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Audetat, Katherine. "Mapping the mop3 gene." Thesis, The University of Arizona, 2009. http://hdl.handle.net/10150/192275.
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Malik, Sajid Perwaiz. "Gene mapping in syndactyly families." [S.l.] : [s.n.], 2005. http://archiv.ub.uni-marburg.de/diss/z2005/0262/.
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Backström, Niclas. "Gene Mapping in Ficedula Flycatchers." Doctoral thesis, Uppsala universitet, Institutionen för evolution, genomik och systematik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9513.
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In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.
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Söderhäll, Cilla. "Gene mapping of atopic dermatitis /." Stockholm : [Karolinska institutets bibl.], 2001. http://diss.kib.ki.se/2001/91-7349-088-1/.
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Setakis, Efrosini. "Gene mapping using DNA pools." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615651.
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Bryant, Stephen Paul. "Pedigree analysis and gene mapping." Thesis, Open University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390811.
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Hernandez-Sanchez, Jules. "Gene mapping using linkage disequilibrium." Thesis, University of Edinburgh, 2002. http://hdl.handle.net/1842/14058.
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The power of QTL detection was studied both empirically and deterministically for several methods. TDT was more powerful than a linkage test, but less powerful than a pure association test. There were no great differences in power between TDTs. One of the TDTs was implemented in BLUP (Best Linear Unbiased Prediction) to study the effect of a candidate gene, the melanocortin 4- receptor (MC4R), on growth, appetite and fatness in pigs. We found significant effects on growth and fatness but not on appetite. TDT uses within families genetic variation. A novel parameter to estimate gene effects using between families genetic variation was also included. If there is no spurious disequilibrium both estimates should be identical, otherwise only the within-families estimator is unbiased. It was more powerful to simulate missing parental genotypes with Gibbs Sampling than analysing data with sib-ship TDTs disregarding parental information. TDT was also used in a genome-wide search for markers associated with bovine spongiform encaphalopathy (BSE). TDT was implemented using logistic regressions, more amenable to statistical modelling than the original form. Maker loci near the Prion Protein gene did not show any associations with BSE, however, markers located on chromosomes 5, 10 and 20, did. A second study that focused on these three chromosomal regions confirmed the association for the marker on chromosome 5. TDT has shown reasonable power and exceptional robustness when mapping QTL in structured populations. Therefore TDT should be part of the gene cartographers’ continuously evolving arsenal of tools for gene mapping. However, previously published TDTs were developed for analysing human populations, whereas domestic/wild populations have different structures and histories that may require alternative statistical analyses. Linked gene flow (LGF) theory can be used for predicting identity-by-descent (IBD) probabilities between individuals. IBD probabilities are at the core of mixed model equations for mapping QTL in outbred populations via variance components estimation. In this thesis, LGF theory was used for determining inbreeding within each individual and chromosomal location using multi-marker information, hence paving the way for further developments.
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Korn, Richard Mervyn. "Mapping sex determining genes and development of techniques for gene mapping in the domestic fowl." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624653.
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Fasulo, Daniel. "Algorithms for DNA restriction mapping /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/7020.
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Tell, Désirée von. "Welander distal myopathy : gene mapping and analysis of candidate genes /." Stockholm, 2004. http://diss.kib.ki.se/2003/91-7349-764-9.
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Li, Li. "Disease Gene Mapping in General Pedigrees." NCSU, 2004. http://www.lib.ncsu.edu/theses/available/etd-10212004-142157/.
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Disease gene mapping is one of the main focuses of genetic epidemiology and statistical genetics. This dissertation explores some methods and algorithms in this area, especially in pedigrees. The first chapter gives an introduction to human genetics and disease gene mapping. Existing linkage and association methods are introduced and compared. Probabilities of genotypic data from multiple linked marker loci on related individuals are used as likelihoods of gene locations for gene-mapping, or as likelihoods of other parameters of interest in human genetics. With the recent development in genetics and molecular biology techniques, large-scale marker data has become available, which requires highly efficient likelihood calculations especially for complex pedigrees. Algorithms for likelihood calculations for pedigree data are reviewed in chapter 2. Besides exact likelihood calculation methods and MCMC, a Sequential Importance Sampling (SIS) approach has been proposed to enable calculations for large pedigrees with large numbers of markers. However, when the system gets large, the variance of the importance sampling weights increases while both efficiency and accuracy of the method decrease. We propose an optimization algorithm for calculating the likelihood of general pedigrees in Chapter 3. We incorporate a resampling strategy into SIS to reduce the variance inflation problem. A successful linkage analysis may identify a linkage region of interest containing hundreds of genes at a magnitude of perhaps ten to thirty centiMorgans. A follow-up association (or so-called linkage disequilibrium) analysis can provide much finer gene-mapping but is subject to greater multiple testing problems. In Chapter 4, we present a method for determining whether an association result is responsible for a non-parametric linkage result for binary traits in general pedigrees. The correlation between family frequency of a variant of interest and family LOD score is used as a measure of whether the association between a given variant at a marker and the disease status can help to explain a significant linkage result seen in the collection of families in the region around the marker.
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He, Bing. "Susceptibility gene mapping in multiple sclerosis /." Stockholm, 1998. http://diss.kib.ki.se/search/diss.se.cfm?19980608he.
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Parts, Leopold. "Genetic mapping of cellular traits." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609665.
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Mumey, Brendan Marshall. "Some computational problems from genomic mapping /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/6932.
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Slape, Christopher Ian. "Molecular characterisation of translocations involving chromosome band 1p36 in acute myeloid leukaemia." Title page, table of contents and abstract only, 2002. http://web4.library.adelaide.edu.au/theses/09PH/09phs6313.pdf.
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"October 2002" Bibliography: leaves 159-198. This thesis describes the mapping of the breakpoints of three different chromosome rearrangements, all involving 1p36, in acute myeloid leukaemia (AML) patients, and an investigation into the molecular outcomes of these rearrangements.
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Gill, Clare Alexandra. "Use of an ovine bacterial artificial chromosome library for the study of Bovidae genomes." Title page, table of contents and abstract only, 1999. http://web4.library.adelaide.edu.au/theses/09ANP/09anpg475.pdf.
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Kalous, Jay Robert. "Candidate gene association mapping in spring wheat." Thesis, Montana State University, 2011. http://etd.lib.montana.edu/etd/2011/kalous/KalousJ0511.pdf.
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Association mapping (AM) is a form of quantitative trait locus (QTL) mapping that utilizes a collection of germplasm rather than a structured mapping population. Marker/trait associations are made through the application of a mixed-effects model that corrects for population stratification. The objective of this study was to evaluate the application of association mapping on a selection of elite spring wheat cultivars. We tested marker/trait associations for known "perfect" markers and markers identified as controlling traits of interest through traditional bi-parental mapping. We also wanted to evaluate the observed linkage disequilibrium (LD) surrounding genes of interest by utilizing closely linked sets of markers in specific regions of the spring wheat genome. Population structure was estimated with fifty-one unlinked microsatellite markers. Two phenotypic datasets were used for evaluation. The first was an unbalanced historical dataset, and the second was a balanced dataset taken from a two year replicated field trial. Marker/trait associations were identified for plant height, stem solidness, heading date, grain protein content, test weight, and seed color. Our analyses identified significant associations between Rht-D1 and plant height, Ppd-D1 and heading date, and Xgwm340 and stem solidness. No associations were identified between Rht-B1 and plant height, Ppd-B1 and heading date, nor Vrn-B1 and heading date. The extent of LD varied depending on breeding history and selection pressure. One LD block was identified around the stem solidness QTL and two blocks were found surrounding a productive tiller QTL. Smaller blocks of LD were observed surrounding the three genes controlling kernel color. No LD was observed surrounding the Rht-B1 locus.
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Melville, Scott Andrew Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "Disease gene mapping in border collie dogs." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Sciences, 2006. http://handle.unsw.edu.au/1959.4/25511.
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Pedigree dog breeds are genetically isolated and inbred populations with characteristics specific to each breed. Some breeds carry genetic diseases which affect the health of the animals, but may also serve as a valuable model to identify genes involved in human disease. In the Border Collie breed in Australia, the identification of two disease genes would enable breeders to DNA test their animals and prevent future cases. Over 530 samples were collected to identify the genes responsible for these diseases through linkage mapping and candidate gene approaches. Collie Eye Anomaly (CEA) defines a group of symptoms that cause the incorrect development of different regions within the eye, and may also result in the detachment of the retina. The presence of the disease in different breeds of collies suggests that the disease originated before the differentiation of the collie breeds. The CEA gene was mapped to a region of CFA37, but the disease gene was identified by another research group. Neuronal Ceroid Lipofuscinosis (NCL) is a fatal neurodegenerative disorder that affects Border Collie dogs from approximately 16 months of age. The disease is inherited in an autosomal recessive manner and affected animals display a range of physiological and behavioural symptoms that include loss of muscular control, nervousness and sometimes aggression. Due to the debilitating nature of the disease, dogs rarely survive beyond 28 months of age. Microsatellite markers were used to exclude the Border Collie NCL gene from the region of the English Setter NCL gene (homolog of human NCL gene CLN8). Further work mapped the disease gene to CFA22, in a region containing the homolog for CLN5, one of the identified human disease genes for NCL. Subsequent sequencing of canine CLN5 revealed a nonsense mutation (c.619C>T, Q206X) that co-segregated with NCL in Border Collie pedigrees. This truncation mutation resulted in a protein product of similar size to some mutations identified in human CLN5 and therefore the Border Collie may make a good model for future NCL studies. With DNA testing now available, breeders of Border Collies can now ensure that no animal will die of NCL.
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Li, Jingyi. "Gene Mapping of Morphological Traits in Chickens." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85397.
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Chickens exhibit considerable variation in morphological traits, with some populations having undergone intensive selection for uniqueness and uniformity. These populations are a source of experimental material to study the genetics of morphological traits. An important first step in such studies is to map the genes and the causal mutations that influence these traits. This research focused on gene mapping of 12 morphological traits including 4 intra-feather color patterns (Pattern, Columbian, Melanotic, and mottling), 2 inter-feather color patterns (Blue and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Ten backcross and/or F2 populations were designed to produce 1,880 individuals. An additional 339 DNA samples from other populations were included. The procedures for gene mapping were: 1. Pooling of DNA samples of backcross or F2 individuals based on their shared phenotypes, followed by microarray assays for genotyping, a cost-effective initial screen for the candidate genomic regions, 2. Linkage mapping to narrow the range of candidate genes, 3. Sequencing to identify the candidate mutations, 4. Diagnostic tests to confirm the association between the candidate mutation and the phenotype. Of the 12 traits studied, 3 (mottling, Blue, and chocolate) made progress into step 4. Complexities due to genomic context, modifiers, and environmental factors precluded step 4 for the first form of the feathered-leg gene, step 3 for the mapping of Melanotic, and earlier stages for the mapping of Pattern, Columbian, dark brown egg, vulture hock, and the second form of feathered-leg. These findings provide insights of the complexity of how background genome can influence the phenotypic expression of single genes (gene genetic background interactions) and an understanding of cellular and molecular mechanisms involved in morphogenesis.Ph. D.
Chickens, one of the major protein sources in diets for humans, have a long cultural, sport and religious history since their initial domestication during the neolithic period. Darwin wrote of the importance of variation, which today we see for example in size of body, length of shank, number of toes, distribution of feathers, comb types, and plumage color patterns resulting in a plethora of breeds of chickens that differ in appearance. Some of these traits are "simply" inherited, which in the molecular era facilitates the study of relationships between DNA sequences and phenotypes. This dissertation focuses on identification of differences in DNA sequences among chickens responsible for these "simply" inherited phenotypes. The 12 phenotypes that were studied included 6 plumage color patterns (Pattern, Columbian, Melanotic, mottling, Blue, and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Designed were ten 3-generation populations to produce 1,880 chickens. An additional 339 DNA samples from other populations were included. Of the 12 phenotypes, 8 involved genotyping of pooled DNA samples, a cost-effective initial screen to target DNA sequences. This was followed by genotyping individual samples in 5 of the more promising studies. Candidate genes identified as associated with these 5 phenotypes underwent further studies which identified differences in DNA sequences associated with 4 of them (mottling, feathered-leg, Blue, and chocolate). These findings provide insights of how DNA sequences contribute to the phenotypic appearance of animals.
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Hoffman, Lori A. "Disease Gene Mapping Under The Coalescent Model." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1282058674.
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Duran, Alonso Maria Beatriz. "Genetic mapping of the rat agu gene." Thesis, University of Glasgow, 1997. http://theses.gla.ac.uk/39021/.
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In 1993, a mutant strain, AS/AGU arose spontaneously in an enclosed colony of the Albino Swiss (AS) strain of rat. AS/AGU animals exhibit a set of locomotor abnormalities. They display a general instability and whole body tremor, are slow at initiating movement, show reductions in purposeful action, and perform poorly at locomotor tests such as mid-air righting. L-dopa administration or fetal midbrain transplants reverse the majority of the symptoms, resembling the observations made on Parkinson's disease patients. These features make the AS/AGU strain a useful model for movement disorders due in significant part to failure of the dopaminergic transmission system. Crosses of AS/AGU to other laboratory rat strains point to a single recessive mutation with essentially complete penetrance (agu/agu) as the cause of the abnormal phenotype. There is no evidence of sex linkage or maternal inheritance. In the absence of any evidence of the function of the agu gene product, positional cloning of this locus was begun. The first step was the establishment of a genetic map location for the agu locus. A large series of microsatellite markers were analysed and used to identify which of the strains PVG, BN, and F344 differed to a greater extent from AS/AGU. Differences at 43%, 62% and 47% of the loci were recorded, respectively. BN and F344 were therefore selected as the reference strains in backcrosses to AS/AGU, in an attempt to maximise the number of informative markers which could be used to type the progeny.
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Guo, Wei. "Some topics of statistical methods in gene mapping." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36873688.
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Wang, Min. "Fine mapping and candidate gene analysis of murine lung tumor susceptibility genes." Connect to this title online, 2003. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1054682174.
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Thesis (Ph. D.)--Ohio State University, 2003.Title from first page of PDF file. Document formatted into pages; contains xvi, 150 p.; also includes graphics (some col.) Includes bibliographical references (p. 129-150). Available online via OhioLINK's ETD Center
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Hinkley, Craig S. (Craig Steven). "Gene Dosage Study on Human Chromosome 22." Thesis, North Texas State University, 1986. https://digital.library.unt.edu/ark:/67531/metadc500617/.
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A gene dosage study was conducted on a rare complete trisomy 22 human fibroblast cell line utilizing three lysosomal enzymes, ∝-iduronidase, ∝-galactosidase B, and arylsulfatase A, whose genes are located on chromosome 22 and two control enzymes, ,β-hexosaminidase A and -- fucosidase, with genes not on chromosome 22. A gene dosage effect was clearly demonstrated for an early passage number of the fibroblasts; however, later passage numbers gave inconclusive results. This study suggests that gene dosage studies must be carefully designed to be conducted only on early, matched passage number cells. ∝-fucosidase gave anomalous results most likely due to pleiotropic effects. The present gene dosage study confirmed the trisomic nature of the cell line studied and suggests that this type of study may be a useful diagnostic tool for small deletions, additions, or unbalanced translocations.
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Lee, Jun Heon. "Characterising and mapping porcine endogenous retroviruses." Connect to full text, 2000. http://hdl.handle.net/2123/366.
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Thesis (Ph. D.)--University of Sydney, 2000.Includes tables. Title from title screen (viewed Apr. 22, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the Dept. of Animal Science, Faculty of Agriculture. Includes bibliography. Also available in print form.
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Sieberts, Solveig K. "Joint relationship inference from three or more individuals in the presence of genotyping error /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/8970.
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Kwan, Sheung-him. "Statistical methods and analyses in human gene mapping." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43759117.
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Black, Graeme. "The mapping of X-linked ophthalmic disease." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358590.
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Wang, Luping. "Physical Mapping of Human Transfer RNA Gene Clusters." Thesis, University of North Texas, 1989. https://digital.library.unt.edu/ark:/67531/metadc500957/.
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Two plaque-pure phage lambda clones designated as λhtX-l and λhtX-2 that hybridized to unfractionated bovine liver tRNA were isolated from a human X chromosome-specific library. The λDNAs were characterized by restriction mapping and Southern blot hybridization techniques. The human DNA segment in λhtX-l contains five or more presumptive tRNA genes and at least one Alu family member. The 19-kilobase human DNA insert in λhtX-2 contains two or more presumptive tRNA genes and at least three Alu family members. Another human genomic clone designated λhVKV7 hybridized to mammalian valine tRNA IAC. The clone was characterized by physical mapping and Southern blot hybridization techniques. The 18.5-kilobase human DNA fragment in λhVKV7 contains a cluster of three tRNA genes and at least nine Alu family members.
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De, Poli Emma. "The gene mapping of Senegalese sole (S. senegalensis)." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amslaurea.unibo.it/15863/.
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The Senegalese sole (S. senegalensis) is a common flatfish, distributed over the eastern Atlantic coast from the Northern part of Senegal. Senegalese sole aquaculture has aroused great interest in the marine aquaculture in Spain and Portugal because of its relatively rapid growth rate, but it presents limits due to the poor reproduction of captive breeders in many facilities. In fact gonad development during sexual maturation results in major growth reduction, and increased susceptibility to diseases (Felip et al., 2006). Senegalese sole has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. In S. senegalensis, these problems are aggravated because of the lack of knowledge concerning sex.
This study fits into a detailed project of Senegalese sole knowledge, promoted by University of Cádiz, providing new information about the karyotype characterization, the chromosome structure of certain genes involved in sex determination and sexual differentiation processes, which may be relevant for improving the commercial production of this species. This piece of information not only helps to understand the development and evolutionary mechanism in vertebrates, but will also contribute to improving the production of target species for aquaculture.
For this purpose, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (Vitellogenin, Otospiralin, R-spondin-1, Steroidogenic Factor1 and Tetkin-2) were analyzed and compared, where possible, with the same genes in other species.
In this study it was possible to describe a part of those four genes, using 3’ RACE method. The BAC-FISH results showed the position of different genes in different chromosome, to improve the knowledge of Senegalese sole karyotype. In particular, the localization of steroidogenic factor 1 (SF1) in the chromosome 1 that is involved in the sex determination.
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Nicholson, Sharon Joycelyn. "Mapping of Loa : a mouse motor deficit gene." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.344089.
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Durrant, Caroline. "Haplotype clustering methods : application to disease gene mapping." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432561.
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方頌恩 and Chung-yan Gardian Fong. "Electro-clinical study and gene mapping of epilepsies." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31981781.
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Kwan, Sheung-him, and 關尚謙. "Statistical methods and analyses in human gene mapping." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43759117.
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Nebbali, M. "Human gene mapping using the polymerase chain reaction." Thesis, University of Nottingham, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317395.
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Baird, Nathan Alder. "Hypoxic gene regulation and high-throughput genetic mapping. /." Connect to title online (ProQuest), 2008. http://proquest.umi.com/pqdweb?did=1525703731&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.
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Thesis (Ph. D.)--University of Oregon, 2008.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 45-52). Also available online in ProQuest, free to University of Oregon users.
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Fong, Chung-yan Gardian. "Electro-clinical study and gene mapping of epilepsies." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B24463826.
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Baird, Nathan Alder 1979. "Hypoxic gene regulation and high-throughput genetic mapping." Thesis, University of Oregon, 2008. http://hdl.handle.net/1794/7505.
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xi, 52 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries under the call number: SCIENCE QH445.2 .B35 2008Activation of Heat shock proteins (Hsps) is critical to adaptation to low oxygen levels (hypoxia) and enduring the oxidative stress of reoxygenation. Hsps are known to be regulated by Heat shock factor (Hsf), but my results demonstrate an unexpected regulatory link between the oxygen sensing and heat shock pathways. Hsf transcription is upregulated during hypoxia due to direct binding by Hypoxia-inducible Factor-1 (HIF-1) to HIF-1 response elements in an Hsf intron. This increase in Hsf transcripts is necessary for full Hsp induction during hypoxia and reoxygenation. The HIF-1-dependent increase in Hsps has a functional impact, as reduced production of Hsps decreases viability of adult flies exposed to hypoxia and reoxygenation. Thus, HIF-1 control of Hsf transcriptional levels is a regulatory mechanism for sensitizing heat shock pathway activity in order to maximize production of protective Hsps. This cross-regulation represents a mechanism by which the low oxygen response pathway has assimilated complex new functions by regulating the heat shock pathway's key transcriptional activator. Beyond studying the regulation of specific genes. I have also developed a method to identify small, yet important, changes within entire genomes. Genetic variation is the foundation of phenotypic traits, as well as many disease states. Variation can be caused by inversions, insertions, deletions, duplications, or single nucleotide polymorphisms (SNPs) within a genome. However, identifying a genetic change that is the cause of a specific phenotype or disease has been a difficult and laborious task for researchers. I developed a technique to quickly and accurately map genetic changes due to natural phenotypic variation or produced by genetic screens. I utilized massively parallel, high-throughput sequencing and restriction site associated DNA (RAD) markers, which are short tags of DNA adjacent to the restriction sites. These RAD markers generate a genome-wide signature of fragments for any restriction enzyme. Taken together with the fact that the vast majority of organisms have SNPs that disrupt restriction site sequences, the differences in the restriction fragment profiles between individuals can be compared. In addition, by using bulk segregant analysis, RAD tags can be used as high-density genetic markers to identify a genetic region that corresponds to a trait of interest. This dissertation includes both previously published and unpublished co-authored materials.
Adviser: Eric Johnson
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Dash, D. P. "Mapping of a gene causing cataract and keratoconus and analysis of candidate genes." Thesis, Queen's University Belfast, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.419498.
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Maher, Bridget Helen. "Identification of X-Linked Genes in Migraine: Fine Mapping and Candidate Gene Studies." Thesis, Griffith University, 2012. http://hdl.handle.net/10072/367770.
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Migraine is a painful temporarily incapacitating disorder that affects an estimated 12% of the general population including 18% of adult women and 6% of adult men. The disorder involves two main subtypes termed migraine with or without aura (MA and MO respectively). Migraine can present with a variety of symptoms that vary between individuals and between episodes experienced by a single individual. This disorder causes significant social and economic burden and alarmingly is often poorly treated. A direct cause of this is a lack of understanding of the underlying pathology of migraine.
Migraine is believed to be a neurogenic disorder that involves temporary disruption of pathways that receive and respond to sensory signals. While numerous environmental triggers may have been identified the exact mechanisms that cause the disruption are still largely unknown. However, familial aggregation of migraine suggests significant genetic contributors.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Medical Science
Griffith Health
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Sugar, Robert. "Genome analysis in three dimensions : functional analysis of Hi-C derived datasets." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708667.
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Li, Miaoxin. "Development of a bioinformatics and statistical framework to integrate biological resources for genome-wide genetic mapping and its applications." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43572030.
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Neves, Pereira Maria de Lurdes Marques. "A Gene for Autism Identified by Translocation Breakpoint Mapping." Thesis, University of Aberdeen, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485663.
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Autistic disorder (AD). is a common form of childhood neurodevelopmental disorder, characterized by severe and sustained impairment of social interaction and social communicative abilities, as well as a markedly restricted repertoire of activities and interests (American Psychiatric Association, 1994). Microscopic chromosomal rearrangements are seen in 3-6% of cases. Submicroscopic copy number variations (CNVs) were recently.identified in 10% patients with sporadic autism. Intriguingly, these were only found in 2% of patients with an affected first-degree relative, and in 1.0% of controls. Similar findings were reported by the Autism consortium, suggesting that single gene defects are more likely to be causative where autism is familial. We have used molecular analysis of a de:110vo balanced translocation in a case of classic autism independently to implicate the mRNA cap binding translation initiation factor EIF4E, already a strong positional candidate in autism. A de novo apparently balanced reciprocal translocation between the long arms of chromosomes 4 and 5 (46,XY,t(4:5)(q23;q31.3)) was identified in a child with classic AD. Linkage has been reported in autistic families to EIF4E region on chromosome 4, but not to the NR3C1 region on chromosome five. We thus sequenced the EIF4E promoter, and its seven exons in 120 multi-case families from the Autism Genetic Research Exchange collection (AGRE; www.agre.org).Asingle base C insertion was identified within the previously identified 12 base pair critical region of the EIF4E promoter in a parent and both affected siblings from two different families. Electrophoretic mobility shift assays (EMSA) demonstrated that this promoter variant had an increased affinity for a nuclear factor, presumably hn-RNPK and when tested in a promoter activity assay using luciferase as reporter gene demonstrated a higher increase in EIF4E promoter activity in the presence of the single base insertion. Expression analysis failed to identify a significant difference in levels of EIF4E in transformed lymphocyte cell lines in either the translocation case or the cases with the promoter variant, indicating that subtle changes in EIF4E expression, perhaps occurring only in the brain/ nervous system/neurons may be sufficient to affect function. EIF4E is a eukaryotic translation initiation factor involved in directing ribosomes to the cap structure of mRNAs, to initiate protein synthesis. In molecular pathology, EIF4E is best known for its role as an oncogene, but it has been recently recognized to be important in memory because of its key role in mediating synaptic plasticity through translation initiation. Other molecules that interact with EIF4E or modulate its activity have been implicated in the control of translation initiation and synaptic plasticity, and also in the pathogenesis of autism. Yonan and co-workers showed linkage to the EIF4E region as part of a large genome wide scan of AGRE families, and suggested this gene as one of many positional candidates. Linkage to 4q21-31 has been confirmed in two other analyses of the AGRE cohort. We now:provide dire.ct evidence for a role of EIF4E in autism. Genetically determined up-regulation of synaptic translation is associated with autistic features in humans, and mice. In Fragile X, a severe learning disability syndrome frequently associated autistic features, synaptic mRNA translation is up-regulated through inactivation of the protein FMRP, causing an increase in the number of dendritic spines present on cortical neurons. EIF4E is the rate limiting component of eukaryotic translation, and thus is fundamental to the process of LTP.
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Mucklow, Stuart. "Characterization and mapping of the murine sialoadhesin gene, Sn." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337593.
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Palma, Federica Di. "Analysis and mapping of bovine MHC class I gene." Thesis, University of Reading, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.248145.
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Jansen, Suzaan. "Linkage mapping in Haliotis midae using gene-lnked markers." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/20347.
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Thesis (MSc)--Stellenbosch University, 2012.ENGLISH ABSTRACT: Haliotis midae, or more commonly known as Perlemoen, is an abalone species found along the coast of South Africa. It is the only cultured abalone species in South Africa and has a high demand abroad. Due to its popularity as a seafood delicacy, illegal harvesting has taken its toll on Perlemoen numbers. This increases the need for sustainable farming efforts and efficient implementation of law enforcement practices against poachers. Abalone farms make use of a limited number of broodstock for breeding, so it is necessary to ensure that genetic effects such as inbreeding and bottlenecks do not interfere with the viability of the offspring. Research that focuses on the genetics of Perlemoen will greatly aid the farms to continue sustainable production of this species as well as enhance their breeding efficiency. This study focuses on the construction of a linkage map for H. midae that will allow the future identification of markers associated with genes important to production, such as growth and disease resistance. Identification of these genes will allow breeders to select genetically superior abalone that will be used for breeding programmes in which the phenotype of the offspring will be enhanced. For the construction of a linkage map it is necessary to have enough informative markers for mapping. In this study, gene-linked microsatellite markers were developed by screening a contig assembly of H. midae’s transcriptome. Ninety-eight primer pairs could be developed from the contigs and 60 loci produced amplification products. Twenty-six microsatellites were found to be polymorphic (27% success rate). In addition to these markers, 239 previously developed microsatellites and 48 gene-linked SNPs were used to develop sex-average and sex-specific linkage maps in four full-sib families consisting of approximately 100 offspring each. Of these markers 99 were informative in family DS1 (31% success rate), 81 in family DS2 (26%), 77 in family DS5 (24%) and 71 in family DS6 (23%). These markers were used for linkage analysis (LOD>3). The average number of linkage groups for the sex-average maps ranged from 17-19. The average genome length for these maps ranged from 700cM to 1100cM with an average marker spacing of 8cM. The sex-specific maps’ linkage groups ranged from 13-17 with an average genome length of 600cM to 1500cM. The average marker spacing was approximately 16cM. The integrated map was constructed by merging the sex-average maps. This map contained 25 linkage groups with an average genome length calculation of 1700cM and an average marker spacing of 9.3cM. The linkage maps created in this study are the first to utilize SNPs in H. midae. Further incorporation of SNPs into linkage maps will enhance the density. The maps created in this study are of medium-density (65%) and provide a link to the development of high-density linkage maps to facilitate associations of phenotypic traits to certain markers, to so that QTL mapping can be performed. This information can be used for marker-assisted selection to produce genetically superior abalone.
AFRIKAANSE OPSOMMING: Haliotis midae, of meer algemeen bekend as Perlemoen, is 'n klipkous spesie wat langs die kus van Suid-Afrika voorkom. Dit is die enigste gekweekte klipkous spesie in Suid-Afrika en het 'n hoë aanvraag in die buiteland. As gevolg van sy gewildheid as 'n seekos lekkerny, het onwettige stropery sy tol geneem op Perlemoen getalle. Hierdie verhoog die behoefte vir volhoubare boerdery pogings en doeltreffende implementering van wetstoepassing teen stropers. Perlemoenplase maak gebruik van 'n beperkte aantal broeidiere vir teling, dus is dit nodig om te verseker dat genetiese effekte soos inteling en genetiese bottelnekke nie inmeng met die lewensvatbaarheid van die nageslag nie. Navorsing wat fokus op die genetika van Perlemoen sal grootliks die plase steun om die volhoubare produksie van hierdie spesie voort te sit, sowel as hul teling doeltreffendheid te verbeter. Hierdie studie fokus op die ontwikkeling van 'n genetiese koppelingskaart vir H. midae, wat die toekomstige identifisering van die merkers wat verband hou met die gene wat belangrik is vir die produksie, soos groei en weerstand teen siektes sal verbeter. Identifisering van hierdie gene sal toelaat dat telers genetiese voortreflike Perlemoen kan kies vir teelprogramme waartydens die fenotipe van die nageslag sal verbeter word. Vir die ontwikkeling van 'n genetiese koppelingskaart is dit nodig om genoeg informatiewe merkers vir die kartering te hê. In hierdie studie, is geen-gekoppelde mikrosatelliet-merkers ontwikkel deur ‘contig’ data van H. midae se transkriptoom te ondersoek. Agt en negentig inleier pare kon ontwikkel word uit die ‘contigs’ en 60 loki kon ‘n amplifiseringsproduk lewer. Ses-en-twintig mikrosatelliete was polimorfies (27% suksessyfer). Bykomend tot hierdie ontwikkelde merkers is 239 voorheen ontwikkelde mikrosatelliete en 48 geen-gekoppelde SNPs gebruik om geslagsgemiddelde en geslagspesifieke koppelingskaarte in vier volsib families, wat uit ongeveer 100 nageslag elk bestaan, te ontwikkel. Van hierdie merkers was 99 informatief in familie DS1 (31%), 81 in die familie DS2 (26%), 77 in die familie DS5 (24%) en 71 in die familie DS6 (23%). Hierdie merkers is gebruik vir 'n koppelingsanalise (LOD>3). Die gemiddelde aantal koppelingsgroepe vir die geslagsgemiddelde kaarte het gewissel van 17-19. Die gemiddelde genoom lengte vir hierdie kaarte het gewissel van 700cM tot 1100cM met 'n gemiddelde merker spasiëring van 8cm. Die koppelingsgroepe van die geslagspesifieke kaarte het gewissel van 13-17 met 'n gemiddelde genoom lengte van 600cM tot 1500cM. Die gemiddelde merker spasiëring was ongeveer 16cm. Die geïntegreerde kaart is saamgestel deur die samesmelting van die geslagsgemiddelde kaarte. Die kaart toon 25 koppelingsgroepe met 'n gemiddelde berekende genoom lengte van 1700cM en' n gemiddelde merker spasiëring van 9.3cM. Die genetiese koppelingskaarte wat in hierdie studie ontwikkel is, is die eerste om SNPs te gebruik in H. midae. Verdere insluiting van SNPs in koppelingskaarte sal die digtheid verhoog. Die kaarte wat in hierdie studie ontwikkel is, is van medium digtheid (65%) en bied 'n stap nader aan die ontwikkeling van hoë digtheid koppelingskaarte om fenotipiese eienskappe met sekere merkers te assosieer, vir kwantitatiewe kenmerk lokus kartering. Hierdie inligting kan gebruik word vir merker bemiddelde seleksie om geneties verbeterde Perlemoen te produseer.
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Kibar, Zoha D. "Mapping of Clouston hidrotic ectodermal dysplasia." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0016/NQ55347.pdf.
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Apostolou, Sinoula. "Physical mapping of human chromosome 16." Title page, contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09pha645.pdf.
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Craig, Nicola Jane. "Genetic and physical mapping of the rat agu locus." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341722.
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Sundholm, James, and n/a. "Analysis of Specific Migraine Candidate Genes Mapping to Human Chromosome 1." Griffith University. School of Health Science, 2003. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030829.153348.
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Migraine, comprised of migraine with aura (MA) and migraine without aura (MO), is a painful neurovascular disease, affecting approximately 16% of the general population. It is characterised by a wide variety of symptoms including headache, nausea and vomiting, and photo- and phonophobia. The disorder is complex involving not only multiple genes, but also specific environmental factors, which can induce attacks in genetically predisposed individuals. Hyperhomocysteinaemia is a known risk factor for cerebrovascular, peripheral vascular and coronary heart disease. The Methylenetetrahydrofolate Reductase (MTHFR) enzyme is involved in homocysteine metabolism. Furthermore, it has been reported that a homozygous mutation (677C to T; Ala to Val) in the 5,10-MTHFR gene is associated with an elevation in plasma homocysteine levels (Frosst et al., 1995). This common mutation in the MTHFR gene has recently been associated with migraine with aura in a Japanese cohort (Kowa et al., 2000). The present study was designed to determine the prevalence of the MTHFR C677T mutation in Australian patients with migraine and to determine whether this mutation is associated with the disease in Caucasians. A large case-control study, consisting of 270 patients with migraine (167 with aura and 103 without aura), and 270 normal matched controls was investigated. Genotypic results indicated that the prevalence of the homozygous (T/T) genotype in migraine sufferers (15%) was higher than that of controls (9%) (P = 0.084). Furthermore, the frequency of the mutant (T/T) genotype in individuals with MA (19%) was significantly higher than in controls (9%) (P = 0.006). Interestingly, the risk of MA was ~2.5-fold higher in suffers possessing the homozygous variant (OR = 2.52, CI: 1.42 - 4.47, P = 0.0012). To confirm the MTHFR allelic association with MA, family-based tests were performed in an independent pedigrees group, where only those with MA were considered affected. Results from both the Pedigree Disequilibrium Test (PDT) and Family-Based Association Test (FBAT) analysis revealed slight, although not significant (PDT test, P = 132; and FBAT test, P = 0.390), over-transmission of the mutant allele (T) from parents to affected offspring. However, despite the MTHFR variant having a high heterozygosity (0.48), there were a limited number of informative transmissions for the MTHFR variant in the pedigree group resulting in reduced power for these tests. In conclusion, our results support the trends reported in the Japanese migraine study and suggest that the homozygous 677T gene variant causing mild hyperhomocysteinaemia, is a genetic risk factor for migraine, and indicate that further studies investigating the role of this gene are warranted. Mutations in various ion channel genes are responsible for neurovascular and other neurological disorders. Inherited ion channel mutations or "channelopathies" are increasingly found to be the cause of various neurological disorders in humans. Wittekindt and colleagues (1998) reported that the calcium-activated potassium channel (hKCa3) gene is a good candidate for schizophrenia and bipolar disorder (BD), as well as for other neurological disorders such as migraine. The hKCa3 gene is a neuronal small conductance calcium-activated potassium channel, which contains a polyglutamine tract, encoded by a polymorphic CAG repeat in the gene. The hKCa3 gene encodes a protein of 731 amino acids containing two adjacent polyglutamine sequences in its N-terminal domain separated by 25 amino acids. The C-terminal polyglutamine sequence is highly polymorphic in length (Austin et al., 1999). hKCa3 plays a critical role in determining the firing pattern of neurons via the generation of slow after-polarization pulses and the regulation of intracellular calcium channels (Kohler et al., 1996). Three distinct mutations in the a1 calcium channel gene have been shown to cause SCA-6, episodic ataxia-2 and familial hemiplegic migraine (FHM) (Ophoff et al., 1996). The hKCa3 gene contains a highly polymorphic CAG repeat that was initially mapped (Chandy et al., 1997) to a schizophrenia locus on chromosome 22 (Pulver et al., 1994). Recently Austin et al (1999) re-mapped hKCa3 and found it to reside on chromosome 1q21, a region that has been linked to FHM (Austin et al., 1999), a rare subtype of MA (Ducros et al., 1997; Gardner et al., 1998), and a region recently showing genetic linkage to typical migraine (Lea et al., 2002). The hKCa3 polymorphism results in small variations in polyglutamine number, similar to those that occur in the calcium channel a1a subunit gene (CACNA1A), which is encoded by CAG expansions and thought to cause Spinocerebellar Ataxia Type 6 via loss of channel function (Austin et al., 1999). Given the recent linkage of FHM to the region of chromosome 1q21, to which hKCa3 resides, and also linkage of typical migraine to this region, a large case-control study investigating this hKCa3 CAG marker and consisting of 270 migraine and 270 stringently matched healthy controls was undertaken. Our results indicated that there was no statistically significant difference in allele distributions for this marker between migraine and non-migraine patients (P >0.05). No significant difference in the allelic distribution was observed in the MA or MO groups when compared to controls (P >0.05) and there was no significant difference in CAG repeat length distribution between the migraine group and controls (P = 0.92), or between the MA and MO groups (P = 0.72) collectively. Hence, the CAG repeat in this gene does not show expansion in migraine. Overall, our results provide no genetic evidence to suggest that the hKCa3 CAG repeat polymorphism is involved in migraine aetiology in Australian Caucasians. Thus the involvement of the hKCa3 gene in migraine is not likely, although the hKCa3 gene remains an important candidate for other neurological disorders that may be linked to the 1q21.3 chromosomal region.