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With the abundance of genomic data after the Human Genome Project, the need for analysis, and annotation of these data arise. Annotation of genomes helps us understand the functionality of different parts of the genomes of various species. In this thesis, we propose a simple, and fast homology-based gene prediction method called Exon Hunter (EH) that achieves a performance comparable with state-of-the-art methods in mitochondrial genomes. Mitochondria are crucial for a eukaryotic cell, and mutation in its DNA has connections with disorders such as Alzheimer and cancer. We used Hidden Markov Model (HMM) Protein Profile of a number of genes to search for protein-coding genes in different genomes. Our method forms every subset of the hit set, and calculates a score for each subset according to an objective function. Then it chooses the subset with the\ highest score. Finally, we analyze the codon usage bias of our dataset, and we discuss how it can help us improve this prediction. ExonHunter is written in Python and is publicly available on github.com/amirh-hajianpour/ExonHunter.

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TCC(graduação) - Universidade Federal de Santa Catarina. Centro de Ciências Biológicas. Biologia. / Submitted by Gabriela Farias Gubert null (gabriela.gubert@grad.ufsc.br) on 2017-07-14T14:00:05Z No. of bitstreams: 1 Gabriela Farias Gubert.pdf: 903100 bytes, checksum: 8ad4192c07dd690dabcaa005dbeea52b (MD5) / Approved for entry into archive by Philipi Schneider (p.schneider@ufsc.br) on 2017-07-14T14:15:24Z (GMT) No. of bitstreams: 1 Gabriela Farias Gubert.pdf: 903100 bytes, checksum: 8ad4192c07dd690dabcaa005dbeea52b (MD5) / Made available in DSpace on 2017-07-14T14:15:24Z (GMT). No. of bitstreams: 1 Gabriela Farias Gubert.pdf: 903100 bytes, checksum: 8ad4192c07dd690dabcaa005dbeea52b (MD5) / O biocombustível tornou-se uma alternativa ao uso do petróleo. Nesse cenário o Brasil apostou no etanol. Industrialmente, sua produção acontece através do processo de fermentação alcóolica pela levedura Saccharomyces cerevisiae em matéria vegetal, como a cana-de-açucar (Saccharum spp.). Porém, a levedura não apresenta o metabolismo necessário para fermentar pentoses, como a xilose, um dos carboidratos mais abundantes em matéria lignocelulósica. Investigando leveduras que fermentam xilose, encontramos um processo de redução e oxidação mediado pelas enzimas Xilose Redutase (XR) e Xilitol Desidrogenase (XDH). Portanto, uma maneira de aumentar a produção de etanol no país, sem aumentar a área plantada de cana-de-açucar, é a criação de linhagens de S. cerevisiea transformantes com as enzimas supracitadas. Para isso, buscamos as enzimas com maior atividade entre as espécides fermentadoras de xilose, chegando as seguintes duas espécies: Spathaspora arborarie e Spathaspora passalidarum. Sendo que a enzima XR de S. arborarie, além de apresentar alta atividade, apresenta atividade com dois cosubstratos, NADPH e NADH. Já a enzima XDH de S. passalidarum apresentou a maior atividade entre as enzimas XDH já descritas, e uma dependência do cosubstrato NAD+. O uso conjunto das enzimas é interessante pela reciclagem dos cosubstratos. Portanto, nesse trabalho, buscamos criar um plasmídeo com um forte promotor constitutivo PGK para XR e TEF para XDH com a intenção de transformar o organismo S. cerevisiae para futura produção de etanol a partir de xilose. Além disso, estudos de engenharia genética demonstraram um efeito positivo da deleção do gene PHO13 de S. cerevisiae, já que essa mudança parece aumentar a expressão de enzimas da Via Glicolítica e da Via das Pentoses Fosfato. Por isso, utilizamos linhagens recombinantes pho13∆ com expressão das enzimas heterólogas supracitadas e comparamos seu perfil fermentativo com linhagens com a mesma expressão de enzimas, porém não pho13∆. Como resultado, percebemos que a expressão das enzimas permite o consumo de xilose, porém percebemos pouca produção de etanol. A linhagem pho13∆ se torna vantajosa em fermentação com alta densidade de xilose, 10%, produzindo o dobro de etanol da linhagem não pho13∆.

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Submitted by FERNANDA DA SILVA VON PORSTER (fdsvporster@univates.br) on 2014-06-02T17:12:47Z No. of bitstreams: 3 license_text: 21393 bytes, checksum: 7c4ecb3427d83129a338fc10c55e726a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) 2014AdrianaReginaBitello.pdf: 740341 bytes, checksum: 3038e78bbc36511e66c5eab91ca5e5f3 (MD5) / Approved for entry into archive by Ana Paula Lisboa Monteiro (monteiro@univates.br) on 2014-06-05T12:30:58Z (GMT) No. of bitstreams: 3 license_text: 21393 bytes, checksum: 7c4ecb3427d83129a338fc10c55e726a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) 2014AdrianaReginaBitello.pdf: 740341 bytes, checksum: 3038e78bbc36511e66c5eab91ca5e5f3 (MD5) / Made available in DSpace on 2014-06-05T12:30:58Z (GMT). No. of bitstreams: 3 license_text: 21393 bytes, checksum: 7c4ecb3427d83129a338fc10c55e726a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) 2014AdrianaReginaBitello.pdf: 740341 bytes, checksum: 3038e78bbc36511e66c5eab91ca5e5f3 (MD5) / Introdução: O aumento da obesidade mundial é motivo de preocupação, sendo considerado fator de risco para o desenvolvimento de diversas doenças crônicas: como obesidade, diabetes mellitus tipo 2, a hipertensão, a hipercolesterolemia e doenças cardiovasculares. A ciência da nutrigenética vem sendo estudada com o intuito de desvendar a forma com que os fatores ambientais, principalmente a dieta se relacionam com os fatores genéticos, influenciando no aparecimento destas patologias. Objetivo: Esta dissertação teve como objetivo investigar a relação entre o consumo alimentar e o polimorfismo rs9939609 no gene Fat Mass and Obesity Associated (FTO). O gene FTO está relacionado com massa gorda e aumento do índice de massa corporal sobre parâmetros bioquímicos e antropométricos. Metodologia: Participaram da pesquisa 346 indivíduos, de ambos os gêneros, frequentadores do ambulatório de nutrição do Universidade do Vale do Taquari Univates-RS-Brasil. Dados do perfil antropométrico (peso, altura, medidas de circunferências e percentual de gordura corporal) e de consumo alimentar (carboidratos, proteínas, gorduras, fibras, colesterol e micronutrientes) dos indivíduos foram coletados por profissionais treinados no ambulatório de Nutrição. As variáveis do consumo alimentar foram obtidas através do método de recordatório alimentar de 24 horas, utilizando o software DietWin Professional (versão 2008). Os parâmetros bioquímicos (glicose de jejum, colesterol e triglicerídeos) foram determinados usando kits comerciais da marca Bioclin®. O Ácido desoxirribonucléico (DNA) dos participantes foi extraído pelo método de sal. O polimorfismo rs9939609 foi genotipados através da técnica de discriminação alélica Taqman (Applied Biosystems). As frequências alélicas foram estimadas por contagem direta e o Equilíbrio de Hardy-Weinberg calculado através do teste do qui-quadrado. A comparação entre o consumo alimentar de macronutrientes e micronutrientes, glicemia de jejum, perfil lipídico e parâmetros antropométricos foram realizada através de modelos lineares gerais univariados. As interações gene-nutriente foram testadas por meio de regressão linear múltipla, com modelagem backward stepwise manual. Resultados: Na população estudada o peso e índice de massa corporal (IMC) apresentaram-se limítrofes. Não foi observado diferenças significativas no consumo alimentar de macronutrientes e micronutrientes, de fibras totais e de colesterol entre os genótipos. Quando analisado glicemia, perfil lipídico, parâmetro antropométricos e gasto calóricos apenas o Colesterol HDL e Colesterol LDL (mg/dl) apresentaram significância (P=0,041 e 0,044) respectivamente em relação ao genótipo heterozigoto TA. Foram detectadas interações significativas entre o genótipo TA e o consumo alimentar elevado de carboidratos em relação ao aumento do Colesterol HDL (P=0,012), assim como a relação do consumo baixo de vitamina B12 em aumento ao percentual de gordura corporal (P=0,0003). Em relação ao genótipo AA observamos uma interação significativa quanto ao consumo baixo de proteínas e o aumento dos níveis de triglicerídeos (P=0,0182), bem como nos parâmetros antropométricos, que os indivíduos homozigotos A que consumiam doses baixas de vitamina A e gorduras, apresentavam relação cintura-quadril (RCQ) aumentada (P=0,020 e 0,0022) respectivamente. Conclusão: O alelo A, inicialmente considerado de risco para obesidade nesta população caracterizada saudável não apresentou risco quanto ao IMC elevado. A variante genética do gene FTO apresentou influencia sobre alguns parâmetros bioquímicos e antropométricos, em relação ao consumo de carboidratos e proteínas sobre o perfil lipídico e também sobre o consumo das gorduras e vitaminas sobre o percentual de gordura corporal e razão cintura-quadril. Considerando os poucos achados nesta área até o momento, ressalta-se a importância da realização de novas pesquisas, de forte impacto estatístico, para confirmar nossos achados.

<i>Pyrenophora teres</i> Drechs. (anamorph: <i>Drechslera teres</i> (Sacc.) Shoem.) is the causal agent of barley net blotch. Net blotch is an economically important disease commonly found throughout the barley producing regions of the world. Significant financial losses result from yield reductions, ranging from 15-35%, and decreased grain quality. Despite its prevalence, it is unclear if the P. teres-barley pathosystem follows a gene-for-gene model, and more generally, little is known about its genetic organization. Three studies were initiated to address these questions.<p>The first study investigated the genetic control of avirulence in <i>P. teres.</i> To establish an appropriate study system, a collection of ten net form (<i>P. teres f. teres</i>) and spot form (<i>P. teres f. maculata</i>) isolates were evaluated on a set of eight differential barley lines to identify two isolates with differential virulence on a specific host line. WRS 1906, exhibiting low virulence on the cultivar Heartland, and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for virulence on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (Chi-square = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism (AFLP) markers closely linked to the avirulence gene (AvrHeartland). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model.<p>In the second study, five isolates of P. teres, representing both net and spot forms, were analyzed by the germ tube burst method (GTBM) and pulsed field gel electrophoresis (PFGE) to determine the species karyotype. Nine chromosomes were observed in all isolates using the GTBM and estimation of chromosome lengths varied from 0.5 to 3.0 µm. PFGE separated 7 to 8 bands depending on isolate, but analysis of bands by densitometry indicated nine chromosomes. Chromosome size ranged from 1.8 to ~6.0 Mb providing a genome size estimate of 32 to 39 Mb. Significant chromosome-length polymorphisms (CLP) were observed between isolates. These CLP did not hinder mating between mating-type compatible net form isolates. No particular CLP or individual chromosome could be associated with differences in disease symptoms observed between pathogen forms. This study provides the first karyotype of both P. teres forms and will assist genetic mapping of this pathogen.<p>A genetic linkage map of <i>P. teres f. teres</i>, was constructed in the third study using the population of 67 progeny derived from the WRS 1906  WRS 1607 cross. The map consists of 138 markers including 114 AFLPs, 21 telomere RFLPs, the mating-type (MAT) locus and an avirulence locus (AvrHeartland) controlling interaction with barley cultivar Heartland. Markers were distributed across 24 linkage groups ranging in length from 2 to 110 cM with an average marker interval of 8.5 cM. The total map length was 797 cM. A telomere-specific probe, consisting of the sequence (TTAGGC)4, was used to map 15 of the 18 telomeres. One of these telomeres mapped to within 3 cM of the AvrHeartland locus. Attempts to consolidate linkage groups by hybridizing markers to the electrophoretically separated chromosomes was unsuccessful because probes bound to multiple chromosomes, likely due to repetitive DNA within the probe. This is the first genetic map reported for this species and it will be a useful genetic tool for map-based cloning of the AvrHeartland gene tagged in this study. <p>This research has provided a number of new insights into the net blotch pathogen and provides a useful research tool in the form of a genetic map. This information lays the foundation for further genetic study of P. teres and will complement studies on barley resistance to net blotch that may potentially lead to more durable resistance.

<i>Pyrenophora teres</i> Drechs. (anamorph: <i>Drechslera teres</i> (Sacc.) Shoem.) is the causal agent of barley net blotch. Net blotch is an economically important disease commonly found throughout the barley producing regions of the world. Significant financial losses result from yield reductions, ranging from 15-35%, and decreased grain quality. Despite its prevalence, it is unclear if the P. teres-barley pathosystem follows a gene-for-gene model, and more generally, little is known about its genetic organization. Three studies were initiated to address these questions.<p>The first study investigated the genetic control of avirulence in <i>P. teres.</i> To establish an appropriate study system, a collection of ten net form (<i>P. teres f. teres</i>) and spot form (<i>P. teres f. maculata</i>) isolates were evaluated on a set of eight differential barley lines to identify two isolates with differential virulence on a specific host line. WRS 1906, exhibiting low virulence on the cultivar Heartland, and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for virulence on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (Chi-square = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism (AFLP) markers closely linked to the avirulence gene (AvrHeartland). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model.<p>In the second study, five isolates of P. teres, representing both net and spot forms, were analyzed by the germ tube burst method (GTBM) and pulsed field gel electrophoresis (PFGE) to determine the species karyotype. Nine chromosomes were observed in all isolates using the GTBM and estimation of chromosome lengths varied from 0.5 to 3.0 µm. PFGE separated 7 to 8 bands depending on isolate, but analysis of bands by densitometry indicated nine chromosomes. Chromosome size ranged from 1.8 to ~6.0 Mb providing a genome size estimate of 32 to 39 Mb. Significant chromosome-length polymorphisms (CLP) were observed between isolates. These CLP did not hinder mating between mating-type compatible net form isolates. No particular CLP or individual chromosome could be associated with differences in disease symptoms observed between pathogen forms. This study provides the first karyotype of both P. teres forms and will assist genetic mapping of this pathogen.<p>A genetic linkage map of <i>P. teres f. teres</i>, was constructed in the third study using the population of 67 progeny derived from the WRS 1906  WRS 1607 cross. The map consists of 138 markers including 114 AFLPs, 21 telomere RFLPs, the mating-type (MAT) locus and an avirulence locus (AvrHeartland) controlling interaction with barley cultivar Heartland. Markers were distributed across 24 linkage groups ranging in length from 2 to 110 cM with an average marker interval of 8.5 cM. The total map length was 797 cM. A telomere-specific probe, consisting of the sequence (TTAGGC)4, was used to map 15 of the 18 telomeres. One of these telomeres mapped to within 3 cM of the AvrHeartland locus. Attempts to consolidate linkage groups by hybridizing markers to the electrophoretically separated chromosomes was unsuccessful because probes bound to multiple chromosomes, likely due to repetitive DNA within the probe. This is the first genetic map reported for this species and it will be a useful genetic tool for map-based cloning of the AvrHeartland gene tagged in this study. <p>This research has provided a number of new insights into the net blotch pathogen and provides a useful research tool in the form of a genetic map. This information lays the foundation for further genetic study of P. teres and will complement studies on barley resistance to net blotch that may potentially lead to more durable resistance.