Orientador: Anita Jocelyne Marsaioli / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-10T04:53:28Z (GMT). No. of bitstreams: 1 Mantovani_SimoneMoraes_M.pdf: 1495773 bytes, checksum: 493a0576675a8aad3c2879147aa7745f (MD5) Previous issue date: 2007 / Resumo: Nas últimas décadas as reações utilizando biocatalisadores tem sido amplamante aplicadas na síntese orgânica, como componentes chave de muitos processos químicos industriais, levando ao aumento na demanda por novas enzimas. A maneira mais rápida e simples de detectar enzimas é através de metodologias de triagem de alto desempenho (HTS) que permitam identificação rápida da atividade enzimática, como por exemplo, os ensaios utilizando compostos fluorogênicos e cromogênicos. Nesse trabalho nós aplicamos HTS baseado em substratos fluorogênicos para detecção de epóxido-hidrolases e esterases em microrganismos brasileiros. Inicialmente foram selecionados cinco microrganismos com alta atividade epóxido-hidrolase, e 18 pela a presença de esterases. Inspirados nesse principio nós adaptamos a metodolgia conhecida como "Quick E" para a avaliação rápida das enantiosseletividades de epóxido-hidrolases em células íntegras através de medidas das velocidades iniciais de substratos fluorogênicos quirais avaliados separadamente com adição de um competidor. Os ensaios de enantiosseletividade mostraram que os experimentos com competidor apresentaram valores de enatiosseletividade muito próximos dos valores de E determinados via biocatálise convencional. Além disso, alguns microrganismos selecionados por HTS foram testados para reações de biotransformação frente a substratos de interesse sintético, o que permitiu, além da confirmação das atividades enzimáticas e seletividades observadas, detectar a capacidade do microrganismo C. albícans CCT 0776 de desracemizar álcoois secundários por estereoinversão, fornecendo o (S)-1,2-octanodiol com 100 % de rendimento teórico e ee > 99 %, e o (S)-4-fenilmetoxi-1,2-butanodiol com ee 45 % / Abstract: Since the past decades the biocatalysts have been applied in organic chemistry, as key components of many industrial chemical processes, thus increasing the demand for novel enzymes. High-Throughput Screening (HTS), using fluorogenic probes are among the best assays to discovery new enzymes, easily adapted to whole cells format. In this work, have been applied fluorogenic probes to screen epoxide hydrolases and esterases in Brazilian Collection Cultures of microorganisms, which allowed to detect epoxide hydrolases in five microorganisms, and esterases in 18 microrganisms. Additionally, were used chiral probes to implement a Quick E assay, for a fast valuation of epoxide hydrolases enantioselectivity by measuring initial rates of pure enantiomers. Optimization of the methodology revealed that almost true E were obtained by competitive experiments of each enantiomer and a substrate of similar reactivity. The quick E assay was validated by determining conversion and ee using GC/MS and NMR (using mandelic acid derivatives) and is now a new method to determine the enantiomeric ratio for epoxide hidrolases. Finally, the outstanding HTS results were better investigated by conventional catalysis detecting a stereoinversion process performed by C. albicans CCT 0776, which furnished (S)-1 ,2-octanodiol in 100 % theoretical yield and ee of 100%, and (S)-4-fenilmetoxi-1,2-butanodiol in ee of 45% / Mestrado / Quimica Organica / Mestre em Química

Master of Science / Department of Biology / Stephen K. Chapes / Immunoglobulins are receptors expressed on the outside of a B cell that can specifically bind pathogens and toxic substances within a host. These receptors are heterodimers of two chains: heavy and light, which are encoded at separate loci. Enzymatic splicing of gene segments at heavy and light chain loci within the genomic DNA in every B cell results in a highly diversified and specific repertoire of immunoglobulins in a single host. Spaceflight is known to affect reduce splenic B cell populations and B cell progenitors within the bone marrow, potentially restricting the diversity of the immunoglobulin repertoire (Ig-Rep). The objective of this thesis project was to characterize the impact of spaceflight on the kappa light-chain Ig-Rep of the C57BL/6 mouse. High-throughput sequencing (HTS) technologies have enabled the rapid characterization of Ig-Reps, however, standard Ig-Rep workflows often rely the amplification of immunoglobulin sequences to ensure the capture immunoglobulin sequences from rare B cell clones. Additionally, the Ig-Rep is often assessed in sorted B cell populations. Opportunities for spaceflight experiments are limited and costly, and the exclusive amplification of immunoglobulin sequences prior to HTS results in a dataset that cannot be mined for additional information. Furthermore, due to the difficulties of tissue collection in spaceflight, HTS of sorted B cell populations is not feasible. We optimized a protocol in which the Ig-Rep was assessed from unamplified whole tissue immunoglobulin transcripts. The Ig-Rep was characterized by gene segment usage, gene segment combinations and the region in which gene segments are joined. HTS datasets of ground control animals and animals flown aboard the International Space Station were compared to explore the impact of spaceflight on the unimmunized murine Ig-Rep.

Lignin is a major chemical component of plants and the second most abundant natural polymer after cellulose. The concerns and interests of agriculture and industry have stimulated the study of genes governing lignin content in plants in an effort to adapt plants to human purposes. Arabidopsis thaliana provides a convenient model for the study of the genes governing lignin content because of its short growth cycle, small plant size, and small completely sequenced genome. In order to identify the genes controlling lignin content in Arabidopsis accessions using Quantitative Trait Locus (QTL) analysis, a rapid micro-scale method of lignin determination is required. The acetyl bromide method has been modified to enable the rapid micro-scale determination of lignin content in Arabidopsis. Modifications included the use of a micro-ball mill, adoption of a modified rapid method of extraction, use of an ice-bath to stabilize solutions and reduction in solution volumes. The modified method was shown to be accurate and precise with values in agreement with those determined by the conventional method. The extinction coefficient for Arabidopsis lignin, dissolved using acetyl bromide, was determined to be 23.35 g-iLcm-1. This value is independent of the Arabidopsis accession, environmental growth conditions and is insensitive to syringyl/guaiacyl ratio. The modified acetyl bromide method was shown to be well correlated with the 72% sulfuric acid method once the latter had been corrected for protein contamination and acid-soluble lignin content (R² = 0.988, P < 0.0001). As determined by the newly developed acetyl bromide method and confirmed by the sulfuric acid method, lignin content in Arabidopsis was found to be a divergent property. Lignin content in Arabidopsis was found to be weekly correlated with growth rate among Arabidopsis accessions (R² = 0.48, P = 0.011). Lignin content was also found to be correlated with plant height among Arabidopsis accessions (R² = 0.491, P < 0.0001). / Forestry, Faculty of / Graduate

É conhecido que muitos softwares deixam de ser utilizados por sua complexa usabilidade. Mesmo ferramentas conhecidas por sua qualidade na execução de uma tarefa são abandonadas em favor de ferramentas mais simples de usar, de instalar ou mais rápidas. Na área da anotação funcional a ferramenta Sifter (v2.0) é considerada uma das com melhor qualidade de anotação. Recentemente ela foi considerada uma das melhores ferramentas de anotação funcional segundo o Critical Assessment of protein Function Annotation (CAFA) experiment. Apesar disso, ela ainda não é amplamente utilizada, provavelmente por questões de usabilidade e adequação do framework à larga escala. O workflow SIFTER original consiste em duas etapas principais: A recuperação das anotações para uma lista de genes e a geração de uma árvore de genes reconciliada para a mesma lista. Em seguida, a partir da árvore de genes o Sifter constrói uma rede bayesiana de mesma estrutura nas quais as folhas representam os genes. As anotações funcionais dos genes conhecidos são associadas a estas folhas e em seguida as anotações são propagadas probabilisticamente ao longo da rede bayesiana até as folhas sem informação a priori. Ao fim do processo é gerada para cada gene de função desconhecida uma lista de funções putativas do tipo Gene Ontology e suas probabilidades de ocorrência. O principal objetivo deste trabalho é aperfeiçoar o código-fonte original para melhor desempenho, potencialmente permitindo que seja usado em escala genômica. Durante o estudo do workflow de pré-processamento dos dados encontramos oportunidades para aperfeiçoamento e visualizamos estratégias para abordá-las. Dentre as estratégias implementadas temos: O uso de threads paralelas; balanceamento de carga de processamento; algoritmos revisados para melhor aproveitamento de disco, memória e tempo de execução; adequação do código fonte ao uso de bancos de dados biológicos em formato utilizado atualmente; aumento da acessibilidade do usuário; expansão dos tipos de entrada aceitos; automatização do processo de reconciliação entre árvores de genes e espécies; processos de filtragem de seqüências para redução da dimensão da análise; e outras implementações menores. Com isto conquistamos aumento de performance de até 87 vezes para a recuperação de anotações e 73,3% para a reconstrução da árvore de genes em máquinas quad-core, e redução significante de consumo de memória na fase de realinhamento. O resultado desta implementação é apresentado como Sifter-T (Sifter otimizado para Throughput), uma ferramenta open source de melhor usabilidade, velocidade e qualidade de anotação em relação à implementação original do workflow de Sifter. Sifter-T foi escrito de forma modular em linguagem de programação Python; foi elaborado para simplificar a tarefa de anotação de genomas e proteomas completos; e os resultados são apresentados de forma a facilitar o trabalho do pesquisador. / It is known that many software are no longer used due to their complex usability. Even tools known for their task execution quality are abandoned in favour of faster tools, simpler to use or install. In the functional annotation field, Sifter (v2.0) is regarded as one of the best when it comes to annotation quality. Recently it has been considered one of the best tools for functional annotation according to the \"Critical Assessment of Protein Function Annotation (CAFA) experiment. Nevertheless, it is still not widely used, probably due to issues with usability and suitability of the framework to a high throughput scale. The original workflow SIFTER consists of two main steps: The annotation recovery for a list of genes and the reconciled gene tree generation for the same list. Next, based on the gene tree, Sifter builds a Bayesian network structure in which its leaves represent genes. The known functional annotations are associated to the aforementioned leaves, and then the annotations are probabilistically propagated along the Bayesian network to the leaves without a priori information. At the end of the process, a list of Gene Ontology functions and their occurrence probabilities is generated for each unknown function gene. This work main goal is to optimize the original source code for better performance, potentially allowing it to be used in a genome-wide scale. Studying the pre-processing workflow we found opportunities for improvement and envisioned strategies to address them. Among the implemented strategies we have: The use of parallel threads; CPU load balancing, revised algorithms for best utilization of disk access, memory usage and runtime; source code adaptation to currently used biological databases; improved user accessibility; input types increase; automatic gene and species tree reconciliation process; sequence filtering to reduce analysis dimension, and other minor implementations. With these implementations we achieved great performance speed-ups. For example, we obtained 87-fold performance increase in the annotation recovering module and 72.3% speed increase in the gene tree generation module using quad-core machines. Additionally, significant memory usage decrease during the realignment phase was obtained. This implementation is presented as Sifter-T (Sifter Throughput-optimized), an open source tool with better usability, performance and annotation quality when compared to the Sifter\'s original workflow implementation. Sifter-T was written in a modular fashion using Python programming language; it is designed to simplify complete genomes and proteomes annotation tasks and the outputs are presented in order to make the researcher\'s work easier.

<div>The present work seeks to use high throughput experimentation (HTE) to guide chemical synthesis. We demonstrate the use of an HTE system utilizing a robotic liquid handler to prepare arrays of reactions and print them onto a surface to be analyzed by desorption electrospray ionization mass spectrometry (DESI-MS) as a tool to guide reaction optimization, synthetic route selection, and reaction discovery. DESI-MS was employed as a high throughput experimentation tool to provide qualitative predictions of the outcome of a reaction, so that vast regions of chemical reactivity space may be more rapidly explored and areas of optimal efficiency identified. This work is part of a larger effort to accelerate reaction optimization to enable the rapid development of continuous-flow syntheses of small molecules in high yield. In the present iteration of this system, reactions are scaled up from these nanogram surface printed reactions to milligram scale microfluidic reactions, where more detailed analysis and further optimization may be performed. In the earliest iterations of this screening system prior to the use of DESI, the initial screening reactions were performed in electrospray (ESI) droplets and leidenfrost droplets before scaling up to microfluidic reactions which were analyzed by ESI-MS. The insights from this combined droplet and microfluidic screening/rapid ESI-MS analysis approach, helped guide the synthesis of diazepam. The system was further refined to by the use of liquid handling robots and DESI-MS analysis, greatly accelerating the overall pace of screening. In order to build confidence in this approach, however, it is necessary to establish a robust predictive connection between reactions performed under analogous DESI-MS, batch, and microfluidic reaction conditions. To achieve this goal, we first explored the potential of high throughput DESI-MS experiments to identify trends in reactivity based on chemical structure, solvent, temperature, and stoichiometry that are consistent across these platforms. While DESI-MS narrowed the scope of possibilities for reaction</div><div>13</div><div>selection with some parameters such as solvent, others like stoichiometry and temperature still required further optimization under continuous synthesis conditions. With our increased confidence in DESI-MS HTE, we proceeded to explore it’s application to rapidly evaluate large sets of aldol reactions of triacetic acid lactone (TAL), a compound well studied for use as a bio-based platform molecule that may be converted to a range of useful commodity chemicals, agrochemicals, and advanced pharmaceutical intermediates. Our DESI-MS HTE screening technique was used to rapidly evaluate known reactions of triacetic acid lactone, in an effort to accelerate reaction discovery with platform chemicals. Our rapid experimentation system, when applied to reaction discovery in this manner, may help to shorten the time scale of platform chemical development.</div>

Salt stress severely constrains plant performance and global agricultural productivity. 5% of arable land, 20% of irrigated areas and 98% of water reserves worldwide are saline. Improving the salt tolerance of major crop species could help attenuate yield losses and expand irrigation opportunities and provide in situ relief in areas where poverty, food and water scarcity are prevalent. Increasing the salt tolerance of crops with high commercial and nutritional value, such as tomato (Solanum lycopersicum L.), would provide particularly significant economic and health benefits. However, salt tolerance is a complex trait with a limited genetic repertoire in domesticated crop varieties, including tomato, frustrating attempts to breed and engineer tolerant crop varieties. Here, a genome-wide association study (GWAS) was undertaken, leveraging the rich genetic diversity of the wild, salt tolerant tomato Solanum pimpinellifolium and the latest phenotyping technologies to identify traits that contribute to salt tolerance and the genetic basis for variation in those traits. A panel of 220 S. pimpinellifolium accessions was phenotyped, focusing on image-based high-throughput phenotyping over time in controlled and field conditions in young and mature plants. Results reveal substantial natural variation in salt tolerance over time across many traits. In particular, the use of unmanned aerial vehicle (UAV)-based remote sensing in the field allowed high-resolution RGB, thermal and hyperspectral mapping that offers new insights into plant performance in the field, over time. To empower our GWAS and facilitate the identification of candidate genes, a new S. pimpinellifolium reference genome was generated, 811Mb in size, N50 of ~76kb, containing 25,970 annotated genes. Analysis of this reference genome highlighted potential contributors to salt tolerance, including enrichments in genes with stress response functions and a high copy number of the salt tolerance-associated gene inositol- 3-phosphate synthase (I3PS). A recently completed full genome re-sequencing of the panel, along with a newly available pseudomolecule-level assembly of the S. pimpinellifolium genome with N50 of ~11Mb, will serve to drive a GWAS to identify loci associated with traits that contribute to salt tolerance. Further research including gene validation, breeding, genetic modification and gene editing experiments will drive the development of new salt tolerant tomato cultivars.

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Mutagenesis following peer review. The definitive publisher-authenticated version is available online at:http://mutage.oxfordjournals.org/content/early/2015/08/03/mutage.gev055.full. / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19588号 / 医博第4095号 / 新制||医||1014(附属図書館) / 32624 / 京都大学大学院医学研究科医学専攻 / (主査)教授 小泉 昭夫, 教授 渡邊 直樹, 教授 高田 穣 / 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(農学) / 甲第19769号 / 農博第2165号 / 新制||農||1040(附属図書館) / 学位論文||H28||N4985(農学部図書室) / 32805 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 井鷺 裕司, 教授 北山 兼弘, 教授 神﨑 護 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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Forensic scientists and ancient DNA researchers face similar challenges with respect to genetic information acquisition and analysis. However, these communities differ in one critical aspect: while forensic science is regulated by the strict guidelines of the judicial community, ancient DNA is a research-based academic field free to explore emerging technologies as they arise. This thesis investigates the application of two methodologies, developed in ancient DNA research, to challenging extracts, in hopes of modernizing forensic models while maintaining compatibility with current standards. The first chapter focuses on blunt-end sequencing library preparation protocols previously optimized for ancient DNA specimens. Forensically-relevant extracts were converted into libraries and typed by short tandem repeats (STR) amplification. When compared to STR profiles from pre-library extracts, a significant decrease in the quality was observed, in the form of allelic drop-out, heterozygous peak imbalance and increased stutter ratios. The second chapter discusses the efficacy of two enzymatic DNA repair methods, “PreCR® Repair” and “Nelson”, on typical ancient DNA specimens. Based on endogenous sample content, fragment length variation and base misincorporation rates, some DNA repair was reported when using PreCR®. However, the use of the Nelson protocol is not recommended for use in its current state. Both sequencing library preparation and enzymatic DNA repair show potential application to forensic evidential material, but require further analyses to confirm hypotheses and observations outlined in this thesis. / Thesis / Master of Science (MSc)