<p>The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity (&gt / 1%) was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study.</p>

Different species are separated by pre-zygotic reproductive barriers which impede gene flow between them. Rarely, when pre-zygotic barriers break down, interspecific hybrids are produced that display abnormal phenotypes, collectively called hybrid dysgenesis effects. Interspecies hybrid placental dysplasia (IHPD) in the genus Mus is a very consistent X-linked hybrid dysgenesis effect. Reproductive cloning and mutation of the gene Esx1 lead to placental hyperplasias with phenotypic similarities to IHPD. Comparative gene expression analysis of these three different models of placental hyperplasia showed that different mechanisms underlie these placental hyperplasias. We also identified several genes for which roles in placentation had not been studied earlier. We screened five of these genes, Car2, Ncam1, Fbln1, Cacnb3 and Cpe for their functions in placentation. Analysis of the spatio-temporal expression patterns of these genes during mouse placental development showed that they are ectopically expressed in IHPD placentas. Placental phenotype and gene expression was then studied in mice mutant for these genes. Our results show that complicated by the expression of functional counterparts, deletion of these genes failed to produce any consistent phenotype. Incompletely penetrant phenotypes were found in Cacnb3 and Cpe mutants. The Cpe mutant placentas recapitulated some IHPD phenotypes, despite co-expression of Cpd, a functionally redundant gene. Deregulated expression of Cpe and Cpd prior to manifestation of IHPD phenotype indicated that these are causally involved in IHPD and might be speciation genes in the genus Mus. We found that AT24 placentas also exhibit deregulated expression of these genes and could be used as a model to study IHPD. We tried rescuing the AT24 placental phenotype, by decreasing the expression of the over expressed genes. Normalization of transcript levels of these genes did not rescue the AT24 phenotype, thus indicating that up-regulation of these genes is a down-stream event in the generation of IHPD.

<p>The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity (&gt / 1%) was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study.</p>

Les anticorps monoclonaux (mAb) sont depuis les années 2000 devenus des médicaments incontournables et de routine en thérapie et notamment en cancérologie. Le domaine continue à croître très rapidement et devant l’abondance des molécules disponibles, il est de plus en plus important d’apporter des molécules innovantes à haute valeur ajoutée pour la thérapie. Deux grandes approches sont utilisées pour sélectionner ces mAbs : l’hybridation lymphocytaire à partir de souris normales ou humanisées ; Les systèmes de display comme le phage-display. Les intérêts majeurs du phage display sont la rapidité de développement des mAbs, la facilité de manipulation chez E. coli, l’accès aux techniques de "protein engineering". Classiquement, les anticorps sont d’abord sélectionnés sur leur capacité de liaison à l’antigène puis ensuite testés pour leur efficacité fonctionnelle dans des modèles cellulaires. Cependant, seulement une partie de l'activité des anticorps est expliquée par leur liaison à l’antigène et l’activité thérapeutique dépend aussi fortement de leur capacité à recruter le système immunitaire (ADCC) et à activer la cascade du complément (CDC).Ce projet de thèse consiste à développer un nouveau format de banque d'anticorps recombinants combinant la puissance de la sélection par phage display à un criblage fonctionnel au format IgG entières produites en cellules eucaryotes. Ce nouveau système est basé sur des régions initiatrices hybrides contenant à la fois des promoteurs et des séquences signal procaryotes et eucaryotes permettant l’expression dans ces deux systèmes cellulaires, et des évènements de recombinaisons sites-spécifiques transférant le fragment Fab du vecteur de display vers le chromosome d’une lignée cellulaire de mammifère spécialement développée pour aboutir à la sécrétion d’un anticorps humain monoclonal par la cellule. L’approche habituelle de reclonage un par un du vecteur E. Coli au format IgG n’est plus nécessaire puisqu’il se fait directement par transfection. Ce nouveau système rend possible le couplage d’une sélection par phage display à un criblage fonctionnel direct sur une large population de clones monoclonaux humains. / Since 2000, monoclonal antibodies (mAb) have become essential and routine drugs in therapy and particularly in oncology. The field continues to grow very quickly and given the abundance of molecules available, it is increasingly important to bring innovative molecules with a high added value for therapy.Two main approaches are used to select these mAbs: hybridoma technology using normal or humanized mice; display systems such as phage-display. The major interests of phage display are the speed of mAb development, the facilities offered by E. coli and the easy access to protein engineering techniques. Typically, antibodies are first selected on their ability to bind to the antigen, and then tested for their functional efficiency in cellular models. However, only a part of the activity of antibodies is explained by their binding to the antigen, and the therapeutic activity also depends strongly on their ability to recruit the immune system (ADCC) and activate the complement cascade (CDC).This thesis project consists in the development of a new recombinant antibody library format combining the power of phage display selection with functional screening in a whole IgG format produced in eukaryotic cells. This new system is based on hybrid promoter and signal peptide regions allowing expression both in prokaryotic and eukaryotic cells, and a site-specific recombination event that exchanges the Fab between the display vector and the chromosome of an especially developed mammalian cell line resulting in the secretion of a monoclonal human antibody by the cell. The usual approach of recloning one by one from E.Coli vector to an IgG format is no more needed since it is done directly by transfection. This new system makes possible to couple selection by phage display with a direct functional screening of a large population of human monoclonal clones.

Magister Scientiae - MSc / The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study. / South Africa

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20563号 / 医博第4248号 / 新制||医||1022(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 生田 宏一, 教授 髙折 晃史, 教授 前川 平 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Short open reading frames (sORFs) are codon sequences with a start and stop codon within atmost 100 codons. Cells produce many transcripts from them and some sORFs have been found to have function. sORFs have been associated with embryogenesis, myogenesis, immunity and various diseases including cancers. Cell culture screening is a common method to study function in sORFs. By inserting mutations in known sORF locations one can affect their translation by removing start codons, inserting premature stop codons, or removing native stop codons. A new tool set to do this isCRISPR technology, where single guide RNA (gRNA) can be used to make more precise genome edits. Unfortunately, such design is nontrivial and suggests a lot of variants for testing. It results in a back-and-forth testing process involving different available design tools. In this project, a comprehensive way was developed to see and iterate over the many test combinations. This intends to ease the process and decrease the likelihood for errors. The developed solution is a tool that integrates the currently best design tools. It also introduces a method in the form of a new quality summary score that can evaluate the estimated outcomes of the various designed guide variants. The tool was tested, and it was found that the score simplifies and amplifies the earlier usedscore methods. The pipeline is simple to install and use, integrates the currently most actively developed tools, and an installation is as future proof as can be made in a rapidly evolving field.

Le gliome infiltrant du tronc cérébral est une tumeur rare, non opérable et inéluctablement fatale. En raison du manque de ressource biologique disponible, aucun progrès dans la compréhension de la biologie de ces tumeurs n’a été fait jusqu’à ces dernières années, laissant la radiothérapie pour seul traitement efficace, et seulement transitoirement. Enfin, grâce à la mise en place de collecte d’échantillons de gliomes infiltrant du tronc cérébral au diagnostic ou à l’autopsie, un nombre sans précédent d’analyses biologiques et génomiques a pu être mené et améliorer la connaissance de ces tumeurs. Si ces études ont montré que ces gliomes pédiatriques étaient bien différents de ceux de l’adulte, elles ont aussi fait apparaître la présence d’anomalies génétiques récurrentes spécifiques de ces tumeurs sous-tentorielles. Ainsi le Platelet-Derived Growth Factor Receptor Alpha (PDGFRα) est apparu comme cible prédominante dans ces tumeurs compte tenu des nombreuses anomalies génétiques constatées. La recherche d’un médicament efficace pouvant inhiber cette voie nous a conduit à évaluer l’effet du dasatinib qui est un inhibiteur multi-ciblé. Nous en rapportons ici l’efficacité in vitro sur de nouvelles lignées cellulaires de gliomes infiltrants du tronc cérébral établies à partir de biopsies stéréotaxiques réalisées au diagnostic. Sachant néanmoins que les thérapies ciblées restent peu efficaces en clinique quand elles sont utilisées seules, nous mettons en évidence l’intérêt de combiner le dasatinib avec un inhibiteur de MET, 2ème oncogène fréquemment amplifié dans ces tumeurs. D’autre part, une stratégie originale de criblage médicamenteux a été mise en œuvre. Celle-ci a permis de définir de manière fonctionnelle de nouveaux médicaments potentiellement efficaces dans les gliomes infiltrants du tronc cérébral, incluant les inhibiteurs d’Histone deacetylases (HDAC), les inhibiteurs des Cyclin-Dependent Kinases (CDK) ou encore les inhibiteurs du protéasome. Enfin par la technique de séquençage génome-entier, de nouvelles anomalies génétiques jamais rencontrées dans aucun autre cancer ont été détectées. Parmi celles-ci se trouvent des mutations d’histone H3K27M dont la fréquence élevée (80%) suggère leur rôle fondamental dans la genèse de ces tumeurs. Des mutations activatrices d’ACVR1/ALK2 ont été également mises en évidence. Celles-ci représentent désormais de nouvelles cibles à explorer.Ce travail de thèse rapporte la recherche de nouvelles cibles thérapeutiques d’une part, via une approche exploratoire par criblage médicamenteux et recherche d’anomalies génétiques par séquençage « génome-entier », et d’autre part, via une approche de validation préclinique sur le plan des thérapies ciblées de type inhibiteurs de tyrosine-kinases. / Diffuse Intrinsic Pontine Glioma (DIPG) is a rare, unresectable and universally fatal tumor. Due to the lack of available material, no improvements have been made in the knowledge of the biology of this tumor until recent years, leaving radiotherapy as the only efficient treatment, and only transiently. Recently, the effort engaged for collecting samples in this disease at the diagnosis or at the autopsy resulted in an unprecedented number of analyses consequently improving our knowledge in DIPG. Those studies bring evidences for their differences with adult gliomas, but also with other pediatric supratentorial glioma showing specific genomic alterations. Thus, Platelet-Derived Growth Factor Receptor Alpha (PDGFRα) appeared to be one of the major target given its frequent aberrations found in those tumors. Investigating an effective drug to inhibit this pathway led us to evaluate the effect of dasatinib, which is known as a multi-targeted inhibitor. We report here the in vitro efficacy of dasatinib on new cell lines of DIPG developed from stereotaxic biopsy at diagnosis. Because therapies are largely inefficient in the clinic when they are used as a monotherapy, we bring out our interest on combining dasatinib with an inhibitor of MET, which is the 2nd most common amplified oncogene in these tumors.Additionally, an innovative strategy of pharmacological screening has been successfully tested. New drugs, potentially efficient in DIPG, have been fonctionnaly-defined, including Histone deacetylase inhibitors (HDACi), Cyclin-Dependent Kinases inhibitors (CDKi) and proteasome inhibitors as well.Finally, by using whole genome sequencing (WGS), we have been able to discover new genetic abnormalities, never encountered before in other cancers. Among those, mutations of histone H3K27M with a high frequency of 80% were found, suggesting that they have a fundamental role in tumors genesis. Moreover, ACVR1/ALK2 activating mutations have been identified as well. And this gene now represents a new target to explore. This work reports the research of new therapeutic targets through an exploratory approach using drug screening and WGS on the one hand, and on the other hand through a preclinical validation approach in terms of targeted therapies with tyrosine-kinases inhibitors.

A compensação da dosagem gênica entre fêmeas XX e machos XY em mamíferos é adquirida através de um complexo mecanismo epigenético que resulta na inativação de grande parte de um dos cromossomos X nas células femininas. O processo de inativação do cromossomo X (XCI) se inicia cedo durante a embriogênese, concomitantemente à diferenciação celular, e envolve a aquisição de modificações epigenéticas características do cromossomo X inativo (Xi). Uma estabelecido, o padrão de inativação é estavelmente mantido através de todas as mitoses celulares subsequentes e por toda a vida do organismo (exceto para células germinativas que sofrem reativação do Xi). Os mecanismos envolvidos na iniciação e estabelecimento da XCI foram extensivamente estudados, especialmente em camundongos. Embora algumas características epigenéticas associadas à manutenção da XCI tenham sido descritas, a identidade e modo específico de ação de fatores envolvidos durante essa fase da XCI são aspectos ainda não bem compreendidos. Além disso, o processo de XCI apresenta diferenças importantes entre humanos e camundongos e estudos direcionados para a identificação de novos componentes envolvidos na manutenção da XCI em humanos tornam-se de fundamental importância. Triagens funcionais genômicas por bibliotecas de shRNAs constituem uma ferramenta poderosa para a identificação de genes envolvidos em diferentes mecanismos celulares e vias bioquímicas. Sendo assim, utilizamos essa ferramenta para triar genes envolvidos na manutenção da XCI em humanos. Células somáticas femininas primárias HPRT+/-/HPRT- foram transduzidas com uma biblioteca lentiviral de shRNAs e posteriormente tratadas em meio de cultura contendo a droga HAT para seleção de células HPRT+ nas quais esperava-se que o cromossomo Xi presente tivesse sofrido reativação em decorrência do knockdown de genes envolvidos na manutenção da XCI. Essa estratégia nos permitiu identificar 20 novos genes candidatos a estarem envolvidos na manutenção da XCI. Esses candidatos deverão ser avaliados individualmente para confirmar seu papel no processo de controle epigenético do cromossomo X / Transcriptional dosage compensation between mammalian XX females and XY males is acquired through a complex epigenetic mechanism that leads to the inactivation of most part of one of the X chromosomes in the female cells. The X chromosome inactivation (XCI) process takes place early during embryogenesis and involves the acquisition of epigenetic modifications that are characteristic of the inactive X chromosome (Xi). Once silencing is established, the inactivation pattern is maintained in through all the subsequent mitosis and the same X chromosome remains stably silenced in all the descendant cells and throughout the life of the organism (except for the germ line cells that undergo X chromosome reactivation). The initiation of XCI has been studied extensively, especially in mice. Although some epigenetic features associated with the maintenance of XCI have already been described, the identity and specific mode of action of the factors involved in this phase of XCI are largely unknown. Moreover, the XCI process presents important differences between mice and humans, and studies directed to the identification of new players involved in the maintenance of human XCI are fundamentally important. Functional genome-wide screens using multiplex shRNA libraries are a powerful tool for the identification of genes involved in different cellular mechanisms and biochemical pathways. In order to screen for genes involved in the maintenance of XCI in humans, a population of HPRT+/-/HPRT- primary somatic female cells were transduced with a multiplex lentiviral shRNA library and subsequently treated in HAT medium to select for HPRT+ cells in which we expected that the Xi would undergo reactivation as a result of the knockdown of genes involved in the maintenance of XCI. As a result, we identified 20 new candidate genes that could potentially be involved in the maintenance of XCI. These candidates should be individually evaluated in order to confirm their role in the epigenetic control of the X chromosome

Thesis (MSc (Genetics. Institute of Plant Biotechnology))--Stellenbosch University, 2008. / Traditional methods used for the discovery of novel genes have previously relied upon the ability to culture the relevant microbes and then demonstrate the activity of a specific enzyme. Although these methods have proved successful in the past, they severely limit our access to the genomes of organisms which are not able to be cultured under laboratory conditions. It was therefore the aim of this project to use metagenomic strategies for the identification of novel polymer-producing genes with the prospect of commercial exploitation. In this study, soil-derived metagenomic libraries were functionally screened for potential -glucan producing clones using aniline blue staining. Positive reacting clones were selected and sequenced. Initial sequencing revealed a gene with high homology to previously described glucan synthases, the products of these genes all having significant industrial value. The clone was transformed into a suitable bacterial host, cultured and allowed to produce the polymer of interest. The polysaccharide was purified and subjected to various chemical analyses so as to confirm its monosaccharide composition. Data suggests that this polymer is composed mainly of glucose units and that it may be secreted out of the cell. Purification of the active enzyme was attempted using classical protein purification methods with faint activity being detected using Native polyacrylamide gel electrophoresis (PAGE). Further attempts to demonstrate activity were made through the construction of a GST (glutathione S-transferase) tagged fusion protein. The second part of this study focuses on the construction and screening of a metagenomic DNA library from whey, a by-product of the cheese manufacturing process. It was envisaged that this could provide a resource for the identification of high value polymers when lactose is provided as a sole carbon source. The library was screened for function using Congo Red for the detection of extra-cellular polysaccharides.