La fièvre Q se traduit par de graves conséquences obstétricales chez la femme enceinte. La voie principale de la contamination humaine par Coxiella burnetii, l’agent de la fièvre Q, est constituée des aérosols provenant des placentas d’animaux infectés. La nature des cellules placentaires cibles de C. burnetii reste totalement inconnue. J’ai montré que C. burnetii infecte les trophoblastes des lignées BeWo et JEG et que les bactéries se répliquent fortement dans les cellules BeWo et survivent dans les cellules JEG. Une analyse par microarray montre que C. burnetii induit une réponse inflammatoire dans les cellules BeWo qui lui est spécifique. Ces résultats suggèrent que les trophoblastes pourraient constituer une niche pour C. burnetii. Les macrophages placentaires pourraient également servir de réservoir pour C. burnetii. J’ai montré que les macrophages placentaires CD14+ sont des macrophages qui présentent des caractéristiques phénotypiques, transcriptionnelles et fonctionnelles différentes de celles des monocytes circulants et des macrophages dérivés de monocytes. Ils forment en outre des cellules géantes multinucléées qui pourraient réguler l’activité cytolytique des macrophages dans le contexte placentaire puisque les macrophages placentaires CD14+ ne sont ni de type M1 ni de type M2. / In pregnant women Q fever presents obstetrical complications. The principal way of human contamination by Coxiella burnetii, the agent of Q fever, is due to aerosols from placentas of infected animals. The nature of placenta cells that are targeted by C. burnetii remains unknown. I showed that C. burnetii infects BeWo and JEG trophoblastic cells and that organisms intensively replicated in BeWo cells and survived in JEG cells. A microarray analysis showed that C. burnetii induced a specific inflammatory response in BeWo cells. These results suggest that trophoblasts may serve as a reservoir for C. burnetii. Placenta macrophages placentaires may also targeted by C. burnetii. I showed that placenta CD14+ macrophages were characterized by phenotypic, transcriptional and functional properties different from those of circulating monocytes and monocyte-derived macrophages. In addition, placenta CD14+ macrophages differentiate into multinucleated giant cells that may regulate the cytolytic activity of macrophages in the placenta context since placenta CD14+ macrophages were not polarized in M1 or M2 macrophages. While M1/M2 polarization of macrophages is well established, that of monocytes remains an important question. We activated monocytes with canonical agonists of M1 and M2 profiles in macrophages using microarrays. The early response, 6 hours, of monocytes corresponded to a type M1/M2 response but the delayed response, 18 hours, did not correspond to the M1/M2 dichotomy, demonstrating a new level of heterogeneity of myeloid cells.

Análise de expressão gênica em larga escala é de fundamental importância para a biologia molecular atual pois possibilita a medida dos níveis de expressão de milhares de genes simultaneamente, o que torna viável a realização de trabalhos voltados para biologia de sistemas (systems biology). Dentre as principais técnicas experimentais disponíveis para esta finalidade, a tecnologia de microarray tem sido amplamente utilizada. Este procedimento para medida de expressão gênica é bastante complexo e os dados obtidos são freqüentemente observacionais, o que dificulta a modelagem estatística. Não existe um protocolo padrão para a geração e avaliação desses dados, sendo portanto necessário buscar procedimentos de análise que sejam adequados para cada caso. Assim, os principais métodos matemáticos e estatísticos aplicados para a análise desses dados deveriam estar disponíveis de uma forma organizada, coerente e simples em um ambiente computacional que confira robustez, confiabilidade e reprodutibilidade às análises realizadas. Uma forma de garantir estas características é através da representação (e documentação) de todos os algoritmos utilizados na forma de um grafo direcionado e acíclico que descreva todo o conjunto de transformações, ou operações, aplicadas seqüencialmente ao conjunto de dados. De acordo com esta filosofia, um ambiente foi implementado neste trabalho incorporando diversos procedimentos disponíveis na literatura atual, além de outros que foram aprimorados ou propostos nesta tese. Dentre os métodos de análise já disponíveis que foram incorporados destacam-se aqueles para a construção de agrupamentos, busca de genes diferencialmente expressos e classificadores, construção de redes de relevância e classificação funcional de grupos gênicos. Além disso, o método de construção de redes de relevância foi revisto e aprimorado e um modelo estatístico para a classificação funcional de redes de regulação gênica foi proposto e implementado. Esses dois últimos métodos surgiram a partir de problemas biológicos para os quais não existiam procedimentos de análise adequados na literatura. Finalmente, são apresentados dois conjuntos de dados que foram analisados utilizando diversas ferramentas disponíveis neste ambiente computacional. / High throughput gene expression analysis has a great importance to molecular biology nowadays because it can measure expression profiles for hundreds of genes, and this turn possible studies focused in systems biology. Between the main experimental techniques available in this direction, the microarray technology has been widely used. This experimental procedure to quantify gene expression profiles is very complex and the data obtained is frequently observational, what difficult the statistical modelling. There is not a standard protocol for the generation and evaluation of microarray data, therefore it is necessary to search by adequate analysis methods for each case. Thus, the main mathematical and statistical methods applied to microarray data analysis would have to be available in an organized, coherent and simple way in a computational environment that confer robustness, reliability and reproducibility to the data analysis. One way to guarantee these characteristics is through the representation (and documentation) of all used algorithms as a directed and acyclic graph that describes the set of transformations, or operations, applied sequentially to the dataset. According to this philosophy, an environment was implemented in this work aggregating several data analysis procedures already available in the literature, beyond other methods that were improved or proposed in this thesis. Between the procedures already available that were incorporated we can distinguish that ones for cluster analysis, differentially expressed genes and classifiers search, construction of relevance networks and functional classification of gene groups. Moreover, the method for construction of relevance networks was revised and improved and an statistical model was proposed and implemented for the functional classification of gene regulation networks. The last two procedures was born from biological problems for which adequate data analysis methods didn?t exist in the literature. Finally, we presented two datasets that were evaluated using several data analysis procedures available in this computational environment.

O controle de Listeria monocytogenes (Lm) nas plantas processadoras de alimentos é uma tarefa difícil, devido à sua capacidade em formar biofilmes e se adaptar às condições adversas do ambiente. A sobrevivência a altas concentrações de cloreto de sódio, além da multiplicação em temperaturas de refrigeração são outras duas importantes características de isolados de Lm, incluindo os dois sorotipos mais prevalentes da espécie (4b e 1/2a). Os objetivos deste estudo foram avaliar o comportamento de multiplicação, da expressão gênica global e da virulência dos dois principais sorotipos de Lm em ambientes de estresse encontrados por esses micro-organismos na indústria de alimentos. Para tanto, 22 cepas de Lm - 12 isoladas de casos clínicos (seis cepas sorotipo 4b e seis sorotipo 1/2a) e 10 isoladas de alimentos (seis sorotipo 4b e quatro sorotipo 1/2a) - além de uma cepa de Listeria monocytogenes Scott A e outra de Listeria innocua, foram inoculadas em caldo BHI com atividade de água (aw) 0,94 (11% NaCl) e incubadas a 4°C, 10°C e 25°C durante 73, 42 e 15 dias, respectivamente. A 4°C, a maior parte das cepas, tanto clínicas como de origem alimentar, conseguiu se manter viável ou ainda se multiplicar e aumentar até 2 log UFC/ml a partir da população inicial. Já a 10°C, a maioria das cepas conseguiu se multiplicar, porém diferenças significativas (p < 0,05) na duração da fase lag entre as cepas dos sorotipos 1/2a e 4b, independentemente da origem das mesmas, foram observadas (lag1/2a > lag4b). Diferenças estatísticas também foram observadas no que diz respeito às cepas de Lm sorotipo 4b, quando incubadas a 25°C em meio de cultura BHI com aw 0,94, apresentando maiores taxa de multiplicação e concentração populacional máxima (p < 0,05) em comparação às cepas de Lm sorotipo 1/2a submetidas às mesmas condições. Já com relação ao potencial de virulência das cepas, não foram detectadas diferenças estatísticas entre os sorotipos com relação a sua capacidade hemolítica, entretanto, a capacidade de invasão das cepas sorotipo 4b em células Caco-2 foi maior (p < 0,05) em comparação ao sorotipo 1/2a. Além disso, análises comparativas pré e pós-estresse osmótico confirmaram o aumento no potencial de invasão (p < 0,05) tanto das cepas sorotipo 1/2a, quanto 4b após o contato com elevadas concentrações de sal. O papel dos reguladores de transcrição Sigma B e PrfA na sobrevivência de Listeria monocytogenes, sob condição de estresse osmótico, também foi avaliado. Ensaios de microarray com cepas das linhagens I e II demonstraram maiores níveis de transcrição para 173 e 68 genes, respectivamente, na cepa selvagem quando comparada à cepa mutante &#916sigB, incluindo genes relacionados à virulência (internalinas), sobrevivência a condições de estresse e metabolismo. Os resultados obtidos confirmam a habilidade de cepas de Lm se manterem viáveis ou mesmo se multiplicarem em baixas temperaturas, bem como em ambientes com elevada pressão osmótica, independentemente do sorotipo ou origem, enfatizando a necessidade de tomada de medidas efetivas de controle desse patógeno pela indústria de alimentos uma vez que cepas de Lm podem, além de sobreviver às condições adversas, ter seu potencial de virulência aumentado. Os dados obtidos também indicam a necessidade de mais estudos de avaliação comportamental e viabilidade de Lm em ambientes com concentração de sal modificada, uma vez que a discussão sobre a diminuição nos teores de sal em alimentos vem ganhando importância mundialmente. / The control of Listeria monocytogenes (Lm) in food processing plants is difficult due to its ability to form biofilms and adapt to adverse environmental conditions. The survival at high concentrations of sodium chloride and growing at low temperatures are two other important features of Lm isolates, including the two most prevalent serotypes (1/2a and 4b). The objectives of this study were to evaluate the growing behavior, global gene expression profile and virulence potential of the two main serotypes of Lm under osmotic stress environments encountered by these microorganisms in the food industry. 22 Lm strains - 12 isolated from clinical cases (six strains serotype 4b and six serotype 1/2a) and 10 isolated from food (six serotype 4b and four serotype 1/2a) - plus one L. monocytogenes Scott A and one Listeria innocua were inoculated into BHI broth with water activity (aw) 0.94 (11% NaCl) and were incubated at 4°C, 10°C and 25°C during 73, 42 and 15 days respectively. At 4°C, the majority of strains both clinical and food were able to remain viable and to grow (up to 2 log CFU/ml). At 10°C, most strains could grow but significant differences (p < 0.05) on the lag phase duration between the serotypes 1/2a and 4b strains, regardless their origin, were observed (lag1/2a > lag4b). Statistical differences were also observed related to Lm serotype 4b strains when grown in BHI with aw 0.94 at 25°C, that showed higher maximum growth rate and final density (p < 0.05) compared to Lm serotype 1/2a strains. Regarding the virulence potential, there were no statistical differences among serotypes with respect to its hemolytic activity, however, the invasiveness of serotype 4b strains in Caco-2 cells was higher (p <0.05) than serotype 1/2a. Furthermore, comparative analyzes before and after osmotic stress confirmed the increased potential for invasion (p < 0.05) in both serotypes (1/2a and 4b) after being submitted to high salt concentrations. The role of transcription regulators sigma B and PrfA in L. monocytogenes survival under osmotic stress condition was also evaluated. Microarray assay using lineage I and II strains showed increased transcription levels in 173 and 68 genes, respectively, when comparing the wild type strains to the mutant &#916sigB strain. This included genes related to virulence (internalina), survival under stress conditions and metabolic genes. The results confirm the ability of Lm strains in remain viable or even grow at low temperatures and in high osmotic pressure environments, regardless of serotype or origin. They also emphasize the need for effective measures to control this pathogen by food industry since it is possible that Lm strains survive under adverse conditions and also increase its virulence potential. The data also indicate the need for additional studies regarding the behavior of Lm in environments with modified sodium chloride concentration since the discussion about salt levels in foods is increasing worldwide.

Esta dissertação de mestrado tem como finalidade descrever o trabalho realizado em uma pesquisa que envolve a análise de expressões gênicas provenientes de microarrays com o objetivo de encontrar genes importantes em um organismo ou em uma determinada doença, como o câncer. Acreditamos que a descoberta desses genes, que chamamos aqui de genes de predição intrinsicamente multivariada (genes IMP), possa levar a descobertas de importantes processos biológicos ainda não conhecidos na literatura. A busca por genes IMP foi realizada em conjunto com estudos de modelos e conceitos matemáticos e estatísticos como redes Booleanas, cadeias de Markov, Coeficiente de Determinação (CoD), Classificação em análise de expressões gênicas e métodos de estimação de erro. No modelo de redes Booleanas, introduzido na Biologia por Kauffman, as expressões gênicas são quantizadas em apenas dois níveis: \"ligado\'\' ou \"desligado\'\'. O nível de expressão (estado) de cada gene, está relacionado com o estado de alguns outros genes através de uma função lógica. Adicionando uma perturbação aleatória a este modelo, temos um modelo mais geral conhecido como redes Booleanas com perturbação. O sistema dinâmico representado pela rede é uma cadeia de Markov ergódica e existe então uma distribuição de probabilidade estacionária. Temos a hipótese de que os experimentos de microarray seguem esta distribuição estacionária. O CoD é uma medida normalizada de quanto a expressão de um gene alvo pode ser melhor predita observando-se a expressão de um conjunto de genes preditores. Uma determinada configuração de CoDs caracteriza um gene alvo como sendo um gene IMP. Podemos trabalhar não somente com genes alvo, mas também com fenótipos alvo, onde o fenótipo de um sistema biológico poderia ser representado por uma variável aleatória binária. Por exemplo, podemos estar interessados em saber quais genes estão relacionados ao fenótipo de vida/morte de uma célula. Como a distribuição de probabilidade das amostras de microarray é desconhecida, o estudo dos CoDs é feito através de estimativas. Entre os métodos de estimação de erro estudados para este propósito podemos citar: Holdout, Resubstituição, Cross-validation, Bootstrap e .632 Bootstrap. Os métodos foram implementados para calcular os CoDs, permitindo então a busca por genes IMP. Os programas implementados na pesquisa foram usados em conjunto com uma pesquisa realizada pelo Prof. Dr. Hugo A. Armelin do Instituto de Química da USP. Este estudo em particular envolve a busca de genes importantes relacionados à morte de células tumorigênicas de camundongo disparada por FGF2 (Fibroblast Growth Factor 2). Nesta pesquisa observamos sub-redes de genes envolvidos no processo biológico em questão e também encontramos genes que podem estar relacionados ao fenômeno de morte das células de camundongo ou que estão, de fato, participando de alguma via disparada pelo FGF2. Esta abordagem de análise de expressões gênicas, juntamente com a pesquisa realizada pelo Prof. Armelin, resulta em uma metodologia para buscas de genes envolvidos em novos mecanismos de células tumorigênicas, ativados pelo FGF2. Na realidade esta metodologia pode ser aplicada em qualquer processo biológico de interesse científico, desde que seja possível modelar o problema proposto no contexto de redes Booleanas, coeficientes de determinação e genes IMP. / This Master\'s degree dissertation describes a research that involves an analysis of gene expression data from microarray experiments with the purpose to find important genes in certain organisms or diseases such as cancer. We believe that these type of genes, called intrinsically multivariately predictive genes (IMP genes), can lead to the discovery of important biological process that are unknown in the literature. The search for IMP genes was done with the study of mathematical and statistical models such as Boolean Networks, Markov Chains, Coefficient of Determination (CoD), Classification and Error Estimation Methods. In the Boolean network model, introduced in Biology by Kauffman, the gene expression is quantized in only two levels: ON and OFF. The expression level (state) of each gene is related with the state of some other genes through a logical function. Adding a random perturbation to this model, we have a more general Boolean-type model called Boolean network with perturbation. The dynamical system represented by this network is an ergodic Markov chain and thereby it possesses a steady-state distribution. We have the hypothesis that the microarray experiments follow this steady-state distribution. The CoD is a normalized measure of how much a gene expression of a target gene can be better predicted observing the expression of a set of predictor genes. A certain configuration of CoDs characterizes a target gene as an IMP gene. We can deal not only with target genes, but also with target phenotypes, where the phenotype of a biological system could be represented by a binary random variable. For example, we could be interested in knowing which genes are related to a life/death cell phenotype. Since the joint probability distribution of the gene expressions is unknown, the CoDs must be computed through estimated values. Among the error estimation methods studied we can cite: Holdout, Resubstitution, Cross-validation, Bootstrap and .632 Bootstrap. Those methods were implemented as a software in order to compute the CoDs and thereby allowing us to search for IMP genes. The software we implemented in this research was used within a research developed by Professor Dr. Hugo A. Armelin from the Instituto de Química - University of Sao Paulo. This particular research involves the search for important genes related to the death of tumorigenic mouse cells triggered by FGF2 (Fibroblast Growth Factor 2). From this research cooperation, we built some gene subnetworks involved in the target biological process and we found some genes that could be related to the death phenotype of mouse cells. This approach of gene expression analysis, together with the research developed by Professor Armelin, results in a methodology to search for important genes that could be involved in new mechanisms of tumorigenic cells triggered by FGF2. Actually, this methodology can be applied to any biological process of scientific interest, if one can model the proposed problem in the context of Boolean Networks, Coefficient of Determination and IMP genes.

Modern high-throughput technologies like DNA microarrays are powerful tools that are widely used in biomedical research. They target a variety of genomics applications ranging from gene expression profiling over DNA genotyping to gene regulation studies. However, the recent discovery of false positives among prominent research findings indicates a lack of awareness or understanding of the non-biological factors negatively affecting the accuracy of data produced using these technologies. The aim of this thesis is to study the origins, effects and potential correction methods for selected methodical biases in microarray data. The two-species Langmuir model serves as the basal physicochemical model of microarray hybridization describing the fluorescence signal response of oligonucleotide probes. The so-called hook method allows to estimate essential model parameters and to compute summary parameters characterizing a particular microarray sample. We show that this method can be applied successfully to various types of microarrays which share the same basic mechanism of multiplexed nucleic acid hybridization. Using appropriate modifications of the model we study RNA quality and sequence effects using publicly available data from Affymetrix GeneChip expression arrays. Varying amounts of hybridized RNA result in systematic changes of raw intensity signals and appropriate indicator variables computed from these. Varying RNA quality strongly affects intensity signals of probes which are located at the 3\'' end of transcripts. We develop new methods that help assessing the RNA quality of a particular microarray sample. A new metric for determining RNA quality, the degradation index, is proposed which improves previous RNA quality metrics. Furthermore, we present a method for the correction of the 3\'' intensity bias. These functionalities have been implemented in the freely available program package AffyRNADegradation. We show that microarray probe signals are affected by sequence effects which are studied systematically using positional-dependent nearest-neighbor models. Analysis of the resulting sensitivity profiles reveals that specific sequence patterns such as runs of guanines at the solution end of the probes have a strong impact on the probe signals. The sequence effects differ for different chip- and target-types, probe types and hybridization modes. Theoretical and practical solutions for the correction of the introduced sequence bias are provided. Assessment of RNA quality and sequence biases in a representative ensemble of over 8000 available microarray samples reveals that RNA quality issues are prevalent: about 10% of the samples have critically low RNA quality. Sequence effects exhibit considerable variation within the investigated samples but have limited impact on the most common patterns in the expression space. Variations in RNA quality and quantity in contrast have a significant impact on the obtained expression measurements. These hybridization biases should be considered and controlled in every microarray experiment to ensure reliable results. Application of rigorous quality control and signal correction methods is strongly advised to avoid erroneous findings. Also, incremental refinement of physicochemical models is a promising way to improve signal calibration paralleled with the opportunity to better understand the fundamental processes in microarray hybridization.

No description available.

Shiga Toxin produzierende Escherichia coli (STEC) sind wichtige Erreger von Lebensmittelinfektionen und gelten als Hauptverursacher für die Ausbildung einer hämorrhagischen Colitis und dem lebensbedrohlichen hämolytisch-urämischen Syndrom. Als Hauptvirulenzfaktor und wichtigstes Charakteristikum der STEC wird die Fähigkeit angesehen, Shiga Toxine (Stx) zu produzieren. Die genetische Information für deren Produktion ist im Genom lambdoider Prophagen kodiert. Eine Antibiotikatherapie bei STEC-assoziierten Infektionen wird sehr kontrovers diskutiert, da sowohl die Produktion der Stx als auch die Freisetzung der Bakteriophagen in vitro durch antibiotisch wirkende Substanzen stimuliert werden kann. Der enterohämorrhagische E. coli O157:H7 Stamm EDL933 beherbergt insgesamt 18 lambdoide Prophagen und prophagenähnliche Elemente, darunter den Stx1-kodierenden Phagen CP-933V und den Stx2-kodierenden Phagen BP-933W. Ziel der vorliegenden Arbeit war es, den Einfluss des Gyrasehemmers Norfloxacin auf das Gesamttranskriptom von EDL933 mit Hilfe der DNA-Microarraytechnologie und unter Verwendung des MWG E. coli O157 Arrays umfassend zu untersuchen und insbesondere die Expression der Prophagengene zu analysieren. Hierfür wurde der E. coli O157:H7 Stamm EDL933 mit 200 ng/ml Norfloxacin inkubiert, Gesamt-RNA isoliert und diese mittels reverser Transkription in cDNA synthetisiert, wobei ein Einbau von fluoreszenzmarkierten Nukleotiden erfolgte. Diese cDNA wurde mit den auf dem E. coli O157 Array befindlichen Oligonukleotiden hybridisiert. Die Auswertung der Fluoreszenzintensitäten ermöglicht eine Analyse der Genexpression. Infolge der Induktion von EDL933 mit 200 ng/ml Norfloxacin zeigten 118 Spots eine Hochregulation und 122 eine Deregulation von Genen an. Bei genauerer Betrachtung resultierte auf Grund der Inkubation mit Norfloxacin eine erhöhte Expression von 52 Genen der Stx-kodierenden Phagen CP-933V und BP-933W. Insbesondere erfolgte eine erhöhte Regulation von Genen der späten Region des BP-933W. Das stxA2-Gen wurde dabei im Vergleich zur nicht-induzierten Kultur 158-fach stärker exprimiert. Im Falle des Stx1-Phagen wiesen nur einige Gene der frühen Region eine gesteigerte Genaktivität auf. Auffallend war die Hochregulation einzelner Gene der nicht Stx-kodierenden Phagen. Gene des Primärstoffwechsels, u. a. Gene der Aminosäurebiosynthese, des Energiehaushaltes und der Zellteilung zeigten eine verminderte Genaktivität nach Induktion. Diese Ergebnisse weisen darauf hin, dass die verwendete Konzentration von Norfloxacin große Auswirkungen auf das Gesamttranskriptom des untersuchten Stammes haben und insbesondere die Genexpression von zehn im Genom des EDL933 befindlichen Prophagen erhöht wurde. Die durch die Microarrayversuche erhaltenen Expressionsraten wurden durch Quantifizierung der cDNA mittels RT Real-Time PCR Untersuchungen überprüft. Zusammenfassend ist festzustellen, dass Norfloxacin neben der antibiotischen Wirkung in der hier verwendeten geringen Konzentration multiple Effekte auf E. coli O157:H7 ausübt und die Auswirkungen in Zukunft noch detaillierter untersucht werden müssen. Die DNA-Microarraytechnologie und der kommerziell erhältliche E. coli O157 Array ermöglichen diese umfassenden Analyse des Transkriptionsprofils. Im Rahmen dieser Arbeit konnte diese Technologie für Untersuchungen der Genexpression von E. coli O157 etabliert und validiert werden. / Infection with Shiga toxin producing Escherichia coli (STEC) is a serious cause of bloody diarrhea and sporadic cases and outbreaks of food-related diseases such hemorrhagic colitis and the hemolytic uremic syndrome (HUS) worldwide. The use of antibiotics in therapy of STEC-associated diseases has been discussed controversially. Release of phage-encoded Shiga toxins is the major virulence factor of enterhemorrhagic Escherichia coli (EHEC). The genome of the EHEC strain E. coli O157:H7 EDL933 contains 18 prophages or prophages elements, including the Stx1- and Stx2-encoding phages CP-933V and BP-933W. Stx-production and Stx-prophage induction can be stimulated by certain antibiotics, e.g. mitomycinC or UV light. The aim of this study was to investigate the influence of a low concentration of the gyrase inhibitor norfloxacin on the whole transcriptom of E. coli O157:H7 strain EDL933 and particularly on the gene expression of prophages using the DNA-microarraytechnology and the commercial available MWG E. coli O157 Array. To determine this, E. coli O157:H7 cultures were incubated with 200 ng/ml norfloxacin. Total RNA was isolated and labelled with fluorescence dyes during reverse transcription. Following this, the labelled cDNA was hybridized with the commercial E. coli O157 Arrays and the fluorescence intensities were measured, analysed and evaluated with appropriate software. Results of this study have indicated that a low concentration of norfloxacin have profound effects on the trancriptome of E. coli O157:H7. Under the conditions applied (200 ng/ml norfloxacin) and an incubation time of 120 minutes, 118 spots indicated a transcriptional upregulation and 122 spots a transcriptional downregulation of E. coli O157:H7 genes present on the array. In detail, 85 spots could be ascribed to EDL933 phage genes. Fifty-two of them could be assigned to the Shiga toxin encoding phages CP-933V and BP-933W, the others belonged to the non-Stx encoding phages or prophages elements existing in the EDL933 genome. Conspicuous, genes present in the late region of the BP-933W prophage were induced most strongly, up to 158-fold in the case of stxA2. Only some genes present in the early region of the Stx1 encoding phage CP-933V were induced upon induction with norfloxacin. Notably, only some genes of the non-Stx phages of EDL933 appeared to be induced after induction. The additional upregulated genes were related to recombination and stress functions and to E. coli O157:H7 RIMD0509952 genes. The majority of downregulated genes belonging to primary metabolism, such as amino acid biosynthesis, cell division and energy metabolism. In conclusion, an induction of E. coli O157:H7 strain EDL933 with 200 ng/ml norfloxacin has profound effects on the transcriptome of E. coli O157:H7, in particular on the global gene expression of more then ten prophages. The DNA-microarray technology and especially the E. coli O157 Array offer a modern tool for analysis of transcription profiles of the serious pathogen EHEC O157 in response to stress, e.g. antibiotics. In the context of this work, the DNA-microarraytechnology could be established and validated to provide the opportunity for further studies about the global effects on the whole transcriptome of E. coli O157.

Due to the current rise of exposure to natural and synthetic compounds in our daily life, the debate concerning the safety of many substances is becoming increasingly relevant. The estrogenic activity of various compounds, described as xenoestrogens, is the major part of this debate. Humans beings are exposed to these substances from different environmental contaminations ranging from conscious intake of estrogenic substances, as in contraception or in hormone replace therapy (HRT), to unconscious exposure, from food, the use of synthetic material in daily life and air and water pollution. At this point the need for methods to investigate the activity and the safety of these substances is becoming increasingly important. Classical methods for the analysis of the estrogenic activity of substances, like batteries of in vivo test systems on the rat uterotrophic assay are not able to describe the different pathways of action of recently discovered estrogenic substances. This evidence was already shown by the Organization for Economic Cooperation and Development (OECD), introducing new test guidelines for the investigation of effects of endocrine disruptors (according to enhanced Test Guideline 407). As reviewed by Nilsson (Nilsson et al., 2001), after the interaction of the estrogens with the Estrogen Receptor (ER) in the cells, the mechanism of activation possible is not only via direct binding of the ER to the Estrogen Responsive Elements (EREs) present in the promoter region of the target gene, very well described for many target genes, but that also other mechanisms are used: the interaction of the ER with the AP 1, Sp 1 and NFkB modes, that are discovered but not yet comprehensively described. The aim of my work is to produce a microarray DNA chip for the investigation of the estrogenic activity of different compounds present in the environment. The chip will consist of a selection of 100 genes that are estrogen responsive and it will cover the spectrum of activities of estrogenic compounds in various organs of the body. In the gene selection, genes were chosen that are estrogen responsive in the classical target tissues of estrogens, linked to reproduction, like uterus and mammary gland, and also in tissues not related to reproduction like liver, bones and capillars. In addition, other genes are included to monitor different pathways that are related to disease states; control of cell proliferation, apoptosis or cancer related genes. Currently these kinds of investigations are already in process, but by other methods which are more time consuming and with a lower throughput e.g. the gene expression profiling using the real time RT-PCR. The use of microarray’s satisfies the need for a less time consuming, high throughput method, to obtain a fast characterization of the gene expression finger print of the candidate substances and their mechanism of action in the organism. In my work I investigated the estrogenic potency of different Xenoestrogens that commonly occur in our daily life, in rat cells and tissue using well known estrogen sensitive genes like C3, Clu, IGFBP1 and CaBP9k. I focused on their effect on cell proliferation, studying PCNA expression. For the first time sensitivity of the gene CA2 was proofed in liver and uterus. A new identified mRNA sequence, r52, was characterized for its sensitivity to estrogenic exposure. This sequence was investigated at the molecular level expanding the known nucleic sequence. I produce a microarray chip with 16 genes to investigate the estrogenic potency of different compounds. As proof of principle of the microarray method completely produced in house I compared the result of gene expression obtained by the chip to that obtained by real time RT PCR finding a similarity of results. This new established method is less sensitive than the real-time RT PCR but allows a high throughput of gene expression analysis producing at the end a more complete picture of the expression signature of a compound.

Shiga Toxin produzierende Escherichia coli (STEC) sind wichtige Erreger von Lebensmittelinfektionen und gelten als Hauptverursacher für die Ausbildung einer hämorrhagischen Colitis und dem lebensbedrohlichen hämolytisch-urämischen Syndrom. Als Hauptvirulenzfaktor und wichtigstes Charakteristikum der STEC wird die Fähigkeit angesehen, Shiga Toxine (Stx) zu produzieren. Die genetische Information für deren Produktion ist im Genom lambdoider Prophagen kodiert. Eine Antibiotikatherapie bei STEC-assoziierten Infektionen wird sehr kontrovers diskutiert, da sowohl die Produktion der Stx als auch die Freisetzung der Bakteriophagen in vitro durch antibiotisch wirkende Substanzen stimuliert werden kann. Der enterohämorrhagische E. coli O157:H7 Stamm EDL933 beherbergt insgesamt 18 lambdoide Prophagen und prophagenähnliche Elemente, darunter den Stx1-kodierenden Phagen CP-933V und den Stx2-kodierenden Phagen BP-933W. Ziel der vorliegenden Arbeit war es, den Einfluss des Gyrasehemmers Norfloxacin auf das Gesamttranskriptom von EDL933 mit Hilfe der DNA-Microarraytechnologie und unter Verwendung des MWG E. coli O157 Arrays umfassend zu untersuchen und insbesondere die Expression der Prophagengene zu analysieren. Hierfür wurde der E. coli O157:H7 Stamm EDL933 mit 200 ng/ml Norfloxacin inkubiert, Gesamt-RNA isoliert und diese mittels reverser Transkription in cDNA synthetisiert, wobei ein Einbau von fluoreszenzmarkierten Nukleotiden erfolgte. Diese cDNA wurde mit den auf dem E. coli O157 Array befindlichen Oligonukleotiden hybridisiert. Die Auswertung der Fluoreszenzintensitäten ermöglicht eine Analyse der Genexpression. Infolge der Induktion von EDL933 mit 200 ng/ml Norfloxacin zeigten 118 Spots eine Hochregulation und 122 eine Deregulation von Genen an. Bei genauerer Betrachtung resultierte auf Grund der Inkubation mit Norfloxacin eine erhöhte Expression von 52 Genen der Stx-kodierenden Phagen CP-933V und BP-933W. Insbesondere erfolgte eine erhöhte Regulation von Genen der späten Region des BP-933W. Das stxA2-Gen wurde dabei im Vergleich zur nicht-induzierten Kultur 158-fach stärker exprimiert. Im Falle des Stx1-Phagen wiesen nur einige Gene der frühen Region eine gesteigerte Genaktivität auf. Auffallend war die Hochregulation einzelner Gene der nicht Stx-kodierenden Phagen. Gene des Primärstoffwechsels, u. a. Gene der Aminosäurebiosynthese, des Energiehaushaltes und der Zellteilung zeigten eine verminderte Genaktivität nach Induktion. Diese Ergebnisse weisen darauf hin, dass die verwendete Konzentration von Norfloxacin große Auswirkungen auf das Gesamttranskriptom des untersuchten Stammes haben und insbesondere die Genexpression von zehn im Genom des EDL933 befindlichen Prophagen erhöht wurde. Die durch die Microarrayversuche erhaltenen Expressionsraten wurden durch Quantifizierung der cDNA mittels RT Real-Time PCR Untersuchungen überprüft. Zusammenfassend ist festzustellen, dass Norfloxacin neben der antibiotischen Wirkung in der hier verwendeten geringen Konzentration multiple Effekte auf E. coli O157:H7 ausübt und die Auswirkungen in Zukunft noch detaillierter untersucht werden müssen. Die DNA-Microarraytechnologie und der kommerziell erhältliche E. coli O157 Array ermöglichen diese umfassenden Analyse des Transkriptionsprofils. Im Rahmen dieser Arbeit konnte diese Technologie für Untersuchungen der Genexpression von E. coli O157 etabliert und validiert werden. / Infection with Shiga toxin producing Escherichia coli (STEC) is a serious cause of bloody diarrhea and sporadic cases and outbreaks of food-related diseases such hemorrhagic colitis and the hemolytic uremic syndrome (HUS) worldwide. The use of antibiotics in therapy of STEC-associated diseases has been discussed controversially. Release of phage-encoded Shiga toxins is the major virulence factor of enterhemorrhagic Escherichia coli (EHEC). The genome of the EHEC strain E. coli O157:H7 EDL933 contains 18 prophages or prophages elements, including the Stx1- and Stx2-encoding phages CP-933V and BP-933W. Stx-production and Stx-prophage induction can be stimulated by certain antibiotics, e.g. mitomycinC or UV light. The aim of this study was to investigate the influence of a low concentration of the gyrase inhibitor norfloxacin on the whole transcriptom of E. coli O157:H7 strain EDL933 and particularly on the gene expression of prophages using the DNA-microarraytechnology and the commercial available MWG E. coli O157 Array. To determine this, E. coli O157:H7 cultures were incubated with 200 ng/ml norfloxacin. Total RNA was isolated and labelled with fluorescence dyes during reverse transcription. Following this, the labelled cDNA was hybridized with the commercial E. coli O157 Arrays and the fluorescence intensities were measured, analysed and evaluated with appropriate software. Results of this study have indicated that a low concentration of norfloxacin have profound effects on the trancriptome of E. coli O157:H7. Under the conditions applied (200 ng/ml norfloxacin) and an incubation time of 120 minutes, 118 spots indicated a transcriptional upregulation and 122 spots a transcriptional downregulation of E. coli O157:H7 genes present on the array. In detail, 85 spots could be ascribed to EDL933 phage genes. Fifty-two of them could be assigned to the Shiga toxin encoding phages CP-933V and BP-933W, the others belonged to the non-Stx encoding phages or prophages elements existing in the EDL933 genome. Conspicuous, genes present in the late region of the BP-933W prophage were induced most strongly, up to 158-fold in the case of stxA2. Only some genes present in the early region of the Stx1 encoding phage CP-933V were induced upon induction with norfloxacin. Notably, only some genes of the non-Stx phages of EDL933 appeared to be induced after induction. The additional upregulated genes were related to recombination and stress functions and to E. coli O157:H7 RIMD0509952 genes. The majority of downregulated genes belonging to primary metabolism, such as amino acid biosynthesis, cell division and energy metabolism. In conclusion, an induction of E. coli O157:H7 strain EDL933 with 200 ng/ml norfloxacin has profound effects on the transcriptome of E. coli O157:H7, in particular on the global gene expression of more then ten prophages. The DNA-microarray technology and especially the E. coli O157 Array offer a modern tool for analysis of transcription profiles of the serious pathogen EHEC O157 in response to stress, e.g. antibiotics. In the context of this work, the DNA-microarraytechnology could be established and validated to provide the opportunity for further studies about the global effects on the whole transcriptome of E. coli O157.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Ludek Zurek / Transfer of bacteria, including antibiotic resistant strains between companion animals and people is likely due to close physical contacts. However, surveillance programs on prevalence of antibiotic resistance are focused mainly on food animals and very little is known about the role of companion animals in the development and spread of antibiotic resistant bacteria. For this study, enterococci were chosen as model organism due to intrinsic and acquired antibiotic resistance and several virulence traits that make them the 3rd most important nosocomial pathogens. In addition, increased fecal shedding of antibiotic resistant bacteria from stressed animals has been reported from studies on food animals. To determine whether the gut microbiota of pet animals serves as a reservoir of clinically important enterococci, 360 enterococcal isolates from two groups: healthy group and pyoderma (stressed) group with 9 dogs in each were identified and screened for resistance to 10 antibiotics and 4 virulence traits. The transferability of resistance determinants and clonality of selected isolates were assessed by horizontal gene transfer assays and pulsed-field gel electrophoresis, respectively. In addition, overall diversity of bacteria as well as antibiotic and metal resistance genes in feces of healthy dogs was assessed by tag-encoded parallel pyrosequencing and microarray analysis, respectively. The most prevalent enterococcal species identified was E. faecalis: healthy group (70.5%); pyoderma group (44.0%). In the pyoderma group, antibiotic resistance and virulence traits (esp, gelE) were more frequent than in the healthy group; however, the overall prevalence of antibiotic resistant strains was low (< 37%) in both groups. The most prevalent resistance genes were tet(M)and tet(S). The antibiotic resistance traits were transferable in-vitro in E. faecalis (tetracycline, erythromycin, doxycycline) and E. faecium (tetracycline). Genotyping revealed less diverse E. faecalis community in pyoderma infected dogs. Pyrosequencing (~7,500 sequences per dog) revealed Firmicutes as the dominant phylum and most common genera included Turicibacter, Lactobacillus, Ruminococcus, Clostridium, and Fusobacterium. Two phyla Lentisphaerae (<1%) and Fibrobacteres (<1%) are reported for the first time from healthy dogs. Microarray data revealed the presence of several tetracycline, erythromycin, aminoglycoside, and copper resistance genes; however, most of these originated from one animal with history of chronic skin infection two year prior to our sampling. Higher prevalence of antimicrobial resistance in pyoderma infected dogs may be related to stress; however, this requires further investigation. In conclusion, based on our data, healthy and pyoderma infected dogs do not represent an important reservoir of clinically significant antibiotic resistant microbiota.