Parmi les stratégies visant à contrôler la croissance de microorganismes pathogènes dans un aliment, la biopréservation qui s’appuie sur l’utilisation des capacités inhibitrices d’autres microorganismes offre une grande diversité d’opportunités. Il est cependant nécessaire de comprendre les mécanismes moléculaires et physiologiques régissant l’antagonisme du microorganisme protecteur vis-à-vis de la bactérie indésirable. L’objectif de cette thèse était de caractériser l’antagonisme de L. garvieae N201, isolé de fromage, vis-à-vis de souches de S. aureus par des approches in vitro : génomique, transcriptomique (ciblée concernant S. aureus, globale concernant L. garvieae) et phénotypique. Un acteur avait déjà été identifié : le peroxyde d’hydrogène (H2O2) produit par L. garvieae sous un niveau d’aération élevé. Lors de ces travaux de thèse, il a été montré que le peroxyde d’hydrogène serait également produit par L. garvieae sous une faible aération en quantité faible (indétectable par spectrophotométrie) mais suffisante pour induire une inhibition de S. aureus. Les gènes de production du H2O2 de L. garvieae (poxB, sodA) seraient exprimés constitutivement quel que soit le niveau d’aération. Les gènes de dégradation du H2O2 (katA, sodA, ahpC / ahpF) seraient plutôt surexprimés sous une faible aération, suggérant leur rôle dans un mode de contrôle de la concentration en H2O2 autogène par L. garvieae. En parallèle, trois autres mécanismes potentiellement impliqués dans l’antagonisme ont été mis en évidence : i) la répression de gènes de réponse au stress (clpC, ctsR, dnaK) de S. aureus par L. garvieae et l’aération, ii) la répression de gènes de division cellulaire de S. aureus (mraZ, mraW, potentiellement le cluster dcw) par L. garvieae, iii) la production d’un effecteur extracellulaire par L. garvieae dont la nature reste à caractériser. Ajouté à cela, la présence de L. garvieae modulerait l’expression des principaux gènes de virulence de S. aureus, réprimant ceux codant pour les entérotoxines sous une faible aération. Ainsi, la souche L. garvieae N201 s’est révélée être une candidate intéressante comme agent de biopréservation. Cependant, son innocuité pour l’Homme devra être vérifiée et son antagonisme sur S. aureus devra être évalué en matrice alimentaire. Les données générées ainsi que la démarche développée pourront être utilisées afin d’étudier des interactions entre d’autres espèces d’intérêt et dans des écosystèmes différents. / Among strategies aiming to control the growth of spoilage microorganisms in food, the biopreservation is based on the inhibitory capacities of other microorganisms and presents a considerable variety of opportunities. A good understanding of the molecular and physiologic mechanisms underlying the antagonism of the preservative microorganism against the spoilage bacterium is also required. This thesis aimed to characterize the antagonism of L. garvieae N201 dairy strain against S. aureus strains combining in vitro strategies: genomic, transcriptomic (targeted concerning S. aureus, global concerning L. garvieae) and phenotypic. The involvement of hydrogen peroxide (H2O2) produced by L. garvieae under high aeration was already known. Although H2O2 concentration was undetectable using spectrophotometry method, it was produced by L. garvieae under low aeration at sufficient concentration to induce S. aureus inhibition. L. garvieae H2O2 -synthesis genes (poxB, sodA) seemed constitutively expressed whatever the aeration level. L. garvieae H2O2-degradation (katA, sodA, ahpC / ahpF) genes were overexpressed under low aeration, suggesting their involvement in control of autogenous H2O2 level. In parallel, three other mechanisms may be involved in this antagonistic relationship: i) the repression of S. aureus stress-response genes (clpC, ctsR, dnaK) by L. garvieae and / or under high aeration, ii) the repression of S. aureus cell-division genes (mraZ, mraW and probably the dcw cluster) by L. garvieae, iii), the production by L. garvieae of an extracellular effector which has to be characterized. Additionally, L. garvieae can modulate the expression of S. aureus major virulence genes, repressing those coding for enterotoxins under low aeration. Thus, L. garvieae N201 turned out to be an interesting candidate for biopreservative applications. However, its safety for humans should be approved and its antagonism against S. aureus has to be investigated in food matrices. The data resulting from this work may be used to study other interactions between other valuable species and in other ecosystems.

Depuis leur apparition, les séquenceurs haut débit ont révolutionné l'étude des transcriptomes à l'échelle du génome. En effet, ils offrent la possibilité de générer des millions, voire des milliards de séquences, appelées reads. Des nouvelles approches transcriptomiques, telles que la Digital Gene Expression (DGE) et le RNA-Sequencing (RNA-Seq), permettent aujourd'hui de répertorier, de quantifier, voire reconstruire tous les transcrits d'une cellule, même les plus rares. Parmi ce type de transcrits se trouvent des ARN non-codants régulateurs ; des variants d'épissages créateurs de protéines ; et aussi des chimères (par fusion de gènes ou trans-épissage). La caractérisation de l'ensemble de ces transcrits représente un réel défi algorithmique, mais suscite aussi un défi biologique car certains peuvent être impliqués dans de nombreux processus cellulaires physiologiques et pathologiques et sont fréquemment décrits dans les cancers.Dans ce travail, nous proposons des algorithmes et des méthodes pour la caractérisation et l'annotation des transcriptomes. Tout d'abord, nous proposons une étude statistique sur la DGE afin d'évaluer l'impact des erreurs de séquences lors de l'analyse des reads. À partir de cette analyse, nous avons développé un pipeline d'annotation pour la DGE. Par le biais de ce premier travail, nous avons pu démontrer que de nombreuses informations étaient partagées entre les reads. Cela nous a amené à concevoir la structure d'indexation Gk arrays qui permet d'organiser une quantité massive de reads de façon à pouvoir interroger rapidement la structure sous forme de requêtes. Enfin, en s'appuyant sur les Gk arrays, nous avons développé CRAC qui est un logiciel spécialisé dans le traitement du RNA-Seq. En intégrant sa propre phase de mapping, CRAC est capable de distinguer les phénomènes biologiques des erreurs de séquences. Ilpermet notamment l'identification de chimères qui sont souvent très faiblement exprimées dans un transcriptome et sont par nature complexe à détecter avec des parties localisées à différents endroits sur le génome. / Since their introduction, high-throughput sequencers have revolutionized transcriptomic studies at genome scale. Indeed, they have the ability to generate millions, or even billions of short sequences, called reads. New transcriptomic approaches, such as Digital Gene Expression (DGE) and RNA-sequencing (RNA-Seq), enable the identification, quantification, and reconstitution of all transcripts of the cell, even rare ones. Among these transcripts are regulatory non-coding RNAs, alternative splice variants, which code for novel proteins, but also non colinear transcripts termed chimeras (generated by either gene fusion or trans-splicing). The characterization of these transcripts constitutes a sheer algorithmic,but also a biological challenge due to their differences in nature, their diverse implications in physiological and cellular processes, and for some their role in cancer development.In this work, we focus on algorithms and methods for the characterization and annotation of transcriptomes. First, we proposed a statistical study on DGE to assess the impact of sequence errors on the analysis. Therefrom, we developed a pipeline for the DGE annotation. Through this initial work,we demonstrated that a lot of information is shared between the reads. This property led us to design, the Gk arrays, an indexing data structure for organizing huge amounts of reads in memory and algorithms to quickly query this structure. Finally, based on the Gk arrays we have conceived, CRAC,a software specialised in the RNA-Seq processing. By integrating its own mapping process, CRAC is able to distinguish the biological phenomena from sequence errors. Moreover, it allows to identify chimeric RNAs, which may be weakly expressed in a transcriptome and are inherently complex to detect since their fragments originate from different places on the genome.

The 15q13.3 microdeletion is a common genetic disorder associated with multiple neurodevelopmental disorders including autism spectrum disorder, epilepsy, and schizophrenia. Patients have diverse clinical presentations, often prompting genetic assays that identify the CNV in the clinic. This late-stage screening leaves a considerable gap in our understanding of the prenatal and prediagnostic developmental impairments in these individuals, providing a barrier to understanding the disease pathobiology. We provide the first investigation into embryonic brain development of individuals with the 15q13.3 microdeletion by generating multiple 3D neural organoid models from the largest clinical cohort in reported literature. We incorporated unguided and guided forebrain organoid models into our multi-transcriptomic phenotyping pipeline to uncover changes in cell type emergence and disruptions to circuit development, all of which had underlying changes to cell adhesion pathways. Specifically, we identified accelerated growth trajectories in 15q13.3del unguided neural organoids and used single cell RNA sequencing to identify changes in radial glia dynamics that affect neurogenesis. We measured changes in the pseudotemporal trajectory of matured unguided neural organoids, and later identified disruptions in synaptic signaling modules amongst the primary constituents to neural circuitry, excitatory and inhibitory neurons. We leveraged dorsal and ventral forebrain organoid models to better assess circuit dynamics, as they faithfully produce the excitatory and inhibitory neurons in the pallium and subpallium, respectively. We then used the entire 15q13.3del cohort and performed bulk RNA sequencing on each tissue type at two timepoints and discovered convergence on transcriptional dysregulation and disruptions to human-specific zinc finger proteins localized to chromosome 19. We also identified cell type-specific vulnerabilities to DNA damage and cell migration amongst the dorsal and ventral organoids, respectively, which was consistent with the excitatory and inhibitory neural subpopulations amongst the unguided neural organoids scRNA Seq, respectively. We then examined neuron migration in a 3D assembloid model by sparsely labeling dorsal-ventral forebrain organoids from multiple genotype-lineage combinations. Light sheet microscopy identified deficits in inhibitory neuron migration and morphology, but not migration distance, suggesting a complex disruption to cortical circuitry. This novel combination of cell type characterization, pathway identification, and circuitry phenotyping provides a novel perspective of how the 15q13.3 deletions impair prenatal development and can be applied to other NDD models to leverage understanding of early disease pathogenesis. / Dissertation / Doctor of Science (PhD) / The development of the human brain is a highly complex and tightly regulated process that requires the participation of multiple cell types throughout development. Disturbances to the emergence, differentiation, or placement of these cell types can cause disruptions and local miswiring of neural circuits, which is often associated with neurodevelopmental disorders (NDDs). The 15q13.3 microdeletion syndrome is a highly complex condition associated with multiple NDDs and has seldom been studied in a human context. To address this, we used stem cells derived from a 15q13.3 microdeletion syndrome cohort and their typically developing familial controls to generate unguided (“whole brain”) and region-specific organoids to investigate early fetal development across time. We used the largest 15q13.3 microdeletion cohort in reported literature to identify shared disruptions in early developmental milestones such as neurogenesis, neural migration, and neural patterning. We identified expansion of specific cell populations, including progenitors that later give rise to mature neurons. Abnormalities persisted in more mature cell populations, including the inhibitory neurons responsible for establishing critical microcircuitry in the human cortex. By generating guided organoids that enrich for excitatory and inhibitory neural populations, we were able to merge the models to form assembloids, where we captured early migratory and morphological deficits in inhibitory neuron populations, which is supported by the multi-transcriptomics experiments performed in both organoid models. This study provides a framework for examining fetal development in a neurodevelopmental disorder context. By using the 15q13.3 microdeletion background, we found novel disruptions in cell type emergence and circuit formation previously unreported in mouse or 2D neuron models, highlighting the utility of the phenotyping platform for disease modeling.

Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics. Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper II on generating strand specific RNA-seq libraries. Paper III and IV deal with current biological issues. In paper III, whole exomes of cancer patients undergoing chemotherapy are sequenced and their genetic variants associ- ated to their toxicity induced adverse drug reactions. In paper IV a comprehensive view of the gene expression of the endometrium is assessed from two time points of the menstrual cycle. Together these papers show relevant aspects of contemporary sequencing technologies and how it can be applied to diverse biological topics. / <p>QC 20160329</p>

Il mais è uno dei cereali maggiormente diffusi perché utilizzato in ambito alimentare umano e animale, per la produzione di materiale biodegradabile e di bioetanolo. I processi fisiologici che coordinano la crescita della cariosside vengono regolati principalmente dall’auxina che agisce a livello trascrizionale e post-traduzionale. Attraverso analisi comparative tra il mutante de18 (defective endosperm 18), deficitario nella produzione di acido indolo-3-acetico (IAA), e del suo corrispettivo wild-type, è stato possibile individuare i geni coinvolti nella determinazione delle dimensioni della cariosside. In particolare, sono state effettuate analisi morfologiche e di quantificazione dell’amido su cariossidi de18 e wild type negli stadi precoci di sviluppo. E’ stato inoltre allestito un esperimento di RNA sequencing sull’endosperma dei due genotipi a 8 e 12 DAP (Days After Pollination). L’analisi dei geni differenzialmente espressi attraverso la classificazione GO (Gene Ontology) ha permesso di studiare l’effetto della carenza di auxina sull’espressione genica. Nel mutante si riscontra l’attivazione tardiva della sintesi dell’amido e l’incremento delle proteine di riserva. Inoltre, la carenza di auxina determina una riduzione dell’attività mitotica ed endoreduplicativa, confermata dalla repressione dell’attività di geni legati al ciclo cellulare. / Maize is one of the world’s leading cereal grains due to its diverse functionality as a food source for both humans and animals, as well as a source of raw materials and biofuel. The physiological processes responsible for the growth of the kernel are regulated mainly by auxin acting at the transcriptional and post-translational level. Through comparative analysis between mutant de18 (defective endosperm 18), defective in indol-3-acetic acid (IAA) production, and its wild-type B37, it has been possible to identify the genes involved in the determination of the final seed size. Morphological analysis and quantification of starch were done on seed mutant and wild-type in the early stages of their development. Finally, an RNA sequencing analysis was carried out on mutant and wild-type endosperm at 8 and 12 DAP (Days After Pollination) and differentially expressed genes were classified by Gene Ontology. Down-regulation of genes related to sugar metabolism suggested a delayed activation of starch biosynthesis. This finding was confirmed by the determination of starch content that was lower in the mutant endosperms respect to the normal in the early stages of gran filling (12 and 16 DAP). The reduced auxin level affected the mitotic and endoreduplication activities as suggested by the repression of genes involved in the cell cycle.

In order to study the potential effects of an oil spill on coral reef organisms, the marine sponge, Cinachyrella spp. was investigated. In this study, Cinachyrella spp. was placed in a closed aquaculture system and exposed to sub-lethal water-accommodated fractions (WAFs) of Macondo crude oil and chemically-enhanced water accommodated fractions (CE-WAFs) of the dispersant, Corexit 9500, over a 24-hour time course, in order to model the BP Deepwater Horizon oil spill and oil spill sponge response. Illumina RNA sequencing and gene expression analysis utilizing hierarchical clustering, principal component analysis, and KEGG bioinformatic database generated 34,147 unique transcripts with differential expression of 483 transcripts across all samples related to metabolism, genetic, environmental, and cellular processes, and associations with pathways involved in human disease development and progression. These pathways highlight the induction of Rac1, a GTPase in the Ras superfamily responsible for cell proliferation, differentiation, and senescence and SOS, a set of specialized Ras-GTP activators. These Ras-regulated signaling proteins are thought to play a significant role in the development of human malignancies, specifically Rac1. The data reported here helps support the possible role of Cinachyrella spp. as an ecotoxicological model for oil and dispersant pollution as well as the identification of potential biomarkers of stress and environmental perturbation. These results have important implications in identifying stress response in coral reef associated communities, and will ultimately be useful in coral reef conservation, management, and oil spill mitigation activities.

Canola (Brassica napus) contributes $19.3 billion dollars to the Canadian economy each year as a result of its oil- and protein-rich seeds. These economically important seed products are produced in highest concentration in the embryo. Embryo development is supported nutritionally and structurally by the maternal subregions, which include the inner (ISC) and outer distal seed coat (OSC), the chalazal seed coat (CZSC), and the chalazal proliferating tissue (CPT). Research on the maternal seed subregions is limited to the SC as a result of its accessibility; the embedded CZSC and CPT subregions have yet to be characterized in canola. Using light and transmission electron microscopy, I found the CZSC and CPT to be anatomically distinct and experience profound changes throughout seed development. To understand these changes at the RNA level, laser microdissection and RNA sequencing were used to profile these subregions spatially and temporally from the ovule to mature green stage of seed development. Employing vigorous bioinformatics analyses, I found that the maternal subregions are transcriptomically distinct and possess unique RNA populations. From here I began to elucidate the biological processes operating within the maternal subregions. As a whole, the maternal subregions appear to have a critical role in transporting nutrients to the filial subregions as well as in coping with oxidative stress produced during these energy-rich processes. Additionally, using CanEnrich, I was able to generate predictive transcriptional circuits regulating the biological processes occurring within the maternal seed. This research has produced the most comprehensive dataset on the canola seed to date and will provide a valuable resource for research on seed development as well as seed improvement. / October 2016

No description available.

A teca é uma árvore de grande importância comercial pelas características de cor e durabilidade de sua madeira. Devido a sua rusticidade e fácil adaptação ao clima, plantios de teca tornam-se cada vez mais atrativos ao redor do mundo. Contudo, esta espécie apresenta escassez de estudos genéticos moleculares a respeito tanto de sua madeira, quanto de sua tolerância às variações ambientais. Uma vez que o transcriptoma pode apresentar grande quantidade de informação a respeito dos genes expressos por um conjunto celular, neste trabalho foi realizado o primeiro transcriptoma de teca, onde foram sequenciadas flores, folhas, raízes e seedlings pela tecnologia Illumina. A montagem do transcriptoma foi realizada com o programa Trinity acima de 100 milhões de reads e gerou mais de 400 mil contigs, os quais tiveram as anotações funcionais adquiridas com o programa Blas2GO. 51% dos contigs foram anotados, mostrando alta similaridade com as espécies Vitis vinifera e Solanum licopersicum; destes, 78% obtiveram anotações funcionais com o Gene Ontology, totalizando 5.165 termos para Processo Biológico, 2.846 termos para Função Molecular e 742 para Componente Celular. A expressão diferencial foi obtida com o programa edgeR a 5% de probabilidade de erro e mostrou que, para 187.315 contigs montados através da fusão de todas as bibliotecas sequenciadas, 18 mostraram expressão diferencial para flor, 14 para folha, 13 para raiz e 29 para seedling. Após a etapa de caracterização do transcriptoma, foi realizado um experimento de estresse por déficit hídrico em casa-de-vegetação, onde plantas de teca foram submetidas a estresse Moderado (40% de água no substrato por 20 dias), estresse Severo (20 a 40% de água por 30 dias) e tratamento controle (substrato saturado). As medições através de analisador de gases por infravermelho (IRGA) mostraram queda na fotossíntese (até 70% a menos do que o controle), na transpiração (até 77%) e na condutância estomática (até 85%) entre os tratamentos; além disto, o conteúdo relativo de água foliar caiu 13% entre o tratamento severo e o controle, e níveis de prolina livre foram até 3,5 vezes mais altos nos tratamentos de estresse. A temperatura foliar aumentou significativamente com o aumento da irradiância de fótons aplicada. A busca por genes relacionados ao estresse por déficit hídrico na biblioteca de transcritos de Raiz retornou 1.145 sequências, e destas, 4 foram caracterizadas: TgTPS (trealose 6-fosfato sintase), TgPIP (aquaporina, proteína intrínseca de membrana plasmática), TgDREB2 (proteína de ligação a elemento responsivo a desidratação) e TgAREB (proteína de ligação a elemento responsivo a ácido abscísico). Apenas TgTPS, TgPIP e TgDREB2 mostraram alto grau de conservação entre as espécies, podendo ser corretamente amplificadas via PCR e validadas por sequenciamento. Assim, com o banco de dados de transcritos obtido pelo RNA-seq, foi possível identificar genes candidatos ao estudo de características vegetativas e reprodutivas de teca, contribuindo para entender os mecanismos moleculares desta espécie florestal. / Teak is a tree of great commercial importance by the characteristics of color and durability of its wood. Due to its hardiness and easy adaptation to climate, teak plantations become increasingly attractive around the world. However, this species has a lack of molecular genetic studies on both of its wood, as their tolerance to environmental variations. Once the transcriptome can provide lots of information about the genes expressed by a cell group, this work represents the first transcriptome teak, which were sequenced flowers, leaves, roots and seedlings by Illumina technology. The transcriptome assembly was performed with Trinity program above 100 million reads and generated more than 400,000 contigs, which have acquired the functional annotations with Blas2GO program. 51% of the contigs were annotaded, showing high similarity to Vitis vinifera and Solanum licopersicum; of these, 78% had functional annotations with the Gene Ontology, totaling 5,165 terms for Biological Process, 2846 terms for Molecular Function and 742 for Cell Component. The differential expression was obtained with the edgeR program at 5% probability of error and showed that for 187,315 contigs assembled by merging all sequenced libraries, 18 showed differential expression to flower, 14 to leaf, 13 to root and 29 for seedling. After this step of characterization of the transcriptome, we performed a stress experiment by water deficit at greenhouse, where teak plants were subjected to Moderate stress (40% of water in the substrate for 20 days), Severe stress (20 to 40% water for 30 days) and control treatment (saturated substrate). Measurements by infrared gas analyzer (IRGA) showed a decrease in photosynthesis (up to 70% less than the control), transpiration (up 77%) and stomatal conductance (up 85%) between treatments; furthermore, leaf relative water content dropped 13% between the treatment control and severe, and free proline levels were up to 3.5 fold greater in stress treatments. The leaf temperature increased significantly with increasing irradiance of photons applied. The search for genes related to stress by water deficit in the root transcripts library returned 1,145 sequences, and these, 4 were characterized: TgTPS (trehalose 6-phosphate synthase), TgPIP (aquaporin, protein intrinsic of plasma membrane), TgDREB2 (dehydration responsive element binding protein) and TgAREB (abscisic acid responsive element binding protein). Only TgTPS, TgPIP and TgDREB2 showed a high degree of conservation between species, and can be properly amplified by PCR and validated by sequencing. Thus, with the database of transcripts obtained by RNA-seq, candidate genes were identified for the study of vegetative and reproductive characteristics teak, helping to understand the molecular mechanisms of this forest species.

The recent technology of single-cell RNA sequencing can be used to investigate molecular, transcriptional, changes in cells as they develop. I reviewed the literature on the technology, and made a large scale quantitative comparison of the different implementations of single cell RNA sequencing to identify their technical limitations. I investigate how to model transcriptional changes during cellular development. The general forms of expression changes with respect to development leads to nonparametric regression models, in the forms of Gaussian Processes. I used Gaussian process models to investigate expression patterns in early embryonic development, and compared the development of mice and humans. When using in vivo systems, ground truth time for each cell cannot be known. Only a snapshot of cells, all being in different stages of development can be obtained. In an experiment measuring the transcriptome of zebrafish blood precursor cells undergoing the development from hematopoietic stem cells to thrombocytes, I used a Gaussian Process Latent Variable model to align the cells according to the developmental trajectory. This way I could investigate which genes were driving the development, and characterise the different patterns of expression. With the latent variable strategy in mind, I designed an experiment to study a rare event of murine embryonic stem cells entering a state similar to very early embryos. The GPLVM can take advantage of the nonlinear expression patterns involved with this process. The results showed multiple activation events of genes as cells progress towards the rare state. An essential feature of cellular biology is that precursor cells can give rise to multiple types of progenitor cells through differentiation. In the immune system, naive T-helper cells differentiate to different sub-types depending on the infection. For an experiment where mice were infected by malaria, the T-helper cells develop into two cell types, Th1 and Tfh. I model this branching development using an Overlapping Mixture of Gaussian Processes, which let me identify both which cells belong to which branch, and learn which genes are involved with the different branches. Researchers have now started performing high-throughput experiments where spatial context of gene expression is recorded. Similar to how I identify temporal expression patterns, spatial expression patterns can be identified nonparametrically. To enable researchers to make use of this technique, I developed a very fast method to perform a statistical test for spatial dependence, and illustrate the result on multiple data sets.