Microarray experiments are used to perform gene expression profiling on a large scale. E- and A-optimality of mixed designs was established for experiments with up to 26 different varieties and with the restriction that the number of arrays available is equal to the number of varieties. Because the IBD setting only allows for a single blocking factor (arrays), the search for optimal designs was extended to the Row-Column Design (RCD) setting with blocking factors dye (row) and array (column). Relative efficiencies of these designs were further compared under analysis of variance (ANOVA) models. We also compared the performance of classification analysis for the interwoven loop and the replicated reference designs under four scenarios. The replicated reference design was favored when gene-specific sample variation was large, but the interwoven loop design was preferred for large variation among biological replicates. We applied mixed model methodology to detection and estimation of gene differential expression. For identification of differential gene expression, we favor contrasts which include both variety main effects and variety by gene interactions. In terms of t-statistics for these contrasts, we examined the equivalence between the one- and two-step analyses under both fixed and mixed effects models. We analytically established conditions for equivalence under fixed and mixed models. We investigated the difference of approximation with the two-step analysis in situations where equivalence does not hold. The significant difference between the one- and two-step mixed effects model was further illustrated through Monte Carlo simulation and three case studies. We implemented the one-step analysis for mixed models with the ASREML software. / Ph. D.

Among sheep producers, the parasitic nematode Haemonchus contortus is a major animal health concern. Caribbean hair sheep are more resistant than conventional wool breeds to this blood-feeding, abomasal parasite. Our objective was to determine differences in the immune response associated with parasite-resistant hair and susceptible wool lambs infected with 10,000 H. contortus and in uninfected controls. Animals were sacrificed and abomasum and lymph node tissues were collected at 3 or 27 days post-infection (PI), and for controls on day 17, 27, or 38 relative to d 0 of infected animals. Blood and fecal samples were collected throughout the study. Lower fecal egg counts, higher packed cell volumes, and heavier lymph nodes of infected hair compared to wool lambs, suggests hair lambs have increased parasite resistance. Greater tissue infiltration of eosinophils (P < 0.05) was observed in hair compared to wool sheep by 3 days PI, with no breed differences in globule leukocytes. Total serum IgA and IgE were greater in control hair versus wool sheep (P < 0.05). After 3, 5, and 21 of infection, total serum IgA (P< 0.05), total lymph node IgE (P < 0.01), but not total serum IgE were greater in hair sheep compared to wool sheep. Gene expression was measured between hair and wool lambs for abomasal and lymph node tissues using bovine cDNA microarrays and real-time RT-PCR. Microarray analysis revealed cell survival, endosome function, gut motility, and anti-coagulation pathways are important in abomasal and lymph node tissues during H. contortus infection. Immune genes, including IL-4, IL-4 Ra, IL-12 Rb1, and IL-12 Rb2, are also highly represented in abomasal or lymph node tissue of infected animals. Eleven genes were evaluated using real-time RT-PCR and included TH1 and TH2 cytokines, cytokine receptors, and IgE. Parasite infection leads to increased expression of IL-13 and IgE in both tissues and breeds when compared to control animals. Breed comparison of gene expression shows resistant hair sheep produce a stronger modified TH2-type immune response during infection. Differential cell infiltration, antibody production, and regulation of TH2 cytokines between breeds may be partially responsible for differences in parasite resistance. / Ph. D.

The widespread use of high-throughput experimental assays designed to measure the entire complement of a cells genes or gene products has led to vast stores of data which are extremely plentiful in terms of the number of items they can measure in a single sample, yet often sparse in the number of samples per experiment due to their high cost. This often leads to datasets where the number of treatment levels or time points sampled is limited, or where there are very small numbers of technical and/or biological replicates. If the goal is to use this data to infer network models, these sparse datasets can lead to under-determined systems. While model parameter variation and its effects on model robustness has been well studied, most of this work has looked exclusively at accounting for variation only from measurement error. In contrast, little work has been done to isolate and quantify the amount of parameter variation caused by the uncertainty in the unmeasured regions of time course experiments. Here we introduce a novel algorithm to quantify the uncertainty in the unmeasured inter- vals between biological measurements taken across a set of quantitative treatments. The algorithm provides a probabilistic distribution of possible gene expression values within un- measured intervals, based on a plausible biological constraint. We show how quantification of this uncertainty can be used to guide researchers in further data collection by identifying which samples would likely add the most information to the system under study. We also present an application of this method to isolate and quantify two distinct sources of model parameter variation. In the concluding chapter we discuss another source of uncertainty in systems biology, namely gene function prediction, and compare several algorithms designed for that purpose. / Ph. D.

Energy balance includes energy intake and energy expenditure. Either excessive food intake or insufficient physical activity will increase the body mass and cause obesity, a worldwide health problem. In the US, more than two-thirds of people are obesity or overweight. Conversely, it is well accepted that reducing energy intake can increase the life span and the resistance to age-related diseases. MicroRNAs are highly conserved non-coding RNA molecules with a length of 21-23 nucleotides. Recent studies show that numerous microRNAs are associated with the regulation of oxidative stress, inflammation, insulin signaling, apoptosis, and angiogenesis that relate to obesity. However, the role of microRNAs in the regulation of energy balance in central nervous system remains unknown, especially within the hypothalamus, a primary site of energy balance control. In this project, microRNA, and mRNA were profiled using microarray technology. Furthermore, quantitative proteomics were used to identify differential protein levels during fasting, and in a genetically obese mouse model, Mice were given either a 24-hour fast, or ad libitum access to food. Hypothalamic RNA and microRNA samples were analyzed by microarray, using both the Affymetrix and Toray 3D mRNA and microRNA platforms. No microRNAs were found to be differentially expressed between two treatments, whereas numerous mRNAs were significantly regulated by fasting, including 7 cell cycle related genes. Hypothalamic protein samples from WT and N2KO mice treated either to ad lib feeding or 24-hour fasting were analyzed by MSE quantitative proteomics. Over 650 proteins were identified with some proteins showing significantly different abundances between or among the four groups. Between ad lib fed WT and N2KO mice, 53 proteins were differentially expressed, with some of these linked to neurodegeneration, NAD synthesis, and the citrate acid cycle (TCA). Overall, the results of this study suggest that while microRNA-mediated mechanisms are not significant modulators of hypothalamic gene expression upon a 24 hour fast, cell cycle gene expression changes represent a major contributor to the fasting response. Moreover, Nlhl2 might play an important role in the neurodegeneration and mitochondrial metabolism. / Ph. D.

The parasitic angiosperm Orobanche aegyptiaca (Pers.) (Egyptian broomrape) is a root holoparasite that causes severe losses in yield and quality of many crops. Control of Orobanche is extremely challenging, in part because the parasite is hidden underground for most of its life cycle. However, the dependence of the parasite on the host suggests that broomrape-resistant hosts could be an ideal control method. Genetic engineering strategies may facilitate realization of this goal, but require an understanding of host defense responses to parasitism. Previous studies with tobacco indicated that broomrape parasitism induces host genes associated with jasmonic acid (JA)-mediated defenses such as wound responses and localized production of phenylpropanoid and isoprenoid phytoalexins. However, the gene for the pathogenesis-related (PR) protein, PR-1a, was not induced by parasitism in tobacco. Expression of PR-1a is correlated with the salicylic acid (SA)-mediated defense pathway that leads to systemic acquired resistance (SAR). The objective of this research was to extend the characterization of PR gene expression in order to define the scope of host defense response. Analyses of gene expression using RNA hybridization and RT-PCR in broomrape-parasitized Arabidopsis thaliana roots indicated that PR-1, PR-2, PR-5, as well as the JA-associated PDF1.2, were slightly induced by parasitism. Expression of PR-1, PR-5, and PDF1.2 in parasitized roots was not detectable by RNA hybridization analysis, but was demonstrated by RT-PCR. Interestingly, shoots of the parasitized plants showed greater PR gene expression levels than roots, indicating that O. aegyptiaca induced a response in the host that was systemic and amplified in shoots. Microarray analysis of parasitized Arabidopsis roots demonstrated a broad range of host gene expression changes including both defense- and non-defense-related genes. Genes induced were consistent with O. aegyptiaca preferentially stimulating JA-mediated responses. The failure of O. aegyptiaca to elicit SA-mediated defenses in host roots suggested that exogenous induction of this signaling pathway could enhance host resistance to parasitism. Treatment of O. aegyptiaca-inoculated tobacco with BTH, a SA analog that activates SAR, caused a 49% reduction in O. aegyptiaca numbers. Analysis of PR-1a using RNA hybridizations and protein immunoblots in treated plants showed the expected induction in shoots, but not in roots, confirming the organ-specific differences in defense response observed in Arabidopsis. Experiments using a strategy to engineer the hypersensitive response via the gene-for-gene interaction confirmed previous findings that parasite-specific activation of an R/Avr interaction in tobacco reduced parasitism by approximately 50%. This research suggests that approaches to stimulate SAR in susceptible host plants may be useful for reducing Orobanche parasitism / Master of Science

In the past decade it has become increasingly clear that a biological response is rarely caused by a single gene or protein. Rather, it is a result of a myriad of biological factors, constituting a systematic network of biological variables that span multiple granularities of biology from gene transcription to cell metabolism. Therefore it has become a significant challenge in the field of bioinformatics to integrate different levels of biology and to think of biological problems from a network perspective. In my thesis, I will discuss three projects that address this challenge. First, I will introduce two novel methods that integrate quantitative and qualitative biological data in a network approach. My aim in chapters two and three is to combine high-throughput data with biological databases to identify the causal mechanisms of action (MoA), in the form of canonical biological pathways, underlying the data for a given phenotype. In the second chapter, I will introduce an algorithm called Latent Pathway Identification Analysis (LPIA). This algorithm looks for statistically significant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. In chapter three, I will introduce a new method that focuses on the identification of perturbed pathways from high-throughput gene expression data, which we approach as a task in statistical modeling and inference. We develop a two-level statistical model, where (i) the first level captures the relationship between high-throughput gene expression and biological pathways, and (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation. In the fourth chapter, I will focus on the integration of high throughput data on two distinct levels of biology to elucidate associations and causal relationships amongst genotype, gene expression and glycemic traits relevant to Type 2 Diabetes. I use the Framingham heart study as well as its extension, the SABRe initiative, to identify genes whose expression may be causally linked to fasting glucose.

Orientia tsutsugamushi, l'agent pathogène responsable du typhus des broussailles, est une bactérie cytosolique qui envahit l'endothélium et les monocytes/macrophages. La réponse immune à l'infection par O. tsutsugamushi reste à ce jour mal connue. L'objectif de cette thèse est de mieux comprendre la réponse des cellules de la réponse immune innée humaine à O. tsutsugamushi. Nous avons montré que O. tsutsugamushi se réplique dans les monocytes humains. En utilisant un microarray portant sur la totalité du génome, nous avons également montré que les bactéries vivantes induisent de profondes modifications du profil transcriptionnel des monocytes. C'est ainsi que l'expression des gènes codant l'interféron de type I et des gènes stimulés par l'interféron est fortement augmentée. Les monocytes infectés expriment plusieurs gènes codant des cytokines et des chimiokines inflammatoires, ce qui montre qu'ils sont polarisés vers un phénotype M1 (classically-activated phenotype). Les bactéries vivantes induisent également la sécrétion de l'interleukine-1&#946; et probablement l'activation des inflammasomes et de la caspase-1. O. tsutsugamushi affecte enfin l'expression des gènes associés à l'apoptose et induit la mort d'une partie des monocytes infectés. Nous avons en outre étudié le profil transcriptionnel de patients atteints d'un typhus des broussailles et avons trouvé une signature spécifique incluant la modulation de gènes de type M1 et de gènes stimulés par l'interféron. Nous avons finalement étudié la réponse des macrophages humains dérivés des monocytes à O. tsutsugamushi. / Orientia tsutsugamushi, the causative pathogen of scrub typhus, is a cytosolic bacterium that invades endothelium and monocytes/macrophages. So far, the knowledge of immune response to O. tsutsugamushi is still limited. The objective of this thesis is to better understand the response of human innate immune cells against this pathogen. We demonstrated that O. tsutsugamushi was able to replicate in human monocytes. Using whole genome microarrays, we showed that live O. tsutsugamushi induced robust changes in the transcriptional profiles of monocytes. First, type I interferons and interferon-stimulated genes were remarkably up-regulated. Second, infected monocytes expressed several inflammatory cytokine and chemokine genes, and were polarized toward the classically-activated M1 phenotype. Third, live bacteria induced interleukin-1&#946; secretion and likely inflammasome and caspase-1 activation. We also showed that O. tsutsugamushi altered the expression of apoptosis-related genes and induced cell death in monocytes. We extended our work to the study of the transcriptional profiles of patients with scrub typhus and found a specific signature in patients that included the modulation of M1-associated genes and interferon-stimulated genes. We finally studied the response of human monocyte-derived macrophages to O. tsutsugamushi. The transcriptional and functional responses of macrophages to O. tsutsugamushi were roughly similar to those observed in circulating monocytes including type I IFN response, pro-inflammatory cytokine gene expression and IL-1&#946; secretion.

Estudos epidemiológicos estabelecem uma associação evidente entre poluição do ar e o aumento de morbimortalidade cardiovascular e respiratória. No entanto, os mecanismos moleculares subjacentes aos efeitos do material particulado fino (MP2,5) sobre o organismo ainda estão pouco esclarecidos. O objetivo deste trabalho foi caracterizar o impacto da exposição ao MP2,5 sobre a biologia do endotélio pulmonar e do coração, através da avaliação do perfil de expressão gênica por microarray. Camundongos adultos fêmeas foram anestesiados e submetidos à instilação intratraqueal de MP2,5 (grupo exposto) ou veículo (grupo controle). Os animais foram sacrificados 12 a 18 horas após a instilação e pulmão, coração e sangue da veia cava inferior foram coletados. Os pulmões foram dissociados com colagenase tipo I e células endoteliais foram positivamente selecionadas por captura imuno-magnética através de micro-ímãs acoplados a anti-CD31. O cRNA derivado de endotélio pulmonar e de coração total foi hibridizado em membrana de microarray de baixa densidade desenhada para representar genes relevantes à biologia endotelial. Os genes encontrados diferencialmente expressos no pulmão foram Itgb1, Cxcl1, Tnf, Ecgf1 e Tnfaip3 (hiper-expressos em expostos a MP2,5) e Enpep, Pdgfra, Gzmb, Birc2, Npr1, Angpt1, Cxcl5 e Il7 (hipo-expressos). Não foi possível realizar análise de inferência estatística de membranas do coração neste trabalho. Não houve diferença estatisticamente significativa entre os grupos exposto e controle na contagem sangüínea de neutrófilos, linfócitos ou plaquetas, apesar dos dois grupos apresentarem plaquetose. Os achados indicam que MP2,5 altera a transcrição de genes envolvidos não só na inflamação e estresse oxidativo, mas também no tônus e remodelamento vascular, que podem ser os responsáveis pelos efeitos cardiovasculares agudos do MP2,5 / Epidemiological studies establish a clear association between air pollution and increased cardiovascular and respiratory morbidity and mortality. However, the molecular mechanisms underlying the effect of fine particulate matter (PM2,5) are still poorly understood. The aim of this study was to characterize the impact of exposure to PM2,5 on the biology of pulmonary endothelium and the heart, through the assessment of gene expression profiling by microarray. Adult female mice were anesthetized and submitted to intratracheal instillation of either PM2,5 (challenged group) or vehicle (control group). The animals were sacrificed 12 to 18 hours after instillation and lung, heart and blood samples from the inferior vena cava were collected. The lungs were dissociated with collagenase type I and endothelial cells were positively selected by immuno-magnetic capture through microbeads coupled to anti-CD31. The cRNA derived from the pulmonary endothelial cells and heart were hybridized to low-density microarray designed specifically to represent genes relevant to endothelial biology. Genes found differentially expressed in the lung were Itgb1, Cxcl1, Tnf, Ecgf1, and Tnfaip3 (over-expressed in challenged group) and Enpep, Pdgfra, Gzmb, Birc2, Npr1, Angpt1, Cxcl5 and IL7 (under-expressed). It was not possible to perform statistical inference of heart samples in this study. There was no statistically significant difference between challenged and control groups in blood counts of neutrophils, lymphocytes or platelets, despite both groups presented increased number of platelets. The findings indicate that PM2,5 alters transcription of genes involved not only in inflammation and oxidative stress, but also in vascular tonus and remodeling, which may be responsible for the acute cardiovascular effects of PM2,5

O carbaril (metilcarbamato de naftila), um inseticida de amplo espectro, foi recentemente associado ao desenvolvimento de melanoma cutâneo em estudo epidemiológico de coorte com trabalhadores agrícolas norte-americanos, expostos também à radiação solar, o principal fator etiológico para o desenvolvimento de tumores cutâneos. Apesar de abrangente e bem planejado, aquele estudo epidemiológico não é suficiente para caracterizar a contribuição direta do inseticida e da radiação solar na melanomagênese. Diversos estudos têm explorado o efeito sinérgico de determinadas substâncias químicas à radiação UV, potencializando seus efeitos deletérios sobre a pele, e possivelmente contribuindo para o desenvolvimento de tumores. A hipótese deste trabalho é de que a exposição ao carbaril associada à radiação solar possa estimular a transformação de melanócitos. Esse estudo visou caracterizar melanócitos humanos após exposição individual ou combinada ao carbaril (100uM) e à radiação solar (375 mJ/ cm2). Em ensaio de microarray, o carbaril, mas não a radiação solar, induziu uma importante resposta a estresse oxidativo, evidenciada pelo aumento da expressão de genes antioxidantes, como o Hemeoxigenase-1 (HMOX1), e pela diminuição da expressão do gene MiTF, regulador da atividade melanocítica; os resultados foram confirmados por qRT-PCR. Além disso, tanto o carbaril quanto a radiação solar induziram respostas que sugerem dano ao DNA e alteração de ciclo celular. A expressão dos genes nestas categorias, como p21 e BRCA1/2, foi notavelmente mais intensa no grupo de tratamento combinado e de fato, ensaios por citometria de fluxo demonstraram parada de ciclo celular na fase S, redução do número de células em apoptose e indução mais rápida de lesões do tipo CPD neste grupo experimental. Nossos dados sugerem que o carbaril é genotóxico para melanócitos humanos, especialmente quando associado à radiação solar / Carbaryl (1-naphthyl-methylcarbamate), a broad spectrum insecticide, has recently been associated with the development of cutaneous melanoma in an epidemiological cohort study with U.S. farm workers also exposed to ultraviolet radiation, which is known to be the main etiologic factor for skin carcinogenesis. Although comprehensive and well designed, the epidemiological study is not sufficient to characterize the direct contribution of the insecticide and solar radiation in melanomagenesis. Several studies have explored the synergistic effect of certain chemicals with UV radiation, increasing its deleterious effects on the skin, possibly contributing to tumor development. We hypothesized that Carbaryl exposure associated with UV solar radiation may induce melanocyte transformation. This study aims to characterize human melanocytes after individual or combined exposure to Carbaryl (100uM) and solar radiation (375 mJ/ cm2). In a microarray analysis, Carbaryl, but not solar radiation, induced an important oxidative stress response, evidenced by the upregulation of antioxidant genes, such as Hemeoxygenase-1 (HMOX1), and downregulation of MiTF, the main regulator of melanocytic activity; results were confirmed by qRT-PCR. Moreover, both Carbaryl and solar UV induced a gene response that suggests DNA damage and cell cycle alteration. The expression of genes in these categories, such as p21 and BRCA1/2, was notably more intense in the combined treatment group in an additive manner and in fact, flow cytometry assays demonstrated cell cycle arrest in S phase, reduced apoptosis induction and faster induction of CPD lesions in this experimental group. Our data suggests that carbaryl is genotoxic to human melanocytes, especially when associated with solar radiation

A busca por melhores resultados nas biotecnologias reprodutivas leva a um estudo dos mecanismos fisiológicos básicos dos gametas e embriões em estágios iniciais. Entender como funciona o desenvolvimento destes, quais os nutrientes que eles precisam para se desenvolver in vitro e quais as condições ambientais necessárias permitem maiores taxas de sucesso. Tendo em vista a heterogeneidade dos complexos cumulus-oócito (COC) bovinos recuperados de ovários obtidos em frigorífico para a maturação in vitro e a relação entre oócito e células do cumulus nos resultados da produção in vitro de embriões, esse trabalho visa a identificação de fatores moleculares que possam explicar as melhores taxas de blastocistos obtidas por COCs com mais de três camadas de células do cumulus compactas e ooplasma homogêneo (COCI) quando comparados com COCs com menos de duas camadas de células do cumulus, com parte da zona pelúcida exposta e ooplasma homogêneo ou heterogêneo (COCIII). Para isso, COCI e III foram maturados in vitro separadamente, foram vortexados para retirada das células do cumulus e os oócitos foram submetidos a extração de RNA. O RNA foi amplificado em aRNA, marcado com biotina, fragmentado e hibridizado em microarray. Os arrays foram escaneados e os dados gerados analisados pelo métodos Significance Analysis of Microarrays e Rank Products em busca de genes diferencialmente expressos (DEG). A análise funcional in silico foi realizada com a ferramenta Ingenuity Pathway Analysis. Os resultados mostraram que o perfil de expressão dos oócitos de COCIII é diferente do perfil dos oócitos de COCI, como pode ser observado pelos 446 DEGs identificados, sendo 24 com expressão aumentada em oócitos de COCIII. Os genes com expressão alterada estão envolvidos em processos básicos da célula, como reassumição da meiose, metabolismo do oócito e maturação molecular, o que corrobora a ideia de que uma grande quantidade de células do cumulus interagindo com o oócito é crucial para a competência de desenvolvimento. / The researches for better results in reproductive biotechnologies have leading to studies of the basic physiological mechanisms of gametes and embryos in the early stages of developmental. Understand about their development, which nutrients they need and what environmental conditions are necessary to allow higher success rates. Because of the cumulus-oocyte complexes (COC) heterogeneous recovered from bovine ovaries obtained from an abattoir used for in vitro maturation and the relationship between oocyte and cumulus cells in the in vitro production of embryos, this study aims to identify molecular factors which might explain the improved rates of blastocyst obtained by COCs with more than three compact layers of cumulus cells and homogeneous ooplasm (COCI) compared with COC with less than two layers of cumulus cells, with part of the zona pellucida exposed and homogeneous or heterogeneous ooplasm (COCIII). For this, COCI and III were matured in vitro separately, their cumulus cells were removed and oocytes were subjected to RNA extraction. The RNA was amplified in aRNA, biotin labeled, fragmented and hybridized on microarray. The arrays were scanned and the data generated analyzed by the Significance Analysis of Microarrays and Rank Products methods in search of differentially expressed genes (DEG). In silico functional analysis were performed using Ingenuity Pathway Analysis. The results showed that the expression profile of COCIII oocytes is different from the profile of COCI oocytes. 446 DEGs were identified of which 24 presented increased expression in COCIII oocytes. Genes with altered expression are, in general, involved in the basic processes of the cell, as reassume of meiosis, metabolism of the oocyte and molecular maturation, which confirms the idea that a large amount of cumulus cells interacting with the oocyte is crucial for the development of competence.