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1
Nordquist, Niklas. "Genetic Studies of Rheumatoid Arthritis using Animal Models." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5117-9/.
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Souleman, Dima. "Genetic consequences of colonization of a metal-polluted environment, population genetics and quantitative genetics approaches." Thesis, Lille 1, 2017. http://www.theses.fr/2017LIL10006/document.
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Les habitats naturels sont de plus en plus détruits et fragmentés par l'expansion urbaine et les activités humaines. La fragmentation des espaces naturels et agricoles par les bâtiments et les nouvelles infrastructures affecte la taille, la connectivité et la qualité des habitats. Les populations d’organismes vivants sur ces territoires anthropisés sont alors plus isolées. Or, la différenciation entre populations d’un même organisme dépend de processus démographiques et génétiques tels que la dérive génétique, le flux génétique, la mutation et la sélection naturelle. La persistance et le développement des populations dans des conditions environnementales modifiées dépendent de mécanismes de tolérance. Dans ce contexte, l'introduction de contaminants tels que des métaux dans l'environnement peut influencer l'évolution des plantes et des animaux en modifiant les forces évolutives et en créant des différences entre populations. Dans ce travail, l’attention a été portée sur les conséquences génétiques de la pollution métallique sur deux espèces, le ver de terre Lumbricus terrestris et une plante modèle Arabidopsis halleri. Deux approches différentes ont été utilisées pour étudier la réponse génétique à la contamination métallique : une approche de génétique des populations chez L. terrestris et une approche de génétique quantitative chez A. halleri. Tout d’abord, il s’est agi d’identifier et de valider de nouveaux marqueurs microsatellites chez L. terrestris. Ensuite, ces marqueurs ont été utilisés afin de caractériser la diversité génétique neutre chez des vers collectés sur des sites agricoles et urbanisés. Parallèlement, l'architecture génétique de la tolérance et de l'hyperaccumulation de Zn chez A. halleri a été explorée à l’aide d’un croisement intraspécifique entre une population métallicole et une population non métallicole. Une densité élevée de marqueurs SNP a été utilisée pour procéder à l'étape de cartographie QTLNatural habitats are more and more destructed and fragmented by urban expansion and human activities. The fragmentation of natural and agricultural areas by buildings and new infrastructures affects the size, connectivity and the quality of habitats. The populations of organisms inhabiting these anthropized territories are then more isolated. However, differentiation between populations of the same organism depends on demographic and genetic processes such as genetic drift, gene flow, mutation and natural selection. Only species that have developed special tolerance mechanisms can persist under changed environmental conditions. The introduction of contaminants such as metals in the environment may influence plants and animals evolution by modifying the evolutionary forces and thus generating differences between populations. In this work, attention was focused on the genetic consequences of metallic pollution on two species, the earthworm Lumbricus terrestris and the plant model Arabidopsis halleri. Two different approaches have been used to study the genetic response to metallic contamination: a population genetic approach was performed in L. terrestris and a quantitative genetic approach was carried on in A. halleri. First, it was a question of identifying and validating new microsatellite markers in L. terrestris. These markers were then used to characterize the neutral genetic diversity in worms collected from agricultural and urban sites. Secondly, genetic architecture of Zn tolerance and Zn hyperaccumulation was conducted investigated for the first time using an intraspecific crossing between metallicolous and non-metallicolous individuals of A. halleri. High density of SNP markers was used to proceed to the QTL mapping step
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Wright, Galen Egan Buckley. "Molecular genetic analysis of two genes, CYP2D6 and COMT, in the schizophrenia-susceptibility locus on chromosome 22q in the Xhosa population." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/20366.
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Cowie, Philip David. "Analysis of the effects of disease-associated variation within a cis-regulatory element of the CNR1 locus on CNR1 promoter dynamics." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=225652.
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Genetic variation within the cannabinoid 1 receptor (CB1R) locus (CNR1) has been repeatedly associated with drug addiction pathologies. Genomic annotation of CNR1 indicates the vast majority of this genetic variation likely results in altered transcriptional regulation of the CNR1 gene as a mechanistic link to the disease phenotype. There is a lack of information describing the regulation of CNR1 transcription and the potential impact of disease-associated variation within the CNR1 locus on its transcriptional regulation. This study investigates the impact of an evolutionary conserved regulatory region of CNR1, termed ECR1, and the disease-associated variation contained within, on the transcriptional activity of the cognate CNR1 promoter region. Reporter assays conducted in primary hippocampal cells demonstrate that CNR1 promoter exhibits variable transcriptional activity during periods of CB1R signalling and cell depolarisation. Coupled to allelic variants of ECR1, the CNR1 promoter shows significant changes in transcriptional activity under resting conditions indicating that disease-associated variation within ECR1 may decrease CNR1 transcription. Further, alleles of ECR1 can drive allele-specific transcriptional responses from the CNR1 promoter during periods of CB1R stimulation and cell depolarisation. The results highlight the potential for disease-associated regulatory variation of the CNR1 locus to create stratified transcriptional responses to specific cell signalling scenarios and putatively to clinical strategies employing pharmacological agents. Furthermore, investigation of DNA-protein interactions at the allelic ECR1 region demonstrate that disease-associated variation within ECR1 alters DNA-protein interactions within the nucleus consistent with a decrease in transcriptional activity in the disease-associated allele variant. Collectively the current work supports the hypothesis that disease-associated variation within the ECR1 regulatory region of the CNR1 locus has the capacity to significantly impact on CNR1 promoter transcriptional activity. It is posited that allele-specific transcriptional effects may have a major impact on the susceptibility of individuals to drug addiction or on responses to clinical pharmacological treatments.
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Armbruster, Steven C. (Steven Christopher). "Characterization of the OCT Plasmid-Encoded Mercury Resistance Genetic Locus in Pseudomonas putida." Thesis, University of North Texas, 1989. https://digital.library.unt.edu/ark:/67531/metadc500381/.
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A 17.1 Kb genetic element encoding for mercury resistance (OCT-Hg^r) was shown to translocate from its original location on the OCT plasmid to the resistance plasmid, RPl, in Pseudomonas putida. Analysis of RPl-Hg^r recombinant plasmids revealed that insertion of mercury resistance genes into RPl could occur at a variety of sites, with all recombinants having common EcoRI restriction fragments of 9.4, 3.8, 2.3, and 1.6 Kb, derived from the insertion. Hybridization analysis suggested the existence of extensive homology between this insertion and the prototypic mercury resistance transposon, Tn501, as well as the location of a similar merA sequence. Although the overall size was shown to be quite different from Tn501, striking physical similarities are shared between these two elements.
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Porter, Susan Dorothy. "Molecular genetic analysis of the saccharomyces cerevisiae Mat Locus." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/29166.
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The MAT∝ locus of the yeast Saccharomyces cerevisiae encodes two regulatory proteins responsible for determining the ∝cell type. The MAT∝1 gene encodes ∝1, a positive regulator of ∝cell-specific genes, whereas the MAT∝2 gene encodes a negative regulator of a cell-specific genes (∝2). MAT∝2. (in conjunction with the MATα1 gene) also determines the α/∝ diploid cell type by repressing haploid-specific genes. ∝2 exerts its effect at the transcriptional level in the ∝ cell by binding to a sequence located upstream of α cell-specific genes.
The present study undertook to examine, through in vitro genetic manipulation, the structure/function relationship of the MAT∝ regulatory proteins, particularly∝2, in their role as gene regulators. The construction of mutant MAT∝2 genes containing termination codons at various points within the gene, and subsequent transformation of the mutant genes into mat∝2 yeast, indicated that the carboxy-terminal one-third of the gene product was necessary for full repressor activity in the haploid as well as in the diploid.
A segment within the carboxy-terminal one-third of ∝2 displays some homology to the higher eukaryote homeo domain as well as to a prokaryotic bihelical DNA-binding structural motif. This region of the gene was subjected to semi-random missense mutagenesis in vitro and the mutant genes were analyzed by transformation into strains containing chimaeric genes that encode β-galactosidase from ∝2 and a1/∝2. repressible promoters.
In this manner it was demonstrated that most of those residues in ∝2. which correspond to conserved amino acids in the prokaryotic DNA-binding structure and in the homeo domain are essential for the two repressor activities of ∝2. Several mutations more severely affected the ability of ∝2 to repress α-specific genes than haploid-specific genes.
Analysis of the temperature dependence of the activities of some of the mutants was consistent with the existence of a helix-turn-helix structure at this region of the protein. Finally, further analysis of some of these mutants in vitro confirmed that the observed defect correlated with a loss of DNA-binding activity.Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Laurencikiene, Jurga. "Regulation of germline transcription in the immunoglobulin heavy chain locus /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-989-7/.
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Farquhar, R. "The spoIVC locus of Bacillus subtilis." Thesis, University of Oxford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370251.
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Wilkes, David Charles. "Molecular analysis of the Friedreich's ataxia locus." Thesis, Imperial College London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309737.
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Nicholls, R. D. "Molecular genetics of the human #alpha#-globin locus." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.375277.
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Puri, V. "Molecular genetics of the 1q23.3 schizophrenia susceptibility locus." Thesis, University College London (University of London), 2008. http://discovery.ucl.ac.uk/1444474/.
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Family based linkage studies have confirmed that part of chromosome lq23.3 contains a susceptibility gene for schizophrenia. This region was investigated by tests of allelic and haplotypic association in order to fine map a specific gene in the lq23.3 region. Previously published studies claimed that the genes RGS4 and CAPON on lq23.3 were associated with schizophrenia. For this research thesis multiple markers were genotyped at the RGS4 and CAPON loci in a London based case control sample, no evidence for association was found. Therefore further fine mapping was carried out in the region between the RGS4 and CAPON genes. Allelic and haplotypic associations with schizophrenia were found with three microsatellite and four SNP markers within the serine threonine kinase (UHMK1) gene. A replication study using an Aberdeen based case control sample also found statistically significant evidence of allelic and haplotypic association between TJHMK1 and schizophrenia. Re-sequencing of the UHMK1 gene was carried out in those individuals who had inherited alleles and haplotypes associated with schizophrenia. Three genetic variants were found. Genotyping of the whole case control sample showed that these changes were not associated with schizophrenia. The previously reported associations between schizophrenia and RGS4 as well as CAPON could possibly be explained by linkage disequilibrium between UHMK1 and both CAPON and RGS4. Alternatively there could be two or even three susceptibility genes within the 700 Kb region. At present no potential aetiological base pair changes have been detected in any of the three genes. UHMK1 is known to be highly expressed in regions of the brain implicated in schizophrenia and was found to be significantly down regulated in mice treated with the antipsychotic drug Clozapine. Further confirmation of the involvement of this gene in schizophrenia is needed followed by further efforts to detect genetic variation in or next to the gene which has an effect on expression and function of UHMK1.
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Stone, Caroline. "Molecular and genetic mapping of the haemochromatosis locus." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306980.
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Mathieu, Stephanie. "The Genetics of Arbuscular Mycorrhizal Fungi." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42770.
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Sexual reproduction is an important process amongst eukaryotic organisms, with one function being to maintain genetic variation. The idea that complex eukaryotic species can persist for millions of years in the absence of sex defies fundamental evolutionary dogma, yet a group of organisms known as ancient asexuals were thought to have evolved clonally under deep evolutionary time. Prominent among these are the arbuscular mycorrhizal fungi (AMF), which are obligate plant symbionts that colonize the root cells of plants and extend their hyphae into the soil assisting the plant in acquiring key nutrients. Unlike most eukaryotes, AMF cells are multinucleate with thousands of nuclei moving through a continuous cytoplasm. Genomic analyses have identified a putative mating-type (MAT) locus within the nuclear genomes of model AMF Rhizophagus irregularis, a region that in other fungi dictates the process of sexual reproduction. Additional findings demonstrated that AMF strains carry one of two nuclear organizations. They can be either homokaryotic (AMF homokaryons), where all nuclei within the cytoplasm are virtually identical, or heterokaryotic (AMF dikaryons), where two MAT-locus variants co-exist within the cytoplasm. Despite a lack of observable traits indicative of sex, this homo/heterokaryotic dichotomy is reminiscent of the nuclear organization of sexual fungi.
My research aims to build on these findings to investigate the actual role of the MAT-locus in driving AMF reproduction. To address this, I build my thesis into three main chapters. The first chapter reviews our current understanding of AMF genetics and what drives genome evolution in these organisms. The second chapter establishes a relatively easy, inexpensive, and reproducible approach to genotype known MAT variants of R. irregularis in natural and experimental conditions. The last chapter uses experimental crossings between strains to assess cytoplasmic compatibility and nuclear exchange. I demonstrate that dikaryotic spore progenies can be formed after co-culturing two distinct AMF homokaryotic strains. Further analyses of various genomic regions also reveal possible recombination in homokaryotic spore progenies from co-cultures. Overall, this research provides new experimental insights into the origin of genetic diversity in AMF. These findings open avenues to produce genetically new AMF strains in the lab using conventional crossing procedures and provide a glimpse of the mechanisms that generate AMF genetic diversity in the field.
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El-Gouhary, Inas. "Targeted transgenesis : the hypoxanthine phosphoribosyl transferase (HPRT) gene locus." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80256.
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To overcome the limitations that accompanied traditional transgenesis using pronuclear injections, multiple methods have been employed to target a single copy of a transgenic sequence to a chosen location in the genome. One of which is the introduction of a construct as a single copy, in a known orientation, upstream of the hprt (hypoxanthine phosphoribosyl transferase) gene. The present study is designed to characterize the influence this locus could impose on the expression capability of the docked sequence.Consistent ectopic expression of reporter constructs bearing different Myelin Basic Protein (mbp) regulatory elements and docked at the hprt locus was noted in cardiomyocytes and major CNS blood vessels; two sites in which mbp is not thought to be expressed. This ectopic expression originated from endogenous hprt enhancer activity as similar mbp reporter constructs, randomly inserted, did not reproduce the same expression phenotypes.
In addition, this work also unraveled aspects of the complex nature of mbp gene regulation. The results obtained from this study reveal that reporter constructs containing mbp enhancer elements docked in hprt locus expressed ectopically in the cartilagenous cells of the vertebral bodies during the mouse mid-fetal development period.
Finally, analysis of the "enhancer trap" construct exposed additional ectopic expression in the muscles of the back and tongue uncovering further hprt enhancer activity. Surprisingly, when mbp enhancer sequences were added to the "enhancer trap" construct, marked reduction in muscle expression was noted.
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Hostert, Arnd Marti. "Identification of regulatory elements in the CD8 gene locus." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286250.
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Spiden, Sarah Louise. "Molecular characterisation of the primary ciliary dyskinesia locus C1LD2." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271037.
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Pardo, Eneida Hamam. "Organisation of the A mating type locus of Coprinus cinereus." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297260.
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Yip, Shea Ping. "Studies of intragenic recombination in the human phosphoglucomutase(PGM1) locus." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267301.
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Gupta, Amit. "Prokaryotic metallothionein locus and cadmium tolerance in Synechococcus PCC 6301." Thesis, Durham University, 1992. http://etheses.dur.ac.uk/6085/.
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The aim of this study was to investigate the molecular mechanism of Cd-tolerance in the cyanobacterium Synechococcus PCC 6301 and to establish whether the prokaryotic metallothionein (MT) locus, smt, is involved. Cd-tolerant cell lines of Synechococcus PCC 6301 were developed by step-wise selection, of a culture that had undergone prolonged maintenance in liquid medium. The Cd-tolerant cell lines AO.8, A1.3 and A1.7 (tolerant to 0.8, 1.3, 1.7 µM Cd, respectively) were phenotypically different to the non-selected line AO. Genomic DNA from AO and the Cd-tolerant lines AO.8, A1.3 and A1.7 was analysed by Southern hybridisation. A ca. 4-fold increase in hybridisation to radiolabelled smtA (prokaryotic metallothionein gene), relative to AO, was observed in genomic DNA from A1.7. Equivalent amounts of DNA were loaded onto each track, and no difference in hybridisation to a control gene, psaE (photosystem I gene), was observed. Indeed, the hybridisation of DNA from Al .7 to psaE was slightly less than that observed in AO. Genomic DNA isolated from AO, AO. 8, A1.3 and A1.7 was also analysed after 2, 4, 7 and 12 subcultures in the presence of the respective Cd concentrations. An increase in hybridisation to smtA, relative to AO, was observed in DNA from all Cd-tolerant cell lines. Additionally, unique additional restriction fragments, both larger and smaller than that in AO, were observed in DNA from A1.3 and A1.7. A similar restriction pattern was observed in 3 independent restrictions of DNA from A1.3 after 2 subcultures. Cd-tolerant cell lines were also developed from a 'clonal' culture of Synechococcus PCC 6301. An increase in tolerance was marked by an increase in growth lag, which reduced upon subsequent maintenance of the Cd-tolerant line in the presence of Cd. Genomic DNA from the non-selected line CO and Cd-tolerant lines C1.4, CI.8, C2.6 and C3.2 (tolerant to 1.4, 1.8, 2.6, 3.2 µM Cd, respectively) were analysed after 1, 2, 3, 4 and 5 subcultures. In all the Cd-tolerant lines, an increase in hybridisation to smtA, and additional larger (ca. 11 kb) and smaller (ca. 5.45 kb) restriction fragments, relative to CO (ca. 5.8 kb), were observed. However, amplification and rearrangement in DNA from CI .4 were evident only after 2 subcultures. Additionally, restriction fragment equivalent in size to that observed in CO was lost in CI.8, C2.6 and C3.2, and the presence of Cd did not affect DNA restriction with Sah under in vitro and short term in vivo conditions. The rearrangement in Cd-tolerant line C3 .2 was observed on a minimal HindIII-SalI fragment (ca. 350 bp smaller than that in CO) and isolated from size-fractionated genomic libraries. The alteration was mapped by PCR to a 600 bp region in the 5' flank of smtA. Nucleotide sequence analysis of the clones identified a deletion of 352 bp within a region of 360 bp encoding the C- terminal end of smtB (repressor of smtA transcription), rendering it non-functional. Increased basal level of smtA expression (derepressed expression) and indications for complete loss of the excised fragment were observed in Cd-tolerant line C3.2. Rearrangement was detected in DNA from C3.2 even after maintenance in the absence of Cd for 3 subcultures. The clone bank pPLAN Bal-Ba7 and pPLAN B2 (carrying Bamm restriction fragments of Synechococcus PCC 7942 plasmids) were used to study the plasmid/chromosomal localisation of smtA. Weak hybridisation of pPLAN Ba2 to smtA was observed, but further Southern analysis of plasmid and genomic DNA suggested chromosomal localisation of smtA. PCR and Southern hybridisation were used to detect homologues of smtA in other cyanobacterial strains. Putative homologues were identified in Synechococcus PCC 7942, Synechococcus D562, Oscillatoria D814 and Synechocystis D840 (= PCC 6803) by heterologous probing. However, no hybridisation to smtA was observed in DNA isolated from Calothrix D184 and Microchaete D578.
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Crompton, Douglas Ewan. "Molecular analysis of the shaking-B locus of Drosophila melanogaster." Thesis, University of Glasgow, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309523.
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Krausa, Peter. "Defining HLA-A locus alleles from DNA using ARMS-PCR." Thesis, Open University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338340.
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Abukashawa, Sumaia. "Patterns of molecular evolution at the amylase locus in Drosophila." Thesis, University of Ottawa (Canada), 1990. http://hdl.handle.net/10393/5995.
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Genes encoding the starch-degrading enzyme, alpha-amylase, are found in all major groups of animals, plants and microbes. In this thesis, amylase-coding sequences have been chosen as a model system to investigate the patterns of molecular evolution in an enzyme-coding gene. Previous phylogenetic comparisons of amylase-coding sequences have shown high levels of primary sequence conservation over long evolutionary periods. The studies described here have concentrated on the evolution of these genes within the genus Drosophila. I have studied patterns of genetic variation within populations of a single species, Drosophila melanogaster, using two techniques: (i) allozyme variation and (ii) restriction fragment length polymorphisms (RFLPs). In order to get more precise information on the intraspecific patterns of variation, I have also isolated and partially sequenced the amylase genes from a wildtype strain of D. melanogaster. This sequence was compared to the known sequences which have already been described for laboratory strains. The work was extended to interspecific comparisons by studying amylase sequences from species that were closely-related to D. melanogaster (in this case D. erecta), and also a distantly-related species (D. virilis). This involved the isolation and sequencing of the amylase gene from a D. virilis genomic library. The results revealed several interesting patterns in the evolution of: (i) the primary gene sequences (e.g., gene conversion and codon bias), (ii) gene structure (e.g., changes in intron frequency and location) and (iii) gene organization (e.g., variation in the number of gene copies). These results, concerning both short-term and long-term patterns of molecular evolution within the genus Drosophila, are discussed in the context of what is currently known about patterns of molecular evolution in general, and about the molecular evolution of amylases in particular.
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Boddhireddy, Prashanth. "Development of highly recombinant inbred populations for quantitative-trait locus mapping." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1671.
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Pimm, Jonathan. "Molecular genetics of the 5q22-23 schizophrenia susceptibility locus." Thesis, University College London (University of London), 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.497294.
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Howard, K. R. "Molecular genetics of the hairy locus of Drosophila melanogaster." Thesis, Imperial College London, 1986. http://hdl.handle.net/10044/1/38040.
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Smith, Sarah Elizabeth. "The function and genetics of the host IFITM locus." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708762.
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MacNeil, Angus. "An investigation of gene regulation in the murine #lambda# immunoglobulin locus." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252431.
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Brian, Paul. "A developmentally regulated spore pigment locus from Streptomyces coelicolor A3(2)." Thesis, University of East Anglia, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333649.
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Xinmin, Li. "Experimental studies of pleiotropy at the Adh locus of Drosophila melanogaster." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276173.
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Sharif, Abid Latif. "A molecular study of the Li locus of Trifolium repens L." Thesis, University of Newcastle Upon Tyne, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265140.
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Lally, Geraldine M. "Characterisation of an enhancer trap transgene integration locus involved in behaviour." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364327.
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Andersson, Tove. "Transcription factors regulating the immunoglobulin heavy chain locus /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3559-9/.
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Budu-Aggrey, Ashley. "Investigation of a susceptibility locus for Psoriatic Arthritis." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/investigation-of-a-susceptibility-locus-for-psoriatic-arthritis(ad7d8704-84ba-45c4-8841-2948d4a188b1).html.
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Psoriatic arthritis (PsA) is an inflammatory arthritis that is associated with psoriasis. PsA is a complex disease that is influenced by both genetic and environmental factors. Genetic studies have been successful in identifying risk loci for PsA, the majority of which also confer risk for psoriasis. As PsA has been estimated to have a stronger genetic component compared to psoriasis, this suggests that there should be genetic loci that are associated with PsA and not with psoriasis, which I have defined to be PsA-specific. Therefore, the overall aim of my PhD project is to apply genetic experimental techniques to identify a novel risk locus that is associated with PsA and not psoriasis. Firstly, genotyping of 1,962 PsA cases was performed with the Immunochip, where I contributed to the identification of a novel PsA-specific association on chromosome 5q31, mapping to rs715285 (P=4.38x10-13). Bioinformatic analysis within the association region identified 3 potential causal genes and 4 potential causal variants. Statistical analysis identified CD8+ memory T cells to be the most critical cell type for PsA, and also gave evidence to suggest that rs10065787 is the causal variant within the 5q31 region. A cell-specific eQTL study was performed within this cell type which identified SLC22A5 to be a potential causal gene for PsA. The findings may suggest a potential mechanism by which the 5q31 region contributes towards PsA susceptibility. Variants that reached nominal association during the Immunochip study (P <1.0x10-4) were selected to follow-up in a candidate SNP study, in addition to other SNPs of interest which had been investigated for psoriasis risk but not PsA alone. This was performed within an independent cohort (914 PsA cases, 6,945 controls). Analysis of the independent samples replicated a PsA-specific association with rs12044149 (P = 4.03x10-6) at the IL23R locus. This association reached genome-wide significance during meta-analysis with the discovery Immunochip genotype data (P = 1.28x10-20). The PsA association with IL23R was found to be independent of the psoriasis association at the same locus when performing conditional analysis (Pcond = 4.86x10-06). The effect estimates for rs12044149 in PsA and psoriasis were found to be significantly different (P = 2.0x10-3). Furthermore, direct comparison of the genotypes for rs12044149 showed a significantly increased risk for PsA compared to psoriasis. Functional annotation was performed with credible SNPs sets defined for the PsA and psoriasis association signals at IL23R. This also revealed potential differences in the mechanisms of the two diseases, supporting the independence of their association with IL23R.A rare variant study was also performed as part of this PhD in order to identify a casual gene for PsA. 1,980 PsA cases and 5,913 controls were genotyped with the Illumina HumanCoreExome and HumanExome chips. Single-variant analysis was performed using the Fisher's Exact test. Analysis of common variants (MAF > 0.05) uncovered associations at known PsA and psoriasis loci that reached genome-wide significance, including TRAF3IP2 (P = 3.88x10-18). Analysis of rare (MAF <0.01) and low-frequency (MAF <0.05) variants identified an association with a coding-variant at IFIH1 (rs35667974, P = 2.39x10-6). This association was replicated within an independent cohort, and was found to be significantly associated during multiple-variant testing (P = 2.30x10-6, Pcorr = 5.60x10-6). The minor allele of the rare variant was found to exist in the same haplotype as the minor allele of the PsA-associated common variant at the IFIH1 locus. The rs36557974 SNP found to be associated with PsA independently of the common variant during conditional logistic regression and conditional haplotype analysis. Although the rare-coding variant has been previously reported for psoriasis, these findings demonstrate the use of rare variant analysis to find evidence of a casual gene for PsA.In summary, genetic and statistical approaches have been used to find evidence of causal genes and variants within PsA-specific association regions, as well as to identify a PsA association mapping to a coding region.
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Williams, Carol Jane. "Conservation and mutational analysis of the suppressor-of-forked locus of Drosophila." Thesis, Imperial College London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294847.
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O'Neill, Rosemary. "Genetic and cytogenetic studies of the aprt locus of mouse friend cells." Thesis, Queen's University Belfast, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336006.
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Hu, Song. "The molecular genetics of the raspberry locus in Drosophila melanogaster." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp03/NQ34780.pdf.
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MacLeod, Malcolm R. "Analysis of an allelic series of mutants of the r locus of pea." Thesis, University of East Anglia, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240305.
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Erriquez, Daniela <1983>. "Transcriptional dynamics of the human DMD locus." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6498/.
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The human DMD locus encodes dystrophin protein. Absence or reduced levels of dystrophin (DMD or BMD phenotype, respectively) lead to progressive muscle wasting. Little is known about the complex coordination of dystrophin expression and its transcriptional regulation is a field of intense interest. In this work we found that DMD locus harbours multiple long non coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. These lncRNAs are tissue-specific and highly expressed during myogenesis, suggesting a possible role in tissue-specific expression of DMD gene isoforms. Their forced ectopic expression in human muscle and neuronal cells leads to a specific and negative regulation of endogenous dystrophin full lenght isoforms. An intriguing aspect regarding the transcription of the DMD locus is the gene size (2.4Mb). The mechanism that ensures the complete synthesis of the primary transcript and the coordinated splicing of 79 exons is still completely unknown. By ChIP-on-chip analyses, we discovered novel regions never been involved before in the transcription regulation of the DMD locus. Specifically, we observed enrichments for Pol II, P-Ser2, P-Ser5, Ac-H3 and 2Me-H3K4 in an intronic region of 3Kb (approximately 21Kb) downstream of the end of DMD exon 52 and in a region of 4Kb spanning the DMD exon 62. Interestingly, this latter region and the TSS of Dp71 are strongly marked by 3Me-H3K36, an histone modification associated with the regulation of splicing process. Furthermore, we also observed strong presence of open chromatin marks (Ac-H3 and 2Me-H3K4) around intron 34 and the exon 45 without presence of RNA pol II. We speculate that these two regions may exert an enhancer-like function on Dp427m promoter, although further investigations are necessary. Finally, we investigated the nuclear-cytoplasmic compartmentalization of the muscular dystrophin mRNA and, specifically, we verified whether the exon skipping therapy could influence its cellular distribution.
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Dunn, Michael G. "Molecular characterisation of a Bacillus thuringiensis genetic locus." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360025.
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Cowley, Catherine Mary. "Genetic analysis of the human desmosomal cadherin locus." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264340.
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Fairweather, Nicholas D. "Genetic and molecular investigation of the CMTX1 locus." Thesis, University of Aberdeen, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387254.
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X-linked Charcot-Marie-Tooth disease (CMTX1), a peripheral neuropathy, is clinically characterised by slow progressive weakness and wasting of the distal muscles with associated sensory loss. The CMTX1 locus had previously been localised to the pericentromeric region of the X chromosome. Our initial linkage analysis utilising Restriction Fragment Length Polymorphisms (RFLPs) confirmed that CMTX1 mapped proximally to the DXYS1X locus (Xq21.31). Subsequent linkage analysis, carried out as part of an international consortium, utilising microsatellite polymorphisms further delineated the CMTX1 locus to a 2cM region around DXS453 (Xq31.1). To help with this analysis new microsatellites are generated at the loci DXS106 and DXS227. In parallel with the linkage analysis a physical map of the region was under construction simultaneously with candidate gene evaluation. The physical map was constructed by Pulsed Field Gel Electrophoresis (PFGE) used in conjunction with partial digestion of Yeast Artificial Chromosomes (YACs). The physical map of nine YACs had been obtained in which seven potential CpG islands were identified. Candidate genes were investigated by sequencing Polymerase Chain Reaction (PCR) amplified gene fragments from DNA isolated from patients with CMTX1. This led to the identification of missense, nonsense and base pair deletion mutations within the previously described GJβ1 gene. This gene encodes, connexin 32, a gap junction subunit. Gap junctions are channels which allow direct transfer of cellular components, which are below 900D in diameter, between coupled cells. It is proposed that mutations affecting the GJβ1 gene are the underlying biological defect which results in the CMTX1 phenotype.
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Specht, Christian. "Characterisation of an inbred mouse strain with a deletion of the alpha-synuclein locus." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272172.
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Bhatia, Simran Sukhmani. "Genetic Association of the APOEAPOC1APOC4 Locus with Coronary Artery Disease." Thesis, University of Ottawa (Canada), 2010. http://hdl.handle.net/10393/28712.
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Genome-wide association studies identified a 5' APOC1 single nucleotide polymorphism (SNP), rs4420638 (minor allele frequency (MAF)=0.18) at 19q13.2, with a CAD risk odds ratio (OR) of 1.17 (1.08-1.28) in linkage disequilibrium with apoE4 risk SNP rs429358 (r 2=0.70; OR=1.06 (0.99-1.13), MAF=0.15). Differing OR and MAF led to the hypothesis that rs4420638 risk is partially independent to rs429358. Additional SNPs not in HapMap were genotyped by sequencing, however no strong linkage existed. Genotypically associated traits include serum apoE, as determined by ELISA (rs4420638 AA: 25.5+/-4.8; AB: 44.8+/-3.1; BB: 69.9+/-3.7ug/ml; p=7.27E-07, rs429358 AA: 14.8+/-3.4; AB: 40.1+/-3.1; BB: 67.0+/-3.4ug/ml; p=1.73E-08) and LDL (linear regression rs4420638 p=0.0007; rs429358 p=0.003) but not apoC1. Haplotype analysis indicated that rs429358 risk allele confers a greater CAD risk than rs4420638: rs4420638 risk allele alone is 6% in cases and 4% in controls; rs429358 risk allele is 3% in cases and 0.3% in controls. Likelihood ratio test confirms this conclusion.
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Griffin, Alan. "Characterisation of the genomic region in and around the shaking-B locus of Drosophila melanogaster." Thesis, University of Glasgow, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320284.
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Usher, Christina Leigh. "Structural Forms of the Human Amylase Locus and Their Relationships to SNPs, Haplotypes, and Obesity." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467224.
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Hundreds of human genes reside in structurally complex loci that elude molecular analysis and assessment in genome-wide association studies (GWAS). One such locus contains the three different amylase genes (AMY2B, AMY2A, and AMY1) responsible for digesting starch into sugar. The copy number of AMY1 is reported to be the genome’s largest influence on obesity, yet has gone undetected in GWAS. Using droplet digital PCR (ddPCR), sequence analysis, and optical mapping, we characterized eight common structural forms of the amylase locus, their mutational histories, and their relationships to SNPs. We found that AMY1 copy number has a unique distribution undetectable to earlier methods that can be understood from an underlying set of structural forms and their allele frequencies. Despite a history of recurrent structural mutations, AMY1 copy number has maintained partial correlations to nearby SNPs; these SNPs do not associate with body mass index (BMI). To directly test for association, we measured amylase gene copy number using ddPCR in 1,000 Estonians selected for being either obese or lean and in two cohorts totaling ~3,500 individuals using sequence analysis. We had 99% power to detect even the lower bound of the reported effects on BMI and obesity, yet found no association. This study model of using multiple methods to analyze the copy number, structural haplotypes, and surrounding SNP haplotypes of multi-allelic variants will likely facilitate more robust disease association results in future studies.Medical Sciences
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Turner, Jennifer Susan. "Functional analysis of the prokaryotic metallothionein locus, smt." Thesis, Durham University, 1993. http://etheses.dur.ac.uk/5701/.
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The localisation of the prokaryotic metallothionein (MT) divergon smt (which includes the MT gene smtA and a divergently transcribed gene smtB] was examined, and smt deficient mutants of Synechococcus PCC 7942 (strain R2-PIM8) have been generated by insertional inactivation/partial gene deletion mediated by homologous recombination. The structure and homozygosity (of the smt region) of these mutants, designated R2-PIM8(smt), was confirmed by Southern analyses and plasmid recovery in Escherichia coli (involving the generation of a ca. 7.8 kb plasmid from Soil digested R2-PIM8(smt) DNA). Furthermore, smtA transcripts were not detected in R2-PIM8(smt) RNA. Viability of R2-PIM8(smt) reveals that smt performs no essential role in Synechococcus under these culture conditions. R2-PIM8(smt) has reduced tolerance to Zn(^2+) and Cd(^2+), and short term reduced resistance to Ag(^+). Restoration of Zn(^2+) tolerance was used as a phenotypic selection to isolate recombinants derived from R2-PIM8(smt) after reintroduction of a linear DNA fragment containing an uninterrupted smt divergon. These smt-restored cells also exhibited restored Cd(^2+) tolerance. Hypersensitivity to Cu(^2+) or Hg(^2+)was not detected in R2-PIM8(smt) indicating independence of Cu(^2+) and Hg(^2+) resistance to smt-mediated metal tolerance. Sequences upstream of smtA (Including smtB and/or the smt operator-promoter) fused to a promoterless locZ, conferred metal-dependent β-galactosidase expression in R2-PIM8. At maximum permissive concentrations for growth, β-galactosidase assays revealed Zn(^2+) to be a more potent elicitor of metal-dependent expression from the smtA operator-promoter than Cd(^2+). Equivalent experiments, in R2-PIM8(smQ and R2-PIM8(smtA+/B-) (containing functional chromosomal smtA and non-functional chromosomal smtB), revealed that smtB encodes a repressor of smtA transcription. In addition, it is demonstrated that SmtB can act in trans. It is proposed that Zn(^2+) is the most potent (metal ion) inducer of SmtB mediated derepression of smtA transcription. Furthermore, β-galactosidase assays indicated that, in addition to SmtB, other regulatory elements (including a transcriptional activator) are involved in the regulation of expression from the smt operator-promoter. Restoration of Zn(^2+) tolerance was also used as a phenotypic selection to isolate recombinants derived from R2-PIM8(smt) after reintroduction of a linear DNA fragment, containing functional smtA and non-functional smtB. The resulting transformants, R2-PIM8(smtA+/B-), exhibited increased (early) tolerance to Zn(^2+) and Cd(^2+) as compared to R2-PIM8(smt-. reintroduced ) (equivalent to R2-PIM8).The work presented in this thesis proposes a role for SmtA in Zn(^2+) homoeostasis/metabolism and Cd(^2+) detoxification. SmtB is confirmed to be a trans-acting inducer- (metal ion) responsive negative regulator of smtA. The phenotype of R2-PIM8(sm(A+/B-) (with respect to metal tolerance) has significance regarding previous work (Gupta et al., 1993. Molecular Microbiology 7, 189-195), in which analysis of the smt region of Synechococcus PCC 6301 cells selected for Cd(^2+) resistance, by stepwise adaptation, revealed the functional deletion of smtB. It was proposed that loss of smtB may be beneficial for continuously metal challenged cells. Loss of smtB, now shown to encode a repressor of smtA transcription, is shown to confer constitutive derepressed expression from the smtA operator- promoter and determine an (early) increase in metal (Zn(2+)/Cd(^2+)) tolerance.
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Lindsay, Robert C. "QUANTITATIVE AND MOLECULAR ANALYSIS OF HABITUATION AT THE MAIZE r1 LOCUS." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5655.
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Epigenetics is the study of heritable changes in phenotypes that are not the result of changes in DNA sequence. Examples of epigenetic affecters include methylation changes, chromatin modifications, transcription factors, and RNA-based changes. The molecular mechanisms behind epigenetic changes are not fully understood. Canalization is the buffering of gene expression against environmental changes over time, while habituation is semi-stable expression change over time due to selection. This work characterized the molecular changes associated with the kernel color changes of the R-sc:86-17pale allele at the maize red color1 (r1) locus to determine if the changes are epigenetic in nature. The research; 1) quantified the color differences between the progenitor and habituated sublines; 2) Determined that there are not sequence differences between the progenitor and habituated sublines at the 3` end of the Sc||nc1 gene that could account for changes in seed color; 3) and examined the cytosine methylation patterns at the 3` end of the Sc||nc1 gene of the habituated sublines and the progenitor to determine whether there are methylation differences that correspond with the kernel color changes. Quantification of the kernel colors of the R-sc:86-17pale selection sublines showed that there was a statistically significant difference in kernel color. The identical sequence of the R-sc:86 line and the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines at the 3` end of the Sc||nc1 gene is evidence that the kernel color change is not driven by differences in sequence within the r1 gene. The methylation data suggests that some methylation differences in the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines are present, and suggests that the molecular basis of the kernel color is epigenetic in nature.
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Saunders, Matthew A. "Patterns of nucleotide variability within and around G6PD, a locus under positive natural selection in humans." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280745.
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Some mutations at the gene coding for glucose-6-phosphate dehydrogenase (G6PD) cause a clinical condition of G6PD deficiency, however these alleles have also been shown to confer resistance to malaria based on geographical allele distributions that coincide with malaria, epidemiology, and in vitro studies. A detailed study of nucleotide variability at G6PD can shed light on the signature of selection on the human genome and can also provide insight into the natural history of human malaria. In Appendix A, patterns of nucleotide variability are described in a worldwide panel of humans at G6PD and at a neighboring locus ( L1CAM). Patterns at G6PD do not significantly differ from patterns found at other loci. Nonetheless, significant long-range linkage disequilibrium (LD) is associated with a selected G6PD deficiency allele from Africa (G6PD A-), implying that the allele is young, and that malaria is a recent agent of selection in humans (within the past 10,000 years). In Appendix B, patterns of nucleotide variability are examined in a panel from sub-Saharan Africa at G6PD and at nine loci located around G6PD. LD and reduced nucleotide variability are observed spanning a region of >1 Mb around G6PD, confirming a young age for G6PD A- and implying that the allele has been under strong selection (0.05 < s < 0.20). In Appendix C, a comparable survey of nucleotide variability was conducted in a Eurasian panel with respect to G6PD med, an independently arisen selected G6PD deficiency allele. Patterns of LD provide strong evidence for independent origins of G6PD med in two geographic regions, and that resistance to malaria arose at approximately the same time in Africa and Eurasia. In Appendix D, a panel of Kurdish Jews was studied at G6PD, at neighboring loci, and at 2 unlinked loci to determine if the remarkably high frequency of G6PDmed in this population is attributable primarily to selection or to a severe bottleneck. Patterns of nucleotide variability that are consistent with selection are observed around G6PD, while nucleotide variability at unlinked loci is typical of other non-African populations, suggesting that natural selection is largely responsible for the high frequency of G6PDmed among Kurdish Jews.
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Todman, Martin. "Investigation of the shaking-B locus of Drosophila melanogaster using RNA in situ hydridisation and transgenics." Thesis, University of Sussex, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362273.
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MacGregor-Pryde, Susan Elizabeth. "A molecular investigation of the otrB locus of Streptomyces rimosus." Thesis, University of Glasgow, 1995. http://theses.gla.ac.uk/2076/.
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The gene cluster encoding production of oxytetracycline (OTC) by Streptomyces rimosus (the commercial producer) has been studied in this laboratory. The topic of this thesis was the region of the otc cluster including and upstream of the OTC-resistance gene otrB, which has been shown previously to be responsible for reduced accumulation of the antibiotic. The otrB gene was sequenced. The sequence revealed some discrepancies with previously-published data on tet347 (Reynes et al., 1988; Journal of General Microbiology 134: 585-598), an OTC-resistant determinant from another strain of S.rimosus. The deduced gene product of the otrB showed considerable identity with efflux proteins from other Gram-negative and Gram-positive bacteria. These proteins contain conserved functional motifs, and OtrB was analysed in this context. The transcriptional start of otrB was identified. Several short investigations were undertaken into the physiology of antibiotic production. (1) A transcriptional fusion vector (pIJ2843) using catechol oxygenase as a reporter was used to monitor the response of transcription of various regions of the otc cluster (cloned from a high-producing strain) to changes in external phosphate concentration. These data were compared in relation to antibiotic production by the wild-type strain. (2) A transposon mutagenesis strategy was used to attempt to generate novel mutations within the otc cluster. (3) The presence of genetically-engineered haemoglobin cloned into S.rimosus production strains was investigated. The relationship between expression of the recombinant protein, antibiotic production and the aeration of the S.rimosus cultures is discussed.