Global ETD Search

61	Deriving a mathematical framework for data-driven analyses of immune cell dynamics Burt, Philipp 06 January 2023 (has links) 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. quantitative Modellierung Zell-Zell Kommunikation T Zell Differenzierung Kinetische Genexpression Data-driven modeling Cell-cell communication Cell fate-decision T cell differentiation Kinetic transcriptome analysis 570 Biologie ddc:570
62	Study of the kinase MAP4K4 in collective migration of cancer cells Alberici Delsin, Lara Elis 08 1900 (has links) 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. MAP4K4 Migration Cellulaire Collective Collective Cell Migration Métastases Metastasis Jonction Cellulaire Cell-Cell Junction Adhésion Focale Focal Adhesion Cytosquelette Cytoskeleton Forces Communication Cellule Cell-Cell Communication Câbles d'Actine Supracellulaires Supracellular Actin Cables
63	Stochastic Modelling of Calcium Dynamics Friedhoff, Victor Nicolai 20 December 2023 (has links) Calcium (Ca2+) ist ein in eukaryotischen Zellen allgegenwärtiger sekundärer Botenstoff. Durch Inositoltrisphosphat (IP3) ausgelöste Ca2+-Signale von IP3-Rezeptoren (IP3Rs) sind eines der universellsten Zell Signalübertragungssysteme. Ca2+ Signale sind fundamental stochastisch. Dennoch hat sich die Modellierung dieser Ca2+-Signale bisher stark auf deterministische Ansätze mit gewöhnlichen Differentialgleichungen gestützt. Diese wurden als Ratengleichungen etabliert und beruhen auf räumlich gemitteltem Ca2+ Werten. Diese Ansätze vernachlässigen Rauschen und Zufall. In dieser Dissertation präsentieren wir ein stochastisches Modell zur Erzeugung von Ca2+ Spikes in Form einer linearen Zustands-Kette. Die Anzahl offener Cluster ist die Zustandsvariable und Erholung von negativem Feedback wird berücksichtigt. Wir identifizieren einen Ca2+ Spike mit dem ersten Erreichen eines kritischen Zustands und sein Interspike Intervall mit der first-passage time (FPT) zu diesem Zustand. Dafür entwickeln wir einen allgemeinen mathematischen Rahmen zur analytischen Berechnung von FPTs auf solch einer Kette. Wir finden z.B. einen allgemein verringerten CV, der ein deutliches Minimum in Abhängigkeit der Zustandskettenlänge N aufweist. Dies nennen wir resonante Länge. Danach ergänzen wir positives Feedback und wenden das Modell auf verschiedene Zelltypen an. Es erfasst alle verfügbaren allgemeinen Beobachtungen zu Ca2+ Signalvorgängen. Es erlaubt uns Einblicke in den Zusammenhang von Agonistenstärke und Puffraten. Auch werden einzelne Ca2+ Spikes in Purkinje Neuronen, welche eine Rolle für Lernen und Erinnerung spielen, als stochastisches reaction-diffusion Model in einer 3D Dornenfortsatz Geometrie modelliert. Ataxia, eine Krankheit, die zum Verlust der Feinmotorik führt, wird auf defekte IP3R zurückgeführt, die abnormale Ca2+ Spikes erzeugen. Dieser Zustand wird ebenfalls untersucht und es wird ein Weg zur Wiederherstellung normaler Ca2+ Spikes vorgeschlagen. / Calcium (Ca2+) is a ubiquitous 2nd messenger molecule in all eukaryotic cells. Inositol trisphosphate (IP3)-induced Ca2+ signalling via IP3 receptors (IP3Rs) is one of the most universal signalling systems used by cells to transmit information. Ca2+ signalling is noisy and a fundamentally stochastic system. Yet, modelling of IP3-induced Ca2+ signalling has relied heavily on deterministic approaches with ordinary differential equations in the past, established as rate equations using spatially averaged Ca2+. These approaches neglect the defining features of Ca2+ signalling, noise and ﬂuctuations. In this thesis, we propose a stochastic model of Ca2+ spike generation in terms of a linear state chain with the number of open clusters as its state variable, also including recovery from negative feedback. We identify a Ca2+ spike with reaching a critical state for the first time, and its interspike interval with the first passage time to that state. To this end, a general mathematical framework for analytically computing first-passage times of such a linear chain is developed first. A substantially reduced CV with a pronounced minimum, dependent on the chain length N, termed resonant length, are found. Positive feedback is then included into the model, and it is applied directly to various cell types. The model is fundamentally stochastic and successfully captures all available general observations on Ca2+ signalling. Also, we specifically study single Ca2+ spikes in spines of Purkinje neurons, assumed to be important for motor learning and memory, using MCell to simulate a reaction-diffusion system in a complex 3D Purkinje spine geometry. The model successfully reproduces experimentally findings on properties of Ca2+ spikes. Ataxia, a pathological condition resulting in, e.g., a loss of fine motor control, assumed to be caused by malfunctioning IP3Rs, is modelled and a possible way of recovery is suggested. Physik Biophysik Calcium Zellkommunikation erste Durchgangszeit Stochastische Prozesse IP3 Purkinje synaptische Plastizität Zellvariabilität Wahrscheinlichkeitstheorie Variationskoeffizient Modellierung Physics Biophysics Calcium Cell Communication First Passage Time stochastic processes Cell Signalling IP3 Purkinje synaptic plasticity cell variability probability theorie statistics Coefficient of variation Modelling 530 Physik ddc:530
64	Structural Investigation of Processing α-Glucosidase I from Saccharomyces cerevisiae Barker, Megan 20 August 2012 (has links) 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. Biomolecular structure Eukaryotic glycosylation glycosylation N-glycan N-linked glycosylation Carbohydrate biochemistry Inhibitor antiviral therapeutic Structure-based drug design glucosidase glycosidase glycoside hydrolase post-translational modification enzyme enzyme mechanism inverting mechanism structural biology protein structure 6xHis tag Crystal packing sugar substrate X-ray crystallography single anomalous dispersion PHENIX heavy-atom phasing docking autodock autodock vina biophysical methods tryptophan fluorescence glucose oxidase activity assay enzyme inhibition Protein expression Protein purification Pichia pastoris Saccharomyces cerevisiae fondue AOX1 promoter glycoside hydrolysis substrate binding model molecular dynamics molecular dynamics Binding site Active site cleft Endoplasmic reticulum Glycan processing Glycan trimming protein-protein interactions cell-cell communication X-ray diffraction crystallization secreted protein substrate selectivity kojibiose glucotriose miglitol deoxynojirimycin Glc3Man9GlcNAc2 free oligosaccharide species GluI Cwh41 Cwh41p Cwht1p 0306 0307 0760
65	Structural Investigation of Processing α-Glucosidase I from Saccharomyces cerevisiae Barker, Megan 20 August 2012 (has links) 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. Biomolecular structure Eukaryotic glycosylation glycosylation N-glycan N-linked glycosylation Carbohydrate biochemistry Inhibitor antiviral therapeutic Structure-based drug design glucosidase glycosidase glycoside hydrolase post-translational modification enzyme enzyme mechanism inverting mechanism structural biology protein structure 6xHis tag Crystal packing sugar substrate X-ray crystallography single anomalous dispersion PHENIX heavy-atom phasing docking autodock autodock vina biophysical methods tryptophan fluorescence glucose oxidase activity assay enzyme inhibition Protein expression Protein purification Pichia pastoris Saccharomyces cerevisiae fondue AOX1 promoter glycoside hydrolysis substrate binding model molecular dynamics molecular dynamics Binding site Active site cleft Endoplasmic reticulum Glycan processing Glycan trimming protein-protein interactions cell-cell communication X-ray diffraction crystallization secreted protein substrate selectivity kojibiose glucotriose miglitol deoxynojirimycin Glc3Man9GlcNAc2 free oligosaccharide species GluI Cwh41 Cwh41p Cwht1p 0306 0307 0760

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