Family, twin, and adoption studies have indicated that human intelligence quotient (IQ) has significant genetic components. We performed a low-density genome-wide association analysis with a family-based association test to identify genetic variants influencing IQ, as measured by Wechsler Adult Intelligence Scale full-score IQ (FSIQ). We examined 11,120 single-nucleotide polymorphisms (SNPs) from the Affymetrix GeneChips 10K mapping array genotyped in 292 nuclear families from Genetic Analysis Workshop 14, a subset from the Collaborative Study on the Genetics of Alcoholism (COGA). A replication analysis was performed using part of International Multi-Center ADHD Genetics Project (IMAGE) dataset. Twenty-two SNPs were identified as having suggestive associations with IQ (p<10-3) in the COGA sample and eleven of the SNPs were located within known genes. In particular, NTM at 11q25 (rs411280, p=0.000764) and NR3C2 at 4q31.1 (rs3846329, p=0.000675) were two novel genes which have not been associated with IQ in other studies. It has been reported that NTM might play a role in late-onset Alzheimer disease while NR3C2 may be associated with cognitive function and major depression. The associations of these two genes were well-replicated by single-marker and haplotype analyses in the IMAGE sample. In conclusion, our findings provide evidence that chromosome regions of 11q25 and 4q31.1 contain genes affecting IQ. This study will serve as a resource for replication in other populations.

京都大学 / 0048 / 新制・課程博士 / 博士(医科学) / 甲第21698号 / 医科博第102号 / 新制||医科||7(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 藤渕 航, 教授 齊藤 博英, 教授 小杉 眞司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Bipolar disorder is a relatively common form of mental illness that depends strongly on genetic inheritance for expression. The author of this study has sought to evaluate whether the gender of subjects influences which genetic variants are associated with the disease. A portion of the cases from a previously published study were analyzed using PLINK software and the association of single-nucleotide polymorphisms was evaluated separately for all cases, for female subjects alone, and for male subjects alone. The results obtained for male subjects alone reached higher levels of statistical significance than when both genders were evaluated together or when female subjects were evaluated alone. The most significantly scoring polymorphisms were distinctly different for the 2 genders. In particular, a site downstream of the ion exchanger SLC24A3 and upstream of the Rab5-interacting protein RIN2 gene on chromosome 20 (rs6046396) yielded very high significance in men (p=3.91 X 10-9).

The design of probes for the selective recognition of biopolymers (nucleic acids and proteins) is a fundamental task for studying, diagnosing, and treating diseases. Traditional methods utilize a single component (small molecule or oligonucleotide) that binds directly to the target biopolymer. However, many biopolymers are unable to be targeted with this approach. The overarching goal of this dissertation is to explore a new, binary approach for designing probes. The binary approach requires two components that cooperatively bind to the target, triggering a recognition event. The requisite binding of two-components allows the probes to have excellent selectivity and modularity. The binary approach was applied to design a new sensor, called operating cooperatively (OC) sensor, for recognition of nucleic acids, including selectively differentiating between single nucleotide polymorphisms (SNPs). An OC sensor contains two oligonucleotide probe strands, called O and C, each with two domains. The first domain contains a target recognition sequence, whereas the second domain is complementary to a molecular beacon (MB) probe. Binding of both probe strands to the fully matched analyte generates a full MB probe recognition site, allowing a MB to bind and report the presence of the target analyte. Importantly, we show that the OC sensor selectively discriminates between single nucleotide polymorphisms (SNPs) in DNA and RNA targets at room temperature, including those with stable secondary structures. Furthermore, the combinatorial use of OC sensors to create a DNA logic gate capable of analyzing DNA sequences of Mycobacterium tuberculosis is described. The binary approach was also applied to design covalent inhibitors for HIV-1 reverse transcriptase (RT). In this application, two separate pre-reactive groups were attached to a natural RT ligand, deoxythymidine triphosphate (dTTP). Upon binding of both dTTP analogs in the RT active site, the pre-reactive groups are brought into the proper proximity and react with each other forming an intermediate that subsequently reacts with an amino acid side chain from the RT. This leads to covalent modification of RT, and inhibition of its DNA polymerase activity. This concept was tested in vitro using dTTP analogs containing pre-reactive groups derived from ?-lactamase inhibitors clavulanic acid (CA) and sulbactam (SB). Importantly, our in vitro assays show that CA based inhibitors are more potent than zidovudine (AZT), a representative of the dominant class of RT inhibitors currently used in anti-HIV therapy. Furthermore, molecular dynamics simulations predict that complexes of RT with these analogs are stable, and point to possible reaction mechanisms. The inhibitors described in this work may serve as the basis for the development of the first covalent inhibitors for RT. Moreover, the pre-reactive groups used in this study can be used to design covalent inhibitors for other targets by attaching them to different ligands. Overall, the work presented herein establishes the binary approach as a straightforward way to develop new probes to selectively recognize nucleic acids and proteins.

Holistic and growth stage-specific screening is needed for identifying tolerant genotypes and for formulating strategies to mitigate the negative effects of abiotic stresses on crops. The objectives of this study were to characterize the genetic variability of 100 rice lines for early-season vigor, growth and physiological plasticity, and drought and temperature tolerance. Five studies were conducted to accomplish these objectives. In study 1 and 2, 100 rice genotypes consisting of several cultivars and experimental breeding lines were characterized for early-season vigor using several shoot and root morphological, physiological, and yield related traits. In study 3, low- and high-temperature tolerance assessed on select rice cultivars/hybrids during early-season. In study 4, genotypic variability in response to drought stress tolerance using morpo-physiological traits including roots was assessed under pot-culture conditions in a mini-greenhouse conditions. In study 5, the 100 rice genotypes were used to identify and validate SNP markers, and genome-wide association study (GWAS) to generate genotypic and phenotypic data with the objective of identifying new genetic loci controlling drought stress traits. Significant variability was recorded among rice genotypes and treatments for many traits measured. Early-season cumulative vigor response indices (CVRI) developed by summing individual responses indices for each trait varied among the rice genotypes, 21.36 (RU1404196) to 36.17 (N-22). Based on means and standard deviation of the CVRI, rice genotypes were classified as low- (43) and moderately low- (33), high- (16), and very high-vigor (5) groups. Total low-temperature response index values ranged from 18.48 to 23.15 whereas total high-temperature responses index values ranged from 42.01 to 48.82. Antonio, CLXL 745, and Mermentau were identified as sensitive to cold- and heat, and XL 753 was highly cold and heat tolerant genotypes tested. A cumulative drought stress response index (CDSRI) values varied between 14.7 (CHENIERE) and 27.9 (RU1402174) among the genotypes tested. This preliminary analysis of GWA indicated that substantial phenotypic and genotypic diversity exists in the 100 rice genotypes, despite their narrow genetic pool. The stress tolerant and high vigor rice genotypes will be valuable for rice breeders for developing new genotypes best suited under growing environments prone to early-season drought and temperature.

No description available.

This thesis presents a new ant-optimized biclustering technique known as SNAP biclustering, which runs faster and produces results of superior quality to previous techniques. Biclustering techniques have been designed to compensate for the weaknesses of classical clustering algorithms by allowing cluster overlap, and allowing vectors to be grouped for a subset of their defined features. These techniques have performed well in many problem domains, particularly DNA microarray analysis and collaborative filtering. A motivation for this work has been the biclustering technique known as bicACO, which was the first to use ant colony optimization. As bicACO is time intensive, much emphasis was placed on decreasing SNAP's runtime. The superior speed and biclustering results of SNAP are due to its improved initialization and solution construction procedures. In experimental studies involving the Yeast Cell Cycle DNA microarray dataset and the MovieLens collaborative filtering dataset, SNAP has run at least 22 times faster than bicACO while generating superior results. Thus, SNAP is an effective choice of technique for microarray analysis and collaborative filtering applications. / Master of Science

Since the late 1990s, common carp and koi production enterprises around the world have suffered enormous losses due to a viral disease caused by cyprinid herpesvirus-3 (CyHV-3). Genetic variation in resistance to CyHV-3 infection was observed in different common carp strains, indicating that disease resistance can be improved by selective breeding. Marker-assisted selection is a breeding strategy that can accelerate genetic gain; however, this approach requires genetic markers and a genetic linkage map. To develop molecular tools for breeding CyHV-3-resistant aquaculture stock, several candidate genes for antiviral innate immune response from common carp were isolated, and single nucleotide polymorphisms (SNPs) were identified. SNP markers for common carp immune response genes were developed for testing their linkage to disease resistance and for generating a genetic linkage map. Common carp immune response genes were isolated using degenerate primers developed from conserved peptide regions among other fish species for polymerase chain reaction (PCR) amplification. The amplified products were cloned and sequenced. Gene-specific primers were designed based on the isolated carp gene sequences to amplify gene fragments from genomic DNA of three carp strains and koi. The amplified products were cloned and sequenced to identify SNPs. For the genes that are duplicated, locus-specific primers were used for PCR amplification. SNPs were identified in several genes, including TLR2, TLR3a, TLR3b, TLR4a, TLR4b, TLR7a, TLR7b, TLR9, TLR21, TLR22, MyD88a, MyD88b, TRAF6a, TRAF6b, type I IFN, IL-1β, IL10a and IL10b. Putative SNPs were genotyped in a SNP discovery panel consisting of different common carp strains and koi to evaluate their allele frequencies and in a full-sib family to validate their segregation patterns using the SNaPshot method. Validated SNPs were used to genotype a mapping family. Twenty-three SNPs (19 exonic and 4 intronic SNPs) were informative in a mapping family. Among these genes, polymorphisms in IL10a suggested a possible association with resistant and susceptible phenotypes of CyHV-3-challenged fish. These SNPs will be analyzed with a set of approximately 300 microsatellites to generate a second-generation genetic map and to identify quantitative trait loci (QTLs) affecting resistance to CyHV-3. Among the common carp genes that were isolated and sequenced, TLR9 is known for its ability to detect viral DNA and requires adaptor molecules MyD88 and TRAF6 for signal transduction. Therefore TLR9, MyD88 and TRAF6 may be important candidate genes for mediating host antiviral response to CyHV-3. To elucidate possible functions of these genes, full-length cDNAs of common carp TLR9, MyD88 and TRAF6 were isolated and tissue-specific mRNA expression was determined. cDNA sequences of MyD88 and TRAF6 revealed that these genes are duplicated. These findings were the first report of MyD88 and TRAF6 duplications in a vertebrate. Protein domain characterization demonstrated that structural characteristics of these genes are conserved and resemble those of other vertebrates, indicating that common carp TLR9, MyD88 and TRAF6 genes may have identical functions with their mammalian orthologs. The mRNA expression of TLR9, MyD88a and b, and TRAF6a and b varied among tissues. Differential expression of the MyD88 and TRAF6 paralogous transcripts were observed in muscle tissues, suggesting that one paralog has evolved and attained a non-immune function. This genomic information will facilitate further research to better understand the ligand specificity of TLR9 and the role of TLR9, MyD88 and TRAF6 in the common carp immune response. / Ph. D.

This study explores the use of coding-region, forensically-relevant single nucleotide polymorphisms (SNPs) from RNA sequencing data. SNPs present distinct advantages over short tandem repeat (STR) typing, particularly in niche scenarios, such as in samples with low-quantity DNA templates or in degraded samples with substantially fragmented DNA. While RNA is susceptible to rapid ex-vivo degradation, mRNA has demonstrated unexpected stability in dried body fluid stains, contingent upon the storage conditions. This paper presents a pipeline designed to identify forensically relevant coding region single nucleotide polymorphisms (cSNPs) from RNA-seq data. The forensically relevant cSNPs utilized in this study were sourced from a previously published paper that identified a panel of 35 body fluid-specific cSNPs. Our pipeline demonstrated effectiveness in identifying forensically relevant cSNPs across various tissue categories. However, the final analysis raises concerns about the overall specificity of this panel of cSNPs and issues with cross-reactivity for different body fluids. Overall, this study contributes to the advancement of forensic genetics by providing a robust and standardized pipeline for identifying cSNPs from RNA-seq data. While further evaluation and optimization are necessary, the demonstrated efficacy of this pipeline holds promise for enhancing genetic profiling in forensic contexts.

S'ha estudiat la variabilitat genètica de les poblacions del nord d'Àfrica a partir de l'anàlisi de diverses regions genòmiques per tal d'entendre les poblacions analitzades d'una banda, i comprendre la dinàmica del genoma per l'altra. Els resultats obtinguts ens han permès verificar diferents hipòtesis sobre la història de les poblacions d'aquesta regió com són l'efecte paral·lel i independent de l'onada de difusió del neolític des de l'Orient Mitjà al llarg d'ambdues ribes de la Mediterrànea; i l'efecte de l'arabització. S'ha pogut estimar també la contribució genètica masculina nord africana a la península ibèrica i detectat certa contribució genètica del pobles sub-saharians a les poblacions nordafricanes. Per altra banda, el tipatge de marcadors genètics que evolucionen a velocitats diferents al cromosoma Y ha permès mostrar que el background genètic predomina sobre el background poblacional en l'estructura de la variació genètica dels microsatèl·lits en la regió no recombinant del cromosoma Y humà. / The genetic variability of the North African populations has been studied through the analysis of different genomic regions in order to understand both the analysed populations and the dynamics of the genome. The obtained results allow us to verify different hypotheses about the population history of this region including the parallel and independent effect of the Neolithic wave of advance from the Middle East and along both Mediterranean coasts; and the effect of Arabization phenomena. We also tried to estimate the North African male genetic contribution to the Iberian peninsula and detected Sub-Saharian genetic influences to the North African peoples. Moreover, the typing of genetic markers with different evolutionary rates on the Y chromosome allowed us to demonstrate that variation in microsatellites is deeply structured by genetic background on the non-recombining region of the human Y chromosome.