Bacillus cereus est une bactérie aéro-anaérobie facultative à Gram positif ubiquiste pouvant s’adapter à de nombreux environnements et s’y développer. C’est un agent pathogène de l’homme capable de produire tout un éventail de protéines extracellulaires et de toxines jouant un rôle majeur dans la pathogénicité de ce micro-organisme. B. cereus croit suivant un métabolisme de type respiratoire en aérobiose et fermentaire en anaérobiose en l’absence d’accepteur final d’électrons. En aérobiose, la chaine respiratoire est une source majeure des dérivés réactifs de l'oxygène (ROS) endogènes. En anaérobiose, les ROS endogènes sont générés en réponse au stress oxydant secondaire au stress nutritionnel et au stress réducteur, lorsque les cultures sont réalisées à bas potentiel d’oxydo-réduction (POR). Les résidus méthionines (Met) sont particulièrement sensibles à l’oxydation par les ROS. L’oxydation des Met conduit à la formation de méthionine sulfoxyde (Met(O)), un dérivé oxydé stable détectable par spectrométrie de masse (MS). L'oxydation des résidus Met est réversible : leur réduction est catalysée par des méthionines sulfoxyde réductases (Msr). Pour déterminer le rôle de l’oxydation des résidus Met, nous avons réalisé une étude exhaustive par MS de la dynamique de l’exoprotéome de la souche ATCC 14579 (pBClin 15) de B. cereus en aérobiose (pO2 = 100%) et en anaérobiose (pO2 = 0%) à haut (POR initial = +140 mV) et bas potentiel redox (PORi= -350 mV). Les résultats ont montré que la dynamique des toxines était représentative de la dynamique de l’exoprotéome à la fois en termes d’abondance relative de protéines et d’oxydation des Met dans les trois conditions testées. L’analyse des résultats suggèrent que (i) l’abondance des toxines et leur taux de méthionines oxydés reflètent le niveau d’oxydation cellulaire et (ii) la sécrétion de toxines au cours de la croissance cellulaire contribue au maintien de l'homéostasie redox intracellulaire en piégeant les ROS endogènes, en particulier en phase active de croissance en aérobiose et en fin de croissance en anaérobiose. Pour étayer l’hypothèse selon laquelle, les Met des protéines extracellulaires, et des toxines en particuliers sont des composants de la machinerie cellulaire antioxydante, nous avons construit une souche mutante ne synthétisant plus MsrAB et comparer le protéome et l’exoprotéome de cette souche mutante avec celle de la souche parentale en aérobiose et anaérobiose à haut POR. Cette étude a mis en évidence l’implication de MsrAB mais également du plasmide cryptique pBClin15 dans la sécrétion des toxines et le maintien de l'homéostasie redox intracellulaire / Bacillus cereus is a Gram-positive aerobic or facultative anaerobic worldwide-distributed bacterium. In addition, B. cereus is a human pathogen able to produce a range of extracellular enzymes and toxins playing a major role in the virulence of the bacteria. In presence of oxygen, B. cereus performs respiration. Without oxygen or other electron acceptors, it performs mixed-acid fermentation. Under aerobiosis, the respiratory electron transport chain is a major source of endogenous reactive oxygen species (ROS). Under anaerobiosis, endogenous ROS are generated in response to reductive stress (mainly under high-reductive anaerobiosis) and to starvation (nutrient stress), i.e. in response to secondary oxidative stresses. Methionine residues (Met) of proteins are vulnerable to oxidation by free radicals. Oxidation of Met leads to the formation of methionine sulfoxide (Met (O)), a stable by-product detectable by mass spectrometry (MS). Met(O) can be reduced back to Met by the action of methionine sulfoxide reductase (Msr). To determine the role of oxidation of Met residues, B. cereus exoproteome time courses were monitored by MS under low oxidation-reduction potential (ORP) anaerobiosis (initial ORP = +140 mV and pO2 = 0%), high-ORP anaerobiosis (iORP = -350 mV and pO2 = 0%), and aerobiosis (pO2 = 100%). The results indicated that toxin-related proteins were the most representative of the exoproteome changes, both in terms of protein abundance and their Met(O) content in the presence and in the absence of oxygen. The analysis results suggest that (i) the abundance of toxins and their oxidized methionines rates reflect the cellular oxidation level and (ii) the secretion of toxins during growth helps to maintain redox homeostasis by keeping endogenous ROS at bay, during the exponential growth phase under aerobic conditions and at the end of growth under anaerobiosis. To support our hypothesis that Met residues of extracellular proteins, particulars of toxins are components of the cellular machinery antioxidant, we constructed a mutant strain by deleting the gene of MsrAB and compare the cellular proteome and exoproteome of this mutant strain with the wild-type strain under aerobiosis and high-ORP anaerobiosis. This study highlighted the involvement of MsrAB but also pBClin15 plasmid in the secretion of toxins and maintain of the intracellular redox homeostasis.

Mudanças nos hábitos alimentares dos consumidores têm aumentado a demanda por frutas frescas e polpas de frutas. Com isso, a busca por novos compostos com atividade antimicrobiana é de grande interesse, já que a aplicação de aditivos químicos convencionais em alimentos tem sido reavaliada devido à potencial toxicidade de alguns desses compostos. As bacteriocinas ou BLIS, produzidas por diferentes gêneros bacterianos, têm despertado grande interesse industrial para aplicação em alimentos em processos de bioconservação. No presente trabalho, foram obtidos 3 isolados bacterianos (A, B e C) a partir de polpa de abacaxi, produtores de substância antagonista frente a diferentes linhagens de Listeria monocytogenes e Bacillus sp. A natureza proteica das substâncias antagônicas produzidas pelos isolados foi confirmada pela sensibilidade à enzima ? - quimotripsina. As linhagens foram identificadas através de provas bioquímicas e moleculares como Bacillus cereus, com a colaboração da Fundação Oswaldo Cruz (Rio de Janeiro, Brasil). Para estudos mais detalhados da BLIS foi selecionado o isolado C denominado Bacillus cereus LFB-FIOCRUZ 1640. A melhor condição de incubação para produção da BLIS foi a 30ºC/24 horas, em caldo MRS. A BLIS apresentou estabilidade térmica por até 30 minutos a 80ºC e em ampla faixa de pH frente a L. monocytogenes. A purificação da BLIS foi realizada com resina Amberlite XAD-16 e de troca catiônica SP-Sepharose \"Fast Flow\", tendo o extrato apresentado um fator de purificação de 4,1 vezes e rendimento de 30%. O extrato obtido foi liofilizado e uma alíquota foi analisada por SDS-PAGE, o que permitiu a estimativa da massa molecular da BLIS de 25 kDa. A Concentração Bactericida Mínima (CBM) de 2 mg/mL foi determinada frente ao indicador L. monocytogenes e esta concentração de extrato foi aplicada em sistema modelo contendo polpa de abacaxi. A BLIS teve ação bactericida inibindo completamente L. monocytogenes por 24h/ 37ºC. Neste sentido, a aplicação da BLIS na área de alimentos e outras áreas farmacêuticas poderá ser explorada em outros trabalhos. / Changes in habits of consumers, with preference for healthy foods, have increased the demand for fruits and fruit pulps. Thus, there is great interest in searching new compounds with antimicrobial activity, since the application of conventional additives in foods is of concern due to the toxicity of some of these compounds. The bacteriocins or BLIS, produced by different bacteria genera, have increased the interest for its industrial application in food technology in processes of biopreservation. In this study, three isolates were obtained (A, B and C) from pineapple pulp, which produce antagonistic substances with activity against Listeria monocytogenes and Bacillus sp. The proteinaceous nature of the antagonistic substance produced by the isolates was confirmed by susceptibility to the enzyme ? - chymotrypsin. The strains were identified by biochemical and molecular tests as Bacillus cereus, in collaboration with Fundação Oswaldo Cruz (Rio de Janeiro, Brazil). Isolate C of Bacillus cereus was named LFB-FIOCRUZ 1640. The best condition of incubation for the BLIS production was 30°C for 24 hours in MRS broth. The BLIS was thermostable (up to 30 minutes at 80°C) and it was partially stable in the range of pH 2 to 9. The purification of the BLIS was performed with Amberllite XAD-16 and cation-exchange SP-Sepharose \"Fast Flow\" resins. The extract presented a purification factor of 4.1 times and 30% of yield. The extract was lyophilized and analyzed by SDS-PAGE. The molecular mass of the BLIS was estimated as 25 kDa. The Minimum Bactericidal Concentration (MBC) of 2 mg/mL was determined with the indicator L. monocytogenes, and this concentration of extract was applied in a model system containing pineapple pulp. The BLIS had bactericidal action which completely inhibited L. monocytogenes for 24h/37°C. The BLIS of B. cereus 1640 presents potential for application as an antimicrobial in food and other pharmaceutical areas.

Há controvérsia sobre os processos responsáveis pela atual distribuição de Florestas Tropicais Sazonalmente Secas (FTSS) na América do Sul. Este tipo de vegetação compreende uma grande proporção de todas as espécies neotropicais. Entender o que modela a sua distribuição pode fornecer novas perspectivas para a evolução deste bioma e contribuirpara os aspectos de sua conservação. O trabalho avaliou a evolução deste bioma no sul do Brasil, onde as FTSS e as Florestas Tropicais (FT) são amplamente intercaladas. Para isso, foi reconstruídaa história filogeográfica do cacto, Cereus hildmannianus, uma espécie característica e abundante das FTSS. Métodos de datação molecular, estrutura populacional e filogeografia foram realizadas para avaliar os eventos histórico-demográficospor meio de uma amostragem densa que compreendeu 24 populações e cerca de 150 amostrasde, pelo menos, uma dentre as seis regiões genômicas nuclear e cloroplastidiais selecionadas. A partir disso, foi investigado um possível cenário da dinâmica populacional de C. hildmannianus. Os resultados indicam uma separação da espécie em dois grupos principais (ST: 0,788) com eventos de expansão populacional: umem regiões costeiras e o outro no interior do sul do Brasil, concondante com a distribuição dos núcleos das FTSS. O tempo do ancestral comum mais recente de C. hildmannianus, há 2,56 milhões de anos, remete a especiação deste ao período pré-Glacial. Os resultados do padrão de distribuição de C. hildmannianus foram concordantes com as áreas de endemismo para outros táxons das FTSS. Os eventos de dispersão e de vicariância entre as FTSS e as FT podem estar associados às mudanças paleoclimáticas durante os períodos glaciais do Quaternário, promovendo eventos de retração/expansão nestas florestas. A compreensão desses padrões na história biogeográfica de populações naturais podem auxiliar futuros planos de conservação deste bioma, na América do Sul. / There is controversy about the processes responsible for the current distribution of Seasonally Dry Tropical Forests (SDTF) in South America. This vegetation type comprises a large proportion of all Neotropical species. Understanding what shapes your distribution may provide new insights into the evolution of this ecosystem and contribute to aspects of conservation. The study evaluated the evolution of this biome in southern Brazil, where SDTF and Rainforests are widely interspersed. For this, we reconstructed the phylogeographic history of the cactus, Cereus hildmannianus, a kind of characteristic and abundant SDTF. Molecular dating methods, population structure and phylogeography were performed to evaluate the historical and demographic events through a dense sampling which comprised 24 populations and about 150 samples of at least one among the six nuclear and chloroplast genomic regions selected. From this, we investigated a possible scenario of population dynamics of C. hildmannianus. The results indicate a separation of the species into two main groups (ST: 0.788) with events of population expansion: one in coastal regions and the other inside the south of Brazil, concondante with the distribution of the nuclei of SDTF. The time of the most recent common ancestor of C. hildmannianuswere 2.56 million years ago, this speciation refers to the pre-Glacial. The results of the distribution pattern C. hildmannianus were consistent with areas of endemism for other taxa of SDTF. The events of dispersal and vicariance between SDTF and Rainforests may be related to paleoclimatic changes during glacial periods of the Quaternary, promoting events shrinkage /expansion in these forests. Understanding these patterns in the biogeographic history of natural populations may aid future conservation plans this biome in South America.

Les personnes âgées sont souvent victimes de dénutrition pouvant conduire à de multiples dégradations de la santé. La prévention de cet état de dénutrition est une des principales préoccupations des autorités de santé. C’est dans cet objectif que le projet OPTIFEL a conçu de nouveaux produits alimentaires optimisés, afin d’améliorer l’alimentation des personnes âgées, en tenant compte de leurs besoins et souhaits, tout en préservant leur sécurité sanitaire. Bacillus cereus est une bactérie pathogène sporulée capable de se développer dans des conditions variables comme le froid, l’absence d’oxygène, des bas pH ainsi que des matrices alimentaires diverses. Elle est l’une des principales causes de Toxi-Infection Alimentaire Collective (TIAC) surtout en Institut Médico-Sociaux (IMS). Ce travail de thèse avait donc pour objectif de déterminer le comportement de B. cereus à différentes étapes de la vie d’un produit alimentaire. La conservation au froid peut permettre la multiplication de souches psychrotolérantes de B. cereus qui peuvent alors représenter un risque d’infection pour le consommateur. Les conditions anaérobies réduisent la capacité d’adaptation de B. cereus au froid et aux bas pH. La composition de l’aliment et sa préparation influence également le comportement de B. cereus, comme nous l’avons constaté avec un bouillon de carotte dans lequel la présence d’oxygène crée un effet létal pour la bactérie. Certaines souches psychrotolérantes de B. cereus sont capables de produire de la toxine émétique appelée céréulide. Nous avons montré que cette production peut se faire à partir de 8°C et atteindre des concentrations pouvant causer des intoxications à partir de 10°C. S’il est produit dans l’aliment, le cereulide ne serait pas détruit lors de la préparation de l’aliment. Par contre les cellules végétatives de B. cereus sont très thermosensibles et celles qui auraient pu se développer pourront être détruites par un réchauffage du produit avant sa consommation. Ce travail a permis de définir les paramètres importants pour limiter le risque d’infection alimentaire par B. cereus. / Elderlies are often victims of undernutrition which can lead to multiple health damages. Prevention of this state of undernutrition is one of the main concerns of health authorities. With this objective, the OPTIFEL project designed new optimized foodstuffs, to improve foods for elderlies, by taking into account their needs and wishes, while preserving their safety. Bacillus cereus is a spore-forming bacterial pathogen able to grow in various conditions as low temperature, absence of oxygen, low pH and in different types of food. It is one of the main causes of foodborne outbreaks, particularly in socio-medical institutions. The aim of this work was to determine the behavior of B. cereus at different steps of the life of the food product. Cold storage can allow multiplication of psychrotolerant B. cereus strains that can represent a risk of infection for consumers. Anaerobic conditions reduce the adaptation capacity of B. cereus at low temperature and low pH. The composition and the preparation of the food product also influence the behavior of B. cereus, as we showed with carrot broth in which oxygen created a lethal effect for the bacterium. Certain psychrotolerant B. cereus strains are able to produce an emetic toxin named cereulide. We showed that this production starts at 8 °C and can reach at 10 °C concentrations sufficient to cause intoxications. If this toxin is produced in food, it would not be destroyed during the food preparation. In contrast, vegetative cells of B. cereus are very heat-sensitive and those who would have been able to develop could be destroyed by a reheating of the food product before its consumption. This work allowed the identification of important parameters to limit the risk of foodborne disease by B. cereus.

Chez les bactéries sporulantes du genre Bacillus, des mécanismes importants tels que la sporulation et la virulence sont régulés par des systèmes de communication cellulaire qui impliquent des peptides de signalisation et des régulateurs de la famille RNPP (Rap, NprR, PlcR, PrgX). L'objectif de mon travail de thèse a été de déterminer le rôle du régulateur NprR chez les bactéries du groupe B. cereus. Ce travail se divise en trois parties complémentaires. La première partie a consisté à montrer que NprR est impliqué dans un système de communication cellulaire. Nous avons montré que NprR est un régulateur transcriptionnel de début de phase stationnaire qui est dépendant du peptide de signalisation NprX. Associé à NprX, NprR active la transcription du gène nprA qui code pour une protéase extracellulaire. Nous avons démontré que le peptide NprX est sécrété, maturé puis réimporté dans la cellule bactérienne par deux systèmes d'oligopeptide perméase (Opp et Npp). Une fois dans la cellule, la forme mature de NprX (vraisemblablement l'heptapeptide SKPDIVG) se lie à NprR et permet la transcription du gène nprA. Nous avons ensuite cherché à déterminer la fonction de ce régulateur au cours du cycle infectieux de B. thuringiensis (Bt) chez l'insecte. Nous avons montré que NprR est actif après la mort de l'insecte et permet aux bactéries de survivre, sous forme de cellules végétatives, dans les cadavres. Une analyse transcriptomique indique que NprR régule l'expression d'au moins 41 gènes qui codent notamment pour des enzymes dégradatives et un locus de gènes impliqués dans la production d'un peptide synthétisé de façon non ribosomique (la kurstakine). Nous avons démontré que les gènes codant pour les enzymes dégradatives s'expriment spécifiquement après la mort de l'hôte et que les produits de ces gènes sont essentiels pour hydrolyser différents substrats (protéines, lipides, chitine), ce qui suggère que Bt a un mode de vie nécrotrophe dans le cadavre. La kurstakine est essentielle pour la survie de Bt pendant son développement nécrotrophe et nous avons montré que cette molécule est nécessaire pour le swarming et la formation de biofilm. Par ailleurs, un mutant du gène nprR ne se développe pas et ne sporule pas efficacement dans le cadavre. L'ensemble de nos résultats indiquent que le necrotrophisme est un mode de vie hautement régulé, qui est essentiel dans le cycle infectieux de Bt car il contribue à la transmission horizontale de ce micro-organisme. Enfin, nous avons étudié la régulation de l'expression des gènes nprR et nprX. Nous avons montré que les gènes nprR-nprX sont co-transcrits à partir d'un promoteur dépendant de sigma-A (PA) situé en amont du gène nprR. La transcription à partir de ce promoteur débute lors de l'entrée en phase stationnaire et est contrôlée par deux régulateurs transcriptionnels: CodY et PlcR. Le répresseur CodY pourrait se lier à l'ADN en amont du promoteur PA et réprimer la transcription des gènes nprR-nprX pendant la phase exponentielle de croissance. Au début de la phase stationnaire, le contrôle négatif de CodY est levé et PlcR active la transcription de nprR-nprX en se liant à une boîte PlcR située en amont de PA. Nos résultats indiquent que nprX est également transcrit indépendamment de nprR à partir de deux promoteurs, PH et PE, respectivement dépendant de sigma-H et sigma-E. Les deux promoteurs permettent d'assurer la transcription de nprX en phase stationnaire tardive alors que la transcription à partir du promoteur PA est achevée. Cette étude met en évidence le role clé des régulateurs CodY, PlcR and Spo0A dans la régulation de l'expression des gènes nprR-nprX. / In sporulating Bacillus, major processes like virulence gene expression and sporulation are regulated by communication systems involving signaling peptides and regulators of the RNPP family. In this work, we investigated the role of one such regulator, NprR, in bacteria of the Bacillus cereus group. This work can be divided into three complementary parts.The first part consisted to demonstrate that NprR is involved in a quorum-sensing system. We showed that NprR is a transcriptional regulator whose activity depends on the NprX signalling peptide. In association with NprX, NprR activates the transcription of an extracellular protease gene (nprA) during the first stage of the sporulation process. We demonstrated that the NprX peptide is secreted, processed and then reimported within the bacterial cell by two oligopeptide permease systems (Opp and Npp). Once inside the cell, the mature form of NprX, presumably the SKPDIVG heptapeptide, directly binds to NprR allowing nprA transcription. The second part was to explore the function of NprR during the infectious cycle of B. thuringiensis (Bt). We showed that NprR is active after death of the insect and allows Bt to survive in the cadavers as vegetative cells. Transcriptomic analysis revealed that NprR regulates at least 41 genes encoding degradative enzymes or involved in the synthesis of a non-ribosomal peptide named kurstakin. The degradative enzymes include chitinases, proteases and lipases. The corresponding genes are specifically expressed after host death suggesting that Bt has an active necrotrophic lifestyle in the cadaver. We showed that kurstakin is essential for Bt survival during necrotrophic development. It is required for swarming mobility and biofilm formation, presumably through a pore forming activity. A nprR deficient mutant does not develop necrotrophically and does not sporulate efficiently in the cadaver. Altogether, our results show that necrotrophism is a highly regulated mechanism essential for the Bt infectious cycle, contributing to horizontal transmission. Finally, the last part of my PhD consisted to study the regulation of nprR and nprX expression. We showed that the nprR-nprX genes are cotranscribed from a sigma A-dependent promoter (PA) located upstream from nprR. The transcription from PA starts at the onset of the stationary phase and is controlled by two transcriptional regulators: CodY and PlcR. The nutritional repressor CodY binds a DNA target site upstream from PA and represses nprR-nprX transcription during the exponential growth phase. At the onset of the stationary phase, the negative control of CodY is relieved and PlcR activates nprR-nprX transcription by binding a PlcR box located upstream from PA. We showed that nprX is also transcribed independently of the nprR transcription from two promoters, PH and PE, dependent on sigma-H and sigma-E, respectively. Both promoters ensure nprX transcription during late stationary phase and sporulation while transcription from PA is complete. This study highlights the key role played by CodY, PlcR and Spo0A in nprR-nprX transcription.

Les bactéries utilisent un mode de communication appelé quorum sensing pour régulerl’expression des gènes en fonction de la densité de population et contrôler ainsi de façonmulticellulaire des processus tels que la sporulation, la compétence ou la virulence. Chez les bactériesà Gram-positif, le quorum sensing repose principalement sur la production, la sécrétion et la détectionde petits peptides de signalisation.Le projet porte sur l’étude du système quorum sensing: NprR/NprX chez Bacillus cereus, oùNprR est l’effecteur qui reconnait spécifiquement le peptide de signalisation NprX. NprR est uneprotéine bi-fonctionnelle. Seule, elle agit en tant qu’inhibiteur de la sporulation, en complexe avecNprX, elle perd sa fonction initiale au profit d’une activité facteur de transcription impliquée dans lavirulence. NprR appartient à une famille d’effecteurs de quorum sensing appelée RNPP (Rap, NprR,PlcR et PrgX) encore mal caractérisée au niveau structural. Mon projet de thèse a consisté en l’analysestructure-fonction du système NprR/NprX.Pour comprendre la régulation fonctionnelle de NprR par NprX, des études en solution (SECMALSet DLS) ont permis de mettre en évidence un switch moléculaire qui repose sur un changementd’oligomérisation. Ainsi NprX fait basculer NprR d’une conformation Apo dimérique à uneconformation compléxée tétramérique.L’étude structurale par cristallographie a aboutit à la résolution de la structure du complexeNprR/NprX. L’analyse de ce tétramère suggère la reconnaissance de 2 sites distincts sur l’ADN.L’étude structurale par SAXS, a quant à elle, permis de proposer une conformation dimérique de laforme Apo NprR, modèle conforté grâce à une étude par mutagénèse dirigée des résidus d’interface. Ils’agit d’un mode de dimérisation semblable à celui des protéines Rap (membres de la famille RNPP).La caractérisation par ITC de l’interaction NprR/NprX avec différentes formes du peptide,ainsi que l’analyse de la poche de fixation du complexe, ont permis de mieux comprendre la spécificitéd’interaction et de mettre en évidence deux résidus clés de l’effecteur : l’Asn275 essentielle à lafixation du peptide et l’Arg 126 essentielle à l’activation de la fonction facteur de transcription.Ces travaux ont contribué à une meilleure compréhension du système quorum sensingNprR/NprX grâce à l’élucidation du switch moléculaire contrôlé par NprX mais aussi à une meilleureconnaissance de la famille d’effecteurs RNPP. / Bacteria use a communication mode named quorum sensing to regulate gene expression depending on the population density and thus to control processes such as sporulation, competence or virulence in a multicellular manner. In Gram-positive bacteria, the quorum sensing relies mostly on the production, the secretion and the detection of small signaling peptides. The project focuses on the study of the quorum sensing system NprR/NprX in Bacillus cereus, where NprR is the effector, which recognizes specifically the signaling peptide NprX. NprR is a bi-functional protein. In the absence of peptide, it acts as a sporulation inhibitor while in complex with NprX, it acts as transcription factor implicated in virulence. NprR belongs to a family of quorum sensing effectors named RNPP (for the first identified members: Rap, NprR, PlcR and PrgX) still not well characterized at a structural level. My PhD project consisted to perform the structure/function analysis of the NprR/NprX system. To understand the functional regulation of NprR by NprX, I carried out different studies in solution (SEC-MALS and DLS). These results allowed me to highlight a molecular switch based on a changing of the oligomerisation state of the protein. NprX binding switches NprR from an Apo dimeric conformation to a tetrameric complex. The structural study by crystallography led to the resolution of the tetrameric NprR/NprX complex structure. The analysis of this tetramer suggests the recognition of 2 DNA binding sites. The structural study of the dimeric conformation of Apo NprR by SAXS, allowed me to propose a model similar to that of the Rap dimers (members of RNPP family). This model is supported by a directed mutagenesis study of interface residues. The characterization by ITC of the NprR/NprX interaction with different forms of the peptide, as well as the analysis of the binding pocket in the complex, led to a better understanding of the specificity of the interaction. Two key residues of the effector were highlighted: Asn275, essential to peptide binding and Arg126, essential to the activation of the transcription factor function. These results have contributed to a better understanding of the NprR/NprX quorum sensing system thanks to the elucidation of the molecular switch controlled by NprX but also in a better knowledge of the RNPP effectors family.

As bactérias patogênicas são os principais agentes que contaminam alimentos e podem prejudicar a saúde humana. Para tentar combater e controlar a contaminação de alimentos investigam-se novos compostos que apresentam atividade antimicrobiana. O ramnolipídeo (RL) é um biossurfatante (BS) produzido por Pseudomonas spp. que apresenta elevada biodegradabilidade e, baixa toxicidade além de potencial antimicrobiano. O objetivo desse trabalho foi estudar a atividade antimicrobiana do RL frente às bactérias patogênicas Gram positivas, Bacillus cereus (ATCC 33018), Listeria monocytogenes (ATCC 19112), Staphylococcus aureus (ATCC 8095) e Gram negativas, Escherichia coli (EHEC) (ATCC 43895) e Salmonella enterica (ATCC 13076) além de contribuir na elucidação do mecanismo de ação destes compostos. Os testes de susceptibilidade ao RL foram realizados a partir da determinação da concentração inibitória mínima (CIM) e concentração bactericida mínima (CBM) utilizando a técnica de micro-diluição. O efeito do pH sobre a atividade antimicrobiana foi avaliado na faixa de pH 5 a 9. Para avaliação do mecanismo de ação foram realizados ensaios de permeabilidade celular, espectroscopia de infravermelho e hidrofobicidade celular. O RL apresentou atividade antimicrobiana para as bactérias B. cereus em CIM 19,5 &#956g/mL e CBM 39,1 &#956g/mL, e para L. monocytogenes CIM 156,2 &#956g/mL e CBM 312,5 &#956g/mL. Para B. cereus apresentou efeito bactericida a partir de 30 minutos na CBM, e para L. monocytogenes em 8 horas de incubação com o RL na CBM. As bactérias Gram negativas E. coli e S. enterica mostraram-se resistentes ao RL. O pH influenciou a ação antimicrobiana do RL sendo mais efetivo em pH mais ácidos. O tratamento com RL promoveu redução da hidrofobicidade da superfície celular das bactérias sensíveis. Os espectros infravermelhos evidenciaram alterações na composição química da membrana/parede celular principalmente para bactérias Gram positivas. A permeabilidade da membrana celular aumentou de acordo com o aumento da concentração de RL. A atividade antimicrobiana do RL foi evidenciada para as bactérias Gram positivas sendo mais sensíveis B. cereus e L. monocytogenes. Os resultados obtidos neste trabalho sugerem que o RL promove alterações na permeabilidade e composição química da membrana celular bacteriana sendo um agente potencial para controle de bactérias Gram positivas de importância alimentar. / Pathogenic bacteria are main agents that contaminate food and are harmful to human health. The search for new compounds to combat and control food pathogens is of increasing interest. Rhamnolipid (RL) is a biosurfactant (BS) typically produced by Pseudomonas spp., showing high biodegradability, low toxicity and antimicrobial activity. This study aimed to evaluate the antimicrobial activity of RL against the food pathogenic Gram positive bacteria Bacillus cereus (ATCC 33018), Listeria monocytogenes (ATCC 19112), Staphylococcus aureus (ATCC 8095) and Gram negative, Escherichia coli (EHEC) (ATCC 43895) and Salmonella enterica (ATCC 13076) and also contribute to the elucidation of RL mechanism of action. Susceptibility tests were performed by determination of the minimum inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) using the broth microdilution method. The effect of pH on antimicrobial action was also investigated ranging from 5 to 9. Mechanism of action was studied using membrane permeability, infrared spectroscopy and cell hydrophobicity assays. The MIC value for B. cereus was 19.5 &#956g/mL and MBC was 39.1 &#956g/mL. L. monocytogenes was inhibited at concentration 156.2 &#956g/mL showing MBC of 312.5 &#956g/mL. B. cereus presented bactericidal effect after 30 minutes and for L. monocytogenes after 8 hours. The Gram-negative E. coli and S. enterica were resistant to RL. The pH influence antimicrobial activity of the RL showing decreasing MIC values at acidic conditions. Cell hydrophobicity was reduced by RL for the sensitive bacteria. Infrared spectroscopy showed that RL induced changes in chemical composition of cell membrane/ wall especially for the Gram positive bacteria. Cell permeability also increases as RL concentration increases. Antimicrobial activity of RL was evidenced for Gram positive bacteria and the most sensitive were B. cereus and L. monocytogenes. The results of this study suggest that rhamnolipid biosurfactant promotes changes in the permeability and membrane chemical composition showing potential to control foodborne Gram positive bacteria.

Diarrhoe ist eines der häufigsten Probleme beim equinen Neonaten. Nahezu alle Fohlen entwickeln Durchfall innerhalb der ersten Lebenswochen. Unterschiedliche virale, bakterielle und parasitäre Ursachen werden diskutiert. In diesen Zeitraum fällt ebenfalls die erste Rosse der Stute, sodass der Durchfall um den 5. - 15. Lebenstag (LT) bei den Fohlen als „Fohlenrossedurchfall“ bezeichnet wird. Es wird vermutet, dass die Entwicklung der intestinalen Mikroflora und die Reifung der Darmschleimhaut im Wesentlichen für das Durchfallgeschehen verantwortlich sind. Bisher ist jedoch wenig bekannt über die Entwicklung der intestinalen Mikroflora bei Fohlen. Einige Probiotika sind als Darmflorastabilisatoren bei Tieren zugelassen. Studien belegten positive Effekte von Toyocerin® (B. cereus var. toyoi) auf die Darmgesundheit bei anderen Tierarten wie z.B. Kälbern, Ferkeln, Broilern, Puten und Mastkaninchen. Die vorliegende Arbeit sollte klären, ob die Supplementierung von B. cereus var. toyoi zu einer Stabilisierung der sich entwickelnden intestinalen Mikroflora und damit zu einer Verringerung der Durchfälle bei Fohlen führt. Die Untersuchung wurde an 25 Mutterstuten eines Vollblutgestüts und ihren Fohlen durchgeführt. Alle Fohlen wurden von Februar bis Mai 2011 geboren. Von Geburt an wurden die Fohlen randomisiert in drei Behandlungsgruppen eingeteilt: Placebo-Gruppe (10 ml isotone Kochsalzlösung, n=8), 50 mg Toyocerin-Gruppe (5 x 108 KbE B. cereus var. toyoi gelöst in 10 ml isotoner Kochsalzlösung, n=7) und 200 mg Toyocerin-Gruppe (2 x 109 KbE B. cereus var. toyoi gelöst in 10 ml isotoner Kochsalzlösung, n=10). Die Placebo- und Behandlungsgruppen wurden einmal täglich vom 1. – 58. LT supplementiert. Herz- und Atemfrequenz, Körperinnentemperatur und die Körpermasseentwicklung wurden nach einem standardisierten Protokoll erhoben. Kotproben konnten mit Hilfe von Kotsammelbeuteln oder durch rektale Entnahme innerhalb von 24 Stunden nach der Geburt sowie an LT 9, 16, 23, 30, 44, 58 und am ersten Durchfalltag gewonnen werden. Blutproben wurden aus der Vena jugularis externa am 1., 9., 16., 30., 58. LT sowie am ersten Durchfalltag entnommen. Die bakteriologische Untersuchung erfolgte mit Hilfe des Kulturverfahrens. Die Bestimmung der Gesamt-IgG-Werte wurde mit einem kompetitiven ELISA, die Bestimmung der spezifischen Antikörper IgG-anti-LPS von E. coli J5 und IgG-anti-PLC-von-C. perfringens-1a mit einem indirekten ELISA durchgeführt. 88 % der Fohlen entwickelten Durchfall (Placebo 7/8, 50 mg Toyocerin 5/7, 200 mg Toyocerin 10/10) mit einer hohen Inzidenz zwischen dem 8. und 16. LT. Das Allgemeinbefinden und die Bewegungs- und Sauglust blieben dabei unbeeinflusst. Zum Zeitpunkt des ersten Östrus der Stute zeigten 59 % der Fohlen Diarrhoe. Unter den 41 %, die keinen Durchfall zum Zeitpunkt der Fohlenrosse hatten, waren Fohlen, die nie Durchfall vom 1. – 58. LT zeigten, aber auch welche die Diarrhoe entwickelten, als die Mutterstute sich nicht in Rosse befand. Ein Zusammenhang zwischen der Fohlenrosse der Stute und Durchfall bei ihrem Fohlen konnte nicht hergestellt werden. Es zeigte sich eine Tendenz, dass hohe Spiegel der Gesamt-IgG (>20 mg/ml) und IgG-anti-LPS von E. coli J5 (>120 RE/ml) nach der Kolostrumaufnahme im Zusammenhang mit einer geringeren Anzahl von Durchfalltagen innerhalb der ersten zwei Lebensmonate standen. C. perfringens und Enterobakterien waren gleichermaßen nachweisbar bei Fohlen mit Durchfall als auch bei unauffälligen Fohlen. Aus der Supplementierung von B. cereus var. toyoi ergab sich kein Effekt auf die Kotflora der Fohlen, außer auf die Gesamtkeimzahlen (GKZ) der aeroben Bakterien. Bei den Aerobiern im Fohlenkot konnte ein signifikanter Behandlungseffekt (p=0,012) festgestellt werden. Im ersten Milchkot der Fohlen waren GKZ von 4,5 x 104 KbE/g (200 mg Toyocerin-Gruppe) bis 5,0 x 105 KbE/g (50 mg Toyocerin-Gruppe) bei den aeroben Bakterien und GKZ von 2,4 x 105 KbE/g (200 mg Toyocerin-Gruppe) bis 4,7 x 106 KbE/g (50 mg Toyocerin-Gruppe) median bei den Anaerobiern nachweisbar. Danach stieg der Gehalt der aeroben und anaeroben Bakterien weiter bis zum 3. LT und stagnierte bis zum 16. LT. Während dieser Stagnationsphase trat bei 92 % der Fohlen (23/25) eine Veränderung der Kotkonsistenz bis hin zu Durchfällen auf. Vom 16. bis zum 58. LT sanken die Gehalte moderat bei den Aerobiern median am 58. LT auf 2,7 x 105 KbE/g (Placebo-Gruppe) bis 2,2 x 106 KbE/g (50 mg Toyocerin-Gruppe) und bei den Anaerobiern median am 58. LT auf 3,8 x 105 KbE/g (Placebo-Gruppe) bis 2,9 x 106 KbE/g (200 mg Toyocerin-Gruppe). Bis zum 58. LT näherte sich der Medianwert der aeroben und anaeroben Bakterien im Kot der Placebo-Gruppe dem Wert der Mutterstuten (gemessen am ersten Tag nach der Geburt) an. Innerhalb der ersten Lebenstage war eine hohe aerobe sowie anaerobe Keimzahl im Kot der Fohlen nachzuweisen, die sich oberhalb der Keimzahlen befand, die im Kot der Mutterstuten zum Zeitpunkt der Geburt gemessen wurde. Im Rahmen der Entwicklung und Etablierung der bakteriellen intestinalen Mikroflora wurde das Fohlenrossedurchfallgeschehen bei den Fohlen beobachtet. B. cereus var. toyoi hatte dabei keinen Einfluss auf die Anzahl der Fohlen mit Durchfall und den Gesundheitsstatus der Fohlen. / Diarrhoea is probably one of the most common problems in equine neonates. Almost all foals develop transient diarrhoea within the first weeks of life. Different viral, bacterial and parasitic causes are discussed. Between the 5th and the 15th day of the foal’s life, when their dam’s first post partum (p.p.) oestrus is expected, diarrhoea in foals is observed quite often. That is why it’s called “foal heat diarrhoea”. In literature establishment of intestinal microflora and maturation of the intestinal mucosa is responsible for the occurrence of diarrhoea in this period of life. But little is known about the development of the intestinal microflora in foals. Many probiotics are authorised as gut flora stabilisers in animal nutrition. Some studies proved positive effects of Bacillus (B.) cereus var. toyoi (Toyocerin®) on intestinal health in other species e.g. calves, piglets, broiler chicken, poultry and growing rabbits. The present study deals with the question if a supplementation of B. cereus var. toyoi lead to a stabilisation of the developing intestinal microflora and therefore to a reduction of diarrhoea in foals. A total of 25 mares and foals of a thoroughbred stud were included into the study. Foals were born between February and May 2011. From birth, the foals were randomly assigned to three treatment groups: placebo group (10 ml isotonic saline solution, n=8), 50 mg Toyocerin group (5 x 108 cfu B. cereus var. toyoi solved in 10 ml isotonic saline solution, n=7) and 200 mg Toyocerin group (2 x 109 cfu B. cereus var. toyoi solved in 10 ml isotonic saline solution, n=10). Placebo- and treatment groups were orally supplemented once a day starting on the 1st through to the 58th day of life. Determination of heart and respiratory rate, body temperature, body weight was realised according to a standardised protocol. Within the first day of life, on day 9, 16, 23, 30, 44, 58 and on the first day of diarrhoea faecal samples has been taken from the rectum or by the use of a collection bag. Blood samples were taken via jugular venipuncture on day 1, 9, 16, 30, 58 and on the first day of diarrhoea. Culture-depend methods were used to analyse the bacterial microflora. Serum IgG was analysed by a competitive ELISA, IgG-anti-LPS from E. coli J5 and IgG-anti-PLC-from-C. perfringens-1a by an indirect ELISA. 88 % of the foals developed diarrhoea (placebo 7/8, 50 mg Toyocerin 5/7, 200 mg Toyocerin 10/10) with a high incidence between the 8th and the 16th day of the foal’s life. Meanwhile, foals remained bright and alert and continued to nurse. At the time point of the first p.p. oestrus in the mares, 59 % of their foals showed signs of diarrhoea. Within the remaining 41 % there are foals that had no diarrhoea but there are also foals which had diarrhoea when the mare had not been in heat. Neonatal diarrhoea in foals is not linked to p.p. oestrus in their mares. There was a tendency, that high serum-IgG (> 20 mg/ml) and IgG-anti-LPS from E. coli J5 (> 120 RE/ml) after colostrum uptake were associated with lower diarrhoea severity in the first 58 days of the foal’s life. C. perfringens and enterobacteria can be found equally in foals with diarrhoea and in foals which are not afflicted. B. cereus var. toyoi supplementation had no effect on faecal bacteria in foals, except on aerobic bacteria (p=0,012). In the first milk faeces aerobic bacteria were detected in median from 4,5 x 104 cfu/g (200 mg Toyocerin-group) to 5,0 x 105 cfu/g (50 mg Toyocerin-group) and anaerobic bacteria were detected in median from 2,4 x 105 cfu/g (200 mg Toyocerin-group) to 4,7 x 106 cfu/g (50 mg Toyocerin-group). Afterwards the counts increased towards the 3rd day of life and stayed on a high level till the 16th day of life. During this stagnation in 92 % of the foals a change in faecal consistency and diarrhoea was observed. Afterwards, from the 16th though to the 58th day of life, the bacteria counts in the faeces moderately decreased in median for the aerobic bacteria on the 58th day of life down to 3,8 x 105 cfu/g (placebo-group) till 2,9 x 106 cfu/g (200 mg Toyocerin-group). On the 58th day of life the counts of aerobic and anaerobic bacteria in the faeces of the placebo-group approached the counts in the faeces of the mare (measured at the time point of birth). In the first days of foals’ life detection of aerobic and anaerobic bacteria in the faeces were high, and above the level of the bacteria counts in the faeces of the mare at the time point of birth. Foal heat diarrhoea is observed as a part of the development and establishment of bacterial intestinal microflora. B. cereus var. toyoi had no effect on the percentage of foals with diarrhoea and health status in the foals at that point.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2015-12-15T18:11:14Z No. of bitstreams: 1 PedroEtelvinoDeGoesNeto_DISSERT.pdf: 761420 bytes, checksum: 21159a91fec1afc40804e76ee1ca9c94 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2015-12-30T17:48:01Z (GMT) No. of bitstreams: 1 PedroEtelvinoDeGoesNeto_DISSERT.pdf: 761420 bytes, checksum: 21159a91fec1afc40804e76ee1ca9c94 (MD5) / Made available in DSpace on 2015-12-30T17:48:01Z (GMT). No. of bitstreams: 1 PedroEtelvinoDeGoesNeto_DISSERT.pdf: 761420 bytes, checksum: 21159a91fec1afc40804e76ee1ca9c94 (MD5) Previous issue date: 2014-02-28 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / O objetivo do presente trabalho foi avaliar o efeito da utiliza??o de cact?ceas nativas e ex?ticas ao n?vel de 50% na MS de inclus?o na dieta total, sobre o consumo de nutrientes, ingest?o de ?gua, produ??o e composi??o f?sico-qu?mica do leite, com cabras em lacta??o. Foram utilizadas 5 cabras Saanen plur?paras (50?4 kg) alocadas em quadrado latino de acordo com cact?ceas fornecidas nas dietas, constando de cinco per?odos de 17 dias, sendo 10 dias de adapta??o e 7 para coleta de dados, cinco tratamentos com as seguintes cact?ceas: xiquexique, mandacaru, facheiro, palma mi?da e palma orelha de elefante mexicana. O consumo de mat?ria seca variou de 1.967,58 a 2.602,46 (g/dia) entre as cact?ceas e teve uma m?dia de 2.251,84 (g/dia). Observou-se que o consumo de mat?ria seca CMS (g/kg0,75) variou de 102,75 ? 136,78 entre as cact?ceas estudadas. O consumo de mat?ria seca (%PV) variou de 3,84 ? 5,11 com m?dia de 4,47. A produ??o de leite em (g/dia) variou de 1.692,60 a 2.090,40. O consumo de ?gua oferecida variou entre 4.549g (xiquexique) a 8.749 (palma mi?da). As cabras alimentadas com palma mi?da apresentaram-se com as maiores produ??es de leite (g/dia) com valores m?dio de 2.091. N?o houve diferen?a na composi??o f?sico-qu?mica do leite estando os teores de gordura, prote?na bruta, lactose e s?lidos totais a cima do m?nimo permitido pela legisla??o para leite de cabra no Brasil. A utiliza??o de cact?ceas ao n?vel de 50% MS na inclus?o da dieta total proporcionou consumo de nutrientes suficientes para atender as exig?ncias dos animais para a produ??o de leite sem alterar a sua composi??o f?sico-qu?mica. / The objective of this research was to evaluate the production of dairy goats fed different species of cactus. Pluriparous five Saanen goats were used, with nine weeks of lactation, and average live weight of 50 kg ? 4 kg. The animals were distributed in latin square design (5x5) with 5 diets and 5 periods. No differences (P>0,05) were observed in the DM of the experimental diets by getting average values of 2.251,84 g dia-1 , 4,46 %PV e 118,91g kg0,75 . The DM contents of the diets were 50,55 to 55,92% by presenting a maximum variation of 10% between them. A significant difference (P<0,05) water consumption way tendered, between diets with different cactus species. The treatments cactus ?Orelha de Elefante Mexicana? and Facheiro had lower water consumption compared to cactus ?Palma Mi?da. For milk yield no significant difference (P> 0,05) between diets formulated with cactus species, with an average of 1,90 kg/day treatments. The analysis of variance show a significant difference (P<0,05) among treatments for milk corrected to 4% fat and fat production. There was an effect (P<0,05) of the diets with different cactus on the crude protein (CP) and lactose in milk. All treatments with different cactus species can be used for dairy goats in view consumption have afforded sufficient to meet the nutritional requirements for milk nutrients, besides presenting the higher than levels of physical and chemical composition to minimum levels established by current legislation

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-21T09:27:02Z (GMT). No. of bitstreams: 1 Araujo_FranciscaDianadaSilva_D.pdf: 5387746 bytes, checksum: ae8110c020cf470d09fb0e22f670508f (MD5) Previous issue date: 2012 / Resumo: Aspectos distintos da ecologia química de bactéria, fungo e abelha foram investigados e abordados em três capítulos. O primeiro capítulo descreve o estudo das moléculas sinalizadoras envolvidas no processo de quorum-sensing da bactéria Enterobacter sakazakii (Cronobacter spp.), que resultou na identificação de três acil-homosserina lactonas (acil-HSLs): (S)-(-)-N-heptanoil-HSL, (S)-(-)-N-dodecanoil-HSL e (S)-(-)-N-tetradecanoil-HSL. Estes semioquímicos foram degradados por enzimas de Bacillus cereus. No segundo capítulo o estudo do fungo Epicoccum nigrum possibilitou o isolamento de meleína, 4,5-dimetil-resorcinol, flavipina e de um novo metabólito, denominado epicolactona. O monitoramento destas substâncias em três mutantes de E. nigrum apontou para a produção de 5-hidroxi-meleína, ausente no fungo selvagem, indicando que a rota biossintética de policetídeos em E. nigrum foi alterada, ativando a ação de uma mono-oxigenase responsável pela oxidação da meleína. No terceiro capítulo, foram investigados feromônios produzidos por diferentes castas da abelha social Tetragonisca angustula. Bioensaios com as rainhas indicaram que lipídios cuticulares são possíveis responsáveis pela indução da cópula nos machos. Operárias fundadoras e guardas foram diferenciadas quimicamente por compostos presentes em seus extratos cefálicos e abdominais. Extratos cefálicos de machos em diferentes ciclos de vida mostraram-se semelhantes / Abstract: Different aspects of bacteria, fungus and bee chemical ecology were investigated and discussed in three chapters. First chapter describes the study of signaling molecules involved in the Enterobacter sakazakii (Cronobacter spp.) quorum sensing process that resulted in the identification of three acyl-homoserine lactones (acyl-HSLs): (S)-(-)-N-heptanoyl-HSL, (S)-(-)-N-dodecanoyl-HSL and (S)-(-)-N-tetradecanoyl-HSL. These semiochemicals were modified by Bacillus cereus enzymes. Second chapter describes the study of Epicoccum nigrum (fungus) revealing the isolation of mellein, 4,5-dimethylresorcinol, flavipin and of a novel metabolite, named epicolactone. Monitoring these compounds in three E. nigrum mutants pointed to the production of 5-hydroxymellein, absent in wild fungus strain, indicating that biosynthetic route of polyketides in E. nigrum has been modified, activating a monooxygenase responsible for mellein oxidation. Third chapter describes pheromones produced by different castes of Tetragonisca angustula social bee. Bioassays with queens indicated that cuticular lipids might be responsible for copulation induction in males. Cephalic and abdominal extracts of founded and guard workers were chemically different, while cephalic extracts of males at different life cycles were similar / Doutorado / Quimica Organica / Doutora em Ciências