meat weight, eviscerated body weight and leg weight, and the body composition traits analyzed were
2006 abdominal fat weight, liver weight and heart weight. Meat quality traits analyzed were initial pH, pH at
Production and metabolism of indole acetic acid in roots and root
nodules of Phaseolus mungo
The mature root nodules of Phaseolus mungo (L.), a leguminous pulse, contain
higher amount of indole acetic acid (IAA) than non-nodulated roots. The tryptophan pool present in
the mature nodule and young roots might serve as a precursor for the IAA production. Presence of
IAA metabolising enzymes - IAA oxidase and peroxidase - indicate the metabolism of IAA in the
nodules and roots. In culture, the symbiont, isolated from the nodules, produced a high amount of
IAA, when tryptophan was supplied in the medium as a precursor. The symbiont preferred l-isomer
over the dl- or d-isomer of tryptophan for IAA production. The important physiological implication of
the IAA production in the legume-Rhizobium symbiosis is discussed.
Reference: Ghosh, S., & Basu, P. (2006). Production and metabolism of indole acetic acid in roots
and root nodules of Phaseolus mungo. Microbiological Research,161(4), 362-366.
doi:10.1016/j.micres.2006.01.001. https://jmg.bmj.com/. Date Accessed 26 January 2019.
The low level expression of chloramphenicol acetyltransferase (CAT)
mRNA in Escherichia coli is not dependent on either Shine-Dalgarno or
the downstream boxes in the CAT gene
Recent studies have shown that the canonical Shine-Dalgarno (SD)-anti-SD
interaction is dispensable for the initiation of translation of certain mRNAs in Escherichia coli.
Alternative non-SD sequences (located upstream from the initiation codon) and also downstream
sequences ("downstream boxes") complementary to 16S rRNA were found to be involved in the
initiation of translation of mRNAs devoid of either SD or any leader sequences. In this study the
chloramphenicol acetyltransferase (CAT) gene was modified to remove the 5' terminal non-translated
region and/or the two potential downstream boxes in the CAT gene. Thus a series of ten CAT gene
constructs was created and expressed in E. coli under a strong constitutive promoter. The results
showed that CAT mRNAs devoid of both leader sequence nucleotides and the two downstream
boxes in the CAT gene remained active in vivo and produced CAT protein in sufficient amounts for
survival of the transformed cells at chloramphenicol concentrations up to 20-30 micrograms/ml.
Reference: Odjakova, M., Golshani, A., Ivanov, G., Haidar, M. A., & Ivanov, I. (2006). The low level
expression of chloramphenicol acetyltransferase (CAT) mRNA in Escherichia coli is not dependent
on either Shine-Dalgarno or the downstream boxes in the CAT gene. Microbiological
Research,153(2), 173-178. doi:10.1016/s0944-5013(98)80037-2. https://jmg.bmj.com/. Date
Accessed 26 January 2019.
Genetic study of meat quality of a male border lines
This research was conducted to estimate genetic and phenotypic parameters of
meat quality, performance,carcass and body composition traits in amale broiler line. Broilers studied
belonged to a sib testprogram, in which data from sibs of the individuals to be selected in this line,
called eliteflock, are collected. Performancetraits analyzedwere body weight at selection, body
weight at slaughter and ultrasound records of pectoral muscle. Carcass traits analyzed were breast
6 h after slaughter, final pH, initial range of pH decline, final range ofpH decline, lightness,redness,
yellowness, weep losses, drip losses, shrink losses, and shear force. (Co)variance components were
estimated by the restricted maximum likelihood method, usingthe MTDFREML software. The
numerator relationship matrix was composed of 107,154 individuals. For pH at 6 h after slaughte4
final pH and lightness, moderate heritability coefficients were estimated; forthe other traits these
coefficients were low Genetic correlation estimates obtained indicated a small association between
meat quality traits and performance, carcass andbody composition traits, except for the selection to
body weight atselection, which seemed to be able to reduce water losses of meat. Genetic
correlation estimates among meat quality traits could orient the understanding of the mechanisms
related to meat quality in the analyzed line; drip losses, shear force and lightness seemed to be able
to determine favorable correlated responses, so their use was recommended as selection criteria if
there was a need for improving meat quality in the analyzed line. However this necessity was not
apparent, since the genetic trends of meat quality traits were small and favorable for meat quality in
the broiler line analyzed.
Reference: Karamichou, E., & Bishop, S. (2006). Genetic and genomic approaches to improving
sheep meat quality. Improving the Sensory and Nutritional Quality of Fresh Meat.
doi:10.1201/9781439829165.ch11. https://jmg.bmj.com/. Date Accessed 26 January 2019.
Biological considerations for a new approach to regulating
genetically modified crops in the United States
Genetic engineering allows scientists to select genes from a variety of species, modify
them, and insert these genes into another organism. This endows an organism not only with a new
segment of DNA, but with a new trait, ability, or phenotype (Table 1). An additional benefit of this
technology is that it is very precise compared to traditional breeding, enabling single genes to be
specifically modified (Fernandez-Cornejo and Caswell 2006). This technology is often used for a
variety of purposes, such as using bacteria to produce pharmaceutical products, or to aid in basic
genetic research. Genetically engineered crops are subject to governmental regulation under three
agencies: the Environmental Protection Agency (EPA), the United States Department of Agriculture
(USDA), and the Food and Drug Administration (FDA), depending on the crop and the type of
modification.
Reference: Liu. (2006). Regulating genetically modified crops in view of environmental risks.
doi:10.26481/dis.20190222al. https://jmg.bmj.com/. Date Accessed 26 January 2019.
Comparative and Integrative genomic approach toward disease gene
ident.
The identification of disease genes (genes that when mutated cause human diseases)
is an important and challenging problem. Proper diagnosis, prevention, as well as care for patients
require an understanding of disease pathophysiology, which is best understood when the underlying
causative gene(s) or genetic element(s) are identified. While the availability of the sequenced human
genome helped to lead to the discovery of more than 1,900 disease genes, the rate of disease gene
discovery is still occurring at a slow pace. The use of genetic linkage methods have successfully led
to the identification of numerous disease genes. However, linkage studies are ultimately restricted by
available meioses (clinical samples) which result in numerous candidate disease genes. This thesis
addresses candidate gene prioritizations in disease gene discovery as applied toward a genetically
heterogeneous disease known as Bardet-Biedl Syndrome (BBS). Specifically, the integration of
various functional information and the development of a novel comparative genomic approach
(Computational Orthologous Prioritization - COP) that led to the identification of BBS3 and BBS11.
Functional data integration and application of the COP method may be helpful toward the
identification of other disease genes.
Reference: Chiang, A. P. (2006). Comparative and integrative genomic approach toward disease
gene identification. doi:10.17077/etd.v3b1w8k9. https://jmg.bmj.com/. Date Accessed 26 January
2019.
Isolation and characterization of high persistence mutants of
Salmonel.
A small fraction of bacterial populations consist of "persistent" cells that are
phenotypically distinct from the majority of cells by their ability to avoid killing by a variety of
antimicrobial challenges. Persistence is distinct from resistance in that persistent cells are unable to
grow in the presence of the antimicrobial agent or treatment, but resume growth after the selection
has been removed. Presently, little is known about the genetic or physiological basis of persistence.
In this study we demonstrate that Salmonella enterica serovar Typhimurium (S. typhimurium)
displays the persistence phenotype. To better understand persistence in this important food-borne
pathogen, we have isolated 6 mutants that show an increased ability to survive exposure to a variety
of antibiotics without an increase in MIC values. All of the mutants isolated were found to have an
extended lag phase, but had wild type growth rates in exponential phase. Characterization of the
mutants indicates that multiple loci appear to contribute to persistence. Mapping the genes for the
high persistence phenotype will reveal new insights into this widely observed phenomenon.
Reference: Slattery, A. R. (2006). Isolation and characterization of high persistence mutants of
Salmonella enterica serotype Typhimurium. doi:10.31274/rtd-180813-8316. https://jmg.bmj.com/.
Date Accessed 26 January 2019.
Genomic and population Genetic studies on THEILEIRA ANNULATA
Tropical theileriosis, caused by the tick-transmitted protozoan Theileria annulata, is a
major disease of cattle in many regions of the developing world. Current research is directed towards
developing a sub-unit vaccine, and it is therefore important that genetic diversity in field populations
of the parasite is investigated and quantified. The recently completed genome sequence provided an
opportunity to develop a panel of genetic markers for population studies and also enabled the
identification of novel antigen genes. The genome was bioinformatically screened to identify micro-
and mini-satellite loci, several of which were PCR amplified from a series of diverse parasite stocks
in order to characterise their polymorphism and to determine their species-specificity. A panel of ten
markers were selected for population genetic studies and were used to genotype
laboratorymaintained cell lines and clonal stocks of T. annulata isolated from different countries. Cell
lines comprised a multiplicity of genotypes, while clonal stocks showed evidence of a single haploid
genome. Preliminary population genetic analysis revealed a large amount of genotypic diversity both
between and within countries and indicated that the parasite population is geographically sub-
structured. Comparison of a limited number of stocks isolated in different countries demonstrated
that genetic differentiation between populations positively correlates with intervening physical
distance. A low standard index of association (I S A) suggested that the population in Tunisia is in
linkage equilibrium, indicating that the parasite possesses a panmictic (randomly mating) population
structure. To confirm these findings, a large number of field isolates from Tunisia and Turkey were
analysed (n = 305). This supported the earlier finding that geographical sub-structuring separates
panmictic populations and an almost identical amount of genetic differentiation between countries
was evident (FST = 0.05). Limited linkage disequilibrium was observed in some populations and this
was attributed to several factors including inbreeding and the Wahlund effect, caused by putatively
immigrant sub-populations. A similar multiplicity of infection was demonstrated in vaccinated and
unvaccinated animals and the immunising genotype did not appear to establish in the field
population. Multiplicity of infection was instead shown to positively correlate with the host age in
several sampling locations.
Reference: Edwards, J. H., Fuhrmann, W., & Vogel, F. (2006). Genetic Counseling. Population
Studies,26(2), 326. doi:10.2307/2173594
Pine Martin CSI: Gaining from tongues and Faces
As a biology student, specializing in animal ecology, this thesis research was an
ideal opportunity to be able to gain more knowledge about genetics and the use of genetic
techniques in the field of animal ecology. I have learned a lot in this respect and I think I am now
able to combine my knowledge by designing genetic based methods to gain more insight into the
ecology of animals. At first, my report was only going to incorporate the part of my research on the
Dutch pine marten genetics, which is now Chapter 2. But as I have spent a lot of time in the lab,
working on the non-invasive genetics study, I decided to also add this part of my research to this
report. The analysis of Chapter 1 is however not very extensive, as I spend most of my time
analysing the data for Chapter 2. The working environment at Alterra gave me the opportunity to
think about my ideas, optimise my results and get the best out of my research. Therefore, I would
like to thank Jan Bovenschen, Hans Peter Koelewijn, Dennis Lammertsma, and Ivo Laros for helping
me during the study, both by discussing my ideas and helping me to get a grip on the ins and outs of
working in a molecular lab. Furthermore, I would like to thank my supervisors Fons Debets and Hugh
Jansman for supporting me during my research and making this thesis research possible.
Reference: Hofmeester. Tim. (2006). Gaining from Decline? International Studies Review,13(3), 526-
528. doi:10.1111/j.1468-2486.2011.01055.x. https://jmg.bmj.com/. Date Accessed 26 January 2019.
New Roles for Model Genetic Organisms in Understanding and Treating
Human Disease: Report From The 2006 Genetics Society of America
Meeting
Fundamental biological knowledge and the technology to acquire it have been immeasurably
advanced by past efforts to understand and manipulate the genomes of model organisms. Has the
utility of bacteria, yeast, worms, flies, mice, plants, and other models now peaked and are humans
poised to become the model organism of the future? The Genetics Society of America recently
convened its 2006 meeting entitled “Genetic Analysis: Model Organisms to Human Biology” to
examine the future role of genetic research. (Because of time limitations, the meeting was unable to
cover the substantial contributions and future potential of research on model prokaryotic organisms.)
In fact, the potential of model-organism-based studies has grown substantially in recent years. The
genomics revolution has revealed an underlying unity between the cells and tissues of eukaryotic
organisms from yeast to humans. No uniquely human biological mechanisms have yet come to light.
This common evolutionary heritage makes it possible to use genetically tractable organisms to
model important aspects of human medical disorders such as cancer, birth defects, neurological
dysfunction, reproductive failure, malnutrition, and aging in systems amenable to rapid and powerful
experimentation. Applying model systems in this way will allow us to identify common genes,
proteins, and processes that underlie human medical conditions. It will allow us to systematically
decipher the gene–gene and gene–environment interactions that influence complex multigenic
disorders. Above all, disease models have the potential to address a growing gap between our ability
to collect human genetic data and to productively interpret and apply it. If model organism research
is supported with these goals in mind, we can look forward to diagnosing and treating human
disease using information from multiple systems and to a medical science built on the unified history
of life on earth.
Rference: Cara, F. D., Rachubinski, R. A., & Simmonds, A. J. (2006). Distinct Roles for Peroxisomal
Targeting Signal Receptors Pex5 and Pex7 in Drosophila. Genetics,211(1), 141-149.
doi:10.1534/genetics.118.301628. https://jmg.bmj.com/. Date Accessed 26 January 2019.
Analysis of Repeat Induced Point (RIP) Mutations in Leptosphaeria
maculans Indicates Variability in the RIP Process Between Fungal Species
Gene duplication contributes to evolutionary potential, yet many duplications in a
genome arise from the activity of “selfish” genetic elements such as transposable elements. Fungi
have a number of mechanisms by which they limit the expansion of transposons, including Repeat
Induced Point mutation (RIP). RIP has been best characterized in the Sordariomycete Neurospora
crassa, wherein duplicated DNA regions are recognized after cell fusion, but before nuclear fusion
during the sexual cycle, and then mutated. While “signatures” of RIP appear in the genome
sequences of many fungi, the species most distant from N. crassa in which the process has been
experimentally demonstrated to occur is the Dothideomycete Leptosphaeria maculans. In the current
study, we show that similar to N. crassa, nonlinked duplications can trigger RIP; however, the
frequency of the generated RIP mutations is extremely low in L maculans (< 0.1%) and requires a
large duplication to initiate RIP, and that multiple premeiotic mitoses are involved in the RIP process.
However, a single sexual cycle leads to the generation of progeny with unique haplotypes, despite
progeny pairs being generated from mitosis. We hypothesize that these different haplotypes may be
the result of the deamination process occurring post karyogamy, leading to unique mutations within
each of the progeny pairs. These findings indicate that the RIP process, while common to many
fungi, differs between fungi and that this impacts on the fate of duplicated DNA.
Reference: Van, Angela P. (2006). F1000Prime recommendation of Analysis of Repeat Induced
Point (RIP) Mutations in Leptosphaeria maculans Indicates Variability in the RIP Process Between
Fungal Species. F1000 - Post-publication Peer Review of the Biomedical Literature.
doi:10.3410/f.734368915.793554519. https://jmg.bmj.com/. Date Accessed 26 January 2019.
Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and
Segregation in Saccharomyces cerevisiae
Pif1 family helicases are found in virtually all eukaryotes.  Saccharomyces
cerevisiae (Sc) encodes two Pif1 family helicases, ScPif1 and Rrm3. ScPif1 is multifunctional,
required not only for maintenance of mitochondrial DNA but also for multiple distinct nuclear
functions. Rrm3 moves with the replication fork and promotes movement of the fork through ∼1400
hard-to-replicate sites, including centromeres. Here we show that ScPif1, like Rrm3, bound robustly
to yeast centromeres but only if the centromere was active. While Rrm3 binding to centromeres
occurred in early to mid S phase, about the same time as centromere replication, ScPif1 binding
occurred later in the cell cycle when replication of most centromeres is complete. However, the
timing of Rrm3 and ScPif1 centromere binding was altered by the absence of the other helicase,
such that Rrm3 centromere binding occurred later in pif1-m2 cells and ScPif1 centromere binding
occurred earlier in rrm3Δ cells. As shown previously, the modest pausing of replication forks at
centromeres seen in wild-type cells was increased in the absence of Rrm3. While a lack
of ScPif1 did not result in increased fork pausing at centromeres, pausing was even higher
in rrm3Δ pif1Δ cells than in rrm3Δ cells. Likewise, centromere function as monitored by the loss rate
of a centromere plasmid was increased in rrm3Δ but not pif1Δ cells, and was even higher
in rrm3Δ pif1Δ cells than in rrm3Δ cells. Thus, ScPif1promotes centromere replication and
segregation, but only in the absence of Rrm3. These data also hint at a potential post-S phase
function for ScPif1 at centromeres. These studies add to the growing list of ScPif1 functions that
promote chromosome stability.
Reference: Chen, C., Pohl, T. J., Pott, S., & Zakian, V. A. (2006). Two Pif1 Family DNA Helicases
Cooperate in Centromere Replication and Segregation in Saccharomyces
cerevisiae. Genetics,211(1), 105-119. doi:10.1534/genetics.118.301710. https://jmg.bmj.com/. Date
Accessed 26 January 2019.
MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming
in Caenorhabditis elegans
Chromatin regulators play important roles in the safeguarding of cell identities by
opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell
identities by reprogramming approaches. Our knowledge of chromatin regulators acting as
reprogramming barriers in living organisms needs improvement as most studies use tissue culture.
We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase
RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells
against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells
against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene
on chromosome 15) and is required during germline development in C. elegans. However, MRG-1’s
function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further
provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions.
Conserved chromatin regulators may have similar functions in higher organisms, and therefore,
understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human
cells.
Reference: Herman, R. K. (2006). F1000Prime recommendation of MRG-1/MRG15 Is a Barrier for
Germ Cell to Neuron Reprogramming in Caenorhabditis elegans. F1000 - Post-publication Peer
Review of the Biomedical Literature. doi:10.3410/f.734438782.793555622. https://jmg.bmj.com/.
Date Accessed 26 January 2019.
Distinct Roles for Peroxisomal Targeting Signal Receptors Pex5 and
Pex7 in Drosophila
Peroxisomes are ubiquitous membrane-enclosed organelles involved in lipid
processing and reactive oxygen detoxification. Mutations in human peroxisome biogenesis genes
(Peroxin, PEX, or Pex) cause developmental disabilities and often early death. Pex5 and Pex7 are
receptors that recognize different peroxisomal targeting signals called PTS1 and PTS2, respectively,
and traffic proteins to the peroxisomal matrix. We characterized mutants of Drosophila melanogaster
Pex5 and Pex7 and found that adult animals are affected in lipid processing. Pex5 mutants exhibited
severe developmental defects in the embryonic nervous system and muscle, similar to what is
observed in humans with PEX5 mutations, while Pex7 fly mutants were weakly affected in brain
development, suggesting different roles for fly Pex7 and human PEX7. Of note, although no PTS2-
containing protein has been identified in Drosophila, Pex7 from Drosophila can function as a bona
fide PTS2 receptor because it can rescue targeting of the PTS2-containing protein thiolase to
peroxisomes in PEX7 mutant human fibroblasts.
Reference: Cara, F. D., Rachubinski, R. A., & Simmonds, A. J. (2006). Distinct Roles for
Peroxisomal Targeting Signal Receptors Pex5 and Pex7 in Drosophila. Genetics,211(1), 141-149.
doi:10.1534/genetics.118.301628. https://jmg.bmj.com/. Date Accessed 26 January 2019.
 Conidial Morphogenesis and Septin-Mediated Plant Infection Require
Smo1, a Ras GTPase-Activating Protein in Magnaporthe oryzae

The pathogenic life cycle of the rice blast fungus  Magnaporthe oryzae involves a series
of morphogenetic changes, essential for its ability to cause disease. The smo mutation was identified
> 25 years ago, and affects the shape and development of diverse cell types in M. oryzae, including
conidia, appressoria, and asci. All attempts to clone the SMO1 gene by map-based cloning or
complementation have failed over many years. Here, we report the identification of SMO1 by a
combination of bulk segregant analysis and comparative genome analysis. SMO1 encodes a
GTPase-activating protein, which regulates Ras signaling during infection-related development.
Targeted deletion of SMO1 results in abnormal, nonadherent conidia, impaired in their production of
spore tip mucilage. Smo1 mutants also develop smaller appressoria, with a severely reduced
capacity to infect rice plants. SMO1 is necessary for the organization of microtubules and for septin-
dependent remodeling of the F-actin cytoskeleton at the appressorium pore. Smo1 physically
interacts with components of the Ras2 signaling complex, and a range of other signaling and
cytoskeletal components, including the four core septins. SMO1 is therefore necessary for the
regulation of RAS activation required for conidial morphogenesis and septin-mediated plant infection.

Reference: Kershaw, M. J., Basiewicz, M., Soanes, D. M., Yan, X., Ryder, L. S., Csukai, M., . . .
Talbot, N. J. (2006). Conidial Morphogenesis and Septin-Mediated Plant Infection Require Smo1, a
Ras GTPase-Activating Protein in Magnaporthe oryzae. Genetics,211(1), 151-167.
doi:10.1534/genetics.118.301490. https://jmg.bmj.com/. Date Accessed 26 January 2019.

Epidermal Remodeling in Caenorhabditis elegansDauers Requires the Nidogen

Domain Protein DEX-1

Phenotypic plasticity is a critical component of an organism’s ability to thrive in a

changing environment. The free-living nematode Caenorhabditis elegans adapts to unfavorable
environmental conditions by pausing reproductive development and entering a stress-resistant larval
stage known as dauer. The transition into dauer is marked by vast morphological changes, including
remodeling of epidermis, neurons, and muscle. Although many of these dauer-specific traits have
been described, the molecular basis of dauer-specific remodeling is still poorly understood. Here we
show that the nidogen domain-containing protein DEX-1 facilitates stage-specific tissue remodeling
during dauer morphogenesis. DEX-1 was previously shown to regulate sensory dendrite formation
during embryogenesis. We find that DEX-1 is also required for proper remodeling of the stem cell-
like epidermal seam cells. dex-1 mutant dauers lack distinct lateral cuticular alae during dauer and
have increased sensitivity to sodium dodecyl sulfate. Furthermore, we find that DEX-1 is required for
proper dauer mobility. We show that DEX-1 is secreted from the seam cells during dauer, but acts
locally in a cell-autonomous manner. We find that dex-1 expression during dauer is regulated
through DAF-16/FOXO–mediated transcriptional activation. Finally, we show that dex-1acts with a
family of zona pellucida domain-encoding genes to regulate dauer-specific epidermal remodeling.
Taken together, our data indicate that DEX-1 is an extracellular matrix component that plays a
central role in C. elegans epidermal remodeling during dauer.

Reference: Flatt, K., Beshers, C., Unal, C., & Schroeder, N. (2006). The nidogen-domain containing
protein DEX-1 is required for epidermal remodeling inC. elegansdauers. doi:10.1101/277798.
https://jmg.bmj.com/. Date Accessed 26 January 2019.