Stem cells have great potential value for treating a number of diseases and conditions, including diabetes, Parkinson's, and spinal cord injuries. Applying stem cells for therapeutic purposes will require an in-depth understanding of their biology, not only of the genes they express, but also the functions of the proteins encoded by the genes. The goal of the project presented in this thesis was to develop a method for high-throughput analyses of protein localization in mouse stem cells. Localization information can provide insight into the functions and biological roles of proteins. <br /><br /> One means of studying protein localization involves creating proteins with a green fluorescent protein (GFP) reporter gene and analyzing their localization using fluorescence microscopy. The research outlined in this thesis focused on developing a system to create a large number of GFP-tagged proteins by constructing a cDNA?GFP fusion library. This involved exploring methods for optimizing cDNA synthesis, designing a retroviral vector (pBES23) for the expression of cDNA?GFP fusions in mouse stem cells, and constructing a cDNA?GFP fusion library in this vector using R1 mouse embryonic stem cell mRNA. The library constructed was not successfully delivered to target cells for GFP-tagged protein expression; it was therefore not possible to characterize protein localization in mouse stem cells. Suggestions are given as to how the methods used in this thesis might be optimized further.

RNA localization, a regulated step of gene expression, is fundamentally important in development and differentiation. In multidisciplinary experiments, we discovered that RNA (mis)localization underlies the human disease myotonic dystrophy (DM). DM, the most prevalent adult muscular dystrophy, is caused independently by two alleles: DM1 is characterized by a (CTG)n expansion in the DM kinase (DMPK) gene 3' untranslated region while DM2 has a mutation in a small presumptive RNA binding protein. These analyses were guided by disease characteristics and have provided insights to DM's cytopathology, cell biology and molecular genetics. Examining muscle biopsies, it is demonstrated here that DM kinase mRNA is specifically subcellularly localized within normal human muscle and that DM kinase mRNA harboring the 3’UTR mutation (DM1) is mislocalized in DM patient muscle to cytoplasmic areas characteristic of DM disease pathology. Thus, the disease mutation alters the cellular distribution of the effected message. DMPK mRNA mislocalization causes altered DM kinase protein localization, correlates with novel phosphoprotein appearance and can account for DM’s diseased phenotype. While we were fortunate to access DM patient tissue to establish these key findings, the system does not lend itself to experimental manipulation. Hence, I established a disease- relevant tissue culture system, which recapitulates DMPK trafficking, Employing this system; I elucidate a complementary role for the DM2 gene product as a localization factor for DMPK mRNA (DM1 gene product). Comprehensive RNA-protein interaction experiments reveal the DM2 protein specifically and selectively recognizes a small, definitive area within the DMPK RNA 3'UTR. Detailed biochemical, cytological and functional experiments reveal 1) the DM2 protein colocalizes with DMPK mRNA, 2) the small area of the DMPK 3’UTR bound by pDM2 acts to properly localize a reporter construct and 3) disruption of the DM2 protein results in DMPK mRNA mislocalization. These data establish mRNA localization as a vital process underlying human disease etiology. Moreover, they reveal DM1 and DM2 gene products function in the same molecular pathway and that mutation of either causes DMPK mRNA mislocalization, leading to disease. These data have apparent application to several neuromuscular disorders and open a plethora of novel research avenues, both basic and applied. / text

Nos organismos eucariotos, aproximadamente 50% das proteínas traduzidas no citoplasma são transportadas para as organelas, onde irão desempenhar suas funções. Com isso, surgiu um intricado sistema de transporte intracelular de proteínas. Nas plantas, a presença de uma segunda organela endossimbionte, o plastídio, tornou este sistema mais complexo e gerou demanda adicional por transporte. Ainda, grande maioria das proteínas mitocondriais e plastidiais são codificadas por genes nucleares e importadas do citosol. O dogma uma proteína-uma localização foi associado ao conceito de um gene-uma proteína na biologia celular. Entretanto, proteínas individuais podem ter mais de uma função, e mais recentemente, proteínas codificadas por um único gene foram identificadas em mais de um compartimento subcelular, o que deu origem ao conceito de duplo direcionamento (DD). Um exemplo bem estudado de DD vem das proteínas da família das aminoacil-tRNA sintetases (aaRS), que participam da síntese protéica ao acoplar o aminoácido ao seu tRNA cognato. Dentre as aaRSs, a glutamil-tRNA sintetase citosólica (GluRS), através de sua extensão N-terminal, parece estar envolvida com outras funções além da tradução. Em Arabidopsis thaliana, há dois genes nucleares que codificam a GluRS, um para uma proteína de duplo direcionamento (DD) e outro para uma proteína citosólica. Resultados recentes em nosso laboratório mostraram que a GluRS citosólica pode estar relacionada ao controle da localização subcelular de proteínas organelares em Arabidopsis. Para verificar um eventual papel desta proteína na localização subcelular de outras proteínas, foram realizados ensaios de duplo-híbrido em levedura, os quais mostraram interação entre a GluRS e a glutamina sintetase (GS) de Arabidopsis thaliana, proteína de DD para mitocôndrias e cloroplastos Esta interação foi confirmada in planta, sendo a sequência da GluRS responsável pela interação localizada na região N-terminal, do resíduo 207 ao 316. Análises filogenéticas apontam que esta região encontra-se ausente nas bactérias e que originou-se provavelmente em Archea, entre 2,6 e 1,8 bilhões de anos. Além disso, observa-se que esta sequência é conservada em fungos, musgos e plantas vaculares, tendo originado-se em Arabidopsis há cerca de 2 bilhões de anos. / In eukaryotic organisms, about 50% of cytoplasmic translated proteins are transported to the organelles, where they can play their roles. Thus, a complex system for intracellular transport was established. In plants, the presence of a second endosymbiont organelle, the plastid, turned this system still more intricated and required an additional transport mechanism. Besides, most of organellar proteins are coded by nuclear genes and imported from the cytosol. The one protein-one localization was associated to the idea of one gene-one protein, which has long been established in molecular biology. However, individual proteins can show more than one function, and recently, proteins coded by one single gene were identified in more than one subcellular compartment, which has originated the concept of dual targeting. One of the most studied example of dual targeted proteins is the aminoacyl-tRNA synthetase (aaRS) family, which are related to protein synthesis by attaching the correct amino acid onto the cognate tRNA molecule. Among the aaRSs, cytosolic glutamyl-tRNA synthetase (GluRS), through its N-terminal extension, seems to be involved in other cellular role beyond translation. In Arabidopsis thaliana, there are two genes encoding GluRS, one for a dual-targeted protein and other for a cytosolic protein. Recent results in our laboratory showed that GluRS interacts with proteins destinated to other organelles, which suggest that this protein might have a role in interfering on protein localization in Arabidopsis. In order to gain some information on the role of this protein in subcellular localization, yeast two-hybrid assays were performed. These studies showed the interaction between GluRS and glutamine synthetase (GS), a mitochondrial and chloroplastic dual-targeted protein. This interaction was confirmed in planta. In addition, the GluRS sequence associated to protein interaction was localized at its N-terminal portion, between the residues 207 316. Phylogenetic analysis revealed that this region is absent in bacteria and it probably arose from Archea between 2.6 and 1.8 billion years ago. Also, this sequence is conserved in fungi, moss and all the green plants investigated. Finally, datation analysis showed that this sequence arose in Arabidopsis between 2 and 1.7 billion years ago.

A regulação da localização de proteínas é um dos aspectos fundamentais na biologia celular vegetal. Os cloroplastos importam mais de 90% de suas proteínas do citosol, portanto, é importante caracterizar os fatores citosólicos que podem estar envolvidos no direcionamento de proteínas para as organelas. Um ensaio de duplohíbrido em leveduras com as proteínas cloroplastidiais HMPPK/TMPPase (TH1) e Glutamina Sintetase (GS) II usados como iscas revelou que a forma citosólica da glutamil-tRNA sintetase - GluRS (At5g26710) de Arabidopsis thaliana interagiu com ambas as proteínas. Estudos de Complementação da Fluorescência Bimolecular (BiFC) confirmaram tais interações in planta. Estudos com deleções na região Nterminal da GluRS mostraram que esta região é responsável pelas interações com HMPPK/TMPPase e GSII. Além disso, seis resíduos de aminoácidos parecem ser cruciais para a interação entre as proteínas. Curiosamente, foi mostrado que a GluRS está envolvida na localização de proteínas em leveduras. A fim de obter mais informações sobre o envolvimento da GluRS ns localização de proteínas nos cloroplastos, foram produzidos plantas de tabaco transgênicas expressando uma proteína quimérica, feita pela fusão do gene codificador da HMPPK/TMPPase, TH1- GFP, e GSII-GFP e posteriormente usados em ensaios de agroinfiltração com RNA de interferência (RNAi) para GluRS. Análises em microscópio confocal mostraram que TH1-GFP e GSII-GFP acumulam no citosol em vez de serem direcionados aos cloroplastos. Neste trabalho, mostramos pela primeira vez que a GluRS está envolvida na localização de proteínas cloroplastidiais em plantas e esse mecanismo é também conservado em Saccharomyces cerevisiae. / Regulation of protein localization is one of the key aspects in plant cell biology. Chloroplasts import more than 90% of their proteins from the cytosol, therefore, it is important to identify and characterize cytosolic factors that might be involved in protein delivery to the organelar envelope. A yeast two-hybrid screen with a chloroplastlocalized HMPPK/TMPPase protein and glutamine synthetase (GS), used as baits, revealed that the cytosolic form of the glutamyl-tRNA synthetase (GluRS) (At5g26710) from Arabidopsis thaliana interacted with both proteins. Bimolecular Fluorescence Complementation (BiFC) studies confirmed such interactions in planta. Deletion studies of GluRS showed that the N-terminal region of the protein is responsible for proteinprotein interactions (PPI) with TH1 and GS. In addition, six amino acid residues appeared to be crucial for PPI. Interestingly, GluRS has been also shown to be involved in regulating protein localization in yeast. In order to gain more information about the involvement of GluRS on protein localization in chloroplasts, we produced transgenic tobacco plants expressing a chimeric protein made by the fusion of TH1- GFP and GSIIGFP and agroinfiltrated with a RNA interference (RNAi) construct against GluRS. Confocal analysis showed that TH1-GFP and GSII-GFP accumulated in the cytosol instead of being targeted to chloroplasts. Here, we show for the same time that GluRS is involved in protein localization in plants and this mechanism is also conserved in Saccharomyces cerevisiae.

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix protein (M), glycoprotein (G), and large polymerase protein (L). The features of each protein including a nuclear localization signal, isoelectric point, and transmembrane domain, were determined by predictive algorithms. The gene coding region was flanked by leader and trailer, and each ORF was separated by a conserved intergenic junction. In the intergenic junctions, the highly conserved cis-regulatory elements, polyadenylation signal, gene spacer, and transcription start site, were identified. The similarities of amino acid sequences between each cognate protein of SYDV and CYDV were higher than 80% except for X and P proteins. The protein localization and interaction assays of each CYDV protein identified strain-specific associations in comparison with those of SYDV and generated unique protein interaction and localization map compared to SYDV. Phylogenetic analysis using L protein identified that CYDV forms a clade with other leafhopper-transmitted rhabdoviruses. Protein sequence comparisons revealed that CYDV X has greater similarity to the cognate protein of Eggplant mottle disease virus than to SYDV X. The localization patterns of CYDV-N and -Y were different compared the cognate proteins of SYDV. The functional nuclear export domain of SYDV M was identified using c-terminal fragments of the Mwt(aa 211-243), MLL223AA(aa 211-243), and MKR225AA(aa 211-243). Based on the data, the functional domains M mediating membrane association, nuclear import and export were mapped for both strains and suggested a model whereby M mediates intra- and intercellular movement of PYDV nucleocapsid.

Rubella virus (RUBV) is a positive-strand RNA virus and the causative agent of rubella and congenital rubella syndrome in humans. To replicate its RNA, RUBV forms membrane-associated spherules, called replication complexes (RCs), the induction of which requires the two virus nonstructural proteins (NSPs), P150 and P90. Interestingly, late in infection the NSPs form a unique cytoplasmic fiber network, similar in appearance to microtubules, the function of which is unknown. Little is known about the roles of the RUBV NSPs in forming these structures and, to this end, we scrutinized the behavior and biochemical properties of the NSPs, both after expression from plasmids and during RUBV infection, using mutagenic, biochemical and pharmacological approaches. The following findings were made: First, the precursor from which P150 and P90 are produced via an embedded protease at the C-terminus of P150, called P200, was required for initial targeting to cytoplasmic foci. P150 was the determinant of fiber formation and while P90 had no specific targeting sequences on its own, P90 sequences within P200 were required for correct targeting of P200. An alpha-helix at the N-terminus of P150 was also important for correct targeting of P200, putatively by mediating the interaction between P150 and P90 within the precursor. Second, the membrane binding domain within the NSPs was within the N-terminal ~450 amino acids of P150. P150 is in an exceptionally tight association with membranes. Third, both the N- and C-terminal regions of P150, and specifically long alpha-helices within these regions, are necessary for fiber formation. Fiber formation relied on an intact microtubule network, but neither microtubule repositioning nor dynamic movement along microtubules was required. Additionally, it was shown that microtubules were not necessary in RUBV replication. Finally, P150 fibers were not required for RUBV replication; however, it was shown that the fibers are likely important in formation of cytoplasmic extensions through which a novel system of cell-to-cell transport of viral RNA in the absence of virus particles appears to occur.

Cette thèse s'inscrit dans le contexte de diagnostic assisté par ordinateur pour la localisation subcellulaire des protéines dans les images microscopiques. L'objectif est la conception et le développement d'un système de classification automatique permettant d'identifier le compartiment cellulaire dans lequel une protéine d'intérêt exerce son activité biologique. Afin de surmonter les difficultés rencontrées pour discerner les compartiments cellulaires présents dans les images microscopiques, les systèmes décrits dans la littérature proposent d'extraire plusieurs descripteurs associés à une combinaison de classifieurs. Dans cette thèse, nous proposons un schéma de classification différent répondant mieux aux besoins de généricité et de flexibilité pour traiter différentes bases d'images.Dans le but de fournir une caractérisation riche des images microscopiques, nous proposons un nouveau système de représentation permettant d'englober de multiples descripteurs visuels identifiés dans les différentes approches d'extraction de caractéristiques : locale, fréquentielle, globale et par région. Nous formulons ensuite le problème de fusion et de sélection des caractéristiques sous forme d'un problème de sélection de noyaux. Basé sur l'apprentissage de noyaux multiples (MKL), les tâches de sélection et de fusion de caractéristiques sont considérées simultanément. Les expériences effectuées montrent que la plateforme de classification proposée est à la fois plus simple, plus générique et souvent plus performante que les autres approches de la littérature. Dans le but d'approfondir notre étude sur l'apprentissage de noyaux multiples, nous définissons un nouveau formalisme d'apprentissage MKL réalisé en deux étapes. Cette contribution consiste à proposer trois termes régularisant liés à la résolution du problème d'apprentissage des poids associés à une combinaison linéaire de noyaux, problème reformulé en un problème de classification à vaste marge dans l'espace des couples. Le premier terme régularisant proposé assure une sélection parcimonieuse des noyaux. Les deux autres termes ont été conçus afin de tenir compte de la similarité entre les noyaux via une métrique basée sur la corrélation. Les différentes expérimentations réalisées montrent que le formalisme proposé permet d'obtenir des résultats de même ordre que les méthodes de référence, mais offrant l'avantage d'utiliser moins de fonctions noyaux. / This thesis arises in the context of computer aided analysis for subcellular protein localization in microscopic images. The aim is the establishment of an automatic classification system allowing to identify the cellular compartment in which a protein of interest exerts its biological activity. In order to overcome the difficulties in attempting to discern the cellular compartments in microscopic images, the existing state-of-art systems use several descriptors to train an ensemble of classifiers. In this thesis, we propose a different classification scheme wich better cope with the requirement of genericity and flexibility to treat various image datasets. Aiming to provide an efficient image characterization of microscopic images, a new feature system combining local, frequency-domain, global, and region-based features is proposed. Then, we formulate the problem of heterogeneous feature fusion as a kernel selection problem. Using multiple kernel learning, the problems of optimal feature sets selection and classifier training are simultaneously resolved. The proposed combination scheme leads to a simple and a generic framework capable of providing a high performance for microscopy image classification. Extensive experiments were carried out using widely-used and best known datasets. When compared with the state-of-the-art systems, our framework is more generic and outperforms other classification systems. To further expand our study on multiple kernel learning, we introduce a new formalism for learning with multiple kernels performed in two steps. This contribution consists in proposing three regularized terms with in the minimization of kernels weights problem, formulated as a classification problem using Separators with Vast Margin on the space of pairs of data. The first term ensures that kernels selection leads to a sparse representation. While the second and the third terms introduce the concept of kernels similarity by using a correlation measure. Experiments on various biomedical image datasets show a promising performance of our method compared to states of art methods.

Myxococcus Xanthus possède un cycle developpemental multicellulaire entièrement sous la dépendance de la capacité des cellules à se déplacer sur des surfaces solides. M. xanthus possède deux systèmes de motilité génétiquement séparé, une motilité Sociale dépendant des pili de Type IV et une motilité Aventurière dont le mécanisme est encore peu compris. Notre hypothèse de travail est que la motilité Aventurière est qu’en des points régulièrement répartis le long du corps cellulaire soient couplés adhésion et traction de ce corps par une interaction entre des moteurs moléculaire et le cytosquelette d’Actine bactérienne MreB. Mon projet est de caractériser la relation qu’il pourrait y avoir entre le cytosquelette et les points d’adhésion durant la motilité. Pour étudier l’implication du cytosquelette MreB durant le mouvement, nous avons utilisé une approche pharmaceutique utilisant l’A22, une drogue permettant la dépolymérisation rapide et spécifique du cytosquelette sans affecter la viabilité des cellules à court terme. De plus j’ai aussi étudier les interactions possible entre MreB et différentes protéines de motilité comme la petite GTPase MglA, qui est connue pour est essentielle au recrutement des machineries de motilité. / Myxococcus xanthus has a multicellular developmental cycle which is dependent on the capacity of the cells to move accross solid surfaces. M. xanthus uses two motility systems: Social motility system is dependent on Type-IV pili, and the Adventurous motility system, the mechanism of which is poorly understood. Our working hypothesis is that Adventurous motility is performed by adhesion points localized along the cell body where a molecular machinery pulls the cell body by interacting with the MreB cytoskeleton. My project aims to characterize the relationship between the adhesion points and the cytoskeleton during movement. To study the involvement of MreB during motility we use A22, a drug known to rapidly and specifically depolymerise in live microscopy assays. Furthermore, I have study also the interactions between MreB and differents proteins like MglA a small GTPase, which we belive is essential for the recruitment of the machineries.

<p dir="ltr">Primary cilia are hair-like structures found on nearly all mammalian cell types, including cells in the developing and adult brain. Cilia establish a unique signaling compartment for cells. For example, a diverse set of receptors and signaling proteins localize within cilia to regulate many physiological and developmental pathways including the Hh pathway. Defects in cilia structure, protein localization, or cilia function lead to genetic disorders called ciliopathies, which present with various clinical features including several neurodevelopmental phenotypes and hyperphagia associated obesity. Despite their dysfunction being implicated in several disease states, understanding their roles in CNS development and signaling has proven challenging. I hypothesize that dynamic changes to ciliary protein composition contributes to this challenge and may reflect unrecognized diversity of CNS cilia. The proteins ARL13B and ADCY3 are established ciliary proteins in the brain and assessing their localization is often used in the field to visualize cilia. ARL13B is a regulatory GTPase important for regulating cilia structure, protein trafficking, and Hh signaling, while ADCY3 is a ciliary adenylyl cyclase thought to be involved in ciliary GPCR singaling. Here, I examine the ciliary localization of ARL13B and ADCY3 in the perinatal and adult mouse brain by defining changes in the proportion of cilia enriched for ARL13B and ADCY3 depending on brain region and age. Furthermore, I identify distinct lengths of cilia within specific brain regions of male and female mice. As mice age, ARL13B cilia become relatively rare in many brain regions, including the hypothalamic feeding centers, while ADCY3 becomes a prominent cilia marker. It is important to understand the endogenous localization patterns of these proteins throughout development and under different physiological conditions as these common cilia markers may be more dynamic than initially expected. Understanding regional and development associated cilia signatures and physiological condition cilia dynamic changes in the CNS may reveal molecular mechanisms associated with ciliopathy clinical features such as obesity.</p>

The detection and analysis of biomolecules, such as proteins, are of great interest since these molecules are fundamental for life and our health. Due to the complexity of biological processes, there is a great advantage of studying proteins in their natural context, for example by using bioimaging. The objective of this doctoral thesis has been to develop, implement and evaluate techniques for the use of proteinspecific affinity reagents in diverse bioimaging platforms for analysis of protein expression in situ in cells and tissues. To be able to visualize a desired protein in situ using affinity reagents, reporter labels are needed. A novel technique for labeling of antibodies on solid phase was developed. This method offers simultaneous purification, concentration and labeling of an antibody sample, giving highly predictable and reproducible results, in a miniaturized format. Another study demonstrates the use of an alternative affinity reagent, the Affibody molecule, in bioimaging as well as other immunoassays. As a relevant proof-of-principle, an Affibody molecule binding the HER2 receptor was site-specificly labeled and employed for analysis of HER2 protein expression in cells and tissue using immunofluorescence (IF), immunohistochemistry (IHC), immunoprecipitation and flow cytometry. Furthermore, it is shown how antibody-based bioimaging approaches can be applied for systematic analysis of protein expression in terms of subcellular localization and expression levels in cell lines. The systematic subcellular localization of nearly 500 proteins was performed using IF and confocal microscopy. Global analysis of expression levels of nearly 2000 proteins in a panel of cell lines using IHC and automated image analysis, revealed that most proteins are expressed in a cell size dependent manner. Two normalization approaches were evaluated and found to allow for protein profiling across the panel of morphologically diverse cells, revealing patterns of protein over- and underexpression, and proteins with stable as well as with lineage specific expression were identified. Finally, the value of antibody-based, bioimaging proteomics as a platform for biomarker discovery is demonstrated. The identification and in depth study of a candidate biomarker for colorectal cancer, SATB2, is described using both IHC and IF bioimaging. Results from extended analyses of tumor biopsies showed that detection of SATB2 protein using IHC provides a clinically relevant diagnostic tool with high specificity and sensitivity to aid in diagnosis of colorectal cancer. Furthermore, the study demonstrated a potential prognostic role of SATB2, as decreased expression was associated with a significantly shorter overall survival in patients with advanced colorectal cancer. / QC 20100824