Quantitative resistance is controlled by multiple genes and has been shown to be a durable form of resistance to pathogens affecting cultivated crops including soybeans (Glycine max L. Merr). Root rot of soybean caused by Phytophthora sojae ranks among the most damaging soybean diseases. Quantitative resistance has proven durable in soybean against P. sojae, however the molecular mechanisms underlying this form of resistance are still unknown. The objective of this project is to gain insight into molecular basis of quantitative resistance in the soybean-P. sojae pathosystem. The approach was to use global transcriptional profiling based on microarray technology to identify genes that were differentially expressed in four cultivars of soybeans with varying levels of quantitative resistance at different time points during infection by P. sojae. Our results provide a better understanding of the potential regulatory factors that may contribute to quantitative resistance during early hours of P. sojae infection. / Ph. D.

Embryonic stem (ES) cell pluripotency is sustained by a network of transcription factors centred on Oct4, Sox2 and Nanog. Whilst Oct4 and Sox2 expression is relatively uniform, ES cells fluctuate between states of high Nanog expression possessing high self-renewal efficiency, and low Nanog expression exhibiting increased differentiation propensity. Moreover, modulation in the level of Nanog expression determines the efficiency of ES cell self-renewal. To identify genes regulated by Nanog, genome-wide transcriptional profiling was performed on ES cells expressing different Nanog levels and Nanog-null ES cells expressing a Nanog-ERT2 fusion protein in which nuclear Nanog activity can be regulated by tamoxifen. Surprisingly, only a minor fraction of the genes to which Nanog binds showed significant changes in response to Nanog induction. Prominent amongst Nanog-responsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding and pause-release of RNAPolII from the Esrrb promoter and stimulates Esrrb transcription. Consistent with these findings, elevation of Nanog produces a cell population that expresses uniformly high Esrrb levels. Moreover, double fluorescent reporter lines show that Esrrb and Nanog levels are strongly correlated in individual cells. Loss of Nanog is required for downregulation of Esrrb, which coincides with commitment to differentiate. Esrrb overexpression results in LIF independent self-renewal, and blocks neural differentiation, even in the absence of Nanog. Cell fusion experiments between ES and neural stem (NS) cells show that elevated Esrrb levels allow the reprogramming of the NS cell genome in the absence of Nanog. Esrrb can rescue stalled reprogramming during the derivation of Nanog-/- induced pluripotent stem (iPS) cells. Moreover, targeted knock-in of Esrrb at the Nanog locus rescues the ability of Nanog null ES cells to maintain germ cell development beyond E12. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent selfrenewal to ES cells. Together these data identify Esrrb as a critical downstream mediator of Nanog function.

Chromatin structure is a fundamental determinant of eukaryotic gene expression and it is composed of two chromatin environments, euchromatin and heterochromatin. Euchromatin provides an accessible platform for transcription factors; hence it is permissive for gene expression. Heterochromatin on the other hand is highly compacted and inaccessible, which in most cases leads to transcriptional repression. A locus that is composed of both of these environments is the ribosomal DNA (rDNA). In eukaryotes the rDNA is composed of hundreds to thousands of tandemly repeated genes where maintaining both silent and active copies is fundamental for the stability of the genome. The aim of this research was to investigate the role of the rDNA in gene expression in Drosophila melanogaster. In D. melanogaster the rDNA loci are present on the X and Y chromosomes. This research used the Y-linked rDNA array to investigate the role of this locus on gene expression. A genetic and molecular strategy was designed to create and quantify specific, graded and isogenic Y- linked rDNA deletions. Then the deletions were used to address the effect of rDNA deletions on gene expression using reporter genes sensitive to Position Effect Variegation (PEV). In addition, the effect of the deletions in nucleolus size and structure as well as the effect of spontaneous rDNA deletions on gene expression were tested in this study. This research found that changes in rDNA size change the chromatin balance, which resulted in increased expression of the reporter genes, decreased nucleolus volume, and altered nucleolus structure. These findings prompted a further research question on whether this effect on gene expression occured globally in the genome. This was addressed by performing microarray analysis where the results showed that rDNA deletions affect about half of the genes on the genome. Presented in this dissertation is evidence that suggest a novel role for the rDNA is a global modulator of gene expression and also is a contributor to the gene expression variance observed in natural populations.

The PhD thesis is focused on a transcriptomics-based comparison of barley cultivars differing with respect to their low temperature acclimation capacity, with a particular focus on genes transcribed in the leaf and crown. The crown was of interest because of its importance for the winter survival of the plant. To involve both the first and the second phase of hardening, the test plants were exposed first to +3řC for 21 days, followed by - 3řC for one day. Freezing damage was assessed by measuring electrolyte leakage (Papers 2 and 3), using a modified version of a protocol developed by Prášil and Zámečník (1998). The same protocol was adapted to evaluate crown regrowth (Paper 2); for this purpose, the plants were cooled, then replanted and cut above the crown, and their survival rate calculated over the following week. Each RNA sample was queried by hybridization to an Affymetrix 22 K Barley1 GeneChip Genome Array (Close et al. 2004). The data were statistically analysed with the help of the software packages R, MAS 5.0 (Ihaka & Gentleman 1996) (Papers 2 and 3), Gene Spring GX 7.3 (Agilent Technologies, Santa Clara CA) and MapMan (Thimm et al. 2004; Usadel et al. 2005) (Paper 2), the "Self-Organizing Maps" algorithm (Kohonen et al. 1996) (Paper 3) and MIPS FunCat (Ruepp et al. 2004) (Paper 2). Paper...

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Le virus de l’immunodéficience humaine de type 1 (VIH-1) altère les fonctions du système immunitaire pour promouvoir sa persistance. Les composantes de l’immunité ciblées par le VIH-1 incluent les lymphocytes Th17 et les cellules dendritiques dérivées des monocytes (CDDMs). Deux sous-populations de lymphocytes Th17, nommées Th17 et Th1Th17, ont précédemment été décrites avec des propriétés transcriptionnelles et des spécificités antigéniques distinctes. Les cellules Th17 et Th1Th17 sont hautement permissives à l’infection par le VIH et leur fréquence est diminuée chez les sujets chroniquement infectés sous trithérapie antirétrovirale. Toutefois, seulement une fraction des lymphocytes Th17 est infectée par le VIH, indiquant l’existence de Th17 résistants à la réplication virale. Également, il est connu que l’infection à VIH induit une altération de la fréquence des monocytes reflétée par l’expansion de la population monocytaire exprimant le récepteur Fcγ de type III/CD16. Les monocytes sont des précurseurs de cellules dendritiques et une altération de ratio entre les monocytes CD16+ et CD16- pourrait avoir des conséquences délétères sur la qualité des réponses immunitaires. Le rôle fonctionnel des CDDM exprimant ou non CD16 dans le contexte de la pathogénèse à VIH-1 demeure inconnu. Ce projet de thèse est divisé en 2 parties: 1) l’étude de l’hétérogénéité des cellules Th17 et 2) la caractérisation approfondie des CDDM CD16+ et CD16- dans le contexte d’homéostasie et de la pathogénèse de l’infection à VIH. Dans la première partie, nous avons fonctionnellement caractérisé deux nouvelles sous-populations de lymphocytes Th17 avec une expression différentielle des récepteurs de chimiokines CXCR3 et CCR4 : nommés CCR6+DN et CCR6+DP, exprimant toutes les deux CCR6, marqueur de lymphocytes Th17. Nous avons démontré que les cellules CCR6+DN et CCR6+DP partagent des caractéristiques biologiques communes avec les cellules Th17 et Th1Th17 incluant la permissivité au VIH. Nos résultats indiquent que les cellules CCR6+DN représentent un stade précoce de différentiation des lymphocytes Th17 et expriment des marqueurs de cellules T folliculaires. De plus, comparativement aux sous-populations Th17, Th1Th17 et CCR6+DP, la fréquence et le compte des CCR6+DN sont préservés au sein des sujets chroniquement infectés sous thérapie antirétrovirale. Nous proposons un modèle dans lequel les cellules CCR6+DN représentent des lymphocytes Th17 résistantes à l’effet cytopatique du virus qui contribuent à la persistance virale par leur capacité de porter un virus compétent en matière de réplication. Dans la deuxième partie, nos résultats révèlent que les CDDMs CD16+ et CD16- représentent deux populations uniques avec des propriétés transcriptionelles et fonctionnelles distinctes. Les CDDMs CD16- détiennent un potentiel immunogène supérieur tandis que les CDDMs CD16+ ont une meilleure capacité de transmettre le virus aux cellules T CD4+ au repos. Également, nous confirmons l’effet néfaste du VIH sur les fonctions immunologiques des cellules DC à stimuler la prolifération et la polarisation des cellules Th17 spécifiques à C. albicans et à S. aureus. En conclusion, les résultats inclus dans cette thèse fournissent une compréhension détaillée sur l’hétérogénéité présente au sein des lymphocytes Th17 et des CDDMs et révèlent de nouveaux déterminants moléculaires de l’immunité exploités par le VIH au profit de sa persistance. / The ultimate aim of immunity is to restrict the emergence of exogenous pathogens while providing immune tolerance to self-antigens. The human immunodeficiency virus type 1 (HIV-1) disrupts the functions of the immune system to promote its own dissemination and persistence. The components of the host immunity targeted by HIV-1 include the Th17 lineage and the monocytes. The Th17 lineage was previously reported to include two different populations referred to as the Th17 and Th1Th17 cells exhibiting different transcriptional profiles and antigenic specificities. Both Th17 and Th1Th17 cells are permissive to HIV and their frequency is reduced in the blood and gut mucosa of chronically HIV-infected subjects. Nevertheless, HIV-1 infects only a fraction of the Th17 pool, suggesting the existence of Th17 cells resistant to HIV. In addition, it well documented that HIV-1 infection alters the pool of peripheral blood monocytes and induces the expansion of a monocytic population expressing the Fcγ receptor III/CD16. Monocytes are precursors for dendritic cells (DCs) and an altered CD16+/CD16- monocyte ratio may have deleterious consequences on the quality of immune responses. The functional features of CD16+ versus CD16- monocyte-derived DCs (MDDCs) in the context of HIV infection remain to be elucidated. This thesis is divided in two parts: 1) the study of Th17 cell heterogeneity and 2) the in depth characterization of CD16+ and CD16- monocytes-derived DCs (MDDCs) at homeostasis and during HIV-1 infection. In the first part, we have identified and functionally characterized two new previously uncharacterized subsets of CCR6+ T-cells with differential expression of CXCR3 and CCR4, double negative CCR4-CXCR3- (CCR6+DN) and double positive CCR4+CXCR3+ (CCR6+DP) subsets. We demonstrated CCR6+DN and CCR6+DP share cytokine production, antigenic specificity, lineage plasticity and HIV permissiveness with the previously characterized Th17 (CCR6+CCR4+CXCR3-) and Th1Th17 (CCR6+CCR4-CXCR3+) subsets. Among these four Th17 subsets, CCR6+DN cells were found to represent an early stage of Th17 differentiation and expressed features of T follicular helper T-cells. Moreover, in contrast to Th17, Th1Th17 and CCR6+DP subsets, the frequency and counts of CCR6+DN cells was preserved in chronically HIV-infected subjects under antiretroviral treatments compared to uninfected controls. Our results suggest that CCR6+DN represent long-lived Th17 cells contributing to HIV persistence by carrying replication-competent virus. In the second part, our results reveal that CD16+ and CD16- MDDCs represent two distinct populations with unique transcriptional programs and immunological functions. CD16- MDDCs displayed a superior immunogenic potential, whereas CD16+ MDDCs exhibited a higher capacity to induce HIV replication in resting CD4+ T-cells. Also, we confirmed the negative effect of HIV on DCs immunogenic function involving the stimulation of T-cell proliferation and Th17 polarization in response to pathogens such as C. albicans and S. aureus. Overall, in this thesis we provide a better understanding on Th17 and MDDC heterogeneity and reveal new molecular determinants of pathogenicity in immune cells that are exploited by HIV-1 to insure its persistence in the infected host.

Lors du développement, la coordination d’évènements moléculaires et cellulaires mène à la production du cortex qui orchestre les fonctions sensori-motrices et cognitives. Son développement s’effectue par étapes : les cellules gliales radiaires (RGs) – les cellules souches neurales (NSCs) du cerveau en développement – et les cellules progénitrices de la zone ventriculaire (VZ) et de la zone sous ventriculaire (SVZ) génèrent séquentiellement des vagues distinctes de nouveaux neurones qui formeront les différentes couches corticales. Autour de la naissance, les RGs changent de devenir et produisent des cellules gliales. Cependant, une fraction persiste tout au long de la vie dans la SVZ qui borde le ventricule, perdant au passage leur morphologie radiale. Ces NSCs produisent ensuite les différents sous types d’interneurones du bulbe olfactif ainsi que des cellules gliales en fonction de leur origine spatiale dans la SVZ. Ces observations soulèvent d’importantes questions non résolues sur 1) le codage transcriptionnel régulant la régionalisation de la SVZ, 2) le potentiel des NSCs postnatales dans la réparation cérébrale, et 3) le lignage et les spécificités transcriptionnelles entre les NSCs et leur descendants. Mon travail de doctorat repose sur une étude transcriptionnelle des domaines de la SVZ postnatale. Celle-ci soulignait le fort degré d’hétérogénéité des NSCs et progéniteurs et identifiait des régulateurs transcriptionnels clés soutenant la régionalisation. J’ai développé des approches bio-informatiques pour explorer ces données et connecter l’expression de facteurs de transcription (TFs) avec la genèse régionale de lignages neuraux distincts. J’ai ensuite développé un modèle d’ablation ciblée pour étudier le potentiel régénératif des progéniteurs postnataux dans divers contextes. Finalement, j’ai participé au développement d’une procédure pour explorer et comparer des progéniteurs pré et postnataux à l’échelle de la cellule unique. Objectif 1 : Des expériences de transcriptomique et de cartographie ont été réalisées pour étudier la relation entre l’expression régionale de TFs par les NSCs et l’acquisition de leur devenir. Nos résultats suggèrent un engagement précoce des NSCs à produire des types cellulaires définis selon leur localisation spatiale dans la SVZ et identifient HOPX comme un marqueur d’une sous population biaisé à générer des astrocytes. Objectif 2 : J’ai mis au point un modèle de lésion corticale qui permet l’ablation ciblée de neurones de couches corticales définies pour étudier la capacité régénérative et la spécification appropriée des progéniteurs postnataux. Une analyse quantitative des régions adjacentes, incluant la région dorsale de la SVZ, a révélé une réponse transitoire de progéniteurs définis. Objectif 3 : Nous avons développé la lignée de souris transgénique Neurog2CreERT2Ai14, qui permet le marquage de cohortes de progéniteurs glutamatergiques et de leurs descendants. Nous avons montré qu’une large fraction de ces progéniteurs persiste dans le cerveau postnatal après la fermeture de neurogénèse corticale. Ils ne s’accumulent pas pendant le développement embryonnaire mais sont produits par des RGs qui persistent après la naissance dans la SVZ et qui continuent de générer des neurones corticaux, bien que l’efficacité soit faible. Le séquençage d’ARN sur cellule unique a révélé une dérégulation transcriptionnelle qui corrèle avec le déclin progressif observé in vivo de la neurogénèse corticale. Ensemble, ces résultats soulignent le potentiel des études transcriptomiques à résoudre mais aussi à soulever des questions fondamentales comme les changements trancriptionnels intervenant dans une population de progéniteurs au cours du temps et participant aux changements de leur destinée. Cette connaissance sera la clé du développement d’approches novatrices pour recruter et promouvoir la génération de types cellulaires spécifiques, incluant les sous-types neuronaux dans un contexte pathologique. / During development, a remarkable coordination of molecular and cellular events leads to the generation of the cortex, which orchestrates most sensorimotor and cognitive functions. Cortex development occurs in a stepwise manner: radial glia cells (RGs) - the neural stem cells (NSCs) of the developing brain - and progenitor cells from the ventricular zone (VZ) and the subventricular zone (SVZ) sequentially give rise to distinct waves of nascent neurons that form cortical layers in an inside-out manner. Around birth, RGs switch fate to produce glial cells. A fraction of neurogenic RGs that lose their radial morphology however persists throughout postnatal life in the subventricular zone that lines the lateral ventricles. These NSCs give rise to different subtypes of olfactory bulb interneurons and glial cells, according to their spatial origin and location within the postnatal SVZ. These observations raise important unresolved questions on 1) the transcriptional coding of postnatal SVZ regionalization, 2) the potential of postnatal NSCs for cellular regeneration and forebrain repair, and 3) the lineage relationship and transcriptional specificities of postnatal NSCs and of their progenies. My PhD work built upon a previously published comparative transcriptional study of defined microdomains of the postnatal SVZ. This study highlighted a high degree of transcriptional heterogeneity within NSCs and progenitors and revealed transcriptional regulators as major hallmarks sustaining postnatal SVZ regionalization. I developed bioinformatics approaches to explore these datasets further and relate expression of defined transcription factors (TFs) to the regional generation of distinct neural lineages. I then developed a model of targeted ablation that can be used to investigate the regenerative potential of postnatal progenitors in various contexts. Finally, I participated to the development of a pipeline for exploring and comparing select populations of pre- and postnatal progenitors at the single cell level. Objective 1: Transcriptomic as well as fate mapping were used to investigate the relationship between regional expression of TFs by NSCs and their acquisition of distinct neural lineage fates. Our results supported an early priming of NSCs to produce defined cell types depending of their spatial location in the SVZ and identified HOPX as a marker of a subpopulation biased to generate astrocytes. Objective 2: I established a cortical lesion model, which allowed the targeted ablation of neurons of defined cortical layers to investigate the regenerative capacity and appropriate specification of postnatal cortical progenitors. Quantitative assessment of surrounding brain regions, including the dorsal SVZ, revealed a transient response of defined progenitor populations. Objective 3: We developed a transgenic mouse line, i.e. Neurog2CreERT2Ai14, which allowed the conditional labeling of birth-dated cohorts of glutamatergic progenitors and their progeny. We used fate-mapping approaches to show that a large fraction of Glu progenitors persist in the postnatal forebrain after closure of the cortical neurogenesis period. Postnatal Glu progenitors do not accumulate during embryonal development but are produced by embryonal RGs that persist after birth in the dorsal SVZ and continue to give rise to cortical neurons, although with low efficiency. Single-cell RNA sequencing revealed a dysregulation of transcriptional programs, which correlates with the gradual decline in cortical neurogenesis observed in vivo. Altogether, these data highlight the potential of transcriptomic studies to unravel but also to approach fundamental questions such as transcriptional changes occurring in a population of progenitors over time and participating to changes in their fate potential. This knowledge will be key in developing innovative approaches to recruit and promote the generation of selected cell types, including neuronal subtypes in pathologies.

The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.