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Xia, Shuang. "Detecting Rare Haplotype-Environment Interaction and Dynamic Effects of Rare Haplotypes using Logistic Bayesian LASSO". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1406246686.
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Janyakhantikul, Somwang. "Evolution of CCL3L1/CCL4L1 haplotypes". Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/13404/.
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CCL3LI and CCL4LI are chemokine genes, located on chromosome 17q12. They are copy number variable genes which share 95% sequence identity with their non-copy number variable paralogues CCL3 and CCL4. The copy number of these genes varies between populations and has been reported to be associated with phenotypes such as susceptibility to HIV infection, hepatitis C virus infection, Kawasaki disease and SLE. The aim of this study is to understand the evolutionary history of variation at the CCL3L1/CCL4LI cluster. To accomplish this goal, several approaches including typing microsatellites, single nucleotide polymorphisms (SNPs) and CCL3L 1/CCL4L 1 sequence haplotypes were used to investigate the association with CCL3L 1 and CCL4L 1 copy number. However, the results showed that there is no strong association between a single-copy marker and CCL3L 1 and CCL4LI copy number, but there is evidence of recombination. Therefore, this may suggest that CCL3L 1/CCL4L 1 is a complex region and one plausible hypothesis is that there is a high rate of recombination in this region. This study of the evolution of CCL3L 1/CCL4L 1 haplotypes showed that a major one-copy CCL3L 1/CCL4L I haplotype (about 70% haplotype frequency) identified in humans, represents the ancestral state, as inferred from comparison with chimpanzee.
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Zhang, Han. "Detecting Rare Haplotype-Environmental Interaction and Nonlinear Effects of Rare Haplotypes using Bayesian LASSO on Quantitative Traits". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu149969433115895.
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Martinez, Cadenas Conrado. "Y chromosome haplotypes and Spanish surnames". Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559800.
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In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships but most data has been collected so far only from the British Isles. In order to provide additional in sights into the con-elation between surnames and Y chromosomes, this study focuses on the Spanish population and investigates Y chromosome SNP/STR variation by analysing a total of 1,766 DNA samples from unrelated Spanish male volunteers belonging to 37 surnames and 355 controls. The results suggest that the degree of coancestry within surnames is highly dependent on surname frequency. Within-surname genetic variation, as measured by different statistics, con-elates well with surname frequency, though a few exceptions are found. In addition, geographic distance between the individuals' place of origin influences Significantly the con-elation between Y chromosome and surnames: men with the same surname tend to have more similar Y chromosomes if their paternal grandfathers were born geographically close to each other. Therefore, it seems that Y chromosome coancestry within surnames is as much about surname frequency as it is about geographical proximity.
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Brennan, Patrick J. "An Investigation of Personal Ancestry Using Haplotypes". University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744.
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Nicholls, Samuel. "Computational recovery of enzyme haplotypes from a metagenome". Thesis, Aberystwyth University, 2018. http://hdl.handle.net/2160/cfc1d884-cc17-439f-be6e-c3ab6d79ee1d.
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Population-level diversity of microbial communities (microbiomes) represent a biotechnological resource for biomining, biorefining and synthetic biology; but industrial exploitation of enzymes responsible for catalyzing reactions of interest requires the recovery of the exact DNA sequences (or "haplotypes") that encode the genes. However, haplotype reconstruction is an extremely difficult computational problem, further complicated by the infancy of techniques for the handling of environmental sequencing data (metagenomics). Current haplotyping approaches cannot choose between alternative haplotype reconstructions and fail to provide biological evidence of correct predictions. Additionally, there is no philosophical framework under which we can consider the variation of genes within a microbial community, such as those that encode isoforms of enzymes of interest to us. To address this, my thesis proposes the "metahaplome" as a definition for the set of haplotypes for a genomic region of interest within a microbial community. This work will offer the first formalisation of the problem of recovering haplotypes from a metagenomic data set, and present Hansel and Gretel: a novel probabilistic framework that reconstructs the most likely haplotypes from complex microbiomes. The framework is robust to sequencing error and uses all available evidence from aligned reads, without altering or discarding observed variation. The approach is verified with multiple in silico experiments, including two de facto data sets that are currently used to benchmark algorithms for the recovery of viral quasispecies, and strain identification. With long-read sequencing, this thesis will demonstrate in vitro verification of the approach, presenting the first biologically validated method for the recovery of haplotypes from a microbial community. Finally, I will introduce the "Rumen Landscape" pilot study to demonstrate the sort of research questions and novel biological insight that can be obtained through exploration of the metahaplome.
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Higgins, Thomas John Diatchenko Luda. "Molecular characterization of [beta]2 adrenergic receptor haplotypes". Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1602.
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Thesis (M.S.)--University of North Carolina at Chapel Hill, 2008.Title from electronic title page (viewed Sep. 16, 2008). "... in partial fulfillment of the requirements for the degree of Master's of Science in the Curriculum in Neurobiology." Discipline: Neurobiology; Department/School: Medicine. On title page, [beta] appers as Greek character and 2 appears in subscript.
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Bradman, Neil. "A Y chromosome history of the Jews". Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275330.
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Lo, Wing Sze. "Association of SNPs and haplotypes in GABRB2 with schizophrenia /". View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20LO.
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King, Turi E. "The relationship between British surnames and Y-chromosomal haplotypes". Thesis, University of Leicester, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.484806.
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Abstract In Britain surnames are paternally inherited and they are thus analogous to the paternally inherited Y chromosome. Therefore, males who share surnames might be expected to share Y-chromosomes. However, this simple relationship is complicated by the multiple origins of many surnames, non-paternity, and mutations on the Y chromosome. Y-chromosomal DNA polymorphisms provide us with a set of tools to directly test, at a molecular level, this hypothetical link. Since surnames are highly geographically localized, local geographical patterning of Y haplotypes is a potential confounding factor: genetic structure within names could arise as a result of geographical structure within Britain, rather than due to descent. Geographical structure was examined using samples from this research but little evidence of such structure was found. Then, to ask if a signal of haplotype sharing exists within surnames, 150 pairs of men were recruited, each sharing a British surname, and Y-haplotype sharing assessed within each pair. The signal of coancestry exhibited constituted powerful evidence for common origins of men sharing surnames. It also has forensic implications and this research shows that it could allow the prediction of surname from crime-scene samples. . These findings for pairs of men sharing surnames suggested that a larger scale' study of larger sample sizes would be worthwhile, so a set of 40 surnames with an average sample size of 42 apparently unrelated men was investigated using Y markers. Correlations between surname rank and degree of diversity exist: the more common the surname, the greater the diversity of Y-chromosomal haplotypes associated with the name. Furthermore, an individual is far more likely to share a Y-chromosome haplotype with another person sharing their surname if the surname is rare. While a handful of surnames show some evidence of having a single founder, overall the picture is one of far more complex surnames histories.
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Paracchini, Silvia. "Y-chromosomal DNA haplotypes in male infertility and cancer". Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270655.
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Lemnrau, A. G. "Identification of human leukocyte antigens (HLA) haplotypes using tagSNPS". Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1344057/.
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Matching for HLA alleles between patients and their potential donors is critical for the success of haematopoietic stem cell transplantation. Current genotyping methods identify HLA alleles but not the haplotypes in which they reside, although both are important for transplantation outcome. The aim of this thesis was to identify HLA specific polymorphisms and tagSNPs that could identify 3 common HLA haplotypes present in population of Northern European (NE) Caucasian ethnicity, HLA-A*01-B*08-DRB1*03, HLA-A*02-B*44-DRB1*04, and HLA-A*03-B*07-DRB1*15. Phylogenetic and bioinformatics methods were used to select polymorphisms for each of the nine HLA alleles that were unique, or only found at low frequency in other HLA alleles. PCR -sequence specific priming (SSP) was used to validate the nine selected polymorphisms, which were then incorporated into a multiplex SSP-PCR assay. However, this method does not differentiate between homozygous and heterozygous samples positive for the HLA alleles and therefore an allele specific primer extension (ASPE)-Luminex assay was developed to allow the simultaneous detection of the selected HLA polymorphisms. In order to determine the HLA haplotypes, sets of tagSNPs exhibiting high specificity for the common haplotypes were then identified. This was achieved by using British Birth Control Cohort (~2,000 samples) SNP genotyping data generated from Illumina and Affymetrix gene chips. Eight tagSNPs were identified; rs2187668 and rs2734986 for HLA-A*01-B*08-DRB1*03; rs2844821, rs2596477 and rs660895 for HLA-A*02-B*44-DRB1*04 and rs3094170, rs3129860 and rs3130933 for HLA-A*03-B*07-DRB1*15 haplotypes. These tagSNPs capture the three haplotypes with a specificity ranging from 96 to 100 %. Luminex-ASPE multiplex assays were developed to validate the eight tagSNPs using 59 homozygous and 70 heterozygous samples previously typed at high resolution level by sequence-based typing. A further validation was then performed using a blind cohort of 93 previously HLA typed samples. This Luminex-ASPE tagSNP multiplex method correctly identified the three most common HLA haplotypes present in the Northern European population. In summary, this is the first time when a novel tagSNPs HLA genotyping assay has been developed and successfully applied to detect three common HLA haplotypes in a blinded retrospective study.
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Attaoua, Redha. "Déterminisme génétique de la résistance à l'insuline dans les maladies complexes : application des stratégies de criblage dense du génome basées sur les profils de déséquilibre de liaison dans la génétique du syndrome des ovaires polykystiques". Montpellier 1, 2009. http://www.theses.fr/2009MON1T011.
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La résistance à l'insuline est un désordre métabolique caractérisé par la diminution de l'action de l'insuline sur ses tissus cibles. Elle caractérise un ensemble de maladies mendéliennes comme le syndrome de type A, ou complexes comme le diabète de type 2 ou le syndrome des ovaires polykystiques (SOPK). Dans ma thèse, nous avons étudié l'association de trois gènes au SOPK dans une population de femmes d' Europe Centrale. Il s'agit du VNTR du gène de l'insuline, du gène du récepteur de l'insuline (INSR) et du FTO (fat mass ans obesity associated gene). Les marqueurs génétiques utilisés dans ces études sont les SNP, des polymorphismes mononucléotidiques et bialléliques que nous avons génotypés par séquençage en fluorescence ou par SSO-PCR (sequence specific oligonucleotide-PCR). Dans l'exploration de INSR, le microsatellite D19S884 situé à 1 mb du gène a été criblé par PCR fluorescente. Le déséquilibre de liaison (DL) entre les SNP a été mesuré par HAPLOVIEW 3. 31 et la combinaison de ces polymorphismes en haplotypes dans la population a été déterminée par le logiciel PHASE 2. 1. Le logiciel StatView and SAS a été utilisé pour calculer les associations génétiques par régression logistique ou pour mesurer les corrélations génotype-phénotype par ANOVA. L'étude du VNTR (en criblant 7 SNP) a été réalisée chez 160 femmes avec SOPK et 95 contrôles. L'exploration du gène INSR (par génotypage de 5 SNP et de 1 microsatellite) a été établie chez 115 femmes avec SOPK et 111 contrôles tandis que l'investigation du FTO (en criblant le SNP rs1421085) a été effectuée chez 207 cas et 100 contrôles. Le gène FTO a été également exploré dans l'obésité de la population générale des femmes, dans une cohorte du Sud de la France (71 avec obésité simple, 48 avec obésité morbide et 128 contrôles). Nous avons constaté l'association du VNTR, par SNP et par son haplotype H5, à un effet protecteur contre le SOPK (OR=0,54, P<0,03), tandis que le gène INSR nous est apparu plutôt pathogène en s'associant par son haplotype H9 au SOPK et à l'infertilité (OR=3,0; P<3,1. 10 ˉ³) et en corrélant avec l'hyperandrogénisme et avec les degrés de sévérité du syndrome. Le FTO quant à lui ne s'associe pas au phénotype SOPK comme l'est INSR, mais s'associe plutôt à l'obésité, au syndrome métabolique (SMet) et à la résistance à l'insuline dans la maladie (OR = 3,2; P < 0,0001). Cette donnée a été confirmée dans l'obésité de la population générale des femmes, où FTO a été associé au phénotype obèse comme c'est d'ailleurs le cas du gène IRS-2, un gène également génotypé dans cette étude. Cependant, et contrairement au FTO, l'association de IRS-2 se limite à l'obésité (OR = 4,4; P < 0,01) mais pas au SMet et à ses composantes comme l'intolérance au glucose (IGT) et l'insulinorésistance. En conclusion, cette thèse m'a permis d'une part de montrer l'intérêt de l'utilisation des haplotypes comme marqueurs dans l'étude génétique des maladies complexes, et d'autre part de constater la nécessité de l'exploration génétique des désordres métaboliques dans SOPK pour rechercher des inividus à risque cardiovasculaire ou de diabète de type 2Insulin resistance is a metabolic disorder characterized by a decrease of insulin activity on its target issues. It characterizes a panel of Mendelian diseases as type A syndrome or complex affections as type 2 diabetes or polycystic ovary syndrome (PCOS). In my thesis, we focused on the study of 3 genes in PCOS, in a women population from Central Europe. Genes explored were VNTR of insulin gene, insulin receptor gene (INSR) and FTO (fat mass and obesity associated gene). Genetic markers used in these studies were SNPs, a mononucleotidic and biallelic polymorphisms which we genotyped using fluorescent sequencing or SSO-PCR (sequence specific oligonucleotide-PCR). For INSR, the microsatellite D19S884 located at 1 Mb from the gene genotyped by fluorescent PCR. Linkage disequilibrium between SNPs was measured using HAPLOVIEW 3. 31 and the combination of these polymorphisms into haplotypes in the population was determined by the software PHASE 2. 1. The software StatView ans SAS was used to calculate genetic association by logistic regression or to assess genotype-phenotype correlations by ANOVA. Exploration of VNTR (by genotyping 7 SNPs) was achieved in a population of 160 women with PCOS and 95 controls. INSR was explored (by genotyping 5 SNPs and one microsatellite) in a population of 115 women with PCOS and 11 controls, while FTO gene was investigated (by genotyping one SNP : rs1421085) in 207 cases and 100 controls. FTO was also studied in the obesity of the general women population, in a cohort from Southern France (71 women with simple obesity, 48 others with morbid obesity and 128 controls). We observed that VNTR associates to a prospective effect against PCOS by its SNPs and haplotype H5 (OR = 0. 54; P< 0. 03) while insulin receptor gene appeared as pathogenic by its haplotype H9 which associates to PCOS and infertility (OR = 3. 0, P < 3. 1. 10ˉ³) and correlates with hyperandrogenism and the severity of the disease. FTO did not associate to the phenotype PCOS like INSR but to metabolic syndrome (MetS) and insulin resistance in PCOS (OR = 3. 2; p <0. 0001). This findind was confirmed in obesity of the general women population where FTO was associated as IRS-2, also genotyped in this cohort, to obesity. However, the association of IRS-2 was limited to obesisty (P < 0. 01, OR = 4. 4) and did not extend to MetS and its components as impaired glucose tolerance (IGT) and insulin resistance. In conclusion, my thesis demonstrates the importance of using haplotypes as markers in genetic studies of complex diseases but also allows to note the necessity of investigating the genetic background of metabolic disorders in PCOS aiming individuals of a high cardiovascular and type 2 diabetes risk
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Chacon, Sanchez Maria Isabel. "Chloroplast DNA polymorphisms and the evolution and domestication of the common bean (Phaseolus vulgaris L.)". Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367751.
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Gornall, Robert J. "TP53 polymorphisms and haplotypes in breast, cervical and ovarian cancer". Thesis, University of Southampton, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310562.
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Salome, Nathalie. "Haplotypes chromosomiques et mutations β-Thalassémiques dans la population algérienne". Lyon 1, 1985. http://www.theses.fr/1985LYO11650.
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Maxey, Gail D. "Identification of major histocompatibility complex haplotypes in goldfish, Carassius auratus". Thesis, This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-08042009-040408/.
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Obregon, Tito Alexandra de. "APOE haplotypes in health, lessons from an Oklahoman African American population". Oklahoma City : [s.n.], 2010.
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Norwich, Jemma Townsend. "The sequence and characterisation of α-globin haplotypes in human populations". Thesis, University of Oxford, 1996. https://ora.ox.ac.uk/objects/uuid:470b6750-3284-45af-8f3d-3acfe655e929.
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Genetic variation at the human a-globin gene complex has only been characterised to date as haplotypes - a linked set of 7 RFLPs and 2 VNTRs - and not at the sequence level. However, an understanding of the extent of sequence variability at this locus, and its relation to underlying mutational processes, is of interest to studies of both molecular and population genetics. This variation has been investigated by the development of a PCR haplotyping and direct sequencing protocol. Sequencing of 6 RFLP-containing regions of the haplotype in different human populations demonstrates that all (-) RFLPs have the same sequence, regardless of geographical origin. Additional sequence variation is found surrounding the RFLP sites, indicating that the overall level of variation at this locus is comparable to that at other loci, although a higher mutation rate is shown in an inter-species comparison. The additional polymorphic sites are concentrated in only three regions; a survey comprising a total ~280kb indicates that this sequence polymorphism is generated and influenced by localised gene conversion, which was not evident at the RFLP level. PCR analysis of the 2 VNTRs in human populations demonstrates considerable size variation in human populations, not detected by previous haplotyping protocols. There is also extensive internal sequence variation in the VNTRs (in a total survey of ~50 kb), apparently accumulating in a polar fashion and governed primarily by gene conversion, as reported at other VNTR loci. In addition, flanking sequence variation is identified which undergoes conversion, although not in concert with changes in the nearby repeat structure. Consideration of the association of variation, at both the unique and repeated sequence regions, with RFLP α-haplotypes demonstrates that haplotypes differ in age, and allows relationships between them to be determined. The resulting haplotype network has similarities to that determined from β-globin gene variation; the implications for recent human evolution are discussed.
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Sanassy, Shane. "Functional study of ubiquitin C-terminal hydrolase-L1 gene promoter haplotypes". Thesis, University of Southampton, 2007. https://eprints.soton.ac.uk/64912/.
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The Ubiquitin Conjugating System (UCS) describes a system in which the 96-amino acid residue Ubiquitin can be selectively covalently linked to intracellular proteins. This endows cells with an indispensable level of regulation to determine protein fate in a wide range of basic cellular events. The abundant, neuron specific Ubiquitin Carboxyl-Terminal Hydrolase-L1 (UCH-L1) is intimately involved with the UCS – both in a hydrolase and ligase capacity. Mutations in UCH-L1 have clearly been associated with various neurodegenerative disorders, including Alzheimer’s, Huntington’s and particularly Parkinson’s disease. The main and unique objective of this study was to identify any common Caucasian sequence variants in UCH-L1’s promoter, and to investigate whether they are associated with neurodegenerative symptoms, and any change in UCH-L1 transcriptional activity. Seven novel UCH-L1 Single Nucleotide Polymorphisms (SNPs), as well as the C54A documented coding region polymorphism (Ser18Tyr), were identified using both denaturing High Performance Liquid Chromatography (dHPLC) and DNA sequencing analysis. In relation to the translational start site, the novel SNPs elucidated were: A-307G, A-306G, G-234A, A-24G, C-16T, G12A and G21A. Restriction Fragment Length Polymorphism (RFLP) genotyping analysis was then employed within Caucasian DNA sample sets of 31 and 480 individuals, to firstly elucidate the common UCH-L1 promoter haplotypes that exist within the population, and secondly, in an attempt to uncover any association between the polymorphic alleles and general neurodegenerative symptoms - no association was uncovered. Using pGEM-T Easy as an initial ‘holding vector’, the three common UCH-L1 promoter haplotypes elucidated – AAGAC, GAGGT and AGAAC - were incorporated into a modified pGL3 vector to ascertain transcriptional activity rates. This was done by Luciferase expression analysis, and the results identified the GAGGT promoter haplotype as having a significantly increased transcriptional activity in all human cell lines tested. It is my contention, that the pronounced increase in transcriptional activity elucidated for the GAGGT UCH-L1 promoter haplotypes, potentially indicates a primary genetic risk factor for sporadic Parkinson’s disease in the Caucasian population – a novel pathogenic model of which is proposed in this thesis. The fact that RFLP genotyping analysis uncovered no association of the promoter polymorphic alleles with more general neurodegenerative symptoms, indicates the need for further studies to be focused more specifically towards Parkinson’s disease.
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McCullagh, Bonnie. "Sequence evolution among divergent mitochondrial haplotypes within species of Junonia butterflies". Journal of Asia-Pacific Entomology, 2015. http://hdl.handle.net/1993/31105.
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The New World Junonia butterflies include well-studied model organisms yet their phylogeny remains unresolved by traditional cox1 DNA barcodes. Sixteen Junonia mitochondrial genomes were sequenced using next generation MiSeq technology. Junonia lemonias, an Old World species, has mitochondrial genome features typical of Ditrysian Lepidoptera, and synteny is maintained throughout Junonia. Analysis of Junonia mitogenomes produced a robust phylogeny that was used with biogeographic information to infer that Junonia crossed the Pacific Ocean to invade the New World on 3 separate occasions. Junonia vestina, a high elevation species from the Andes Mountains, shows high altitude adaptation in the mitochondrial protein coding loci atp6, atp8, cox1, cob, nad1, and nad2, with the strongest effects seen in cox1 and nad1. There is some overlap between these genes with human loci that have disease associations with the same amino acid positions which could help elucidate the function of high elevation mutations in J. vestina.February 2016
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Zou, Meilin. "Haplotypes of cleistogamous flowering gene cly1 and association with temperature stress". Thesis, Zou, Meilin (2017) Haplotypes of cleistogamous flowering gene cly1 and association with temperature stress. Honours thesis, Murdoch University, 2017. https://researchrepository.murdoch.edu.au/id/eprint/37942/.
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Cleistogamy refers to a type of sexual breeding system, a floret type with closed flowers. Cleistogamous flower sheds its pollen before flower opening, so this behavior leads to a great mass of autogamy. Furthermore, the cleistogamy has been found and presented widely in the angiosperm. In recent years, the cleistogamy has been regarded as an important reproductive system in various plant taxa and already attracted widespread attention in the world. However, the understanding of the molecular mechanism of the cleistogamous trait was very limited. It is valuable to explore the cleistogamy gene cly1 in barley.
Cly1 has been cloned, and two SNPs within the open reading frame region were identified to be associated with floral types. New markers were developed to genotype 672 barley accessions. Among them, the floral types of 436 lines were investigated. A total of 45 novel lines were identified as the genotype of the two markers could not explain their phenotypes. Five novel lines which showed non-cleistogamous types in the field but had cleistogamous genotype were sequenced. Thirteen SNPs were detected among the gene region. But no SNPs were associated with non-cleistogamy. Promoter region, methylation, and miR172 gene sequence need to be investigated in the future.
The purposes of this article are to investigate the occurrence mechanism of cleistogamy, particularly on genetic aspects in barley. Temperature stress including frost stress and heat stress is one of the biggest obstacles to crop production. So the impacts of cleistogamy against temperature stress were discussed in the present study. Grain fertility rate was investigated in the four field trials. Katanning experienced frost stress in 2016 with the lowest temperature of -3.4°C. Grain fertility percentage was as low as 85% in Katanning, while in other three trials, the grain fertility percentage ranged from 92% to 96%. The correlation coefficient of grain fertility between cleistogamous type and non-cleistogamous type was analyzed. No significant difference was detected in the four trials between the two floral types.
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Van, Dorp L. "Investigating processes driving genetic diversity in human populations using dense haplotypes". Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1542974/.
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Although it is well established that DNA varies substantially among different world-wide human groups, the principal forces driving this genetic diversity are not well understood. This PhD thesis aims to describe genetic patterns among a wide range of human groups and characterize the primary historical, anthropological and sociological factors that contribute to observed levels of genetic diversity among these groups. In particular, through development and application of sophisticated haplotype-based techniques to several diverse human datasets, this work sheds light on the effects on genetic diversity of genetic isolation, migration, and other factors in specific geographic regions at different times in history. For example, this thesis explores the impact of recent marginalisation on genetic diversity in the Ethiopian Ari and shows that recent isolation in the Ari Blacksmiths can lead to strong genetic differentiation over a relatively short time scale. It also explores population structure in the Democratic Republic of Congo through analyses of novel genome-wide genotype data, relating these patterns to oral traditions, social practices and migration history. Studying the impact of much older events on present day population structure, this thesis also presents the first application of haplotype-based methods to study ancient DNA from some of the earliest known farmers recovered in Greece, Anatolia and Iran. Using this data, evidence is provided for demic diffusion of a Neolithic way of life into Europe, as well as documenting the presence of strong genetic structure in the first farmers of the Eastern Fertile Crescent. Finally this thesis presents preliminary work that synthesises global patterns of genetic diversity in relation to Africa as a method for investigating the temporal nature of the initial Out of Africa migrations that have contributed enormously to human genetic diversity observed today. Overall through merging these unique methods and diverse datasets, this thesis answers a number of important questions about human evolution.
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Ribeiro, Daniela Maria. "Influencia dos polimorfismos do elemento regulatorio maior dos genes do cluster da globina alfa humana na expressão genica in vitro". [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/310876.
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Orientador: Maria de Fatima SonatiTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas
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Resumo: A expressão dos genes do cluster da globina a em humanos é regulada pelo a-MRE ( a-Major Regulatory Element), um elemento localizado 40 kb à montante do respectivo cluster na região telomérica do braço curto do cromossomo 16. O a-MRE é geneticamente polimórfico e seis diferentes haplótipos, nomeados de A a F, foram determinados em alguns grupos populacionais da África, Europa e Ásia e em indivíduos pertencentes a duas populações indígenas brasileiras. As substituições de base que resultaram nestes haplótipos estão localizadas entre sítios de ligação para fatores nucleares ou em um sítio não ocupado in vivo, exceto no caso do haplótipo D, em que o polimorfismo altera a seqüência de um dos sítios ocupado in vivo pelo fator NF-E2. Não há, de nosso conhecimento, nenhum estudo experimental feito para avaliar se essa variabilidade pode influenciar a expressão gênica. Assim, no presente trabalho foi analisada e comparada a expressão do gene repórter da luciferase em células K562 transientemente transfectadas com construções que tiveram como enhancers os diferentes haplótipos do a-MRE, além de 3 dos polimorfismos isoladamente (+130, +199 e +209). Os resultados revelaram redução da expressão do gene da luciferase com todas as construções em relação à do haplótipo selvagem A: os haplótipos B e C corresponderam a 19% do grau de expressão do haplótipo A, o D a 21%, o E a 15%, o F a 3%, o polimorfismo +130 a 24%, o +199 a 32% e o +209 a 3%. Em seu conjunto, eles demonstram que os polimorfismos responsáveis pelos diferentes haplótipos do a-MRE, em sua maioria situados nas seqüências flanqueadoras dos sítios de ligação para proteínas regulatórias, reduzem a expressão gênica in vitro
Abstract: The expression of human a-like globin genes is regulated by the a-MRE (a-Major Regulatory Element), an element located 40 kb upstream of the a cluster in the short arm of chromosome 16. The a-MRE is genetically polymorphic and six different haplotypes, named A to F, have been identified in some population groups from Europe, Africa and Asia and in native Indians from two Brazilian Indian tribes. The base substitutions that resulted in these haplotypes are located between binding sites for nuclear factors or in a site that is considered not to be active in vivo, with the exception of haplotype D, in which the polymorphism changes the first binding site for the NF-E2 factor occupied in vivo. To our knowledge, there are no experimental studies evaluating whether this variability may influence gene expression. Thus, the present work analyzed and compared the expression of the luciferase reporter gene in K562 cells transiently transfected with constructs that have, as enhancers, the different a-MRE haplotypes, besides three isolated polymorphisms (+130, +199 and +209). The results demonstrated a reduction in luciferase gene expression with all the constructs compared with the wild type a-MRE (A haplotype): the B and C haplotypes corresponded to 19% of the A haplotype expression, the D to 21%, the E to 15%, the F to 3%, the polymorphism +130 to 24%, the +199 to 32% and the +209 to 3%. They demonstrate that the polymorphisms responsible for the a-MRE haplotypes, most located in the flanking sequences of the regulatory protein binding sites, decrease in vitro gene expression
Doutorado
Ciencias Biomedicas
Doutor em Ciências Médicas
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Angelo, Sandro Nunes. "Influencia dos polimorfismos T6235C e A4889G, do gene CYP1A1, e dos haplotipos NAT1*3, NAT1*4 e NAT1*10 do gene NAT1, associados com o metabolismo de carcinogenos, na susceptibilidade ao adenocarcinoma colorretal esporadico". [s.n.], 2008. http://repositorio.unicamp.br/jspui/handle/REPOSIP/308618.
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Orientadores: Carmen Silvia Passos Lima, Claudio Saddy Rodrigues CoyDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas
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Resumo: A exposição das células do cólon e do reto a substâncias carcinogênicas está associada ao consumo de alimentos que constituam fonte de substratos, como aminas aromáticas e hidrocarbonetos aromáticos policiclícos. Enzimas como a mono-oxigenase do citocromo P450, codificada pelo gene CYP1A1 e a N-acetiltransferase, codificada pelo gene NAT1, estão relacionadas com o metabolismo dessas substâncias. Os polimorfismos T6235C e A4889G, do gene CYP1A1, e o haplótipo NAT1*10, do gene NAT1, foram associados ao risco do câncer colorretal (CC) em indivíduos do hemisfério norte. Não há descrições sobre as influências desses polimorfismos no risco do CC em nossa população, sendo este o objetivo do estudo. O DNA de 254 pacientes com adenocarcinoma colorretal esporádico (ACE) e 255 controles foi analisado por meio da reação em cadeia da polimerase e digestão enzimática. Foi avaliado também, o padrão dietético de pacientes e controles por meio do recordatório de freqüência alimentar. Houve risco maior de ocorrência do ACE em indivíduos com os genótipos variantes dos polimorfismos T6235C e A4889G do gene CYP1A1 e com consumo excessivo de carnes. A frequência do haplótipo NAT1*10 foi maior em pacientes do que em controles, havendo risco maior de ocorrência do ACE nesses indivíduos. Maior risco de ocorrência da doença foi também observado em indivíduos com os haplótipos NAT1*10 do gene NAT1 e consumo excessivo de carnes e escasso de verduras e frutas. Os resultados deste estudo sugerem que as vias herdadas do metabolismo de carcinógenos, CYP1A1 e NAT1, associadas ao padrão da dieta influenciam o risco de ocorrência do ACE em nosso meio.
Abstract: The exposure of the cells of the colon and rectum to carcinogenic substances is associated with the consumption of foods that are source of substrates, such as aromatic amines and polycyclic aromatic hydrocarbons. Enzymes such as cytochrome P450 monooxygenase, encoded by the CYP1A1 gene, and acetyltransferase, encoded by the NAT1 gene, are related to the metabolism of these substances. T6235C and A4889G polymorphisms, of the CYP1A1 gene, and NAT1*10 haplotype of the gene NAT1 were associated with incidence of colorectal cancer (CC). There are no descriptions about the influences of these polymorphisms on the risk for the CC in our population, which is the objective of the study. DNA from 254 sporadic colorectal adenocarcinoma (SCA) patients and 255 controls were analysed by polymerase chain reaction and restriction digestion. It was also assessed the dietary pattern pacients and controls through the recall of food frequency. There was a greater risk of the occurrence of SCA in individuals with the variant genotypes of the T6235C and A4889G polymorphisms, of the CYP1A1 gene, associated with high consumption of meat. The frequency of the NAT1*10 haplotype was greater in pacients than in controls, with increased risk of occurrence of SCA these individuals. Increased risk of occurrence of the disease was also observed in individuals with NAT1*10 haplotype of the gene NAT1 and excessive consumption of meat and little vegetables and fruits. The results of the study suggest that the pathaway inherited from the metabolism of carcinogens, CYP1A1 and NAT1, associated with the pattern of diet influences the risk of occurrence of SCA in our country.
Mestrado
Cirurgia
Mestre em Cirurgia
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Bardel, Claire. "Mise en évidence de facteurs génétiques de risque en utilisant des phylogénies d'haplotypes". Paris 6, 2005. http://www.theses.fr/2005PA066616.
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Lavelle, Suzanne Patricia. "Autosomal haplotypes as markers for the histories and structures of human populations". Thesis, University of Leicester, 2010. http://hdl.handle.net/2381/8374.
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The demographic history of humans is very complex. Populations have undergone bottlenecks, isolation, migration, admixture and expansions. All of these have added to the complexity of what makes a population and how that population has changed over time. A record of these events can be found in our DNA. This project used autosomal DNA to trace the histories and structures of human populations by using a combination of a SNP (single nucleotide polymorphism) and an STR (short tandem repeat) – SNPSTR (Mountain et al. 2002). Forensic STRs formed the basis for the SNPSTR systems because their allelic diversity is well characterised, their mutation rates have been reliably measured and they are robust in PCR amplification. Four SNPSTR systems were found, using SNPs which had been verified by HapMap and/or Perlegen and which were < 500 base pairs away from the forensic STRs. These SNPSTRs were typed on DNAs from the HapMap project, the CEPH-HGDP, Cornwall, UK African Caribbeans, Danes and Greenland Inuit. They were analysed using an ABI3100 and GeneMapper software. Data from the combined SNPSTRs allowed inferences to be made about population structures, and also enabled the calculation of the TMRCA of the derived SNPs associated with the forensic STRs. Population structure was evident in the MDS plots where rudimentary population groupings could be seen. The Americas were outliers, reflecting their later peopling some 15,000 years ago (Jobling et al. 2003). Haplogroup analysis highlighted population isolates, such as the Surui in Brazil. The STRUCTURE analysis of the SNPSTR data has also provided some insights into the admixed nature of the autosomal DNA in known admixed populations such as the Greenland Inuit and to some extent, the African Caribbeans. One SNPSTR was expanded into a larger haplotype block - a PHAX - Phylogeographically informative Haplotypes on the Autosomes and seX chromosomes, by means of a SNaPshot reaction. The preliminary data from this suggested that this would allow us to gain a more complete insight into the histories and structures of human populations.
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Kamihara-Ting, Junne. "Studies at the hemochromatosis (HFE) locus : gene conversions, haplotypes, and association analysis". Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/34193.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, February 2006.Includes bibliographical references.
Haplotype-based association studies offer an exciting potential methodology for the identification of genes that contribute to complex traits. There is thus great interest in understanding the biological forces that shape haplotypes. We have studied a well-characterized genetic locus surrounding the gene responsible for hereditary hemochromatosis (HFE) to investigate the impact of meiotic recombination events upon haplotype structure in this region. First we identified crossover hotspots in order to define the boundaries of haplotype blocks in this locus. We then found that gene conversion events play a significant role in shaping haplotype structure within these haplotype blocks. These gene conversion events were not limited to recombination hotspots and occurred with a frequency as high as 1 in 104 per site per generation. Gene conversions lead to the creation of new haplotypes and we suggest that they are important for the spread of disease alleles in a population. In addition, we discuss how these events can be used as important tools in haplotype-based association studies. We also present an association study in a large Venezuelan cohort to search for genes that contribute to residual age of onset in Huntington's disease. We demonstrate significant association between multiple alleles in a region on chromosome 6p21.3.
(cont.) We identify two candidate genes in this region, HFE and histone Hlt and demonstrate significant association of this region with age of onset in a male-specific model.
by Junne Kamihara-Ting.
Ph.D.
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Jiang, Wei. "Killer-cell immunoglobulin-like receptor gene copy number, haplotypes and disease association". Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607691.
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Serao, Nick, Dianelys Gonzalez-Pena, Jonathan Beever, Dan Faulkner, Bruce Southey i Sandra Rodriguez-Zas. "Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle". BioMed Central, 2013. http://hdl.handle.net/10150/610391.
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BACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide bindingion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.
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Dicks, Kara Leanne. "Unravelling major histocompatibility complex diversity in the Soay sheep of St Kilda". Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31412.
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The major histocompatibility complex (MHC) is one of the most variable regions in the vertebrate genome. Many genes within the MHC play important roles in the development of an immune response, including the response to pathogens, by presenting pathogen fragments to T cells. Pathogen-mediated balancing selection is thought to be important in maintaining the high levels of allelic variation at these loci, though the precise mechanism remains unclear. The number of studies of MHC diversity in non-model organisms has increased dramatically in recent years as genotype data have become cheaper and easier to generate; however, key limitations in many such studies remain a lack of high quality MHC genotypes and associated phenotype data. Many studies focus on a single MHC locus, assuming that one locus will represent the full range of variation within each MHC haplotype. Alternatively, the products of different loci may co-amplify, preventing locus-specific genotypes and hence heterozygosity being accurately determined. Non-model systems are also often limited by small sample sizes and limited recording of associated host and pathogen measures, which, combined with high levels of allelic variation at MHC loci, can limit statistical power. Finally, few MHC studies control for the general effect of relatedness in explaining host traits before testing for MHC effects. With so many methodological impediments, it is challenging to identify robust associations between MHC variation and host phenotypes, such as parasite burden or fitness, and to draw conclusions about the mechanisms underpinning the maintenance of diversity at MHC loci. In this thesis, I address these problems by developing a SNP-based haplotyping system for a population of unmanaged Soay sheep (Ovis aries) on Hirta, St. Kilda, for which data is available on pedigree, phenotypic traits and fitness and its components over a 30- year study period. The ovine MHC consists of four classes of loci, within which loci are tightly clustered and show reduced recombination rates compared to the genome average. Although the mammalian MHC is usually highly variable, one would expect that the number of haplotypes within an MHC class in an island population of sheep with no immigration to be limited. The class IIa region of the ovine MHC includes the classical class II loci which are typically thought to be involved in the presentation of peptides derived from extracellular pathogens, including gastrointestinal helminths, in sheep and other mammals. In chapters 2 to 4, I describe the characterisation of class IIa haplotypic diversity in the Soay sheep using direct Sanger sequencing of PCR amplified fragments, which, in combination with cloning, revealed eight distinct haplotypes. With this knowledge of haplotypic diversity, and genotypes for a sample of Soay sheep typed on the Ovine Infinium HD chip (approximately 600K SNPs), I developed a panel of 13 SNPs which could be used to impute the class IIa haplotypes. This panel was genotyped by KASP (Kompetitive Allele Specific PCR) in 6034 samples and used to impute the class IIa haplotypes. After quality control measures, class IIa haplotypes were successfully imputed for 5349 individuals. Evidence of balancing selection was identified using the Ewens-Watterson test at different life history stages and within the standing population each year between 1985 and 2012, showing that allele frequencies were more even than would be expected under neutrality. However, there was no evidence of deviation from Hardy-Weinberg equilibrium identified at different life stages or in the standing population in any year. In chapter 5, I investigate associations between the MHC class IIa haplotypes and individual-level data on host phenotypes - body weight, plasma immunoglobulin levels (measured as anti-Teladorsagia circumcincta third larval stage IgA, IgE and IgG) and strongyle faecal egg counts (FEC). Associations were tested within mixed effects models which were used to account for repeated measures and control for fixed effects known to affect the response variables, as well as within an animal model framework to account for relatedness between individuals. Haplotype heterozygosity was unrelated to any of the traits investigated, suggesting a general heterozygote advantage is unlikely to be operating within the Soay sheep. Six of the eight class IIa haplotypes were associated with multiple traits in different age-sex classes, although many of these associations were removed after inclusion within animal models. The evidence of balancing selection and associations between class IIa haplotypes and phenotypes related to health offers a promising glimpse into the evolutionary mechanisms which may be operating to maintain diversity within this region.
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Howie, Bryan. "Statistical methods for phasing haplotypes and inputing genotypes in large population genetic datasets". Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531825.
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Salgado, Teixeira Duarte Carolina. "The role of lupus susceptibility MHC haplotypes and interferon-alpha in gene regulation". Thesis, King's College London (University of London), 2017. https://kclpure.kcl.ac.uk/portal/en/theses/the-role-of-lupus-susceptibility-mhc-haplotypes-and-interferonalpha-in-gene-regulation(7430456f-6cca-47e0-b9f4-a89a22e1991f).html.
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Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by B cell dysregulation and type 1 interferon (IFN) activity. Variants in the major histocompatibility complex (MHC) region confer the greatest genetic risk for SLE; however, the underlying causes of association remain elusive. One mechanism by which causal variants may drive genetic associations at the MHC is through regulating gene expression in a context-specific manner. This project investigates the effect of (i) SLE-associated MHC haplotypes, and (ii) IFN-α stimulation on gene regulation in ex vivo B cells, in order to further our understanding of how these factors contribute to disease risk. Expression quantitative trait loci (eQTLs) were investigated for variants tagging six SLE-risk or -protective haplotypes: DRB1*03:01 (rs2187668), DRB1*15:01 (rs3135391), DPB1 (rs3117213, rs2071351, rs2071349), and MSH5 (rs409558). eQTL analyses were conducted using publicly-available data sets. Additionally, gene expression data were generated from resting and IFN-α-stimulated ex vivo B cells. Several cis-eQTLs were identified and replicated in the publicly-available data sets. A novel trans-eQTL was identified for DRB1*03:01 haplotypes in the exon array data set, in both resting and IFN-α-stimulated cells, involving down-regulation of BTN3A2 (P < 2.63 × 10-6). These results suggest a regulatory role for disease-associated MHC haplotypes, and implicate BTN3A2 as a novel candidate gene on the DRB1*03:01 haplotype. The global effect of IFN-α stimulation on the B cell transcriptome was also explored. Several SLE susceptibility genes outside canonical type 1 IFN signalling pathways were differentially expressed in response to IFN-α. The direction of effect of IFN-α on the expression of SLE candidate genes paralleled the known functional consequences of SLE-associated polymorphisms in those genes. This suggests a previously unrecognised role for SLE candidate genes following activation of the type 1 IFN pathway, and sheds light into the role of IFN-α in the aetiopathogenesis of SLE.
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Wang, Meng. "Family-Based Bayesian LASSO for Detecting Association of Rare Haplotypes with Common Diseases". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1398896091.
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Menard, Katrina Louise. "Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes". Texas A&M University, 2006. http://hdl.handle.net/1969.1/4210.
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Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems
since they burrow into pine cone tissues for egg deposition, causing the death of the
seeds. Management of these beetles in natural and commercial stands of pines has been
problematic due to lack of understanding about species limits and distribution. This study
was conducted to investigate the phylogeography and phylogenetics of the genus. Several
species represented by disjunct populations appear to be monophyletic including
Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C.
ponderosae is polyphyletic with many distinct clades isolated by geography. This study
explored whether host use or geography has played a greater role in the diversification of
this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis.
In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a
phylogeny of the genus, and the distribution and host use were compared to investigate
whether these factors were significantly associated. The second study addressed
population structure and possible historical influences on the C. edulis and C. ponderosae
populations using a nested clade analysis of the mtDNA haplotypes. Despite potential
limitations due to sampling, several conclusions could be drawn. Three separate
haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was
significantly associated with the phylogeny at greater distances (>900km), but host use
was not significant. At the species level, association with geography is variable.
Population structure for C. ponderosae at the species level is minimal, and suggests that
there has not been much time for lineage sorting of the haplotypes based on the nested
clade analysis as compared to C. edulis.
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Spinka, Christine Marie. "Gene-environment interactions in genetic epidemiology". Texas A&M University, 2004. http://hdl.handle.net/1969.1/1399.
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Gene-environment interactions are an area of increasing interest in complex hu-
man diseases. The first step in any study of the interactions between genes and the
environment involves identifying genes which influence the trait of interest. In this
dissertation, a new method for using the information in complex pedigrees to per-
form a joint linkage disequilibrium and linkage mapping of quantitative trait loci is
developed. Subsequently, methods are needed to determine the interaction, if any,
between these genes and environmental risk factors. Many of these factors, such as
weight or age, are continuous and little is known about their distributions. Thus, we
introduce a new method for estimating the gene-environment interaction parameters
in a logistic regression for the case-control study design. In doing so, we make the
assumption that in the underlying population, the distributions of the genetic factors
and the environmental covariates are independent. Additionally, we treat the envi-
ronmental parameters nonparametricly, utilizing the profile likelihood. Furthermore,
the methodology we develop is also general enough to be used on many different types
of genetic information, including haplotypes, and can accommodate missing genotype
data. The method is also extended to allow analysis in the presence of population
stratification or genotype misclassification. We show that the standard errors of pa-
rameter estimates using our method are smaller than those found using complete data
only. These methods are illustrated using simulations and are applied to a real data
set exploring the interaction between genotype and environment in disease risk.
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Gündüz, Islam. "Evolutionary genetics of the house mouse (Mus musculus domesticus) with particular emphasis on chromosomal and mitochondrial DNA variation". Thesis, University of York, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369328.
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Moreira, Juliane Almeida. "Impacto dos haplÃtipos do gene ΒS sobre os marcadores de hemÃlise em pacientes com anemia falciforme em estado basal". Universidade Federal do CearÃ, 2013. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=12359.
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CoordenaÃÃo de AperfeÃoamento de Pessoal de NÃvel SuperiorA anemia falciforme (AF) Ã uma doenÃa hereditÃria resultante de uma mutaÃÃo pontual (GAG GTG) no cÃdon do gene da βS - globina, levando a uma substituiÃÃo de Ãcido glutÃmico por valina na sexta posiÃÃo da cadeia polipeptÃdica, gerando uma hemoglobina (Hb) anormal denominada de HbS, em homozigose. A AF se caracteriza por anemia hemolÃtica crÃnica associada a mÃltiplos eventos tais como processo inflamatÃrio crÃnico, aumento do estresse oxidativo, dano endotelial, diminuiÃÃo da biodisponibilidade do Ãxido nÃtrico (NO), ativaÃÃo da coagulaÃÃo, dentre outros. Os biomarcadores de hemÃlise tais como: contagem de reticulÃcitos, lactato desidrogenase (LDH), Ãcido Ãrico e arginase I sÃo fundamentais na avaliaÃÃo do grau da hemÃlise, principalmente, de natureza intravascular contribuindo com o monitoramento da anemia nesses pacientes. O presente estudo teve como objetivo avaliar o impacto dos haplÃtipos do gene βS sobre os marcadores de hemÃlise em adultos com AF em estado basal, acompanhados no ambulatÃrio do serviÃo de hematologia no Hospital UniversitÃrio Walter CantÃdio (HUWC). Um total de 50 pacientes adultos com AF foi selecionado, com diagnÃstico confirmado por estudo molecular. Os pacientes se encontravam em uso de hidroxiurÃia (HU), dose variando de 500 mg a 1,5 g/kg/dia por no mÃnimo seis meses. Um grupo controle foi elaborado, sendo constituÃdo por 20 indivÃduos supostamente saudÃveis. Foram coletados 10 mL de sangue venoso em tubo de coleta a vÃcuo, contendo o anticoagulante EDTA (etileno-diamino-tetracÃtico), para a realizaÃÃo da contagem de reticulÃcitos e 6 mL de sangue venoso em tubo de coleta a vÃcuo contendo gel separador, sem anticoagulante, para as dosagens sÃricas de LDH , Ãcido Ãrico e arginase I. As variÃveis idade, sexo, dosagem e tempo de uso do medicamento, concentraÃÃo da Hb e da hemoglobina fetal (HbF) foram obtidas nos prontuÃrios mÃdicos no momento da realizaÃÃo do estudo. As anÃlises estatÃsticas foram realizadas no programa GraphPad Prism (versÃo 5.0) e o nÃvel de significÃncia estabelecido foi p < 0,05. Foi verificado aumento significante nos nÃveis de reticulÃcitos, LDH, Ãcido Ãrico e arginase I nos pacientes com AF em relaÃÃo ao grupo controle (p < 0,05). Foi observada diferenÃa significativa na Hb nos grupos Bantu/Benin em relaÃÃo aos demais haplÃtipos do cluster da βs-globina. Os nÃveis de HbF apresentaram uma tendÃncia a aumento no haplÃtipo Benin/Benin em relaÃÃo aos demais. Foi verificada uma tendÃncia no aumento de LDH no genÃtipo Bantu/Bantu em comparaÃÃo com os demais haplÃtipos. Foi observada diferenÃa significativa da arginase I entre os grupos Bantu/Bantu vs Bantu/Benin e Bantu/Bantu vs Benin/Benin. Os resultados do presente estudo reforÃam a hipÃtese de que a arginase I possa ser utilizada como possÃvel indicador de gravidade uma vez que a mesma foi associada ao haplÃtipo Bantu.
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Jacobs, Clifford Winston. "Pharmacogenomics of solute carrier transporter genes in the Xhosa population". University of the Western Cape, 2014. http://hdl.handle.net/11394/4450.
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Philosophiae Doctor - PhDSolute carrier transporters belonging to the major facilitator family of membrane transporter are increasingly being recognized as a possible mechanism to explain inter-individual variation in drug efficacy and response. Genetic factors are estimated to be responsible for approximately 15-30% of inter-individual variation in drug disposition and response. The aims of this study were to determine the minor allele frequencies of 78 previously identified single nucleotide polymorphisms in the pharmacogenetically relevant SLC22A1-3 and SLC47A1 genes in the indigenous African population of South Africa. Secondly, to determine whether allele and genotype frequencies for these SNP were different from that reported for other African, Caucasian, and Asian populations. Thirdly, to infer haplotypes from the genetic information which can potentially be used in future to design and interpret results of pharmacogenetics association studies involving these genes and their substrate drugs. Finally, to determine whether the Xhosa population harbour novel SNPs in the SLC22A2 gene, that encodes the kidney-specific hOCT2. SNaPshot™ multiplex single base minisequencing systems were developed and optimized for each of SLC22A1, SLC22A2, SLC22A3, and SLC47A1 covering the previously identified 78 SNPs. These systems were then used to genotype the alleles of 148 healthy Xhosa subjects residing in Cape Town, South Africa. In addition, the proximal promoter region and all 11 exons and flanking regions of the SLC22A2 gene of 96 of the participants were screened for novel SNPs by direct sequencing. The Xhosa subjects investigated lacked heterozygosity and were monomorphic for 91% of the SNPs screened. None of the SLC22A3 and SLC47A1 SNPs investigated was observed in this study. Sequencing of the SLC22A2 gene revealed 28 SNPs, including seven novel polymorphic sites, in the 96 Xhosa subjects that were screened. The minor allele frequencies of the seven previously identified variant SNPs observed in this study were different compared to that observed for American and European Caucasian, and Asian populations. Moreover, the allele frequencies for these SNPs differed amongst African populations themselves. Eight and seven haplotypes were inferred for SLC22A1 and SLC22A2, respectively, for the Xhosa population from the information gathered with SNaPshot™ genotyping. This study highlights the fact that African populations do not have the same allele frequencies for SNPs in pharmacogenetically relevant genes. Furthermore, the Xhosa and other African populations do not share all reduced function variants of the SLC22A1-3 and SLC47A1 genes with Caucasian and Asian populations. Moreover, this study has demonstrated that the Xhosa population harbours novel and rare genetic polymorphisms in the key pharmacogene SLC22A2. This study lays the foundation for the design and interpretation of future pharmacogenetic association studies between the variant alleles of the SLC22A1-3 and SLC47A1 genes in the Xhosa population and drug disposition and efficacy.
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Wilson, Lyle. "Genetic analysis of the Cape Sand Frog, Tomopterna delalandii (Tschudi 1838)". University of the Western Cape, 2015. http://hdl.handle.net/11394/4866.
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Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol)Tomopterna delalandii occurs throughout the west coast, Western Cape and south coast of South Africa. This range stretches across three distinct biogeographical assemblages. Based on historical records and the fact that Tomopterna is a genus of cryptic frogs, it is possible that there are unknown genetic variations within the species. To investigate whether population structure is present within T. delalandii a mitochondrial gene and nuclear gene, 16S and Tyrosinase, was sequenced from across the range. Haplotype networks and cladograms were constructed to look at the relationship between the genetic samples. This revealed definite population structuring between samples from the western edge of the range and samples from the eastern edge of the range. It also revealed that samples taken from the northern edge of the range, while matching general T. delalandii tadpole morphology, are genetically different. Further study needs to be made into the identity of this new form. This study shows that by using both mitochondrial and nuclear DNA patterns can be discovered about the genetic structure of a species as well as revealing a new one.
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Utsunomiya, Yuri Tani. "Sobre a origem e dispersão da mutação do gene PLAG1 em bovinos". Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/152438.
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O gene 1 do adenoma pleomórfico (PLAG1) apresenta evidência de seleção positiva recente e associação com tamanho corporal e fertilidade em um grande número de raças bovinas ao redor do mundo. Tendo em vista sua recentemente descoberta função como fator de transcrição para o gene do fator de crescimento semelhante à insulina 2 (IGF2), o PLAG1 possui papel emergente como um dos principais reguladores do crescimento e da reprodução em bovinos. Apesar de sua importância, a variante de sequência de DNA responsável pelos efeitos pleiotrópicos atribuídos ao PLAG1 em bovinos permanece desconhecida. Também não está claro se a mesma mutação explica as associações fenótipo-genótipo encontradas em diferentes populações bovinas. Além disso, ainda é incerto onde e quando ocorreu a pressão de seleção responsável pelo aumento da frequência da mutação do PLAG1. No presente trabalho, reportamos o desenvolvimento de um pacote para o software estatístico R, o qual é direcionado à análise de haplótipos como preditores para variantes genéticas não observadas. Através da aplicação desta ferramenta a dados genômicos de bovinos oriundos de diversas regiões do mundo, encontramos evidência indicando que um único alelo derivado do PLAG1 aumentou em frequência rapidamente em bovinos Bos taurus do noroeste europeu entre os séculos XVI e XVIII. Este período é reconhecido como a última onda de aumento de estatura em bovinos por meio de registros arqueológicos. Os dados também sugerem que o alelo foi introgredido em B. taurus não europeu e raças Bos indicus entre os séculos XIX e XX, adquirindo uma distribuição quase global no último século. Análises de DNA antigo revelaram que esta mutação segrega em gado do noroeste europeu há pelo menos 1.000 anos. Em conjunto, estes resultados implicam um papel central da mutação do PLAG1 em recentes mudanças de tamanho corporal em bovinos.
The pleomorphic adenoma gene 1 (PLAG1) presents both evidence of recent positive selection and association with body size and fertility in a wide range of worldwide cattle breeds. Considering its recently uncovered function as a transcription factor for the insulin-like growth factor 2 gene (IGF2), PLAG1 is emerging as a major regulator of bovine growth and reproduction. In spite of its importance, the causal DNA sequence variant underlying the pleiotropic effects of PLAG1 in cattle remains unknown. It is also unclear whether the same mutation accounts for the phenotype-genotype associations detected across different cattle populations. Furthermore, when and where the selective pressure responsible for increasing the frequency of the PLAG1 mutation occurred is still uncertain. Here, we report the development of a package for the R statistical software to analyze haplotypes as surrogates for unobserved genetic variants. By applying this tool to genomic data of worldwide cattle breeds, we found evidence that a single bovine PLAG1 derived allele increased rapidly in frequency in Northwestern European Bos taurus populations between the 16th and 18th centuries. This period is recognized as the last wave of increase in bovine stature from archaeological data. The data also suggested that the allele was introgressed into non-European B. taurus and Bos indicus breeds towards the 19th and 20th centuries, achieving an almost global distribution in the last century. Ancient DNA analyses further revealed that this mutation has been segregating in Northwestern European cattle for at least 1,000 years. Altogether, these results implicate a major role of the PLAG1 mutation in recent changes in body size in cattle.
2014/01095-8
2016/07531-0
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Froimzon, Melanie. "Identification of D21S11 haplotypes based on single nucleotide polymorphisms found in the 5' flanking sequence". FIU Digital Commons, 2005. http://digitalcommons.fiu.edu/etd/3420.
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Several studies have suggested a relationship between the rate of mutation of a microsatellite locus and the content of its flanking sequences. D21S11 is one of the thirteen microsatellites that constitute the FBI's CODIS Core. It is a complex microsatellite which exhibits high levels of polymorphism and microvariation. The goal of this project was to determine D21S11 haplo pes based on the new SNPs found in approximately 800 bp of associated flanking sequence. The region surrounding the microsatellite was amplified and sequenced. In 150 samples, two SNPs were identified upstream (5') of D21S11. None of them revealed any association with a specific allele.
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Boettger, Linda M. "Complex Forms of Structural Variation in the Human Genome: Haplotypes, Evolution, and Relationship to Disease". Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226090.
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Genomic mutations arise in many forms, varying from single base pair substitutions to complicated sets of overlapping copy number variants (CNVs). While each type of variation contributes to phenotype, complex structural variation, which contains multiple mutations, is difficult to type across many individuals and is largely omitted from genomic studies. This thesis presents methods to type complex structural variation, understand how it evolves, and integrate these complex variants into association studies to phenotypes.
We focused on four structurally complex regions in the human genome. The 17q21.31 region contains an inversion, previously uncharacterized overlapping copy number variants, and SNPs that associate to the female meiotic recombination rate and female fertility1. The haptoglobin (HP) gene at chromosome 16q22.2 contains a 1.7 kb tandem duplication2, previously uncharacterized paralogous gene conversion, and nearby SNPs that associate to cholesterol levels3. The haptoglobin related gene (HPR) at chromosome 16q22.2, segregates as a multi-allelic copy number variant (mCNV) specifically in African populations. Lastly, complement component 4 (C4) at chromosome 6p21.3, contains a length polymorphism, paralogous sequence variation, and copy number variation segregating in humans and non-human primates4.
We developed methods to characterize the complex structural variation in each of these four regions, type the variation at the population level and integrate it into association studies. Briefly, we determined the breakpoints of each individual structural variant, typed each variant in a population cohort, and learned which variants segregate together through trio inheritance patterns. Once these structural haplotypes were defined, we phased them with surrounding SNP haplotypes and used this data as a reference panel for imputation into disease cohorts, and to better understand their evolutionary history.
We found that two overlapping duplications in the 17q21.31 region rose rapidly and independently to high frequency within European populations, and may account for the regional association to female fertility and the female meiotic recombination rate. We also found that a recurrent deletion in the HP gene associates to total cholesterol and LDL cholesterol levels. The methods developed in this thesis enable the integration of structurally complex variation into future association studies so that we can begin to understand their effects on phenotypes.
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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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Santoro, Andreia [UNESP]. "Identificação de Single Nucleotilde Polymorphisms (SMPs) no gene Nove-cis-epoxicaroteníde dioxigenase (NCED) em Eucalyptus". Universidade Estadual Paulista (UNESP), 2010. http://hdl.handle.net/11449/92455.
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santoro_a_me_botib.pdf: 947565 bytes, checksum: 9b8b73aa8568ce2e4062e8221c067755 (MD5)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Florestas de eucalipto no Brasil estão entre os ecossistemas mais produtivos do mundo. A madeira do eucalipto é principalmente utilizada pelas empresas de papel e celulose. Contudo, fatores abióticos e bióticos afetam a expansão dessas florestas. A disponibilidade de água é uma das maiores limitações para o desenvolvimento das espécies, afetando a produção de biomassa. O hormônio ácido abscísico (ABA) desencadeia respostas de resistência a estresses abióticos, em particular a seca. O objetivo deste trabalho foi identificar Single Nucleotide Polymorphisms (SNPs) no gene NCED (nove-cis-epoxicarotenóide dioxigenase), da rota biossintética do ácido abscísico (ABA), em Eucalyptus. Através da utilização da sequencia de aminoácido da enzima de Arabidopsis (AtNCED3) e do banco de dados de Expressed Sequence Tags (ESTs) de Eucalyptus foi possível o desenvolvimento de três oligonucleotídeos, os quais amplificaram a região desejada do gene. Então, primers específicos foram desenhados e os produtos de amplificação de diferentes indivíduos submetidos ao sequenciamento direto. O alinhamento e as análises das sequencias revelaram a ocorrência de sete SNPs no gene NCED, em uma região de 1230 pares de bases. A razão transição/transversão foi 1.33. Após a predição da proteína, no site Softberry e Expasy, foram verificados cinco SNPs presentes na região codificadora, os quais geraram mutações sinônimas. Através do software DnaSP, sete haplótipos foram encontrados na amostra de 65 indivíduos gerando 15 genótipos, distribuídos entre as espécies E. grandis, E. urophylla e no híbrido Urograndis. Para os sete sítios polimórficos foram desenhados conjuntos de primers específicos que permitirão a genotipagem em larga escala para estudos de genética de população e em programas de melhoramento assistido
Eucalyptus plantations in Brazil are among the most productive ecosystems in the world. The eucalyptus wood has its principal use in the paper and cellulose industry. However, abiotic and biotic factors affect the expansion of forest plantation. Water availability is the major limitation to development of species affecting biomass production. The plant hormone abscisic acid (ABA) triggers resistance responses to abiotic stresses, in particular to drought. The objective of this study was to identify Single Nucleotide Polymorphism (SNPs) in nine-cis-epoxycarotenoid dioxygenase (NCED), enzyme of ABA biosynthetic pathway, in Eucalyptus. Through the utilization of amino acid sequence of this enzyme of Arabidopsis (AtNCED3) and using availability Expressed Sequence Tags (ESTs) database of Eucalyptus, as possible the development of three PCR primers that amplified the desirable regions of the gene. Thus, specifics primers were designed and amplification products of different individuals submitted to direct sequencing. The alignment and analysis of sequences revealed the occurence of seven SNPs in NCED gene, in a region of 1230 base pairs. The rate of transition/transversion was 1.33. After the prediction of protein, by the sites Softberry and Expasy, it was verified five SNPs, in coding region, that generated synonymous substitutions. Using the DnaSP program, seven haplotypes were found in a sample of 65 individuals, consisting of the species E. grandis, E. urophylla and the hybrid Urograndis. For these seven polymorphic sites were designed SNPs markers sets that will allow large-scale genotyping for population genetic studies and assisted breeding programs
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Certain, Laura K. "Genetic profiling of drug resistance in Plasmodium falciparum /". Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/10252.
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Silva, Lilianne Brito da. "CaracterizaÃÃo clÃnica, hematolÃgica e molecular dos pacientes com anemia falciforme em Fortaleza, CearÃ". Universidade Federal do CearÃ, 2009. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=3637.
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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgicoIntroduÃÃo: A anemia falciforme à o resultado de uma mutaÃÃo pontual (GAGGTG) no cÃdon do gene da globina β, conduzindo a uma substituiÃÃo de Ãcido glutÃmico por valina na sexta posiÃÃo da cadeia polipeptÃdica. A anemia falciforme apresenta manifestaÃÃes clÃnicas heterogÃneas, que podem ser relacionadas ao tipo de haplÃtipo associado ao gene da HbS e aos nÃveis de HbF. Objetivo: CaracterizaÃÃo clÃnica, hematolÃgica e molecular dos pacientes com anemia falciforme em Fortaleza, CearÃ. Metodologia: Foram analisados 47 pacientes com anemia falciforme, adultos e de ambos os sexos. A determinaÃÃo dos valores hematolÃgicos foi realizada em contador automÃtico de cÃlulas sangÃÃneas; a determinaÃÃo da presenÃa de HbSS foi realizada por eletroforese em pH alcalino em fitas de acetato de celulose e por eletroforese de diferenciaÃÃo em Ãgar-fostato pH 6.2; os nÃveis de HbF foram determinados pela tÃcnica da desnaturaÃÃo alcalina; e a anÃlise dos haplÃtipos da mutaÃÃo ÃS foi realizada por meio da tÃcnica da reaÃÃo em cadeia mediada pela polimerase para polimorfismo dos comprimentos dos fragmentos de restriÃÃo (PCR-RFLP). As anÃlises estatÃsticas foram desenvolvidas no programa GraphPad Prism (versÃo 5.0) e o nÃvel de significÃncia estabelecido foi p < 0,05. Resultados: A distribuiÃÃo dos haplÃtipos do gene da βS-globina, 63% do tipo Bantu, 25% do tipo Benin e 12% do tipo AtÃpico, està em conformidade com a observada para a populaÃÃo brasileira, em que o haplÃtipo Bantu à o mais prevalente, seguido pelo Benin e Senegal. NÃo houve diferenÃa significativa entre o presente estudo e os resultados encontrados no Rio de Janeiro, Porto Alegre, Campinas e RibeirÃo Preto; porÃm uma diferenÃa significativa foi observada quando o estudo foi comparado aos resultados obtidos em Salvador, BelÃm, Amazonas e por outros pesquisadores no CearÃ. A distribuiÃÃo das freqÃÃncias dos haplÃtipos do gene da βS-globina nos diferentes estudos està condizente com a histÃria da formaÃÃo da populaÃÃo brasileira, exceto nos resultados do estudo anterior realizado no CearÃ, que obteve o haplÃtipo Benin com maior prevalÃncia. Conforme os dados histÃricos sobre as origens da populaÃÃo negra trazida ao estado do CearÃ, o haplÃtipo Bantu seria o mais prevalente. Na comparaÃÃo entre os haplÃtipos e as caracterÃsticas hematolÃgicas estudadas, apenas os valores de HbF e Ht apresentaram diferenÃa estatisticamente significativa. Os nÃveis de HbF foram maiores no haplÃtipo Benin, seguido do haplÃtipo Bantu, o que està em conformidade com os dados da literatura. Foi demonstrada maior presenÃa de crises vaso-oclusivas e episÃdios de pneumonia no haplÃtipo Benin/AtÃpico do que no haplÃtipo Bantu/AtÃpico; e maior presenÃa de crises de infecÃÃo urinÃria no haplÃtipo Benin/AtÃpico do que no haplÃtipo Benin/Benin. NÃo houve diferenÃa estatisticamente significativa entre os haplÃtipos Bantu/Bantu e Benin/Benin em relaÃÃo Ãs complicaÃÃes clÃnicas, entretanto foi observado que o haplÃtipo Bantu/Bantu tem uma maior freqÃÃncia em todos os eventos clÃnicos estudados quando comparado ao Benin/Benin. Dentre os resultados foi demonstrada uma tendÃncia de menor nÃmero de pacientes com crises vasos-oclusivas e Ãlceras de perna com o aumento dos nÃveis de HbF. NÃo houve diferenÃa estatisticamente significativa na comparaÃÃo entre os nÃveis de HbF e os valores de HemÃcias, Hemoglobina, HematÃcrito, LeucÃcitos e Plaquetas. ConclusÃes: A determinaÃÃo dos haplÃtipos da anemia falciforme à de grande importÃncia nÃo sà para o acompanhamento e prognÃstico dos pacientes, como tambÃm como ferramenta para estudos antropolÃgicos que contribuam no esclarecimento da origem dos africanos que tanto contribuÃram na formaÃÃo etnolÃgica, econÃmica, cultural e social do Brasil.
Introduction: The sickle cell anemia is the result of a point mutation in the β-globin gene, leading to a substitution of glutamic acid by valine at the sixth position of the polypeptide chain. The sickle cell anemia presents heterogeneous clinical manifestations, which may be related to the type of haplotype associated with the gene for HbS and HbF levels. Objective: Clinical characterization, molecular and haematological patients with sickle cell anemia in Fortaleza, CearÃ. Methods: We analyzed 47 patients with sickle cell anemia, adults of both sexes. The determination of hematological values was performed on blood cells automated meter; the determination of the presence of HbSS was performed by alkaline hemoglobin electrophoresis on cellulose acetate tapes and by differentiation electrophoresis on agar-phosphate pH 6.2; the levels of HbF were determined by alkali denaturation technique; and the analysis of the haplotypes of the ÃS mutation was done by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Statistical analysis was developed in the program GraphPad Prism (version 5.0) and the level of significance was set p <0.05. Results: The distribution of the haplotypes of βS-globin gene - 63% of the Bantu type, 25% of the Benin type and 12% atypical â was in conformity with that observed for the entire Brazilian population, in which the Bantu haplotype is most prevalent, followed by the Benin and Senegal. There was no significant difference between the results found in this study and those found for the cities of Rio de Janeiro, Porto Alegre, Campinas and RibeirÃo Preto; but there was a significant difference with the results obtained for the cities of Salvador and BelÃm and the state of Amazonas, and by other researchers in CearÃ. The distribution of haplotype frequencies of the βS-globin gene in the different studies is in line with the history of the formation of the Brazilian population, except for the results of a previous study carried out in CearÃ, in which the Benin haplotype was found to be most prevalent. According to the historical information on the origins of the slave population brought to CearÃ, the Bantu haplotype should be the most prevalent. In the comparison between the haplotypes and the haematological characteristics studied, only the values of HbF and Ht showed statistically significant difference. The levels of HbF were higher in the Benin haplotype, followed by the Bantu haplotype, which is in accordance with the literature. Was demonstrated greater presence of painful episodes and episodes of pneumonia in Benin haplotype/Atypical haplotype than in Bantu/Atypical and increased presence of urinary infection crises in Benin haplotype/Atypical haplotype than in Benin/Benin. There was no statistically significant difference between the haplotypes Bantu/Bantu and Benin/Benin for clinical complications, however it was observed that the haplotype Bantu/Bantu has a higher frequency in all studied clinical events when compared to Benin/Benin. Among the results was shown a trend of fewer patients with painful episodes and of leg ulcers with increased levels of HbF. There was no statistically significant difference in the comparison between the levels of HbF and the values of red blood cells, hemoglobin, hematocrit, leukocytes and platelets. Conclusions: The determination of haplotypes of sickle cell anemia is of great importance not only for monitoring and prognosis of patients, but also as a tool for anthropological studies which help in clarifying the origin of Africans who have contributed so much in training ethnological, economic, cultural and social Brazil.
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Borden, William Calvin. "Phylogeography of Smallmouth Bass (Micropterus Dolomieu) and Comparative Myology of the Black Bass (Micropterus, Centrarchidae)". Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1209066783.
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Li, Na. "Modeling and inference for linkage disequilibrium and recombination /". Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/9532.
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Ashford, Blair Donald. "Investigations into the selective neutrality of mitochondrial DNA haplotypes in hatchery strain brook charr (Salvelinus fontinalis)". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24438.pdf.
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