Altered intracellular calcium homeostasis and oxidative stress are involved in the pathophysiology of bipolar disorder (BD)-I. To explore the genes contributing to these abnormalities, we examined the association with BD of the iPLA2β (PLA2G6), a signaling enzyme that mobilizes the arachidonic acid signaling cascade and activates oxidative stress, and assessed whether it interacts genetically with type 2 transient receptor potential channel gene (TRPM2), an oxidative stress-responsive calcium channel implicated both functionally and genetically in BD-I. Two tag single nucleotide polymorphisms rs4375 and rs3788533 in iPLA2β were genotyped in 446 White case-control individuals and 296 BD families using a 5′-nuclease TaqMan assay. The results were analyzed using χ-test and transmission disequilibrium tests, and Haploview. In a secondary analysis, we tested gene-gene interactions between TRPM2 and iPLA2β on BD vulnerability by logistic regression using a case-only design in PLINK. iPLA2β-rs3788533 showed a borderline association with BD-I in patients with a history of psychosis in both case-control and family designs. Association with BD as a whole was observed in the family study (significant over transmissions of rs3788533-allele C, P=0.015, PBonferroni=0.03, TDTPHASE). A borderline interaction was found between rs749909 within TRPM2 and rs4375 within iPLA2β (Puncorrected=0.009), on the basis of the case-only design analyzed with PLINK. A significant association of iPLA2β variants with BD-I and a trend gene-gene interaction between iPLA2β and TRPM2 provides additional support for the notion that genetic variation in these two functionally implicated candidates contributes toward the risk and pathophysiology of this illness.

Objectives: To determine the association between genetic variants on chromosome 4q25 and atrial fibrillation (AF) in a Taiwanese population. Methods: We enrolled 200 patients with AF (mean age: 67 ± 13 years) and 158 controls (mean age: 63 ± 10 years). The genotypes of five SNPs, RS2634073, RS2200733, RS13143308, RS2220427 and RS10033464, were determined using multiplex single base extension methods. Results: The distribution of the RS2200733 and RS10033464 genotypes did not significantly deviate from the Hardy-Weinberg equilibrium in the control group. The distribution of the RS2200733 genotypes differed significantly between the AF group and the controls (p = 0.03), whereas the distribution of the RS10033464 genotypes did not (p = 0.49). At RS2200733, patients with the CC genotype exhibited a 0.45 times higher risk of developing AF than those with the TT genotype (p = 0.02) and a recessive model was suggested (p = 0.01). After adjusting for various covariates, patients with the CC genotype remained recessively associated with a lower risk of developing AF than those with the TT genotype (odds ratio: 0.27, 95% confidence interval: 0.11-0.65; p < 0.01). Conclusions: In the Taiwanese, there is an association between SNP RS2200733 - but not RS10033464 - and the development of AF. Based on a recessive model of inheritance, individuals with SNP RS2200733 genotype CC are at a lesser risk of developing AF.

Wheat is the most widely grown crop in the world and as such, is an essential source of energy and nutrition. The challenges that breeders presently face is to increase production to feed the rising population of the world, while also accounting for climate change, pollution, water and environmental stresses. As genetic uniformity of modern cultivars has increased vulnerability to pests and diseases, the wild relatives of wheat offer a rich source of genetic diversity and stress tolerance traits, that can be harnessed and transferred in to modern wheat. In this study, we used array-based genotyping to explore genetic diversity in 385 domesticated and non-domesticated lines of wheat and their wild relatives. Genetic characterization using the wheat 90K array, and subsequent filtering and validation mapped 9,570 single nucleotide polymorphic markers onto the wheat reference genome. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the domesticated, and the ancient Triticum turgidum species from modern T. turgidum cultivars. Using this diverse germplasm, a genome-wide association study (GWAS) was performed for leaf rust, the most widespread rust disease of wheat. Identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead in the plant-pathogen evolutionary arms race. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3-4 years at 2-3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related nucleotide associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known leaf rust (Lr) resistance genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Future efforts to validate these loci will help understand their role in disease resistance and promote their utility for marker-assisted selection in pre-breeding.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20249号 / 医博第4208号 / 新制||医||1020(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 清水 章, 教授 松田 道行, 教授 武田 俊一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20808号 / 医博第4308号 / 新制||医||1025(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 椛島 健治, 教授 玉木 敬二, 教授 生田 宏一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Arsenic contamination of the environment is a worldwide health hazard. This research project focused on four areas: development and testing of low cost, field portable devices capable of measuring levels of arsenic at 10 μg L-1 or less; specific chemical techniques for such testing; creation of educational tools and techniques to allow operators who lack advanced chemistry training to perform accurate testing; and the determination and use of a biomarker in DNA as a cancer predictor in individuals exposed to environmental arsenic. The analytical techniques explored include: (1) the Gutzeit method of arsenic determination though arsine gas production, which was investigated in three experiments: measuring arsenic levels in soil samples, using Gutzeit-based kits using silver nitrate as a reactant for arsine gas, and sensitivity comparison of three commercial test kits over varying time periods up to twenty-four hours. (2) The molybdenum blue method, technologically quantified through three different experiments: digital photographic analysis, spectroscopic analysis, and flow injection. (3) Filtration of arsenic contaminated water with wood-ash, sand, ferric oxide, and commercially available steel wool; and the construction of a filtering device constructed of recyclable discarded soda bottles. Further, single nucleotide polymorphisms in the DNA of arsenic exposed individuals were studied to determine what immune response genes might be implicated in arsenic susceptibility. The major conclusions of this research were: digital image analysis used with the Gutzeit method improves precision and accuracy; silver nitrate proved to be a better measurement tool at low concentrations of arsenic than mercuric bromide; and the Gutzeit method can be applied to soils in the Hach kit.

Cotton (Gossypium spp.) is the world’s leading textile fiber crop, and an important source of oil and protein. Insufficient candidate gene derived-markers suitable for genetic mapping and limited information on genes that control economically important traits are the major impediments to the genetic improvement of Upland cotton (G. hirsutum L.). The objectives of this study were to develop a SNP marker discovery strategy in tetraploid cotton species, SNP characterization and marker development from fiber initiation and elongation related genes, chromosomal assignment of these genes by SNP marker-based deletion analysis or linkage mapping, and genetic and molecular analysis of mutants affecting cotton fiber development. Phylogenetic grouping and comparision to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). By employing this strategry, a total of 222 and 108 SNPs were identified and the average frequency of SNP was 2.35% and 1.30% in six EXPANSIN A genes and six MYB genes, respectively. Both gene families showed independent and incongruent evolution in the two subgenomes and a faster evolution rate in Dt-genome than that in At-genome. SNPs were concordantly mapped to different chromsomes, which confirmed their value as candidate gene marker and indicated the reliability of SNP discovery stragey. QTL mapping by two F2 populations developed from fiber mutants detected major QTL which explain 62.8-87.1% of the phenotypic variation for lint percentage or lint index in the vicinity of BNL3482-138 on chromosome 26. Single marker regression analyses indicated STV79-108, which was located to the long arm of chromosome 12 (the known location of N1 and perhaps n2 loci), also had significant association (R2 % value 15.4-30.6) with lint percentage, lint index, embryo protein percentage and micronaire. Additional QTL and significant markers associated with other seed and fiber traits were detected on different chromosomes. Inheritance analysis indicated that both genetic models N1N1n2n2 and n2n2li3lisub>3 could lead to the fiberless phenotype. The observation of fuzzless-short lint phenotype indicated fiber initiation and elongation were controlled by different mechanisms. The penetrance of Li2 gene expression was observed in this study.

No description available.

No description available.

O gênero Yersinia pertence à família Enterobacteriaceae e compreende 17 espécies. Y. pestis, Y. pseudotuberculosis e Y. enterocolitica são reconhecidamente patógenos de humanos e animais. Y. pestis cause a peste. Y. pseudotuberculosis e Y. enterocolitica são agentes causadores, sobretudo, de gastroenterites transmitidas por água e alimentos. As demais 14 espécies são, usualmente, consideradas não-patogênicas, com exceção de Y. ruckeri sorogrupo O:1 que causa infecções em peixes. Nas últimas décadas, a tipagem molecular tornou-se uma importante ferramenta nos estudos filogenéticos de numerosos micro-organismos e o desenvolvimento de sistemas de tipagem rápidos e baratos pode facilitar os estudos epidemiológicos de infecções bacterianas. No presente estudo objetivou-se desenvolver um método de genotipagem de Yersinia spp. baseado em high-resolution melting analysis (HRMA) para diferenciar os single-nucleotide polymorphisms (SNPs) presentes nas sequências dos genes 16S rRNA, glnA, gyrB, hsp60 e recA e aplicá-lo na tipagem de 40 linhagens de Y. pseudotuberculosis e 50 linhagens de Y. enterocolitica, bem como separar por HRMA as espécies Y. pseudotuberculosis e Y. enterocolitica. Os SNPs foram determinados nas sequências dos loci acima citados a partir de um conjunto de 119 linhagens de Yersinia spp. depositadas no GenBank/EMBL/DDBJ. Foram encontrados nas sequências dos genes analisados de Y. pseudotuberculosis, Y. enterocolitica, Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii e Y. ruckeri 10, 10, 9, 6, 4, 1 e 1 SNPs, respectivamente. Nenhum SNP foi encontrado nas sequências analisadas de Y. pestis e um grande número de SNPs foi encontrado nas sequências analisadas de Y. frederiksenii, Y. kristensenii e Y. massiliensis, o que impossibilitou a genotipagem dessas espécies por HRMA. As demais espécies não foram analisadas. Foram desenhados pares de primers para flanquear os SNPs encontrados em cada espécie de Yersinia testada. Usando um conjunto de primers espécie-específicos, a diversidade genética de cada espécie de Yersinia foi determinada por HRMA e a análise filogenética foi baseada na sequência concatenada composta pelos nucleotídeos identificados em cada fragmento analisado. O agrupamento foi realizado com o software BioNumerics usando o método UPGMA com 1.000 replicatas de bootstrap. A árvore filogenética ii construída para Y. pseudotuberculosis agrupou as linhagens em clusters bio-sorogrupo específicos. As linhagens do bio-sorogrupo 1/O:1 foram agrupadas em um cluster e as linhagens do bio-sorogrupo 2/O:3 em outro. A árvore filogenética construída para Y. enterocolitica agrupou as linhagens em três grupos. As linhagens altamente patogênicas, do biotipo 1B, foram agrupadas em um cluster, as linhagens de média patogenicidade, dos biotipos 2, 3, 4 e 5, foram agrupadas em um segundo cluster e as linhagens consideradas nãopatogênicas, do biotipo 1A, foram agrupadas em um terceiro cluster. O agrupamento encontrado em Y. pseudotuberculosis e Y. enterocolitica foi consistente com o perfil patogênico característico dessas duas espécies. Nenhuma correlação epidemiológica significativa foi encontrada no agrupamento de Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii e Y. ruckeri de acordo com os resultados de HRMA. Ademais, o método de HRMA aqui desenvolvido foi capaz de separar as espécies Y. pseudotuberculosis e Y. enterocolitica. O método de HRMA desenvolvido nesse estudo pode ser usado como uma alternativa para a genotipagem e para a diferenciação de Y. pseudotuberculosis de Y. enterocolitica. Esse método também pode complementar os métodos baseados em sequências e facilitar os estudos epidemiológicos dessas duas espécies de Yersinia. / The genus Yersinia belongs to the family Enterobacteriaceae and comprises 17 species. Y. pestis, Y. pseudotuberculosis and Y. enterocolitica are well recognized human and animal pathogens. Y. pestis causes plague. Y. pseudotuberculosis and Y. enterocolitica are, usually, causative agents of food-waterborne gastroenteritis. The other 14 Yersinia species are considered to be non-pathogenic, with the exception of Y. ruckeri serogroup O:1 which causes infections in fishes. In the last few decades, molecular typing has become an important tool in phylogenetic studies of several microorganisms and the development of fast and inexpensive typing systems can facilitate epidemiological studies of bacterial infections. The present study aimed to develop a method of Yersinia spp. genotyping based on high-resolution melting analysis (HRMA) in order to differentiate the single-nucleotide polymorphisms (SNPs) present in the 16S rRNA, glnA, gyrB, hsp60 and recA sequences and apply it in the typing of 40 Y. pseudotuberculosis strains and 50 Y. enterocolitica strains, as well as, to separate by HRMA the Y. pseudotuberculosis and Y. enterocolitica species. The SNPs were determined in the sequences of the aforementioned loci using a set of 119 Yersinia strains deposited in the GenBank/EMBL/DDBJ database. It were found in the gene sequences analyzed of Y. pseudotuberculosis, Y. enterocolitica, Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii and Y. ruckeri 10, 10, 9, 6, 4, 1 and 1 SNPs, respectively. No SNPs was found in the analyzed sequences of Y. pestis and a large number of SNPs were found in the analyzed sequences of Y. frederiksenii, Y. kristensenii and Y. massiliensis what prevented their genotyping by HRMA. The remaining Yersinia species were not analyzed. It was designed primer pairs to flank the SNPs found in each Yersinia species tested. Using a specie-specific set of primers, the genetic diversity of each Yersinia species used was determined by HRMA and the phylogenetic analysis was based on the concatenated sequence composed by the nucleotides identified in each fragment analyzed. Clustering was performed with the software package BioNumerics using UPGMA method and 1,000 bootstrap replicates. The phylogenetic tree constructed for Y. pseudotuberculosis grouped the strains into bio-serogroups specific clusters. The strains of 1/O:1 bio-serogroup were grouped into one cluster and the strains of 2/O:3 bio-serogroup into iv other cluster. The phylogenetic tree constructed for Y. enterocolitica grouped the strains in three clusters. The highly pathogenic strains, of biotype 1B, were grouped into one cluster, the moderate pathogenic strains, of biotypes 2, 3, 4 and 5, were grouped into a second cluster and, the non-pathogenic strains, of biotype 1A, were grouped into a third cluster. The clusterization of Y. pseudotuberculosis and Y. enterocolitica were consistent with the pathogenic profile characteristic of these two Yersinia species. No significant epidemiological correlation was found in the grouping of Y. bercovieri, Y. rohdei, Y. intermedia Y. mollaretii and Y. ruckeri according to HRMA results. Moreover, the HRMA-based method develop here was able to separate the Y. pseudotuberculosis and Y. enterocolitica species. The HRMA assay developed in this study can be used as an alternative for the genotyping and the differentiation of Y. pseudotuberculosis and Y. enterocolitica. This method can also complement sequence-based methods and facilitate epidemiological studies of these two Yersinia species.