Les améliorations des technologies de séquençage offrent aujourd’hui la possibilité d’explorer la variabilité intraspécifique au sein d’une espèce à travers le séquençage complet du génome d’un grand nombre d’individus. Dans ce contexte, mes travaux de thèse se sont basés sur l’étude et la comparaison de la variabilité génomique à travers des études de génomique des populations au sein de plusieurs espèces de levures. Dans un premier temps, j’ai réalisé une étude systématique de la variabilité intraspécifique au sein de 6 espèces de levures, me donnant notamment la possibilité d’étudier la variabilité du contenu en gènes entre les espèces. Dans un second temps, je me suis focalisé sur l’utilisation des dernières technologies de séquençage dans l’objectif de produire une séquence de référence de Dekkera bruxellensis, dont l’absence pour un grand nombre d’espèces limite l’établissement d’étude de génomique des populations. Cette séquence a été utilisée dans un dernier temps afin d’étudier l’évolution de l’espèce. Dans l’ensemble, ces travaux apportent de solides fondations dans l’exploration de la diversité génétique au sein d’espèces non-modèles. / Advent of high throughput technologies as well as the reduction of their price open the way to the exploration of the intraspecific genetic variation at the species level by sequencing the complete genome of a wide range of individuals. Doing so, I first produced populations genomics studies of 6 yeast species based on the same framework, allowing the exploration and comparison of the genes repository of each species. I then used new sequencing technologies to produce a reference sequence for the yeast species Dekkera bruxellensis. Using this sequence, I was then able to produce for the first time a population genomic study at the genome wide scale for this species.

No presente trabalho, primeiramente avaliou-se o desempenho fermentativo de 10 cepas de leveduras isoladas de frutas, de mel centrifugado e de resíduo do processamento de mel após a etapa de sedimentação (borra do mel), em tubo de ensaio contendo mosto constituído de Mel 15 °Brix suplementado, individualmente, com diferentes nutrientes, a saber: extrato de levedura comercial (10,0 g/L), farelo de arroz (20,0 g/L), mistura (1,0 g/L) constituída de farelos de milho, arroz e soja na proporção 5:2:5 e nutriente comercial (D&R) (0,15 g/L). Os parâmetros avaliados coexistiram da determinação do número de células em câmara de Neubauer e das concentrações de açúcares e etanol por HPLC, o que permitiu a determinação dos parâmetros rendimento, eficiência de fermentação e produtividade. Estes resultados sustentaram a seleção do mosto suplementado com extrato de levedura comercial e da melhor cepa de levedura que foram posteriormente avaliados em escala piloto. A cepa selecionada foi a levedura isolada a partir da borra de mel, a qual foi posteriormente identificada como Saccharomyces cerevisiae e nomeada Saccharomyces cerevisiae EEL 2009. A avaliação da produção de aguardente de mel em escala piloto foi realizada nas instalações do Alambique da Associação Rural de Canas, Canas-SP e o destilado obtido armazenado em tonel de carvalho de 200 L por 6 meses. Amostras foram coletadas a cada 30 dias para caracterização físico-química em conformidade com os parâmetros estabelecidos na Legislação Brasileira para aguardente de frutas. Em paralelo, as respectivas amostras foram devidamente avaliadas sensorialmente por 120 provadores não treinados, por meio de testes de aceitação, em escala hedônica, considerando os quesitos aparência, aroma, sabor, corpo e impressão global, além da atitude de compra. Estes resultados foram analisados estatisticamente por ANOVA e teste de Tukey, sendo os resultados de aceitação em relação à impressão global, analisados por meio da análise multivariada o que permitiu traçar o Mapa de Preferência Interno - MDPREF. Os resultados referentes à caracterização físico-química das respectivas amostras demonstraram que todas apresentaram os parâmetros de avaliação em conformidade com os padrões estabelecidos pela legislação. Os resultados da análise sensorial revelaram que o tempo de armazenamento de 180 dias em tonel de carvalho não foi suficiente para a ocorrência de reações desejadas, o que influenciaria nas características sensoriais da bebida, tornado-a mais agradável e suave. No entanto, apesar do pouco tempo de armazenamento, a aguardente de mel apresentou uma boa aceitação por parte dos provadores, cuja maioria manifestou sua aceitação em termos de \"gostei ligeiramente\" e \"não gostei, nem desgostei\". No tocante ao MDPREF, este revelou que a amostra referente a 180 dias de armazenamento foi preferida por um maior número de provadores. Em relação à atitude de compra, as amostras armazenadas por 60 (79,17%) e 180 dias (75,83%) apresentaram os melhores resultados. Diante do exposto, conclui-se que o mel se apresenta como uma alternativa viável para a formulação de mosto para produção de aguardente no período de entre safra de cana-de-açúcar, contribuindo para melhor aproveitamento das instalações e como fonte alternativa de renda para o produtor rural. / In this work, first it was evaluated the fermentation performance of 10 yeast strains isolated from fruits, centrifuged honey and residue of honey processing after the sedimentation (sludge honey) step. This experiment was carried out in test tube containing wort made from honey 15 °Brix supplemented individually with different nutrients, namely: commercial yeast extract (10.0 g/L), rice bran (20.0 g/L), mixture (1.0 g/L) consisting of bran corn, rice and soy in the ratio 5:2:5 and commercial nutrient (D&R) (0.15 g/L). The parameters evaluated included the cell number determination in Neubauer chamber, and sugars and ethanol concentrations by HPLC, which allowed to determine the fermentation parameters as yield, fermentation efficiency and productivity. These results supported the selection of the wort supplemented with commercial yeast extract and the best yeast strain, which were subsequently evaluated in a pilot scale. The selected strain was the yeast isolated from the sludge honey, which was later identified as Saccharomyces cerevisiae and named Saccharomyces cerevisiae EEL 2009. The production evaluation of honey spirit on a pilot scale was conducted at the Canas Rural Association Pilot Plant for cachaça production - Canas-SP and distillate was stored in oak barrel of 200 liters per 6 months. Samples were collected every 30 days for physic-chemical characterization in accordance with the guidelines established in the Brazilian Legislation for fruit spirit. Beyond that, the respective samples were properly sensory evaluated by 120 untrained consumers regarding to acceptance testing employing a hedonic scale, considering characteristics as appearance, aroma, flavor, and overall impression, and the attitude of purchase, as well. These results were statistically analyzes by ANOVA and Tukey`s test and the results of acceptance regarding to the overall impression, were analyzed by multivariate analysis which allowed tracing the Internal Preference Map - MDPREF. The results concerning the physic-chemical characterization of the respective samples showed that all presented the evaluation parameters in accordance with standards established by the legislation. The results of sensory analysis revealed that the storage time of 180 days in oak barrel was not enough for the occurrence of desired reactions, which influence the sensory characteristics of the beverage, making it nicer and smoother. However, despite short time storage, honey spirit showed good acceptance by the consumers. Most of them expressed acceptance in terms of \"liked slightly\" and \"not liked nor disliked\". Regarding the MDPREF results, these proved that the sample relating to 180 days of storage was preferred by majority of consumers. Regarding the attitude of purchase, the samples stored for 60 days (79.17%) and 180 days (75.83%) showed the best results. Therefore, we conclude that honey can be considered as a viable alternative for wort formulation for the production of spirit, mainly in the period between harvests of sugar cane, contributing to better utilization of the facilities and as alternative source of income for farmers.

Existe um grande interesse das indústrias farmacêuticas em encontrar um tratamento adequado para os pacientes com câncer que apresentaram resistência aos medicamentos comumente utilizados para o combate dessa neoplasia. Sendo assim, se faz necessário a busca de novos marcadores genéticos que estejam associados à predisposição do paciente a reagir ao efeito da droga de maneira diferente do esperado. Para isso, vários estudos vêm sendo desenvolvidos, baseados nos medicamentos anticancerígenos. Entre esses medicamentos podemos destacar os agentes quimioterápicos a base de platina, como a carboplatina, cisplatina, oxaliplatina e a nedaplatina, que agem eliminando as células cancerosas através da formação de adutos nas bases de purina do DNA nuclear e a rebecamicina, um antitumoral que possui a capacidade de inibir a ação catalítica das topoisomerases I, ainda em teste clínico. Desse modo, este estudo teve a perspectiva de encontrar mutantes de leveduras resistentes a carboplatina e análogos de rebecamicina. Como resultado, identificamos 19 genes associados à resistência a carboplatina, sendo que 6 deles possuem genes ortólogos em humanos associados principalmente ao mecanismo de reparo de DNA e ao transporte celular. Foram também identificadas 9 linhagens que estavam associadas a sensibilidade a carboplatina sendo que 3 delas possuem deleções em genes com ortólogos humanos, que estão associados ao transporte endossomal, ao ribossomo e ao bloqueio do ciclo celular na fase G1. Na busca por um novo composto antitumoral derivado de rebecamicina, identificamos Reb C como um análogo promissor, já que apresentou 9 genes associados a resistência, dos quais 2 deles possuem ortólogos humanos relacionados ao ribossomo e ao proteassoma / There is a strong interest from pharmaceutical companies in finding an appropriate treatment for patients with cancer who had resistance to drugs commonly used to fight this disease. Therefore, it is necessary to search for new genetic markers that are associated with the patient\'s predisposition to react to the drug differently than expected. Aiming this, several studies have been developed based on anticancer drugs. Among these drugs can be highlighted the chemotherapeutic agents based on platinum, such as carboplatin, cisplatin, oxaliplatin and nedaplatin, which act by eliminating cancer cells through the formation of adducts with the purine bases of nuclear DNA and the rebeccamycin, an antitumor that has the ability to inhibit the catalytic action of topoisomerase I, still in clinical trial. This study aimed to find yeast resistant mutants to carboplatin and rebeccamycin analogs. As a result, we identified 19 genes associated with resistance to carboplatin, 6 of them presenting orthologous genes in humans, which are mainly associated to the mechanism of DNA repair and to cellular transport. 9 strains were also identified which are associated with carboplatin sensitivity, 3 possessing their orthologous in humans associated with endosomal transport, ribosome and cell cycle arrest in the G1 phase. In a search for a new antitumor compound derived from rebeccamycin, we identified the Reb C analog as promising, since it featured nine genes associated with resistance to it, among 2 of them have human counterparts related to the ribosome and the proteasome.

Les extrémités des chromosomes portent des structures nommées télomères, nécessaires à la survie des cellules. La sénescence réplicative induite par l’altération des télomères bloque les proliférations cellulaires excessives. Cependant, certaines cellules échappent à ce contrôle et deviennent immortelles. Je me suis intéressée aux mécanismes permettant de reconstituer des télomères fonctionnels par recombinaison chez la levure. Le noyau est divisé en sous-compartiments plus ou moins permissifs pour la recombinaison. J’ai étudié comment la localisation des télomères dysfonctionnels aux pores nucléaires (NPC) conditionne leur réparation et la prolifération des cellules. J’ai montré que les lésions réplicatives au télomères sont relocalisées aux NPC ce qui favorise leur réparation par un mécanisme conservatif. J’ai aussi montré la présence aux NPC de cercles d’ADN télomérique qui pourraient servir de matrice pour allonger les télomères et sortir de la sénescence réplicative. / Chromosome ends are formed by structures called telomeres, which are necessary for genome integrity and cell survival. Upon aberrant proliferation, as in precancerous cells, telomere alterations blocks cell proliferation, a mechanism called replicative senescence. However, some cells escape this control and become immortals. Using budding yeast as model, my work aimed to understand the mechanisms that allow cells to reconstitute functional telomeres using homologous recombination. The nucleus is divided in sub-compartments that are differently permissive for recombination. I investigated how the localization of dysfunctional telomeres to the nuclear pore complex (NPC) determines their repair and favors cell proliferation. I showed that replicative lesions at telomeres relocate to the NPC allowing conservative repair by recombination. I further shed light on the presence at NPC of telomeric DNA circles that may serve as template for telomere elongation and thus escape from senescence.

The herpesvirus life cycle involves a step where newly formed capsids leave the nucleus by translocating across the intact nuclear envelope (NE). Little is known about the role of cellular factors during nuclear egress. We sought to identify novel cellular proteins that interact with the conserved herpes simplex virus-1 (HSV-1) pUL34 by performing a yeast two-hybrid screen. pUL34 was chosen due to its crucial and multifunctional role during nuclear egress. From 42 cellular factors that interacted with pUL34 in yeast, twelve were further evaluated in mammalian cells by co-localization studies using immunofluorescence. No specific co-location between the tested cellular factors and pUL34 was observed in infected cells, thus the screen failed to convincingly identify novel pUL34 interactors. In the second part of the thesis we addressed the functional significance of the cellular protein torsinA (TA) in the HSV-1 life cycle. We became interested in TA due to its role in maintaining normal NE morphology. We showed that perturbing the normal function of TA through overexpression impaired HSV-1 replication and caused a defect in capsid nuclear egress. In mouse embryonic fibroblasts that failed to express TA (TA-/-MEFs), HSV-1 replication was also inhibited, but a defect in capsid nuclear egress was not apparent. Strikingly, infection in TA-null MEFs induced a NE breakdown, the extent of which was dependent on viral products involved in nuclear egress. The viral growth defect and NE envelope breakdown, however, seem to be TA-null cell line specific rather than a functional consequence of TA loss as indicated by TA-/-MEFs reconstituted with TA and 293T with reduced TA levels. In conclusion, overexpression and loss of TA have different effects on the HSV-1 life cycle.

The continued increase in the demand for fossil fuels combined with their ever dwindling supply has prompted the search for a suitable alternative fuel. The research contained within this dissertation seeks to increase the lipid content of cellular feedstocks, improve extraction efficiencies of lipids, and understand the pathways involved in the production of fatty alcohols and triacylglycerides from microbial feedstocks. As part of this research the diatom, Cheatoceros gracilis, was grown at small and large scale to determine optimal growing conditions. No apparent nutrient stress trigger was required to initiate the accumulation of the biodiesel precursor triacylglyceride, unlike other documented algal strains. A follow-up to this project demonstrated that the microalga C. gracilis may utilize light intensity as a trigger for lipid production. A major difficulty in the production of biofuels from microorganisms is the expensive process of dewatering, drying, and extracting the lipid compounds from the cells. As part of this research, a process has been developed that allows for lipid extraction to occur in the presence of water at a point as low as 2 percent solids or 98 percent water. This process utilizes a single organic solvent that mixes well with microbial lipids, but poorly with water allowing for efficient extraction of lipids and fast solvent to water separation. This process greatly decreases the cost of the microbial biofuels production associated with the removal of water from cell slurries. Triacylglycerides and fatty alcohols are oleochemicals that are commonly used in industrial, pharmaceutical, and consumable processes. A predicted fatty acyl CoA reductase enzyme was cloned into an E. coli vector, expressed, characterized and shown to be active as a dual reductive enzyme reducing a fatty acyl CoA to its respective fatty alcohol, constituting the first enzyme of this type discovered in a bacterium. The process of triacylglyceride production in microbes is fairly well understood; however, the process that regulates this production has not yet been fully explored. As part of this research, the model yeast organism, Yarrowea lipolytica, is utilized to identify essential genes for citrate transport that if removed could result in increasing triacylglyceride production in vivo.

The neurodegenerative disorders Alzheimer??s Disease (AD) and Parkinson??s Disease (PD) are characterised by the accumulation of misfolded amyloid beta 1-42 peptide (Aβ1-42) or α-synuclein, respectively. In both cases, there is extensive evidence to support a central role for these aggregation-prone molecules in the progression of disease pathology. However, the precise mechanisms through which Aβ1-42 and α-synuclein contribute to neurodegeneration remain unclear. Organismal, cellular and in vitro models are under development to allow elucidation of these mechanisms. A cellular system for the study of intracellular Aβ1-42 misfolding and localisation was developed, based on expression of an Aβ1-42-GFP fusion protein in the model eukaryote Saccharomyces cerevisiae. This system relies on the known inverse relationship between GFP fluorescence, and the propensity to misfold of an N-terminal fusion domain. To discover cellular processes that may affect the misfolding and localisation of intracellular Aβ1-42, the Aβ1-42-GFP reporter was transformed into the S. cerevisiae genome deletion mutant collection and screened for fluorescence. 94 deletion mutants exhibited increased Aβ1-42-GFP fluorescence, indicative of altered Aβ1-42 misfolding. These mutants were involved in a number of cellular processes with suspected relationships to AD, including the tricarboxylic acid cycle, chromatin remodelling and phospholipid metabolism. Detailed examination of mutants involved in phosphatidylcholine synthesis revealed the potential for phospholipid composition to influence the intracellular aggregation and localisation of Aβ1-42. In addition, an existing S. cerevisiae model of α-synuclein pathobiology was extended to study the effects of compounds that have been hypothesized to be environmental risk factors leading to increased risk of developing PD. Exposure of cells to aluminium, dieldrin and compounds generating reactive oxygen species enhanced the toxicity of α- synuclein expression, supporting suggested roles for these agents in the onset and development of PD. Expression of α-synuclein-GFP in phosphatidylcholine synthesis mutants identified in the Aβ1-42-GFP fluorescence screen resulted in dramatic alteration of α-synuclein localisation, indicating a common involvement of phospholipid metabolism and composition in modulating the behaviours of these two aggregation-prone proteins.

Abstract not available

Along with an increasing understanding of the harmful effects on the environment of a wide range of pollutants has come the need for more sensitive, faster and less expensive detection methods of identification and quantitation. Many environmental pollutants occur in low levels and often in complex matrices thus analysis can be difficult, time consuming and costly. Because of the availability and easy cultivation of the microorganisms with potentially high specificity, there is considerable interest in the use of living microorganisms as the analytical component (the biocomponent) of sensors for pollutants. While a number of biosensors using bacteria have been developed, yeast has been comparatively rarely used as the biocomponent. Yeast are attractive because they are easy to culture and they are eukaryotes which means their biochemistry is in many respects closer to that of higher organisms. This thesis describes the development of whole cell bioassays that use yeast cells as a sensing element and redox mediators to probe the intracellular redox reactions to monitor the catabolic activity of the yeast resulting from the external substrate, steady-state voltammetry is utilised as the electrochemical detection technique. The isogenic differential enzyme analysis (IDEA) concept of Lincoln Ventures Limited, lead NERF funded research consortium uses bacteria that have been cultured using specific organic pollutants as the carbon source which are the biocomponent in sensors. The use of wild type yeast Arxula adeninivorans that has the ability to use a very wide variety of substrates as sources of carbon and nitrogen was used as an alternative to bacteria to validate the “IDEA” concept. Naphthalene and di-butyl phthalate were chosen as model target contaminant molecules. The performance, detection limits and the usefulness of yeast based biosensor applications for environmental analysis are discussed. This thesis also describes the development and optimisation of a simple, cost effective in vivo estrogens bioassay for the detection of estrogens using either genetically modified or a wild type yeast Saccharomyces cerevisiae. In this study, catabolic repression by glucose was exploited to achieve specificity to estrogens in complex environmental samples that eliminates the requirement for conventional sample preparation. This is the first time that the use of wild type yeast to quantify estrogens has been reported. The attractive features of the bioassay are its use of a non-GMO organism, its speed, its high specificity and sensitivity with a detection limit of 10-15 M. The similarity of binding affinities for major estrogens to those of human estrogens receptors makes this in vivo estrogen bioassay very useful for analytical/screening procedures. The electrochemical detection method also makes it easy to interface with a variety of electronic devices.

Includes bibliographies. This thesis describes the isolation of putative promoter sequences that can produce differential expression of a gene during anaerobic wine fermentations, the use of these sequences in the development of expression vectors and the application of this work to the production of genetically engineered wine yeasts for commercial purposes.