Chez les plantes, l'oxyde nitrique (NO) est impliqué dans de nombreux processusbiologiques tels que la germination ou le développement racinaire et intervient dans les réponses àdivers stress biotiques ou abiotiques. Ainsi, en situation de stress en fer, la production de NOconstitue un événement précoce dans la voie de signalisation qui aboutit à l'induction desferritines. Les cibles du NO demeurent toutefois mal connues, mais il est établi qu'un effet majeurest la S-nitrosylation de cystéines dans les protéines. Dans ce travail, nous avons cherché àidentifier les protéines (et les cystéines) qui constituent les cibles moléculaires du NO dans deuxsituations de stress abiotique chez Arabidopsis thaliana. Dans ce but, une démarche deprotéomique post-traductionnelle dédiée, fondée sur la méthode classique dite du «Biotin-switch»(BS), a été privilégiée pour l'identification des protéines nitrosylées. Par ailleurs, afin de pouvoirévaluer les variations de nitrosylation et analyser des réponses physiologiques, nous avonsintroduit une dimension quantitative en combinant le BS à un marquage des thiols par des réactifsdifférant par la présence d'isotopes lourds (Isotope coded affinity tag, ICAT). La méthode ainsidéveloppée (BS-ICAT) a permis de caractériser des variations de nitrosylation de protéines lorsd'un stress ferrique et d'un stress salin. A côté de l'identification de cibles potentielles du NO, lesrésultats ont également attiré l'attention sur certaines limites du BS. Sur cette base, la méthodeBS-ICAT a été utilisée pour revisiter quantitativement le BS. Nous avons montré que le blocagedes thiols libres, étape initiale-clé fondant le BS, n'est que partiel et conduit à l'apparition de fauxpositifs. Simultanément, de nouveaux contrôles de spécificité ont été éprouvés. La combinaisonBS-ICAT constitue l'une des toutes premières tentatives pour la caractérisation quantitative àlarge échelle de réponses de nitrosylation. A côté d'un premier répertoire de sites de Snitrosylationchez les plantes et de l'identification de candidats potentiellement impliqués dans lesréponses aux stress en fer et en sel, l'analyse quantitative permet de proposer une utilisation du BSintégrant ses limites de façon plus contrôlée. Cette analyse souligne le besoin de méthodesalternatives où le marquage soit réalisé directement sur les nitrosothiols. / In plants, nitric oxide (NO) is involved in many biological processes such as germination or roots development and in responses to various biotic and abiotic stresses. Thereby, in iron stress situations, NO production is the earliest signaling pathway event leading to ferritins induction. NO targets remain largely unknown but it is now stated that cysteine S-nitrosylation in proteins is the main NO consequence. The present work aims at identifying NO target proteins in Arabidopsis thaliana in the context of two abiotic stresses. For this purpose, a posttranslational proteomics approach based on the classical “Biotin-Switch” method (BS) was favored to identify nitrosylated proteins. Moreover, in order to estimate changes in nitrosylation and analyze physiological responses, a quantitative dimension combining the BS and a differential isotope based labeling of thiol with the ICAT reagents (Isotope Coded Affinity Tag) was introduced. This method named BS-ICAT allowed us to characterize quantitative variations of S-nitrosylation during an iron and a salt stress. Beside the identification of potential NO targets, our results highlighted limitations of BS method through incomplete free thiol blockage, the key initial step in BS, leading to false positive identifications. Simultaneously, new control have been introduced to test the specificity of the labeling. The combination of BS and ICAT is one the first attempt to quantitatively characterize the NO response at a large scale. This quantitative analysis results in one of the first repertoire of S-nitrosylation sites in plant proteins under abiotic stress and highly suggests a careful use of BS under strict control conditions. Moreover this analysis re-enforces the emerging need for alternative methods where the labeling molecules react directly with the nitrosothiols.

Many research institutes produce a huge amount of data. It was said by someone that “We are drowning in data, but starving of information”. This is particularly true for scientific data. The needs and the advantages of being able to search data from different experiments are increasing in order to look for differences and similarities among them and thus doing Meta studies. A Meta-study is the method that takes data from different independent studies and integrate them using statistical analysis. If data is well described and data access is flexible then it is possible to establish unexpected relationships among data. It also helps in the re-using of data from studies that have already been conducted which saves time, money and resources. In this thesis, we explore at the ways to store data from experiments and to make finding cross-experiments more efficient. The main aim of this thesis work is to propose a database solution for storing time series data generated by different simulators and to investigate the feasibility of using it with ICAT. ICAT is a metadata system used for searching and browsing of scientific data. This thesis has been completed in two steps. The first step is aimed at proposing an efficient database solution for storing time series data. The second step is aimed at investigating the feasibility of using ICAT and proposed database solution together. We found out that it is feasible to use ICAT as a metadata system for scientific studies. Since it is free and open source, it can be linked to any system and customized according to the needs.

Statens väg- och transportforskningsinstitut (VTI) utför tillämpad forsknings- och utveck-lingsverksamhet inom samtliga transportslag. Inom VTI genomförs ett antal olika projekt inom en stor variation av områden. Det kan handla om t.ex. människors beteende i trafiken, en körbanas hållbarhet eller, som denna rapport handlar om, trafikflödet över en viss geografisk punkt under ett förutbestämt tidsspann.Detta gör att en stor varierad mängd data produceras inom de olika avdelningarna då VTI har ca 35 olika testsystem och instrument som producerar mycket varierad data. Data kan be-stå av allt från relativt enkla heltalsserier till stora komplexa matriser. För att försvåra det hela så kan flera av de olika systemen och instrumenten producera flera olika sorters resultat bero-ende på vilken typ av studie som genomförs.Denna rapport beskriver arbetet att undersöka metadatasystemet ICAT som system. Rap-porten beskriver även arbetet med att skapa en prototyp, som en del av den förstudie som av-gör om VTI skall fortsätta arbetet med ICAT.Prototypen gör resultatdata från instrumentet Trafikanalysator 89(TA89) tillgänglig genom ICAT. Prototypen består av en webbportal, som är tillgänglig från samtliga datorer inom det lokala nätverket, med en underliggande databas för lagring av olika data relaterad till de olika studier som utförts. När studien är genomförd och resultatet förs in i prototypen, överförs me-tadata från prototypen till ICAT. Genom metadata kan andra forskare söka på resultatet, häm-ta insamlad forskningsdata och använda den i sin egen forskning. ICAT ger även forskare en överblick över de olika projekt och studier som vederbörande är eller har varit involverad i.

Enteropathogenic bacteria, such as Shigella and Salmonella, are associated with diarrheal diseases, which remain a significant cause of infant mortality worldwide. The secretion of protein effectors by the type III secretion apparatus (T3SA) is used by these pathogens to invade human cells and modulate host cell functions. First, we used RNA-Seq to analyze the differential transcriptome of Shigella flexneri when the T3SA is active or inactive. This allowed us to identify two uncharacterized genes that were temporarily named gem1 and gem3 and whose expression was regulated by MxiE and IpgC as other late substrates of the T3SA. Finally, we pursued the characterization of gem1 and gem3 at the protein level and renamed them icaT and icaR, respectively, when we found their protein products were secreted by the T3SA. Furthermore, we find homologs of icaT and icaR with a conserved MxiE box in several E. coli phylogroups. We also demonstrated that these homologous genes could be reactivated when both MxiE and IpgC were introduced in these strains. This discovery paved a new perspective on the evolution of pathogenesis into the E. coli lineage as both commensal and pathogenic strains harbored these genes. Treating infections caused by Enterobacteriaceae is becoming more challenging due to growing antibiotic resistance and no vaccines are widely available. Accordingly, the World Health Organization (WHO) recognized that we entered the "post-antibiotic era," where new antibiotics or antivirulence drugs are urgently needed, including for Shigella. The T3SA is an attractive target for antivirulence drugs, which may become alternative to classical antibiotics. Through screening 3,000 compounds, we found two novel inhibitors of the T3SA. Our data suggested that one of these candidate inhibitors, a dipyridyl-containing compound, reduces the virulence of Shigella at the transcriptional level. Indeed, the virulence inhibition occurs via the repression of the transcriptional activator VirB by the small chromosomal RNA RyhB, which is upregulated by this compound through an unknown mechanism involving the pyridyl groups. The repression of VirB induced by this molecule reduce the expression of several genes encoding parts of the T3SA. In comparison, the second compound is a quinone that seems to affect the assembly of the T3SA.

Ptf1a/p48 is a pancreas specific bHLH transcription factor that is required at early stages of embryonic development for pancreas formation and, during adulthood, for the proper exocrine pancreatic function. P48 also exerts an antiproliferative effect, which may exert a tumor suppressor activity. In this study, based on a yeast two-hybrid approach, we have identified new p48 partners that modulate the activity of p48. Among the newly identified putative interactors we found p/CAF, which is a coactivator that potentiates its transcriptional activity, and ICAT, an inhibitor of the β-catenin/TCF signaling pathway. ICAT binds to p48 and is coexpressed with it in the pancreas during development and postnatally. Using different cellular models, ICAT overexpression in acinar tumor cells resulted in changes of the pancreatic specific gene expression pattern. Furthermore, high levels of ICAT inhibited the interaction between p48 and p/CAF. While this hetero-oligomeric complex is required for the acinar gene expression, ICAT itself is shown to be present in a reconstituted PTF1 complex in vivo. Importantly, altered ICAT expression is demonstrated in several histological types of pancreatic tumors, possibly contributing to their differentiation phenotype and neoplastic properties. / Ptf1a/p48 es un factor de transcripción bHLH específico del páncreas necesario durante los estadios tempranos del desarrollo embrionario para la formación del mismo, y para el correcto funcionamiento del páncreas exocrino en el adulto. P48 desempeña también una función antiproliferativa, la cual puede resultar en una actividad de supresión tumoral. En el presente estudio, basado en una estrategia de cribado de doble-híbrido en levadura, han sido identificadas nuevas proteínas que interaccionan y que modulan la actividad específica de p48. Entre las posibles proteínas que interaccionan y han sido identificadas de novo se encuentra p/CAF, un co-activador que potencia la actividad transcripcional de p48, y ICAT, un inhibidor de la vía de señalización de la β-catenina. Se ha demostrado que ICAT se une a p48 y ambos son co-expresados en el páncreas durante el desarrollo y en el adulto. Utilizando diferentes modelos celulares, la sobreexpresión de ICAT en células tumorales acinares resultó en un cambio en el patrón de expresión de genes específicos del páncreas. Al mismo tiempo, se observó que niveles elevados de ICAT inhiben la interacción entre p48 y su co-activador p/CAF. Mientras que este complejo hetero-oligomérico es necesario para la expresión de los genes acinares, se demostró que ICAT está presente en un complejo PTF1 reconstituido in vivo. Finalmente, se observaron alteraciones en la expresión de ICAT en varios tipos histológicos de tumores pancreáticos, que posiblemente contribuyen a su fenotipo de diferenciación y propiedades neoplásicas.

Technological advances will allow virtual agents to increasingly help individuals with daily activities. As such, virtual agents will interact with users of various ages and experience levels. Facial expressions are often used to facilitate social interaction between agents and humans. However, older and younger adults do not label human or virtual agent facial expressions in the same way, with older adults commonly mislabeling certain expressions. The dynamic formation of facial expression, or motion, may provide additional facial information potentially making emotions less ambiguous. This study examined how motion affects younger and older adults in recognizing various intensities of emotion displayed by a virtual agent. Contrary to the dynamic advantage found in emotion recognition for human faces, older adults had higher emotion recognition for static virtual agent faces than dynamic ones. Motion condition did not influence younger adults' emotion recognition. Younger adults had higher emotion recognition than older adults for the emotions of anger, disgust, fear, happiness, and sadness. Low intensities of expression had lower emotion recognition than medium to high expression intensities.