In the development of multicellular organisms, tissue development and homeostasis require coordinated cellular motion. For example, in conditions such as wound healing, immune and epithelial cells need to proliferate and migrate. Deregulation of key signalling pathways in pathological conditions causes alterations in cellular motion properties that are critical for disease development and progression, in cancer it leads to invasion and metastasis. Consequently there is strong interest in identifying factors, including drugs that affect the motion and interactions of cells in disease using experimental models suitable for high-content screening. There are two main modes of cell migration; individual and collective migration. Currently analysis tools for robust, sensitive and comprehensive motion characterisation in varying experimental conditions for large extended timelapse acquisitions that jointly considers both modes are limited. We have developed a systematic motion analysis framework, Motion Sensing Superpixels (MOSES) to quantitatively capture cellular motion in timelapse microscopy videos suitable for high-content screening. MOSES builds upon established computer vision approaches to deliver a minimal parameter, robust algorithm that can i) extract reliable phenomena-relevant motion metrics, ii) discover spatiotemporal salient motion patterns and iii) facilitate unbiased analysis with little prior knowledge through unique motion 'signatures'. The framework was validated by application to numerous datasets including YouTube videos, zebrafish immunosurveillance and Drosophila embryo development. We demonstrate two extended applications; the analysis of interactions between two epithelial populations in 2D culture using cell lines of the squamous and columnar epithelia from human normal esophagus, Barrett's esophagus and esophageal adenocarcinoma and the automatic monitoring of 3D organoid culture growth captured through label-free phase contrast microscopy. MOSES found unique boundary formation between squamous and columnar cells and could measure subtle changes in boundary formation due to external stimuli. MOSES automatically segments the motion and shape of multiple organoids even if present in the same field of view. Automated analysis of intestinal organoid branching following treatment agrees with independent RNA-seq results.

Made available in DSpace on 2015-03-13T17:10:31Z (GMT). No. of bitstreams: 1 ValdembergAAS.pdf: 4975019 bytes, checksum: f75f416655ac17172121b061a2d7e7f8 (MD5) Previous issue date: 2008-10-10 / This study was developed in the northern coast of the city of Macau, a total area of 88,52 km?, located in the State of Rio Grande do Norte. It presents relatively plain surface, with interlaced of streams and gamboas, characterized by contributions of oceanic water, flooding areas of swamps. Altogether, the climatic and topographical conditions provide an ideal environment for the development of saline activity. Inserted in the geologic context of the Potiguar Basin, the region presents favorable conditions for the production of hydro-carbons. It still presents natural conditions for shrimp breeding and artisanal fishing. This work analyzes the transformations occurred in the land use, using air photographs of 1978, Landsat 5 ETM Images of 1988, 1998 and 2008. A secular analyzes was carried through the dynamics of the use of the territory and the transformations occurred in the landscape due to the increment of the productive activities. In the survey of the data for study of the area, it was verified that little alteration occurred in the 30 years. The saline activity that was present since the year of 1978 having an increase of about 5% in thirty years; the shrimp breeding activity that had its presence in the decade of 1990, presented a high growth in the land use, therefore in 1998 it presented 0.45% and currently it presents 6.59%. In the field it was observed that great areas used previously for the saline activity, today it is prepared for shrimp breeding and that the areas of petroleum exploration occupy salt mines, beaches and trays. In 1988 it presented a percentage of 0, 07% and currently it occupies 0.46%, having grown 50% in the last 10 years. Although the variation of the occupation of the area has been little expressive, shrimp breeding showed a growth of 1,200% in only 10 years. In regards to petroleum activity, there wasn t any demonstration of an increasing impact in the land use in the area of study in 26 years of exploration / Este estudo foi desenvolvido no litoral setentrional do munic?pio de Macau, localizado no Estado do Rio Grande do Norte, totalizando uma ?rea de 88,52 km?. Apresenta superf?cie relativamente plana, com entrela?ados de riachos e gamboas, caracterizada por contribui??es de ?guas oce?nicas, alagando ?reas de manguezais. Somadas ?s condi??es clim?ticas e topogr?ficas proporcionam um ambiente ideal para o desenvolvimento da atividade salineira. Inserida no contexto geol?gico da Bacia Potiguar, a regi?o apresenta condi??es favor?veis para a produ??o de hidrocarbonetos. Apresenta, ainda, condi??es naturais para a carcinicultura e pesca artesanal. Este trabalho analisa as transforma??es ocorridas no uso do solo, utilizando fotografias a?reas de 1978, Imagens Landsat 5 ETM de 1988, 1998 e 2008. Foi realizada uma an?lise temporal da din?mica do uso do territ?rio e as transforma??es ocorridas na paisagem, devido ao incremento das atividades produtivas. No levantamento dos dados para estudo da ?rea, foi verificado que pouca altera??o ocorreu nos 30 anos em tela. A atividade salineira que estava presente desde o ano de 1978, tendo um aumento aproximado de 5 % em trinta anos; a carcinicultura que teve sua presen?a na d?cada de 1990 apresentou um elevado crescimento no uso do solo, pois em 1998 apresentava 0,45% - atualmente 6,59%. No campo, observou-se que grandes ?reas utilizadas anteriormente para a atividade salineira, hoje se encontram preparadas para a carcinicultura e que as ?reas de explora??o petrol?fera ocupam salinas, praias e tabuleiros. Em 1988, ela apresentou uma porcentagem de 0,07% e atualmente ocupa 0,46%, tendo crescido 50% nos ?ltimos 10 anos. Embora a varia??o da ocupa??o da ?rea tenha sido pouco expressiva, a carcinicultura mostrou um crescimento de 1200% em apenas 10 anos. No tocante ? atividade petrol?fera, n?o houve demonstra??o de um aumento impactante no uso do solo na ?rea de estudo em 26 anos de explora??o

Les tourbières couvrent 3 % des surfaces continentales et jouent un rôle important dans le cycle du carbone en stockant le tiers du carbone des sols. L'accumulation de tourbe est liée au déséquilibre production primaire/décomposition du à une activité microbienne limitée par les conditions environnementales. L'infection et la lyse virale ont un impact sur la diversité et l'activité des communautés microbiennes, et influent sur le cycle du carbone. Cependant, le fonctionnement de ce compartiment viral n'avait jamais été pris en compte dans les études de fonctionnement des tourbières. Le but de ce travail de thèse était d'analyser et comprendre la dynamique spatiale et temporelle de l'abondance et de la diversité virale des tourbières à Sphagnum. L'analyse de l'abondance virale et procaryote et de 12 metaviromes en lien avec la physico-chimie d'une tourbière tempérée en France montre une forte variation saisonnière des communautés virales. Cette variation semble très liée aux conditions environnementales générées par la fluctuation de la nappe d'eau. Dans cette même tourbière, l'analyse de la diversité taxonomique et fonctionnelle des communautés de microorganismes présents (métagénomes) et métaboliquement actifs (métatranscriptomes) indique que la structure taxonomique est différente entre les des deux principaux stades, le fen et le bog, mais que ces communautés présentent une diversité fonctionnelle similaire, dont l'expression est liée aux changements des conditions environnementales avec la profondeur. L'abondance des particules virales étudiées dans 5 tourbières à Sphagnum réparties en Finlande, au Canada, en France, et sur l'île subantarctique d'Amsterdam varie fortement avec les sites. L'analyse de la diversité virale de la matrice et de l'eau de tourbe du Canada et de Finlande montre que la diversité virale est structurée par le site, puis le stade dynamique, puis la profondeur, avec un rôle important de la saturation en eau au niveau du site. Ces résultats valident le fonctionnement proposé du compartiment viral et de la communauté d'hôtes procaryotes. Ces connaissances ont été utilisées pour analyser le fonctionnement du compartiment microbien de tourbières à Sphagnum soumises à des perturbations d'origine anthropique. Les 31 métaviromes produits pour cette thèse constituent l'une des plus grandes bases de données sur la diversité virale des écosystèmes alors que la diversité virale des sols n'avait presque jamais été étudiée auparavant. / Peatlands cover 3 % of the continental surfaces but represent up to a third of the soil carbon stock. Peat accumulation results from the imbalance between primary production and decomposition due to the limitation of the prokaryote activity caused by the environmental conditions. Viral infection and lysis impact the diversity and the activity of the microbial communities and influence the carbon cycle. However, the functioning of the viral compartment had never been taken into account in peatlands. The aim of this thesis was to gain knowledge about the spatio-temporal dynamic of viral abundance and diversity in Sphagnum-dominated peatlands. Spatio-temporal analysis of viral and prokaryote abundance and of 12 metaviromes (viral diversity) in relation to the physico-chemical features in a temperate Sphagnum-dominated peatland in France revealed the high seasonal variability of the viral communities. This dynamic appeared mainly related to the environmental conditions shaped by the fluctuation of the water-table level. In the same peatland the taxonomic diversity of the present microorganisms (metagenomes) differed between the fen and the bog, but these communities present a similar functional diversity, which expression in selected in the same way in the two dynamic stages, in relation to depth-related environmental conditions. Viral abundance analyzed in 5 Sphagnum-dominated peatlands from Finland, Canada, France and subantarctic Amsterdam Isle presented a high geographical variability. Investigation of the diversity of the viral communities from the peat matrix and the pore-water in Finland and Canada emphasized the structuration of the viral communities by the site, then the dynamic stage, and finally depth. These results confirm the first hypotheses about the functioning of the viral compartment depending on environmental conditions and prokaryote activity. Effects of human-derived disturbances on viral ecology in peatlands were investigated based on this knowledge. While soil viral diversity was poorly documented at the start of this thesis, the collection of 31 metaviromes from Sphagnum-dominated peatlands produced for this project represents the second largest dataset representing the viral diversity from environmental samples.