins, required for wound-induced gene expression. jaundice A yellow appearance resulting from increased bile pigment in the plasma. joint molecule An intermediate in the DNA recombination process consisting of single-stranded DNA paired to a homologous region within a double-stranded DNA molecule. Jurassic period The middle major division of the Mesozoic era. just-so-story An adaptationist explanation for a trait that relies on plausible but generally untestable claims about the circumstances under which the trait is supposed to have evolved. A just-so-story is a ‘how possibly’ explanation as opposed to a ‘how actually’ it happened.

K antigen Bacterial capsular antigen used for serotyping. K homology (KH) motif An RNA-binding domain in proteins that consists of ~60 amino acids and contains a conserved octapeptide, Ile-Gly-X2-Gly-X2-Ile, where X varies among the different KH motifs but is usually a positively charged amino acid. kairomone (1) A substance produced by a predator that induces an adaptive change in the development of the prey. (2) Plant chemical that attracts herbivores. kala-azar Visceral leishmaniasis. kaliuresis Increased potassium in the urine. Kaposi’s sarcoma-associated herpesvirus A herpesevirus associated with the vascular cancer, Kaposi’s sarcoma. karyogamy Fusion of two nuclei (usually haploid nuclei). karyogram Representation of an entire chromosome set that has been stained by one of several possible methods to yield discrete banding patterns. karyonide In ciliate protozoans, a vegetative cell lineage that is derived from an exconjugant cell with a single newly formed macronucleus. karyopherin See importin. karyotype A complete description of the number and morphology (often a photograph) of all the chromosomes in a cell as they appear at mitosis or meiosis. kb Kilobase, a unit of measurement of the length of nucleic acid molecules (DNA or RNA). It is 1000 nucleotides or base pairs. kcat The first-order rate constant that describes the rate of an enzyme-catalysed chemical transformation of substrates to products. kcat/Km Parameter that describes the catalytic efficiency of an enzymatic reaction involving a particular substrate. The larger the value, the more efficient the reaction for a particular enzyme– substrate pair. keratinized epithelium The hard, dry, ‘horny’ outer surface found on skin and related structures.

keratinocyte The predominant cell within the epidermis, containing large amounts of the protein keratin. keratins The protein subunits of certain cytoskeletal intermediate filaments. They interact with integrins, thereby contributing to cell strength and to cell motility during migration. ketogenic Describes metabolites that result in the production and excretion of ketone bodies. ketone body Acetoacetate, D-b-hydroxybutyrate or acetone, which are water-soluble derivatives of fatty acids produced by the liver during starvation or in uncontrolled type I diabetes. key innovation A novel character that may have been important in the origin of an adaptive radiation. Kimmeridgian The middle stage of the Upper Jurassic. kin selection Selection that results from close kin behaving in ways that favour each other, resulting in increased inclusive fitness. kinase An enzyme that catalyses the transfer of the terminal gphosphoryl group of ATP to an acceptor molecule, with the formation of ADP and the phosphorylated acceptor. Protein kinases are enzymes that transfer phosphoryl groups in this way to proteins, thus phosphorylating them at specific sites and often changing their activity as a result. kinematics The study of the characteristics of motion. kinesin A member of a superfamily of motor proteins with ATPase activity that are present in most eukaryotic cells. They associate with microtubules and move along them, hydrolysing ATP to produce the energy to power the movement. kinesis Mobility of a structure (of a skull, typically) about particular joints. kinetics (1) A branch of chemistry that deals with the study of rates and rate laws of chemical reactions. (2) The study of how forces act on a system to create movement. kinetochore Specialized structure that forms at the centromere and to which the microtubules attach during mitosis and meiosis. kinetoplast Organelle containing mitochondrial DNA that characterizes the protozoan order Kinetoplastida. kinetosome Subpellicular, cylindrical structures composed of nine longitudinal equally spaced peripheral tubules each composed of three microtubules. The embedded basal body produces a cilium or flagellum. kinety A row formed by kinetosomes, the basal bodies of cilia. Kingdom In taxonomy, the second highest level of biological classification. kissing complex Complex formed by two stem–loops in a nucleic acid base pairing in their respective loop regions. Klenow fragment The fragment of Escherichia coli DNA polymerase I derived by removal of the 50 –30 exonuclease domain. It has the function of adding bases to the unpaired stretch of DNA at the end of a growing DNA duplex. kleptoplastidy The capacity of certain microorganisms to use the chloroplasts of the prey they ingest in order to photosynthesize. Km The Michaelis constant. A kinetic constant related to Ks, and which describes the concentration of substrate required to halfsaturate the enzyme molecules during steady-state catalysis. KNM-ER Abbreviation of the prefix ‘Kenya National Museum – East Rudolf’. knockout mouse A mouse in which a given predetermined gene has been inactivated. It is generated by first targeting the gene in cultured embryonic stem cells and then introducing the altered stem cells into a blastocyst. knot A closed circular DNA including a knot which cannot be removed without double-strand breakage.

196

Glossary

Kranz anatomy The wreath-like arrangement of bundle-sheath cells and mesophyll cells within the leaves of C4 plant species. Krebs cycle The tricarboxylic acid cycle, a metabolic pathway within mitochondria by which carbohydrates and fats are fully combusted during aerobic respiration. krill Large schools of planktonic euphausiacean crustaceans (subclass Eumalacostraca) typically found in Antarctic waters. Also refers to the euphausiaceans themselves. Ks The equilibrium dissociation constant for the binary complex between an enzyme and its substrate molecules. K-shell The innermost shell or orbital of electrons in an atom. K-shell binding energy The energy required to expel an electron from the K-shell of an atom. Kyte and Doolittle hydropathy analysis Method of assessing the hydrophobicity of amino acids in a protein. This information is used to predict membrane-spanning domains and topology.

labelling index In studies of actively growing and dividing cells, the percentage of cells labelled with tritiated thymidine ([3H]TdR), which reflects DNA replication, is known as the labelling index. labyrinth The inner layers of the placenta in rodents. lacteal Lymph vessels of small intestine. LAG See line of arrested growth. ¨ ¨ Lagerstatte (plural Lagerstatten) A fossil deposit of exceptional preservation. This is a specialized use of a German word that originally referred to a rich mineral deposit. lagging strand In a replicating DNA, the strand that is synthesized discontinuously and in the opposite direction to fork movement, as a series of short Okazaki fragments. lambdoid bacteriophages The family of related phages of which l is the prototype. lamella See bilayer lamellar bone Bone in which fine collagen fibre bundles are arranged in thin plates, or lamellae, with different orientations in successive lamellae. lamellated bone Bone that has a gross layered structure due to variation in the mineral structure. lamellipodia (singular lamellipodium) Actin-based motile veillike protrusions from the leading edge of a migrating eukaryotic cell, which assist in locomotion. laminar Sheet-like. lamivudine Nucleoside analogue inhibitor of human immunodeficiency virus (HIV) reverse transcriptase. Used as an anti-HIV drug. Lancefield groups A serotyping scheme (devised by Rebecca Lancefield) for streptococci, based on antigenic cell wall polysaccharides. Grouping is usually accomplished by precipitation reactions with group-specific antisera. landrace A local or regional crop variety that has arisen from farmlevel seed production and selection, often over centuries. Langerhans cells Immature dendritic cells of epithelium, particularly the skin, which pick up antigen and carry it to draining lymphoid organs. lariat The looped structure formed in the intron as a result of the formation of a 20 –50 phosphodiester bond between the first base of the intron and an adenosine (branchpoint adenosine) in the first step of splicing.

laser ablation Experimental technique used on C. elegans in which a single cell is killed by means of a microscopically focused laser beam. late genes Viral genes transcribed late in the replication cycle, mainly virion proteins. latency The activity of a mitochondrial enzyme following the disruption of mitochondria minus its activity in the intact preparation. Enzyme latencies are used to assess the integrity of mitochondria. latent period (1) The time needed for a vector that has completed the acquisition of virus to become infective. (2) The entire period during which phage reproduction is occurring. It comprises the interval between adsorption of phage to the cell and lysis of that cell. lateral Away from the midline. lateral diffusion Movement by lipids and by proteins in the plane of a membrane. lateral geniculate nucleus A nucleus in the thalamus of the brain that relays visual information from the retina to the primary visual cortex. Additional inputs to the lateral geniculate nucleus from the brainstem and primary visual cortex modulate its output. lateral inhibition The process whereby a developing cell inhibits its neighbours from assuming a similar fate. lateral root Plant root formed on a young root that has not yet started secondary growth. Laurasia The northern continental landmass formed during the early Mesozoic. It included what were to become North America, Europe and Asia. Lazarus taxa Taxa that disappear from the geological record, only to reappear at a later time. leading strand In replicating DNA, the strand that is synthesized continuously and in the same direction as the fork moves during DNA replication. ¨ Leao spreading depression Depression of nerve cell function in selected areas of the brain causing the aura of migraine. It also affects cranial blood vessels. leaving group Structural entity produced by cleavage of a chemical bond, requiring stabilization (e.g. by protonation) before release of the product. lecithotrophic Describes the nourishment of larva solely by digesting yolk. lectin A class of proteins first found in plants, but also present in animals, which bind to sugars on e.g. the glycoproteins and glycolipids of the plasma membrane. They are often used as receptors in innate defence reactions. Lectins found in arthropods are known as haemagglutinins or heteroagglutinins. LEF An HMG-box transcription factor that binds DNA with sequence specificity, altering the bending of DNA and thus gene expression. legume Fruit (a dehiscent pod) of the Leguminosae (peas, beans, vetches, etc.). The term is also used to describe the plants of this family. Leishmania Genus in the Trypanosomatidae family of protozoa. lek Mating arena where males display and females come simply to acquire matings. No resources are associated with a lek besides males. lens The transparent structure in the eye that focuses the optical image to the retinal photoreceptor layer. Its shape ranges in different animals from almost spherical to a flat disc with an ellipsoid section.

197

Glossary

lentic Pertaining to slow moving water characteristic of a pond or lake. leptospiraemia Presence of leptospire bacteria in the blood. leptospiruria Presence of leptospire bacteria in the urine. Ler The Arabidopsis ecotype Landsberg erecta. lesion A site of damage. In DNA, the term refers to damage such as an adducted base or a strand break. leucocytes A general term for all white blood cells. Leucocytes include lymphocytes, monocytes, dendritic cells and polymorphonuclear lymphocytes. leucocytosis Increased count of white blood cells in the blood circulation. leukocyte See leucocyte. Lewis acid An electron pair acceptor. Metals often serve as Lewis acids in catalysis by accepting an electron pair from a substrate (to form a coordinate bond), thereby polarizing the electron density of the substrate. library Collection of cloned DNA fragments. Libraries can be composed of genomic DNA clones, generated from fragments of genomic DNA, or of cDNA clones, generated from reverse transcription of cellular mRNAs. life cycle Refers to various developmental stages that one organism, or even one cell, passes through during its life. Some parasites exhibit life cycles involving several hosts. lifetime In regard to a fluorophore, the average amount of time between light absorption and emission. ligand (1) The smaller of two molecules that interact reversibly to form a complex. (2) A molecule that binds to a cell-surface receptor. (3) A molecule or ion that binds to a metal ion by donation of an electron pair. ligase An enzyme that joins two molecules together covalently, e.g. D-alanine ligase, which forms D-alanyl-D-alanine from two Dalanine molecules. light-harvesting complex A protein complex that absorbs light energy and converts it to exciton energy that can migrate to a neighbouring complex or to a reaction centre. The light is absorbed by pigment molecules (e.g. chlorophyll and carotenoids) that are attached to the protein. light-harvesting structure The main light-gathering antenna (complexes of chlorophyll and protein) in photosynthetic organisms. lignocellulose The mixture of polymers found in the cell walls of higher plants. It is composed of cellulose microfibrils associated with smaller, more complex polysaccharides called hemicelluloses embedded in a matrix of lignin. The adjective is lignocellulosic. likelihood A general method of testing hypotheses that contrasts the exact probabilities of observing data given particular hypotheses. likelihood-ratio statistic A statistic based on the ratio of two probabilities, used to test the hypotheses under which the probabilities were generated. limb plexus Region at the base of the developing limb where the incoming axons join together and sort out from one another. limestone Rock composed mostly of calcium carbonate. limited proteolysis Proteolytic hydrolysis of an entire organelle or membrane-bound protein(s) and cleavage of surface-accessible peptide regions.

Limulus lysate test An assay to detect the presence of bacterial lipopolysaccharide based on the ability of this molecule to cause gelation of amoebocyte lysate of the horseshoe crab, Limulus polyphemis. line of arrested growth (LAG) A line that marks a pause in bone growth. lineage (1) A sequence of fossil species, which usually do not overlap in time, but which form part of a distinctive evolutionary trend. (2) Descendants from a particular precursor cell. linear energy transfer Energy deposited in material per unit of track by a transmitting ionizing particle (usually expressed as keV mmÀ1). It can be regarded as a measure of the efficiency of a radiation for producing a biological effect. linkage The situation when two loci are situated close together on the same chromosome, so that their alleles usually stay together at meiosis in gamete formation. linkage disequilibrium Nonrandom association between alleles at different genetic loci such that they tend to be inherited together. It is due either to physical proximity on the chromosome or to selection for a particular combination of traits. linker DNA The DNA joining two nucleosomes, which is lost when a nucleosome is trimmed to a core particle. lipid Substance insoluble in water but soluble in organic solvents such as chloroform and acetone. Lipids include phospho- and glycolipids, sterols, waxes and triacylglycerols. lipid bilayer The structure formed by amphipathic phospholipids in an aqueous environment in response to the hydrophobic effect. The molecules are organized in a double layer in which the polar headgroups face outwards (to the aqueous environment) and the hydrocarbon chains are in the interior. A lipid bilayer is the basic structure of all biological membranes. lipid monolayer A planar array of amphipathic lipid molecules, one molecule thick, where the hydrophobic surface is formed by the lipid hydrocarbon chains and the hydrophilic surface is established by the polar headgroups. lipophilicity A molecular property associated with an affinity for oily or waxy environments as opposed to those that are aqueous in nature. lipopolysaccharide (LPS) A component of the cell walls of Gramnegative bacteria consisting of a lipid A moiety and a highly species- and strain-specific polysaccharide domain. The vertebrate innate immune response has evolved to be exquisitely sensitive to minute amounts of LPS. lipoprotein A complex of proteins and lipids that transports lipids in the blood. liposome A tiny synthetic lipid vesicle into which protein or other materials, e.g. fluorescent molecules, can be incorporated for delivery into cells. liquid crystal The type of organization within the lipid bilayer membranes of cells. There is extensive order in the plane of the membrane. Within this nearly two-dimensional structure, lipid molecules can diffuse laterally in two dimensions but experience very little freedom to move between layers. liquid scintillation Process by which radioactivity in a sample can be quantified through the use of a solvent (a fluor) that has the ability to absorb energy and re-emit it as light. lithification The alteration or hardening of loose sediment into compact, cemented rock. lithosphere The upper layer of the Earth’s crust, which moves in many separate tectonic plates across the weaker, plastic asthenosphere below.

198

Glossary

lithostratigraphic unit A body of rock with certain unifying features that enables it to be recognized, mapped and correlated as a single unit. littoral The seashore, or, living on the seashore. lobopod A limb constructed as a lobe-like outgrowth of the body wall in tardigrades and lacking rigid sections and articulations. local alignment The alignment of two or more sequences at discrete regions of similarity. This type of alignment is well suited for database searching with an uncharacterized query sequence. local response Activation of wound-response genes in damaged tissues of a plant. Usually refers to responses occurring in the leaf that has actually been wounded. locomotion Movement of a cell or organism. locus Position on a chromosome at which the gene controlling a particular trait resides. It can be occupied by different alleles of the gene. locus heterogeneity See genetic heterogeneity. loess Wind-blown silt derived from deserts or from the rock-flour produced by glaciers. long QT syndrome (LQT) A cardiac disorder characterized by prolongation of the QT interval on electrocardiograms, syncope (sudden loss of consciousness), seizures, and sudden death due to a specific ventricular tachycardia called torsade de pointes. long-branch attraction The tendency of parsimony-based methods to group long-branch taxa together. longevity The ability of seeds to maintain their viability over a long period. long-term potentiation (LTP) A long-lasting (41 hour) increase in synaptic strength caused by a brief period of synaptic activity that fulfils special requirements. For many forms of LTP, this requirement is that the postsynaptic cell be strongly depolarized. look-up table (LUT) An array of values that changes a grey value of a pixel to another value. lophophore Tentaculated extension of the mesosome that embraces the mouth, but not the anus, in phoronids. Its main functions are feeding, respiration and protection. lorica A loosely fitting secreted extracellular shell that can partially or nearly completely envelop the cell body of suctorian protozoa. lotic Pertaining to rapidly moving water characteristic of a river or stream. low-threshold channel A voltage-gated channel that opens when the membrane potential is depolarized only a few millivolts above resting potential. LPS See lipopolysacharide. LQT See long QT syndrome. LTD See long-term depression. LTP See long-term potentiation. lumen (1) The interior space within a hollow structure such as the gut or a blood vessel. (2) The water phase within the thylakoid vesicle of chloroplasts. luminal Pertaining to a lumen, or facing into the lumen. lupus erythematosus An autoimmune disease of unknown aetiology with disseminated proliferative lesions of minute blood vessels and lymphatics. LUT See look-up table. Lyapunov exponent A measure of whether nearby trajectories will tend to converge (negative), diverge (positive) or retain their separation (zero). A positive Lyapunov exponent is a hallmark of chaos. Lyme borreliosis See Lyme disease.

lymphadenopathy Pathological enlargement of one or more lymph nodes. lymphangiogram The detection by radiology of contrast medium injected into the lymphatic system, used to highlight abnormalities of that system, including lymph nodes. lymphangion A collecting lymphatic segment with an upstream and downstream valve, and intrinsic smooth muscle to compress the lymphatic lumen. lymphatic system The lymphatic vessels and lymphoid tissues. lymphatic vessels, lymphatics Vessels that carry the lymph formed in various tissues to lymph nodes and eventually from there to the blood circulation. lymphocyte The cell type mediating the antigen-specific part of the adaptive immune response. It is a type of white blood cell with a large, spherical nucleus surrounded by a thin layer of nongranular cytoplasm. The two main classes of lymphocytes are the T lymphocytes (or T cells) and the B lymphocytes (or B cells). B cells develop into antibody-secreting cells, while T lymphocytes become either cytotoxic T cells or helper T cells. lymphocyte homing Migration of lymphocytes that directs them to particular tissues where they may develop further and/or carry out their effector function. lymphocyte recirculation The process in which naı¨ ve lymphocytes are continuously migrating from the bloodstream into secondary lymphoid organs and returning to the blood via efferent lymphatics. lymphoedema Oedema resulting from lymphatic obstruction. lymphoid cells Lymphocytes or their precursors. lymphoid follicle An accumulation of rapidly proliferating B lymphocytes in a secondary lymphoid tissue. lymphoid progenitor A cell that is committed to a developmental pathway that will result in lymphocytes. lymphokines Cytokines produced by lymphocytes. lymphoma A cancer of lymphoid tissue. lymphopenia A deficiency of lymphocytes in the blood circulation. lymphoproliferative A disease or disorder that results in a population of lymphocytes that proliferate in an uncontrolled manner. lymphotoxin Cytokin produced by activated T cells and which is toxic to some cell types. Also known as tumour necrosis factor-b (TNF-b). lyophile A sample that has been preserved by freeze-drying. lyriform organ A sensory organ unique to arachnids that is formed by several closely spaced slit sensilla and is used in detecting compressional forces in the exoskeleton. lyse To rupture a cell, releasing its contents and resulting in cell death. lysis Rupture of a cell, resulting in the release of its contents and cell death. lysis inhibition A delay in the metabolic death of a phage-infected cell, with consequent delay in lysis, caused by infection of a previously infected cell. lysogen A bacterium that harbours a phage chromosome in a stable inactive association with the bacterial chromosome. lysogenic Describes a type of bacteriophage that can integrate into the host DNA and remain inactive there for many cell generations. See lysogeny. lysogenization The establishment of a lysogen.

199

Glossary

lysogeny A stable state in the life cycle of a temperate phage, in which the phage genome is integrated into the host cell chromosome in an inactive state (prophage), with no synthesis of progeny virions. lysophospholipid Glycerolipid that contains an unesterified hydroxyl group and a single acyl chain substituent on the glycerol backbone. lysosome A specialized membrane-bounded acidic vacuole in animal cells that contains hydrolytic enzymes. Material that is internalized via endosomes is ultimately degraded in lysosomes. lysosomotropic Describes a chemical that tends to concentrate within the lysosomes of a cell. lysozyme Antibacterial mucolytic enzyme that attacks bacterial cell walls, resulting in bacterial lysis. It is present in lysosomes and is secreted in certain bodily secretions, such as tears. lytic Causing cell lysis. lytic bacteriophage Bacteriophages whose infection cycle ends with formation of new progeny phages and their release by cell lysis. lytic enzymes Enzymes, typically found in phagocyte lysosomes, that attack cell constituents, causing cell lysis. lytic phage See lytic bacteriophage.

MA See mechanical advantage. m7G cap The methylated nucleotide that is added at the 50 end of fully processed eukaryotic mRNA. This nucleotide, 7-methylguanosine diphosphate, is linked in a unique 50 –50 triphosphate bridge with the first transcribed nucleotide in the mRNA. m7G50 ppp50 Gm cap A modified nucleotide structure characteristic of the 50 terminus of eukaryotic mRNAs. m7GDP 7-Methylguanosine 50 -diphosphate. MAC See membrane-attack complex. Mac-1 An integrin present on leucocytes which is comprised of the subunits CD11b and CD18 and recognizes the complement fragment iC3b. Also known as the complement receptor CR2. macrocarrier See macroprojectile. macrocyst The sexual stage of dictyostelid cellular slime moulds. Macrocysts form from aggregations of cells in response to environmental conditions of excess moisture and absence of light. Two of the cells fuse to form a giant cell that ingests all the others. macroevolution Large-scale evolution, usually interpreted to mean all processes and patterns of phenotypic and genetic change at and above the species level. macrogamete Female gamete. macromolecular crowding The notion that a significant percentage of the intracellular volume is occupied by macromolecules. macronucleus The somatic nucleus in protozoa (such as ciliates) that have nuclear dimorphism. macrophage Large phagocytic cell present in almost all tissues and derived from circulating monocytes. It scavenges tissue debris and has effector roles in both innate and adaptive immunity in vertebrates. As well as phagocytosing and killing microorganisms, the macrophage can act as a professional antigen-presenting cell to activate T lymphocytes and secretes numerous cytokines that influence inflammatory and immune responses. Granulocytes and/or plasmatocytes perform a similar phagocytic function in arthropods. macropodid A member of the kangaroo and wallaby family of marsupials.

macroprojectile Any macroscopic object that can be accelerated to high velocity, which can thereby accelerate the microcarriers placed on its surface. macula An enlarged region of the inner ear containing densely packed sensory hair cells specialized for detecting sound, vibration, acceleration or gravity. maculopapular Describes a nonvesicular skin eruption containing macules (small spots) and papules (red elevated areas of skin). magnetic field The pattern of the magnetic influence derived from the presence of a magnetized entity. magnetic resonance spectroscopic imaging (MRSI) A method of acquiring nuclear magnetic resonance spectral information in a spatially dependent manner. Data can be displayed as images in which image intensity (or colour) represents the intensity in any portion of the spectrum. magnetosomes Intracellular membrane-bound bodies of magnetic minerals present in magnetotactic bacteria. magnetotaxis Bacterial orientation and migration along the lines of a magnetic field. magnitude amplification The production of a high concentration of active signalling molecules in response to a low concentration of stimulus molecules. major histocompatibility complex (MHC) A large cluster of highly polymorphic genes that encode a family of cell-surface glycoproteins (MHC molecules) which bind intracellularly processed peptides and display them for recognition by T-cell antigen receptors. As well as controlling antigen recognition and the ability to mount an immune response to a given antigen, this region is responsible for tissue incompatibility. major histocompatibility complex antigens See MHC molecules. major histocompatibility complex molecules See MHC molecules. malacologist Someone who studies molluscs. malacology The study of molluscs. malaise A general feeling of illness, body weakness and discomfort. malignant melanoma A malignancy of melanocytes, almost always arising in skin. management Accomplishing a defined objective by implementing a plan. In the case of conservation management, a plan involving a protected area or species. mandibles The third pair of appendages on the crustacean head, usually reduced and specialized for food-processing. maniraptoriform theropods Subgroup of predatory dinosaurs that includes the ornithomimids, troodontids, oviraptorids and dromaeosaurids. mantle cavity The space under the shell or between the valves of a mollusc or brachiopod, bounded by the mantle and the anterior body wall. It contains the lophophore in brachiopods. mantle plume A body of molten material (magma) that originates in the Earth’s lower mantle, migrates upward through the mantle and crust, and emerges on the surface as a geographically stable centre of basaltic volcanic activity (a ‘hot spot’) that can persist for millions of years (e.g. the hot spot beneath the Hawaiian Island chain). MAP kinase Mitogen-activated protein kinase. An intracellular serine/ threonine protein kinase that is part of a signalling pathway which is activated by the action of extracellular signals at a variety of receptors. it is involved in stimulating cell proliferation and gene expression. Also known as extracellular signal-regulated kinase (ERK). marboran The first antiviral agent against smallpox. marine regression A period of falling sea level.

200

Glossary

marine transgression A period of rising sea level. marker In genome mapping, any feature (such as a known DNA sequence) whose location in the genome can be determined. marker vaccines Vaccines that allow animals that are vaccinated to be distinguished from those that have been exposed to natural infection and therefore may be carriers of the disease. marsupial mammals (Metatheria) The marsupials. Ovoviviparous mammals, nourished from the yolk sac until hatching, when the very immature young crawl out to the teats (in a pouch in many species) to complete their development. Examples are the kangaroos, opossums and bandicoots. Marsupialia The marsupials. The name of the clade stemming from the most recent common ancestor of all modern ‘pouched’ mammals. See marsupial mammals. marsupials See marsupial mammals. mass extinction Episodic events of global extent that lead to the demise of numerous diverse groups of organisms in a variety of environments. They are caused by major environmental disturbances. mast cell A cell that resides in tissues and mucosal surfaces and binds IgE on its surface. Binding of antigen to the cell-bound IgE triggers the release of chemicals largely responsible for the clinical symptoms of allergy. master sequence The dominant genomic sequence in a viral quasispecies. maternal antibodies Antibodies in newborns that are passively acquired through transplacental transfer or colostral/enteral uptake. maternal-effect genes Genes that are expressed by the mother during oogenesis and exert their function in the early embryo, resulting in an embryonic phenotype. maternal-effect mutation A mutation that affects only the progeny of a homozygous mutant mother, and is rescued by a maternal wild-type allele. It usually represents a mutation in a maternal-effect gene. mating The coming together of two organisms or cells for the purposes of sexual reproduction. matrix protein A structural protein of a virus particle which lies under the envelope and links it to the core. matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) Mass spectrographic method used for rapid identification of proteins in which the polypeptide is applied to a target mixed with a suitable matrix (organic acid) that generates crystals coated with protein. By laser flashes on to the target the matrix molecules are evaporated together with the peptide or protein molecules and yield ions that fly into a time-of-flight detector where the molecular ions are separated according to their respective masses. maturation (1) The final stage of differentiation of a cell or tissue, in which it becomes fully functional. (2) The stage of viral replication at which a virus particle becomes infectious. maximum parsimony methods Construction of a phylogenetic tree based on the smallest number of evolutionary changes to explain the differences observed among the operational taxonomic units. MDR Multiple drug resistance. MDR proteins Proteins that confer multiple drug resistance on tumour cells. measles inclusion body encephalitis An inflammatory disease of the brain caused by measles virus in immunocompromised patients.

mechanical advantage (MA) The ratio of exerted to applied force in a mechanical system. For example, the ratio of lever arm length to load arm length. Meckel diverticulum A small pouch projecting from the ileum, first described by Johann Meckel in the eighteenth century. meconium Fetal faeces that are dark green due to a high content of biliverdin. The passage of meconium by the fetus in utero suggests some form of hypoxic stress, which may be temporary. Inspiration of meconium by the fetus causes airway obstruction. meconium ileus Intestinal obstruction due to retained meconium. media A layer of the pulmonary vascular wall lying between the endothelium and the adventitia. The media typically consists of vascular smooth muscle cells. medial Towards, or close to, the midline. medical images Pictures of the human body taken using X-rays, ultrasound or any other technology in order to detect disease. medullary cord Cellular cord between the lymphatic sinuses in the central or medullary region of a lymph node. Contains B lymphocytes, plasma cells, reticulum cells and macrophages. medusa The disc-like to bell-shaped sexual form (phenomorph) in the life cycle of medusozoans, commonly called a jellyfish. megadont Large-toothed relative to body mass when compared with species in the same, and closely related, genera. megafaunal mammals Mammalian species whose adults are heavier than 40 kg. megalopa A developmental stage of crustaceans between larva and adult. meiofauna The aquatic fauna inhabiting the interstitial water of soils, marine or freshwater sediments, moss cushions, etc. meiosis The type of nuclear and cell division that occurs in gamete formation to produce four haploid gametes (n) from a diploid precursor (2n). It involves duplication of the chromosomes followed by two reduction divisions, without further DNA synthesis, resulting in haploid cells. meiosis I and II Specialized cell division producing haploid germ cells from a diploid precursor. Reduction in chromosome number occurs during meiosis I and separation of haploid chromatids occurs at meiosis II. meiotic drive A distortion in the transmission rate of a particular chromosomal rearrangement at meiosis in favour of one allele. Certain genetic elements cause distorted segregation in heterozygotes, such that more than 50% of gametes contain the element in question. melanocyte Specialized cell in the basal layer of the epidermis which synthesizes and transfers melanin pigments to surrounding keratinocytes. melanoma A malignant tumour of melanocytes, usually occurring in the skin. Overexposure to sunlight is believed to be most common aetiological agent. membrane A bilayer of amphipathic phospholipids, also containing other lipids and proteins, that forms the boundary of the cytoplasm in all living cells and also delimits intracellular organelles in eukaryotic cells. The protein and, to a lesser extent, the lipid composition of biological membranes varies from cell to cell and compartment to compartment. membrane asymmetry The differences in the lipid and protein composition, and physicochemical and functional properties, of the two layers of a biological membrane. membrane conductance The ability of a biological membrane to conduct ions, primarily through ion channel proteins. membrane depolarization See depolarization.

201

Glossary

membrane hyperpolarization See hyperpolarization. membrane potential A measure of the voltage difference between the inside and outside of a cell membrane, which results from an unequal distribution of charged molecules. The membrane potential of a cell refers to the voltage across the plasma cell membrane, which is usually in the range of –40 to –80 mV, negative inside with respect to outside. membrane recycling Recovery of plasma membrane by endocytosis or molecular recycling. membrane resistance The ability of a biological membrane to act as a barrier against ionic movement. The inverse of membrane conductance. membrane skeleton A matrix of glycoproteins beneath the red cell plasma membrane that has an essential role in maintaining the shape and flexibility of the cell. membrane translocator An integral membrane protein which facilitates the passage of a chemical species through a membrane. membrane-attack complex (MAC) A multimeric complex of complement components (C5b–C9) that generate a transmembrane pore in eukaryotic and some prokaryotic cells, causing lysis of the cell. membranelle A compound structure in which numerous cilia are attached to each other, forming a flattened waving structure. memory cell A B or T lymphocyte that has been activated by the appropriate antigen and has not undergone differentiation into an effector cell but has become a long-lived cell that can react rapidly to re-exposure to antigen by immediately proliferating and differentiating into effector cells. MENA A member of the VASP protein family. Mendelian (1) Consistent with Mendel’s laws of segregation and independent assortment of genes. (2) Applied to traits caused by a single gene. Meniere disease A disorder characterized by fluctuating hearing loss, episodic vertigo and tinnitus due to endolymphatic hydrops. meniscus The upward- or downward-curving boundary between a liquid and a solid surface (such as the edge of container) that forms as a result of capillarity. menstrual migraine Migraine attacks confined to the 48 hours before, or the first day of, menstruation. meristems The growth regions of plants, where cells are proliferating. The primary meristems are located at the tips of the shoot and root. Some cells of the meristem are perpetuated in an undetermined state, and thus share characteristics with animal stem cells. merogony Asexual schizogony. meromictic lake A stable type of lake, independent of temperature, built up of a mixolimnion (upper free circulating water layer) and a monimolimnion (lower isolated layer of water with high concentration of chemical substances) kept separate by a chemocline. meront Intracellular stage of sporozoan protozoan parasites, in which asexual division usually occurs. merosporangium (plural merosporangia) A cylindrical sporangium containing a row of sporangiospores. merozoite Infectious stages of sporozoan parasites that are the product of merogony (schizogony). mesenchyme (1) Unpolarized cells located in connective tissue. (2) Non-epithelial undifferentiated embryonic cells which can give rise to a variety of differentiated tissues.

mesenteric Pertaining to the mesentery, which is the fibrous and vascular membrane from which the gut is suspended in the abdomen. mesoderm The middle of the three primary germ layers formed by gastrulation in triploblastic embryos. It lies between the ectoderm and endoderm and will develop into the musculoskeletal system, circulatory system and parts of the internal organs. mesoglea A generally acellular layer of the body wall of cnidarians, separating ectoderm and endoderm. mesohyl That region of the sponge body enclosed by pinacoderm and choanoderm. mesonephros The second kidney formed in the embryo of vertebrates. It forms the adult kidney in anamniotes, such as fish and amphibia, but is superseded in adult mammals by the metanephros. mesoplastra Paired bony elements present in the primitive turtle plastron between the hyoplastra and hypoplastra. mesosome Second body section, especially that formed by the lophophore in adult phoronids and the tentacular collar in the actinotroch larva. messenger RNA (mRNA) An RNA molecule that represents a meaningful transcript of a gene (or an operon in bacteria), that can be translated into protein. The mRNAs of eukaryotes encode a single protein, whereas those of bacterial operons encode more than one protein. messenger RNAase (mRNAase) An RNA-degrading enzyme dedicated primarily or solely to degrading messenger RNAs. meta-analysis Statistical combination of the results of several studies. metabasidium An outgrowth of a teliospore that bears basidiospores, developing in certain basidiomycete fungi following meiosis. Also called promycelium. metabolic complementation The ability of the products of different defective genes to reconstitute metabolic flux of a pathway. Rarely, complementation errors in the same gene give rise to intragenic complementation. metabolic pathway A successive series of reactions catalysed by different enzymes which result in the conversion of a molecule into one or more products with the production or consumption of energy. metabolic poisons Agents that inhibit the cell’s ability to use or gain energy. metabolic rate A measure of total metabolic energy use (or total turnover of ATP) by an organism. It is generally determined by measuring either oxygen consumption or metabolic heat production. metabolic scope The range in rate of metabolism, expressed either as the difference between maximal and minimal rates, or as a ratio of maximal to minimal rates. metabolism All of the chemical reactions within an organism that transform molecules and consume and generate energy. metabolite channelling The direct transfer of a metabolite from one enzyme to another. metabotropic Describes the action of a neurotransmitter through a G-protein-coupled receptor in contrast to the action of the same neurotransmitter acting through ionotropic receptors. metabotropic glutamate receptors (mGluR) G-proteincoupled receptors for the neurotransmitter glutamate. There are three classes of metabotropic glutamate receptors (I, II, III) that differ in their pharmacological profiles.

202

Glossary

metabotropic receptor A G-protein-coupled neurotransmitter receptor, in contrast to an ion channel-linked receptor for the same neurotransmitter. metacentric A chromosome with a centromere at or near its midpoint and two arms of about equal length. metachronal rhythm, metachronal waves Successive synchronized waves of movement, travelling forward along the body, typical of arthropod locomotion. metacyclic Refers to a developmental form of the protozoan parasite Trypanosoma cruzi which is released in the faeces and urine of the insect host, and is the form in which the parasite is transmitted from the invertebrate to the vertebrate host. metagenesis See alternation of generations. metal leaching Degradation of water-insoluble heavy metal salts by microbes. metalloenzyme An enzyme that contains a bound metal ion. metalloprotease, metalloproteinase A protease that contains a bound metal ion. metanephric mesenchyme Mesenchyme tissue destined to be induced by the ureteric bud to form the metanephros (kidney). metanephridium Adult excretory organ in invertebrates, opening at its inner end by one or two funnels and exteriorly by the nephridiopore. metanephros The embryonic kidney that develops into the adult kidney in mammals. metaphase The phase of mitosis when the duplicated chromosomes are near maximum contraction, and lie together at the equator of the spindle. metapodials The metatarsals and metacarpals, the bones distal to the ankle or wrist, respectively. metapopulation A set of individual populations of a species, usually within a given area, analogous to a collection of islands in an archipelago. metasome Third body section of arachnids and some crustaceans. it is cylindrical and contains the digestive tract, gonads, nephridia, and the main circulatory system. metastases Secondary tumours away from the primary site of origin that arise as a result of the invasive spread of tumour cells. metastasis The spread of tumour cells through the lymph system or blood circulation to near or distant sites where they form secondary tumours. metastatic Pertaining to the transfer of disease from one part of the body to another. metastatic tumour Secondary growth of a tumour at a site at a distance from the primary tumour. Metatheria See marsupial mammals. metazoa All multicellular animals whose tissues form organs. Methanoarchaea A group of prokaryotic microorganisms, the methanogens, belonging to the domain Archaea that generate methane as a by-product of carbon fixation. methanochondroitin An archaeal analogue of human chondroitin, a nonsulfated polysaccharide that occurs in the cell wall of Methanosarcina. methanogens Prokaryotic microorganisms capable of producing methane (CH4). All methanogens belong to the Kingdom Euryarchaeota of the Archaea. They subsist entirely on inorganic nutrients (gaseous hydrogen, nitrogen and carbon dioxide) in the complete absence of light and oxygen. Methane gas is released as a result of the carbon fixation process.

methanoreductosome An enzyme complex consisting of a stalk and head which is attached to the inner face of the plasma membrane of methanogenic archaea and has methyl coenzyme M reductase activity. methanosomes Intracytoplasmic invaginations of the plasma membrane in methanogenic archaea which have been implicated in methanogenesis. methionyl-tRNA synthetase Enzyme that aminoacylates the isoaccepting methionine tRNAs. methionyl-tRNA transformylase Enzyme that catalyses the transfer of a formyl group from N10-formyl-tetrahydrofolate to the a-amino group of methionyl-tRNAfMet. methylated cytosine Cytosine in GC dinucleotides in DNA that has become modified by the addition of a methyl group. methylation (1) The addition of a methyl group to a molecule. (2) Modification of a cytosine residue in DNA by the addition of a methyl group. Methylation of some genes appears to prevent their expression. Mg branch A pathway for synthesizing chlorophylls and bacteriochlorophylls from protoporphyrin IX that branches from a pathway common to haem biosynthesis. MHC See major histocompatibility complex. MHC molecules Cell-surface proteins encoded by the major histocompatibility complex of genes (MHC). They bind intracellularly processed peptide epitopes of protein antigens and display them on the cell surface for presentation to T cells. MHC class I molecules present peptides to CD8 T cells and MHC class II molecules to CD4 T cells. MHC molecules themselves are the antigens primarily responsible for the rejection of tissue grafts. MHC restriction Refers to the phenomenon by which an immunocompetent T cell recognizes a foreign peptide antigen only if it is presented in association with a particular MHC molecule, i.e. T-cell receptors recognize unique ligands of peptide and MHC molecule. MIC See minimum inhibitory concentration. MIC genes MHC class I-related genes that have limited polymorphism. micelle (1) Small molecular aggregates formed in the presence of bile salts and allowing the absorption of lipid digestion products into the epithelial cells. (2) A cluster of detergent molecules. Michael addition Condensation of a nucleophile into an a,bunsaturated ketone. Michaelis complex The binary complex formed between enzyme and substrate molecules preceding catalysis. It is also known as the ES (enzyme–substrate) complex. Michaelis constant Ratio between the sum rate constants of processes leading to disintegration and to formation of a substrate–enzyme complex. It is a ‘pseudo-equilibrium’ constant related to the steady state in enzyme systems. Michaelian response In an individual level of a regulatory cascade (such as an intracellular signalling pathway), an amplification response that has Michaelis–Menten-type kinetics: e.g., as the stimulus increases, the resulting increment of response becomes progressively smaller; the response is highly graded; and it is also relatively insensitive to change. microbial fermentation Anaerobic breakdown of polysaccharides and sugars by microbes to produce various products, such as ethanol and short-chain fatty acids.

203

Glossary

microcalcification Small aggregates of calcium phosphate or oxalate occurring in secretions or in necrosis within the terminal duct lobular unit of the glandular system of the breast, which can produce characteristic patterns on mammography. microchimaerism A chimaeric condition in which an individual contains only a small fraction of genetically different haematopoietic and/or lymphoid cells. microdeletion The absence of a small piece of chromosome. microdialysis Technique by which a substance can be measured in fluid based on passage of the compound through a dialysis membrane without removing actual fluid samples. microfilament One of the three principal cytoskeletal components in eukaryotic cells. Microfilaments are narrow (8 nm diameter) linear polymers of actin subunits. They act as architectural elements, are involved in motility, and also act as trackways for intracellular transport of materials. microfossils Any small fossils, such as foraminifera or spores that must be studied microscopically. microgamete A male gamete. microglia Resident population of bone marrow-derived cells within the central nervous system, resembling tissue macrophages. microinvasion Foci of invasive carcinomas, none which exceed 1 mm in diameter, arising from ductal carcinoma in situ. micrometeorite A particle from space that is small enough to be slowed down when it reaches the Earth’s atmosphere without being burnt up. micronucleus The generative (sexual) nucleus in protozoa, such as ciliates, that have nuclear dimorphism. micronutrient An essential mineral nutrient that is only required in small quantities. Tissue concentrations of micronutrients are equal to or less than 100 mg per kg dry matter (or less than 0.005% body weight). microorganisms Living organisms that are too small to be seen with the naked eye, e.g. bacteria, fungi, protozoa and single-celled algae. Viruses are also considered as microorganisms. microphyllous leaves Elongate leaves with a single (or occasionally two parallel) veins running along their length. microprojectile/microcarrier Any microscopic and coherent particle that when sufficiently accelerated can penetrate cells and tissues. micropylar end The part of a seed in which the embryo grows. micropyle The small channel through which a pollen tube enters an ovule prior to fertilization. microsatellites Tandem arrays of very short, moderately repetitive, localized DNA sequences (e.g. (CA)15) present in mammalian and other genomes. microscope slide A rectangular sheet of thin glass used to support thin sections or smears of the specimen for optical microscopy. microspike See filopodia. microstromatolite Fossilized layers of bacterial mats and sediment, producing a very finely laminated rock stratum. microtomy Use of a mechanical device (a microtome) to cut thin sections for microscopy from a larger specimen. microtubule-organizing centre (MTOC) The major origin of microtubules in a living cell. microtubules One of the three principal cytoskeletal components of the eukaryotic cell. Microtubules are stiff hollow tubes of protein (25 nm in diameter) composed of tubulin subunits. They act as architectural elements and also as trackways for intracellular transport of materials. Movement of cilia and flagella is based on microtubules, and they also form the mitotic and meiotic spindles.

midbrain The central subdivision of the brain, which contains the tectum. midgut The small intestine in many species. midtarsal joint The joint in the tarsus between the talus and calcaneus (heelbone) proximally and the cuboid and navicular distally. migraine Paroxysmal severe headache with pain-free intervals. Pulsating and throbbing qualities and unilateral distribution are characteristic. Nausea and vomiting, and phobias for light and sound often accompany the headache. ´e migraine accompagne See complicated migraine. migraine sine cephalgia The occasional occurrence of migrainous auras (warning symptoms) without the accompanying headache. It usually occurs in middle-aged or elderly patients. migraine variants, migraine equivalents Unusual symptoms such as periodic abdominal pain and travel sickness, usually in children, believed to be of migrainous origin. migraine without aura Common migraine. A throbbing, aching headache, often but not always one-sided, with sickness and photophobia, but no specific warning symptoms (aura). migrant pool colonization The founding of a new population with colonists chosen at random from all populations in the metapopulation. migration In the context of population genetics, this term refers to gene flow and is measured as that proportion of a local population that arrives in each generation from other populations of the same species. Milankovitch cycles Astronomically determined climatic cycles with dominant periodicities of 100 000, 41 000 and 22 000 years. Milankovitch theory Explanation of the timing of glacial–interglacial climate based on changes in the Earth’s orbit. Miller indices In X-ray crystallography, a set of three integer values, denoted (h,k,l), used to label a reflection or structure factor according to the direction and angle of scattering of the X-ray beam. miniature postsynaptic potential (MPSP) A postsynaptic potential caused by the spontaneous secretion of a single presynaptic vesicle of transmitter. minimal effective concentration An in vitro measure that defines the effective concentration of an agent against a fungal organism. minimal medium The standard medium having the fewest and simplest compounds upon which an organism will grow well. minimal inhibitory concentration See minimum inhibitory concentration minimally invasive therapy The performance of an interventional procedure with the minimum of trauma to the patient. Also known as minimal access surgery. minimum resolved distance (MRD) The least distance between two points that can be resolved by an imaging system. minimum viable population The minimum size of population that ensures a greater than 95% chance that the population will persist for 100 years into the future. minisatellites Tandem arrays of moderately repetitive, localized sequences with repeat size ~15 bp, longer than that of microsatellites. minus end The end of a microtubule that is slowest growing. MIP Major intrinsic protein of bovine lens. It was the first defined member of a family of presumed channel proteins that includes the aquaporins.

204

Glossary

missense error An error in translation that results from a codon being incorrectly decoded. It results in the incorporation of the incorrect amino acid into the protein. missing self model The hypothesis that natural killer cells survey cells for the presence of MHC class I molecules, killing those in which it is missing. Originally proposed in 1985 and now supported by a large body of evidence. mitochondria (singular mitochondrion) Energy-generating organelles of eukaryotic cells. They are bounded by two membranes, the inner one being folded into cristae that carry the electron transport chains that generate the energy for the production of ATP by oxidative phosphorylation. The tricarboxylic acid cycle occurs in the central mitochondrial matrix. Mitochondria carry a small DNA genome that encodes some mitochondrial proteins. mitochondrial bottleneck Genetic term to explain how a mitochondrial DNA polymorphism can rapidly become predominant between generations. It is suggested that only a small subset of mitochondrial DNA molecules is selectively amplified during oocyte maturation. mitochondrial DNA (mtDNA) Small circular DNA molecules present in mitochondria, and which encode some mitochondrial proteins. mitochondrion See mitochondria. mitogen A chemical or physical agent that nonspecifically induces cells to enter mitosis. mitogen-activated protein kinase See MAP kinase. mitoplast A mitochondrion with a ruptured outer membrane that has lost the soluble content of the intermembrane space but is otherwise intact. mitosis A type of nuclear division that produces two daughter nuclei containing chromosome sets identical to each other and to that of the parent cell. mitotic parthenogenesis Development of an individual from an unfertilized egg not undergoing meiotic divisions. Such individuals are genotypically identical to the mother. mixed lymphocyte reaction A test for histocompatibility. When lymphocytes (effectively T cells) from two incompatible people are cultured together, they will recognize each other as foreign and start to proliferate and differentiate into helper T cells and cytotoxic T cells. This test mimics allograft recognition. mixed semidiurnal tides A sequence of tides consisting of two high and two low tides over approximately 24 hours and 50 minutes. The high tides are of unequal amplitude, as are the low tides. mixotrophic Capable of using two or more modes of nutrition (e.g. phototrophic and heterotrophic) during the life cycle, as in some protists. mixotrophy Nutritional mode exhibited by some protozoa and other protists in which two or more methods of satisfying metabolic needs, e.g. photoautotrophy and heterotrophy, may be combined in a single organism. mmc Megaspore mother cell, a diploid cell that gives rise via meiosis to four megaspores. mobile phase Buffer used to equilibrate affinity chromatography columns. mobilization Conjugal transfer of a plasmid lacking a complete set of transfer functions, which is not capable of autonomous transfer and requires transfer functions supplied by a coresident conjugative plasmid.

modulus A measure of the stiffness of a material, which helps determine the degree to which it deforms if forces are applied. molecular chaperones Proteins that aid in protein folding, protein associations or protein transport, but are not part of the final protein complex. molecular clock The theory that mutations accumulate in DNA sequences at an approximately constant rate, and thus can be used as a measure of the absolute time of divergence of two sequences. It it most likely to hold for sequences that still encode proteins with the same function. molecular marker See marker. molecular mimicry (1) The case when a parasite antigen resembles that of a host antigen. In some cases this may mean that an immune response is not mounted against that parasite. In other cases, it can result in a transient autoimmune reaction as antibodies evoked by the parasite cross-react with the host antigen. (2) Similarity in the three-dimensional structures of divergent molecules which facilitates recognition by common elements. molecular phylogenetics The study of the evolution of molecules (DNA and proteins), generally by constructing phylogenetic trees from DNA and amino-acid sequences. molecularity The number of molecules of reactants involved in the transition state of an elementary chemical process. monoamines The neurotransmitters dopamine, noradrenaline (norepinephrine), serotonin and adrenaline (epinephrine). monobrachial homology Sharing of a chromosome arm in double Robertsonian heterozygotes. monociliated epidermis Epidermis in which each epidermal cell has only one cilium. monocistronic Describes a messenger RNA that encodes a single protein. monoclonal antibody Antibody of one specificity produced by a single clone of antibody-secreting cells. They can be produced in culture by fusing a single B cell with a myeloma cell to yield a specific antibody-secreting hybridoma cell line. monoclonal gammopathy Pertaining to or originating in a single clone of B cells. All the cells in such a clone will produce an identical specific immunoglobulin. monoclonal (M) component Immunoglobulins produced by a plasma cell dyscrasia. These are seen as a sharp discrete band on protein electrophoresis. monoclonal Arising from a single clone of cells. monocotyledonous Belonging to the group of plants called monocotyledons, which have a single cotyledon in the seed. monocotyledons A major division of the flowering plants having only one seed leaf or cotyledon. Most monocotyledons have narrow, parallel-veined leaves, as in grasses and lilies. monocyclic cascade A simple system where a signalling protein A can be converted between active and inactive forms by opposing activator and inactivator enzymes. monocytes Circulating white blood cells that are the source of tissue macrophages. monocytoid B cells B cells with the cytological appearance of histiocytes, which may collect in lymph node sinuses in some reactive states. monodisperse suspension of particles A suspension of particles of very uniform diameter. They are all the same size and therefore alter in an exactly reproducible fashion the properties of cells to which they attach, e.g. the magnetic properties if they themselves are magnetic.

205

Glossary

monogenic Applied to traits that are caused by a single gene. monomer (1) A single subunit of a dimer or a larger multimeric complex. (2) A single repeating unit of a polymer. mononegavirales Order of viruses consisting of four families with nonsegmented negative-stranded RNA genomes. mononuclear With a single nucleus. Applied, e.g. to those white blood cells, such as monocytes, that have a single round nucleus. mononuclear phagocyte system A family of widely distributed macrophage-related cells, usually phagocytic, that are derived from blood mononuclear cells, as opposed to polymorphonuclear (neutrophil) leucocytes. This term has not entirely replaced the older term, reticuloendothelial system. monophyletic Describes a phylogenetic group (a clade) that consists of a common ancestor and all of its descendants. Accordingly, such a group should be definable by the possession of one or more shared characters derived from the ancestor (synapomorphies). monophyletic group A group of species that includes their single common ancestor and all of this ancestor’s descendants. monophyletic origin Describes a trait that has been established once and then transmitted to different systematic categories during evolution. monophyly See monophyletic. monosaccharide A molecule consisting of a single sugar. monosome A messenger RNA molecule with a single attached ribosome. monosomy A condition in which one chromosome of a pair is missing. monoxenic culture A culture in which only one species of bacteria or other food organism is allowed to be present with a cultured protist. monoxenous life cycle The life cycle in which the sexual and asexual stages of a parasite occur in the same host. monozygotic twins Genetically identical twins, derived from the same egg. morph A phenotypic variant, usually one of two or more possible developmental outcomes. morphallaxis Regeneration process by which new structures are formed in the absence of cell proliferation. It relies on migration and terminal differentiation of precursor cells or possibly on transdifferentiation. morphogen Molecule that is distributed in a gradient and subdivides a field of cells into more than two domains. morphogenesis The development of form, or morphology, in organisms during embryogenesis. morphogenetic movement Cell or tissue migrations that lead to changes in organ or body shape. morphogenetic phenomena Developmental processes associated with cell division in ciliates. These include the development of a new oral apparatus (stomatogenesis), assembly and positioning of new organelles, as well as degradative processes. morphological species concept The differentiation of species on morphological grounds, providing the baseline for taxonomic description. morphology (1) The shape and form of a cell or organism. (2) The scientific discipline that studies the diversity of shapes of biological organisms. morphometrics The application of multivariate methods to the analysis of size and shape in organisms. morphotype A taxon diagnosed by a unique combination of characters.

morula The mammalian conceptus at the 16–32-cell stage. mosaicism Condition in which an individual is composed of cells of two different genotypes. mosasaurs A group of large, extinct marine monitor lizards that might be closely related to snakes. motif A characteristic or conserved amino-acid sequence containing functionally important residues. motional freedom The ability to change conformation. In an amphipathic lipid, the hydrocarbon chains have considerable motional freedom at their methyl termini and less towards the polar headgroup. motional order Lipid hydrocarbon chains have considerable conformational freedom at their methyl termini, and the motional order is low. Conversely, their degree of conformational freedom towards the polar headgroup is low and the motional order there is high. motor learning The adaptive changes occurring in the brain that allow movements to be executed skilfully, and to be well adjusted to the mechanical loads that must be moved. motor proteins Enzymes that move along the surface of microtubules or microfilaments. Depending on the other structures with which they interact, they can move cytoplasmic constituents along the cytoskeletal polymers, or they can move the cytoskeletal structures themselves. moult cycle The time between two moults (ecdyses). Divided into a period of preparation for moult (called pro-ecdysis) and a period of normal life activities (called anecdysis). moulting In arthropods, the process of shedding the cuticle at periodic intervals during the growth period. mounting Immersion of a stained tissue section or smear, attached to a microscope slide, in a medium of high refractive index, the whole usually being overlaid with a thin glass coverslip. Mr Relative molecular mass. MRD See minimum resolved distance. mRNA See messenger RNA. mRNAase See messenger RNAase. mRNA stability determinant A segment of an mRNA that helps to determine the mRNA half-life. mRNA turnover The rate at which an mRNA is degraded, usually defined in terms of mRNA half-life. MRS See nuclear magnetic resonance spectroscopy. MSP Major sperm protein, a protein from the sperm of certain nematodes (e.g. Ascaris) that polymerizes to drive the cell forward in a manner similar to that proposed for actin in most other eukaryotic cells. mtDNA See mitochondrial DNA. MTOC See microtubule-organizing centre. mucopolysaccharides Gelatinous carbohydrates of high Mr (~5 Â 106) that both lubricate and serve as a sticky cement. mucormycosis Invasive infection caused by the fungus Mucor racemosus. mucosa (plural mucosae) General term for the secretory epithelia lining the gastrointestinal, respiratory and urinogenital tracts. multifunctional protein A protein containing two or more discrete and different enzyme catalytic centres, on separate domains. multigene family Family of DNA or amino-acid sequences in which some sequences or groups of sequences have evolved by gene duplication events.

206

Glossary

multinet growth hypothesis Physical explanation that plant cell elongation results from passive reorientation of the cellulose microfibrils from transverse to longitudinal in the outer layers of the wall to affect growth along the entire axis. multiphoton microscope A microscope in which the illumination is confined to a spot in the specimen by means of two- or threephoton excitation of a fluorescent probe using a high-power pulsed laser. multiple alleles The existence in a population of more than two variant forms of a gene at a given locus. multiple cloning site A short sequence of DNA that contains the recognition sites for several restriction enzymes and thus can accept DNA fragments cut with a variety of restriction enzymes. multiplicity of infection Number of infectious particles per host cell in the initial infective dose. multipotential progenitor A cell that can produce daughter cells that will give rise to multiple lineages. multiregional hypothesis The hypothesis that modern humans are diffusely descended from precursor populations, called archaic Homo sapiens, distributed over much of the tropical and temperate Old World. multispot array A set of immobilized capture molecules (probes) that participate in a solid–liquid interfacial interaction with target molecules contained in the sample solution applied to the surface of the multispot array. multituberculate mammals An extinct order of mammals, common in the Mesozoic era, that were ecologically equivalent to modern-day rodents. murein Cell wall peptidoglycan of the Bacteria. mutagenesis The process of causing a change in a DNA sequence. mutagens Agents that will induce a change in a cell’s DNA. mutant spectrum The set of variant genomes present in an evolving quasispecies. mutation A permanent heritable change in the genetic material of a cell or organism. This could be a change in the base sequence of the DNA that affects a single gene, or a change in the number or structure of the chromosomes. In classical genetics, the term usually refers to a change that has a demonstrable effect on the phenotype. mutualism Persistent and intimate association between two (or more) dissimilar organisms that provides advantages, particularly in terms of fitness, to all partners. mutualistic interaction An interaction between organisms in which the darwinian fitness of both (or all) interacting species is increased as a result of the interaction. mutualistic symbiosis A symbiosis that is beneficial to all the partners in the association. myalgia Muscle pain. Myb proteins, MYB proteins Transcription factors structurally homologous to the mammalian cellular proto-oncogene c-Myb. They have common DNA-binding domains that are involved in the control of gene expression of various metabolic and developmental processes. Myb-related transcription factor See Myb proteins. mycelium The vegetative part of a fungus, composed of a network of hyphae. mycetocyte Also called mycetome, an evagination of the midgut of certain insects.

mycoheterotroph A plant that in the juvenile stages or throughout its life lacks chlorophyll (i.e. is heterotrophic). Instead of photosynthesizing it receives all of its carbon by way of its mycorrhizal fungal symbionts. mycoparasite A fungus that parasitizes another fungus. mycorrhiza (plural mycorrhizae) A symbiotic relationship between a fungus and plant roots. mycorrhizal mushroom Describes a mushroom-forming basidiomycete fungus, whose mycelium forms a mutually beneficial association with the roots of a plant. Thus, the mushroom is typically found near the plant host. mycorrhizosphere The zone surrounding the mycelium of a mycorrhizal fungus as it extends into soil. mycosis (plural mycoses) Any disease caused by a fungus. mycotroph A plant that is dependent upon, or highly responsive to, the provision of nutrients by a fungus. myelin A discontinuous fatty insulating sheath formed around the axons of certain neurons, which facilitates fast nerve conduction. It is produced by Schwann cells in the peripheral nervous system and oligodendrocytes in the central nervous system, which wrap their cell processes around the axon, forming a sheath of layers of membrane. myeloid progenitor A cell that is committed to a pathway that will give rise to mononuclear and polymorphonuclear leucocytes. myoblasts Undifferentiated cells that develop into muscle cells during development. myocarditis Inflammation of the myocardium or the muscle of the heart. myoclonus Pathological sudden involuntary muscle jerking. myofibroblast A fibre-forming cell of the connective tissue, which contains large amounts of contractile assemblies of smooth muscle actin and myosin. Myofibroblasts are regarded as contractile cells. myofilaments Actin and myosin protein filaments that are linked by cross-bridges and slide relative to each other to produce force. myoglobin A haemoprotein that reversibly binds dioxygen and stores it in muscle tissue. myopathy A neurological disorder affecting muscles. myosin Any of a superfamily of motor proteins (17 classes identified so far) present in probably all eukaryotic cells. They bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments. myotube Multinucleate cell that develops from fusion of several myoblasts and develops into a skeletal muscle cell. myotubules The earliest muscle structures formed during development. myristoylation The covalent attachment of a myristoyl group (derived from the fatty acid myristic acid) to the N-terminal glycine residue of a nascent polypeptide. This posttranslational modification can provide a way of attaching a protein to a membrane. myrmecophagous Feeding on ants and termites.

NA See numerical aperture. Na1 , K1-ATPase A transmembrane protein with ATPase activity that uses the energy released by hydrolysis of ATP to transport three Na1 out of the cell and two K1 into the cell per ATP hydrolysed. It is chiefly responsible for generating the membrane potential in animal cells, maintaining the ion gradients that are used by other transport proteins.

207

Glossary
NADP1 Oxidized form of nicotinamide adenine dinucleotide phosphate. NADPH Reduced form of nicotinamide adenine dinucleotide phosphate, a small water-soluble molecule that acts as a hydrogen carrier in biochemical reactions. NADPH oxidase A multicomponent enzyme that oxidizes intracellular NADPH (the reduced form of nicotinamide adenine + dinucleotide phosphate) to NADP and reduces molecular oxygen, O2, to superoxide anions, OÀ. 2 naive lymphocyte Lymphocyte that has not previously been stimulated by its specific antigen. nascent polymer A polymer molecule in the process of being synthesized. nascent strand A polymer strand in the process of being synthesized. native Describes the three-dimensional conformation of a protein or peptide that represents the biologically active structure. natriuretic Causing an enhanced tendency for urinary excretion of sodium. natural cytotoxicity The ability of natural killer (NK) cells to kill certain target cells without preactivation. Also known as spontaneous cytotoxicity. natural immunity See innate immunity. natural killer cell (NK cell) A type of antigen-nonspecific non-T, non-B cytotoxic lymphocyte that plays a crucial role in innate immunity to viruses and other intracellular pathogens. Unlike cytotoxic T lymphocytes, NK cells can lyse target cells without the need for previous antigen recognition or sensitization. NK cells are also able to kill certain tumour cells, and are the cells mediating antibody-dependent cell-mediated cytotoxicity. natural killer cell receptor (NK cell receptor) Receptors on NK cells that can either activate or inhibit the cytotoxic activity of the cell. Examples are KIR (killer cell inhibitory receptor) and KAR (killer cell activating receptor). natural product A compound produced by a living organism. natural selection The evolutionary process by which the organisms in a population that are best adapted to the environment increase in frequency relative to less well-adapted forms over a number of generations. naturalized Describes introduced (alien) species that have formed self-sustaining populations in the wild at their new location. nauplius larva The characteristic larvae of crustaceans, with a median simple eye and three pairs of appendages, which will become the antennae and mandibles of the adult. NBS See nucleotide-binding site. necrosis Pathological cell death and tissue destruction, usually in a localized area, which is due to cell lysis as opposed to programmed cell death due to apoptosis. necrotizing Causing cell or tissue death. needle core biopsy A biopsy taken by inserting a sharpened cutting needle into a tissue. negative chemotactic stimulation A decreasing gradient of chemoattractant or an increasing gradient of chemorepellent. negative eugenics Use of programmes, techniques or social policies with the goal of reducing or eliminating negative (harmful or undesirable) genes in a population, often by preventing reproduction of individuals believed to be carrying such genes. negative selection The process whereby self-reactive clones of T cells or B cells are deleted from the developing lymphocyte repertoire, principally by apoptosis.

negative-stranded RNA virus A virus whose RNA genome is complementary to its mRNA. neighbour-joining analysis A statistical method that sequentially identifies neighbour pairs (operational taxonomic units connected through a single internal node) that minimize the total length of the phylogenetic tree. nektic, nektonic A term applied to aquatic organisms that actively swim. nematocyst Any of 30 types of adhesive, ensnaring, coiling and penetrating cnidocysts present in cnidarians. nematodes A large phylum of organisms commonly known as round worms. They include the model organism Caenorhabditis elegans. Neognathae A taxonomic group that includes all modern extant birds. Members of this group have a prokinetic skull, keratincovered and toothless jaws (the beak) and several other characters such as a keel on the sternum (breastbone) for the attachment of large flight muscles. These characters separate this taxon from the Palaeognathae. neonatal alloimmune thrombocytopenia purpura Destruction of platelets of the fetus or the newborn by platelet-specific alloantibodies derived from the mother. neonate Newborn. In humans, it refers to an infant of up to 4 weeks old. neoplasia Abnormal proliferation of cells (‘new growth’). The word generally refers to tumour cell growth and behaviour that is initiated by genetic alteration, and which persists after removal of the agent that caused the change. neoplasm An abnormal growth, caused by proliferation of cells. The term is synonymous with tumour, either benign or malignant. neoteny (1) The persistence of embryonic characters into adulthood. (2) The attainment of sexual maturity in an immature stage. nephridium (plural nephridia) An invertebrate organ that serves excretory or osmoregulatory functions. nephron An individual functional unit of the vertebrate kidney. It is composed of the glomerulus and a tubule draining the glomerular filtrate. nephrotoxicity The property of being toxic to kidney cells. nerve regeneration Regrowth of nerve fibres after injury. nerve ring A visible ring of fibrous material of the nervous system which usually encircles the nematode pharynx. NES See nuclear export signal. network A system of wires and communication standards that allow computers to communicate with one another. neural activity The all-or-none electrical discharge of a neuron that is propagated along its axon with the resultant release of neurotransmitter from synaptic vesicles. neural crest An embryonic tissue that gives rise to many tissues, including the neurons and glia of the peripheral nervous system. neural plate The flattened plate of neural ectoderm on the dorsal side of a vertebrate embryo that will give rise to the nervous system. It becomes evident after gastrulation and neural induction. neural tube In vertebrate embryos, the precursor to the central nervous system which is formed when the lateral edges of the neural plate roll dorsally and fuse at the dorsal midline to form a tube. neuraminidase An enzyme with sialidase activity. It is present in some viruses.

208

Glossary

neuroblast An embryonic progenitor cell of a neuron. In arthropods, neuroblasts can also give rise to glial cells as well as to neurons. In vertebrates, the name refers to the postmitotic but immature neuron. neurofilaments Intermediate filaments of neurons, which act as internal support for the axon. neurogenesis The ‘birth’ or formation of new neurons during embryonic development. It occurs in the ventricular zones lining the lumen of the neural tube. neurogenic Describes genes whose loss of activity (defined originally by mutants) leads to neural hypertrophy. neuromast Individual sensory organs of the lateral line, composed of hair cells and supporting cells. neuromodulator A neurotransmitter whose main effect is to modify the properties of an ion channel that primarily responds to another factor, such as voltage. neuron A nerve cell, the principal information-processing and signalling cell of the nervous system. Neurons develop elongated processes, dendrites and axon, that receive and transmit information, respectively. Information travels as electrical signals within neurons and is transmitted between neurons by chemical neurotransmitters released at specialized cell junctions called synapses. neuropathy A neurological disorder affecting the peripheral nerves. neuropil Regions of densely intertwined dendrites and axons of neurons, excluding the cell bodies. neuroscience The study of the brain and nervous system. neurotoxicity The disturbance of neuronal function or causation of neuronal death by an external agent. neurotransmitter A signalling molecule released from the presynaptic axon at a synapse after the arrival of an action potential at the axon terminal. It diffuses across the synpatic cleft and, depending on the type of neurotransmitter and neuron involved, can cause either depolarization or hyperpolarization of the postsynaptic cell. neurotrophins Proteins important for neuronal growth and survival. An example is neuronal growth factor (NGF). They act at specific receptors (neurotrophin receptors). neurulation Formation of the neural tube during embryogenesis by the rolling up of the neural plate and fusion of the neural folds. neutral allele, neutral mutation A mutation that has no apparent favourable or unfavourable effect on phenotype and whose fate in a population is determined solely by random genetic drift. neutral substitutions Base changes in the reading frame of a gene that do not alter the encoded amino-acid sequence. neutral theory The proposal that the majority of sequence differences observed between the DNA or proteins of two species are the result of fixation of neutral or nearly neutral mutations by random genetic drift, rather than the result of natural selection. neutropenia A reduction in the blood neutrophil count below normal. neutrophil A phagocytic white blood cell with a distinctive lobed nucleus and granules that stain with neutral dyes. It is one of the first defences against many types of bacterial infection, ingesting and killing bacteria. Acting in both innate and adaptive immunity, neutrophils bear complement and Fc receptors and migrate from the blood into sites of infection or inflammation. neutrophiles Microorganisms that grow with a pH optimum near neutrality.

Newtonian flow Flow of a fluid whose viscosity does not change with changes in shear rate or over time. Newton’s rings A circular pattern of fringes with alternating intensity that arises from the interference of monochromatic light partially reflected from a flat glass surface with the light partially reflected from a concave glass surface. NF-kB Nuclear factor kB. A transcription factor that enhances transcription of a number of genes, particularly those involved in inflammation and immunity. niche specialization The particular habitat and mode of life sustenance of a given species. niche The geographic location, habitat, activity pattern and diet that characterizes a given species (or group of species) and according and to which it is particularly adapted. See also fundamental niche, realized niche. nick A discontinuity in the phosphodiester backbone of duplex DNA in which no base pairs are missing. nicotine An alkaloid that acts as a nonphysiological agonist at the ion channel type of acetylcholine receptor, which is thus known as the nicotinic acetylcholine receptor (nAChR). Nieuwkoop centre A region of the dorsal endodermal mass in the Xenopus blastula that induces the adjacent marginal zone cells to become dorsal mesoderm (notochord and paraxial mesoderm). nif Gene designation for the molybdenum nitrogenase system. nitric oxide A short-lived membrane-permeable signalling molecule. nitrogen fixation The conversion of molecular nitrogen (N2) into metabolically usable nitrogen, principally NH+. Biological 4 nitrogen fixation can be carried out only by a few species of free-living and symbiotic bacteria. NK cell See natural killer cell. NK cell receptor See natural killer cell receptor. NLS See nuclear localization signal. NMDA receptor A type of receptor that responds to the excitatory neurotransmitter glutamate and which is distinguished from other glutamate receptors by its selective response to N-methylD-aspartate and activation of calcium currents. NMDA N-methyl-D-aspartate. A chemical used to distinguish a particular type of glutamate receptors. NMR See nuclear magnetic resonance. NMRS See nuclear magnetic resonance spectroscopy. NNS RNA virus Nonsegmented negative-strand RNA virus nomenclature The assignment of taxonomic rank to the groups resulting from classification and naming the organisms according to their rank. nominalism The philosophical thesis that individuals are real but classes are not real, sometimes associated with the notion that all groups are purely arbitrary or mental constructs. noncanonical splice site Unconventional splice site. noncentromeric chromosome A DNA molecule (with associated protein) that lacks spindle attachment regions (centromeres). Such entities are sometimes considered not to be true chromosomes, and then are called ‘autonomously replicating pieces’. nondisjunction Failure of chromosome pairs or sister chromatids to separate at cell division, resulting in aneuploidy in the daughter cells. nonhomologous end-joining enzyme One of a group of enzymes that form complexes capable of joining, or religating, double-stranded ends of DNA which has been cleaved or broken, when the double-stranded ends have no sequence homology.

209

Glossary

nonhomologous recombination Recombination between DNA molecules sharing little or no homology. Also known as endjoining. nonpersistent transmission See stylet-borne transmission. nonselective cation channel An ion channel that is selective for cations (positively charged ions) over anions (negatively charged ions), but shows little selectivity between Ca21 , Na1 and K1 . nonself Everything that is not part of the body’s own tissues and may be recognized by the immune system. nonsense codons Codons that do not specify an amino acid but signal the end of the region of an mRNA to be decoded. Also known as termination or stop codons. nonsense suppressors tRNAs with anticodon mutations that allow translation of stop codons. nonsense-mediated mRNA decay The process whereby the cell recognizes and rapidly degrades mRNAs with premature nonsense (termination) codons. nonstructural proteins Virus-encoded proteins that function in the replication of the virus and are not part of the viral particle. nonunion distal (NUd) A type of deletion in sister chromatids in which the broken ends of the remaining sister chromatids fuse but the broken ends of the deleted acentric portions do not. nonunion proximal (NUp) A type of deletion in sister chromatids in which the broken ends of the remaining sister chromatids do not fuse, but the broken ends of the deleted acentric portions do. nonzonal bone Bone tissue that does not show zonal ‘growth rings’. noradrenaline The catecholamine neurotransmitter of the sympathetic nervous system. Called norepinephrine in North America. norepinephrine See noradrenaline. NOR See nucleolar organizing region. norm of reaction See reaction norm. normal pressure hydrocephalus (NPH) Syndrome of ventricular enlargement with normal intracranial pressure, characterized by a symptom complex of dementia, gait instability and incontinence. nosocomial infection Infection pertaining to or originating in hospital. notochord A rod-like mesodermal structure that forms just ventral to the neural plate and tube in vertebrate embryos. It provides a primitive backbone for the embryo. novelty A new structural character arising in a phylogenetic lineage that is neither homologous to any structure in the ancestral species, nor serially homologous to any other structure within the same organism. NOx The nitrogen oxides (NO, NO2, N2O, N2O3, etc.) collectively. In literature on the effects of air pollutants on vegetation, often only NO and NO2 are referred to as NOx as these two substances contribute most to the nitrogen load of terrestrial ecosystems. NPC See nuclear pore complex. NPH See normal pressure hydrocephalus. nt An abbreviation for nucleotide(s). nuclear DNA The DNA found in the chromosomes contained in the nucleus of a eukaryotic cell, as opposed to the DNA of mitochondria and chloroplasts. nuclear export signal (NES) Sequence of amino acids that targets a protein for export from the nucleus. nuclear lamina A layer of proteins (the lamins) on the inner side of the nuclear membrane, to which nuclear pore complexes are thought to be anchored.

nuclear localization signal (NLS) Sequence of amino acids that targets a protein for import into the nucleus. nuclear localization Present in the cell nucleus. nuclear magnetic resonance (NMR) A technique that examines the structure of molecules by detecting nuclear spin reorientation (radiofrequency transitions) in an applied magnetic field. nuclear magnetic resonance spectroscopy (MRS/NMRS) A branch of spectroscopy operating in the radiofrequency region of the electromagnetic spectrum, roughly from 0 to 109 Hz. The signal arises from the interaction between atomic nuclei and a magnetic field. nuclear pore complex (NPC) A large multiprotein complex inserted into the double membrane around the nucleus that mediates all communication between the cytoplasm and the nuclear interior. nuclear receptors Receptor proteins, such as those for some steroid hormones, that are located within the nucleus, or translocate to the nucleus after binding their ligand. nuclear reprogramming The resetting of the pattern of gene expression that occurs in a differentiated somatic cell nucleus following its transfer to an enucleated oocyte. After reprogramming the nucleus can support normal embryogenesis. nuclear transfer The method of reconstructing a one-cell embryo from an enucleated oocyte and the nucleus of a donor cell to generate an embryo and ultimately a cloned animal. nuclease An enzyme that degrades nucleic acids (DNA or RNA) by cleaving phosphodiester bonds. Endonucleases attack internal bonds of the polymer, whereas exonucleases attack from the end, usually liberating mononucleotides. nucleocapsid The nucleoprotein core of a virus, consisting of the nucleic acid genome and associated proteins. nucleoid In prokaryotes, the region of the cytoplasm occupied by the DNA and associated proteins. nucleolar organizing region (NOR) The chromosomal regions that form the nucleolus in interphase eukaryotic cells. nucleolus Region in the nucleus where rRNA is transcribed and ribosomes partially assembled. nucleophile An atom (or chemical group) with an available lone pair of electrons that can act as an electron donor in a chemical reaction. Common active-site nucleophiles in enzymes are the hydroxyl group of serine and threonine, the sulfhydryl group of cysteine, and the imidazole group of histidine. nucleophilic attack The reaction of an electron-rich atom with an electron-deficient atom to form a bond. An example is the attack of the e-amino group nitrogen of a lysine residue of DNA ligase on the a-phosphorus of ATP to give a P–N bond. nucleophilic Describes an electron-rich atom or chemical group that readily reacts with compounds (electrophiles) containing positive charge or that are electron deficient. nucleophilic substitution Chemical reaction whereby a nucleophile attacks an atom and often leads to the dissociation of another group covalently bound to that atom, called the leaving group. nucleoporin A protein component of the nuclear pore complex. nucleoprotein filament A complex of RecA protein, DNA and a nucleoside triphosphate cofactor. nucleoside Molecule consisting of a purine or pyrimidine base attached to a pentose sugar (e.g. ribose, deoxyribose).

210

Glossary

nucleosome The basic structural unit of eukaryotic chromatin, consisting of an octamer of histone molecules ((H2A, H2B)2 (H32, H42)) plus one molecule of H1, around which is wrapped about 1.7 turns (180–200 base pairs) of DNA double helix. nucleosome core particle The histone octamer and the length of DNA (146 base pairs) wrapped round it that resists digestion by micrococcal nuclease. nucleosome position Nonrandom contacts of histones with DNA with respect to sequence. nucleotide excision repair A DNA repair process whereby damaged nucleotides in the cell’s DNA are removed as part of a short single-stranded DNA fragment and the integrity of the DNA restored to its normal state by new DNA synthesis using the exposed normal strand as template. nucleotide-binding site (NBS) Amino-acid residues that form the binding pocket for nucleoside triphosphates on various enzymes. nucleotide Phosphate ester derivative of a nucleoside, the phosphate group (or groups) being attached to the sugar. Nucleotides are the monomer units of DNA and RNA. nucleus (1) The large and usually prominent organelle in a eukaryotic cell that contains the cell’s chromosomal DNA, and is the site of DNA replication and transcription and RNA processing. The nucleus is bounded by a double membrane that is a continuation of the endoplasmic reticulum. (2) Anatomically discrete collection of functionally related nerve cell bodies in the central nervous system. NUd See nonunion distal. NUp See nonunion proximal. null allele An allele that produces either no protein product or a nonfunctional protein product (under the conditions analysed). nullizygous The absence of a particular gene product as a result of the presence of two null alleles at a locus. numerical aperture (NA) The sine of half the intake angle of a lens, multiplied by the refractive index of the medium between lens and object. nutritional ecology The study of the interrelationships between food resources in the environment and the consumptive use of these food resources by animals. nystagmus Rhythmic oscillation of the eye during vestibular or full-field visual stimulation. Each oscillation is composed of a slow, compensatory and a fast, anti-compensatory phase.

O antigen A branched polysaccharide portion of lipopolysaccharide that extends out from the bacterial surface. observational study A study of whether an exposure (a measure at recruitment to the study, such as increased cholesterol concentration) is associated with an outcome (e.g. myocardial infarction) at follow-up. ochre mutation Mutation that produces TAA, a nonsense codon that will signal the termination of translation. ocular dominance columns Alternating, regularly spaced, bands of left- and right-eye inputs in layer 4 of the primary visual cortex. oedema Swelling due to abnormal collection of fluid in the extracellular spaces of tissues. It manifests as a boggy swelling and excessive weight gain. In the context of haemolytic disease of the newborn, oedema occurs because of cardiac failure due to anaemia. OH Abbreviation of the prefix ‘Olduvai Hominid’.

Ohm’s law The relationship between current (I), voltage (V) and resistance (R): a current of 1 ampere (1 coulomb sÀ1) flowing through a resistance of 1 ohm will generate a voltage drop across that resistor equal to 1 volt (V 5 IR). Okazaki fragment A short length of DNA that is synthesized during discontinuous synthesis on the lagging strand of replicating DNA. Okazaki fragments are 1000–2000 nucleotides in prokaryotes and 50–200 nucleotides in eukaryotes. After their 50 RNA primers are removed, the fragments are joined together by DNA ligase to form a complete DNA strand. Oldowan The name of a type of stone tool industry that comprises crude chopping tools and flakes. oligoastrocytoma A brain tumour arising either from an oligodendrocyte or an astrocyte. oligoclonal Made up of only a few clones, as, e.g., an immune response involving only a few clones of lymphocytes. oligoclonal bands Two or more discrete bands on electrophoresis that are produced by a few clones. oligodendrocyte Myelinating glial cell of the vertebrate central nervous system. oligogenic Describes a trait controlled by several genes, one of which usually has a major effect. oligohydramnios Reduction in the volume of amniotic fluid around the fetus to below 100 ml. Usually the diagnosis is made by ultrasound scan and the finding of a deepest pool of less than 2 cm is taken as diagnostic. oligomer A molecule formed by connecting several (2, 3, 4, 5) smaller molecules (monomers), usually in the form of a chain or network. oligonucleotide A short chain of nucleotides, often made using a DNA synthesizer to create primers that can be used in PCR and sequencing applications. oligonucleotide hybridization probing A method of detecting particular DNA sequences in a mixture. After dissociation into single strands, the DNA is hybridized with a labelled, singlestranded oligonucleotide complementary to the target sequence. oligonucleotide primer A short piece of single-stranded DNA, generally 17–30 nucleotides in length, that is used in PCR and DNA sequencing methods to start DNA replication at a particular sequence. oligosaccharide A series of monosaccharides (from 2–20) linked together by glycosidic bonds through their hydroxyl groups into linear or branched polymers. oligotrophic Describes an aqueous environment with low levels of nutrient supply. ommatidia (singular ommatidium) The individual units in an arthropod compound eye, each containing a crystalline ‘lens’, a set of photoreceptor neurons and support cells. omnivorous Having a broad diet of both plant and animal origin. omnivory Having a diet that includes both plants and animals. Humans are traditionally categorized as omnivores. oncogene activation The conversion of a proto-oncogene into an oncogene, caused by viral insertion, viral transactivation or through gene mutation. oncogenesis The generation of a tumour, which initially involves the conversion of a cell to a tumour cell by, e.g., activation of oncogenes and/or loss of tumour suppressor genes as a result of mutation. oncology The branch of medicine that deals with cancer, literally the science of new growths. oncoprotein The protein product of a viral or cellular oncogene.

211

Glossary

ontogenetic stage A morphologically distinct stage in development. ontogeny The growth and development of an individual from embryo to adult. ontology The branch of philosophy that is concerned with basic questions about reality and existence. onychomycosis Fungal infection involving the nails. Onychophora A phylum/subphylum of tropical and subtropical carnivorous lobopodial arthropods inhabiting the litter layer. oocyst The cystic stage of a parasite. oocyte An immature egg cell. oocyte maturation The resumption of meiosis in an oocyte at the completion of oogenesis to produce the mature egg. In many species, the egg then undergoes a second meiotic arrest. oogenesis The development of a female egg cell in the mother, from the immature oocyte up to the mature egg. oogonium (plural oogonia) A female gametangium that contains one or more discrete gametes, the oospheres. Oomycetes Also known as water moulds. Genetically, these are quite unique fungi, generally now classified separately from the Fungi, that are commonly plant pathogenic and lack cross walls. oosphere A large naked mass of protoplasm that functions as the female gamete, or egg, in an oogonium. oospore A thick-walled sexual spore that develops from the oosphere after plasmogamy. open complex A complex of RNA polymerase and a promoter in which the duplex DNA is unwound around the transcription start point. open reading frame (ORF) A set of codons (triplets in DNA) uninterrupted by a stop codon and potentially translatable into a protein. operator Site in bacterial DNA to which a regulatory protein binds to exert its effect on gene expression. operon In bacteria and archaea, a series of adjacent genes that are cotranscribed into a single mRNA, and are thus coordinately controlled. An operon comprises a regulatory gene, an operator region, a promoter region and the structural genes. The protein products of these genes are almost always involved in the same metabolic pathway. opines Low-molecular weight molecules produced by Agrobacterium-transformed cells and used by the bacterium for its growth. opioids The opiates (derivatives of opium) and synthetic narcotics resembling opiates. opisthobranch molluscs, opistobranchs A subclass of the class Gastropoda (Opistobranchia) comprising marine molluscs in which the shell is much reduced or absent. opisthosoma The posterior body region of chelicerates. It is composed primitively of 12 segments and houses the heart, respiratory organs, reproductive system and much of the digestive system. opportunistic infection An infection caused by an organism that usually does not cause disease in individuals with a normal immune system. opsonin Any protein (e.g. vertebrate antibodies, complement fragments, and various factors in invertebrates) whose binding to a foreign antigen facilitates the antigen’s recognition and subsequent elimination by phagocytic cells. opsonization A process by which phagocytosis of a foreign antigen is facilitated by its coating with opsonins (e.g. antibody, complement fragments).

optic chiasm Region behind the eyes where some retinal axons cross from one side of the brain to the other. optic lobes Well developed regions of the brain concerned with processing visual data. optic tectum The visual centre in the brain of lower vertebrates, such as fish, amphibia and birds. optical path length The effective distance travelled by a light beam in going from one point to another, allowing for the repertoire end view of the materials through which it passes, and the possibility that it is scattered and does not follow a straight line path. optical section An image produced by some form of noninvasive light microscopical imaging and containing little or no information from above or below the focal plane of interest. order (1) Unit of taxonomic classification that comes between family and class. (2) A very high taxonomic unit used in taxonomic studies of prokaryotes. Ordovician period The second major division of the Palaeozoic era. ORF See open reading frame. organelle A subcellular structure that performs a specialized function. Examples are the nucleus, mitochondrion, endoplasmic reticulum, Golgi body. organizer General term for the embryonic structure formed during gastrulation which has the ability to induce a secondary neural tube when placed into an ectopic site. In the mouse, the node, or anterior condensation of the primitive streak, possesses ‘organizer’ activity. organomegaly Abnormal enlargement of any or all visceral organs. organometallic Involving a direct metal–carbon bond. origin of replication Site on a DNA molecule at which replication is initiated. Bacterial chromosomes and plasmids have a single origin of replication; most eukaryotic chromosomes have multiple origins. origin of transfer Sequence on a plasmid that serves as the starting point for the synthesis of a DNA molecule which can be transferred to a recipient bacterium during conjugation. Ornithischia The ‘bird-hipped’ dinosaurs. These were exclusively herbivorous and are recognized by a bird-like arrangement of their hip bones. Paradoxically, they are not closely related to living birds. Ornithuromorphs A diverse group of birds including all living birds. oropharyngeal washing Garglings. The fluid recovered from washing the mouth and throat by keeping the fluid in motion from air expelled from the lungs. orthodox seeds Seeds whose viability is best maintained by dry storage at temperatures close to or below 01C. orthograde Having upright body posture. orthologous genes The name given to the same gene or DNA sequence when they occur in different species as a result of an ancestor containing that gene giving rise to two or more different species. orthologous sequence See orthologous genes. orthology (1) The situation in which similarities between two species are the result of a common evolutionary origin, and in which the gene product or structure at issue retains the same form and function. (2) The relationship between any two homologous genes that are descended from the same gene in the nearest common ancestor.

212

Glossary

orthorhombic Crystal symmetry group typified by three mutually perpendicular axes of unequal length. orthostatic Related to the upright position of the body. oseltamavir A neuraminidase inhibitor that acts as an antiinfluenza agent. oscillation Any measurable behaviour that is periodic in time. That is, the state of the system repeats at regular intervals called the period of the oscillation. The reciprocal of the period is the frequency. osmolality A measure of the osmotic pressure generated by a solution. It is the concentration of osmotically active molecules, i.e. those that cross semipermeable membranes in solution, measured in osmoles (the standard unit of osmotic pressure) per litre of solution. osmoregulation Regulation of a cell or organism’s water and ion balance. osmotic concentration The number of dissolved particles (ions and molecules) in 1 litre of water. osmotrophy, osmotrophic Heterotrophic nutritional mode in which an organism acquires food material by taking it in (by active transport) through the cell membrane in a dissolved state. It is characteristic of many microorganisms (e.g. several major groups of internal symbiotic or parasitic protozoa). osteoarthritis A degenerative joint disease characterized by erosion of articular cartilage, which can be either primary or secondary to trauma or other conditions. osteoblast Cell that secretes bone matrix and initiates bone mineralization. osteoclast Large multinucleate cell, related to the macrophage, that degrades bone matrix. It is found wherever existing bone tissue is being removed and migrates over the bone surface, creating irregular scalloped cavities. osteocyte An osteoblast after it has been trapped in bone matrix and ceases to deposit bone. It is well connected to a dense network of other osteocytes and bone-lining cells through cytoplasmic extensions which radiate outward from the central vascular canal. osteoderms Bony dermal scutes covered by epidermal scales that make up the carapace of armadillos and glyptodonts and are also present in mylodont sloths. osteogenesis The production of new bone. osteoid Unmineralized bone matrix, deposited by osteoblasts and consisting primarily of type I collagen. As the matrix mineralizes, the collagen infrastructure provides tensile strength. osteon Complex of concentric lamellae, or plates, of bone surrounding a canal containing blood vessels, nerves and loose connective tissue. osteopetrosis An inherited disease that is characterized by an increased density and apposition of bone due to a reduced activity of osteoclasts (macrophage-like cells that degrade bone matrix). osteoprogenitor cells A population of cells with the latent capability to produce bone-forming cells on demand. ostiate heart A heart with pores to permit the entrance of blood from the haemocoel. ostracods A group of small, mostly aquatic crustaceans that have minute, bean-shaped, bivalved, hinged usually calcitic shells. Phylum Arthropoda, subphylum Crustacea, class Ostracoda. They have been present from Cambrian to Recent. otolith ‘Ear stone’, a structure containing calcium carbonate particles embedded in a gelatinous mass, which sits above the hair cells in the maculae of the inner ear.

outgroup In phylogenetic studies, a taxon used to establish the root of a phylogenetic tree. It is chosen from among ancestral groups or species that diverged from the group being studied prior to diversification within that group. outgrowth The growth of a germinated spore as a vegetative organism capable of synthesizing RNA, protein and DNA. outside-in signalling Signalling responses that are triggered within a cell following the binding of integrins to their ligands. overdominance The case when the heterozygote (e.g., Aa) has higher fitness than either of the homozygous genotypes (e.g., AA and aa), thus maintaining polymorphism. That is, the reproductive success of Aa ensures that both the A and a alleles are preserved. ovipary Type of reproduction in which eggs are laid and embryos develop outside the mother’s body. ovulation Process by which an ovum, or egg, is released from the ovary. ovule The organ in which the female gametophyte develops in plants. In angiosperms ovules arise from part of the inner surface of carpels and are enclosed by them. After fertilization and development of the embryo, the ovule matures into a seed. oxidase A haem enzyme that accomplishes the four-electron reduction of dioxygen to water. oxidation A chemical reaction that results in the loss of electrons from the molecule that undergoes oxidation. oxidative burst (1) Rapid production and accumulation of reactive oxygen species in infected plant tissues following pathogen attack. (2) The production of reactive oxygen species in macrophages and neutrophils after pathogen ingestion. oxidative damage Damage caused to biological molecules by free radicals or other reactive oxygen species generated in the normal course of oxygen-dependent metabolism. oxidative pentose phosphate pathway A metabolic pathway by which glucose 6-phosphate is oxidized to finally yield triose phosphates and reducing power in the form of NADPH. oxidative phosphorylation Formation of ATP from ADP and inorganic phosphate (Pi) by an ATP synthase, which is coupled to oxidation of substrates (e.g. NADH) via the electron transport system with the consumption of oxygen. oxidative stress Cellular stress caused by an excess of reactive oxygen species (free radicals). It occurs when there is a serious imbalance between the generation of reactive oxygen species in vivo and the activity of antioxidant defences. oxyanion A negatively charged oxygen atom, usually arising from attack on a carbonyl group. The oxygen atom receives electrons from the double bond upon attack on the carbon, resulting in excess electrons. oxygen debt The amount of lactate accumulated during a bout of activity, which after activity has stopped is reconverted to glucose, a process that requires an increase in the consumption of oxygen. oxygenase A haem enzyme that accomplishes addition of one oxygen atom or two oxygen atoms to a substrate.

P element A transposable element found in Drosophila. P granules Aggregations containing RNA and protein which are found in the germline and in early embryos of Caenorhabditis elegans, where they are segregated to the future germline at each of the early cleavages.

213

Glossary

P site The tRNA-binding site on the ribosome where the peptidyltRNA (P) is located before peptide-bond formation. It involves both the large and small subunits. p53 A regulatory protein of the eukaryotic cell cycle. It acts at one of the checkpoints for detecting DNA damage and is an important tumour suppressor protein. PAC P1-phage derived artifical chromosome. Large-insert cloning system retaining features of both the Escherichia coli F factor and the P1 phage. The vector carries an antibiotic-resistance gene, copy-number control elements and a positive selection system for cloned inserts. pachytene The stage of meiosis I prophase during which bivalent formation is completed and chiasmata appear. packaging signal A motif in a retroviral RNA genome that determines their efficient encapsidation into virions. packing defect Localized defects or voids in the bilayer structure caused by the presence of membrane lipids with cis double bonds. These form kinks in the hydrocarbon chains which prevent effective close-packing of the lipid hydrocarbon chains in the bilayer. PACS See Picture Archiving and Communication System. paedomorphosis One form of heterochrony, in which the juvenile characters of the ancestral form are retained in the adult of the descendant. PAGE See polyacrylamide gel electrophoresis. Palaeognathae The taxon of large running birds that cannot fly, often called ratites. They have a rhynchokinetic skull and a specific palate-reinforcing construction. The group includes the extinct moa, the ostrich, kiwi, rhea, emu and cassowary. palaeontology The study of ancient life from fossils. palaeosol Fossilized soil. palatal detachment An uncoupling of some lower facial and basal skull bones from the braincase, during evolution, through which slenderized bones at the ventrorostral region of the skull formed a movable apparatus that was capable of operating the prokinetic or rhynchokinetic movement of the skull. palindrome A DNA segment in which the sequence is the same on one strand read 50 to 30 as on the other strand. pallial Situated in the mantle cavity. palpation Examination performed by touching and probing with the hands and fingers. PAMPs See pathogen-associated molecular patterns. panbiogeography A methodology for studying the origins of closely related species that tries to reconstruct the events leading to observed distributions of species by connecting the known distributions of related taxa by drawing lines on maps. pancreatitis Inflammation of the pancreas. pandemic A worldwide epidemic of a disease. panmictic Randomly interbreeding. papilloedema Swelling of the optic nerve head visible on fundoscopic examination reflecting increased intracranial pressure. It results from increased pressure in the nerve sheath slowing the axoplasmic transport within the optic nerve. para-aortic Situated beside the aorta. parabasal body Organelle of various shape and size in flagellate protozoans, sometimes wound about the axostyle. It is identical to the Golgi apparatus and forms an identifying feature of the Parabasalea. parabiosis Linking pairs of animals together so that they have a common blood circulation.

paracrine circuit effect Occurs when the effect of a hormone or cytokine is exerted on a cell population that differs from the secreting cells themselves. paracrine growth factor A secreted polypeptide that is made by one cell and acts on a different neighbouring cell. paracrine Describes the local action of a cytokine or hormone on cells close to the producer cell. parallel fibres Nonmyelinated axons of granule cells forming massive parallel bands running through Purkinje cell dendrites in the cerebellar cortex. Each Purkinje cell receives synapses from 100 000 parallel fibres. paralogous genes Homologous genes that have arisen through the process of gene duplication. paralogy The relationship between any two homologous genes descended from the same ancestral gene by gene duplication and divergence. paramutation The heritable modification of the expression state of an allele (the paramutable allele) which depends on the presence of another allele (the paramutagenic allele) that has acquired a repressed state. Paranthropus A genus introduced by Robert Broom in 1938 to accommodate a group of early hominins distinguished by relatively small incisor and canine teeth, large premolars and molars, and a wide, flat face. paranemic joint molecule A DNA strand-exchange intermediate where the individual complementary strands of DNA are base paired but not intertwined. parapatric Describes populations or species with geographical distributions that are contiguous but not overlapping. paraphyletic group A group of species that includes their single common ancestor but not all of this ancestor’s descendants. Thus, members of a paraphyletic genus, for example, can also be closely related to members of other genera. paraphyly See paraphyletic; paraphyletic group. paraplegia Paralysis of the lower extremities. paraprotein Any unknown band of restricted migration seen on electrophoresis, prior to identification. Once identified, the band is then referred to by its specific name. paraptry See parapatric. parasporal crystal A crystalline protein inclusion formed within the sporangium during sporulation of certain bacteria. paratenic host A host that carries a parasite but does not support its growth or reproduction. paratope Single binding site within the V regions of an antibody or T-cell receptor that binds to a particular epitope on a particular antigen. paraxenology Similarity arising by a combination of gene transfer and gene duplication/multiplication. parenchyma (1) Plant cell type with thin-walled cells and living cellular contents at maturity. (2) The tissue occupying the space between the epidermis and the gastrodermis in planarians. It provides support to the internal organs, and is primarily composed of two cell types: the neoblasts and the large, highly interdigitated, fixed parenchymal cells. parenchymella A sponge ‘larva’ composed of an envelope of flagellated cells surrounding an internal cell mass. parental imprinting In relation to genetics, the phenomenon that for some genes the paternal copy or the maternal copy only is expressed in the early embryo, as a result of epigenetic modification in the gamete. Also known as genomic imprinting.

214

Glossary

parts Variables expressed as parts or percentages of a whole. Parts are dependent on each other; if one is omitted, all remaining parts are affected. This is not so for normal variables. pascal The SI unit of pressure or stress (1 Pa 5 newton (N) mÀ2), commonly expressed in units of kPa and equivalent to 100 millibars or 7.5 Â 10À3 mmHg (101 kPa 5 1 atm 5 760 mmHg). PAS See periodic acid Schiff technique. passerine Describes birds of the Order Passeriformes (includes 52% of bird species), which have feet adapted for perching on branches. Three-quarters are songbird families in the Suborder Oscines, characterized by a versatile syrinx (vocal organ). passive antibody Antibody that is present is young animals and is derived from the mother, either in utero or through the milk. The animal’s own immune system is not stimulated. passive transport Transport of molecules across a membrane down a concentration or electrochemical gradient without the use of other cellular energy. passive-margin basin The basin at the edge of a subsiding continental margin as it moves away from the mid-ocean ridge. It is usually filled with shallow marine shelf sediments and deepmarine sediments of the continental slope and rise. patch testing The placing of small amounts of a potential allergen on the skin to determine which agent might be responsible for an allergic contact hypersensitivity reaction. paternalism Interference with or overriding of another’s preferences or choices in order to avoid harm to or benefit the one whose preferences are interfered with. pathogen Any disease-producing agent, especially a virus, bacterium or other micoorganism that is expected to cause disease in a normal host. pathogen-associated molecular patterns (PAMPs) Unique molecular patterns expressed by microorganisms which are recognized by the innate immune system. pathogenesis-related protein A diverse groups of proteins synthesized de novo in response to pathogen infection. They associate with induced defence responses and often possess antimicrobial activity. pathognomonic Specific and characteristic of a given disease or condition, as, e.g., Aschoff bodies are of rheumatic carditis. pathway The succession of different steps in a process. patristic distance Sum of branch lengths connecting two nodes in a phylogenetic tree. PBDs See peroxisome biogenesis disorders. PBPs See penicillin-binding proteins. PCR See polymerase chain reaction. p-distance For DNA and amino-acid sequences, the fraction of sites at which two sequences differ in content. pectates Pectic polysaccharides containing a high proportion of 1,4-linked galactosyluronic acid residues that are not methylesterified. pectic polysaccharides Plant polysaccharides composed predominantly of 1,4-linked galactosyluronic acid residues. pectins Pectic polysaccharides containing a high proportion of methyl-esterified 1,4-linked galactosyluronic acid residues. pedal nerve The large nerve running from the body of a crab into each leg. pedicle (1) The narrow stem of an organ or tumour. (2) The appendage commonly protruding from the larger of the two valves of a brachiopod, and generally responsible for attachment of animal to substratum.

pelagic Living in the water column, not attached to rocks or the seabed. pellicle A set of cortical structures that strengthens the outermost layer of the cell body in ciliates and some flagellates, enabling them to maintain shape. A typical pellicle comprises the plasma membrane, two alveolar membranes and a granular cytoplasm (epiplasm). pelta Crescent-shaped structure composed of microtubules and associated with the axostylar capitulum in flagellates, it may be an extension of the axostyle wrapped around the basal body. penciclovir Nucleoside analogue inhibitor of human herpesvirus 1. penetrance A measure of the ability of an allele to produce a phenotype in the population. penetration The stage of viral replication at which the virus genome enters the cell. penicillin-binding proteins (PBPs) Enzymes located in the bacterial cell membrane and responsible for the terminal stages of bacterial peptidoglycan (cell wall) synthesis. They are usually transpeptidases and carboxypeptidases and are the critical targets for b-lactam antibiotics. pentacyclic triterpenoid A compound, containing five rings, which is made up of three C10 molecules known as terpenes. These compounds are distinct from, though related to, sterols. pentose phosphate pathway A metabolic pathway in which carbon dioxide is produced directly from glucose. A major function of the pathway is the provision of NADPH. pentraxins A family of plasma proteins involved in innate immunity. They are composed of five identical subunits. PEP:PTS See phosphoenolpyruvate: carbohydrate phototransferase system. peptide Any chain of fewer than 100 amino acid residues. Peptides may be synthesized de novo or derived from enzymatic cleavage of proteins. peptide backbone That part of a polypeptide or protein structure that includes the amide bonds and a-carbons but not the individual side chains. peptide nucleic acid (PNA) A synthetic DNA analogue containing a (2-aminoethyl) glycine backbone which forms highly stable duplexes with complementary DNA. peptidergic (1) Describes a neuron that secretes a peptide neurotransmitter. (2) Having an action resembling that of a peptide hormone. The term describes a receptor that is activated or modulated by a peptide. peptidoglycan The complex polymer that forms the major structural element of bacterial cell walls. It is composed of short glycan chains crosslinked by short peptides such as murein and pseudomurein. peptidylprolyl isomerase An enzyme that catalyses the cis/trans isomerization of proline residues. peptidyltransferase Enzymatic activity that transfers an amino acid to the carboxyl end of a growing polypeptide chain by formation of a peptide bond. Peptidyltransferase (transpeptidation) activity resides in large ribosomal subunit RNA, not in a protein. peptidyltransferase centre Catalytic site on the large ribosomal subunit where the bond between tRNA in the P-site and the carboxyl end of the polypeptide is broken, and transferred to the aminoacyl end of the aminoacylated A-site tRNA. peptidyl-tRNA hydrolase Enzyme that catalyses the hydrolysis of all N-blocked aminoacyl-tRNAs with the exception of fMettRNAfMet.

215

Glossary

perforin A pore-forming protein present in the granules of cytotoxic T cells. perfusion The blood flow through tissue. pericardial effusion Fluid collecting in the sac-like membrane around the heart (pericardium) due to anaemia and cardiac failure. pericarp The wall of a fruit. It develops from the ovary wall. pericentric inversion A chromosomal inversion that includes the centromere. periclinal (1) Describes a plane parallel to the outside of the organism or organ. (2) Describes a cell division in which the plane of division is oriented parallel to the surface. pericyclic reactions A large group of organic reactions the stereochemistry of which is controlled by the conservation of orbital symmetry. peridinin Accessory carotenoid pigment present in many dinoflagellates. perinatal mortality Death that occurs just before or just after birth. In humans, the term is used for stillbirths after 24 weeks or 168 days of gestation and deaths within the first 7 days after delivery. periodic acid Schiff technique (PAS) A staining technique in which material containing vicinal glycol groups on their amino or alkylamino derivatives can be oxidized by periodic acid to form dialdehydes that combine with Schiff reagent to form an insoluble magenta compound. periosteum The highly vascularized and innervated fibrous connective tisssue layer surrounding a compact bone. It is rich in collagen, osteoblasts and fibroblasts and can be a site of new bone formation. periostracum Thin, organic external layer of a shell. Peripatus See Onychophora. peripatric speciation Formation of a new species in small peripheral isolated populations or beyond the periphery of the parent species’ range. peripheral circulation The collective name for the blood vessels that supply blood to the body tissues. It is also termed the systemic circulation. peripheral membrane proteins Proteins that are bound to membrane surfaces (usually to integral membrane proteins) but that do not have any of their mass buried in the membrane. peripheral nervous system (PNS) Part of the nervous system encompassing peripheral nerves, sensory and sympathetic ganglia, and nerve roots. periplasm The region between the inner and outer membrane in a bacterium. It contains a large number of transport proteins and enzymes and is the region in which the peptidoglycan is located. Extracellular bacterial proteins fold in the periplasm. periplasmic enzymes Enzymes that function in the space between the inner and outer membranes of Gram-negative bacteria. periplasmic region See periplasm. peripodal cells Cells in the imaginal discs of insects. perissodactyl mammals Hoofed mammals with an odd number of functional toes on each foot, such as horses, tapirs, and rhinoceros perisynaptic glial cells Glial cells anatomically associated with chemical synapses. These are astrocytes in the central nervous system, Bergmann glial cells in the retina and perisynaptic Schwann cells at the neuromuscular synapse.

permeability A measure of how well an ion moves across a cell membrane. Membrane permeabilities for different ions are usually expressed as ratios. permeance A measure of the permeability of a membrane to gases, liquids or solutes with units of m sÀ1 (calculated from the flow rate across the membrane in g mÀ2 sÀ1 divided by the appropriate concentration gradient in g mÀ3). Permian period The last major division of the Palaeozoic era. permineralization The conversion of soft or hard tissues of an organism to mineral. permissive interactions Conditions required for the expression of a new phenotype gained through directive interactions. peroxins Proteins encoded by the PEX genes and involved in the biogenesis of peroxisomes. At least 20 are known and include cytosolic and membrane receptors, putative components of the membrane translocation apparatus, and many proteins of unknown function. peroxisomal targeting sequence type 1 (PTS1) A C-terminal tripeptide based on the SKL amino-acid motif. This is the most common targeting sequence found in peroxisomal matrix proteins. PTS1 proteins interact with the import receptor Pex5p. peroxisomal targeting sequence type 2 (PTS2) An N-terminal sequence based on the XnRLX5H/QLXn amino-acid motif. PTS2s are less common than PTS1s and unlike PTS1s are often cleaved after import. PTS2 proteins interact with the import receptor Pex7p. peroxisome An organelle in eukaryotic cells that is involved the breakdown of peroxides, especially hydrogen peroxide, oxidation of amino acids and lipid metabolism. It is usually characterized by the presence of catalase. peroxisome biogenesis disorders (PBDs) Human genetic diseases in which peroxisomes do not form properly. In many cases the mutant genes have been cloned and shown to encode peroxins. persistent transmission The transmission of a pathogen throughout the life cycle of the vector. PEV See position-effect variegation. Peyer’s patches The organized lymphoid tissue of the small intestine. PFU See plaque-forming unit. PFU assay Plaque-forming unit assay. It is used to determine the infectivity of viruses that can infect and kill cultured cells. PGA See 3-phosphoglycerate. phage See bacteriophage. phage k A temperate phage that infects the bacterium Escherichia coli. phage vector Modified phage genome that is capable of replicating in its host organism and into which foreign DNA (e.g. human DNA) can be inserted for cloning. phagocytes Scavenger cells that take up microorganisms and cell debris by sweeping the plasma membrane around the object and internalizing it in a structure called the phagocytic vacuole or phagosome. In vertebrates, the ‘professional’ phagocytes involved in host defence are the monocytes, macrophages and neutrophils, but other cells have a limited ability for phagocytosis. In invertebrate host defence, the plasmatocytes and granulocytes are the phagocytic cells. phagocytose To actively engulf large particles by the process of phagocytosis.

216

Glossary

phagocytosis The engulfment of particulate material by a cell, by surrounding the particles with the plasma membrane and internalizing them in a membrane-bounded vacuole (a phagosome). phagolysosome A phagosome fused with lysosomes. phagosome A membrane-bounded cytoplasmic vacuole formed around a particle ingested by phagocytosis. phagotrophic Describes a type of heterotrophic nutrition in which particulate food is engulfed in a food vacuole, as in many protozoa. Often whole organisms (usually other protists or bacteria), serve as prey. Phanerozoic The entire span of time since macroscopic fossils first appeared. phantom limb pain Painful sensations referred to an amputated limb. pharmacodynamics The relationship of the pharmacokinetics of a drug to its biological effects, including, in the case of antimicrobial agents, the nature, speed and completeness of the antimicrobial effect. pharmacokinetics The behaviour of a drug in terms of its absorption, distribution, binding, metabolism and elimination. pharynx (1) In nematodes, a muscular pumping organ at the front of the digestive tract. (2) The portion of the gut between the mouth and midgut in chelicerates. It is lined with cuticle and supplied with constrictor and dilator muscles for transporting and processing food. phase II trial An experimental test programme that checks the efficacy of a drug on patients with actual disease symptoms. phase separation Formation of a heterogeneous state of membrane lipid owing to the transition of high-melting point lipids from the fluid phase to the gel phase at low temperature, resulting in the loss of native function of the biological membrane. phase space A conceptual space in which each axis corresponds to one of the state variables, and in which the system is represented by a point at any given moment of time. phase variation The change in antigen specificity demonstrated by some bacteria, caused by their on–off switching of a flagellar protein gene. phase–response curve The graphical representation of how a phase of a rhythmic process changes when perturbed by an external stimulus at different times or phases in its cycle. phasins Small, amphipathic proteins found at the boundary layer between an insoluble inclusion body and the soluble cytoplasm of the bacterial cell. phenetic Describes a grouping of organisms founded on overall similarity, based on all available characters, which may include genotypic and phenotypic data. phenocopy An instance of a trait that has arisen environmentally but simulates a genetically determined trait. phenoloxidase An enzyme that oxidizes o-diphenols to o-quinones, eventually producing melanin. In insects it can be present in both the haemolymph and the cuticle and participates in wound healing and sclerotization. Also called tyrosinase. phenotype The morphological, biochemical and behavioural characteristics of an individual organism or cell. Phenotype is determined by both genetic and environmental factors. phenotypic plasticity The capacity of a given genotype to produce different phenotypes in response to different environmental conditions. phenylalanine hydroxylase (PH) Enzyme that catalyses the conversion of the essential amino acid phenylalanine to tyrosine.

pheromones Secreted compounds that carry information about an individual to other members of the same species, in which they induce a specific response. pH A measure of the active acidity of a solution defined as the negative logarithm of the H 1 ion activity (or concentration). PH See phenylalanine hydroxylase. pilus (plural pili) See fimbriae. phloem The nutrient-conducting tissue of vascular plants, composed of thin-walled living cells. phonophobia An intense dislike of sound which commonly accompanies the headache of migraine. phoresy A condition where a nematode or other potential parasite rides on the body of an animal but does not harm it. It is used as a means of distribution to new habitats. Phoronida, phoronids A phylum of tube-dwelling, worm-like animals having a horseshoe-shaped crown of tentacles (the lophophore) around the mouth. 3-phosphoglycerate (PGA) Three-carbon molecule that is the first three-carbon stable intermediate of the C3 carbon dioxide fixation pathway in plants. phosphatase An enzyme that removes a phosphoryl group from another molecule. phosphate overplus Accumulation of polyphosphate in bacteria on transition from phosphate-poor to phosphate-rich conditions. phosphodiester bond The covalent linkage –O–P(O2)–O– between two nucleotides in a nucleic acid strand. phosphodiesterase Enzyme that catalyses the hydrolysis of phosphodiester bonds. phosphoenolpyruvate:carbohydrate phosphotransferase system (PEP:PTS) A membrane transport system in prokaryotes that catalyses the coupled transport and phosphorylation of a number of sugars. The transported sugar is phosphorylated during transport by a specific kinase, with phosphoenolpyruvate as the phosphate donor. This system is also involved in the chemotactic response to these sugars. phosphoenolpyruvate-dependent sugar phosphotransferase system See phosphoenolpyruvate:carbohydrate phosphotransferase system. phosphoenzyme An enzyme with a covalent bond between a nucleophile on the enzyme and a phosphorylating agent. phospholipase C (PLC) Enzyme that hydrolyses the membrane phospholipid phosphatidylinositol 4,5-bisphosphate to produce inositol 1,4,5-phosphate and diacyglycerol. phospholipids Amphipathic lipids in which a glycerol phosphate backbone is substituted with two fatty acids and a hydrophilic base such as choline. They are the major constituents of the lipid bilayer of biological membranes. phosphorite Sedimentary rock containing calcium phosphate, chiefly as the mineral apatite. Also called phosphatic nodule. phosphorolytic Describes the degradation of starch to glucose phosphate by starch phosphorylase. phosphorylase An enzyme that uses the oxygen of phosphate as the nucleophile in a substitution reaction. photoautotroph, photoautotrophic Organism that utilizes the energy derived from sunlight to build up its organic molecules from inorganic materials available in their surroundings, using carbon dioxide as the carbon source. photobiont The symbiotic alga or cyanobacterium (i.e. the photosynthetic partner) in a lichen. photodiode A semiconductor diode that produces a photovoltage as a result of the absorption of photons.

217

Glossary

photoheterotrophic growth Growth using organic compounds as nutrients and light as a source of energy. photoinhibition Reduction in the capacity for photosynthesis caused by high light levels, which damage the photosynthetic apparatus. photolithotroph Organism that uses sunlight as the energy source and inorganic materials as the source of the elements needed for growth, using carbon dioxide as the carbon source. photolithotrophy See photolithotroph. photomorphogenetic Pertaining to the regulation of morphogenesis by light, other than by the provision of organic matter by photosynthesis. photoperiod The period of time during which a plant is exposed to daylight in the context of the day–night cycle. With respect to the initiation of flowering, different plant species respond to different length of photoperiod. photophobia Intense dislike of light which commonly accompanies the headache of migraine. photophosphorylation The formation of ATP from ADP and PI driven by the energy of sunlight in photosynthetic organisms. photoreceptor neurons The light-sensitive neurons of the retina. They contain specialized structures – rhabdomeres – that absorb light and transduce the energy to a signal that is sent through the axons to the underlying optic lobes of the brain. photorespiration The biochemical reactions initiated by the oxygenase activity of Rubisco, which utilize atmospheric oxygen and serve to recycle some of the reduced carbon fixed by photosynthesis. photosynthate The carbohydrate products of photosynthesis. photosynthesis The physicochemical process by which some organisms (plants, algae and some bacteria) can utilize the energy of sunlight to power the biosynthesis of organic molecules, using carbon dioxide as the carbon source. photosystem A pigment–protein complex that uses light energy to excite specific chlorophylls that then transfer electrons to nearby cofactors, thus setting in motion photosynthetic electron transport. phototherapy Ultraviolet illumination of the skin of a baby to convert unconjugated bilirubin, released from haemolysis of red blood cells, to the conjugated water-soluble form, which will not cross the blood–brain barrier. phototroph, phototrophic See photoautotroph. phototroph Any organism whose principal or only source of primary energy is sunlight. phototrophic Describes an organism that relies on photosynthetic fixation of carbon dioxide as its sole source of carbon. phycobilins Water-soluble blue or red pigments that function in the capture of light energy. The energy is ultimately transferred to chlorophyll a. phycobiliprotein Blue/green or red water-soluble accessory pigments present in the chloroplasts of some algal groups. phycobilisome A light-harvesting structure found in cyanobacteria. It contains allophycocyanin, phycocyanin and phycoerythrin. phycoerythrin Protein involved in collection of light for photosynthesis in cyanobacteria. phyletic gradualism A theory that suggests that most evolution occurs at a phyletic level, that is, within established species. Speciation is regarded as a relatively rare event which results from a gradual divergence in morphologies.

phyllody Transformation of normal floral parts (petals) into leaflike structures. phyllosphere The external surface of plant leaves. phyllotaxis The relative positioning of the leaves (and other aboveground organs) on the shoots. phylogenetic Relating to the evolutionary history of a species, a taxonomic group, or a structure. phylogenetics A branch of systematics that concerns the uncovering of the evolutionary history of organisms and the relationships between different groups. phylogenetic marker Homologous molecule whose nucleic acid or amino acid sequence information may be used to infer the phylogeny of organisms. phylogenetic species concept The idea that a species is the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent. phylogenetic tree A branched, (usually) bifurcating representation of the evolutionary relationships between taxa. They can be based on DNA sequence comparisons or on fossil, anatomical or other similar evidence. phylogeny The evolutionary history of species and the genetic relationships between them. phylum (plural phyla) A major taxonomic grouping of organisms (e.g. Arthropoda, Mollusca), based on a common body organization. physical map An ordered arrangement of loci of genes and DNA markers on a chromosome, based on the number of nucleotide pairs between loci. physician-assisted suicide The act of aiding a patient in suicide by providing effective means such as drugs. physiognomy The shape of the body, as expressed, for example, in indices that relate the lengths of the two limbs to that of the trunk, and to each other, and in indices that reflect the relative lengths of the component segments within each limb. phytanyl Branched-chain hydrocarbons (approximately 20 carbons) which are highly methylated and are ether-attached to the polar headgroups of the lipids in archaeal membranes. phytoalexin A low-molecular weight antimicrobial compound produced as a secondary metabolite by plants. It is synthesized and accumulated in response to infection or other physical or chemical stresses. phytohormone An organic substance that in minute quantities profoundly affects plant growth. Examples include auxins, gibberellins and ethylene. phytosteroid A plant-produced molecule having the ring system of cholesterol. phytosterol A plant produced molecule having a cholestane skeleton and alkyated at C24 in the side chain. pili (singular pilus) Nonflagellar, long filamentous structures on the surface of bacteria. Also called fimbriae. pilin Protein subunit of bacterial pili or fimbriae. pinacoderm The outer epithelial layer of the body wall of a sponge. pinacocyte A cell of the sponge pinacoderm, the cell layer separating the sponge from the external milieu. ping-pong mechanism Catalytic mechanism in which one substrate is bound by an enzyme, transformed to product, and released before the second substrate is bound.

218

Glossary

pinocytosis ‘Cell drinking’. The ingestion by a cell of small droplets of extracellular fluid by endocytosis. pituitary gland Gland situated in the base of the skull, divided into a posterior part derived from nervous tissue and an anterior part from glandular tissue. It secretes several hormones involved in reproduction. pixel A two-dimensional picture element which represents the smallest digital element of an image. PKA See protein kinase A. PKC See protein kinase C. pK The pH at which an acid is half dissociated. placental abruption Bleeding into, and rupture of, the attachment of the placenta to the wall of the uterus. placental viviparity Bearing of young nourished within the maternal uterus by transfer of nutrients through a placenta. Placentalia, placentals The name of the clade stemming from the most recent common ancestor of all modern ‘placental’ mammals (all mammals excluding the marsupials and monotremes). Also known as the Eutheria. placentamegaly Enlargement of the placenta. placode A cake-like thickening of the ectoderm that gives rise to sensory neurons and, in the case of the inner ear and the lateral line, to hair cells. placoid Tooth-like scale structure typical for sharks. planktic Describes aquatic organisms that passively float. plankton Tiny animals and plants that live suspended in the water column, with little or no contact with the bottom. They drift in the ocean and provide food for many marine animals. planktonic Describes aquatic organisms that are floating passively or only weakly swimming. planktotrophic Describes actively swimming larvae that feed within the plankton. planktotrophic larva Larva feeding in the plankton. plant growth regulators Natural and synthetic compounds that modify plant growth and development. plant segmentation Independent responses of different parts of a plant to external conditions. This can be due to localized cambial activity and to vascular conduits favouring one organ over another. planula Pear-shaped to rod-like solid embryo of cnidarians, which develops into a tubular polyp. planum temporale An area of the brain adjacent to the primary auditory cortex of the temporal lobe. The left planum temporale is relatively larger in individuals who have absolute pitch. plaque A small clear area that forms around an initial focus of phage infection on a lawn of susceptible bacteria (or of a virus on susceptible cells), due to lysis of infected cells. With an appropriate concentration of phage (or virus) in the initial inoculum, each plaque will be due to a single initial phage (or virus) particle. plaque-forming unit (PFU) An infectious virus or phage particle that can undergo replication in an infected cell and then reinfect surrounding cells to form an area of cell death termed a plaque. plasma cell dyscrasia Proliferation of a single, usually malignant, clone of plasma cells. Characterized by production of large quantities of identical immunoglobulins. plasma membrane The lipid–protein bilayer that surrounds the cytoplasm. Also called the cell membrane, cytoplasmic membrane, plasmalemma (in plants) or inner membrane (in Gramnegative bacteria).

plasmablast A proliferating B lymphocyte at a stage before final differentiation into a plasma cell. Plasmablasts can migrate, contain large amounts of intracellular immunoglobulin and potentially also secrete it. plasmalemma The plasma membrane of plant cells. It lies immediately under the cell wall and invaginates and proliferates to surround all intrusive hyphal structures produced by mycorrhizal fungi. plasmanyl ether lipids Glycerophospholipids (primarily of the choline-linked family) in which position 1 of the glycerol backbone is linked via an ether linkage to a long-chain alcohol. plasmenyl ether lipids Glycerophospholipids (primarily of the ethanolamine-linked family) in which position 1 of the glycerol backbone is linked via a vinyl ether linkage to a long-chain alcohol. plasmids Extrachromosomal DNA present in bacteria and yeast and capable of replication independently of the chromosome. Most are in the form of a supercoiled circular double-stranded DNA, but some linear plasmids are known. Plasmids are used in recombinant DNA procedures as carriers for foreign genetic material. plasmodesmata (singular plasmodesma) Narrow channels through plant cell walls which provide cytoplasmic continuity between adjacent cells, enabling them to communicate with each other and to exchange metabolites. plasmodium (plural plasmodia) The multinucleated single-cell feeding stage of plasmodial slime moulds and some protostelids. In the plasmodial slime moulds, this cell can be very large and features the fastest rate of cytoplasmic streaming known in nature. plasmogamy The fusion of cytoplasm of two protoplasts. plasmolysis Shrinkage of the plant cell protoplast due to loss of water, forming a space between the plasma membrane and the cell wall. plasticity (1) The property of the potential for change or modification. In life sciences, the term is used, for example, to describe the capacity of a phenotype to vary according to environmental experience, and to describe the ability of the brain to make and reinforce new connections between neurons in response to experience. (2) Term used to describe the ability of a molecule to undergo structural changes without extreme input of energy. (3) The tendency of a material to change shape in response to an applied load. plastids Organelles in plant and algal cells that have a characteristic double membrane or envelope. Examples are chloroplasts and chromoplasts. plastochron, plastochron ratio The time interval between the initiation of successive leaf primordia. plastocyanin A soluble copper-containing protein found in the thylakoid lumen. Plastocyanin carries electrons from the cytochrome bf complex to photosystem I. plastoquinone A small organic molecule involved in electron and proton transfer in photosynthesis. Plastoquinone is found in the hydrophobic core of the thylakoid membranes and in the photosystem II reaction centre and cytochrome bf complex. plate tectonics The movement of segments of the Earth’s crust as a result of its production at mid-ocean ridges and burial in ocean trenches.

219

Glossary

platelet A small membrane-bound enucleate cell fragment (derived from megakaryocytes) present in large numbers in blood plasma (typically 2–2.5 Â 108 per ml). When exposed to extravascular components of injured tissue it releases factors that induce cell division and blood clotting. platelet-activating factor A molecule that induces blood platelets to release factors that induce cell division and blood clotting. It is a 1-alkyl phospholipid with an acetyl group in the 2-position. plating efficiency The proportion of phage particles that, when plated on a lawn of susceptible bacteria, will yield a plaque. platyrrhine A general term of primate classification used for the New World monkeys. PLC See phospholipase C. plectonemic joint molecule A DNA strand-exchange intermediate where the complementary strands of DNA are both base paired and intertwined. pleiotropic Describes a gene or mutation that affects more than one phenotypic characteristic. pleiotropy The multiple effects of a single gene on different organs, or organ systems. pleocytosis The presence of an abnormal (increased) number of cells in the spinal fluid. pleomorphic Exhibiting more than one distinct form. Having morphologically distinct stages in the life cycle. pleopods Abdominal arthropod appendages often used for swimming. plerology Similarity that arises as a result of gene rearrangement, either within or between genes. plesiomorphic Describes an ancestral character, in an evolutionary sense. plesiomorphy The original (primitive) state of a character. pleurae (singular pleura) The lateral parts of the trilobite’s thoracic segments, on either side of the upraised axis. plexus A network of vessels or nerves. In the latter case the nerves may split and exchange nerve fibres. ploidy The number of chromosome sets present in a cell or organism. Haploids have one chromosome set; diploids have two; and polyploids have more than two. plurilocular Describes multicellular gametangia and sporangia, each cell of which produces a single motile cell, which functions as a gamete or asexual spore, respectively. pluripotent Describes a cell that can give rise to a number of different cell types. pluripotent stem cell A stem cell that gives rise to many different types of terminally differentiated cells. plus end The end of a microtubule that is fastest growing. It is the natural end for the assembly of tubulin subunits, the end towards which the b subunits of tubulin dimers are directed, and the end towards which most kinesin motors translocate. plus end, minus end The fast and slow-growing ends, respectively, of a microtubule (occasionally also used to refer to the barbed and pointed ends of actin filaments). pluton A body of magma that has cooled at depth in a magma chamber. PNA See peptide nucleic acid. PNS See peripheral nervous system. PNS See postnuclear supernatant. poikilohydric Describes organisms that require high humidity but tolerate desiccation and rehydrate when favourable conditions resume.

poikilotherm A ‘cold-blooded’ organism whose body temperature is generally very close to environmental temperature. Elevation of body temperature may be produced by behavioural means such as basking, but not via biochemical reactions of heat production. poikilothermy Maintaining a variable body temperature equal to that of the surroundings. pointed end The slow-growing end of an actin microfilament. point mutation A change in a single base pair in the coding or noncoding region of a gene. Poisson correction A transformation applied to raw p-distance measurements to correct for multiple substitutions at a site. polar filament A thin multilayered tube made of protein and coiled around the internal periphery of the microsporidian spore. It is thought to evert when the spore germinates, thus pulling the sporoplasm through and injecting it into the host cell. polar pili Protein filaments located at the extremities of a bacterium. polar tube See polar filament. polarity (1) The direction of change of a character, from one state to another. (2) Having one end morphologically or biochemically distinct from the other. (3) Situation in which electrical charge is not distributed uniformly in an atom or molecule. polarizability Response of a molecule’s electron density to an applied electric field or the reponse of a material to an applied field. polaroplast A highly membranous structure attached near the base of the polar filament and located behind the anchoring disc at the anterior of the microsporidian spore. pollen The mass of male gametophytes, or pollen grains, of a seed plant, which are produced within the anther. Each pollen grain contains three cells: two sperm and a vegetative cell that grows a pollen tube in order to deliver sperm to embryo sac. poly(A) signal DNA sequence transcribed as part of an mRNA that determines the formation of the 30 end of the mRNA and the addition of the polyadenylate tail. poly(A) tail A homopolymer of adenine ribonucleotides that is added to the 30 end of eukaryotic mRNAs after transcription. polyacetate A polyketide metabolite synthesized only from an acetate starter and n-malonyl extenders. polyacrylamide gel electrophoresis (PAGE) A technique for the separation of molecules from complex mixtures (proteins and nucleic acid fragments) by their differential migration in an electric field in a polyacrylamide gel. It is typically used to separate DNA fragments between 10 and 1500 bp long. polyadenylation The post-transcriptional addition of a string of nontemplated adenine nucleotides to the 30 end of an mRNA molecule. polyandry The situation where females mate with several males, usually within the same reproductive period. Poly-b-hydroxyalkanoate granules Intracellular deposits of alkanoate polymers formed in some bacteria. Poly-b-hydroxybutyrate granules A type of polyhydroxyalkanoate granule. polycistronic Describes a bacterial messenger RNA containing the coding sequences for more than one protein. polycistronic transcript An mRNA molecule resulting from the continuous transcription of several adjacent genes. polyclonal Composed of several different clones of cells. polyclonal antibodies The mixture of antibodies usually evoked by a single antigen, which contains antibodies that recognize different epitopes on the antigen.

220

Glossary

polycythaemia An increase in the proportion of cellular components of the blood with an inevitable decrease in the plasma component, which may have adverse effects. polydentate binding An association between different molecular species in which noncovalent interactions (binding) take place at several sites in each molecule. polyembryony The formation of more than one embryo in the ovule. polygenic Caused by or involving many genes. polygonum-type embryo sac The most common type of embryo sac in higher plants (named after the plant Polygonum divaricatum). It is an eight-nucleate embryo sac derived from a single spore. polygyny The situation where males mate with several females, usually within the same reproductive period. polyhedral bodies Inclusions possessing many faces. polyhydramnios An abnormal condition of pregnancy when there is excess production of amniotic fluid in the uterus. polyketide A secondary metabolite formed by a common biosynthetic pathway involving decarboxylative condensation of malonyl units. polymer A large molecule formed by connecting many chemically similar small molecules (monomers) together, usually in the form of a chain or network. Proteins (polypeptides) are polymers of amino acids. Nucleic acids (DNA and RNA) are polymers of deoxyribonucleotides and ribonucleotides respectively. Polysaccharides are polymers of sugars. polymerase In the most general sense, an enzyme that catalyses the reactions that connect molecular subunits to one another to form polymers. Most commonly refers to any of the enzymes that catalyse the assembly of ribonucleotides or deoxyribonucleotides into RNA (transcription) or DNA (replication). DNA polymerases catalyse the production of DNA molecules. RNA polymerases catalyse the production of RNA molecules. polymerase chain reaction (PCR) An in vitro method for specifically amplifying a given sequence in a DNA molecule. polymorphic Existing in many different forms. polymorphism (1) The existence of a character, or a gene, in two or more forms in a population, where the least common form is present in more than 1% of individuals. (2) A region of DNA sequence that differs from allele to allele. polymorphs Polymorphonuclear leucocytes or neutrophils, phagocytic, antimicrobial white blood cells with irregularly shaped nuclei. polymorphonuclear leucocyte See neutrophil. polymyositis polyneuropathy Any systemic disorder of the peripheral nerves of toxic, metabolic or unknown aetiology. polypeptide A linear polymer of amino acids covalently linked to one another through bonds called ‘peptide bonds’. Geneticists tend to distinguish between a polypeptide, by which they mean the linear chain of amino acids, and a protein, in which the chain is folded into a three-dimensional conformation. polyphenism The situation when an organism is able to produce two or more distinctive phenotypes in response to environmental cues. It contrasts with polymorphism, which is based on genetic differences. polyphosphate granules (bodies) Intracellular deposits of condensed phosphates. polyphyletic Having distinct evolutionary histories. The term describes a group of organisms that are classified together, often because of convergent evolution, but are derived from a number of different ancestral species, so that they are not all descended from a common ancestor that was a member of that group.

polyphyletic group A group of species that does not include their single, common ancestor. polyphyletic origin Describes a trait that has been independently established in a number of different lineages. Polyplacophora The chitons, a class of the phylum Mollusca. polyploid (1) Possessing three or more sets of chromosomes. (2) Having more than one copy of the virus genome per virus particle. polyploidy The condition in which there are three or more sets of chromosomes in a cell. polyprotein A long polypeptide which is composed of the sequences of several different proteins, which are subsequently released by protease cleavage. polysaccharide A polymer of more than 20 monosaccharide units joined into a linear or branched chain through glycosidic bonds. polysaccharide-protein A compound of plant origin in which one or more polysaccharide structures are covalently attached to a polypeptide chain. polysialic acids Natural polymers of N-acetylneuraminic acid (sialic acid). polysome A messenger RNA molecule with two or more translating ribosomes attached. polysomnography A formal study of sleep, which is used to detect obstructive sleep apnoea. polyteny The condition when a chromosome is composed of many identical DNA duplexes, which is caused by many rounds of DNA replication not followed by separation. polytypic species A species constituted of two or more locally adapted populations (subspecies), with little gene flow among them. polytypism The existence of two or more genotypically/phenotypically distinct populations of the same species that have been recognized as geographic races or subspecies. poly(U) A polynucleotide composed of uridine nucleotides only. polyuria–polydipsia Combination of excessive thirst (polydipsia) and excessive urine output (polyuria). population A group of organisms of the same species occupying the same area and isolated to some degree from other populations. population bottleneck A period during which a population is of greatly reduced size and genetic drift plays a larger role than usual in changing allele frequencies. population doublings The estimated number of times the cell number in a culture has doubled. population viability analysis The use of mathematical models to determine the likely viability of a population in the future. population-specific allele See private allele pore Conductive pathway through e.g. a membrane, which is generally always open. porphyria A disorder of haem metabolism that can be either genetically transmitted or induced by certain chemicals. portal vein A blood vessel that joins a set of capillaries in one organ with another so that substances can pass directly between the two organs. position effect variegation (PEV) The silencing of a gene in some, but not all, of the cells in which it is normally expressed, which e.g. gives rise to a variegated appearance of the structure. The silencing is due to a chromosomal rearrangement that brings the gene under the influence of heterochromatin. positive chemotactic stimulation An increasing gradient of chemoattractant or a decreasing gradient of chemorepellent.

221

Glossary

positive eugenics Programmes, techniques or social policies that encourage and favour reproduction among individuals believed to carry desirable genes. positive feedback The type of control in a metabolic or signalling pathway in which a late stage in the pathway has a reinforcing effect on early stages. post ribosome The post-translocational state of a ribosome, with deacylated tRNA in the E site and the peptidyl-tRNA in the P site. postcranial That part of the skeleton of vertebrates that is behind, or beneath, the cranium. It includes the vertebral column, both limb girdles and all four limbs. posterior Towards the tail end of an organism. The anteriorposterior axis of a vertebrate organism, for example, runs from the tip of the nose, snout or beak to the tip of the tail. posterior fossa The posterior and inferior portion of the cranium that contains the brainstem and cerebellum. posterior vacuole A large vacuole at the posterior of the microsporidial spore. It is thought to be the part of the extrusion apparatus responsible for pushing the cytoplasm out of the spore during germination. postganglionic sympathetic Describes neurons of the peripheral autonomic nervous system normally projecting from the paravertebral or prevertebral ganglia. postmitochondrial supernatant The fraction of a cell homogenate that remains after removal of mitochondria and other large subcellular particles by centrifugation. postnuclear supernatant (PNS) Cell homogenate containing membranes and cytosol after removal of nuclei by slow-speed centrifugation. postpartum oestrus The oestrus that occurs immediately after giving birth. postsynaptic Refers to the cell that is on the receiving side of a synapse. postsynaptic membrane The plasma membrane of the cell on the receiving side of a synapse. postsynaptic potential (PSP) The change in membrane potential in a postsynaptic (receiving) neuron or muscle cell caused by the action of transmitter released from the presynaptic neuron on postsynaptic receptors. post-temporal canal An opening on each side of the posterior part of the skull in certain reptiles, retained in monotremes. post-tetanic potentiation (PTP) See potentiation. post-transcriptional gene silencing A reduction in gene expression associated with a sequence-specific degradation of RNA in the cytoplasm. post-transfer editing Hydrolysis of misacylated tRNA with the liberation of free noncognate amino acid and tRNA. post-transfusion purpura Thrombocytopenia caused by destruction of transfused and autologous platelets, occurring about 1 week after blood transfusion and associated with the presence of anti-platelet alloantibodies. post-translational Occurring after translation is complete. post-translational modification Any modification that occurs to a polypeptide chain after its synthesis is complete. potentiation Slowest phase of enhanced transmission in shortterm synaptic plasticity, lasting minutes. potocytosis Mechanism for the cellular uptake of small molecules or solutes independent of endocytosis but mediated by caveolae. pouch A fold of abdominal skin around the mammary glands of a monotreme or marsupial.

power Rate of energy use or production or of doing work. It is measured in watts (W) (= joules (J) per second (s)). ppGpp Guanosine 30 ,50 -bis(diphosphate). An ‘alarmone’ synthesized by bacteria to overcome amino acid starvation and involved in growth rate regulation. ppm Parts per million, a measure of concentration. pRb See Rb preacquisition fasting period Fasting of aphids for a defined period prior to allowing acquisition of virus. Such a period is mostly needed for nonpersistent viruses. pre-B cell A stage in the development of B cells that occurs between the pro-B cell and the immature B cell. Pre-B cells express a complete m heavy chain but have not yet rearranged the lightchain genes. Prebilateria A group of primitive animal phyla that do not display bilateral symmetry and are believed to have evolved before the bilaterians. precursor cells Cells that are committed to a particular cell lineage but are still in a process of developing the characteristics of that cell type. precursor frequency The frequency of a lymphocyte subset with a given antigen specificity. pre-eclampsia Pregnancy-specific syndrome associated with new high blood pressure and proteinuria, appearing in the second half of pregnancy and resolving after delivery. pre-mRNA The unspliced precursor to messenger RNA. prenatal diagnosis The detection of fetal abnormality during pregnancy. pre-pro-B cells The earliest precursors of B cells identified so far. They have DH and JH gene segments of the immunoglobulin genes rearranged but not the V gene segments. pre-ribosome The pretranslocational state of a ribosome, with peptidyl-tRNA in the A site and deacylated tRNA in the P site. presoma The anterior portion of the two-segmented preparasitic larva of nematomorphs, which contains the reversible proboscis. Also called the preseptum. presomatic cell A cell that undergoes chromatin diminution in e.g. Parascaris, and thus will become a somatic cell. prespore See forespore. presynaptic Refers to the cell that is on the transmitting side of a synapse. presynaptic facilitation Enhanced transmission from a synaptic terminal of a neuron (the presynaptic cell) onto a target postsynaptic cell that results from the action of a third neuron (the facilitator cell) synapsing onto the axon terminal of the presynaptic cell. pretransfer editing In tRNA synthetase proofreading of amino acids, the destruction of noncognate aminoacyl adenylate, usually by hydrolysis to free noncognate amino acid and AMP. prevacuole A membrane-bounded compartment in eukaryotic cells intermediate between the Golgi and the vacuoles. prevalence The percentage of a host population that is infected by symbionts. primary cell wall A polysaccharide-enriched matrix that encapsulates growing plant cells. primary culture A culture of unpassaged cells isolated directly from tissue, organs or body fluids. primary image plane An image of the object is formed at the primary image plane owing to interference between those beams diffracted by the specimen and the undiffracted (zero order) beam.

222

Glossary

primary immune response The immune response to an initial exposure to antigen. primary immunodeficiency disease Immunological disorder resulting from an inborn defect of the immune system. primary root Root that has its origin in the plant embryo. primary structure The sequence of amino acids along the polypeptide chain of a protein. primary transcript The order or sequence of nucleotides, from the 50 to 30 end, within a strand of RNA exactly as it is transcribed from the DNA, before processing. primer (1) A short sequence of RNA synthesized on the DNA template that provides a startpoint for the synthesis of a DNA strand in DNA replication. After DNA synthesis is complete, the RNA is removed and replaced with DNA by repair enzymes. (2) A short oligonucleotide of specific sequence that is used to define the startpoint for DNA synthesis in the polymerase chain reaction. See also mutagenic oligonucleotide primer. primitive In the context of taxonomy, a species with relatively few specialized features, thus indicating that it is closer to the morphology of the earliest members of an evolutionary lineage. primitive ectoderm See epiblast. primitive haematopoiesis Formation of blood cells that occurs before birth or hatching, usually marked by the expression of different globin genes and cell morphology. primitive life A chemical system capable of self-reproduction and evolution. primitive streak A narrow elongated region of mesoderm internalization in early bird and mammalian embryos, indicating the axis along which gut and notochord will form, and the anteroposterior axis of the embryo. primordial germ cell A cell which is the precursor of germ cells only. primordial leaf A leaf in the earliest stages of its development, as it starts to form on the shoot meristem. primordium (plural primordia) A structure in its most rudimentary form, at a very early stage in its development. PRINS See primed in situ labelling. prion Infectious proteinaceous particle that is a conformational isoform of a normal cellular protein. Prions are thought to be responsible for some degenerative diseases of the central nervous system, such as Creutzfeldt–Jacob disease in humans, and bovine spongiform encephalitis (BSE) in cattle. prismatic Showing crystalline structure. prismatic cartilage Outer layer of cartilage in sharks, arranged in crystalline prisms. private allele A genetic variant, evolved by mutation in a specific population, which did not get a chance to spread to other populations of the species. probe (1) A short oligonucleotide (DNA or RNA), usually labelled, that is used to detect the complementary sequence in a DNA by hybridizing with it. (2) A fluorescently or radioactively labelled antibody or other protein that is used to label a cellular structure or particular molecule in a sample. (3) A fluorescent molecule whose emission is used to analyse a sample. procambial initial A precursor cell in the procambium that can differentiate into various types of vascular cells including tracheary element, xylem parenchyma cell, cambial cell, sieve element and phloem parenchyma cell. procambium Cells destined to become the primary vascular tissue in plants.

processivity The property of DNA and RNA polymerases that enables them, once bound, to move along the template, successively adding nucleotides to the growing DNA or RNA strand. processivity error An error in translation in which peptidyl-tRNA is prematurely released. The corresponding nascent peptide is shorter than the mature protein and is thus usually nonfunctional. procoracoid A bone that connects with the shoulder, the scapula and the interclavicle, forming a bony bridge in the pectoral region. procumbent Protruding anteriorly. prodrome Symptoms of yawning, euphoria, unbridled energy or depression, or craving or distaste for various foods, that occur in the 24 hours before a migraine headache. producer An organism, such as a photosynthetic, photolithotrophic or chemotrophic organism, that can utilize solar energy or energy derived from inorganic chemicals to manufacture its own food (carbohydrates) from carbon dioxide. Producer organisms are the basis of all life on Earth and support the remainder of the food chain. proecdysis See moult cycle. proenzyme A precursor form of an enzyme that has not yet been activated to its final functional form. Activation is usually achieved by cleaving an inhibitor domain from the protein. progametangium (plural progametangia) A swollen hypha that will differentiate into the gametangium and suspensor. progenitor A precursor cell that has not yet undergone maturation of differentiation and maintains the ability to divide. progenote A putative ancestral organism from which all extant organisms are thought to have derived. programmed cell death A regulated mechanism of cell death by apoptosis that eliminates cells in a predictable fashion, without damage to the organism, suggestive of an underlying developmental or genetic programme. It is common during development, e.g. in the formation of the digits of hands and feet, and in the resorption of the tadpole tail during metamorphosis. progress zone Mesenchyme at the distal tip of the limb. The progress zone mesenchyme is kept in an undifferentiated and proliferative state by signals from apical ectodermal ridge. Call fate specification is believed to occur in the progress zone. prohaemocyte A stem cell from which other haemocyte types originate in invertebrates. It is characterized by a nucleus that almost fills the cell and the absence of intracytoplasmic granules. prokaryotes The members of the Bacteria and the Archaea. They are small single-celled micoorganisms (about 1–2 mm in diameter) whose DNA is not enclosed in a nucleus and in which the cytoplasm is not compartmented into membrane-bounded organelles. prokaryotic Pertaining to prokaryotes. prokaryotic cells See prokaryotes. Prolacertiformes An important group of Triassic reptiles closely related to the archosaurs, the group that gave rise to the dinosaurs. They were generally lizard-like in body plan and commonly had a narrow skull and long snout. proliferation Increase in the number of cells by means of mitotic cell division. promastigote The stage of Leishmania that occurs in the insect vector.

223

Glossary

promiscuity In the molecular context, the tendency of a molecule to bind to many alternative ligands rather than to have a strict specificity for only one other molecule. promoter A region of DNA that is typically located immediately before a gene and that contains signals for initiating transcription of the gene. It contains the binding site for RNA polymerase and its ancillary factors. pronephros The first embryonic kidney in vertebrates, maintained only in some fishes. proneural Describes genes whose activity pushes cells towards a neural fate. proofreading In the context of translation, the ability of aminoacyl-tRNA synthetases to prevent or correct mistakes in the aminoacylation of tRNA. pro-oxidant Stimulating or catalysing oxidative reactions potentially damaging to cells. propagule pool colonization The founding of a new population with colonists derived from a single source population. prophage The bacteriophage genome in a state when it is not producing new phage particles. The genome may be integrated into the DNA of the host bacterial cell or be replicating as a plasmid. prophenoloxidase An enzyme precursor stored in granulocytes and which produces a functional phenoloxidase when activated by enzymatic cleavage. prophylaxis Prevention of disease, for example, by antibiotic administration before surgery. prosimian A general term of primate classification that includes the lemurs, lorises and the tarsier, even though tarsiers are more closely related, evolutionarily, to anthropoids. prosoma The anterior body region of chelicerates. It is composed of six appendage-bearing segments and is typically covered by a dorsal carapace bearing the eyes. prosome The first body section of a phoronid, represented by the epistome in the adult and by the preoral lobe in the actinotroch larva. prospective study See observational study. prostaglandins A class of derivatives of the unsaturated fatty acid arachidonic acid, formed via the cyclooxygenase pathway. They are involved in many biological processes, including the contraction of smooth muscle, the development and control of inflammatory responses, the regulation of body temperature, and the sensing of pain. protandry Ambisexuality where the individual functions first as a male, then as a female. protease An enzyme that can cleave a protein at a peptide bond. Some proteases cut nonspecifically, catalysing the breakdown of proteins to peptides and amino acids; others selectively cut at a certain combination of amino acids. proteasome Large catalytic multisubunit protease located in the cytoplasm which degrades cytosolic proteins. protected areas Areas managed primarily for the protection of species, biological communities and other aspects of biological diversity. protein A large organic molecule made up of one or more polypeptide chains folded into the appropriate three-dimensional configurations and sometimes modified by the addition of carbohydrate units, phosphate groups, or other chemical adducts.

protein b sheet A secondary structure in proteins that is formed when two or more almost fully extended polypeptide chains are brought together side by side so that hydrogen bonds form between the peptide amide NH and carbonyl oxygen groups of adjacent chains. protein binding motif An amino-acid sequence that is present in several proteins that can interact with an RNA molecule. protein disulfide isomerase An abundant enzyme in the endoplasmic reticulum that catalyses disulfide bond formation and isomerization during protein folding. protein domain A compact structurally discrete portion of a protein, usually with a particular function. protein electrophoresis A technique used to separate different forms of a protein on the basis of their different rates of movement in response to an applied electric field through a liquid or a gel. protein family A group of proteins that are suspected to be evolutionarily related on the basis of their amino acid sequence or folding pattern. protein folding The process by which a linear polypeptide chain spontaneously folds into its functional three-dimensional native conformation. protein kinase An enzyme that transfers phosphate groups from ATP to proteins, usually phosphorylating the protein at serine, tyrosine or threonine residues, depending on the type of kinase. protein kinase C (PKC) An intracellular enzyme that is activated by a variety of signal transduction events and functions to phosphorylate specific proteins. protein module Any protein domain or protein sequence that is used repeatedly as a building block in diverse, mostly extracellular, proteins. protein phosphorylation The addition of a phosphate group to protein, usually catalysed by a protein kinase. protein synthesis The biosynthesis of a protein on a ribosome by the linking together of amino acids in a sequence directed by a messenger RNA. protein targeting The allocation of a protein to a specific region or organelle within the cell, or for secretion. The targeting is mediated by specific sequences within the protein. protein tertiary structure The overall spatial arrangement of amino-acid residues within a single folded polypeptide chain. proteinase inhibitors Small peptides, rather resistant to degradation, with inhibitory activity towards proteinases (proteases). protein-tyrosine kinase An enzyme that phosphorylates a protein at tyrosine residues. protein-tyrosine phosphatase An enzyme that cleaves phosphate groups from tyrosine residues in a protein. proteinuria The presence of excessive amounts of protein in the urine. Proteobacteria The largest and physiologically most diverse group of bacteria, grouped into five subclasses by probable sharing of ancestry with phototrophic purple bacteria. proteoglycan A protein to which long glycosaminoglycan (carbohydrate) chains are attached. The carbohydrate frequently accounts for much of the net mass of the molecule. proteolytic cleavage Trimming of proteins or peptides into smaller fragments by specific enzymes, i.e. proteases. proteolytic processing The process by which one or more smaller protein molecules are generated from a larger precursor by sitespecific cleavage catalysed by a protease. proteome All the proteins expressed by a cell.

224

Glossary

Protista, protists Unicellular, coenocytic or simple multicellular eukaryotic organisms that are not classified as fungi, animals or plants. protogny Ambisexuality where the individual functions first as a female, then as a male. proton electrochemical potential (DmH1 ) A measure of the potential (typically in mV) across a biological membrane due to a proton (H1 ) gradient. It is composed of a membrane electrical potential (Dy) and an ion concentration gradient (DpH). proton gradient An unequal distribution of H1 ions (protons) on both sides of a membrane. protonephridium (plural protonephridia) Excretory organ in larva of Kinorhyncha, Phoronida and Entoprocta. It is closed at its inner end and opens to the exterior by the nephridiopore. proto-oncogene A gene that encodes a protein required for normal cell survival and/or proliferation, but which can give rise to an oncogene after mutation or activation. When the mutant gene was originally found in a transforming retrovirus, the name of the cellular form of the gene may be prefixed with a ‘c-’, and the viral form prefixed with ‘v-’ (e.g. c-src and v-src). protoperithecium The female sexual organ of certain ascomycetes. protoplast A cell including the plasma membrane but excluding the cell wall. Protostomia, protostomes Animals that are characterized by certain patterns of development, e.g. formation of the mouth at the location of the primary invagination (the blastopore). They include Arthropoda (insects, crustaceans, etc.), Annelida (earthworms, polychaetes, etc.) and Mollusca (clams, snails, etc.). protostomy Describes a pattern of development in which the site of the primary invagination in the early embryo becomes the mouth. prototroph A bacterium (or other microorganism) that has no specific nutritional requirements for growth. prototrophy A phenotypic state in which a particular nutrient does not need to be supplied for growth. A prototrophic strain resembles the wild-type strain with respect to its ability to grow without a particular nutrient. protozoa A large, rather arbitrary, group of single-celled nonphotosynthetic eukaryotic microorganisms lacking cell walls, and thus resembling animal cells rather than plant or fungal cells. protraction Forward and/or upward motion of an anatomical element relative to an overall muscle–bone apparatus. provirus Double-stranded DNA copy of a retroviral genome integrated into host chromosomal DNA. pruritus (1) A condition that has as the dominant symptom a desire to scratch some part of the body to relieve irritation. (2) A sensation that elicits the desire to scratch. pseudarthrosis An ‘artificial joint’ that forms at the site of a fracture as a consequence of persistent nonunion of the fracture ends. pseudoautosomal region A region common to the X and Y chromosomes in which pairing and recombination may take place. pseudocoelom In nematodes, the fluid-filled space separating the ectodermal–mesodermal layer from the endodermal layer. pseudocolour A colour representation of a grey scale, defined by the user. pseudocospeciation A match between host and parasite phylogenies that is due to cospeciation.

pseudogamy A form of apomixis in which meiosis does not occur, but development of the embryo requires fertilization of the central cell by a sperm from pollen. pseudoknot See RNA pseudoknot. pseudomurein An archaeal analogue of peptidoglycan consisting of alternating N-acetylglucosamine and N-acetyltalosaminuronic acid linked by b1,3 bonds. It occurs in Methanobacterium, Methanobrevibacter and Methanosphaera. pseudomurein Cell-wall peptidoglycan of some methanogenic Archaea that lack muramic acid. pseudomycelium A group of budding yeast cells in a tree-like formation of branched chains. pseudopersistent transmission Type of transmission of viruses found in some nematode vectors. it resembles stylet-borne transmission, but with long retention times, giving a false impression of persistent transmission. pseudopodia (singular pseudopodium) Mobile finger-shaped, lobose or net-like projections extended from the surfaces of certain cells, e.g. some protozoa, and typically associated with shape change and movement resulting from cytoplasmic flow within the projection. pseudorevertant Descendant of a mutant in which the negative effect of a mutation has been neutralized by a compensatory mutation at a site in the genome different from that of the initial mutation. pseudotypes Virus particles produced during replication of heterologous viruses in the same host cell in which the genome of one virus is contained within the coat or envelope of another virus. pseudouridine (Y, W) 5-Ribosyluracil, a C-glycoxyl isomer of the classical N-glycosyl nucleoside, uridine (1-ribosyluracil). It contains the only C–C ‘base–sugar bond’ in RNA and is the most abundant modified nucleotide in RNA. PSP See postsynaptic potential. psychrophiles Microorganisms whose optimum temperature for growth is below 201C. Some psychrophilic algae can grow near 01C. pteridophytes Plants (e.g. ferns) in which sexual reproduction does not involve seed production, and in which there are independent alternating sexual (gametophyte) and asexual (sporophyte) generations. pterodactyloids Advanced, short-tailed, Jurassic and Cretaceous pterosaurs 0.3–12 m in wingspan. PTH See phenylthiohydantoin. PTP Post-tetanic potentiation. See potentiation. PTS1, PTS2 See peroxisomal targeting sequence type 1; peroxisomal targeting sequence type 2. P-type ATPases A superfamily of transmembrane proteins with ATPase activity that use the energy released by hydrolysis of ATP to transport ions across membranes. The enzymatic mechanism of P-type ATPases involves a phosphorylated intermediate, hence the name P-type. puberty The time when an animal becomes capable of breeding, normally coincidental with the start of gametogenesis. Pulmonata, pulmonates, pulmonate molluscs Subclass of the class Gastropoda comprising snails and slugs, in which the mantle cavity is used as a lung. pumps Transmembrane proteins that (usually) use the energy of ATP hydrolysis to move ions from one side of the membrane to the other, typically against a concentration gradient.

225

Glossary

punctuated equilibrium A theory of evolution that, in contrast to phyletic gradualism, relates most evolutionary change to rapid branching events, with periods of relative stasis between speciations. purines, purine bases One of the two common types of bases in nucleotides. They are composed of a heterocyclic pyrimidine ring combined with an imidazole ring. The purines in nucleic acids are adenine and guanine. Purkinje cell A type of large neuron that extends characteristic planar dendrites, forming a layer in the cerebellar cortex and providing its sole output. purple membrane Regions of the cell membrane of halobacteria that contain a two-dimensional crystalline array of the lightdriven proton pump bacteriorhodopsin, which has a purple colour. purpura Small bruises on the skin caused by the coalescence of small pinpoint-sized skin haemorrhages called petechiae. purulent infections Infections caused by extracellular pathogens such as streptococci or staphylococci, which cause pus-forming lesions (abscesses) that are composed mainly of polymorphonuclear leucocytes and bacteria. pygidium The tail of a trilobite, often rounded or triangular in form, and made of fused segments like those of the thorax. pyloric caeca Blind, finger-like projections of the proximal intestine just beyond the pyloric sphincter of the stomach. pyrenoid Specialized region in the chloroplast involved in starch formation. pyridone ring Compounds based on the 5- carbon, 1-nitrogen ring system. Pyridones carrying iodine were used as early X-ray contrast agents. pyridoxal phosphate Chemical name for vitamin B6, found as a cofactor in enzymes. pyrimidine tract binding protein (PTB) A protein that binds to pyrimidine-rich sequences in RNA. pyrimidines One of the two types of bases in nucleotides. They are heterocyclic six-membered rings. The pyrimidines in nucleic acids are uracil, cytosine and thymine. pyrophosphate (O)3P–O–P(O)3.

R gene A host resistance gene that specifically recognizes a gene product (Avr) of the pathogen. Note this narrow definition of an R gene, as compared to any other host gene that confers resistance to a pathogen and can be called a ‘resistance gene’. R plasmid A plasmid containing antibiotic-resistance gene(s), which confers resistance to those antibiotics on the bacterium carrying it. R0 Index used in epidemiology, indicating the number of secondary cases that could originate from a single index case of virus infection. RAD52 epistasis group A group of genes, first identified in the yeast Saccharomyces cerevisiae, which act in concert to achieve homologous recombination in eukaryotic cells. radial distribution function (rdf) Probability that one molecule or atom will be at a certain distance from another molecule or atom. radiation hybrid A hybrid cell formed by fusing an irradiated donor with an unirradiated host cell. The hybrid retains some fragments of the donor’s chromosomes.

radiocarbon dating A method of dating based on the decay rate of carbon-14 (14C) in organic materials such as wood. radiograph An image obtained using X-rays and a film (or socalled film-screen combination). radioisotope A radioactive atom possessing a different number of neutrons from its parent atom. In biology, radioisotopes of common biological atoms such as phosphorus and sulphur are used to label biological molecules for detection purposes or for use as tracers. Radiolaria, radiolarians Subclass (phylum Circadian, class Actinopoda) of tiny marine planktonic protozoans that secrete spheroidal to bell-shaped silica tests. They are important sediment formers in the deep sea. Present from the Cambrian to the present-day. Radiology Information System (RIS) A computer system (in the past, usually mainframe types; more recently, powerful PCs) that handles workflow components of a radiology practice including scheduling, billing and reporting. RAG1, RAG2 Recombinase-activating genes that encode the subunits of a heterodimeric protein required for recombination of V, D and J gene segments during antigen-receptor gene rearrangement in lymphocytes. Ran A small, Ras-related GTP-binding protein that is central to the nuclear transport cycle. The yeast homologue is called Gsp1p. random amplified polymorphic DNA (RAPD) DNA synthesized via a polymerase chain reaction using arbitrary primers, which results in DNA fragments of varying lengths that give a specific banding pattern when separated electrophoretically. random genetic drift The chance fluctuations of allele frequencies within a population from generation to generation as a result of chance events such as sampling of gametes. The smaller the population, the greater the random fluctuations in gene frequency will be. random walk A trajectory in space characterized by a sequence of steps in which each new step is taken in a random direction. randomized controlled trial A trial in which participants have been randomly assigned to intervention with a treatment. range In palaeontology, the observed distribution of fossil finds describing the span between the oldest and youngest finds. If sampling were perfect, a taxon’s range would be its duration. range extensions Hypothesized extensions of observed ranges implicit to particular estimates of phylogeny. RAPD See random amplified polymorphic DNA. raphe A longitudinal slit in one or both surfaces of a diatom cell wall, necessary for movement to occur, and found only in pennate diatoms. rare-allele advantage See frequency-dependent selection. rate equation Differential equation describing the change of concentration of a reaction component over time. ratite Describes a bird having a keelless sternum, the converse of carinate. A member of the Ratitae. RB See Rb. Rb The retinoblastoma protein (Rb or RB depending on species), a regulatory protein of the eukaryotic cell cycle. It is an important tumour suppressor protein, whose absence leads to the eye tumour retinoblastoma. RD gene A gene situated in the class III region of the human major histocompatibility complex between the BF and C4A complement genes. rdf See radial distribution function. rDNA Genes that encode the ribosomal RNA (rRNA).

226

Glossary

reaction centre, reaction centre complex A chlorophyll– protein complex that uses light energy to create a stable charge separation from the excited chlorophyll or bacteriochlorophyll. A single electron is transferred energetically uphill from the donor molecule to an acceptor molecule, both of which are located in the reaction centre. reaction coordinate The single vibrational mode of a reaction assembly that has no restoring force, and hence an imaginary frequency. reaction norm The range of possible phenotypes that a single genotype can express along an environmental gradient. reactivation Causing something to function again when it has ceased functioning. For example, the procedure by which isolated subcellular organelles are ‘brought back to life’, usually by the addition of ATP. reactive amyloidosis Extracellular accumulation of amyloid protein fibrils in various organs and tissues of the body secondary to a chronic inflammatory disease. reactive gliosis Strong proliferation of reactive, swollen astrocytes accompanied by an accumulation of microglial cells at affected brain areas. While not specific for prion diseases, gliosis is extremely prominent in Creutzfeldt–Jakob disease and scrapie. reactive oxygen species Collective term used by biologists to designate the oxygen radicals (e.g. O2À, OH) and certain nonradical derivatives of O2, such as hydrogen peroxide (H2O2). reactogenic Capable of causing an unwanted side reaction, as in ‘reactogenic vaccine’, e.g. causing fever, rash or excessive local inflammation. reading frame In a protein-coding mRNA, the translation machinery has to start at a particular point in order to read off the correct sets of three nucleotides (codons) as it moves along the RNA. There are three possible reading frames in any sequence, only one of which usually encodes a functional protein. realism The philosophical thesis that classes are real, contrasted with nominalism. realized heritability A measure of a trait’s heritability based on the trait’s response to selection over multiple generations. reassociation The formation of a duplex by two nucleic acid strands (DNA, RNA or both) having complementary base sequences. reassortment The process of random redistribution of genomic RNA segments into new virions following simultaneous infection of a cell by different strains. The resulting viruses are known as reassortants. RecA protein A 38 kDa bacterial protein that plays a key role in homologous recombination by catalysing homologous pairing and strand exchange between the recombining DNA molecules. recalcitrant seeds Seeds whose viability is lost on drying and also on freezing. recalcitrant Describes a compound that resists breakdown to its mineral constituents. The term should not be confused with xenobiotic, although they are often used with the same meaning. For example, lignin is recalcitrant, but not xenobiotic as it is of organic origin. recapitulation The biogenetic law according to which the evolutionary history of a species (phylogeny) is repeated in a speededup form in the embryological development of the individual organism (ontogeny).

receptor (1) A protein molecule that recognizes and binds another (the ligand) with high affinity and specificity, the binding event usually triggering a biological response in the cell carrying the receptor, although some receptors may simply act as ‘passive’ carriers. (2) A cell-surface protein that is used by a virus for attachment. receptor channel An ion channel in which a receptor site for a neurotransmitter forms an integral part of the channel itself, and binding of the neurotransmitter is responsible for channel opening, for example the nicotinic acetylcholine receptor channel. receptor integral anion channel An anion-selective aqueous pore formed within a receptor protein. receptor-mediated endocytosis Internalization of a protein after it has bound to its receptor at the cell surface. recessive allele Allele that has to be present in two copies at a locus for its phenotype to be expressed. In heterozygotes with a dominant allele, the recessive phenotype is obscured by that of the dominant allele. Recessive alleles usually encode an inactive version of the gene product or an absence of the gene product. recessive mutation A mutation that results in a phenotypic effect only when in the homozygous state. In the heterozygous state the normal allele prevails over the mutant allele. recessiveness When the phenotype of the Aa heterozygote is identical to the phenotype of the AA homozygote, the a allele is said to be recessive to the A allele. reciprocal synapse A specialized type of synapse in which the two cells on either side can both transmit and receive. reciprocal translocation A translocation in which part of one chromosome is exchanged with part of a different, nonhomologous, chromosome. reciprocity The situation in which an action at one point, which produces an effect at a second point, can be assumed to provide an accurate model of the performance at the first object of an action at the second. recirculation Continuous migration of mature lymphocytes from the blood to the secondary lymphoid organs and from there via lymphatic vessels back to the blood. recoding Reprogrammed genetic decoding. Three classes have been identified: the meaning of specific codons can be redefined; reading frames can be switched by ribosomal frameshifting; blocks of nucleotides within a coding sequence can be bypassed by ribosomes. recoding site A sequence in an mRNA that contains special elements, often including a stop signal, and where an alternative genetic event occurs other than those characteristic of normal protein synthesis. recognition (1) The rejection and selection of taxa that occurs during the establishment of a symbiosis, resulting in the observed specificity of a symbiosis. (2) In cell and molecular biology, the highly specific interactions that occur between different proteins and between proteins and DNA sequences. recognition sequence DNA sequences recognized by restriction enzymes. recognition species concept The idea of a species in which the members share a specific mate-recognition system, ensuring effective syngamy within a population occupying a preferred habitat.

227

Glossary

recombinant (1) Pertaining to DNA into which a foreign gene has been introduced by genetic engineering. (2) Pertaining to a protein produced by a microorganism whose DNA has been engineered in order to produce it. recombinant DNA A single DNA molecule formed by joining together DNA molecules from different sources (e.g. genes from different parts of the same genome, or DNA from different organisms). recombinant virus A virus that has been genetically manipulated to incorporate a foreign gene into its genetic material. recombinase A protein that mediates a DNA rearrangement reaction (recombination). recombination (1) The exchange of similar or dissimilar sequences between two DNA molecules. (2) Any process that gives rise to cells or individuals in which parental alleles have been inherited in new combinations. recombination mediators Accessory factors that function to enhance the activity of a recombinase. recombinational repair A DNA repair process involving an interaction between a damaged DNA molecule and a separate DNA duplex with homology to the damaged region. It proceeds by reactions very similar to those of genetic recombination. reconstitution The bringing together of separate cell components, each individually inactive, but which together can carry out a given reaction. reconstruction Process by which data acquired from multiple acquisitions are manipulated to produce an image. rectification The direction in which a cell membrane most easily passes current. For example, a membrane that passes outward current more easily than inward current is said to show outward rectification. recurrent circuit A series of synaptic connections between neurons in which the last neuron connects some of its output back to the first. A recurrent circuit can support positive feedback. recurrent flagellum A posteriorly directed flagellum. recycling compartment Tubular compartment localized in the perinuclear region or subapical region (in polarized epithelial cells), important for recycling receptors and other plasma membrane components. redox The process of reduction or oxidation. redox buffer A mixture of a thiol and its corresponding disulfide. redox reactions Reactions in which the reacting species change oxidation states. reducing terminus The single sugar group at one end of a polysaccharide chain that is not glycosidically bonded to any other group. All the other sugar groups in a polysaccharide chain are nonreducing. reduction A chemical reaction that results in the gain of electrons by the molecules that undergo reduction. redundancy In respect to the genetic code, the fact that there are several different codons for each amino acid. Reed–Sternberg cell The neoplastic element of Hodgkin disease. It is a large cell, either binucleate or with a bilobate nucleus, and possessing prominent nucleoli. reflection A narrow beam of strongly diffracted X-rays produced when a crystal is in a particular orientation in the X-ray beam. refractometric optics Optics based on exploiting the refractive index of the medium through which light is passing. The ultracentrifuge employs a Rayleigh interferometer in which the difference in refractive index between a reference solution and the sample is measured.

refractory period A period following an action potential where it is more difficult (relative refractory period) or impossible (absolute refractory period) to elicit another action potential. refugia (singular refugium) Isolated areas that have served as a refuge for a species during climatic or other changes. regenerative xylem Tracheary elements that are formed from parenchyma cells rather than from the meristematic procambium or cambium. They may connect growing lateral buds, lateral roots, and new strands around wounds. regional specification The case when a group of cells is determined as a whole by cell–cell interactions that depend on their position within the embryo. regiospecificity The exclusiveness of modification of a specific site in a reactant, thereby forming a specific product when two or more sites of modification on the reactant are available. regulatory cascade A sequence of regulatory proteins A, B, C y where protein A catalyses the activation of protein B, which then catalyses the activation of protein C, and so on. regulatory RNA An RNA whose primary function is the regulation of a biological activity. regulon Groups of genes and operons that are coordinately controlled. RE See reproductive effort. reification Examination of the morphometric implications of the components of a latent vector by assigning biological or physical meaning to these. rejection antigen An immunogenic protein in a cell that can induce rejection of that cell by the host’s immune system. RelA (p)ppGpp synthetase I (PSI), an enzyme involved in the ‘stringent response’ linking amino acid availability and RNA accumulation in bacteria. relaxed DNA Closed circular DNA without any supercoiling. release The stage of viral replication at which virus particles escape the infected cell. remodelling In relation to bone, a coupled sequence of resorption and formation events that replace previously existing bone. Also considered as the last stage of bone healing, following the inflammatory and reparative stages. Renette cell A ventrally located gland in nematodes that collects liquids from the body cavity and passes them into the excretory duct from which they are expelled through the excretory pore. repair (1) DNA repair. The cellular processes resulting in the removal of damaged DNA and its replacement with normal undamaged DNA in the genome of an organism. (2) Wound repair. The replacement of lost tissue by connective tissue elements and parenchymal cells in varying proportions. When replaced completely by granulation tissue, which later matures to fibrous tissue, the result is referred to as a scar. repair synthesis of DNA DNA synthesis that fills in gaps generated by the excision of damaged stretches of DNA. repairosome A putative multiprotein complex comprising many, perhaps all, of the proteins involved in nucleotide excision repair of DNA. repeat induced point mutations (RIP) A premeiotic process in Neurospora in which both copies of duplicated DNA are heavily mutated, leading to inactivation of genes. replication See DNA replication. replication band Lightly staining, migrating crossband of a macronucleus, found in all hypotrichous ciliates and in some oligotrichs. The area concerned is involved in DNA replication and histone synthesis.

228

Glossary

replication fork trap Two groups of terminators with opposite orientations arranged to trap replication forks in the terminus region of the chromosome. replication fork Junctions in partially replicated DNA where the newly synthesized daughter strands meet the unreplicated parental DNA. The replication fork is the site at which DNA synthesis occurs. replication origin The point on a genome at which DNA replication initiates. replication protein A (RPA) A heterotrimeric single-stranded DNA-binding protein that plays important accessory roles in DNA metabolism by preventing formation of or disrupting secondary structures within single-stranded DNA. replication slippage Mispairing between DNA strands that can occur during the replication of tandem repeats, leading to repeat amplification or deletion. replicative intermediate A partially double-stranded structure formed during the replication and transcription of RNA viruses. replicative senescence An ‘ageing’ phenomenon in which normal cells proliferating in culture lose their potential for replication and acquire biomarkers of cellular senescence after a certain number of serial passages in culture. replisome A large multiprotein complex, located at the replication fork, that catalyses DNA replication. reporter gene The coding sequence for a protein whose activity can be easily assayed. It can be fused to the sequence of another gene of interest to report on its expression, or it can be placed under the control of enhancer and promoter sequences of interest to report on their activity and tissue-specificity, for example. reporter molecule A molecule used in an indirect assay that detects an event that is otherwise unobservable by direct examination. repressor A gene regulatory protein that shuts off the expression of a particular gene or group of genes by inhibiting the initiation of transcription. In bacteria, classical repressor proteins such as the lac repressor act at sequences known as operators, adjacent to the promoter. reproductive effort (RE) The fraction of resources allocated to reproduction. reproductive isolation Evolutionary independence of populations due to intrinsic features that prevent their successful interbreeding, and thus prevent gene exchange. reproductive value A way of evaluating the relative demographic importance of the different categories (age, size etc.) in a population. The reproductive value of an individual in a particular category is the number of newborns needed to affect population growth as much as that individual. repulsion Mechanism by which an axon or a cell is driven away. Chemorepulsion involves the interaction of the cell with soluble repellent molecules, contact repulsion involves cell–cell interactions. reservoir host Nonhuman natural host for a virus, providing a continual source of the infectious agent. resolution (1) The ability to distinguish between events close together in space, in time or in appearance. (2) The ability of an imaging system to distinguish between two points in a specimen in terms of distance or time, which is often a function of the display device in a digital imaging system.

resolving power In microscopy, the ability to distinguish structures that are close to each other (e.g. the light microscope has a resolving power of 0.4 mm, whereas the transmission electron microscope has a resolving power of 0.2–0.5 nm). resonance a condition occurring when the driving frequency closely matches the natural frequency of the system it is driving. Maximum energy transfer and oscillation amplitude occurs. resource defence polygyny Behaviour in which males defend a necessary or limiting resource and mate with all females that come to that resource. resource tracking The case where a parasite is associated with a set of hosts that share a given resource. respiration (1) Cellular oxidation of chemical fuels, leading to the generation of metabolic energy and reducing power. The term usually refers to aerobic respiration, in which the final electron acceptor is molecular oxygen and which generates large amounts of ATP. (2) A type of metabolism using external electron acceptors (e.g. O2). respirators Filtered breathing devices that can protect culturists from particles and microorganisms. respiratory burst Augmented oxygen consumption and production of reactive oxygen radicals and other microbicidal products which is stimulated in phagocytes (e.g. macrophages and neutrophils) by the phagocytosis of microorganisms or by other external stimuli. respiratory chain A series of redox proteins within a membrane (such as the inner mitochondrial membrane) that couples substrate oxidation to the generation of a proton electrochemical gradient across the membrane. respiratory circulation The collective name for the blood vessels that supply blood specifically to the respiratory organ. It is also termed the branchial or gill circulation in fish and the pulmonary circulation in vertebrates with lungs. respiratory control The tight coupling of the rate of mitochondrial respiration to the ratio of ATP/ (ADP + Pi) in the cell. response regulator In a two-component regulatory system, a protein, that is phosphorylated by a histidine kinase on an aspartate residue as part of the signal transduction process. The response regulators have 120 conserved residues in the N terminus. restoration Returning a species to a habitat where it used to occur, or changing an ecosystem back to its original condition. restriction enzymes Endonucleases from bacteria that recognize specific DNA sequences and cut the DNA at a particular site at or near the recognition sequence. restriction fragment length polymorphism (RFLP) DNA is cut by specific restriction enzymes resulting in DNA-pieces of individually varying lengths, thus giving a specific banding pattern when separated electrophoretically. restriction fragment length polymorphism (RFLP) Genetic variation in a population that manifests itself in the form of variability among individuals of the lengths of restriction fragments produced by cleavage of a given region of the genome by a restriction enzyme. reticular formation A network of neurons and fibres occupying the core of the brainstem. reticulate evolution The fusing of previously separated branches on an evolutionary tree. reticulocyte A red blood cell newly made and released from the marrow. After supravital staining, reticulocytes exhibit a cytoplasmic reticular pattern detectable by light microscopy.

229

Glossary

reticuloendothelial cells, reticuloendothelial system Nonmigratory phagocytic cells in the marrow and lymph nodes and the sinusoids of the liver and spleen, and macrophages in other tissues. retinal error Difference between fovea position and target position in space. retinoblastoma protein See Rb. retinotectal system Chick visual system with topographically ordered projections from retinal ganglion cells to their immediate brain target, the tectum. retrograde transport The movement of materials from the terminals of a neuron to the cell body. retroperitoneum The area behind the rear of the abdominal cavity. retrotransposons See transposable elements. retroviral packaging cell Cell line engineered to contain all the proteins needed for retroviral replication. retroviruses A family of enveloped viruses with RNA genomes that replicate via a DNA intermediate through the use of reverse transcriptase, and in which the double-stranded DNA intermediate may become integrated into the host chromosome as an inactive provirus. In this form the provirus can be passed on from generation to generation. reversal of damage A type of DNA-repair process in which a DNA lesion is repaired without excision and resynthesis of DNA. reverse genetics The term coined to describe the analysis of gene function starting from the gene, into which mutations can be introduced and their phenotypic effect studied, in contrast to classical genetic analysis which starts with a mutant phenotype. reverse transcriptase RNA-dependent DNA polymerase, which catalyses the synthesis of DNA on an RNA template. reverse transcriptase PCR (RT–PCR) Polymerase chain reaction using as template DNA produced by reverse transcription. reverse transcription The synthesis of DNA using RNA as the template. reversed phase high-performance liquid chromatography (RP-HPLC) Chromatographic technique for separating peptides or proteins, in which the sample is run under pressure through a steel column packed with 3–5 mm silica particles that carry extended hydrophobic C2 to C18 chains. The particles have pore ˚ diameters of 100 to 300 A. reversed transport Transport in a direction opposite to that occurring normally. In the case of plasma membrane amine transporters, reversed transport moves the substrate from the cell interior towards the exterior. reversion Restoration of a phenotypic trait to its original state, or restoration of a mutated gene to its original sequence (genetic reversion). A phenotypic trait may revert as a result of a true genetic reversion or through additional, secondary alterations in the genome. reward conditioning See appetitive conditioning. Reynolds number A dimensionless number that represents the ratio of inertial to viscous forces. RF II DNA Full length M13 bacteriophage DNA. RFLP See restriction fragment length polymorphism. RGG motif An RNA-binding motif 20–30 amino acids long that is characterized by arginine–glycine–glycine (RGG) tripeptide repeats interspersed with other, often aromatic amino acids. rhabdomyolysis Necrosis of muscle cells.

rhamnogalacturonan I A pectic polysaccharide with a backbone of alternating rhamnosyl and galacturonosyl residues. Between 20 and 80% of the rhamnosyl residues may be substituted at position 2 with oligosaccharide side chains. rhamnogalacturonan II A structurally complex pectic polysaccharide present in the walls of all higher plants. It contains several unusual glycosyl residues. rhamphorhynchoids Primitive, long-tailed Triassic and Jurassic pterosaurs 0.5–2.5 m in wingspan. rhamphotheca Keratin cover of the upper and lower mandibles, replacing teeth. rhapidosomes Rod-shaped tubular inclusions. rhizomorph A linear aggregation of hyphae, often robust and root-like in appearance and sometimes showing internal differentiation, through which nutrients are transported. rhizosheath A sheath of soil particles bound together with polysaccharides that surrounds the roots of some desert plants. They provide the roots with protection against desiccation. rhombomere Segmental unit of the developing hindbrain. The hindbrain is composed of 7–8 rhombomeres. rhizome A creeping underground stem from which aerial shoots are produced. In ferns, the leaves and roots arise from the rhizome. rhynchokinetic Applied to the skulls of birds that have flexible regions near the tip of the upper beak. rhynchosaurs A common group of large, herbivorous Triassic reptiles closely related to the archosaurs. They were characterized by broad, powerful skulls that were well adapted to grinding up tough plants. ribavirin A broad-spectrum antiviral drug. ribonuclease (RNAase) An enzyme that cleaves RNA into fragments or single nucleotides. ribonuclease H (RNAase H) A nuclease that digests the RNA strand of an RNA–DNA duplex. It is found in association with reverse transcriptase and is essential in reverse transcription replication. ribonucleic acid See RNA. ribonucleoprotein motif An RNA-binding domain in a protein that consists of approximately 80–90 amino acids containing two highly conserved sequence elements, RNP1 and RNP2. ribonucleoprotein (RNP) A complex consisting of one or more RNA components and one or more protein components. Examples include the ribosome, telomerase, RNase P and the spliceosome. ribonucleoprotein shedding Elimination of ribonucleoprotein during meiotic divisions, as described in the oocytes of some species (e.g. Lepidoptera, Trichoptera and others). ribosomal A site See A site. ribosomal frameshifting The programmed alteration of a reading frame by a ribosome during translation. ribosomal P site See P site. ribosomal proteins The stable protein components of ribosomes. In bacteria they are named S1–S21 for the small (30S) subunit, and L1– L36 for the large subunit (50S). ribosomal RNA maturation The cleavage and/or chemical modification of the initial rRNA transcript. The mature rRNA is functional in ribosome assembly and protein synthesis.

230

Glossary

ribosomal RNA (rRNA) The non-coding RNA that is a stable structural component of the ribosomes. Each ribosomal RNA is a single-stranded molecule, generally denoted by its sedimentation coefficient, e.g. 16S rRNA, S5 rRNA. In eukaryotic ribosomes the small subunit contains a 16S rRNA, and the large subunit a 23S and a 5S rRNA. ribosomal subunits The two ribonucleoprotein complexes (the small subunit and the large subunit) that form a functional ribosome. A large and a small subunit come together on messenger RNA at the initiation of protein synthesis. The large and the small subunits have sedimentation coefficients of 50S and 30S in prokaryotes and 60S and 40S in eukaryotes, respectively. ribosome Large nucleoprotein particle, composed of multiple ribosomal proteins complexed to rRNAs. Ribosomes are present in large numbers in the cytoplasm, and are the sites at which messenger RNA is translated to protein. ribosome-binding site Site on bacterial messenger RNA, also called the Shine–Dalgarno sequence, that is required for efficient ribosome binding and translation. ribozyme A polyribonucleotide with enzymatic activity, also known as an RNA enzyme. Natural examples include selfsplicing introns and the peptide-bond forming activity of the ribosome. ribulose 1,5-bisphosphate carboxylase/oxygenase See Rubisco. ribulose 1,5-bisphosphate (RuBP) The five-carbon compound carboxylated by Rubisco in the C3 cycle. richness The number of distinct units within a (usually taxonomic) group (e.g. species richness, generic richness) or within a habitat. Ringer solution A ‘physiological’ salt solution made to be isotonic with serum. It usually contains Na1 , ClÀ, K1 , Mg21 , Ca21 and bicarbonate, as well as lactate or glucose. RIP See repeat induced point mutations. RIS See Radiology Information System. ritonavir Protease inhibitor of human immunodeficiency virus 1 (HIV1). RNA Ribonucleic acid. Nucleic acid, usually single-stranded except in some virus genomes, which is composed of ribonucleotides. The bases in RNA are adenine, cytosine, guanine and uracil. See also messenger RNA, ribosomal RNA, transfer RNA. RNA editing A change in the information content of a messenger RNA by the deletion, insertion or chemical modification of specific bases during or after transcription. These changes are sometimes directed by antisense RNAs. RNA enzyme See ribozyme. RNA hairpin A strand of RNA that is folded back on itself and held together by complementary base pairing. The turning point (the loop) contains a few unpaired nucleotides. RNA helicase An enzyme that unwinds double-stranded RNA in an ATP-dependent reaction. RNA interference (RNAi) The phenomenon whereby a gene’s function can be selectively inhibited by double-stranded RNA corresponding to that gene. The mechanism of this effect is still unclear. RNA maturation The complete set of enzymatic and physicochemical events that convert a primary RNA transcript into a mature functional RNA. RNA modification The chemical changes that occur on individual nucleotides in RNA, e.g. change of functional groups (usually methylation) and isomerization.

RNA polymerase The enzyme that carries out transcription. It catalyses the formation of a complementary RNA strand on a DNA template. RNA polymerase holoenzyme The complete form of bacterial RNA polymerase, containing s factor, which is required to initiate transcription efficiently. After initiation, the s factor is lost and the rest of the polymerase, the core enzyme, is responsible for elongation of the RNA strand. RNA polymerase II The enzyme responsible for synthesis of messenger RNA in eukaryotes. RNA primary structure The sequence of ribonucleotides (G, C, A or U) in the RNA chain. RNA processing The alterations that are made to primary RNA transcripts in order to produce a translatable or functional RNA. These include RNA splicing, polyadenylation, capping, and methylation. RNA pseudoknot A structure in an RNA formed by a stem–loop with a tail that base pairs and forms a helix with part of the loop. RNA secondary structure The three-dimensional conformation of a folded RNA chain resulting from base-pairing between different parts of the chain. The base-pairing generally follows Watson–Crick rules, but G–U pairs are also allowed. RNA splicing The removal of introns from a primary RNA transcript and the rejoining of the exons to form a mature RNA molecule. RNA structure Three-dimensional structure formed by intramolecular interactions between the bases in an RNA molecule. RNA tertiary structure Structure formed by superfolding and long-range interactions in an RNA molecule. RNAase See ribonuclease. RNAase H See ribonuclease H. RNAase P A ribonuclease involved in RNA processing that matures the 50 end of tRNA transcripts. RNAi See RNA interference. RNP See ribonucleoprotein. RNP motif See ribonucleoprotein motif. Robertsonian change Translocation between two nonhomologous acrocentric chromosomes to form a bi-armed chromosome (Robertsonian fusion), or the mutation of a bi-armed chromosome into two acrocentrics (Robertsonian fission). Robertsonian translocation, Robertsonian fusion Chromosomal rearrangement involving two acrocentric chromosomes which fuse near the centromeric region with loss of the short arms. The result is a chromosome with two arms and a centromere in the middle. robusticity A technical term to describe limb bones that are relatively short but which have broad shafts. Long bones are said to be ‘robust’ when the width of the shaft is greater than that for an equivalent modern human bone of the same length. rod elements Arrays of aggregated chlorophyll that form the core of the chlorosome. rod outer segment (ROS) A specialized compartment in the rod cells of the retina that consists of densely packed membrane. rolling The rotating movement of blood cells along the vessel wall that is due to weak interactions between adhesion molecules on the cell and the wall. rolling-circle replication A type of replication of circular DNA or double-stranded RNA in which one strand of the doublestranded circle is nicked, and the 30 end thus generated is used to prime DNA synthesis, displacing a 50 tail. The single replication fork thus formed moves indefinitely around the circular template.

231

Glossary

root exudates Material released by roots including sugars, amino acids, organic acids, proteins, cell debris and carbon dioxide. root pressure An osmotic pressure generated in the roots, pushing water upwards. Thought to have important roles in young plants and in dissolving air bubbles in the xylem at the beginning of the growing season. rosette A structure in the plant cell plasma membrane that is thought to be an enzyme complex responsible for cellulose synthesis. ROS See rod outer segment. rostral Towards the snout or beak end of an animal, i.e. the anterior end. rotavirus Double-stranded RNA virus of the genus Rotavirus, family Reoviridae, that is the major cause of infant diarrhoea. RPA See replication protein A. RP-HPLC See reversed phase high-performance liquid chromatography. rRNA See ribosomal RNA. RS domain A protein domain rich in arginine and serine dipeptides. RS domains are common in splicing factors in multicellular organisms. RTK See receptor tyrosine kinase. RU486 A drug that blocks progesterone receptor function. It is used in breast cancer, induction of labour, and elective pregnancy termination. Rubisco The enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase. The carboxylase function is responsible for the fixation of carbon dioxide to ribulose 1,5-bisphosphate in the first step of the C3 pathway. The oxygenase function is involved in photorespiration. RuBP See ribulose 1,5-bisphosphate. ruffle See lamellipodia. rule-of-six In the canine distemper virus, and similar viruses, the viral genomic RNA needs to be completely enwrapped by nucleocapsid protein (N). A single N protein covers six nucleotides. To fulfil the rule, the number of nucleotides of the genome must be divisible by 6. rumen The first vessel in the multichambered stomach of ruminant animals (including cattle, sheep, goats, deer, elk, bison, marsupials, coloboid and langur monkeys, camels, hippopotamus, llamas, and the hoatzin or stinkbird), in which cellulose is digested. run-through fraction In column chromatography, the portion of a sample that flows unaffected by passage through a column made of some selectively adherent material.

S chlorosomes Chlorosomes found in the anaerobic sulfur bacterial family Chlorobiaceae. S phase The DNA replication phase of the eukaryotic cell cycle. It follows G1 and precedes G2 and mitosis (M phase). S0.5 The concentration of a substrate required to produce halfmaximal activity. saccade A fast jerky angular displacement of the eye. Saccharomyces cerevisiae Baker’s or brewer’s yeast. Commonly referred to simply as yeast, this unicellular fungus is used as a eukaryotic cell model system for scientific and industrial research. saline agglutinin An antibody that directly agglutinates red blood cells suspended in saline. It is usually IgM.

saltation (1) The evolution of new species by sudden, discontinuous steps. (2) A radical and discontinuous reorganization of morphology in a single generation (e.g. through mutation), resulting in a population successfully occupying a new and substantially different ecological niche. saltatory conduction The propagation of action potentials from node to node in myelinated axons. sampling intensity The probability of sampling a taxon over some specified stratigraphic or temporal interval. sandfly The insect vector of leishmaniasis. Santana Formation Early Cretaceous rock sequence in Brazil that has produced many exceptionally well preserved pterosaur remains. SAP See serum amyloid protein. saprotroph An organism, especially a bacterium or fungus, that lives by absorbing nutrients from dead organic matter. saprotrophic Living on dead organic matter. saprotrophy A form of chemo-organotrophy common in bacteria and fungi in which organic compounds are absorbed directly from the substrate of dead organic matter after digestion by extracellular enzymes. saquinavir Protease inhibitor of human immunodeficiency virus 1 (HIV1). sarcoid An unusual granulomatous disease that affects many organs and tissues including lung, skin, spleen and lymph node. Its cause is unknown. sarcolemma The plasma membrane of a muscle fibre. SASP See small acid-soluble spore proteins. satellite A visible block of heterochromatin above the NOR region at the end of the short arm of acrocentric human chromosomes. satellite DNA Localized DNA sequences consisting of large numbers of tandem repeats, which often have base compositions differing from the genomic average, and which therefore form ‘satellite’ bands in caesium chloride equilibrium centrifugation gradients. satellite remote sensing Surveillance by satellite-borne sensors that has been used, e.g. to determine chlorophyll concentrations or water temperatures and can be used for tracking algal blooms in water. saturation (1) In genetics, describes the case where very large numbers of mutants of a sequence are made, so as to ensure that there is a mutant for any particular codon of the squence. (2) The case where two DNA sequences have such frequent multiple mutations at the same site that it is difficult to estimate an accurate genetic distance between them. Such a situation is common among highly divergent sequences. (3) In regard to fatty acids and similar lipids, the case where the hydrocarbon chain has no double bonds, i.e. it contains the maximum possible number of hydrogen atoms. saturated fatty acid Fatty acid that contains no double bonds in the hydrocarbon tail, i.e. all the carbon atoms are ‘saturated’ with hydrogen. Saurischia The ‘reptile-hipped’ dinosaurs. These dinosaurs include both herbivores and carnivores among their members and are characterized by a more typically reptile-like arrangement of their hip bones. sauropod dinosaurs Plant-eating dinosaurs with long neck and tail, small heads, and five-toed feet. Examples include Brontosaurus, Diplodocus and Brachiosaurus. Sauropodomorpha See sauropod dinosaurs. scaffold Protein around which a viral capsid is built.

232

Glossary
secretion leader sequence A sequence at the 50 end of a gene that encodes a signal sequence in the protein which leads to the targeting of that protein to the secretory system of the cell. secretory granule Small intracellular vesicle that is packed with material and is destined for regulated exocytosis. sections, ultrathin Sections (less than 1-mm thick) prepared for electron microscopic resolution. Even bacterial cells must be sectioned into more than 10 slices. Cells are solidified for microtomy with special knives made of diamond or glass. Solidification is achieved either by deep freezing and slicing of the still frozen block at low temperatures (cryosections), or by stepwise replacement of cellular water (in bacteria about 80% w/w) by a synthetic resin. sedimentary rock A rock, such as sandstone or limestone, that was once a sediment such as sand or mud, and which has not been modified substantially after burial. segmenter Intracellular stage in which asexual division of sporozoan protozoa occurs. segmentation The division of the animal body or other structure into a series of segments of rather similar internal structure. segregating site A nucleotide site at which two or more different types of nucleotide are present in a population. selectins A family of cell adhesion proteins present on leucocytes and endothelial cells. They possess an extracellular lectin-like domain that recognizes sugars on cell-surface glycoproteins. selection coefficient A measure of the strength of natural selection. selection Non-random differential survival and reproduction (in a particular environment) that is due to differences in genotype and thus phenotype. selectivity index Ratio of the TC50 to the IC50 (or, more broadly, toxicity to efficacy) for an antiviral drug. Should be as high as possible, with a ratio of 100 often used as a benchmark. selenodont A condition found in some herbivores, in which the cusps of the molars are arranged in crescent-shaped crests. selenoprotein A protein that contains the amino acid selenocysteine. SELEX Systematic evolution of ligands by exponential enrichment. A technique that selects high-affinity nucleic acid sequences from a random pool. self The body’s own tissues. self assembly The ability of a complex macromolecular structure such as a ribosome or virus particle to assemble itself from its components without external assistance. selfish DNA DNA sequences that are maintained solely by their capability to replicate within the genome, despite their capacity to reduce the fitness of their hosts. self-tolerance The normal ability of the immune system to distinguish self from nonself, and to avoid mounting an immune attack on self antigens. semelparity A reproductive pattern in which the females normally give birth only once in their lifetime. semidiurnal tides A sequence of tides consisting of two high and two low tides over approximately 24 hours and 50 minutes. The high tides are of approximately equal amplitude, as are the low tides. semidominant mutation A mutation that results in a phenotypic effect when in the heterozygous state, but which is more severe in the homozygous state.

scale An organic or inorganic cell covering of variable shape that usually occurs in layers upon the plasma membrane of some types of algae. scaling The quantitative influence of body size on organic function, including rate of metabolism. scanning the ATP-dependent, 50 to 30 movement of the 40S subunit along a messenger RNA in search of an initiating AUG codon. scansorial A type of locomotion characterized by rapid scurrying movements that is particularly common among small clawed mammals. scattering The process whereby a wave is diffusely redirected in space. SCE See standard calomel electrode. SCF See stem cell factor. Schiff base The C5N-containing covalent adduct formed by the reaction of a primary amine with either an aldehyde or a ketone. schizogony An asexual multiple fission stage in the life cycle of Apicomplexa (and other protozoa), leading to the formation of merozoites. The multinucleate cell divides into multiple progeny through simultaneous budding from the cell membrane schizont Intracellular stage in which asexual division of sporozoan protozoa occurs. SCID See severe combined immune deficiency. sclerenchyma Plant cell type characterized by the presence of lignified secondary cell walls and the absence of cellular contents at maturity. sclerite A small scale, typically embedded in an epithelium. scleroderma A disease characterized by deposition of fibrous tissue in skin and internal organs. sclerotic cell Thick brown-walled globose to oval cells that reproduce by forming cross-walls and represent the tissue form of fungi causing chromoblastomycosis. scopuloid Ultrastructurally complex area in the suctorian swarmer where the suctorian stalk is secreted. It is not homologous to a ‘scopula’ in other ciliates. score matrix For a dynamic programming algorithm, the matrix that holds the cumulative scores between a query and the target amino acid or nucleotide sequence. scurvy A disease caused by vitamin C deficiency. SDS-PAGE Sodium dodecyl sulfate–polyacrylamide gel electrophoresis. An electrophoretic technique that denatures and separates proteins/peptides on the basis of their molecular mass. SDV See silicon deposition vesicle. second messenger Small diffusible intracellular signalling molecule, produced as a result of receptor stimulation, that conveys the signal from the receptor to some enzyme or molecular system in the cell, which mediates the cell’s response. Common second messengers are cyclic AMP, cyclic GMP, Ca21 , inositol 1,4,5trisphosphate and 1,2-diacylglycerol. secondary chemical Molecular compound produced by an organism but not essential for its basic life functions. secondary root See lateral root. secondary structure Those regular elements of two-dimensional structure common to many proteins that are formed by relatively short-range interactions within the polypeptide chain. Examples are a-helix and b-pleated sheet. secondary wood Woody tissue produced by lateral growth from the stele, and which provides the bulk of the stem in trees and shrubs. secretory antigen Antigens secreted by an organism.

233

Glossary

semi-persistent Describes the relationship between a plant virus and its arthropod vector in which the vector retains the virus for a period of hours to days. senescence The steady decline in many aspects of adaptive performance (e.g. sensory, cardiac, immunological) as a person ages during adult life. sensitivity amplification The production of a large percentage change in the steady-state concentration of an active signalling molecule in response to a small percentage change in a stimulus. sensor In two-component bacterial sensory systems, a histidine protein kinase that can be autophosphorylated and then phosphorylate the response regulator as part of the signal transduction process. sensory learning An improved capacity of the nervous system to process the sensory information related to specific experiences, resulting in a more effective or efficient behaviour. sensory messages Signals recognized by sensory organs and which give information about physical and chemical environmental characteristics (e.g. light, odorants, pheromones). sensory receptor A specialized nerve cell that introduces information into the nervous system by transducing specific events or conditions into a neural code. sensory system A neuronal network made up of the sensory receptors and all successive processing centres of sensory information in the nervous system. Sensory systems organize the activity of large populations of neurons to make information accessible to other brain systems. sensu stricto The most precise, restrictive or exclusive interpretation of a species (contrast with sensu lato). septum (plural septa) A cross wall formed within a fungal hypha or at the base of a reproductive structure. sequence (1) A succession of layers of sedimentary rock. (2) The order of nucleotides in a nucleic acid or of amino acids in a protein. sequence similarity Two amino-acid sequences are said to show similarity when there is a minimum of 30% identical amino acids in comparable sequence regions. sequence-specific DNA-binding proteins Proteins that bind with high affinity to sites on DNA consisting of a particular sequence of base pairs. sequence-tagged site (STS) A short, known DNA sequence which can be detected using the polymerase chain reaction. sequestration (1) Withdrawal of the more mature stages of the malaria parasite Plasmodium from the peripheral circulation and their adherence to endothelial cells lining the deep tissues. (2) Keeping a reserve of some molecule in a particular form or location. serine proteases A family of proteolytic enzymes that contain the active-site triad of serine, aspartic acid and histidine residues in their catalytic site. They include trypsin, chymotrypsin and elastase. seroconversion The appearance of antibodies in the serum after exposure to an antigen. serogroup A subdivision of a species (especially of bacteria) based on differences in surface antigens. serotype A subdivision of a serogroup, e.g. Leptospira interrogans serogroup icterohaemorrhagiae serotype icterohaemorrhagiae. serovar See serotype. serum amyloid protein (SAP) A protein of the pentraxin family which is an acute-phase protein in mice and is found in amyloidosis.

serum sickness The clinical symptoms that accompany an allergic reaction to the horse serum that formerly was administered to protect against diphtheria or tetanus. seta (plural setae) A small hair-like projection formed from the insect cuticle. severe combined immune deficiency (SCID) Inherited immune deficiency, usually rapidly fatal without treatment, in which both T cells and B cells are very few or absent. It can be due to a variety of causes. severing Of actin, breaking of an actin microfilament. sex chromosome The chromosomes responsible for sex determination (e.g. X and Y in humans) and which are present in different numbers or combinations in the different sexes. sex determination The genetic, molecular and cellular mechanisms which direct development as a male or a female. sex differentiation Implementation of a sex-specific programme of development. sex linkage The association of a genetic trait with one sex only, which is usually due to the location of the gene for that trait on one of the sex chromosomes. sex pilus See F pilus. sex-linked Describes a genetic trait associated with one sex only. In mammals the clinically important sex-linked traits are usually specified by genes on the X chromosome. sexual dimorphism The existence of a difference in structure and appearance between males and females of the same species. The term is sometimes also used to describe functional differences, such as the frequency with which particular behaviours are displayed. sexual reproduction Type of reproduction in which, at some stage of the life cycle, haploid gametes (or haploid nuclei) are produced as a result of meiosis. A gamete subsequently fuses with another gamete of different ‘sex’ or mating-type (often from a different individual) to produce a diploid cell (or nucleus) from which a new reproductive individual will develop. SF1 See splicing factor 1. shape The geometry of an organism after information about scale, position and orientation has been removed. Sharpey fibres Extrinsic collagen fibre bundles by which bones and teeth attach to muscles, tendons and ligaments. shear Deformation of a material caused by coplanar but noncollinear forces. shift-up An experiment in which cells growing slowly are suddenly shifted to a medium that allows more rapid growth. shoot apex The tip of a plant shoot, defined as the summit of the apical meristem. This is the most central point of the meristem and is often the highest point of the meristem where undifferentiated meristematic cells reside. shoot apical meristem The meristem located at the apex or growth tip of the shoot. shoulder dystocia Difficulty in delivering the shoulder encountered with abnormally broad-shouldered, big babies. Birth injury may result. Shungura Formation Block of sediments that lie to the west of the Omo River just before it drains into Lake Turkana. siamois A homeobox gene in Xenopus that encodes a likely transcription factor which plays a role in inducing the Spemann organizer. sick euthyroid syndrome Abnormal thyroid function blood tests in the absence of thyroid disease.

234

Glossary

side chain The group of atoms that are connected to the a-carbon of an amino acid. siderite An iron carbonate mineral, FeCO3. siderophore A chelating protein, produced by both plants and microorganisms, with a high affinity for metal ions. sigma factor A subunit of bacterial RNA polymerase that is required for initiation of transcription. Some sigma factors confer the ability to recognize and bind to a particular promoter, thus changing the pattern of gene expression. signal peptidase A protease that specifically cleaves the signal peptide from the N terminus of a protein. signal peptide A stretch of amino acids, located at the N terminus of a protein, that targets it to be secreted. signal transducers and activators of transcription (STATs) A family of transcription factors that are defined by sequence homology and are considered to be the primary substrates of the receptor-linked Janus kinases. signal transduction A series of interlinked biochemical reactions in which a signal initiated at the cell surface is transmitted inside the cell to cause a specific cellular response. silicon deposition vesicle (SDV) A special endomembrane component of golden algae where silica-complexed coverings are produced within the cell. similarity search A search for sequences similar to a query sequence in the DNA and amino-acid sequence databases by pairwise comparison of sequences using alignment tools. simple spike Action potential with a simple configuration, induced in a Purkinje cell by activation via parallel fibres. single-strand annealing A DNA repair process involving digestion of the opposing single strands of a DNA duplex on either side of a double-strand break to expose regions of homology on the remaining strands. These regions can then pair to facilitate repair. single-stranded DNA-binding protein Protein that binds nonspecifically to single-stranded DNA with much higher affinity than to either RNA or double-stranded DNA. sink tissues Tissues dependent upon the inward flow of nutrients for growth. sink A region of a plant in which the net flux of solutes into sieve elements is sufficient to produce net export from them. sinter Porous silica-rich deposit of hot springs and geysers. It forms terraces and mounds in hot-spring areas. sister chromatids The two copies of a chromosome after its replication and while they are still attached to each other. sister group In phylogenetic systematics (cladistics), either of two species groups that arose from the stem species of a monophyletic group in the same splitting (speciation) event. Sister groups have the same rank. Furthermore, any newly arising species has a sister group by definition. sister taxa Taxa sharing a more recent common ancestor with each other than with any other known taxa. sister union (SU) A type of deletion in sister chromatids in which the remaining sister chromatids become united at the break point, and the deleted acentric portions also become fused at the broken ends. site-directed mutagenesis The production of defined mutations at defined positions in a DNA sequence. site-specific recombination Process in which specific segments of DNA are synapsed by site-specific recombinase proteins which then catalyse conservative breakage–rejoining reactions to generate recombinant DNA.

¨ Sjogren syndrome A syndrome involving dryness of mucous membranes and inflamed parotid glands. skeleton The supporting hard tissues in an organism, either internal or external. skewness Pertaining to the asymmetry of a frequency function as a departure from the normal distribution. skull The bony casing of the brain (the cranium) and the mandible. skull roof A series of dermal bones of the skull that protect the braincase from above, including (in turtles) the nasal, prefrontal, frontal, parietal, jugal, quadratojugal, squamosal and postorbital bones. S-layer Self-assembled paracrystalline surface arrays consisting of protein or glycoprotein which reside on top of the cell wall of prokaryotes. sleeping sickness Disease caused by Trypanosoma brucei gambiense or T. b. rhodesiense, restricted to sub-Saharan Africa. slime Polysaccharide- and/or glycoprotein-rich material secreted by many types of organism. In bacteria, it is similar to the capsular material but is not attached to the cell wall. slimy Describes a fluid with a low degree of shear thinning. A slimy food material is one that coats and does not clear the mouth; it may also be difficult to swallow. slit sensillum (plural slit sensilla) A sense organ unique to arachnids that appears as a small slit in the cuticle. It is sensitive to compressional forces in the exoskeleton that act perpendicular to the long axis of the slit. small acid-soluble spore proteins (SASP) Low-molecular weight proteins produced during bacterial endospore formation that bind to DNA to protect it against damage and serve as a source of metabolizable amino acids for germinating spores. small nuclear ribonucleoprotein particle (snRNP) A stable complex of small nuclear RNAs with proteins. Such particles are involved in the RNA splicing reaction in the nucleus. small nuclear RNA (snRNA) Small RNA molecules present in the nucleus usually complexed with protein to form small nuclear ribonucleoproteins. The snRNAs involved in pre-mRNA splicing are U1, U2, U4, U5 and U6, and, for the splicing of U12-dependent introns, U11, U12, U5, U4atac and U6atac. smectite Clay mineral with a very high proportion of the mineral montmorillonite. smoker A hot deep-sea vent with precipitate-forming plume (‘smoke’). The precipitates may be black or white (‘black smokers’ and ‘white smokers’). smooth muscle Type of muscle found e.g. in blood vessel walls, gut walls and in other organs that are under involuntary control by the nervous system. When looked at under a microscope, the small cells making up this type of muscle have no crossbands or striations. SN2-reaction Nucleophilic substitution. The first and rate-limiting step of the reaction is a collision of the original complex with the nucleophile. The reaction is therefore bimolecular and of the second order. SNC meteorites A group of meteorites originating from the same parent body, probably Mars. snRNA See small nuclear RNA. snRNP See small nuclear ribonucleoprotein particle. social behaviour A behaviour that affects not only the fitness of the individual performing it, but also the fitnesses of nearby organisms of the same species.

235

Glossary

sodium channel A voltage-sensitive transmembrane ion channel present in the membranes of most neurons. When this channel is opened by a depolarizing voltage, sodium ions selectively pass through. sodium dodecyl sulfate–polyacrylamide gel electrophoresis See SDS-PAGE. soft selection Selection based on the relative fitness (rank) of individuals in a population. It is usually frequency dependent. solfatara A hot, sulfur-rich, often acidic environment. The name is derived from the Solfatara Crater near Naples (Italy). solid-phase immunoassay Type of immunoassay, such as ELISA, in which one of the reactants (antigen or antibody) is linked to a solid support. Solnhofen limestone Sequence of Late Jurassic calcareous deposits famed for the excellent preservation of many different types of fossils including pterosaurs and Archaeopteryx. solvation Transfer of solute from the gas phase to solution. solvent transfer The solvent transfer free energy of a molecule is a measure of the propensity of the molecule to dissolve in a nonaqueous liquid such as cyclohexane rather than in water. soma (1) The animal body, with the exception of the cells of the germline. (2) The neuronal cell body containing the cell nucleus. somatic cell Any of the cells that make up the body of an animal, with the exception of the germ cells. somatic fate All cell fates other than the germline. somatic hypermutation An accumulation of point mutations that occurs in the variable regions of rearranged immunoglobulin genes in activated B cells. It results in a further diversification of antibody specificity and binding strength for the antigen. somatic mutation Mutations that occur in somatic cells, not germ cells, and thus are not passed on to the next generation. somatic Describes a cell or structure that does not produce reproductive structures or gametes. sonic hedgehog A gene related to the hedgehog gene, first characterized as encoding a secreted protein signal in Drosophila. It has been found in many mammalian species, including humans, and plays a critical role in patterning of vertebrate embryonic tissues. sorocarp A fruiting body produced by cellular slime moulds in which the spores are not contained within a common wall but are instead suspended in a matrix of slime. sorus (plural sori) The mass of cells within a sorocarp. SOS mutagenesis An error-prone DNA repair mechanism in bacteria that occurs under conditions of extreme DNA damage. source A region of a plant in which there is net efflux of solutes and water from sieve elements, resulting in import into them. source tissues Tissues capable of assimilating carbon by photosynthesis and exporting it to sink tissues. Southern blotting A technique used for detection of a specific restriction fragment against a background of many other restriction fragments. spasticity Muscle tightness and stiffness resulting from injury to the brain or spinal cord. spatiotemporal pattern The information contained within a group of neurons, which is represented both by the time-varying activity of individual neurons and by the particular set of neurons that becomes active. spawn Substrate that has been impregnated by mushroom mycelium and is used for mushroom production. The genetic and cultural characteristics of the mushroom species are carried in the spawn.

special pair chlorophyll A pair of chlorophyll molecules that are arranged in the reaction centre complex to cause charge separation. specialist An organism with a restricted realized niche. speciation Process in which new species are generated either by splitting (cladogenesis) of an ancestral species or the gradual transformation of one species into another (anagenesis). species The most commonly used unit of biodiversity, defined as a group of organisms of the same type that can interbreed with each other. A species thus comprises all the populations that occur across its overall range. specific activity The catalytic activity of an enzyme per milligram protein. specific metabolic rate Metabolic rate per unit body mass, which is useful in comparing metabolism in animals of different sizes. specification Processes by which cell fate is acquired during development. specificity In regard to symbiosis, the taxonomic range of a partner with which an organism forms a symbiosis. The specificity may be narrow (the organism associates with few, closely related taxa) to broad (the organism associates with many, taxonomically diverse taxa). spectrum Absorbance of a substance measured as a function of the wavelength or the frequency of the incident light. Spemann organizer A signalling centre above the dorsal lip of the blastopore in the Xenopus embryo which is responsible for induction of the central nervous system and other tissues of the dorsal axis. When transplanted to the ventral side of a host embryo, it can induce a complete new embryonic axis. Named after its discoverer, the Nobel prize-winning developmental biologist Hans Spemann. spermatogenesis The formation of sperm. spermatogonia (singular spermatogonium) The primitive germ cells that undergo meiosis to produce spermatozoa. spermatophore A sperm package, consolidated by protein or polysaccharide and transferred from male to female in several animal groups. Use of spermatophores circumvents copulation. spheroplast A bacterial or yeast cell from which the bulk of the cell wall has been removed enzymatically under osmotic protection. spherule A sac-like structure producing asexual spores endogenously that is the tissue phase of the fungus Coccidioides immitis. spherulocyte A type of haemocyte characterized by prominent membrane-bounded, electron-dense, intracytoplasmic spherules, which are considerably larger than granules in the granulocytes. spicule A sclerotized intromittent organ that the male nematode employs to hold open the female vulva during the transfer of sperm at mating. spine A protrusion of a postsynaptic dendrite that makes synaptic contact with a presynaptic cell’s axon terminal. spinneret An appendage or projection in arachnids specialized for producing and handling silk. Found on the opisthosoma of spiders and the chelicerae of pseudoscorpions. spiral cleavage Pattern of zygote cleavage found in species of annelids, molluscs, sipunculans, entoprocts, platyhelminths and nemertines. It is characterized by alternation in the direction of the mitotic spindles such that blastomeres are displaced so that they lie in the furrows between one another. spiral valve Intestine with a longitudinal secondary wall laid down as a spiral around a central axis. spiralians Animals with a spiral type of cleavage, e.g. flatworms, ribbon worms, molluscs, annelids.

236

Glossary

¨ Spitzenkorper A cluster of vesicles located just inside the fungal hyphal tip that is believed to be involved in the transport of wall material in a polarized fashion. splanchnomegaly See organomegaly. spliceosome A large complex of RNAs and proteins responsible for pre-mRNA splicing. A spliceosome forms around each intron and dissociates after splicing is complete. splice-site mutation A mutation in a consensus DNA sequence that is essential for effective RNA splicing. Splice-site mutations often result in the loss of exons from the messenger RNA (exon skipping). splicing factor 1 (SF1) A protein that interacts with the premRNA branchpoint during RNA splicing. Also known as BBP (branch site-binding protein). spongiform changes Formation of sponge-like vacuoles within the grey matter of the brain as a characteristic morphological correlate in all prion diseases. spongiotrophoblast The outer layers of the placenta in the rodent. spontaneous cytotoxicity See natural cytotoxicity. sporangiole A very small sporangium that contains only one or two sporangiospores, and also lacks a columella. sporangiophore A modified hypha that supports the sporangium. sporangiospore An asexual spore formed within a sporangium. sporangium (plural sporangia) The mother cell from which asexual spores are formed, and which eventually develops into a sac-like structure containing the asexual spores. spore A general term for a propagule that is formed either asexually or sexually, is usually surrounded by a rigid cell wall, and which is the dissemination stage of the life cycle. sporidium Sexually differentiated basidiospore. sporoblast A cell that develops directly into a spore without further division. sporocarp A multicellular fruiting body in which the spores are contained by a common wall. Sporocarps are produced by the plasmodial slime moulds. sporogenesis See sporulation. sporogony (1) Mitotic fission stage in the life cycle of apicomplexan protozoans, leading to the formation of spores. (2) Development of the fertilized zygote through a process of meiotic and mitotic divisions to form infective sporozoites. (3) In microsporidians, the process of division of the sporont to form a sporoblast. sporomorph Plant spore or spore-like object. sporont In microsporidians, a cell that is committed to sporogony and, after a specific number of divisions, becomes sporoblasts. Sporonts are sometimes characterized by a membrane-dense ribosome-rich cytoplasm and a thickening of the cell membrane. sporophyte Phase of plant life cycle that forms spores. sporotrichosis Invasive fungal infection caused by Sporothrix schenckii. sporulation The formation of spores and their associated specialized supporting and containing structures. SpoT An enzyme with (p)ppGpp 30 pyrophosphohydrolase activity and potential (p)ppGpp synthetic activity, closely involved with RelA in the ‘stringent response’ of bacteria. squamates A group of reptiles (the Order Squamata) consisting of snakes, lizards, and amphisbaenians. They are characterized by reduction or absence of limbs, elongated bodies and tails, keratinous scales, vomeronasal organs and paired copulatory organs called hemipenises. SSV1 Temperate virus of the archaeon Sulfolobus shibatae.

stabilizing selection Selection acting against individuals at both extremes of a phenotypic distribution (e.g. selection against both very small and very large individuals). stable isotopes Isotopes that do not undergo radioactive decay. standard apparent reduction potential E0 1 is the standard reduction potential at a specified pH. It is defined by: E0 5 E0 1 – (ln Q0 (RT/nF)). standard calomel electrode (SCE) A widely used reference for establishing redox potential. Redox potentials vs SCE 5 potentials vs SHE (standard hydrogen electrode) 1 0.242 V (at 251C). Redox potentials vary with temperature and pH. standard rate of metabolism The rate of metabolism in adult ectotherms at rest, at a particular body temperature, and when post-absorptive. stapes A small stirrup-shaped bone in the mammalian middle ear. It transmits sound vibrations to the inner ear, where they are transduced into electrical impulses. start codon The trinucleotide sequence in messenger RNA at which protein synthesis starts. starter and extender units Materials that initiate formation (starter) and elongation (extender) of carbon chains. In general, 1 starter unit + n extender units gives n CO2 + product. statocyst Gravity-detecting sense organ. status migrainosus Daily and continuous headaches associated with psychogenic tension or analgesic or other drug misuse. stavudine Nucleoside analogue inhibitor of human immunodeficiency virus (HIV) reverse transcriptase. Used as an anti-HIV drug. steady state (1) A state of a macromolecule–ligand system in which the equilibrium condition dC/dt is pertinent for only a part of the reaction components and which is temporarily achieved in a finite time interval. (2) A kinetic phase during enzyme catalysis in which the rate of formation of the enzyme–substrate (ES) complex is exactly matched by its rate of consumption. Hence, during steady state, the concentration of ES complex is constant. (3) For a gas-exchange system, a state in which the total masses, concentrations, partial pressures and fluxes of a given moving gas species remain the same with time in all locations, e.g. in which the amounts of gas consumed (oxygen) or produced (carbon dioxide) in the tissues equal those exchanged with the ambient medium. steatosis Accumulations of fatty droplets in a tissue. stele The vascular tissue and associated pith in a stem or root, which translocates substances from one part of a plant to another. stellate Star-shaped. stem cell An undifferentiated cell that is capable of continued indefinite division, giving rise both to more stem cells and to other daughter cells that undergo differentiation into particular cell types. stem cell factor (SCF) A protein required for the in vivo growth of haematopoietic stem cells. In vitro it stimulates the growth of blast cell, erythroid and granulocyte colonies. stem lineage If a species becomes the stem species of a clade through splitting, its lineage becomes the stem lineage of the clade. stem–loop An RNA structure formed by pairing of self-complementary regions flanking an unpaired loop sequence. stenothermal Tolerant of only a narrow range of temperature. stenotopic Having a narrow environmental range. stepping-stone model migration The movement of individuals among neighbouring populations.

237

Glossary

stepwise mutation model A model for the formation of tandem arrays (e.g. a microsatellite array) which proposes an increase or decrease by one repeat unit at a time. stereocilia (singular stereocilium) Modified microvilli of the hair cells of the cochlea that serve as mechanoelectric transducers. stereoelectronic effects Molecular conformation-dependent influences on reaction rates due to the geometric dependence of atomic orbital interactions. stereotyped song Adult stable form of a bird’s song. sterigma (plural sterigmata) A spike-like protrusion on a basidium that supports a basidiospore. sterile cabinet An enclosure that provides an aseptic work area for culture. sterile Tissues or structures that are not producing spores. sterilization The killing of all living organisms on or in a material. Sternberg–Reed cells Large neoplastic binucleate cells characteristic of Hodgkin disease. sternite A cuticular plate that occurs on the ventral surface of each body segment in arthropods. sterol A hydroxylated tetracyclic compound that retains some or all of the carbon atoms of squalene in its nucleus and side chain and partitions nearly completely into the ether layer when it is shaken with equal volumes of water and ether. stewardship The responsibility to protect biological diversity, as given by God or accepted from society. sticking The stationary arrest of blood cells in the presence of fluid shear, mediated by secondary adhesion receptors. stigmata of congenital syphilis The signs that are specific or common in congenital syphilis: saddle nose, interstitial keratitis, fibrosis around angles of the mouth, Hutchinson teeth or Moon molars, palatal gumma, Clutton joints. stochastic Random, by chance. stoichiometric Present in equimolar amounts. stomata (singular stoma) The pores in the underside of a leaf through which gas exchange takes place. Each is composed of a pair of specialized cells whose movement opens or closes the pore. stomatogastric nervous system A part of the nervous system that supplies and controls the anterior part of the gut in arthropods. stomium A cluster of cells that control the rupture or dehiscence of pollen grains. stomodaeum An intucking of ectoderm meeting endoderm in Ctenophora, corresponding to the mouth of higher invertebrates. stop codon The trinucleotide sequence in messenger RNA at which protein synthesis terminates. stopped-flow spectroscopy Method of rapid mixing of two fluids that is used to capture fast reactions. The fluid flow is stopped by a mechanical mechanism, and the mixture is observed immediately. strabismus Commonly known as squinting, an abnormal deviation of an eyeball preventing a binocular focus of the same visual target. strain energy Ability of matter to do work by virtue of internal deformation. strand break A type of DNA damage in which a break occurs in the sugar–phosphate backbone of DNA. A break on one side of the helix is called a single-stranded break, while matching breaks on both sides of the helix are called double-stranded breaks. stratification The difference in density at different depths in a column of water, which is dependent on variation in temperature, pressure and (in seawater) salinity.

stratigraphic debt The sum of range extensions measured in temporal or stratigraphic units. stratigraphy The arrangement of rocks in sequence in the Earth’s crust. The study of the dating and sequence of rocks. stratocladistics An amended version of cladistics in which both implied stratographic gaps and implied homoplasies are considered evidence against a possible phylogeny. strepsirhine A cladistic term of primate classification that includes only the lemurs and lorises. stress (1) Physiologically defined in humans and other mammals as a response of the organism to changes in its homeostasis, specifically involving activation of the hypothalamic-pituitaryadrenocortical (HPA) axis, resulting in the secretion of corticotrophin-releasing factor, adrenocorticotrophic hormone (ACTH) and corticosteroids, and in coactivation of the sympathetic nervous system and the adrenal medulla. (2) The force in a structure acting over an area that resists internal forces. stress fibres Bundles of relatively stable actin filaments spanning the length of cells, involved in maintaining cell shape. stress-induced premature senescence Long-term appearance of the biomarkers of replicative senescence after exposure of human diploid cells to sublethal stress. striated muscle The skeletal muscle that forms the main mass of the limbs and much of the body and is responsible for the ability to move. It is generally under conscious or voluntary control. When looked at under a microscope, the long cells making up this type of muscle have crossbands or striations. stroke volume The volume of blood pumped by one ventricle during a single heartbeat. stroma Liquid phase of the chloroplast, located outside the thylakoid membrane vesicle, where photosynthetic carbon reduction, starch synthesis and other important biosynthetic pathways take place. stromal cell The supportive tissue of an organ. stromal membranes Unstacked thylakoid membranes that extend between grana stacks in chloroplasts. stromatactis A common feature of many Palaeozoic reefs of multiple and controversial origin, consisting of cement-filled laminar voids with flat or undulose lower surfaces and irregular or digitate upper surfaces. stromatolite A laminated calcareous structure produced by the activities of lime-secreting cyanobacteria. strongyles stylet A relatively solid, sclerotized structure in the mouth area of plant-parasitic nematodes. It is used to transfer sap from plant cells to the nematode pharynx. structural imaging The formation of an image of anatomical structure. structure factor The X-ray scattering along a particular direction from a single unit cell, equivalent to the diffraction pattern sample only at reflection peaks. STS See sequence-tagged site. stylet In insects and mites, mouthparts modified into a piercing– sucking instrument. In plant-parasitic nematodes, a single stiletto-like part of the foregut (odontostyl) needed to open epidermal cells or even to reach deeper tissue layers. stylet bundle The feeding organ of the Hemiptera (bugs). It is composed of two external mandibular stylets and two maxillar stylets. Longitudinal grooves in the maxillar stylets form the wide food canal for ingestion and the narrow salivary canal for egestion.

238

Glossary

stylet-borne transmission Common type of transmission for plant diseases with aphid vectors. Acquisition and infection feeding times are short, there is no lag-phase, the vector is infective for short times and infectivity is lost on moulting. subacute sclerosing panencephalitis A rare disease caused by persistent measles virus infection in the central nervous system. subcellular marker A selected biomolecule that is confined to a specific organelle or suborganellar compartment and that may be used to determine the presence of this compartment in a subcellular fraction. subduction The process in which one crustal plate plunges beneath another, eventually reaching the mantle and melting. suberin Aliphatic biopolymer composed of linear, long-chain, lipophilic compounds derived from elongated fatty acids. subgenomic RNA A viral messenger RNA that is identical in sequence to the 30 -end of the genomic RNA. subsensitive response In an individual level of regulatory cascade (such as an intracellular signalling pathway), an amplification response that is more gradual than a Michaelian response. subspecies Fully interfertile geographic races of the same species that have been assigned formal taxonomic names. substituted galacturonans A pectic polysaccharide composed of a 1,4-linked galacturonic acid backbone that is substituted at C2 and/or C3 with mono- or oligosaccharide side chains. substitution (1) A mutation that replaces one nucleotide with another in a DNA molecule, or results in the substitution of one amino acid with another in a protein molecule. (2) Replacement of one allele by another in a population. substitution matrix A matrix containing scores for weighting the various possible substitutions between different characters, most commonly amino-acid residues. substrate (1) The molecule(s) of reactant that are acted upon by an enzyme and thus converted to the products of the reaction. (2) The surface upon which an animal is positioned or moving, such as the ground, a tree branch, etc. substrate specificity The property of an enzyme that it will act only (or most efficiently) on one substrate. substrate-level phosphorylation Process in which the generated phosphoryl group is formed attached to the actual substrate of an enzyme. substratum (plural substrata) Organic matter that serves as a food source and support for fungal growth. subtilisin A serine protease produced by sporulating cells of Bacillus subtilis and which is used in washing powders. subunit vaccine A vaccine that contains only one or a few individual purified components from the microorganism it is designed to protect against. sugar mimic A substance that, although not a sugar, has a similar molecular shape and can therefore lodge at the active site of an enzyme. This prevents the sugar docking with the enzyme and thus prevents metabolism of the sugar. SU See sister union. sulfate reduction Anaerobic bacterial metabolism that utilizes sulfate (SO42À) dissolved in sea water in the metabolism of organic matter, and produces hydrogen sulfide (H2S) and bicarbonate (HCO3) as byproducts. sulfur globules Deposits of organosulfanes present in the periplasmic region of certain bacteria.

superantigens Proteins that stimulate large numbers of T cells in an antigen-nonspecific fashion. They simultaneously bind certain types of T-cell receptors and MHC class II molecules (at a site distinct from the regular antigen-binding site). supercoiled Describes a closed DNA double helix which is itself coiled around its own axis. supercoiled DNA Closed circular DNA formed from linear DNA after twisting (positive) or untwisting (negative) the DNA helix. supercoiling Coiling superimposed on that of the helix of the DNA molecule itself. supercooling point Temperature below the freezing point to which a solution can be cooled before spontaneously freezing. superficial Describes a noninvasive cutaneous or subcutaneous infection. superinfection immunity The inability of a bacteriophage to infect a bacterial cell lysogenic for the same phage. This is due to the turn-off of genes on the infecting genome by the resident prophage repressor. superior Towards the head. supermolecule A discrete structure comprised of more than one compound, usually polymers. supernova An explosion of a massive star which ejects most of the original mass into space. superoxide anion A derivative of oxygen capable of oxidative destruction of cellular components. superoxide dismutase Enzyme that converts superoxide radicals formed after photosynthetic reduction of oxygen to hydrogen peroxide (H2O2). suppressor mutation A secondary mutation that totally or partially restores a function lost as a result of a primary mutation, and which is located at a site different from that of the primary mutation. suppressor of PEV (Su(var)) A second-site mutation that leads to suppression of the position-effect variegation (PEV) phenotype, i.e. one that results in more expression (less silencing) of a euchromatic gene subject to PEV. suppressor T cells T lymphocytes that negatively regulate the extent of an immune response, and can even promote nonresponsiveness or tolerance to an antigen. supraclavicular In the hollow above and behind the clavicle. supramolecular structure An aggregate of a number of individual molecules held together by noncovalent forces. supraorbital ridges Brow ridges above the eye orbits that are present in some archaic hominid species. In Homo erectus these form a continuous shelf of bone, but in the Neanderthals they are curved over each orbit and do not connect in the midline. supravalvular aortic stenosis (SVAS) A narrowing of the artery that is above the valve of the heart’s aorta. surface coil A radio transmitter/receiver that transmits radiofrequency energy to, or receives signal from, tissue that is immediately adjacent to the plane of the coil. Such coils are typically constructed as one- or two-turn solenoids. surrogate A person appointed to make medical decisions for an individual who is no longer able to make those decisions for themself. suspension feeding Mode of feeding by removal of suspended food particles from the surrounding medium. suspensor A hyphal tip that at first supports the gametangium and then the zygospore.

239

Glossary

sustainability The ability of a society or a particular human activity to continue indefinitely without depleting resources or damaging the environment. SVAS See supravalvular aortic stenosis. swarm cells Uninucleated cells with flagella which emerge from amoebae in the life cycle of Physarum. switch I Structural element in G proteins which changes conformation depending on whether GDP or GTP is bound. switch II Structural element in G proteins which changes orientation depending on whether GDP or GTP is bound. symbionin A GroE-like protein synthesized by the endosymbiotic bacteria of aphid cells. symbiont Most generally, a species partner in a symbiosis. Also frequently used, in contrast to host, to refer to the smaller member of the association. symbiosis An intimate association between two species, which may be advantageous to both partners (mutualism), be of advantage to one partner at the expense of the other (antagonism), or be neither harmful nor advantageous to either (commensalism). symbiosome A membrane-bounded vacuole containing a symbiont(s) within the host tissue. sympatric Occupying the same geographical location. sympatric speciation Formation of a new species without geographical separation from ancestral species. It is considered uncommon, hence the significance of polyploid speciation as an example. sympatry Occurring in the same geographic region, thus having the potential to interbreed. symplasm The interconnected cell contents of a plant. symplast The interconnected cytoplasms of a plant, as a whole. symplastic Describes the supracellular organization of the interconnected cytoplasm in plant tissues. symporter A transmembrane protein that couples the transport of two solutes across a membrane in the same direction. symptomatic infection An infection that produces clinical signs, based on which the infection can be diagnosed. symptomatic migraine Migraine-like attacks that are rarely caused by brain diseases, such as tumours, malformations, raised intracranial pressure, strokes and inflammatory conditions of the blood vessels. synaptic facilitation See facilitation. synanthropic Typical of human dwellings and benefiting from, or able to exploit, human activities. synapomorphic Describes a derived or specialized homologous character found in species of two or more groups that is hypothesized to have arisen in a directly ancestral group and not in any earlier ancestor. The term is popularly used in cladistic studies. synapomorphy A shared derived character. In cladistics, a character that defines a clade. synapse The point of near-opposition of one neuron with another at which signals are passed from one cell to the other. Usually, the end of the axon of one neuron forms a synapse on a dendrite of another. Neurotransmitter is released from the cell on one side of the synapse (the presynaptic side) and triggers an electrical charge in the cell on the other (the postsynaptic side). synapse specificity The phenomenon in neuronal plasticity that not all synapses on the same neuron have to change together. Depending on stimulation conditions, some synapses can get stronger, others can get weaker, and many may not change at all.

synapsis (1) The bringing together of two transposon ends by transposase–transposase interactions. (2) The pairing of two homologous chromosomes during meiosis. synaptic cleft The extracellular-matrix-filled gap separating individual neurons at a synapse. synaptic depression Reduction in synaptic transmission, usually due to depletion of a presynaptic store of transmitter. synaptic eligibility trace A transient neurochemical event that serves as a memory of recent synaptic activity, and indicates that a particular synapse is ‘eligible’ for adaptive modification if an error in performance is subsequently detected. synaptic plasticity The amount of neurotransmitter released at synapses of many neurons can vary with the past history of the synapses. Changes in synaptic strength are thought to be the basis of learning and memory. synaptic potential A brief, graded voltage change in a neuron generated by the opening of ion channels following the release of neurotransmitter from the presynaptic terminal. synaptic strength This is measured by determining the average amplitude of the excitatory postsynaptic response caused by a presynaptic action potential. synaptic vesicles Small membrane-bounded sacs inside the axon terminal that contain chemical neurotransmitters (e.g. acetylcholine) that are released from the axon by exocytosis in response to the arrival of an action potential. synaptosomes Isolated nerve endings in homogenates of neural tissue formed when synapses break off from associated axons and their plasma membrane reseals. syncope Sudden loss of consciousness. syncytium (1) A multinucleated cell formed by the cytoplasmic fusion of individual cells. (2) A population of cells whose cytoplasms are connected by gap junctions is also sometimes referred to as a syncytium or a syncytial network. syndrome A collection of symptoms and features associated with a specific disease. syneresis The expulsion of aqueous solution from a gel caused by shrinking of the gel. Characterized by the formation of droplets or a liquid layer over the surface of the gel. synergism See synergy. synergistic Acting cooperatively to have an enhanced effect, e.g. two mutations which individually have only a mild or no phenotype, but when combined are lethal. synergy, synergism The case when two agents or stimuli acting together have a greater effect than either acting alone. syngeneic graft See isograft. syngeneic mouse strains Strains of mice possessing almost identical genotypes. synteny The occurrence of a given set of genes in the same order on a chromosome in different species. synthetases Enzymes that catalyse the hydrolysis of ATP to ADP and PI coupled to the formation of X-Y from X and Y. syntrophy Microbial interaction in which two species working together carry out a particular chemical transformation that neither organism could perform alone. Literally means ‘eating together’. systematics (1) Study of the diversity of organisms, their classification and nomenclature. (2) The process of organizing taxa (species and higher categories) into a hierarchical pattern that may approximate their evolutionary relationships.

240

Glossary

systemic acquired resistance In plants, a resistance response manifest throughout the whole plant that results from either pathogen infection or chemical treatments, and often confers a durable and broad-spectrum disease resistance. systemic circulation See peripheral circulation. systemic lupus erythematosus An autoimmune inflammatory connective tissue disease with variable features frequently including fever, fatigue, joint pains, and diffuse reddening of the skin of the face and upper body. systemic response Activation of wound-response genes in the undamaged tissues of a wounded plant. The term usually refers to responses occurring in different leaves from the one actually wounded. systemin Peptide of 18 amino acid residues, derived from the Nterminal part of a 200 amino acid precursor protein, apparently of cytosolic location. A potent inducer of proteinase inhibitor expression in tomato plants. systole The period of contraction of the ventricles of the heart. syn conformation Conformation of nucleotide where the Watson–Crick face of the nucleobase is oriented over rather than away from the sugar.

T cell-dependent antigen An antigen that requires the cooperation of CD4 T cells with B lymphocytes for an effective antibody response to be made. Most protein antigens are T-cell dependent. T cells Thymus-derived lymphocytes, the lymphocytes that mature in the thymus and are the cells responsible for antigen-specific cell-mediated immunity and which, in most cases initiate adaptive immune responses. They include the CD4 (helper T cell) subset (which secretes cytokines acting on B cells, macrophages and other T cells) and the CD8 subset, which includes cytotoxic T cells. T lymphocyte See T cells. T7-transcript RNA molecule synthesized in vitro by transcription of a synthetic or natural gene by bacteriophage T7 RNA polymerase. tachyphylaxis Rapid loss of response. tagmata See tagmosis. tagmatization The regional specialization of groups of segments in arthropods to form functional units or tagmata (e.g. head, thorax, abdomen). tagmosis Regional specialization of the body. tail (1) The cytoplasmic portion of a transmembrane receptor molecule, with which signal-transducing proteins associate. (2) Domains of the core histones and linker histones involved in protein–DNA and protein–protein interactions, and which are subject to post-translational modification. talonid The distal part (i.e. towards the back of the mouth) of the crowns of mandibular/lower premolar and molar teeth. tandem fusion Direct fusion of telomeric–centromeric and telomeric–telomeric chromosomal regions (as in Robertsonian rearrangement). tapetum Anther tissue that lines the locules containing the developing male gametophytes (pollen grains) and provides materials necessary for their development. taphocoenosis Mixed fossil community of fauna and flora that lived in the place of its later embedding together with a fauna and flora transported from other biotopes into the sedimentation area.

taphonomy The study of the processes of fossilization, essentially those processes that act on a once-living organism following death. It includes those that act upon a carcass between death and final burial, and the changes in the chemistry of the fossil that mainly occur after burial. It may yield forensic evidence concerning the life habits of the fossilized organism and the circumstances surrounding the death. tautomers Chemical isomers that differ only in the location of hydrogen atoms. They exist in rapid equilibrium, although one form is usually more stable. taxon (plural taxa) A group such as Mammalia or Homo sapiens that is a unit, rather than a kind of unit (e.g. family, class), in a formal classification system. taxonomy The science of identification, classification and nomenclature of organisms. TC50 Drug concentration that is toxic to 50% of cells. T-cell antigen receptor See T-cell receptor. T-cell receptor (TCR) The antigen-specific receptor of T cells, encoded by genes that undergo rearrangement during T-cell development. It is a cell-surface heterodimer of either a and b chains (the majority of T cells) or g and d chains, complexed with signal-transducing proteins. T-cell receptors recognize peptide antigens complexed with MHC molecules, and each T cell bears receptors of only one specificity. Tcf An HMG-box transcription factor that binds DNA with sequence specificity, altering the bending of the DNA and thus gene expression. TCR See T-cell receptor. TDLU See terminal duct lobular unit. T-DNA Fragment of the Ti plasmid transferred to plant cells during Agrobacterium infection (‘transferred DNA’). TdT See terminal deoxynucleotidyltransferase. tectonic Refers to processes or features of deformation of rocks, commonly during mountain building or movement of continents. tectum The dorsal part of the midbrain, which contains maps of the space around an animal and is involved in multisensory integration. teichoic acid, teichuronic acids Polymers of glycerol and ribitol joined by phosphate groups, with amino acids or sugars attached. Major components of the Gram-type positive cell wall, these polymers are found in great variety and are highly antigenic. teleomorph The sexual stage of a fungus, e.g. the cup in an ascomycete or the mushroom of a basidiomycete. teleosemantics A theory of the semantic significance, or meaning, of symbols that explains meaning in terms of the evolutionary history of those symbols. teliospore Thick-walled resting spore where karyogamy occurs in some basidiomycetes. teloblastic growth Growth in which new segments arise during development from a specific budding zone at the rear of the animal. telomerase An RNA-containing enzyme complex that extends chromosome ends (telomeres) by copying its RNA sequence repeatedly into chromosomal DNA. This extension enables DNA replication of the chromosome ends. telomere A specialized non-coding region of repeated sequence (about 15 000 nucleotides long) found at the ends of eukaryotic chromosomes. It is replicated in a way that counteracts the tendency of the chromosome otherwise to be shortened at each round of replication.

241

Glossary

telson A posterior projection on the opisthosoma of certain chelicerates. It takes the form of a tail-like spine in horseshoe crabs, a venomous sting in scorpions and a sensory ‘whip’ in whipscorpions. temnospondyls The most abundant and diverse group of archaic amphibians. They range from early Carboniferous to early Cretaceous and are common in many Triassic fossil assemblages, and were often of large size. The group includes many lizard-like forms. temperate bacteriophage, temperate phage A bacteriophage that can either cause a lytic infection or persist within its host in a prophage state. temperate virus Virus able to persist within the host cell as a provirus integrated within the cell’s DNA. template A nucleic acid sequence that is copied by an RNA or DNA polymerase to produce a new RNA or DNA strand of the exact complementary sequence to the original sequence. temporal cospeciation Strictly contemporaneous cospeciation. tension A lengthening of a structure that results from an applied force (positive linear strain). teratogenic Describes a substance that, when ingested, may cause malformation of the fetus. terbinafine A member of the allylamine class of antifungal drugs currently used to treat superficial infections. tergite The dorsal cuticular plates of arthropods. A single tergite usually surmounts each segment. terminal complexes The cellulose synthetase particles present on the plasma membrane that produce cellulose microfibrils. terminal deoxynucleotidyltransferase (TdT) A template-independent DNA polymerase that adds non-templated nucleotides at the junctions between gene segments during immunoglobulin and T-cell receptor gene rearrangement, thus generating additional functional diversity. terminal duct lobular unit (TDLU) The peripheral secretory unit of the breast, composed of a terminal duct, and a lobular arrangement of complex anastomosing tubules embedded in a specialized connective tissue stroma. terminal oxidase Collective term for cytochrome and quinol oxidases at the ends of electron transport chains that transfer electrons to oxygen, reducing it to form water. terminal rate, terminal velocity The final descent speed of a particle in a fluid, e.g. a person free-falling in air or a cell in a liquid. At the terminal rate the fluid resistance equals the net weight of the particle. terminal redundancy The presence of identical nucleotide sequences at both ends of a linear genome. terminal repeats Repetitive units of DNA sequence found at the ends of linear viral genomes. terminalization In genetic recombination, the movement of the chiasmata to the ends of the chromosomes. termination codon One of three codons (UAA, UAG, UGA) that signal the end of a polypeptide chain. termination Often refers to the termination of polypeptide chain synthesis, triggered by the presence of one of the three termination codons, UAA, UAG or UGA, in the A site. Their presence results in the binding to the ribosome of a release factor instead of an aminoacyl-tRNA. terminator protein A protein which, upon binding to a specific site in the DNA known as a terminator, causes arrest (or pausing) of a replication fork when it approaches from one side of the complex, but not the other.

terminator (1) A DNA site which, upon being bound by a terminator protein, causes arrest (or pausing) of a replication fork when it approaches from one side of the complex, but not the other. (2) Signal sequence that halts formation of an RNA transcript and allows for addition of a poly(A) tail. terminus region A restricted and defined segment of the chromosome in which replication forks meet and fuse. ternary complex (1) A three-component complex, usually consisting of an enzyme protein to which are bound two ligands, such as two substrates, or substrate and cofactor or inhibitor. (2) In respect of translation, refers to the initiation complex that contains the following three components: eIF2, Met-tRNAi and GTP. terrestrial Living on the ground. tertian Associated with fever peaking every 48 hours. Tertiary period The geological period spanning the interval 65 million to about 2 million years ago, characterized by the rise of mammals. tertiary structure The complete three-dimensional conformation of a protein. test A skeletal capsule in some protozoa such as foraminifera and radiolaria, generally covered by an outer layer of living tissue. testa Seed coat. testicond Retaining the testes in the abdominal cavity rather than in a scrotum. testosterone A steroid hormone important in the regulation of masculine anatomy and sexual behaviour. tetanus High-frequency repetitive action potentials, arising either from normal neural synaptic activation or from experimental stimulation. tetrad The group of four haploid products of the meiotic divisions or the immediate derivatives thereof. Often applied to the four spores generated by a single meiosis in fungi. tetraether lipid A membrane lipid in which two acyl (phytanyl) chains extend between the inner and outer faces of the bilayer and which are joined to a polar head group on each face by ether linkage. tetrahydrobiopterin Essential cosubstrate for phenylalanine hydroxylase, tyrosine hydroxylase and tryptophan hydroxylase. It is also referred to as the pterin cosubstrate or, incorrectly, as the pterin cofactor. tetrapods Vertebrate animals with pelvic and shoulder girdles and four limbs, including their descendants in which these structures have been secondarily lost (as is the case in snakes). tetravalent Having four binding sites. TH cell Helper T cell. A type of CD4 T lymphocyte that cooperates in initiating antibody responses. thalamus A collection of nuclei in the dorsal part of the diencephalon, which relays information to the cerebrum. thallic development In fungi, formation of conidia by septation of a conidiogenous cell, which can enlarge after the conidial initials are delimited. thalloblastic development In fungi, formation of conidia by septation of a somatic hypha or conidiophores into discrete conidial initials, which then enlarge. thallus (plural thalli) The somatic fungal or algal body. thanatocoenosis Mixed fossil community of fauna and flora that lived in the place of its later embedding. theca A secreted, tightly fitting yet flexible covering around some unicellular microorganisms, thus distinguishable from an inflexible, rigid, secreted shell or test. See also lorica.

242

Glossary

thecodont Describes a tooth that sits in a socket in the jaw. thecodonts Triassic archosaurs that were the dominant predators throughout the Triassic. Often of large size, they were quadrupeds with a sprawling gait. thermal conductance A measure of the propensity of heat to enter or leave a body as a function of the thermal gradient between the body and environment. Thermal conductance is the inverse of insulation. thermal fluctuations Spontaneous variations in the energy of a system due to energy exchange with a surrounding temperature bath. thermal stability (1) The resistance of DNA or RNA duplexes to dissociation by increased temperature. (2) The ability of a protein to resist denaturation, or unfolding by increased temperature. thermoduric Heat tolerant. thermodynamic cycle A process that compares the effects of two single changes separately with the total effect of making both changes at once. thermodynamics The physics of the relationship between heat and other forms of energy. thermophile A microorganism whose optimum temperature for growth is high, i.e. over 501C. Some thermophilic prokaryotes can survive at temperatures approaching 1001C. thermophilic organism A species that is able to live at high temperatures, i.e. over 501C. Thermoplasma A genus of thermophilic archaea that lack cell walls. Thermotoga maritima Hyperthermophilic, rod-shaped marine bacterium with a coat-like cell envelope (‘toga’). theropod dinosaur Meat-eating dinosaurs that walked on their hind feet. Examples include Allosaurus, Velociraptor and Tyrannosaurus. Theropoda See theropod dinosaurs. thioester Compound (R–CO–S–R0 ) in which a carboxylic acid (R–COOH) is condensed with a thiol (R0 –SH). threes A set of three ciliates united in conjugation, in contrast to the normal pair formation during conjugation. threshold (1) The level that has to be reached by a substance or stimulus before it will trigger a subsequent event. (2) In excitable cells, the membrane potential at which sodium channels open rapidly, depolarizing the cell and causing an action potential. Experimentally, the threshold is determined as the membrane voltage reached by a stimulus that generates an action potential during 50% of trials. thrombin A central protein in haemostasis, generated from its inactive precursor prothrombin. Thrombin converts fibrinogen to fibrin, but can also cause cellular activation of platelets, monocytes and endothelium. thrombocytopenia A decrease in the number of circulating platelets in the blood. thrombogenic A substrate that induces platelet aggregation and activation of the plasma coagulation factors. thrombomodulin A protein expressed on the endothelium of blood vessels, which can form a 1:1 stoichiometric complex with thrombin and thus alter its substrate affinity. The complex of thrombin–thrombomodulin activates protein C. thrombophlebitis Inflammation of a vein leading to a blood clot. thrombosis The formation of an intravascular blood clot (thrombus), consisting of fibrin, aggregated platelets and blood cells, in response to an imbalance between thrombogenic factors and protective, anticoagulant mechanisms.

thylakoid (1) A simple membrane structure that is the photosynthetic apparatus in cyanobacteria and chloroxybacteria. (2) Vesicles, often stacked, formed from the inner membrane of chloroplasts, containing the pigments and enzyme systems essential for photosynthesis. thymine Pyrimidine base, present in DNA but not in RNA. thymus An organ located in the chest cavity behind the sternum. It is the site of T-cell development. thymus-dependent antigen An antigen, e.g. most proteins, that requires an interaction between antigen-specific T cells and B cells to induce an antibody response. thymus-independent antigen Antigen that can induce an antibody response without the help of T cells. Such antigens have repetitive epitopes and are able to crosslink the B-cell antigen receptor efficiently. thyroid-stimulating hormone (TSH) A glycoprotein hormone released by the anterior pituitary which stimulates thyroid hormone production and thyroid cell division. thyrotoxicosis The clinical signs and symptoms caused by an excess of the thyroid hormones thyroxine and triiodothyronine. Ti plasmid Large tumour-inducing plasmid of Agrobacterium tumefaciens, responsible for crown gall induction. Tic Protein translocation machinery at the inner envelope of chloroplasts. tiering Development of a vertical ecological stratification in a forest between the understorey and the canopy. till Sediment produced by glacial action, characterized by coarse stratification, angular fragments, and a wide range of particle sizes from silt to boulders. tillite A sedimentary rock produced from glacial till. TILs See tumour-infiltrating lymphocytes. tinamous A taxon of fowl-like birds found in semi-arid environments which have many characters of the Palaeognathae and therefore systematically are generally placed in or very near to that taxon. tip growth A mechanism of growth of plant cells in which new wall material is added only to one end of certain elongating cells, such as pollen tubes and root hairs. tissue A coherent assembly of cells serving a particular function in an organism. tissue cyst Enlarged host cell containing numerous parasites with reduced activity. It may be strengthened by primary and/or secondary cyst walls. tissue factor A single-chain glycoprotein complexed to phospholipid that is the main physiological activator of blood coagulation. It is expressed on cells within the vessel wall, but not normally on cells in direct contact with the blood. Tithonian The top stage of the Upper Jurassic. titre (1) A measurement of the dilution at which an antiserum can be detected in an assay. (2) Number of infectious virus particles per given volume of a virus stock solution. TLX See trophoblast leucocyte cross-reactive antigen. Toc Protein translocation machinery at the outer envelope of chloroplasts. tolerance Failure to respond to an antigen that is, in other conditions, capable of inducing an immune response. Self tolerance is an essential feature of the immune system and is established by the deletion/inactivation of self-reactive clones during lymphocyte development.

243

Glossary

tolerogenic Able to induce specific immunological ‘tolerance’ (non-reactivity). The test for the tolerant state is to observe zero response following challenge with antigen in a form that would be expected to stimulate an immune reaction. Toll-like receptors A family of mammalian transmembrane receptors related to the Toll protein of Drosophila. They are involved in the recognition of pathogens and microbial products and activate antimicrobial effector pathways in phagocytes. tomography Any technique that allows ‘slices’ of the body to be imaged, with the partial or complete elimination of effects from all other regions of the body. Image data are acquired from a number (often large) of different perspectives round an object, whereby a cross-sectional view of it can be produced. tonoplast Membrane surrounding the vacuole in plant and fungal cells. tool kit Term used by archaeologists to refer to the various types of tools found in ancient tool caches, or in circumstances where natural agencies have brought stone tools together. topographic projections The situation when axons of neighbouring neurons innervate neighbouring areas in their target field. topography A detailed surface map of a region. topoisomerase Class of enzymes involved in controlling the coiled or relaxed state of DNA by catalysing transient breaks. Type I topoisomerases catalyse single-strand breaks and type II doublestrand breaks. topology In regard to phylogenetics, the connectivity relationship of nodes in a phylogenetic tree. Trees with the same topology may have different branch lengths and may be drawn differently, but represent the same branching pattern. top-up transfusion Small amounts of blood given to an infant to increase the haemoglobin concentration. The neonate can tolerate only 10 ml kgÀ1 of concentrated red cells. If it is necessary to give more blood, an exchange transfusion has to be performed. toroid In the shape of a torus, like a doughnut with a hole in the middle. torpor A regulated state of inactivity where the body temperature is regulated somewhere in the region between 01C and euthermy. torque The turning or twisting force, the product of the magnitude of a force, F, and the perpendicular distance between the line of action of the force and the centre of rotation, d. torsion angle The angle between two groups on either side of a freely rotating chemical bond. torsion A counterclockwise 1801 rotation of the visceral part of the body in gastropod development and phylogeny. It is the diagnostic character of the class Gastropoda. torus semicircularis Also known as the inferior colliculus in mammals. It is part of the tectum (or roof) of the midbrain that receives auditory input and, where present, lateral line input. toxicity The intrinsic property of certain substances to be harmful to the normal structure or physiology of cells, tissues or organs. Toxoplasma A protozoan parasite causing a disease of animals and humans, transmitted from cats (the primary host). toxoplasmosis Disease caused by infection with the protozoan parasite Toxoplasma gondii. TPs See transition polypeptides. trabecula A solid strand of connective tissue branching from the splenic capsule into the interior of the spleen. trace fossil Evidence of activity of an ancient animal or plant, such as a burrow, track or faecal pellet.

trachea (plural trachaeae) (1) The windpipe in vertebrates. (2) In arthropods, a thin-walled cuticular tube that opens through small holes in the body surface and extends throughout the body, providing tissues with atmospheric oxygen and a pathway for removing carbon dioxide. tracheid A water-conducting xylem tissue in plants, composed of tapering tracheary elements that do not have open ends. trajectory The sequence of points (in the phase space) visited by a system as time moves forwards. trans-acting Acting on or affecting another molecule. trans-acting determinant A gene product that influences the expression of another gene. trans-acting factor A macromolecule or complex of macromolecules (usually protein and/or RNA) that interacts with RNA (or DNA). transamination The transfer of an amino group from an amino acid to an a-ketoacid to produce a new keto acid and a new amino acid. transcript An RNA molecule produced by transcription. transcriptase DNA-dependent RNA polymerase. An RNA polymerase that catalyses the formation of RNA on a DNA template. transcription The synthesis of RNA molecules using DNA as the template to determine the sequence of bases in the RNA product. The synthesis of RNA is catalysed by the enzyme RNA polymerase. transcription factor A regulatory protein required to initiate, upregulate or repress transcription. The term originally referred especially to those factors involved in the precise binding of RNA polymerases to promoters on the DNA and the initiation of transcription, but is now widely used for any gene regulatory protein. transcription-coupled nucleotide-excision repair A DNA repair process by which nucleotide-excision repair occurs preferentially on the transcribed strand on a transcriptionally active gene, presumably by the coupling of repair and transcription. transcriptome The full complement of RNA species transcribed by a cell. transcytosis A transport process by which molecules cross a cellular barrier in a membrane-bound, or pinocytic, vesicle. The process involves pinocytic uptake, or endocytosis, of the molecule at one surface of the cellular barrier, and pinocytic release, or exocytosis, at the other. transdifferentiation Differentiation of one cell type into another. transduce To infect cells with a virus. transducer (1) A device for converting one form of energy into another. Biologically, a device for converting the energy of a stimulus applied to a tissue into a series of action potentials in an afferent nerve. (2) A device for converting a signal from one form into another, e.g. a cell-surface receptor, which transmits the signal that extracellular ligand has bound to an intracellular signalling pathway. (3) The region of a sensory protein responsible for signal generation. transduction (1) Signal transduction. The process of translating a stimulus into an intracellular response. (2) Virus-mediated transfer of a gene into a cell. transencapsidation The packaging of one type of virus in the other’s protein coat, when two different viruses infect a cell. trans-encoded antisense RNA An RNA encoded by a gene that is not linked to its target gene. Target and trans-encoded antisense transcripts are not completely complementary and form imperfect RNA–RNA duplexes.

244

Glossary

transesterification The reaction where one ester moiety is replaced by another. transfected cell A cell into which a bacterial plasmid that contains a foreign virus or genetic material has been inserted. transfer RNA (tRNA) A family of small RNA molecules that act as ‘adaptors’ in the process of translating the sequence of a messenger RNA into protein. Each tRNA molecule carries an amino acid that matches its anticodon (which will match to the appropriate codon in mRNA). tRNAs are small (75–100 nucleotide) elbow-shaped RNA molecules that carry a threebase sequence (‘anticodon’) on the long arm and an amino acid on the short arm. transferase An enzyme that breaks a bond in a donor substrate and transfers one group from it to an acceptor substrate. The remainder of the donor substrate is the ‘leaving group’. transferrin A transport protein in animals that binds, transports and delivers free iron to cells. transform In image processing, to take an image from one space (domain) to another. The most commonly used transform in image processing is the Fourier transform which takes an image from coordinate space to frequency space. transformation (1) The process by which bacteria and yeast cells take up exogenous DNA. (2) A multistep process involving mutation of cellular genes or viral infection by which cells acquire altered growth properties, usually including the ability to divide indefinitely in culture. The pheotype resembles that of cells from cancerous tissue. transgene A piece of foreign DNA that has become incorporated into the genome of a cell. transgenesis The intentional introduction of foreign genetic material into the genome of plants or animals. transgenic Carrying a foreign gene. Describes an organism in which the deliberate insertion of a foreign gene into the germ cells or into the very early embryo has given rise to a mature organism with the foreign transgene incorporated into the genome of every cell. transgenic animals Animals carrying and expressing a foreign gene. transgenic mice Genetically engineered mice that contain a foreign gene integrated into the germline genome. transgenic plant A genetically engineered plant that contains and expresses a modified gene or a gene from another species. transglycosylation reaction The insertion of a base by cleavage of the N–C glycosidic bond between the nucleobase and the C1 of ribose. transglycosylation Cleavage of a glycosidic bond followed by attachment of the newly formed (potentially) reducing terminus to some other molecule (e.g. another sugar). transgression The drowning of the land by a relative rise in sea level. transition See transition mutation. transition mutation A mutation in which a purine (adenine, guanine) replaces another purine, or a pyrimidine (cytosine, thymine) replaces another pyrimidine. transition polypeptides (TPs) Set of small proteins with mass 33 kDa that are synthesized when a plant is initially exposed to an anaerobic environment. For the first 90 minutes, these are the only proteins that appear to be synthesized. transition state A short-lived, high-energy intermediate molecular state that must be attained in order to complete the transformation of reactants to products in any chemical reaction.

transition-state analogue inhibitor A stable molecule that binds to an enzyme in a manner that is structurally analogous to the transition state. translation The process whereby the nucleotide sequence of a messenger RNA is read out and used to make a polypeptide chain. It takes place on the ribosomes. The process is called translation because the alphabet of nucleic acids (AT/UGC) is converted into sequences of amino acids. translational control Regulation of protein synthesis at the translational stage. translational operator Sequence in mRNA, generally encompassing the translation initiation region, to which translational repressor proteins bind. translational polarity The fact that translation of a message on a polycistronic messenger RNA depends on the translation of a 50 preceding message. translational repressor Protein which binds to an mRNA, usually near the translation start, blocking access of ribosomes and inhibiting protein synthesis. translocase A protein or proteins that promotes movement (translocation) of macromolecular machinery (e.g. ribosome or spliceosome) along an RNA. translocation (1) The step in the elongation cycle of protein synthesis during which A- and P-site tRNAs move to P and E sites, respectively, and the messenger RNA is advanced by one codon. (2) A change in location, as in the movement of a molecule from one compartment of the cell to another. The term often refers specifically to the movement of proteins across a membrane. (3) A chromosome rearrangement in which there is exchange of parts between nonhomologous chromosomes. transmembrane Extending completely across a lipid bilayer, with exposure on both sides of the bilayer to the adjacent aqueous compartments. transmembrane helical domain (TM) a-helical secondary structure in those parts of the protein chain that cross the membrane in integral membrane proteins. transmembrane receptor Cell-surface protein whose extracellular domain recognizes and binds an extracellular signal molecule, and which transduces this information into the interior of the cell by association of the cytoplasmic portion of the receptor with intracellular signalling machinery. transmembrane synthases Enzymes located in the plant cell membrane that extend from the cytoplasmic side of the membrane to the external, environmental, side and that are active in synthesizing cell wall components. transmissible spongiform encephalopathies (TSEs) Diseases caused by defective brain proteins, called prions, that lead to brain degeneration. In humans, they include Creutzfeldt– Jakob disease (CJD), Gerstmann–Straussler–Scheinker ¨ syndrome (GSS) and fatal familial insomnia (FFI). In animals they include bovine spongiform encephalopathy (BSE) and scrapie. transmitter Chemical substance liberated from presynaptic axon terminals when they are invaded by propagating action potentials. It acts on receptors on the postsynaptic cell to generate postsynaptic potentials, thus passing the signal from one cell to the other. transovarial Transfer of infection from the adult female tick to the next generation via the eggs.

245

Glossary

transparent testa Arabidopsis phenotypes recognized by the reduction or absence of pigments in the seed coat (testa), due to the absence of one or more loci required for flavonoid biosynthesis, thus revealing the yellow colour of the underlying tissues. transplantation (1) The surgical implantation of tissue or an organ taken from one individual (the donor) into another individual (the recipient). (2) Insertion of a few cells from a donor embryo into a host of the same age (homochronic) or of a different age (heterochronic). transport Often refers to membrane transport, the transport of substances, typically small molecules and ions, across a membrane, transporters Transmembrane proteins that transport solutes or ions across the membrane, using a variety of energy sources. transporter multimers Functional transporter units consisting of more than one copy of the transporter protein. This is not established or ruled out for plasma membrane transporters. transposable element A DNA sequence that is able to move itself, or a copy of itself, to a new location in the genome (the process of transposition). Such movements often cause mutations. transposase The catalytic protein that carries out the DNA cleavage and strand-transfer reactions of transposition. transposition A process whereby certain DNA elements (insertion elements and transposons) move from one DNA location to another, using enzymes (transposases) usually encoded by the element. transposon See transposable element. trans-splicing Formation of a mature messenger RNA by splicing of exons from different primary RNA transcripts. It is contrasted with the more usual cis-splicing, in which exons from a single transcript are spliced together. TransTerm A database of translational signals including initiation and termination contexts from more than 250 organisms and currently containing nearly 100 000 sequences. transversion See transversion mutation. transversion mutation A mutation in which a purine (adenine, guanine) replaces a pyrimidine (cytosine, thymine) or vice versa. treadmilling A description of the condition in which monomers are being added to one end of a filament at the same time as they are depolymerizing from the other end. triacylglycerol Ester of glycerol with three fatty acyl side chains. triangulation number A description of a triangular face of an icosahedron indicating the number of triangles into which each face is divided when forming an icosadeltahedron. Triassic period First major division of the Mesozoic era. triazole An azole antifungal agent containing an azole ring with three nitrogen atoms. Examples are fluconazole and itraconazole. trichobothrium (plural trichobothria) Long, thin, hair-like structure with a jointed attachment to the cuticle in arthropods. Used in many terrestrial arthropods for sensing slight displacements or vibrations of the air. trichocyst An organelle in the cell cortex which is capable of undergoing an explosive change in shape to extrude a (generally thread-like) projection in response to stimulation. trichogyne A slender hypha originating from the gametic cell of a protoperithecium that will fuse with a cell of the opposite mating type during fertilization.

trigeminovascular reflex Link between nerve cells and vascular mechanisms such that stimulation of nerve cells in the brainstem via the parasympathetic part of the facial nerve increases blood flow to the head. trilete mark Triradiate feature on a plant spore through which germination occurs. trimeric Describes a macromolecule that is composed of three subunits. triple gene block Three contiguous virus genes located at the 30 terminus of the genomic nucleic acids of potexviruses and carlaviruses. trisomy A condition of having three copies of a given chromosome instead of the normal two. trivalent The association of three chromosomes during meiosis I metaphase, typically observed in Robertsonian translocation heterozygotes. tRNA See transfer RNA. tRNAMet Initiator tRNA not carrying its amino acid. f tRNAMet Initiator tRNA in prokaryotes. The methionine aminof acylated to this tRNA is formylated. tRNAMet tRNA from animal mitochondria, which occurs as f/m fMet-tRNAMet and Met-tRNAMet. The formylated form is f/m f/m active in initiation of translation and the non-formylated form in the elongation of protein synthesis. tRNAMet Initiator tRNA in the eukaryotic cytoplasm. i The methionine aminoacylated to this tRNA is not formylated. tRNAMet The methionine-carrying tRNA that acts during elongam tion of the polypeptide chain. trophectoderm Simple squamous epithelium that covers the blastocyst. Its derivatives are giant cells, the ectoplacental cone and extraembryonic ectoderm, all of which contribute to the chorionic disc of the placenta. trophic factors Proteins that support the survival and growth of cells. trophic level The place of an organism in a food chain. trophonemata Vascularized villous extensions of uterine mucosa in stingrays used for nutrient delivery and respiration. trophozoite The feeding, motile stage of a sporozoan protozoan. trypanosomiasis Disease caused by a protozoan parasite of genus Trypanosoma. TSEs See transmissible spongiform encephalopathies. tsetse fly Dipteran fly of genus Glossina restricted to sub-Saharan Africa. TSH receptor Receptor for thyroid-stimulating hormone. It is a member of the G-protein-coupled receptor family. TSH See thyroid-stimulating hormone. tsunami A great sea wave produced by submarine earth movement or volcanic eruption. TTV1 Virus that infects the archaeon Thermoproteus tenax. tubulin The protein monomer that polymerizes to make microtubules. tuff Consolidated ash derived from a volcanic eruption. Tullgren funnel A funnel used for extracting soil fauna. The funnel holds a soil sample on a wire mesh and this is heated from above with an incandescent bulb to drive animals into a collecting vessel below. tumour suppressor A recessive gene normally involved in preventing cell proliferation, which, when eliminated at both alleles, allows uncontrolled proliferation.

246

Glossary

tumour-infiltrating lymphocytes (TILs) T cells isolated from a tumour which, after treatment with interleukin-2 to stimulate cell proliferation, can mediate tumour regression in some cancers when reintroduced. tunnelling The contribution made to chemical reaction rates by virtue of the wave character of matter. turbinates Scroll-shaped bones in the nasal passages of birds and mammals. turgor A positive internal hydrostatic pressure that develops in plant cells as a result of the osmotic intake of water and the presence of the rigid plant cell wall. It is an important driving force for cell growth. turgor pressure The pressure exerted on the plasma membrane in a plant cell due to the osmotic differences between the cytoplasm and the outside environment. twitching motility A form of surface translocation in bacteria that is attributable to type IV fimbriae. two-component system See two-component regulatory system. two-hybrid system A system for examining protein–protein interactions in vivo. It involves specialized genetic constructs transformed into yeast cells, and can be used to test interactions between yeast proteins or to study other proteins expressed in yeast. type A specimen that is irrevocably tied to that species name. type I hair cells, type II hair cells Hair cells in the vestibular system, which have or lack a calyx, respectively. typology See essentialism. tyrosinase See phenooxidase. tyrosine kinase Any enzyme that phosphorylates certain proteins on one or more tyrosine residues. tyrosine phosphorylation A mechanism for activating or inactivating proteins by phosphorylation of specific tyrosine residues. tyrosyl-tRNA synthetase Enzyme that attaches tyrosine to its cognate tRNA, in a reaction that links the carboxyl group of tyrosine in an ester linkage to the phosphate of AMP. Polymers of glycerol and ribitol joined by phosphate groups, with amino acids or sugars attached. Major components of the Gram-type positive cell wall, these polymers are found in great variety and are highly antigenic.

U1 snRNA A highly conserved small nuclear RNA involved in splicing. The U1 snRNP functions in 50 splice site recognition during splicing. U2 auxiliary factor (U2AF) A dimeric protein containing RNA-binding and RS domains that associates with pre-mRNA near the 30 splice site through direct binding of the pyrimidine-rich sequences and through protein–protein contacts. U2 snRNA A highly conserved small nuclear RNA involved in splicing. The U2 snRNP functions in branch site recognition during splicing. U2 remains associated with the pre-mRNA throughout splicing and may form part of the catalytic core of the spliceosome. ultracentrifuge A high-speed centrifuge capable of reaching up to 200 000 g. ultramafic Rocks that are very rich in magnesium and iron, such as peridotites.

ultrasensitive response Also called a sigmoidal response. A response described by an S-shaped stimulus–response curve. Ultrasensitive responses are more switch-like than Michaelian responses. ultrasonography The use of high-frequency sound (usually 1– 10 MHz range) to generate images of the human body. ultrastructure The structure of a cell that is only visible under a high-power optical microscope or an electron microscope. uncoating The stage of viral replication at which structural proteins are lost and the virus genome is exposed to the replication machinery. underdominance The lower fitness of heterozygotes relative to either homozygote. underreplication The failure to completely replicate the DNA of a chromosome. undulating membrane In certain protists, a fold of the cell membrane united with the flagellar membrane, resulting in attachment of the flagellar axoneme to the cell surface. In the trichomonads it results in the formation of the recurrent flagellum. unequal exchange Recombination between tandemly repeated sequences that are aligned out of register. unfolded The state of a protein molecule that exists in a large number (ensemble) of random conformations that are interconverting. Unfolding is often induced by chemical denaturants or increased temperature. unguligrade A foot posture in which the animal stands on the last phalanx of the digit – on tip toes – with the sole or palm of the foot and the digits off the ground. uniform binding Binding that arises from an enzymatic interaction that comparably stabilizes all internal states. Uniform Resource Locator See URL. unilocular Describes a sporangium formed of a single cell, which undergoes meiotic division commonly followed by mitosis after which the cytoplasm divides to produce four or more spores (usually motile). uniparental disomy The situation where both copies of a particular chromosome are inherited from one parent and none from the other. uniporter A transport protein (carrier) that facilitates passive diffusion of a solute across a membrane. unipotent stem cell A stem cell that gives rise to a single type of differentiated cell. unit cell In crystallography, the representative parallelepiped defined within the crystal, which may be tessellated with itself in three dimensions to build up the complete crystal. unmyelinated fibres Nerve cell axons that are wrapped by glial (or Schwann) cells but without the formation of a myelin sheath. unpaired electron An electron that is the sole occupant of an atomic or molecular orbital. unsaturated fatty acid Fatty acid that contains one or more double bonds in the hydrocarbon tail that can accept hydrogen or other substituents. untranslated region (UTR) The untranslated region of an mRNA, located either 50 (50 -UTR) or 30 (30 -UTR) to the coding region. upstream Toward the 50 end, a term used to indicate direction along a DNA or RNA strand. Transcription proceeds from upstream to downstream on DNA (50 to 30 ). upwelling An area in the ocean where water is moving vertically towards the surface.

247

Glossary

uracil A commonly occurring pyrimidine base, found in RNA. urbilaterian The primitive bilaterian from which the protostome and deuterostome lineages diverged. urea CON2H4, a non-toxic product of nitrogen waste formed by the urea cycle in the liver. urea cycle A metabolic pathway in the liver in which amino groups are donated by ammonia and aspartic acid and combine with carbon to form urea. ureotelic Describes organisms that excrete nitrogen principally in the form of urea. uricotelic Describes organisms that excrete nitrogen principally in the form of uric acid. URL Uniform Resource Locator, an information source described by the communications protocols (http), the Internet address of the host computer and the file location of the specific information. uropod The most terminal posterior appendage on the crustacean abdomen. urticaria Hives, an allergic skin condition characterized by dermal oedema (wheal) and surrounding erythema (redness) as a result of the release of histamine and other mediators from mast cells in the skin. utilization See extraction. UTR See untranslated region. U-turn motif A structural motif first found in tRNA anticodon loops. The loop structure is highly constrained by unusual hydrogen-bond interactions within the loop. uveitis Inflammation of the middle epithelial layer (uvea) of the iris of the eye.

Vmax The maximum steady-state velocity achievable by an enzyme at infinite substrate concentration. It is also equivalent to the value of kcat multiplied by the enzyme concentration. vac genes Genes associated with formation of gas vesicles in bacteria. vac operon An operon of gas vesicle genes. vaccination Administration of a pathogen-derived antigen or the whole microorganism (in killed or non-pathogenic form) in order to produce an antigen-specific immune response that will protect against the disease. vaccine Originally, the cowpox material used by Edward Jenner to immunize against smallpox. The term is now used for any preparation used for preventive immunization against a specific disease-causing microorganism. vadose zone The unsaturated zone above the water table. This zone may be considerably deeper than the soil and include underlying materials unsaturated with water. valve One half of the two-part shell of some molluscs (e.g. clams and cockles) and brachiopods. van der Waals forces, van der Waals interaction A relatively weak interaction between any pair of atoms that are in close proximity to each other. They show a weak bonding interaction due to their fluctuating electrical charges. The strength of the interaction falls off rapidly as the distance between the atoms is increased. varanids A group of mostly large, predatory lizards that include the living monitors. They are characterized by light flexible skulls, long necks and retractable, forked tongues.

variable regions The N-terminal domains of antibody heavy and light chains. They vary in amino-acid sequence between different clones and form the antigen-binding site. varicella-zoster An acute infectious viral disease, known commonly as chickenpox. The same virus also causes shingles. vas deferens A muscular duct that carries sperm from the epididymis to the ejaculatory duct. vascular addressins Tissue- or organ-specific endothelial cellsurface molecules that are ligands for homing receptors on lymphocytes, and which direct the migration of lymphocytes into the appropriate target tissue. vascular bundle In plants, a discrete bundle of xylem and phloem providing a conduit for nutrients and water. vascular cambium A band of meristem around the central vascular tissue that produces secondary vascular tissues in woody plants, which is is responsible for the growth in girth of trunks and branches. vasculitis An inflammatory disorder affecting blood vessels and resulting in destruction of vessel walls and reduction of blood flow to tissues. vasoactive Refers to an agent that exerts an effect on the diameter (calibre) of blood vessels. Vasoconstrictive agents decrease calibre and slow blood flow, and vasodilative agents increase calibre and flow. vasoconstriction A reduction in the cross-sectional area of a blood vessel. vasoconstrictor An agent that causes narrowing of the blood vessels. vasodilation, vasodilatation An increase in the cross-sectional area of a blood vessel. vasodilator-stimulated phosphoprotein (VASP) An adaptor protein that binds to ActA, zyxin and viculin through one proline-rich domain and to profilin through a second proline-rich domain. vasomotor responses Constriction (vasoconstriction) or relaxation (vasodilation) of smooth musculature of blood vessels, often with reference to peripheral arterioles. VASP See vasodilator-stimulated phosphoprotein. Vb Any of the V gene segments at the T-cell receptor b-chain locus. The final T-cell receptor will contain one Vb sequence. VDJ recombination The somatic recombination of germlineencoded gene segments (V and J in the case of immunoglobulin light chains and T-cell receptor a chains, and V, D and J in heavy chain and b chain) to generate a sequence encoding a functional variable region. It occurs only in developing T cells and B cells and is a key event in their development. vector (1) A living agent that can act as a vehicle to transmit a disease from one host to another. (2) A piece of DNA that is capable of propagating itself inside cells and is used to carry DNA sequences of interest in cloning and gene expression experiments. A vector that can replicate in different organisms is called a shuttle vector. A vector that carries the foreign DNA in a form in which it can be expressed is called an expression vector. vegetative cell The growing cell that, in the case of a typical prokaryote, divides by binary fission at a rate corresponding with the level of nutrients. velocity In enzyme kinetics, the rate of an enzyme-catalysed reaction, defined as the change in substrate or product concentration per unit time. velvet worms See Onychophora.

248

Glossary

venomous animal Animal that produces and excretes toxic compounds. ventral Front side or underside of a structure or organism (opposite to dorsal). Towards the belly of a vertebrate. vermiform Worm-shaped. vertebrates Animals, including fishes, amphibians, reptiles, birds and mammals, that possess a dorsal nerve cord supported by a cartilaginous or bony vertebrae (the backbone). Phylum Chordata, subphylum Vertebrata. vertical transmission (1) The transfer of symbiotic microorganisms from parent to offspring, often by direct insertion into (or on to) gametes or other reproductive propagules. (2) Transmission of disease from mother to offspring via infection in the womb. vesicles (1) Small membrane-bound structures in eukaryotic cells that carry material from one compartment to another and to the plasma membrane for secretion. (2) Internal particles produced by bacteria to perform a distinct function. For example, gas vesicles adjust cell buoyancy, vesicles containing bacteriochlorophyll are necessary for photosynthesis. vesicular systems In muscle fibres, the internal membranebounded compartment from which calcium is released to raise internal calcium levels to activate the myofilament system. vesiculoviruses Viruses classified in the genus Vesiculovirus of the family Rhabdoviridae. vessel A water-conducting xylem tissue composed of a line of tracheary elements with open ends. VF See ventricular fibrillation. Vg1 A member of the transforming growth factor \beta superfamily of secreted signalling proteins. It is expressed in Xenopus embryos at the vegetal pole. viability (1) An individual’s ability to survive, measured as the probability of surviving from birth to adulthood. (2) Of seeds, the percentage in a sample that germinate to give normal healthy seedlings. vicariance The separation of a formerly continuous, ancestral population into two or more new populations as a result of geological or climatic changes. vicariance biogeography Approach to biogeography that assumes that the modern distribution of a species is caused by the splitting (vicariance) of a former more extensive range rather than by dispersal events. vigour In plants, a measure of the relative rapidity and uniformity of germination, which results in stronger seedlings and better crop establishment. viraemia The presence of virus in blood. viral oncogene A gene carried by a retrovirus or DNA virus whose product causes cellular transformation in vitro, and/or contributes to tumour induction in vivo. viral quasispecies A dynamic distribution of closely related, replicating mutant and recombinant genomes subjected to a process of genetic variation, competition and selection. viral vectors Replication-deficient viral particles that are used as vehicles to introduce genetic material into target cells. Virchow–Robin spaces Extensions of the subarachnoid space along blood vessels which penetrate the brain parenchyma. virion A complete virus particle containing the genetic material, capsid, and envelope (where applicable). It can exist outside living cells and is capable of infecting cells. viroplasm Inclusion body in a cell where viral replication and assembly is taking place.

virulence A measure of the harm that a pathogen can inflict on its host. virulent phage A phage that produces a lytic infection and cannot enter a prophage state. virus attachment protein The protein on the surface of a virus particle responsible for binding the receptor. virus-like particles (VLPs) Particles that self-assemble following overexpression of the virus capsid protein in a baculovirus expression system. The VLPs are antigenically authentic and morphologically resemble virus particles but contain no nucleic acid. viscera The internal organs, such as heart, liver, intestines. visceral endoderm Extraembryonic cell lineage which gives rise to the yolk sac endoderm. visceral Pertaining to the internal organs. visceromegaly See organomegaly. vital rates Birth and death rates, usually age- or stage-specific. vital stain A dye that is taken up differentially by live and dead cells and can be used, for example, to visualize viral plaques. vitamin C deficiency A state of malnutrition due to a lack of ascorbic acid (vitamin C) in daily foods. vitreous ice Also called amorphous ice. Water that has been frozen in such a way that no crystals have been created. Protein imbedded in vitreous ice is thought to keep its original structure. vitrification Cooling a sample rapidly enough to prevent crystal formation. Vitrification of pure water requires an extremely high cooling speed. vivipary The production of live young directly from the mother’s body, either by retention of eggs until hatching or by the intermediary of a placenta. VLP See virus-like particles. vnf Gene designation of the vanadium nitrogenase system. VNTR See variable number of tandem repeats. volcanic arc A chain of volcanic mountains formed above the subduction zone by magma rising up from the melting of the downgoing plate. voltage-dependent calcium channel, voltage-gated calcium channel An ion channel, situated in the plasma membrane, that is selectively permeable to calcium ions and opens in response to membrane depolarization. voltammetry Technique by which substances can be measured in fluid on the basis of oxidation–reduction reactions generated in probes engineered for these electrochemical reactions. volutin Metachromatically staining polyphosphate storage granule found in some microorganisms. vomeronasal organ A sensory structure in the nose or roof of the mouth of many vertebrates. It responds to specific volatile compounds termed pheromones, which animals use to communicate with each other. In snakes it comprises a pair of blindended chambers in the roof of the mouth. They are lined with sensory cells and process the molecules picked up by the tongue during tongue-flicking. voxel The basic volume-element in the MRI/MRSI image being acquired. It is the three-dimensional analogue of the ‘pixel’. VPg A small 15-kDa protein covalently attached to the 50 -end of the genomic and subgenomic RNAs of caliciviruses. vulva Opening in the ventral epidermis of the adult hermaphrodite nematode, connecting the gonads to the outside. It allows mating and egg-laying.

249

Glossary

wall loosening Proposed interruption of biochemical crosslinks between the load-bearing components of the plant cell wall that allows wall expansion. Wallerian degeneration The degenerative changes in the distal stump of a nerve that occur following axonal damage. Named after Waller, who discovered this phenomenon in 1850. warm-reactive autoantibody An antibody to red blood cells that binds to the cells most efficiently at 371C. It is principally IgG. Watson–Crick base pairing, Watson–Crick pairing rules Hydrogen bonding in nucleic acids between A (adenine) and T (thymine) or U (uracil), and between G (guanine) and C (cytosine). wax ester Ester of a long-chain fatty alcohol with a long-chain fatty acid. WD-40 A repetitive tryptophan–aspartic acid motif in Gb subunits. Web The World Wide Web (WWW), a set of communication protocols with hypertext capability developed at the HighEnergy Physics Laboratory, CERN, in Geneva, Switzerland. Weil disease Severe form of leptospirosis with jaundice and renal failure. wet deposition Deposition of (pollutant) material removed from the atmosphere by precipitation. whole-arm fusion (centric fusion, Robertsonian translocation) Fusion of the long arms of two chromosomes following breakage and loss of the small arms of two acrocentric chromosomes. Wiebel–Palade bodies Storage granules present in endothelial cells. They are a component of the secretory pathway of endothelial cells. Factor VIII, von Willebrand factor, P-selectin, interleukin-8, and endothelin are examples of molecules stored in these organelles in endothelial cells. wilderness A large area that remains essentially unmanaged and unmodified by human beings. wild-type Describes the organism as first isolated from nature, prior to introduction of additional mutations. In some genetic studies a natural variant is arbitrarily chosen as the ‘wild-type’ point of reference. window The parameters of grey scale chosen for image viewing. The window level is centred on the attenuation of the tissue in question. The window width refers to the range of other tissues demonstrated. wing-finger Highly enlarged fourth digit of the pterosaur hand that supported the outer part the wing. Wiskott–Aldrich syndrome Genetic disease characterized by eczema, thrombocytopenia and recurrent infections. witches’ broom Symptoms of abnormal, massed, brush-like development of shoots or roots, mainly on woody plants. wobble position Position 34 in a tRNA, 50 -adjacent to the anticodon. The nucleotide at the position is responsible for non-Watson–Crick (wobble) base-pairing.

wobble, wobble base pair A nonstandard base-pair interaction between the third nucleotide of a codon (the wobble base) and the first nucleotide of the anticodon. In this way a single tRNA is able to decode multiple codons. Wolffian duct The mesonephros duct which subsequently gives rise to the ureteric bud that interacts with metanephric mesenchyme to produce metanephros. work The product of force and distance (measured in joules, J, the energy needed to move 1 newton (N) a distance of 1 m). woven bone Bone tissue that has coarse collagen fibre bundles interwoven in varying directions. Wright–Fisher model A model of reproduction which assumes that the alleles present at a given generation are a random sample from the gene pool of the previous generation.

xenoma A hypertrophic growth of host cells of microsporidial parasites, forming giant cells filled with microsporidial spores that are frequently encountered as tumours on fish and other hosts. X-ray film A thin piece of plastic covered by silver halide crystals capable of undergoing oxidation by high-energy species and thus revealing a latent image.

YAC Yeast artificial chromosome, containing yeast telomeres, origin of replication and centromere. There is a multiple cloning site and positive selection for the cloning vector. yolk sac Extraembryonic tissues (ectoderm, mesoderm and endoderm) that surround and digest yolk stores. In some sharks, it forms the yolk sac placenta.

zalcitabine Nucleoside analogue inhibitor of human immunodeficiency virus (HIV) reverse transcriptase. Used as an anti-HIV drug. zanamivir A neuraminidase inhibitor that acts as an anti-influenza agent. zidovudine Nucleoside analogue inhibitor of human immunodeficiency virus (HIV) reverse transcriptase. Used as an anti-HIV drug. zonal bone Periosteal bone with ‘growth rings’. Z-test A statistical test of significance that measures how far an observation is from the mean in units of standard error. zygote The immediate product of fusion of sperm and egg at fertilization. It comprises a single cell that contains two pronuclei: one derived from the egg and one from the sperm, After nuclear fusion, it divides mitotically to form the embryo.

250

Sign up to vote on this title
UsefulNot useful