No description available.

No description available.

No description available.

The development of recombinant proteins for therapeutic applications has revolutionized the pharmaceutical industry. In particular, monoclonal antibodies are the safest class of all therapeutic molecules and account for the majority of recombinant proteins currently undergoing clinical trials. A variety of technologies exist to engineer antibodies with a desired binding specificity and affinity, both of which are a prerequisite for therapeutic applications. This dissertation describes the implementation of a novel combinatorial library screening technology for the discovery and engineering of antibodies with unique binding properties. Combinatorial library screening technologies are used for the in vitro isolation of antibodies from large ensembles of proteins (libraries) typically produced by microorganisms using molecular biology techniques. Our lab has developed a powerful antibody discovery technology that relies on E. coli display by anchored periplasmic expression, otherwise known as APEx. First, I compared the effects of using combinatorial libraries comprising either smaller, monovalent single-chain antibody fragments (scFv), or the much larger, bifunctional full-length IgG antibodies. These technologies were used to isolate a small panel of antigen specific antibodies from the same library of antibody variable domains amplified from a mouse immunized with the Protective Antigen (PA) component from Bacillus anthracis, the causative agent of anthrax. Overall, IgG display resulted in the isolation of a broader panel of variable domain sequences. Most of these variable domains exhibited substantially reduced affinity when expressed as scFvs, which is consistent with the finding that none of these could be isolated from the equivalent scFv library. These results indicate that the antibody format used during in vitro selection affects which antibody variable domains will be discovered. Second, I developed several modifications of the APEx methodology to allow for more efficient recovery of antibodies with desired properties. Specifically, the system was reengineered to simultaneously account for antibody binding and expression levels in order to isolate the highest affinity antibodies with favorable expression characteristics. Third, the new approach, coupled with optimized fluorescence activated cell sorting (FACS) settings, was used to increase the affinity of an antibody by 35-fold resulting in a K[subscript D] of 100 pM. It was demonstrated that genetic transfer of this high affinity antibody specific for the V antigen of Yersinia pestis, the etiologic agent of the plague, conferred increased protection against intranasal challenge with a 363 LD₅₀ of Y. pestis in mice. / text

La plupart des virus ont développé des mécanismes de résistance ou de suppression du système immunitaire pour parvenir à infecter durablement leur hôte. Ces mécanismes demeurent encore imparfaitement connus. Un domaine immunosuppresseur (IS) a été identifié au niveau de la région transmembranaire des protéines d’enveloppe des rétrovirus endogènes ou infectieux. Ce domaine hautement conservé a été décrit par exemple comme inhibant l’activation lymphocytaire. Dans le laboratoire, il a été caractérisé en particulier via des expériences de rejet de cellules tumorales in vivo, ce qui a permis de définir des mutations inactivatrices. Afin de mieux comprendre les mécanismes de résistance des rétrovirus au système immunitaire, mes travaux de thèse ont porté sur l’identification de la ou des protéines capables d’interagir avec le domaine IS. Plusieurs approches cellulaires et moléculaires ont été développées, basées pour la plupart sur l’utilisation de sondes fluorescentes obtenues par synthèse chimique, constituées des domaines IS provenant de différents rétrovirus. Dans un premier temps, les cellules du système immunitaire qui lient les protéines virales ont été identifiées : les lymphocytes B et les cellules myéloïdes (monocytes, cellules dendritiques et macrophages). Dans un second temps, des expériences de co-immunoprécipitation et de chromatographie d’affinité couplées à la spectrométrie de masse ont été réalisées dans le but d’identifier sur ces cellules les protéines membranaires responsables de ces liaisons. Plusieurs agents de couplages chimiques ont été utilisés afin de maintenir les liaisons domaine IS - protéine de faibles affinités. En raison de résultats non-reproductibles obtenus au cours de ces expériences, des tests de liaison du domaine IS sur des cellules transfectées avec des banques d’ADNc, ou lors d’expériences de double hybride ont été réalisées. Ces deux approches ont permis d’identifier des protéines membranaires potentiellement impliquées dans la liaison du domaine IS : les protéines X1 et X2. Les co-transfections de vecteurs d’expression du domaine IS et de X2 ont mis en évidence des interactions protéiques au cours d’expériences de co-immunoprécipitation et de microscopie confocale, en particulier avec le domaine IS du rétrovirus HIV-1. Concernant X1, sa transfection induit la liaison cellulaire des domaines IS de HERV-W et MLV. En revanche, aucune interaction directe entre X1 et le domaine IS n’a pu être démontrée, notamment dans des expériences de co-immunoprécipitation et de microscopie confocale.La découverte des protéines membranaires qui interagissent avec le domaine IS demeure un enjeu critique pour la compréhension des voies de signalisation et de transcription qui permettent aux rétrovirus d’exercer leur effet sur le système immunitaire, l’objectif de ces travaux étant d’identifier à terme des nouvelles cibles thérapeutiques.En conclusion, même si des travaux complémentaires demeurent nécessaires, les protéines X1 et X2 pourraient contribuer à l’immunosuppression rétrovirale. / Most viruses have developed mechanisms of resistance or suppression of the immune system to achieve lasting infection of their host. These mechanisms are still imperfectly known. An immunosuppressive (IS) domain has been identified in the transmembrane region of envelope proteins of endogenous or infectious retroviruses. This highly conserved domain has been described, for example, as inhibiting lymphocyte activation. In the laboratory, it has been characterized by tumor cell rejection experiments in vivo, which has made it possible to define inactivating mutations. In order to better understand the mechanisms of resistance of retroviruses to the immune system, my thesis focused on the identification of the protein(s) interacting with the IS domain. Several cellular and molecular approaches have been developed, based for the most part on the use of fluorescent probes obtained by chemical synthesis, consisting of IS domains from different retroviruses. At first, immune system cells that bind viral proteins have been identified: B cells and myeloid cells (monocytes, dendritic cells and macrophages). In a second step, co-immunoprecipitation and affinity chromatography coupled to mass spectrometry were performed to identify on these cells the membrane proteins responsible for these bonds. Several chemical coupling agents have been used to prevent detachment of low affinity binding between proteins and the IS domain. Due to non-reproducible results obtained during these experiments, IS domain binding assays on cells transfected with cDNA libraries, or in double hybrid experiments were performed. These two approaches made it possible to identify membrane proteins potentially involved in the binding of the IS domain: the X1 and X2 proteins. Co-transfections of IS domain and X2 expression vectors demonstrated protein interactions in co-immunoprecipitation and confocal microscopy experiments, particularly with the IS domain of the HIV-1 retrovirus. Concerning X1, its transfection induces binding of the IS domains of HERV-W and MLV on cells membrane. On the other hand, no direct interaction between X1 and the IS domain could be demonstrated, especially in co-immunoprecipitation and confocal microscopy experiments.The discovery of membrane proteins that interact with the IS domain remains a critical issue for understanding the signaling and transcription pathways that allow retroviruses to exert their effect on the immune system, the aim of this work being to identify new therapeutic targets.In conclusion, although further work is still needed, the X1 and X2 proteins may contribute to retroviral immunosuppression.

No description available.

Background Systematic, large-scale RNA interference (RNAi) approaches are very valuable to systematically investigate biological processes in cell culture or in tissues of organisms such as Drosophila. A notorious pitfall of all RNAi technologies are potential false positives caused by unspecific knock-down of genes other than the intended target gene. The ultimate proof for RNAi specificity is a rescue by a construct immune to RNAi, typically originating from a related species. Methodology/Principal Findings We show that primary sequence divergence in areas targeted by Drosophila melanogaster RNAi hairpins in five non-melanogaster species is sufficient to identify orthologs for 81% of the genes that are predicted to be RNAi refractory. We use clones from a genomic fosmid library of Drosophila pseudoobscura to demonstrate the rescue of RNAi phenotypes in Drosophila melanogaster muscles. Four out of five fosmid clones we tested harbour cross-species functionality for the gene assayed, and three out of the four rescue a RNAi phenotype in Drosophila melanogaster. Conclusions/Significance The Drosophila pseudoobscura fosmid library is designed for seamless cross-species transgenesis and can be readily used to demonstrate specificity of RNAi phenotypes in a systematic manner.

UDP-sugar metabolizing pyrophosphorylases provide the primary mechanism for de novo synthesis of UDP-sugars, which can then be used for myriads of glycosyltranferase reactions, producing cell wall carbohydrates, sucrose, glycoproteins and glycolipids, as well as many other glycosylated compounds. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase) and UDP-N-acety lglucosamine pyrophosphorylase (UAGPase), which can be discriminated both by differences in accepted substrate range and amino acid sequences. This thesis focuses both on experimental examination (and re-examination) of some enzymatic/ biochemical properties of selected members of the UGPases and USPases and UAGPase families and on the design and implementation of a strategy to study in vivo roles of these pyrophosphorylases using specific inhibitors. In the first part, substrate specificities of members of the Arabidopsis UGPase, USPase and UAGPase families were comprehensively surveyed and kinetically analyzed, with barley UGPase also further studied with regard to itspH dependency, regulation by oligomerization, etc. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Frc-1-P, whereas USPase reacted with arange of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P, β-L-Ara-1-P and α-D-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P and, to some extent, with D-Glc-1-P. A structure activity relationship was established to connect enzyme activity, the examined sugar-1-phosphates and the three pyrophosphorylases. The UGPase/USPase/UAGPase active sites were subsequently compared in an attempt to identify amino acids which may contribute to the experimentally determined differences in substrate specificities. The second part of the thesis deals with identification and characterization of inhibitors of the pyrophosphorylases and with studies on in vivo effects of those inhibitors in Arabidopsis-based systems. A novel luminescence-based high-throughput assay system was designed, which allowed for quantitative measurement of UGPase and USPase activities, down to a pmol per min level. The assay was then used to screen a chemical library (which contained 17,500 potential inhibitors) to identify several compounds affecting UGPase and USPase. Hit-optimization on one of the compounds revealed even stronger inhibitors of UGPase and USPase which also strongly inhibited Arabidopsis pollen germination, by disturbing UDP-sugar metabolism. The inhibitors may represent useful tools to study in vivo roles of the pyrophosphorylases, as a complement to previous genetics-based studies. The thesis also includes two review papers on mechanisms of synthesis of NDP-sugars. The first review covered the characterization of USPase from both prokaryotic and eukaryotic organisms, whereas the second review was a comprehensive survey of NDP-sugar producing enzymes (not only UDP-sugar producing and not only pyrophosphorylases). All these enzymes were discussed with respect to their substrate specificities and structural features (if known) and their proposed in vivo functions.

p83 é uma proteína com massa molecular aparente de 83 kDa, supostamente ainda não descrita, específica de sistema nervoso, e desenvolvimento regulada. p83 interage fortemente com laminina, Tau, tubulina e heat shock protein 90. p83 foi inicialmente detectada por imunohistoquímica e western blot usando-se um anticorpo anti-lectina KM+ purificado por afinidade. Sua purificação a partir de cérebro de rato está em progresso. Identificar o envolvimento de p83 em processos do Sistema Nervoso Central humano é um passo necessário em direção à compreensão de sua função biológica. Uma biblioteca de expressão de cDNA de cerebelo de rato (Lambda ZAP II, Stratagene) foi submetida ao screening, usando-se um anticorpo específico para isolar o cDNA de p83. O anticorpo anti-KM+ foi pré-adsorvido contra proteínas de E. coli XL1 Blue MRF, antes de ser usado no screening. As membranas foram reveladas por imunodetecção cromogênica (fosfatase alcalina e NBT/BCIP). A análise de todos os clones Lambda ZAP II foi feita por excisão in vivo do fagomídeo pBluescript, subclonagem em E. coli XL1 Blue MRF, purificação do DNA plasmidial e digestão com Eco RI. A seqüência correspondente ao clone isolado foi analisada usando-se ferramentas e bancos de dados do NCBI. A seqüência nucleotídica mostrou identidade com as isoformas A e E de drebrina. As isoformas A e E de drebrina foram detectadas em adulto e embrião, respectivamente. Drebrina A é uma proteína sistema nervoso-específica, desenvolvimento regulada e associa-se com F-actina. Embora drebrina e p83 compartilhem propriedades em comum, nossos dados de western blot indicaram que parecem não se tratar da mesma proteína. Nós investigamos a expressão de drebrina em Displasia Cortical Focal tipo IIB, comparando com córtex normal. As secções de tecido foram coradas com hematoxilina-eosina e prata (Bielchowsky). Secções foram processadas por imunohistoquímica usando-se os anticorpos anti-drebrina M2F6 e o DAS2, e recuperação antigênica. A detecção foi feita usando-se um anticorpo biotinilado, e DAB como cromógeno. Os tecidos displásicos (13 casos) foram obtidos cirurgicamente de tecidos exibindo epilepsia droga-resistente. Os controles foram obtidos de necrópsia de 15 pacientes sem história prévia de doenças neurológicas ou alterações patológicas. Nossos resultados sugerem uma associação entre drebrina e DCF IIB, um distúrbio do desenvolvimento cortical. / p83 is 83 kDa protein supposedly not yet described, nervous system specific, and developmentally regulated. p83 strongly interacts with laminin, Tau, tubulin and heat shock protein 90. It was initially detected by immunohistochemistry and western blot using an affinity-purified anti-lectin KM+ antibody. Its purification from rat brain is in progress. Identifying the involvement of p83 in human Central Nervous System processes is a required step towards understanding its biological roles. A premade cDNA rat cerebellum expression library (Lambda ZAP II, Stratagene) has been screened, using a specific antibody to isolate p83 cDNA. Anti-KM+ antibody was pre-adsorbed against E. coli XL1 Blue MRF proteins, before using in screening. Membranes were revealed by cromogenic immunodetection (alcaline fostase and NBT/BCIP). The analysis of all positive Lambda ZAP II clones was carried out by in vivo excision of pBluescript, subcloning in E. coli XL1 Blue MRF, plasmidial DNA purification and Eco RI digestion. The sequence corresponding to the clone isolated was analyzed using the NCBI tools and database. The nucleotide sequence showed identity with drebrin A and E isoforms. Drebrin A and E isoforms were detected in adults and embryos. Drebrin A is a neuron-specific, development-regulated F-actin-binding protein. It participates in growth cone extension and dendritic spine formation. Although have same drebrin and p83 properties in common, they not seem to be the same protein. We have investigated the expression of drebrin in Focal Cortical Dysplasia type IIB (FCD IIB) as compared to normal cortex. Tissue sections were stained with hematoxylin-eosin and silver (Bielchowsky). Sections were processed for immunohistochemistry using anti-drebrin antibodies M2F6 and DAS2, and an antigen retrieval technique. Detection was carried out using a biotinylated antibody, using DAB as chromogen. Dysplastic tissues (13 cases) were obtained at surgery for drug-resistant epilepsy. Controls were obtained at autopsy from 15 patients without history of neurological disorder and gross pathological changes. A specific drebrin labeling in dysplastic tissue was more intense than in controls. Indeed, most control cases exhibited at most a slightly higher staining than the background. Balloon, clear and undetermined cells, and giant, dysmorphic neurons, showed a conspicuous labeling by anti-drebrin. These cells showed a thin rim labeling of the nuclear membrane, and a finely punctate nuclear labeling. In contrast, a coarse nuclear, but a faint cytoplasm labeling was observed in autopsy cases. Our data suggest an association between Drebrin expression and the FCD IIB, a disturbance of cortical development.

<p>Enzymes are useful tools as specific analytical reagents. Two different analysis methods were developed for use in the separate fields of protein science and organic synthesis. Both methods rely on the substrate specificity of enzymes. Enzyme catalysis and substrate specificity is described and put in context with each of the two developed methods.</p><p>In <strong>paper I </strong>a method for C-terminal peptide sequencing was developed based on conventional Carboxypeptidase Y digestion combined with matrix assisted laser desorption/ionization mass spectrometry. An alternative nucleophile was used to obtain a stable peptide ladder and improve sequence coverage.</p><p>In paper<strong> II </strong>and <strong>III</strong>, three different enzymes were used for rapid analysis of enantiomeric excess and conversion of O-acylated cyanohydrins synthesized by a defined protocol. Horse liver alcohol dehydrogenase,<em> Candida antarctica</em> lipase<strong> </strong>B<strong> </strong>and pig liver esterase were sequentially added to a solution containing the O-acylated cyanohydrin. Each enzyme caused a drop in absorbance from oxidation of NADH to NAD⁺. The conversion and enantiomeric excess of the sample could be calculated from the relative differences in absorbance.</p>