With the development of sequencing technologies, more and more sequence variants are available for investigation. Different types of variants in the human genome have been identified, including single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and large structural variations such as large duplications and deletions. Of great research interest is the functional effects of these variants. Although many programs have been developed to predict the effect of SNPs, few can be used to predict the effect of indels or multiple variants, such as multiple SNPs, multiple indels, or a combination of both. Moreover, fine grained prediction of the functional outcome of variants is not available. To address these limitations, we developed a prediction framework, HMMvar, to predict the functional effects of coding variants (SNPs or indels), using profile hidden Markov models (HMMs). Based on HMMvar, we proposed HMMvar-multi to explore the joint effects of multiple variants in the same gene. For fine grained functional outcome prediction, we developed HMMvar-func to computationally define and predict four types of functional outcome of a variant: gain, loss, switch, and conservation of function. / Ph. D.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19264号 / 理博第4119号 / 新制||理||1593(附属図書館) / 32266 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 古市 剛史, 教授 湯本 貴和, 教授 中村 克樹 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Orientadores: Anete Pereira de Souza, Ronan Xavier Corrêa / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T22:18:55Z (GMT). No. of bitstreams: 1 Santos_ElisaSusileneLisboa_D.pdf: 19219557 bytes, checksum: 6dd887ae1478926cac4f0e6781200025 (MD5) Previous issue date: 2014 / Resumo: O cacaueiro é uma planta perene amplamente cultivada entre as latitudes 20ºN e 20ºS. O Brasil é o principal produtor das Américas, tendo 62% da sua produção concentrada em áreas de plantio do sudeste da Bahia. A introdução do cacau neste Estado ocorreu a partir de 1746 no município de Canavieiras, primeiro com a chegada da variedade 'Comum¿ e posteriormente com a chegada das variedades 'Pará' e 'Maranhão'. Descendentes destas introduções foram usadas para gerar plantios que predomiram na Bahia por mais de dois séculos e são denominados de 'cacau da Bahia¿ ou variedades locais baianas. Com a crise da vassoura-de-bruxa, a partir de 1989, as variedades locais baianas passaram a ser substituídas por clones resistentes selecionados em fazendas, coleções de germoplasma e programas de melhoramento genético. Embora tenham sido caracterizadas como susceptível à vassoura-de-bruxa, plantas de 'cacau da Bahia¿ ainda são encontradas em 50% da área produtiva, sendo cultivadas principalmente por pequenos produtores. Tendo em vista o exposto, o objetivo desta tese foi contribuir com informações genético-moleculares para o progresso dos programas de melhoramento do cacaueiro da Bahia. Para tanto, 17 marcadores microssatélite polimórficos foram obtidos a partir de bibliotecas genômicas enriquecidas. Estes marcadores foram somados a outros 13 presentes na literatura e empregados na avaliação da diversidade do 'cacau da Bahia¿, presentes em fazendas e em banco de germoplasma. A análise de 176 genótipos coletados em fazendas e institutos de pesquisa baianos (nos municípios de Canavieiras, Camacan, Uruçuca e Gandu) indicou a existência de dois grupos genéticos (denominados de cacau da Bahia (CB) I e II, "GST = " 0,22). Os valores de diversidade apresentados por CB I e CB II foram baixos (riqueza alélica = 1,31 e 1,41 e "HE = " 0,11 e 0,15, respectivamente para CB I e CB II). Alto índice de fixação alélica foi também observado para os cacaueiros baianos (F = 0,28). Análise de nove características de importância econômica a partir de frutos e grãos em 106 genótipos foi realizada e constitui informações preliminares para a escolha de plantas candidatas a novas avaliações. A avaliação de clones pertencentes às seleções do Instituto do Cacau da Bahia (SIC) e do Instituto Agronômico do Leste (SIAL) (representantes do 'cacau da Bahia' em bancos de germoplasma), também indicaram baixa variabilidade genética (2,6 alelos por loco e "HE =" 0,22) e alto índice de fixação alélica (F = 0,38). A variabilidade foi estruturada em dois grupos ("GST" = 0,27), havendo uma tendência de separar os indivíduos de acordo com a série (SIC ou SIAL). A baixa diversidade observada para o 'cacau da Bahia' é reflexo, entre outros fatores, das restritas introduções de plantas que fundaram boa parte do cultivo no Estado. Análises moleculares conjuntas de todas as plantas neste trabalho indicaram que parte da diversidade dos cacaueiros baianos presente em fazendas não está amostrada nas plantas do banco de germoplasma, sendo urgentemente necessário efetuar amostragens adicionais, para incremento da representatividade dos bancos no que tange o 'cacau da Bahia'. Os resultados obtidos ao longo do trabalho de doutorado trouxeram informações e persperctivas úteis tanto para incrementar a conservação do 'cacau da Bahia' quanto para o delineamento de ações visando implementar programas de seleção recorrente em programas de melhoramento direcionados à obtenção de 'cacau da Bahia' mais produtivo, com qualidade superior e também, tolerante às principais doenças que o acometem / Abstract: Theobroma cacao L. is a perennial plant cultivated in latitudes 20ºN and 20ºS. Brazil is the most important cacao-producing country in the Americas and 62% of the Brazilian cacao production is developed in Southern Bahia region (a Brazilian State). The introduction of cacao in Bahia started in 1746, in the municipality of Canavieiras; first with the arrival of the 'Comum¿ variety and next with the 'Pará' and 'Maranhão' varieties. Descendents of these introductions were naturalized as 'Bahian cacao' or Bahian local varieties and have been cultivated for over 200 years. With the witches' broom outbreak on the Bahian farms in 1989, 'Bahian cacao' have been replaced by more resistant clones, obtained by selection on farms, germplasm collection and from breeding programs. Even though local cultivars are susceptible to witches' broom disease, they are still being planted in 50% of farms, especially by smallholders. The goal of this thesis was to contribute to the breeding program of cacao using molecular and genetics characterization of 'Bahian cacao'. Seventeen polymorphic microsatellite markers for cacao were developed from genomic libraries and, in addition to other thirteen, were employed to characterize 'Bahian cacao' plants obtained from farms and in a germplasm collection. One hundred seventy six cacao genotypes of the Bahian cultivars were obtained from farms and institutes of four Bahian municipalities and the analysis indicated structure from genotypes in two groups ('Bahian cacao¿ (BC) I and II, GST = 0.22). Lower genetic diversity were observed for BC I and BC II (allelic richness = 1.31 and 1.41; and HE = 0.11 and 0.15 for BC I and BC II, respectively). High fixation index was observed for 'Bahian cacao¿ (F = 0.28). Phenotypic evaluations of nine characteristic of economic importance from fruits and seeds in 106 farm cacao plants were realized and constituted a preliminary approach for choise of candidate plants for additional analysis. Evaluation of clones representatives of 'Bahian cacao' in germplasm collections and selected by Bahian Cacao Institute and Agronomic Institute of East (these clones designated as SIC and SIAL, respectively), also indicated low genetic diversity (mean alleles per locus=2.60 and HE = 0.22) and high fixation index (F = 0.38). Structure levels were revealed in two groups (GST = 0.27) formed according to clones selection (SIC and SIAL). The low genetic diversity observed for 'Bahian cacao' reflect the founder effect of introduced plants and that served as resource to start almost all 'Bahian cacao¿ plantations. Combined molecular analyzes of all the plants of 'Bahian cacao' used in this study indicated that part of the diversity present on farm is not sampled in plants of germplasms collections, being additional sampling needed. The results presented in this thesis are useful information both for conservation of 'Bahian cacao' plants and to the use of this in recurrent breeding programs in order to obtain 'Bahian cocoa' more productive, with superior quality and tolerant to major diseases. / Doutorado / Genetica Vegetal e Melhoramento / Doutora em Genética e Biologia Molecular

One of the tools a clinician has in disease diagnosis and treatment is genetic testing. To generate value in genetic testing, the link between genetic variants and disease must be discovered, documented, and shared within the community. Working with two existing genomic variation tools, Kafeen and Cordova, a new set of features referred to as Variant-Curation and Database Instantiation (Variant-CADI) was identified, designed, implemented and integrated into the existing Cordova system to unite data collection, management and distribution into one cohesive tool accessible through user interfaces. This eliminates the user needing specialized knowledge of the underlying implementation, data pipeline or data management to collect desired disease specific genetic variations. Using this tool, new disease-specific variation database instances have been initialized and created as demonstrations of the utility of these applications.

Production of bioethanol from crop residues such as wheat straw, has been considered as a viable approach to meet the ever increasing demands for energy without affecting our environment. However, lignin hinders the success of efficient production of bioethanol as it confers recalcitrance of lignocellulosic biomass to hydrolysis. Genetic modification of plant biomass lignin content or composition without affecting its agronomic functions, can reduce biomass recalcitrance, however, application of this strategy requires a detailed understanding of the molecular mechanisms underlying lignin synthesis. This thesis performed comprehensive analysis of the expression of wheat lignin biosynthesis candidate genes and identified genes that are predominant across different tissues. Using three commercial wheat cultivars that exhibit variation in stem resistance to lodging, it investigated the association of expression of these predominant genes with tissue lignin content. Furthermore, this identified transcriptional changes mediating the response of lignin biosynthesis in wheat to changes in soil moisture. / May 2015

Master of Science / Department of Human Nutrition / Kadri Koppel / Understanding the physiological activation and genetic variation of the sweet taste receptor (T1R) can improve formula optimization for products intended for a population of genetically diverse people. Computer modeling and cell culture techniques have thoroughly described the structure and binding sites of the T1R. The structure contains two subunits (T1R2 and T1R3) with multiple domains where sweet molecules can interact. The interaction takes place between individual molecules and amino acid residues of the T1R. The residues with which individual molecules interact differs between sweeteners. Person-to-person differences in the residue sequence of the T1R can arise from variation in the genes that encode the T1R (TAS1R), potentially effecting the function of the receptor. As a result of the specificity of binding interactions, genetic variation may affect sensitivity to some sweeteners, while sensitivity to other sweeteners remains normal. Therefore, it can be hypothesized that the level of person-to-person sweetness sensitivity variation may differ for each sweetener depending on the binding site of the molecule and site of T1R variation. The T1R structure, binding sites, and genetic variation will be reviewed, as well as potential parameters to predict the degree of sensitivity variation and formulation strategies to minimize the effects of sensitivity variation.

Class of 2012 Abstract / Specific Aims: We sought to determine the influence of genetic variation of ADRB2 on the airway response to albuterol in patients with CF when compared to matched healthy controls at baseline and at 60 minutes following the administration of albuterol (2.5mg diluted in 3ml normal saline). Methods: Baseline pulmonary function (forced vital capacity, FVC, forced expiratory flow in 1-second, FEV1, mid-maximal expiratory flow, MMF, and forced expiratory flow at 50% of the FVC) was assessed in 17 patients with CF and 31 healthy subjects. Main Results: As expected, the healthy group had higher baseline pulmonary function when compared to the CF group (FVC=97±3 vs. 83±5; FEV1=95±3 vs. 72±6; MMF=90±4 vs. 54±8, % predicted for healthy and CF, respectively, mean±SE, p<0.05 for all. We compared Arg16Arg to Arg16Gly/Gly16Gly subjects. There was no effect of genotype on the response to albuterol in healthy subjects. However, in the CF group, we found that the Arg16Arg group (n=6) had an attenuated response to β-agonist when compared to the Gly-containing group (n=11) (FVC=0±0.9 vs. 6±3: FEV1=3±1 vs. 7±4: MMF=12±3 vs. 12±5 % change, for Arg16Arg and Gly-containing groups, respectively, p<0.05 for FVC, p=0.06 for FEV1). Conclusions: These results demonstrate a differential response to β-agonists according to genetic variation of the ADRB2 at amino acid 16. Due to the differences in FVC and FEV1 but not in MMF, these data suggest that the genetic difference in airway function is primarily in bronchodilation of the larger airways.

Class of 2010 Abstract / OBJECTIVES: Cystic fibrosis (CF) is a disease that adversely affects the lung resulting in a reduction of lung diffusion. Stimulation of the β2 adrenergic receptors results in mucocilliary clearance, and therefore, lung diffusion. We sought to determine the influence of an inhaled β-­‐agonist on the diffusing capacity of the lungs for carbon monoxide (DLCO), alveolar-­‐capillary membrane conductance (DM), pulmonary capillary blood volume (Vc), and peripheral oxygen saturation (SaO2) in subjects with CF and compare the data to matched healthy subjects. METHODS: To determine this we recruited 20 healthy subjects and 18 subjects with CF (age=23±7 vs. 24±4years, ht=168±8 vs. 174±12cm. wt=64±16 vs. 70±13kg, BMI= 23±4 vs. 23±3kg/m2, FEV1= 72±27 vs. 92±12%pred., VO2peak = 45±25 vs. 99±24%pred., P<0.05 for FEV1 and VO2peak, mean±SD) for the study and measured DLCO, DM, Vc and SaO2 before and 30, 60, and 90 minutes following the administration of inhaled albuterol. RESULTS: Within the healthy subjects, there were no differences in DLCO, DM, Vc, DM/Vc at baseline or in response to albuterol according to genetic variation of the ADRB2 at amino acid 27. Within the CF group, the Glu27Glu/Gln27Glu group had higher DM/Vc when compared to the Gln27Gln group at baseline. Both genotype groups had a significant decline in Vc and a significant improvement in DM/Vc and SaO2 in response to albuterol, but not in DLCO or DM. CONCLUSIONS: These results suggest that there are differences in lung diffusion and peripheral SaO2 according to genetic variants of the ADRB2 at position 27 and could play a potential role in treatment options.

Dans le contexte du changement climatique global, il apparaît essentiel de prendre en compte l?adaptabilité des variétés cultivées à la modification de l?environnement. Dans le cas du peuplier, la sélection de ressources génétiques capables de produire du bois à moindre coût en eau devient alors un critère de choix qui peut être apprécié par l?efficience d?utilisation de l?eau (WUE). De façon à évaluer l?intérêt de développer un programme de sélection sur WUE, il convenait de juger si les variations génétiques de WUE observées sur de jeunes boutures, s?exprimaient encore sur des arbres cultivés en peupleraie sur des sols contrastés. Par ailleurs, afin d?initier une étude du déterminisme moléculaire de WUE, nous avons évalué le degré de variation génétique des protéomes foliaires de huit génotypes de peupliers contrastés pour leur WUE et cultivés dans des conditions d?alimentation en eau variées. Nos travaux ont permis de valider l?existence d?importantes variations génétiques de WUE chez des peupliers cultivés en peupleraie. Toutefois, le type de sol modifiait considérablement le classement des génotypes alors que celui établi sur les sols les plus propices à la populiculture était comparable au classement décrit précédemment en serre. Nos expériences ont également validé la possibilité de distinguer des génotypes contrastés pour WUE à partir de leur protéome foliaire. Nous avons montré que le protéome foliaire de huit génotypes différant par leur WUE présentait d?importantes variations génétiques en réponse à la sécheresse et qu?il existait des liens entre abondances de protéines foliaires et variations génétiques de WUE. / In the actual climate change context, the cultivated varieties will have to cope with the expected environmental modifications. In poplar, the breeding of genetic ressources able to grow with lower water costs becomes therefore, an essential criterion that can be evaluated from water-use efficiency (WUE). In order to assess the interest to develop a breeding program based on WUE, it was agreed to judge if the genetic variation of WUE observed on young cuttings, were still expressed on trees cultivated in poplar plantation on contrasted soils. In addition, in order to initiate a study of the molecular determinism of WUE, we evaluated the degree of genetic variation in the leaf proteome of eight poplar genotypes contrasted for their WUE and cultivated under varied water supply. Our work evidenced consistent genetic variations of WUE in poplars cultivated in a commercial plantation. However, the type of cultivated soil modified considerably the genotypic ranking, whereas ranking established on the most favourable soils for poplar growth, remained comparable with the one described previously in greenhouse. Our experiments also validated the possibility of distinguishing genotypes contrasted for WUE from their leaf proteome. We showed that leaf proteome of eight poplar genotypes differing by their WUE displayed consistent genetic variations in their drought response and that there were relationships between leaf protein abundances and genetic variations of WUE.

Master of Science / Food Science - Food, Nutrition, Dietetics and Health / Kadri Koppel / Understanding the physiological activation and genetic variation of the sweet taste receptor (T1R) can improve formula optimization for products intended for a population of genetically diverse people. Computer modeling and cell culture techniques have thoroughly described the structure and binding sites of the T1R. The structure contains two subunits (T1R2 and T1R3) with multiple domains where sweet molecules can interact. The interaction takes place between individual molecules and amino acid residues of the T1R. The residues with which individual molecules interact differs between sweeteners. Person-to-person differences in the residue sequence of the T1R can arise from variation in the genes that encode the T1R (TAS1R), potentially effecting the function of the receptor. As a result of the specificity of binding interactions, genetic variation may affect sensitivity to some sweeteners, while sensitivity to other sweeteners remains normal. Therefore, it can be hypothesized that the level of person-to-person sweetness sensitivity variation may differ for each sweetener depending on the binding site of the molecule and site of T1R variation. The T1R structure, binding sites, and genetic variation will be reviewed, as well as potential parameters to predict the degree of sensitivity variation and formulation strategies to minimize the effects of sensitivity variation.