During development, cells consume energy, divide, rearrange, and die. Bulk properties such as viscosity and elasticity emerge from cell-scale mechanics and dynamics. Order appears, for example in patterns of hair outgrowth, or in the predominately hexagonal pattern of cell boundaries in the wing of a fruit fly. In the past fifty years, much progress has been made in understanding tissues as living materials. However, the physical mechanisms underlying tissue-scale behaviour are not completely understood. Here we apply theories from statistical physics and fluid dynamics to understand mechanics and order in two-dimensional tissues. We restrict our attention to the mechanics and dynamics of cell boundaries and vertices, and to planar polarity, a type of long-ranged order visible in anisotropic patterns of proteins and hair outgrowth. Our principle tool for understanding mechanics and dynamics is a vertex model where cell shapes are represented using polygons. We analytically derive the ground-state diagram of this vertex model, finding it to be dominated by the geometric requirement that cells be polygons, and the topological requirement that those polygons tile the plane. We present a simplified algorithm for cell division and growth, and furthermore derive a dynamic equation for the vertex model, which we use to demonstrate the emergence of quasistatic behaviour in the limit of slow growth. All our results relating to the vertex model are consistent with and build off past calculations and experiments. To investigate the emergence of planar polarity, we develop quantification methods for cell flow and planar polarity based on confocal microscope images of developing fly wings. We analyze cell flow using a velocity gradient tensor, which is uniquely decomposed into terms corresponding to local compression, shear, and rotations. We argue that a pattern in an inhomogeneously flowing tissue will necessarily be reorganized, motivating a hydrodynamic theory of polarity reorientation. Using such a coarse-grained theory of polarity reorientation, we show that the quantified patterns of shear and rotation in the wing are consistent with the observed polarity reorganization, and conclude that cell flow reorients planar polarity in the wing of the fruit fly. Finally, we present a cell-scale model of planar polarity based on the vertex model, unifying the themes of this thesis.

Apicobasal polarity is essential for epithelia formation and maintenance. Cell junctions, namely the zonula adherens in Drosophila melanogaster, are the morphological landmarks that define and distinguish the apical from the basal surface. This resulting compartmentalisation is key for the cell and consequently the epithelia. To maintain proper junctions, cells make use of several protein complexes and their interactions. Among these complexes, the Crumbs (Crb) network stands out. Mutations in Crumbs (crb11A22) lead to zonula adherens collapse, consequent loss of apical surface and disaggregation of the epithelia. However, the mechanisms behind this are not known and havenʼt been addressed using modern techniques such as live imaging. Several things came out of the dataset obtained from the FRAP experiments. Firstly, protein kinetics are better described when a double exponential fit curve is used, which raises the possibility that two cell processes might be involved in the recovery observed for the different markers. Another finding was the fact that the kinetics of some polarised protein markers is not the same in every region of the embryo. Distinct areas of the embryo with different morphogenetic activity levels show different kinetics for the same compartment marker. That was the case with SpiderGFP (whole plasma membrane marker) and SASVenus (apical plasma membrane marker) where τ2 was lower in the posterior region of the embryo which is characterised by intense cell movements resulting from convergence extension. DE-CadGFP (zonula adherens marker) and lacGFP (basolateral marker) behaved similarly in the whole embryo. This indicates that convergence extension shows different trafficking needs for the apical surface. In crb11A22, SpiderGFP kinetic spatial differences were not observed. τ2 in the anterior (low level of morphogenesis) is affected and similar to wild type τ2 levels in the posterior. This could pinpoint the fact that the epithelia disaggregation is a result of trafficking failure of apical components. Live imaging of DE-CadGFP in crb11A22 background revealed initial disaggregation in the anterior part of the embryo, which strengthens the idea that Crb is required for adherens junction stabilisation and maintenance.

The East African Rift System diverges in the Lake Natron Basin of Northern Tanzania and is a major zone of continental extension and crustal thinning with resulting in active tectonics and volcanism. The discovery of Acheulean technology in Olduvai Gorge and Peninj as well as the presence of significant volcanic centers, has made in the region subject to studies in various disciplines. However, lack of precise radiometric age constraints due to the complex geology of the region is a major drawback. The basin is bordered on the western side by an escarpment that contains thick sequences of volcanic (nephelinites, basanites, hawaiites, alkali basalts), volcaniclastic and lacustrine strata that predates 1.2 Ma. This thesis is based on 41 rock samples that were collected from two geological sections, the Endukai Kete (EK) and Waterfall (WF) sections and aims to establish a preliminary geomagnetic polarity time scale (GPTS) for the Natron Escarpment, together with establishing possible flow directions of the volcanic lavas within these sections. Nephelinites of EK section have an inferred NW-SE direction of flow, based on study of anisotropy of magnetic susceptibility. They record a normal polarity that most likely correspond to the Cobb Mountain Event (CMT; 1.187-1.208 Ma), although there is an 80-ka discrepancy between the CMT event and the dated lavas. The most probable source is the Mosonik that erupted nephelinitic lavas 1.28 Ma ago. The palagonitic tuff layer below the nephelinites displays reverse polarity and a NE-SW direction of flow. Due to the absence of approximately 200 m strata within the basanite series of the section, regional lithological correlation is used to constrain the GPTS pattern. Hajaro Beds of the Peninj Group to the north of the escarpment, postdates the Olduvai Event (1.71 to 1.86 Ma) and lacustrine strata of the escarpment for EK and WF sections are deposited over the same unconformity and share depositional similarities. Therefore, the lacustrine strata are correlative to Hajaro beds and the normal event observed within the basanite series of both sections is attributed to the Réunion Event (2.116 – 2.137 Ma). The establishment of a preliminary magnetostratigraphic sequence presented in this thesis demonstrate that the rift escarpment in northern Tanzania is suitable for paleomagnetic dating. Future studies should be conducted to establish a more detailed and constrained magnetostratigraphic section, which will be of great use in this part of the African Rift where radiometric dating has been challenging.

Diseases caused by bacteria, fungi and viruses pose a significant threat especially to poor rural communities. Viral infections are frequently complicated by secondary bacterial and fungal infections which remain a major challenge globally and in particular, in sub Sahara Africa amongst humans and animals alike. The main aim of this study was to develop a low toxicity plant extract or isolated compound active against viral, bacteria and fungal pathogens from selected plant species. Seven tree species that were investigated were Acokanthera schimperi, Carissa edulis, Ekebergia capensis, Podocarpus henkellii, Plumbago zeylanica, Annona senegalensis and Schrebera alata traditionally used in the treatments of various ailments were selected and extracted using solvents of varying polarity. Extracts of selected plants were tested for activity against two Gram positive and two Gram negative bacterial namely Enterococcus faecalis and Staphylococcus aureus and two Gram-negative species, Pseudomonas aeruginosa and Escherichia coli respectively, three fungal pathogens: Candida albicans, Cryptococcus neoformans and Aspergillus fumigates and four enveloped animal viruses: feline herpes virus–1 (FHV-1, dsDNA), canine distemper virus (CDV, ssRNA), canine parainfluenza virus-2 (CPIV-2, ssRNA) and lumpy skin disease virus strain V248/93 (LSDV, dsDNA). The presence of antioxidant constituents in the different extracts and cytotoxicity against three cell types CRFK, bovine dermis and Vero cells were determined. Bioautography and the serial microplate dilution methods were used to determine the number of antimicrobial compounds and antimicrobial activity of extracts against bacterial and fungal pathogens. Virucidal and attachments assays were used to determine the activity against viral pathogens. Qualitative antioxidant activities of extracts were tested using the DPPH reagent and cytotoxicity using the MTT assay. Biological activity was observed in all the extracts against one or more organisms on bioautography. The intermediately polar system (CEF) separated more active constituents. Some extracts had compounds with similar Rf values active against one or more organisms. In both the antibacterial and antifungal assays, acetone extracts had the highest activity followed by DCM against one or more pathogens. Hexanes extracts were the least active. P. henkellii extracts had more active compounds against the bacteria and Annona senegalensisagainst the fungi. In the micro-dilution assay, S. aureus was the most susceptible bacterial organism to extracts of the different plant, followed by P. aeruginosa andEscherichia coli, and E. faecalis the least. C. neoformans on the other hand was the most susceptible fungal pathogen. In the antiviral assay, although activity was observed with hexane extracts of some plants in the virucidal assay, the most potent inhibition was observed with the acetone and methanol extracts of Podocarpus henkelii against CDV and LSDV in the virucidal assay and acetone extracts in the attachment assay. In general the hexane was the least toxic while the intermediate polarity extracts were generally the most toxic indicating that highly polar compounds were possibly poorly or highly absorbed through membranes in the former and later respectively. Of the three cell types used CRFK was the most sensitive followed by bovine dermis and Vero cells the least. Cytotoxicity studies of extracts of the different plants revealed A. senegalensis and A. schimperi extracts were the most toxic plants in the cellular assay. These plants are toxic to animals and the cytoxicity is in line with the in vivo toxicity. The protective effects of antioxidant constituents in some extracts varied and appear to be influenced by the metabolism of the type of cell in culture. It also appears to suggest that metabolism in kidney derived cells can be influenced by species variation in the origin of cells. P. henkellii was selected for isolation of bioactive compound. Three compounds were isolated and their structure elucidated using 13C and 1H NMR and mass spectrometric data. The antibacterial, antifungal and antiviral activity of the isolated compounds 7’, 4’, 7’’, 4’’’, tetramethoxy amentoflavone (C1), isoginkgetin (C2) and Podocarpusflavone–A (C3) were determined. Compound C2 was the most active against E. coli and S. aureus (MIC = 60 ìg/mE) and a selectivity index (SI) value of 16.67. The compound was also active against A. fumigatus and C. neoformans (SI = 33.33) suggesting both antibacterial and antifungal activity with relative safety. Compound C3 had a broad spectrum of activity against E. faecalis and P. aeruginosa with SI values of 4. A less potent activity of the compounds was obtained in both the virucidal and attachment assays against test pathogens, indicating the lower activity of the compounds against tested viral pathogens. The studies further suggest structural activity relationship in the antimicrobial activity of biflavonoids. The compounds C1 and C2 had no toxic effect on the three cell types and mutagenicity studies indicated no activity of these compounds. Podocarpusflavone-A occurs in every species of Podocarpus so far investigated, except P. latifolius. These studies represent the first isolation of bioactive compounds from P. henkellii. Although a different extractant was used than that used by traditional healers, the presence of antiviral compounds in Podocarpus henkelii against two unrelated viruses may justify on a chemotaxonomic basis the traditional use of related species Podocarpus latifoliusand Podocarpus falcatus in the traditional treatment of canine distemper infection in dogs. / Thesis (PhD)--University of Pretoria, 2011. / Paraclinical Sciences / unrestricted

This thesis aims to shed light on the differences between offensive and a specific version of neoclassical realism on their expectations regarding how a great power shapes its environment. The neoclassical framework proposed in this work constitutes an independent variable captured by the polarity in the system, an intervening variable of state capacity, and a dependent variable of revisionist foreign policy. It is argued that along with multipolarity and bipolarity, there is a need to incorporate unipolarity in structural realist accounts. Analysed from this perspective, great powers feel high external pressure due to the nature of unipolarity, which diminishes the value of pure structural frameworks. In this respect, the incorporation of state-level factors provides more reliable analyses for explaining anxious great powers` strive for regional hegemony. As a result, neoclassical realism is better equipped to explain Russia`s revisionist foreign policy.

Amino acid frequencies in proteins may not be at equilibrium. We consider two possible explanations for the nonzero net residue fluxes in drosophilid proteins. First, protein interiors may have a suboptimal residue composition and be under a selective pressure favoring stability, that is, leading to the loss of polar (and the gain of large) amino acids. One would then expect stronger net fluxes on the protein interior than at the exposed sites. Alternatively, ifmost of the polarity loss occurs at the exposed sites and the selective constraint on amino acid composition at such sites decreases over time, net loss of polarity may be neutral and caused by disproportionally high occurrence of polar residues at exposed, least constrained sites.We estimated net evolutionary fluxes of residue polarity and volume at sites with different solvent accessibility in conserved protein families from 12 species of Drosophila. Net loss of polarity, miniscule in magnitude, but consistent across all lineages, occurred at all sites except the most exposed ones, where net flux of polaritywas close to zero or, in membrane proteins, even positive. At the intermediate solvent accessibility the net fluxes of polarity and volumewere similar to neutral predictions, whereas much of the polarity loss not attributable to neutral expectations occurred at the buried sites. These observations are consistent with the hypothesis that residue composition in many proteins is structurally suboptimal and continues to evolve toward lower polarity in the protein interior, in particular in proteins with intracellular localization. The magnitude of polarity and volume changes was independent from the protein's evolutionary age, indicating that the approach to equilibrium has been slow or that no such single equilibrium exists.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第23571号 / 医博第4785号 / 新制||医||1054(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 齊藤 博英, 教授 大森 孝一, 教授 大鶴 繁 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

La phosphoinositide 3-kinase p110δ (PI3Kδ) est principalement exprimée dans les cellules hématopoïétiques et son inhibiteur, l'idélalisib est approuvé pour le traitement de la leucémie et du lymphome. Cependant, la fonction de cette isoforme dans les cellules non hématopoïétiques reste insaisissable. Dans cette étude, nous rapportons que la formation des canalicules biliaires est dépendante de l’activité de la PI3Kδ lors de la culture en 3D de cellules de carcinome hépatocellulaire. Une étude in-vitro reposant sur la différenciation de cellules souches embryonnaires humaines en hépatocytes révèle que la PI3Kδ est enrichie dans les cellules souches et que son expression diminue au fur et à mesure que les cellules se différencient. Lorsqu’elle est surexprimée, la PI3Kδ reprogramme ces cellules en cellules ressemblant à des cellules souches formant des rosettes polarisées et perdant des marqueurs d’hépatocytes pour acquérir des traits de cholangiocytes. Dans le foie murin, la réexpression de la PI3Kδ entraine des modifications de la morphologie de cellules jouxtant la veine porte, ainsi que l’augmentation de l’expression du gène codant pour EpCAM. Cette reprogrammation dépendante de la PI3Kδ est associée à l'activation de la voie de Notch et requiert l'activation de la protéine Src. Enfin, la PI3Kδ est exprimée dans les lignées cellulaires dérivées d’hépatoblastome humain et le traitement des souris par l’idélalisib diminue la taille des tumeurs formées par les PDX d’hépatoblastome. La PI3Kδ représente donc une cible thérapeutique prometteuse dans ce cancer pédiatrique avec des caractéristiques de cellules souches. / The phosphoinositide 3-kinase p110δ (PI3Kδ) is primarily expressed in the hematopoietic cells and its inhibitor, Idelalisib, is approved for leukemia and lymphoma treatments. Nevertheless, the function of PI3Kδ in the non-hematopoietic cells is still elusive. Here we report that the formation of bile canaliculi is dependent on the PI3Kδ activity using hepatocellular carcinoma (HCC) cells grown in a 3D culture. In-vitro study based on hepatocytes differentiation from human Embryonic Stem Cell (hESC) highlights that PI3Kδ is enriched in hESC and increasingly reduces over time while cells are differentiating. When PI3Kδ is overexpressed, it reprograms those cells into stem-like cells forming polarized rosette structures and losing hepatocyte markers to gain cholangiocyte characteristics. These changes were observed in mice liver overexpressing PI3Kδ. The aforementioned reprogramming, dependent on PI3Kδ, is associated with the Notch pathway activation and requires the Src protein activation. Finally,PI3Kδ is expressed in hepatoblastoma cell lines and idelalisib efficiently reduces tumor size formed by patient derived xenograft (PDX). Therefore, PI3Kδ represents a promising therapeutic target for this pediatric cancer with stem cell features.

Etudiées par la phraséologie, les locutions verbales sont des composantes de la structure du langage naturel qui expriment une idée ou un concept. Ces structures linguistiques sont des unités lexicales composées par plusieurs mots. Elles sont formées par un verbe et une ou plusieurs variables, dont le signifié global n'est pas nécessairement déduit du signifié de chacun de ses composants.Dans ce travail de recherche, nous proposons une méthodologie informatique permettant l’identification semi-automatique des locutions verbales de l’espagnol mexicain. Cette méthodologie contribue tant au domaine de la linguistique qu’à celui de l’informatique. Nous introduisons des méthodes informatiques supervisées et non supervisées pour l’identification et la validation des “locutions verbales candidates” en corpus des différents domaines.Les contributions de cette thèse sont principalement de quatre ordres : a) des corpus manuellement annotés pour les locutions verbales, en incluant leurs contextes, b) un lexique qui estime la probabilité d’occurrence de ces structures linguistiques dans le corpus du genre journalistique, c) diverses hypothèses pour la validation et/ou identification des locutions verbales en textes bruts, et d) l’analyse de la polarité de celles-ci.Les résultats obtenus, en incluant les hypothèses envisagées dans cette thèse, auront un impact futur sur des différentes tâches, tels que la traduction automatique, la construction des dictionnaires et l’apprentissage d’une langue étrangère, pour ne citer que quelques exemples. / Verbal phraseological units are components of the natural language structure, studied by phraseology, which express a concept or an idea. These linguistic structures are multi-word lexical units, made up of one verb and one or more variables, having a meaning which cannot be predicted from the sum of the expression component meanings. In this PhD thesis we proposed a computational methodology for the semi-automatic identification of verbal phraseological units written in Mexican Spanish that aims to contribute in both, the linguistic and computational fields. We introduce unsupervised and supervised computational methods in order to identify and validate “candidate verbal phraseological units” in corpora of different genre.The contributions of this research work are mainly four: a) corpora manually annotated for verbal phraseological units and contexts associated, b) a lexicon in which it is estimated the probability of occurrence of such linguistic structures in a corpus of news genre, c) a number of hypotheses for the automatic validation and/or identification of verbal phraseological units in raw texts, and d) analysis of their polarity.The obtained results, including the hypotheses proposed in the PhD document, will have a future impact in different tasks such as machine translation, dictionaries construction, foreign language learning, among others.