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Prominin-1 (alias CD133) has received considerable interest because of its expression by several stem and progenitor cells originating from various sources, including the neural and hematopoietic systems. As a cell surface marker, prominin-1 is now used for somatic stem cell isolation. Its expression in cancer stem cells has broadened its clinical value, as it might be useful to outline new prospects for more effective cancer therapies by targeting tumor-initiating cells. Cell biological studies of this molecule have demonstrated that it is specifically concentrated in various membrane structures that protrude from the planar areas of the plasmalemma. Prominin-1 binds to the plasma membrane cholesterol and is associated with a particular membrane microdomain in a cholesterol-dependent manner. Although its physiological function is not yet determined, it is becoming clear that this cell surface protein, as a unique marker of both plasma membrane protrusions and membrane microdomains, might reveal new aspects of the cell biology of rare stem and cancer stem cells. The aim of this review is to outline the recent discoveries regarding the dynamic reorganization of the plasma membrane of rare CD133+ hematopoietic progenitor cells during cell migration and division. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

All cells are delimited by membranes that protect the cell from the surrounding environment. In eukaryotic cells the same principle applies at subcellular level where membranes delimit functional cell organelles. The membrane structure, properties and function are defined in part by their lipid composition. Lipidomics is the large‐scale study of pathways and networks of cellular lipids in biological systems. It involves the identification and quantitation of cellular lipid molecular species and their interactions with other lipids, proteins, and other metabolites. Lipidomics has been greatly facilitated by recent advances in ionization technology and mass spectrometric capabilities which have simplified the sample processing prior to analysis, giving rise to shotgun lipidomics. Shotgun lipidomics is fast, highly sensitive, and can identify hundreds of lipids missed by other methods. However, Glycosphingolipids are an important lipid family that was out of the scope of shotgun lipidomics due to the lack of suitable analytical tools. The aim of my thesis was two‐fold. The first aim was the establishment of Glycosphingolipid identification and quantification by shotgun approach. This allowed us to perform lipidomic studies with unprecedented comprehensiveness (~300 lipid species from 15 different lipid classes) from low sample amounts and with minimal sample processing. The second was the application of this technology in studies of the role of lipids in several processes like vesicular carrier formation, cell polarization, protein delivery to the plasma membrane and viral budding. This work resulted in several findings. We found that there is sorting of sphingolipids and sterols into plasma membrane targeted vesicular carriers in budding yeast. When kidney cells change from a mesenchymal to an epithelial morphology there is a profound remodeling of their lipidome, with the synthesis of longer, more saturated, more hydroxylated, and more glycosylated sphingolipids. When these sphingolipids and sterols are depleted in epithelial cells, the apical transport in epithelial cells is impaired. These data strongly support the idea that lipid rafts play an important role in sorting and delivery of lipid and protein cargo to the plasma membrane. Finally, we found that the envelopes of vesicular stomatitis virus and Semliki forest virus assert little specificity in the incorporation of lipids from the plasma membrane. This weak specificity seems to be related to a combination of virus lipid bilayer asymmetry and curvature.

With the dawn of metazoans, the ability of cells to communicate with each other became of paramount importance in maintaining tissue homeostasis. The transforming growth factor β (TGF-β) signaling pathway, which plays important roles during embryogenesis and in the adult organism, signals via a heterodimeric receptor complex consisting of two type II and two type I receptors. After receptor activation through ligand binding, Smads mediate the signal from the receptor complex to the nucleus, where they orchestrate transcription. Depending on the context of activation, TGF-β can mediate a plethora of cellular responses, including proliferation, growth arrest, apoptosis and differentiation. In cancer, TGF-β can act as both as a tumor suppressor and promoter. During early stages of tumorigenesis, TGF-β prevents proliferation. However, TGF-β is also known to promote tumor progression during later stages of the disease, where it can induce differentiation of cancer cells towards a migratory phenotype. The aim of this thesis was to investigate how cells can differentiate their response upon TGF-β pathway activation. The first paper describes the role of Notch signaling in TGF-β induced growth arrest, demonstrating that TGF-β promotes Notch activity and that Notch signaling is required for prolonged TGF-β induced cell cycle arrest. In the second and third paper, we investigate the role of SIK, a member of the AMPK family of kinases, mediating signaling strength of TGF-β through degradation of the TGF-β type I receptor ALK5. While the second paper focuses on the effect of SIK on ALK5 stability and subsequent alterations in TGF-β signaling, the third paper emphasizes cooperation between SIK, Smad7 and the E3 ligase Smurf in degradation of ALK5. Finally, the fourth paper explores a novel role of SIK during TGF-β induced epithelial to mesenchymal transition (EMT). SIK binds to and degrades the polarity protein Par3, leading to enhanced EMT.

Au cours de ce projet de thèse, j’ai étudié le lien fonctionnel entre la morphogénèse épithéliale et la signalisation Delta-Notch, dans le cadre de la formation du tube neural chez le poisson-zèbre. La signalisation Delta-Notch est primordiale pour le développement embryonnaire et le maintien de l’homéostasie des tissus adultes. De façon inattendue, j’ai observé suite à la perte-de-fonction de Mib une perte de la polarité apico-basale dans le neuro-épithélium de la moelle épinière embryonnaire. L’analyse plus poussée de ce phénotype m’a ensuite permis de montrer que l’activité de l’intégralité de la signalisation Notch est requise pour l’établissement de la polarité apico-basale dans le tube neural de poisson-zèbre. En effet, l’inhibition des ligands de Notch et des activateurs transcriptionnels situés en aval, Rbpja et Rbpjb, résulte en l’interruption de la polarité apico-basale. De plus, l’activation ectopique de Notch entraîne un sauvetage complet de la polarité apico-basale dans les embryons déplétés pour Mib. Finalement, le mutant Mib échoue à activer la transcription de protéines de polarité apicale Crumbs1 et Crumbs2a au cours de la formation du tube neural, ce qui suggèrerait que la signalisation Notch agit en amont des complexes de polarité. De façon surprenante, nous avons également montré que le composant de la signalisation Notch, Mib, affecte les mouvements de convergence-extension et la division cellulaire orientée, appelée C-divisions, durant la neurulation et la gastrulation à travers la signalisation PCP. Cet effet de Mib sur la PCP est indépendant de son rôle sur la signalisation Notch. Généralement, cette étude révèle un double-rôle de Mib. / In this Ph.D. project, I study the functional link between epithelial polarity and Delta-Notch signaling in the context of zebrafish neural tube morphogenesis. Notch signaling, one of the major signaling pathways and of prime importance in neurogenesis, has been widely studied for its function in cell fate specifications. Surprisingly, I found that the Notch signaling component Mindbomb (Mib) loss-of-function led to a loss of apico-basal polarity in the neuroepithelium of the embryonic spinal cord. I further explored that the activity of the entire Notch signaling pathway is actually required for the earliest steps of establishment of apico-basal polarity in the zebrafish neural tube. Indeed, inhibition of Notch ligands and downstream transcriptional activators Rbpja and Rbpjb resulted in a disruption of apico-basal polarity. Moreover, ectopic activation of Notch ensued to a complete rescue of apico-basal polarity in Mib loss of function embryos. Furthermore, Mib mutant embryos fail to upregulate the transcription of the apical polarity proteins Crumbs1 and Crumbs2a in the course of neural tube formation, suggesting that Notch signalling might act upstream of polarity complexes. Moreover, I found that Mib affects convergent-extension movements and oriented cell divisions during neurulation and gastrulation through an effect on planar cell polarity. Remarkably, this effect of Mib on PCP is independent of its role in Notch signaling. These results indicate a novel role of Mib in the regulation of PCP signaling. Altogether, this study revealed a dual role of Mib in the epithelial morphogenesis of the zebrafish neural tube.

Algoritmos exatos para fatoração estão limitados a funções Booleanas read-once, onde cada variável aparece uma vez na equação final. No entanto, estes algoritmos apresentam duas restrições principais: (1) eles não consideram funções Booleanas incompletamente especificadas, e (2) eles não são adequados para as funções binate. Para superar o primeiro inconveniente, é proposto um algoritmo que encontra equações read-once para funções Booleanas incompletamente especificadas, sempre que possível, é proposto. Com respeito à segunda limitação, é apresentada uma transformação de domínio que divide variáveis binate existentes em duas variáveis unate independentes. Tal transformação de domínio conduz a funções Booleanas incompletamente especificadas, que podem ser eficientemente fatoradas mediante a aplicação do algoritmo proposto. A combinação das duas contribuições dá resultados ótimos para uma nova classe de funções Booleanas chamada read-polarity-once, onde cada polaridade (positiva ou negativa) de uma variável aparece no máximo uma vez na forma fatorada da expressão Booleana. Resultados experimentais sobre circuitos ISCAS'85 mostrou que funções read-polarity-once são significativamente mais frequentes em circuitos reais quando comparado com a classe de funções read-once, a qual muitos trabalhos já foram dedicados na literatura. / Efficient exact factoring algorithms are limited to read-once functions, in which each variable appears once in the final Boolean equation. However, those algorithms present two main constraints: (1) they do not consider incompletely specified Boolean functions; and (2) they are not suitable for binate functions. To overcome the first drawback, it is proposed an algorithm that finds read-once formulas for incompletely specified Boolean functions, whenever possible. With respect to the second limitation, a domain transformation that splits existing binate variables into two independent unate variables is presented. Such domain transformation leads to incompletely specified Boolean functions, which can be efficiently factored by applying the proposed algorithm. The combination of both contributions gives optimal results for a novel broader class of Boolean functions named as read-polarity-once functions, where each polarity (positive or negative) of a variable appears at most once in the factored form. Experimental results over ISCAS'85 benchmark circuits have shown that read-polarityonce functions are significantly more frequent than read-once functions, for which many works have already been devoted in the literature.

Devido à demanda de aumento de produtividade na indústria, a utilização de materiais mais leves, busca por processos de reparos com melhor custo, em conjunto com o avanço das tecnologias, evolução dos processos de soldagem, e esses fatores aliados aos benefícios de uma maior taxa de fusão, melhor controle da penetração, faz com que o processo MIG/MAG com polaridade variável apresente consideráveis avanços tecnológicos nos dias de hoje. Porém, a seleção dos parâmetros da curva típica de corrente do processo (composta por corrente de pico, corrente de base positiva e corrente negativa), é ainda um desafio. Buscando um melhor entendimento da influência da polaridade negativa no processo de soldagem, em especial para aplicações de revestimento, este trabalho tem como objetivo analisar os parâmetros da polaridade negativa individualmente em relação a geometria do cordão de solda, utilizando aço ao carbono como metal base e aço inoxidável como metal de adição. O planejamento e execução do experimento foi realizado com base na metodologia de projeto de experimentos Box-Behnken, variando três fatores: tempo de corrente negativa, intensidade de corrente negativa e tempo de corrente de base positiva, em três níveis cada um. Primeiramente alcançou-se a minimização da diluição, onde o tempo de corrente negativa apresentou efeito significativo no resultado final, sendo seu nível máximo (15 ms) o responsável pelos menores valores de diluição, aproximadamente 12%, recomendado em soldagem para revestimento. Posteriormente, foi avaliado o efeito dos parâmetros em relação à penetração, altura e largura do cordão de solda, sendo o tempo de corrente negativa em 15 ms e corrente negativa em -150 A os níveis que apresentaram melhores resultados. Após, os parâmetros da polaridade negativa utilizados foram comparados com os termos proporcionais sugeridos pela literatura (%EN). E, por fim, avaliou-se uma forma de curva de corrente sem a corrente de base positiva, onde foi concluído que não há significância das diferentes formas de curva de corrente sobre os resultados na penetração do cordão de solda, assim como a necessidade da corrente de base na estabilidade do arco elétrico do processo. / Due to the demand to increase productivity in the industry, use lighter materials, search for repair processes with better cost, in combination with advancement of technologies, evolution of welding processes, connected with the benefits of a higher melting rate and better control of the process penetration, it was possible to verify advances in the MIG / MAG Variable Polarity welding technique. However, the selection of the parameters of the typical process current curve (composed by peak current, positive current and negative current), is still a challenge today. The aim of this work is to analyze the negative polarity parameters individually in relation to the weld bead geometry, using carbon steel as base metal and stainless steel as addition metal. The planning and execution of the experiment was performed based on the Box-Behnken design methodology, varying three factors: negative current time, negative current intensity and positive base current time, at three levels each one. Firstly, dilution minimization was achieved, which showed that the negative current time had a strong influence on the final result, and the maximum level (15 ms) was responsible for the lowest dilution values, nearby 12%, ideal for welding cladding. Then, the parameters were evaluated in relation to penetration, height and width of the weld bead, which for welding cladding, the negative current time 15 ms and negative current -150 A presented better results. Next, the negative polarity parameters were compared with the proportional terms suggested by the literature (%EN). Finally, a form of current curve without positive base current was evaluated, where it can be concluded that the current curve form does not have significance on the penetration results, as well as the necessity of the base current in the arc electric stability.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / In this work we use the Density Functional Theory (DFT) to analyze the influence of a water environment in the interaction between amino acids and a semiconductor carbon nanotube (CNT). To the study of the interaction in vacuum we use both an ab initio and a parameterized tight-binding method. To the study of the same interactions in water we performed finite temperature (300 K) molecular dynamics calculations, using the parameterized tight-binding method. The selected amino acids have different hydrophobicity and polarity indexes. Our study shows that for the neutral amino acids, a direct relationship between the variation in the bonding distances and the hydrophobicity indexes when changing from vacuum to water environments, with the hydrophobic (hydrophilic) amino acids getting nearer (farther) of the carbon nanotube. The change in the binding energies, when going from the vacuum to the water environments, shows an inverse relationship with the polarity, with the amino acids that have more polar (nonpolar) side chains showing lower (greater) variations in the binding energies. We also analyze the variations in the binding energies in vacuum and water for the neutral and zwitterionic forms of glicine. We show that the zwitterionic form is more stable in the polar environment of water, whereas the neutral form is more stable in vacuum. / Neste trabalho utilizamos a teoria do funcional da densidade (DFT) para analisar a influência de um meio solvente, a água, na interação de aminoácidos com um nanotubo de carbono (CNT) semicondutor. Para o estudo das interações no vácuo utilizamos tanto um método ab-initio quanto um método tight binding parametrizado. Os estudos destas mesmas interações (CNT-aminoácidos) no meio aquoso foram realizados empregando o método de dinâmica molecular a uma temperatura de 300 K usando o método tight binding parametrizado. Os aminoácidos selecionados para o estudo tinham diferentes valores de índice de hidrofobicidade e de polaridade. Nossos resultados mostram que para a forma neutra destes aminoácidos, há uma relação direta entre a variação da distância da ligação, do vácuo em relação a água, e o índice de hidrofobicidade com os aminoácidos mais hidrofóbicos (hidrofílicos) se aproximando (afastando) do nanotubo de carbono. A variação da energia de ligação, quando se passa do vácuo para o ambiente aquoso, apresenta uma relação inversa com a polaridade, com os aminoácidos que possuem a cadeia lateral mais polares (menos polares) apresentado os menores (maiores) variações na energia de ligação. Analisamos ainda as variações na energia de ligação no vácuo e na água para o aminoácido glicina em relação as suas possíveis formas elétricas: neutra e como íon dipolar (zwiteri onica). Mostramos que a forma zwiteriônica é mais estável no ambiente polar da água, enquanto a forma neutra apresenta maior estabilidade no vácuo.

During embryonic development of the nematode Caenorhabditis elegans, cell fates are specified by asymmetric segregation of cell fate determinants and via cell-cell signaling events. Specification of the eight-cell stage blastomere E, the endoderm progenitor cell, requires both cell signaling and asymmetric cell division. At the four-cell stage, a polarity-inducing signal from the P2 cell is required for the EMS cell to divide asymmetrically to produce an anterior daughter MS, and posterior daughter E. In the absence of signal, the EMS cell divides symmetrically to produce two daughters that adopt the MS fate. This thesis describes the identification and analyses of seven genes required to tranduce this polarity-inducing signal and specify endoderm formation. The mom-1, mom-2, mom-5, apr-1, and wrm-1 genes are homologous to components of the Wnt/Wingless signal transduction pathway, and the mom-4, and lit-1 genes are related to components of the mitogen-activated protein kinase pathway. Biochemical analysis of these signaling molecules reveal a novel convergence of these pathways at the level of the LIT-1 and WRM-1 proteins, which appear to function as a kinase complex and are required for the downregulation of POP-1. Together these genes constitute components of a complex genetic pathway required for specification of the E cell fate.

Tous les organismes, les animaux, les plantes et les microbes, sont composés de cellules polarisées, en affichant un positionnement asymétrique des organites sub-cellulaires ou des structures. Le contrôle de polarité a été étudié chez les eucaryotes pendant une longue période, et a été montré pour être impliqués dans de nombreux processus physiologiques, tels que l'embryogenèse, le cancer métastatique et les maladies dégénératives des neurones. Chez les procaryotes, des études de polarité ne sont apparues récemment avec le développement de la microscopie à fluorescence sensibles. Ces études ont révélé que les cellules procaryotes sont en fait très organisé et une masse croissante de la littérature a montré que les cellules bactériennes également utiliser des radeaux lipidiques, courbure membranaire, la paroi cellulaire et un cytosquelette complexe pour diriger le positionnement spécifique de structures subcellulaires.Petites GTPases de la superfamille Ras sont des éléments réglementaires polarisation répandue chez les eucaryotes. Malgré l'existence depuis longtemps de ces petites GTPases dans les génomes procaryotes, leur fonction a jamais été étudiée. Pendant ce travail de thèse, nous avons trouvé, pour la première fois, qu'une petite GTPase, MglA et de sa protéine apparentée Activation GTPase (GAP) MglB, directe une dynamique axe antéro-postérieur à la motilité directe en forme de tige deltaproteobacterium Myxococcus xanthus. Dans ce processus, MglA s'accumule dans son état lié au GTP au niveau du pôle leader de cellules, en activant les machineries motilité. Ce schéma de localisation est maintenue par MglB, qui localise le pôle opposé, le blocage de l'accumulation MglA à ce pôle à travers son activité GAP. Remarquablement, les deux protéines passer leur localisation synchrone, ce qui correspond à un changement dramatique dans la direction du mouvement cellulaire (inversion). Ce commutateur est réglementé par un système chimiosensoriels-like, Frz. Dans une deuxième partie de ce travail, nous avons identifié un régulateur de protéine de réponse, RomR qui est essentiel pour le regroupement polaire de MglA. Interdépendances complexes entre la localisation RomR, MglA et MglB indiquent que ces protéines pourraient constituer un complexe de polarité dynamique de trois protéines qui reçoit Frz de signalisation pour passer l'axe de polarité. En conclusion, les résultats de ce travail de thèse suggère que M. xanthus intégré un module de polarité eucaryotes-like (MglAB) dans un procaryote spécifique (Frz) réseau de signalisation pour réguler sa motilité. Une telle réglementation est distincte sous forme de petites protéines G des règlements, qui sont généralement couplés à la protéine G récepteurs couplés (GPCR) chez les eucaryotes. Enfin, ce travail ouvre la voie pour comprendre comment la réglementation seule la motilité cellulaire sont intégrés pour générer des comportements commandés multicellulaires donnant naissance à des structures primitives de développement, par exemple, la morphogenèse du corps fructifères. D'autre part, ce travail fournit également un exemple d'analyser les étapes évolutives donnant lieu à des réseaux de signalisation. / All organisms, animals, plants and microbes, are composed of polarized cells, displaying asymmetric positioning of sub-cellular organelles or structures. Polarity control has been studied in eukaryotes for a long time, and has been shown to be involved in many physiological processes, such as embryogenesis, cancer metastasis and neuron degenerative diseases. In prokaryotes, polarity studies only emerged recently with the development of sensitive fluorescent microscopy. These studies revealed that prokaryotic cells are in fact highly organized and a growing body of literature has shown that bacterial cells also use lipid rafts, membrane curvature, the cell wall and a complex cytoskeleton to direct the specific positioning of subcellular structures.Small GTPases of the Ras superfamily are widespread polarization regulatory elements in eukaryotes. Despite the long known existence of such small GTPases in prokaryotic genomes, their function has never been studied. During this thesis work, we found, for the first time, that a small GTPase, MglA and its cognate GTPase Activating Protein (GAP) MglB, direct a dynamic anterior- posterior axis to direct motility of the rod-shaped deltaproteobacterium Myxococcus xanthus. In this process, MglA accumulates in its GTP-bound state at the leading cell pole, activating the motility machineries. This localization pattern is maintained by MglB, which localizes at the opposite pole, blocking MglA accumulation at this pole through its GAP activity. Remarkably, both proteins switch their localization synchronously, which correlates with a dramatic change in the direction of cell movement (reversal). This switch is regulated by a chemosensory-like system, Frz. In a second part of this work, we identified a response regulator protein, RomR which is essential for the polar clustering of MglA. Intricate localization interdependencies between Romr, MglA and MglB indicate that these proteins might constitute a dynamic three-protein polarity complex that receives Frz-signaling to switch the polarity axis. In conclusion, the results from this thesis work suggest that M. xanthus integrated a eukaryotic-like polarity module (MglAB) into a prokaryotic- specific (Frz) signaling network to regulate its motility. Such regulation is distinct form small G- protein regulations, which are generally coupled to G-protein coupled receptors (GPCRs) in eukaryotes. Finally, this work paves the way to understand how single cell motility regulations are integrated to generate ordered multicellular behaviors giving rise to primitive developmental structures, for example fruiting body morphogenesis. On the other hand, this work also provides an example to analyze the evolutionary steps giving rise to signaling networks.