Cell-cell communication between bacteria, belonging to the same species or to different species (Intra-kingdom signaling), or communication between bacteria and their animal host (Inter-kingdom signaling) is mediated through different chemical signals that are synthesized and secreted by bacteria or the host and is crucial for the survival of bacteria inside their host. The overall goal of this work was to understand the role of inter- and intra-kingdom signaling in phenotypes such as chemotaxis, colonization and biofilm formation, and virulence that are associated with infections caused by the human gastrointestinal (GI) tract pathogens. A part of our work also aimed at developing microfluidics-based models to study inter- and intra-kingdom signaling in biofilm formation, inhibition, and dispersal. We showed that norepinephrine (NE), an important host signal produced during stress, increases human opportunistic pathogen Pseudomonas aeruginosa growth, motility, attachment, and virulence, and also showed that the actions of NE are mediated primarily through the LasR, and not the RhlR QS system. We investigated the molecular mechanism underlying the chemo-sensing of the intra-kingdom signal autoinducer-2 (AI-2) by pathogens Escherichia coli and Salmonella typhimurium by performing different chemotaxis assays (capillary, microPlug and microFlow assays), and discovered that AI-2 is a potent attractant for E. coli and S. typhimurium, and that the Tsr chemoreceptor and periplasmic AI-2 binding protein LsrB are necessary for sensing AI-2, although uptake of AI-2 into the cytoplasm is not required. We concluded that LsrB, when bound to AI-2, interacts directly with the periplasmic domain of Tsr primarily at the Thr-61 and Asp-63 residues of LsrB, making LsrB the first known periplasmic-protein partner for Tsr. We fabricated a simple user-friendly microfluidic flow cell (microBF) device that can precisely measure the effect of a wide range of concentrations of single or combinations of two or more soluble signals on bacterial biofilm formation and development. We also constructed a synthetic biofilm circuit that utilizes the Hha and BdcA dispersal proteins of E. coli along with a quorum sensing (QS) switch that works based on the accumulation of the signal N-(3-oxo-dodecanoyl)-L-homoserine lactone (3-o-C12HSL) and implemented it in an upgraded �BF device. We showed that a QS system may be utilized with biofilm dispersal proteins to control consortial biofilm formation by removing an existing biofilm and then removing the biofilm that displaced the first one. These types of synthetic QS circuits may be used to pattern biofilms by facilitating the re-use of platforms and to create sophisticated reactor systems that will be used to form bio-refineries.

In order to optimize productivity of a cell culture it is necessary to understand growth and productivity and couple these features of the culture to extracellular nutrients whose profiles can be manipulated. Also, since growth and productivity are directly affected by cell death mechanisms such as apoptosis, it is imperative to understand these mechanisms. This work describes the development of a differential equation based population balance model of apoptosis in a Chinese Hamster Ovary cell culture producing Anti-RhD monoclonal antibody (mAb). The model was verified in isolation and was then coupled to a metabolic flux model. The model distinguishes between various subpopulations at normal healthy states and at various stages of apoptosis. After finding that glucose and glutamine are not limiting nutrients for this culture, different hypotheses were explored to explain growth arrest. Initially, it was hypothesized that there is some unknown nutrient in either media or serum which is depleted, thus causing growth arrest. Accordingly a first model was developed assuming depletion of this nutrient. Subsequent experiments with different additions of media and serum showed that there is no such nutrient limitation for the media and serum conditions used in most of the experiments. Additional experiments with different culture volumes showed that cell growth was actually controlled by a compound that accumulates and causes pH deviation from its optimal range of operation. Since strong correlations were found between culture volume and growth, it was hypothesized that the compound may be carbon dioxide (CO2), which is inhibitory for growth and may accumulate due to mass transfer limitations. Following this finding, a second model was proposed to take into account the accumulation of this inhibitor, although the specific inhibiting compound could not be exactly identified. This second mathematical model of cell growth was then integrated with a metabolic flux model to provide for a link between intracellular and extracellular species balances, since the latter are the ones to be manipulated for increasing productivity. This final model formulation was then used to describe mAb productivity. The model was also able to reasonably predict all cell subpopulations, nutrients, metabolites and mAb. In an attempt to mitigate the effect of CO2 accumulation and renew the cell growth, culture perfusions were performed. Although this approach resulted in some renewal of growth, the cell concentration progressively decreased after each successive perfusion event. This suggests that irreversible cell damage occurs because of CO2 accumulation. The model was used to describe the perfusion experiments. Agreement between data and model predictions were reasonable. In addition, it was shown that operation with successive perfusions results in a significant increase in productivity and therefore it can be used for further process optimization.

Chez les angiospermes, la reproduction passe par la double fécondation. Le tube pollinique délivre deux cellules spermatiques au sein du gamétophyte femelle. Une cellule féconde la cellule œuf pour produire un zygote; l’autre féconde la cellule centrale pour produire l’endosperme. Pour assurer un succès reproductif, le développement du gamétophyte femelle au sein de l’ovule doit établir un patron cellulaire qui favorise les interactions avec le tube pollinique et les cellules spermatiques. Pour ce faire, un dialogue doit s’établir entre les différentes cellules de l’ovule lors de son développement, de même que lors de la fécondation. D’ailleurs, plusieurs types de communications intercellulaires sont supposées suite à la caractérisation de plusieurs mutants développementaux. De même, ces communications semblent persister au sein du zygote et de l’endosperme pour permettre la formation d’un embryon viable au sein de la graine. Malgré les développements récents qui ont permis de trouver des molécules de signalisation supportant les modèles d’interactions cellulaires avancés par la communauté scientifique, les voies de signalisation sont de loin très incomplètes. Dans le but de caractériser des gènes encodant des protéines de signalisation potentiellement impliqués dans la reproduction chez Solanum chacoense, l’analyse d’expression des gènes de type RALF présents dans une banque d’ESTs (Expressed Sequence Tags) spécifiques à l’ovule après fécondation a été entreprise. RALF, Rapid Alcalinization Factor, est un peptide de 5 kDa qui fait partie de la superfamille des «protéines riches en cystéines (CRPs)», dont les rôles physiologiques au sein de la plante sont multiples. Cette analyse d’expression a conduit à une analyse approfondie de ScRALF3, dont l’expression au sein de la plante se limite essentiellement à l’ovule. L’analyse de plantes transgéniques d’interférence pour le gène ScRALF3 a révélé un rôle particulier lors de la mégagamétogénèse. Les plantes transgéniques présentent des divisions mitotiques anormales qui empêchent le développement complet du sac embryonnaire. Le positionnement des noyaux, de même que la synchronisation des divisions au sein du syncytium, semblent responsables de cette perte de progression lors de la mégagamétogénèse. L’isolement du promoteur de même que l’analyse plus précise d’expression au sein de l’ovule révèle une localisation sporophytique du transcrit. La voie de signalisation de l’auxine régule également la transcription de ScRALF3. De surcroît, ScRALF3 est un peptide empruntant la voie de sécrétion médiée par le réticulum endoplasmique et l’appareil de Golgi. En somme, ScRALF3 est un important facteur facilitant la communication entre le sporophyte et le gamétophyte pour amener à maturité le sac embryonnaire. L’identification d’un orthologue potentiel chez Arabidopsis thaliana a conduit à la caractérisation de AtRALF34. L’absence de phénotype lors du développement du sac embryonnaire suggère, cependant, de la redondance génétique au sein de la grande famille des gènes de type RALF. Néanmoins, les peptides RALFs apparaissent comme d’importants régulateurs lors de la reproduction chez Solanum chacoense et Arabidopsis thaliana. / In angiosperms, reproduction occurs through double fertilization. The pollen tube delivers two sperm cells into the female gametophyte. A first sperm cell fertilizes the egg cell to produce a zygote, while the other fertilizes the central cell to produce the endosperm. To ensure reproductive success, the development of the female gametophyte within the ovule must establish a cellular pattern allowing interaction with the pollen tube and sperm cells. To this end, a dialogue must be established amongst the various cells of the ovule during its development, as well as during fertilization. Several types of communication are suggested by the analysis of developmental mutants. These communications must persist in the zygote and endosperm to allow the formation of a viable embryo within the seed. Recent developments have helped to find signaling molecules that support cell interaction models developed by the scientific community, but the signaling pathways are far from complete. In order to characterise genes encoding signaling proteins which are potentially active during reproduction in Solanum chacoense, I undertook the expression analysis of the RALF-like genes present in a bank of ESTs (Expressed Sequence Tags) specific to the ovule after fertilization. RALF, Rapid Alcalinization Factor, is a 5 kDa peptide that is part of the superfamily of Cysteine Rich Proteins (CRPs), which play a wide variety physiological roles within the plant. This expression analysis led to a detailed analysis of ScRALF3, whose expression in the plant is largely restricted to the ovule. The analysis of ScRALF3 RNAi transgenic plants revealed a function during megagametogenesis. The transgenic plants exhibit abnormal mitotic divisions that prevent the maturity of the embryo sac. The positioning of the nuclei, as well as the timing of divisions in the syncytium, appear to be responsible for the arrest of development during megagametogenesis. Isolation of the promoter as well as more accurate analysis of transcript expression reveals localisation within the ovule sporophytic tissue. The auxin signaling pathway is also involved in the regulation of ScRALF3 expression. ScRALF3 is a secreted peptide passing via the endoplasmic reticulum and the Golgi apparatus. In summary, ScRALF3 may be an important factor facilitating communication between the gametophyte and the sporophyte to allow maturation of the embryo sac. The identification of a potential orthologue in Arabidopsis thaliana led to the characterisation of AtRALF34. The lack of a phenotype during embryo sac development, however, suggests that genetic redundancy within the family of RALF-like genes is very complex. Nevertheless, the RALF peptides appear to be important regulators during reproduction in Solanum chacoense and Arabidopsis thaliana.

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<p>In recent years, science has shifted from a focus on reductionist explanations of biological phenomena to a more integrated, systems approach. This shift has made its way into curricular recommendations for undergraduate education. To understand complex biological phenomena, it has been argued that students employ mechanistic reasoning, in which one describes a mechanism by identifying the activities that produce change, the entities which engage in activities, and the starting and ending conditions. Students’ use of mechanistic reasoning requires engaging in the complex task of simultaneously integrating and coordinating multiple elements across space and time. In addition, students must link and organize their scientific ideas and then structure their thoughts into a network of knowledge, as described by the theory of knowledge integration. Previous studies that have explored students’ understanding of scientific concepts using knowledge integration as a lens found that students’ nonmechanistic ideas prevented them from identifying gaps in the connections between their ideas and from forming normative knowledge. Thus, this dissertation investigates the features of undergraduate biology students’ systems thinking using knowledge integration and mechanistic reasoning as conceptual and analytical frameworks. Using a semi-structured interview, we asked students to describe functional definitions of and relationships between three fundamental modules in biology (i.e., gene regulation, cell-cell communication, and the relationship between genotype and phenotype). In the first study, we found that the majority of students did not have normative functional definitions for how and why gene regulation occurs or how phenotype is regulated. When describing the relationships in an open context, most students expressed unidirectional, linear knowledge networks which lacked Mechanistic connections. In our second study, we examined how students described a transition point in biofilm development after being cued to think about the three modules. Though students struggled to transfer over relevant ideas to the biofilm context (such as gene regulation and cell-cell communication processes), we found that explanations were more specified in the nature of connections and content including more Mechanistic descriptions. In the third study, we explored features of biology students’ and instructors’ knowledge networks in an open context and situated to a context of the participants’ choice. Within an open context, most students described multidirectional, non-linear knowledge networks similar to instructors. In the specific context, the majority of students described non-linear knowledge networks, but some students modified their structures to be linear. Although the structures became less complex in the specific context, the nature of connections and content became more specified. Across all studies, we found that context greatly affected students’ systems thinking as revealed by the changing features of the knowledge networks. Specifically, context helped students identify what relationships they deeply understood and could transfer and allowed for the creation of a detailed explanation relevant to the specific biological phenomenon. For students to develop a broad systems perspective of biology, we recommend instructors engage students in the process of knowledge integration. Embed opportunities for students to think about biology concepts in various contexts, particularly where students grapple with nuanced and complex transfer of ideas. These practices will encourage students to form causal, mechanistic linkages between concepts and build an integrated, expert-like understanding of biology.</p>

La coordination du développement par les communications intercellulaires est essentielle pour assurer la reproduction chez les plantes. Plusieurs études démontrent qu’une communication entre le sac embryonnaire et le tissu maternel, le sporophyte, est essentielle au bon développement des gamètes. Les molécules, peptides ou autres protagonistes impliqués dans ces voies de signalisation ainsi que leur mode d’action restent toutefois nébuleux. Les gènes de type RALF codent pour des petits peptides sécrétés retrouvés de manière spécifique ou ubiquitaire dans la plante. Leur structure en font de parfaits candidats pour permettre ces communications cellule-cellule entre les différents tissus. Treize gènes de type RALF ont été isolés actuellement chez la pomme de terre sauvage Solanum chacoense. Maintenant, nous montrons qu’un de ceux-ci, ScRALF3, est impliqué dans la polarisation du sac embryonnaire et dans la synchronicité des divisions mitotiques assurant la formation d’un gamétophyte femelle mature fonctionnel. Étant exprimé de manière spécifique au niveau des téguments de l’ovule, ScRALF3 est un candidat idéal pour réguler les communications cellule-cellule entre le sporophyte et le sac embryonnaire. / Development coordination through intercellular communication is essential for plant reproduction. Several studies show that communication between embryo sac and maternal tissue, the sporophyte, is essential to the development of gametes. These molecules, peptides or other actors involved in these signaling pathways and their mode of action remains unclear. Genes encoding small secreted RALF peptides specifically or ubiquitously expressed throughout the plant are good candidates to allow these cell-cell communications. Thirteen RALF-like genes have been isolated at present from the wild potato Solanum chacoense. Now, we show that one of these, ScRALF3, is involved in the polarization of the embryo sac and the synchronicity of mitotic divisions to ensure the formation of a functional mature female gametophyte. Since it is specifically expressed in the integument of the ovule, ScRALF3 is an ideal candidate to regulate cell-cell communication between the sporophyte and the gametophyte, e.g., the embryo sac.

La coordination du développement par les communications intercellulaires est essentielle pour assurer la reproduction chez les plantes. Plusieurs études démontrent qu’une communication entre le sac embryonnaire et le tissu maternel, le sporophyte, est essentielle au bon développement des gamètes. Les molécules, peptides ou autres protagonistes impliqués dans ces voies de signalisation ainsi que leur mode d’action restent toutefois nébuleux. Les gènes de type RALF codent pour des petits peptides sécrétés retrouvés de manière spécifique ou ubiquitaire dans la plante. Leur structure en font de parfaits candidats pour permettre ces communications cellule-cellule entre les différents tissus. Treize gènes de type RALF ont été isolés actuellement chez la pomme de terre sauvage Solanum chacoense. Maintenant, nous montrons qu’un de ceux-ci, ScRALF3, est impliqué dans la polarisation du sac embryonnaire et dans la synchronicité des divisions mitotiques assurant la formation d’un gamétophyte femelle mature fonctionnel. Étant exprimé de manière spécifique au niveau des téguments de l’ovule, ScRALF3 est un candidat idéal pour réguler les communications cellule-cellule entre le sporophyte et le sac embryonnaire. / Development coordination through intercellular communication is essential for plant reproduction. Several studies show that communication between embryo sac and maternal tissue, the sporophyte, is essential to the development of gametes. These molecules, peptides or other actors involved in these signaling pathways and their mode of action remains unclear. Genes encoding small secreted RALF peptides specifically or ubiquitously expressed throughout the plant are good candidates to allow these cell-cell communications. Thirteen RALF-like genes have been isolated at present from the wild potato Solanum chacoense. Now, we show that one of these, ScRALF3, is involved in the polarization of the embryo sac and the synchronicity of mitotic divisions to ensure the formation of a functional mature female gametophyte. Since it is specifically expressed in the integument of the ovule, ScRALF3 is an ideal candidate to regulate cell-cell communication between the sporophyte and the gametophyte, e.g., the embryo sac.

Zelluläre Entscheidungen, wie z. B. die Differenzierung von T-Helferzellen (Th-Zellen) in spezialisierte Effektorlinien, haben großen Einfluss auf die Spezifität von Immunreaktionen. Solche Reaktionen sind das Ergebnis eines komplexen Zusammenspiels einzelner Zellen, die über kleine Signalmoleküle, so genannte Zytokine, kommunizieren. Die hohe Anzahl der Komponenten, sowie deren komplizierte und oft nichtlineare Interaktionen erschweren dabei die Vorhersage, wie bestimmte zelluläre Reaktionen erzeugt werden. Aus diesem Grund sind die globalen Auswirkungen der gezielten Beeinflussung einzelner Zellen oder spezifischer Signalwege nur unzureichend verstanden. So wirken beispielsweise etablierte Behandlungen von Autoimmunkrankheiten oft nur bei einem Teil der Patienten. Durch Einzelzellmethoden wie Live-Cell-Imaging, Massenzytometrie und Einzelzellsequenzierung, können Immunzellen heutzutage quantitativ auf mehreren Ebenen charakterisiert werden. Diese Ansammlung quantitativer Daten erlaubt die Formulierung datengetriebener Modelle zur Vorhersage von zellulären Entscheidungen, allerdings fehlen in vielen Fällen Methoden, um die verschiedenen Daten auf geeignete Weise zu integrieren und zu annotieren. Die vorliegende Arbeit befasst sich mit quantitativen Modellformulierungen für die Entscheidungsfindung von Zellen im Immunsystem mit dem Schwerpunkt auf Lymphozytenproliferation, -differenzierung und -tod. / Cellular decisions, such as the differentiation of T helper (Th) cells into specialized effector lineages, largely impact the direction of immune responses. Such population-level responses are the result of a complex interplay of individual cells which communicate via small signaling molecules called cytokines. The system's complexity, stemming not only from the number of components but also from their intricate and oftentimes non-linear interactions, makes it difficult to develop intuition for how cellular responses are actually generated. Not surprisingly, the global effects of targeting individual cells or specific signaling pathways through perturbations are poorly understood. For instance, common treatments of autoimmune diseases often work for some patients, but not for others. Recently developed methods such as live-cell imaging, mass cytometry and single-cell sequencing now enable quantitative characterization of individual immune cells. This accumulating wealth of quantitative data has laid the basis to derive predictive, data-driven models of immune cell behavior, but in many cases, methods to integrate and annotate the data in a way suitable for model formulation are missing. In this thesis, quantitative workflows and methods are introduced that allow to formulate data-driven models of immune cell decision-making with a particular focus on lymphocyte proliferation, differentiation and death.

La migration cellulaire collective est essentielle aux processus physiologiques, tels que le dé-veloppement et la réparation des tissus, et aux conditions pathogènes, telles que les métas-tases cancéreuses. Les lésions métastatiques sont à l'origine de la majorité de la mortalité liée au cancer, ce qui incite à comprendre les mécanismes moléculaires régissant la migration collective du cancer et à explorer leur potentiel thérapeutique. Dans ce contexte, la kinase MAP4K4 est apparue comme une kinase pro-métastatique, associée à un mauvais pronostic pour les patients et reconnue pour réguler la migration des cellules cancéreuses. Cependant, son rôle dans la migration collective reste flou. Au cours des dernières années, le groupe de recherche du Dr Emery a dévoilé que Misshapen, l'orthologue drosophile de MAP4K4, est un régulateur central de la migration collective des cellules de bordure, soulevant la question de savoir si MAP4K4 coordonnerait la migration collective des cellules cancéreuses. Le but de cette thèse était d’évaluer la fonction de MAP4K4 dans la migration collective des cellules cancéreuses, incluant deux modes de migration différents : en grappe et en feuillets. En utilisant la lignée cellulaire A431, nous démontrons le rôle de MAP4K4 dans la régulation de la dynamique de protrusion, de rétraction et d’adhésion focale, favorisant la migration des grappes grâce à la régulation des forces de traction cellule-substrat. De plus, nous dévoi-lons un nouveau rôle de MAP4K4 dans l’adhésion cellule-cellule, en contrôlant la charge de tension et la stabilité, et en ajustant les contraintes intercellulaires. Notamment, lors de la migration des feuillets, les cellules A431 forment des structures en forme de doigts, avec une hiérarchie leader-suiveur. En caractérisant ces structures migratrices, nous avons identifié des structures d'actomyosine supracellulaires, ouvrant ainsi de nouvelles questions et voies d'investigation pour explorer les mécanismes de communication cellule-cellule. De plus, nous avons montré que MAP4K4 régule la formation des doigts et la densité des câbles supracellu-laires, nuisant à l'émergence de cellules leader et coordonnant la communication cellule-cellule. Dans l’ensemble, ces travaux soulignent le rôle central de MAP4K4 dans la régulation de la migration collective des cellules cancéreuses par l’adhésion focale et la modulation de la jonction cellule-cellule, ayant finalement un impact sur la génération et la transmission de la force cellulaire, coordonnant ainsi le mouvement collectif. En outre, nous discutons du po-tentiel de l’inhibition de MAP4K4 en tant que stratégie de traitement des métastases. / Collective cell migration is essential for both physiological processes, such as development and tissue repair, and pathogenic conditions, such as cancer metastasis. Metastatic lesions drive the majority of cancer-related mortality, urging the understanding of molecular me-chanisms governing collective cancer migration, and exploring their therapeutic potential. In this context, the kinase MAP4K4 has emerged as a pro-metastatic kinase, associated with poor patient prognosis and recognized for regulating cancer cell migration. However, its role in collective migration remains unclear. In the past years, Dr. Emery's research group unveiled that Misshapen, the MAP4K4 Drosophila orthologue, is a central regulator of border cell col-lective migration, raising the question whether MAP4K4 would coordinate the collective mi-gration of cancer cells. The purpose of this thesis was to assess the function of MAP4K4 in carcinoma cell’s collective migration, including two different migration modes : clusters and sheets. Using A431 cell line, we demonstrate MAP4K4’s role in regulating protrusion, retraction and focal adhesion dy-namics, promoting cluster migration through regulating cell-substrate traction forces. Furthermore, we unveil a new role of MAP4K4 at cell-cell adhesions, controlling tension loa-ding and stability, and tunning the intercellular stresses. Notably, during sheet migration, A431 cells form finger-like structures, with a leader-follower hierarchy. Performing the charac-terization of these migrating structures, we identified supracellular actomyosin structures, opening new questions and investigative pathways to explore cell-cell communication me-chanisms. Moreover, we showed that MAP4K4 regulates finger formation and the density of the supracellular cables, impairing the emergence of leader cells and coordinating cell-cell communication. Overall, this work underscores the central role of MAP4K4 in regulating collective cancer cell migration through focal adhesion and cell-cell junction modulation, ultimately impacting cell force generation and transmission, coordinating collective movement. Furthermore, we dis-cuss the potential of MAP4K4 inhibition as a strategy for metastasis therapy.

N-glycosylation is the most common eukaryotic post-translational modification, impacting on protein stability, folding, and protein-protein interactions. More broadly, N-glycans play biological roles in reaction kinetics modulation, intracellular protein trafficking, and cell-cell communications. The machinery responsible for the initial stages of N-glycan assembly and processing is found on the membrane of the endoplasmic reticulum. Following N-glycan transfer to a nascent glycoprotein, the enzyme Processing α-Glucosidase I (GluI) catalyzes the selective removal of the terminal glucose residue. GluI is a highly substrate-specific enzyme, requiring a minimum glucotriose for catalysis; this glycan is uniquely found in biology in this pathway. The structural basis of the high substrate selectivity and the details of the mechanism of hydrolysis of this reaction have not been characterized. Understanding the structural foundation of this unique relationship forms the major aim of this work. To approach this goal, the S. cerevisiae homolog soluble protein, Cwht1p, was investigated. Cwht1p was expressed and purified in the methyltrophic yeast P. pastoris, improving protein yield to be sufficient for crystallization screens. From Cwht1p crystals, the structure was solved using mercury SAD phasing at a resolution of 2 Å, and two catalytic residues were proposed based upon structural similarity with characterized enzymes. Subsequently, computational methods using a glucotriose ligand were applied to predict the mode of substrate binding. From these results, a proposed model of substrate binding has been formulated, which may be conserved in eukaryotic GluI homologs.