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SUBMITTED TO: MR. HARSH KUMAR (LECT. IN BIOTECH.)
SUBMITTED BY:ROLL NO.R108B039 REG.NO.1040070114 B.TECH. BIOTECH 3RD SEM
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Introduction How do geneticist indicate the location of gene References
I would like to express my gratitude to all those who gave me the possibility to complete this term paper. I want to thank the Department of BIOTECHNOLOGY of LOVELY PROFESSIONAL UNIVERSITY for giving me permission to commence this Term paper, to do the necessary research work and to use departmental data. I have furthermore to thank to Mr. Harsh Kumar, Lect.In Concepts of Biotech., which gave and confirmed this permission and encouraged me to go ahead with my term paper. I am deeply indebted to my supervisor Lect. Harsh Kumar whose help, stimulating suggestions and encouragement helped me in all the time of research for and writing of this term paper.
How do geneticists indicate the location of a gene?
Geneticists use maps to describe the location of a particular gene on a chromosome. One type of map uses the cytogenetic location to describe a gene’s position. The cytogenetic location is based on a distinctive pattern of bands created when chromosomes are stained with certain chemicals. Another type of map uses the molecular location, a precise description of a gene’s position on a chromosome. The molecular location is based on the sequence of DNA building blocks (base pairs) that make up the chromosome.
Geneticists use a standardized way of describing a gene’s cytogenetic location. In most cases, the location describes the position of a particular band on a stained chromosome:17q12 It can also be written as a range of bands, if less is known about the exact location: 17q12-q21 The combination of numbers and letters provide a gene’s “address” on a chromosome. This address is made up of several parts: • The chromosome on which the gene can be found. The first number or letter used to describe a gene’s location represents the chromosome. Chromosomes 1 through 22 (the autosomes) are designated by their chromosome number. The sex chromosomes are designated by X or Y. The arm of the chromosome. Each chromosome is divided into two sections (arms) based on the location of a narrowing (constriction) called the centromere. By convention, the shorter arm is called p, and the longer arm is called q. The chromosome arm is the second part of the gene’s address. For example, 5q is the long arm of chromosome 5, and Xp is the short arm of the X chromosome. The position of the gene on the p or q arm. The position of a gene is based on a distinctive pattern of light and dark bands that appear when the chromosome is stained in a certain way. The position is usually designated by two digits (representing a region and a band), which are sometimes followed by a decimal point and one or more additional digits (representing sub-bands within a light or dark area). The number indicating the gene position increases with distance from the centromere. For example: 14q21 represents position 21 on the long arm of chromosome 14. 14q21 is closer to the centromere than 14q22.
Sometimes, the abbreviations “cen” or “ter” are also used to describe a gene’s cytogenetic location. “Cen” indicates that the gene is very close to the centromere. For example, 16pcen refers to the short arm of chromosome 16 near the centromere. “Ter” stands for terminus, which indicates that the gene is very close to the end of the p or q arm. For example, 14qter refers to the tip of the long arm of chromosome 14. (“Tel” is also sometimes used to describe a gene’s location. “Tel” stands for telomeres, which are at the ends of each chromosome. The abbreviations “tel” and “ter” refer to the same location.)
The CFTR gene is located on the long arm of chromosome 7 at position 7q31.2.
The Human Genome Project, an international research effort completed in 2003, determined the sequence of base pairs for each human chromosome. This sequence information allows researchers to provide a more specific address than the cytogenetic location for many genes. A gene’s molecular address pinpoints the location of that gene in terms of base pairs. For example, the molecular location of the APOE gene on chromosome 19 begins with base pair 50,100,901 and ends with base pair 50,104,488. This range describes the gene’s precise position on chromosome 19 and indicates the size of the gene (3,588 base pairs). Knowing a gene’s molecular location also allows researchers to determine exactly how far the gene is from other genes on the same chromosome. Different groups of researchers often present slightly different values for a gene’s molecular location. Researchers interpret the sequence of the human genome using a variety of methods, which can result in small differences in a gene’s molecular address. For example, the National Centre for Biotechnology Information (NCBI) identifies the molecular location of the APOE gene as base pair 50,100,901 to base pair 50,104,488 on chromosome 19. The Ensemble database identifies the location of this gene as base pair 50,100,879 to base pair 50,104,489 on chromosome 19. Neither of these addresses is incorrect; they represent different interpretations of the same data. Cells become cancerous mainly because they lose control of their growth. To better understand how this happens, a new study at Ohio State University's Comprehensive Cancer Center looks at four genes that help regulate cell growth in embryos and that contribute to cancer in adults. The genes – E2f1, E2f2, and E2f3a and E2f3b – are
generally believed to work together to help control cell proliferation, a belief that comes from experiments using only cells. Cancer researchers at The Ohio State University carried out several studies in an animal model to learn if it is also true in the body during development. The scientists also hoped to learn why many organisms, including humans, have multiple E2F genes of this type, while other animals have just one copy.Their study, published in the Aug. 28 issue of the journal Nature, shows that mice need just one of the four genes to develop from fertilized eggs through adulthood."We found that if E2f3a is present, the animals can develop normally through adulthood, even when all the other genes are absent," says study leader Gustavo Leone, an associate professor of molecular virology, immunology and medical genetics at Ohio State's Comprehensive Cancer Center. Then came the real surprise. To learn if the E2f3a gene was doing something truly critical and different from the other three E2Fs, the scientists swapped it with one of the others – they replaced it first with E2f3 gene, then with the E2f1. Neither change made any difference; these "swapped" mice developed quite normally. "If the E2F3a gene was doing something unique, replacing it with one of the others should prevent development," Leone says. "But the animals still developed just fine. "We conclude from this that it is the gene's location in the genome, plus the timing and level of its activity, that makes it so important during development," he says. But if just one of the genes is sufficient for development, why are the others needed? "Organisms above insects have multiple E2Fs, and these findings don't tell us what the others are doing," Leone says. "We surmise that the other genes are required for adult survival under the stressful conditions in the wild. We are investigating that now."
Chromosomal location of human metallothionein genes: implications for Menkes' disease CJ Schmidt, DH Hamer, and OW McBride
Human metallothioneins are encoded by a complex multigene family. The chromosomal location of these genes has been determined by gel transfer hybridization analysis of the DNA from human-rodent cell hybrids. Chromosome 16 contains a cluster of metallothionein sequences, including two functional metallothionein I genes and a functional metallothionein II gene. The remaining sequences, including a processed pseudogene, are dispersed to at least four other autosomes. The absence of metallothionein sequences from the X chromosome indicates that Menkes' disease, an X-linked disorder of copper metabolism, affects metallothionein expression by a trans-acting mechanism. Mutants of Escherichia coli K-12 unable to synthesize the iron-sequestering compound, enterochelin, from 2,3-dihydroxybenzoate have been isolated and divided into three classes on the basis of tests for enzymatic complementation. The genes affected (designated entD, entE, and entF) have been mapped by cotransduction and are located at about minute 14 on the E. coli genome. They were found to be closely linked to other genes (entA, entB, and entC) concerned with enterochelin biosynthesis and a gene (fep) concerned with the uptake of the iron-enterochelin complex. No detectable diffusible intermediate in the formation of enterochelin from 2,3dihydroxybenzoate was formed by cell extracts of mutants carrying mutations in the entD, entE, or entF genes. Karnal bunt (Tilletia indica Mitra) infestation of wheat (Triticum aestivum L.) kernels reduces grain quality. Deployment of genetic resistance would be preferable to chemical applications for control of the disease. Inoculation studies were carried out in a wheat mapping population with the aim of locating genes for resistance. Recombinant inbred (RI) lines from a cross between resistant synthetic wheat (Triticum turgidum ‘Altar 84’ & T. tauschii) and the susceptible common wheat cultivar ‘Opata 85’ were inoculated with Karnal bunt sporidial suspension and evaluated for symptom development in the field for three seasons and in the greenhouse. Based on restriction fragment length polymorphism (RFLP) analyses, regions on chromosome arms 3BS and SAL carrying marker alleles from the Altar durum parent were consistently associated with reduced kernel disease. Main marker effects accounted for up to 32% of disease variation in the field but only 15% in the greenhouse, where the level of disease was higher, suggesting an environmental component of resistance. The tagging of these Karnal bunt partial-resistance genes in tetraploid and hexaploid backgrounds may facilitate the accumulation of resistance via marker-assisted transfer to susceptible durum and common wheat cultivars. This practice should reduce laborious disease screening requirements.
Location, Location, Location Important For Genes, Too
Cells become cancerous mainly because they lose control of their growth. To better understand how this happens, a new study at Ohio State University’s Comprehensive Cancer Centre looks at four genes that help regulate cell growth in embryos and that contribute to cancer in adults. The genes – E2f1, E2f2, and E2f3a and E2f3b – are generally believed to work together to help control cell proliferation, a belief that comes from experiments using only cells. Cancer researchers at The Ohio State University carried out several studies in an animal model to learn if it is also true in the body during development. The scientists also hoped to learn why many organisms, including humans, have multiple E2F genes of this type, while other animals have just one copy.Their study, published in the Aug. 28 issue of the journal Nature, shows that mice need just one of the four genes to develop from fertilized eggs through adulthood.“We found that if E2f3a is present, the animals can develop normally through adulthood, even when all the other genes are absent,” says study leader Gustavo Leone, an associate professor of molecular virology, immunology and medical genetics at Ohio State’s Comprehensive Cancer Center.Then came the real surprise. To learn if the E2f3a gene was doing something truly critical and different from the other three E2Fs, the scientists swapped it with one of the others – they replaced it first with E2f3 gene, then with the E2f1. Neither change made any difference; these “swapped” mice developed quite normally. “If the E2F3a gene was doing something unique, replacing it with one of the others should prevent development,” Leone says. “But the animals still developed just fine. “We conclude from this that it is the gene’s location in the genome, plus the timing and level of its activity, that makes it so important during development,” he says. But if just one of the genes is sufficient for development, why are the others needed? “Organisms above insects have multiple E2Fs, and these findings don’t tell us what the others are doing,” Leone says. “We surmise that the other genes are required for adult survival under the stressful conditions in the wild. We are investigating that now.” The tetrasomics of the homoeologous groups 2, 5 and 7 of ‘Chinese Spring’ wheat were, together with the euploid standard, screened at the seedling stage for sensitivity to exogenously applied gibberellic acid (GA3). Whilst the seedling length of lines tetrasomic for group 2 chromosomes were taller and those for chromosomes 5A, 5D and 7D shorter in both treatments (with and without GA3) compared to the euploid control, the remaining tetrasomics — 5B, 7A and 7B — were significantly shorter than the euploids in the GA variant only. These results suggest the presence of additional genetic factors for GA insensitivity on chromosomes of the groups 5 and 7 of hexaploid wheat. This corresponds with the localization of GA insensitive dwarfing genes on the homoeologous chromosomes 5R and 7R in diploid rye.
Chromosomal location of the genes encoding complement components C5 and factor H in the mouse
P D'Eustachio, T Kristensen, RA Wetsel, R Riblet, BA Taylor and BF Tack
Complementary DNA probes corresponding to the factor H and C5 polypeptides have been used to determine the chromosomal localizations of these two complement components. Both probes revealed complex and polymorphic arrays of DNA fragments in Southern blot analysis of mouse genomic DNA. Following the distribution of these bands in panels of somatic cell hybrids carrying various combinations of mouse chromosomes on a constant rat or Chinese hamster background allowed the localization of the C5-associated fragments to proximal chromosome 2 and the localization of the factor H-associated fragments to chromosome 1 or chromosome 3. Following the inheritance of DNA restriction fragment-length polymorphisms revealed by the probes in recombinant inbred mouse strains allowed the factor H-associated fragments to be mapped to Sas-1 on chromosome 1, and the C5-associated fragments to be mapped to Hc. Analysis of three-point crosses, in turn, placed the latter locus 19 cM distal to Sd on chromosome 2. We have designated the two loci Cfh and C5, respectively. This genetic analysis raises the possibility that C5 and factor H are both encoded by complex loci composed of distinct structural and regulatory genes.
In Escherichia coli, the following genes are involved in motility and chemotaxis. The H gene is the structural gene for flagellin. Mutation in the mot gene results in
paralysis of the flagella, and mutation in the fla genes leads to an absence of flagella. The cheA, cheB, and cheC genes are required for chemotaxis. The chromosomal location of these genes has now been determined. The majority are clustered in a small region around uvrC, between his and aroD, in the order his-cheC-H-uvrC-motcheA-cheB-aroD. The Fla genes are located in the same region, and also between trp and gal. The results indicate that many of the genes are homologous to those which have been studied in Salmonella typhimurium.
Autonomic location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution.
Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of human X- and Y-borne genes in distantly related mammals and non-mammalian vertebrates has proved valuable to help deduce the evolution of this unique part of the genome. The platypus, a monotreme mammal distantly related to eutherians and marsupials, has an extraordinary sex chromosome system comprising five X and five Y chromosomes that form a translocation chain at male meiosis. The largest X chromosome (X1), which lies at one end of the chain, has considerable homology to the human X. Using comparative mapping and the emerging chicken database, we demonstrate that part of the therian X chromosome, previously thought to be conserved across all mammals, was lost from the platypus X1 to an autosome. This region included genes flanking the XIST locus, and also genes with Y-linked homologues that are important to male reproduction in therians. Since these genes lie on the X in marsupials and eutherians, and also on the homologous region of chicken chromosome 4, this represents a loss from the monotreme X rather than an additional evolutionary stratum of the human X.
Chromosomal location of additional genes for resistance to Corynebacterium (Clavibacter) michiganense ssp. nebraskense
Goss's wilt (Leaf Freckles and Wilt) is a vascular and foliar disease incited by the bacterial pathogen Corynebacterium (Clavibacter) michiganense ssp. nebraskense. We previously reported use of crosses between M14 (resistant) translocation stocks and inbred A632 (susceptible) to locate a gene for resistance on the long arm of chromosome 7 (MGCNL 59:57, 1985). Similar field tests conducted in 1985 indicate that genes for resistance are also located on the short arm of chromosome 4 and the long arm of chromosome 8 (Table 1). These findings are consistent with a quantitative mode of inheritance for resistance to this disease.Environment appears to influence expression of this disease. The genetic stocks involving translocation T4-9e demonstrated a significant difference in 1985 but did not in 1984. T8-9(6673) was not in 1984 tests. The effect of environment was also demonstrated in greenhouse tests. Genetic stocks involving translocations T4-9e, T7-9a and T8-9(6673), all of which demonstrated differences in the field, were greenhouse tested in fall 1985. Only stocks involving translocation T4-9e demonstrated a significant difference.Preliminary results from greenhouse studies conducted with A632 (susceptible) translocation stocks crossed with Mo20W (resistant) are supportive of a quantitative mode of inheritance for susceptibility to this disease. These stocks will be field tested before chromosomal locations of genes effecting susceptibility are reported. Of interest is the potential location of a gene on the short arm of chromosome 4 that causes a susceptible reaction. Many sweet corn and popcorn cultivars have demonstrated susceptibility to this disease. The sugary-1 locus and the gametophyte factor locus, Ga, are both found on the short arm of chromosome 4. It may be worthwhile to evaluate for a possible relationship between selection for sugary-1 in sweet corn or selection for gametophyte factor in popcorn and the level of susceptibility to Goss's wilt.
Divergent location of ribosomal genes in chromosomes of fish thorny-headed worms, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala).
We studied distribution of ribosomal DNA (rDNA) sequences along with chromosomal location of the nucleolar organizer regions (NORs) in males of two fish parasites, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala). Fluorescence in situ hybridization with 18S rDNA probe identified two clusters of rDNA in each species, but revealed a remarkable difference in their location on chromosomes. In P. laevis, the rDNA-FISH signals were found in long arms of the first chromosome pair and in short arms of the second pair. Whereas in P. tereticollis, rDNA clusters were located in long arms of both the first and second chromosome pairs. The divergent location of rDNA clusters in the chromosome No. 2 supports current classification of P. tereticollis, previously considered a synonym of P. laevis, as a separate species. A possible scenario of the second chromosome rearrangement during karyotype evolution of the two species involves two successive pericentric inversions. In both species, one or two prominent nucleoli were apparent within interphase nuclei stained with either silver nitrate or a fluorescent dye YOYO-1. However, a single large nucleolus was observed in early stages of mitosis and meiosis I regardless the number of rDNA clusters. Nevertheless, two bivalents with silverstained NORs in diakinesis and two silver-stained sites in early prophase II nuclei
indicated that all NORs are active. This means that each Pomphorhynchus NOR generates a nucleolus, but the resulting nucleoli have a strong tendency to associate in a large body.
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