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Adaptation aux métaux lourds de populations de rhizobia impliquées dans la phytostabilisation de déblais miniers : Identification des mécanismes d’adaptation au Zn et au Cd, et structuration des populations de rhizobia adaptées aux sites miniers / Heavy metal-adaptated rhizobial populations involved in phytostabilisation strategies : Identification of Zn/Cd-adaptation genes and structural populations of rhizobia adapted to mining soilsMaynaud, Géraldine 18 December 2012 (has links)
La symbiose entre Anthyllis vulneraria et Mesorhizobium metallidurans, mise en évidence dans l'ancienne mine Zn/Pb des Avinières à St Laurent-le-Minier (Gard) permet une entrée d'azote dans les sols grâce à la fixation biologique qui favorise l'installation d'une végétation pérenne d'intérêt pour limiter la pollution métallique via l'érosion éolienne et hydrique. M. metallidurans ayant la particularité de résister à de fortes concentrations en Zn et Cd, la recherche des gènes d'adaptation aux métaux lourds a été mise en œuvre pour mieux connaitre cette bactérie impliquée dans des opérations de phytostabilisation, par des approches de génétique moléculaire et de transcriptomie (RNAseq). Les gènes codant pour des systèmes de séquestration, d'exclusion, de réduction et d'efflux des métaux lourds, dont cadA1, codant pour une PIB-ATPase exportant Cd/Zn ont été identifiés chez deux souches métallicoles associées à Anthyllis ; M. metallidurans STM 2683T (mine des Avinières) et Mesorhizobium sp. STM 4661 (mine d'Eylie). Une étude fonctionnelle de cadA1 a permis de caractériser son rôle dans la résistance aux métaux lourds chez M. metallidurans. Ce gène a ensuite été testé comme marqueur de résistance pour étudier la diversité et la répartition des symbiotes d'Anthyllis sur des sites miniers et non pollués. Pour cela ce travail a été complété par des analyses phénotypiques de tolérance au Zn et Cd et des analyses phylogénétiques basées sur des marqueurs taxonomiques et symbiotiques. La contrainte métallique exercée par les environnements miniers semble influencer la composition et la diversité bactérienne avec une plus forte proportion (i) de phénotype métallicole lié à la présence du gène cadA1 et (ii) de rhizobia appartenant à M. metallidurans ou à une espèce très proche. La plante hôte semble quant à elle influencer la diversité symbiotique des rhizobia, indépendamment de la contrainte métallique. / Efficient nitrogen-fixing symbiosis between Anthyllis vulneraria and Mesorhizobium metallidurans, identified in the highly Zn/Pb polluted mining site of Avinières (St Laurent-le-Minier, Gard county, France) has recently been described as a potential key bioremediation agent for stimulating the growth of a sustainable plant cover and thus limit heavy metal dispersion from contaminated sites. M. metallidurans strains were shown to be resistant to high Zn and Cd concentrations. The aim of our work was to identify and characterize genes involved in heavy metal adaptation in M. metallidurans by using genetic and transcriptomic approaches (RNAseq technology). Putative genes involved in heavy metal adaptation mechanisms such as exclusion, binding, reduction and efflux, like cadA1, encoding an efflux system PIB-type ATPase involved in Zn and Cd export, were identified in two Mesorhizobium strains associated with Anthyllis: M. metallidurans STM 2683T (Avinières mine) and Mesorhizobium sp. STM 4661 (Eylie mine). Functional studies allowed us to characterize the cadA1 efflux protein as involved in metal tolerance in M. metallidurans. Then, cadA1 was used as a metal-resistance marker to study the diversity and the distribution of Anthyllis symbionts from mine soils and unpolluted soils. This work was completed by Zn- and Cd-tolerance phenotype assays and phylogenetic analyses using taxonomical and symbiotic markers. Metals in mine environments seemed to influence the bacterial composition and the diversity with a high proportion of (i) metal-tolerant phenotypes consistent with the detection of the cadA1 gene and (ii) strains belonging to the M. metallidurans species or to a bacterial species close to it. The plant-hosts seemed to impact symbiotic diversity independently of the metal-tolerant property.
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High-field NMR Metabonomics for Investigation of Cancer in Human Populations and Metabolic Perturbations in Model Systems / Métabonomique par RMN à haut champ pour l’étude du cancer sur une grande population et pour l’étude des perturbations métaboliques à travers l’utilisation de systèmes modèlesFages, Anne 17 December 2013 (has links)
La métabonomique est une approche de choix pour l’identification de biomarqueurs d’intérêts pour le diagnostic de pathologies mais aussi pour l’amélioration de notre compréhension des processus physiopathologiques. La métabonomique offre de nouvelles perspectives en épidémiologie moléculaire, objet principale de cette thèse. Nous avons appliqué l’approche métabonomique par RMN à haut champ à l’analyse de sérums sanguins issus de la cohorte prospective EPIC (European Prospective Investigation into Cancer and nutrition) dans le but d’identifier des biomarqueurs de la survenue du cancer du foie et du cancer du pancréas. L’analyse statistique des profiles métaboliques des sérums obtenus par RMN à 800MHz a permis de mettre en évidence une signature métabolique associée à l’occurrence des hépatocarcinomes (HCC) à cinq ans avant diagnostic en moyenne. L’analyse stratifiée des données a révélé des biomarqueurs précoces mais aussi des biomarqueurs de l’étiologie des HCC. L’analyse métabonomique portée sur le cancer du pancréas n’a à l’inverse pas été concluante. Des méthodes pertinentes pour l’analyse des cohortes épidémiologiques par métabonomique ont été développées, telle qu’une méthode de correction d’effet batch rendant possible la comparaison de données RMN acquises au cours d’une longue période de temps. La méthode statistique PCPR2 développée permet de quantifier l’impact de différents facteurs sur les données métabonomique afin d’en révéler les sources de variations systématiques. D’autre part, l’approche métabonomique permet également l’investigation de questions biologiques plus fondamentales. Cette thèse offre une approche de génomique fonctionnelle à l’étude des cibles métaboliques du récepteur aux hormones thyroïdiennes TRβ dans le foie. L’analyse des données HR-MAS de tissus de foie intacts complémentée par l’analyse d’extraits hépatiques sur un modèle de souris a permis d’éclaircir le rôle de ce récepteur nucléaire. / Metabonomics is a recent approach that enables not only to identify relevant biomarkers for disease diagnosis but also to improve our understanding of biological processes by gaining insight into metabolism. This thesis is mainly dedicated to the application of metabonomics to molecular epidemiology. High-field NMR metabonomic approach was applied to the analysis of serum samples from the large prospective cohort EPIC (European Prospective Investigation into Cancer and nutrition) to identify biomarkers of liver cancer and pancreatic cancer occurrence. The statistical analysis of NMR serum metabolic profiles obtained at 800 MHz enabled to highlight a metabolic signature associated with the occurrence of hepatocellular carcinoma (HCC), in average five years before diagnosis. The stratified analysis revealed both early and etiologic biomarkers of HCC. The NMR metabonomic analysis of the pancreatic cancer did not reveal any metabolic signature of this cancer. Moreover, relevant methods to allow the NMR metabonomic analysis of epidemiological cohort were developed. This thesis proposes a method to correct data for batch effect, making possible the comparison of NMR data recorded in a long period of time. The statistical method PC-PR2 developed enables the quantification of the contribution of different factors onto metabonomic data to reveal systematic variation sources. In addition, the metabonomic approach is also suitable to address specific biological questions by providing a new read-out of the metabolism. Functional genomics by NMR metabonomics was used in this thesis to study the metabolic targets of the thyroid hormone nuclear receptor TRβ in the liver. The analysis of HR-MAS data obtained on intact liver tissue in addition to the analysis of NMR data of liver extracts from a mice model enabled to better understand the role of this nuclear receptor.
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VEGF-A et phénotypes intermédiaires des maladies cardiovasculaires : une approche de génomique fonctionnelle / VEGF-A and intermediate phenotypes of cardiovascular diseases : a functional genomics approachAzimi-Nezhad, Mohsen 19 September 2012 (has links)
Le facteur de croissance de l'endothélium vasculaire (VEGF) est une cytokine multifonctionnelle qui a été liée aux maladies cardiovasculaires (MCV) et à des divers troubles/ facteurs de risque cardiovasculaires tel que le syndrome métabolique (SM). L'identification de variants génétiques qui agissent sur les taux de VEGF circulant et leurs associations avec le SM et les molécules d'adhésion et d'inflammation pourraient permettre la compréhension des liens entre les taux de VEGF et les MCV. Par conséquent nous avons recherché l'origine génétique des taux de VEGF, via une étude d'association pangénomique, et les facteurs de variation pré-analytiques et analytiques influant les taux de VEGF mesurés avant d'étudier les implications de cette molécule dans l'inflammation et le SM. Nous avons également examiné le profil du SM dans des populations françaises (cohorte STANISLAS) et iraniennes (cohorte MASHHAD). Les principaux résultats de cette thèse sont : 1) l'identification de variants génétiques rs6921438, rs4416670, rs6993770 et rs10738760 expliquant 47.6% des taux de VEGF circulant, 2) l'association du VEGF et des variants génétiques identifiés avec des molécules d'adhésion et d'inflammation telles que ICAM-1,sélectines E et L,TNF-alpha, IL-6 et CRP au niveau protéique et transcriptomique, 3) l'association du rs10738760 avec le SM, 4) la relation entre le rs6921438 et le HDL-C et le LDL-C, 5) la détermination optimale à la fois des taux de VEGF (le sérum serait plus stable que le plasma) et de son expression génétique en proposant une durée minimale entre le recueil du sang et sa centrifugation, et en évitant des cycles de gel/dégel répétés. 6) la prévalence élevée du SM chez les femmes iraniennes. Nos résultats proposent des liens biologiques entre le VEGF et les molécules d'inflammation et l'adhésion, les lipides et le SM / Vascular endothelial growth factor (VEGF) is a multifunctional cytokine that has been linked to cardiovascular diseases (CVDs) and related predisposing statuses such as metabolic syndrome (MetS).The identification of genetic variants that influence the VEGF circulating levels and their associations with MetS and adhesion and inflammation molecules could enable us to have a comprehensive approach of the relationship of this molecule with CVDs. Therefore, we aimed at first to investigate the genetic background of VEGF levels, via a genome wide association analysis, and the pre-analytical and analytical variation factors of VEGF levels measurements before examining the implication of this molecule in inflammation and in MetS. Also, we examined the differences of MetS between Iranian (MASHHAD cohort) and French (STANISLAS cohort) populations. The main findings of this thesis are: 1) the identification of 4 genetic variants(rs6921438, rs4416670, rs6993770 and rs10738760) that explain 47.6% of circulating VEGF levels, 2) the associations of VEGF and its identified genetic variants with adhesion and inflammation molecules such as ICAM-1, E and L selectins , TNF-alpha, IL-6 and CRP at protein and transcription levels, 3) the association of VEGF-related polymorphism rs10738760 with MetS, 4) the relationship between VEGF regulatory variant, rs6921438, and LDL-C and HDL-C,5) the proposition of the best conditions for measuring both circulating VEGF (serum being the most stable anticoagulant) and its gene expression by reducing time between blood collection and centrifugation, and by avoiding multiple freeze-thaw cycles,6) a high prevalence of MetS in Iranian women. Our results propose the biological connections between VEGF, inflammation and adhesion molecules, lipids and MetS
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Uso de técnicas de proteoma e genoma funcional para revelar as bases moleculares da ação anti-tumoral de ácido retinóico / Use of proteomics and functional genomics to unravel the molecular mechanisms of retinoic acid as an anti-tumor agentMontor, Wagner Ricardo 09 March 2005 (has links)
Controlar a proliferação celular de tumores é um objetivo que vem sendo perseguido há décadas, com moderado sucesso na maioria dos casos. Dentre os diversos tipos de tumores que atingem a humanidade, alguns gliomas são considerados os mais fatais, por haver pouca ou nenhuma alternativa de tratamento efetivo. Agentes que apresentam propriedades anti-tumorais, como glicocorticóides (GC) e a forma all-trans do ácido retinóico (ATRA) são utilizados como adjuvantes no tratamento de alguns tipos de glioma. Entretanto, apesar de serem moléculas bastante conhecidas, pouco se sabe sobre seu mecanismo de ação como anti-tumoral. Para endereçar este problema, nosso laboratório se propôs a isolar e caracterizar genes regulados por estes agentes, utilizando modelos celulares, como as linhagens C6 e ST1 de glioma de rato, e as linhagens T98G e A172 de glioma humano. A linhagem C6 apresenta características de células transformadas e tumorais em cultura, e responde a GC, ou ATRA, com inibição de crescimento e achatamento celular. A linhagem ST1, variante derivado da C6, é hiper-responsiva ao tratamento com GC e, aparentemente, mais responsiva ao tratamento com ATRA, passando por um processo de completa reversão fenotípica tumoral-normal, devido ao expressivo aumento do tempo de dobramento, diminuição da densidade de saturação, recuperação da dependência de fatores de crescimento presentes no soro fetal bovino e da dependência de ancoragem para proliferação e perda do potencial tumorigênico, além de sofrer alterações morfológicas, como um maior achatamento celular e reorganização em feixes paralelos, que a aproximam do fenótipo normal. No presente trabalho buscou-se alterações moleculares induzidas por ATRA em células ST1, para melhor compreender a cascata de eventos desencadeada por ação deste fármaco. Em paralelo foram realizados estudos da ação de ATRA sobre as células T98G, buscando-se correlacionar os dados obtidos em modelo celular murino com modelos humanos. Para tanto, duas metodologias de estudo foram aplicadas: a) análise proteômica através de eletroforese bidimensional de proteínas (2D-PAGE), acoplada à espectrometria de massa (MALDI-TOF), para gerar perfis de expressão protéica na ausência e na presença de ATRA, permitindo comparação e identificação de proteínas moduladas no processo; b) construção de vetores plasmideais e retrovirais para super-expressar ou bloquear a expressão de um inibidor de serina protease de rato (serpinb6), descrito previamente no laboratório como estando potencialmente envolvido no processo de reversão fenotípica de ST1 induzido por ATRA. A abordagem proteômica permitiu a identificação de sete proteínas potencialmente reguladas por ATRA no modelo celular ST1, como as proteínas envolvidas em proliferação celular (c-Fos e SCGF), as proteínas de citoesqueleto (actina e tubulina), as proteínas envolvidas em estresse celular (GRP78 e Hsc70) e a proteína TCTP, classicamente reprimida em processos de reversão do fenótipo tumoral. O uso de construções plasmideais e retrovirais permitiu a obtenção de populações celulares que super-expressam serpinb6 e a análise de fenótipo destas células indicou que serpinb6 também pode ter função citoprotetora em células ST1, o que a coloca junto com as proteínas GRP78 e Hsc70 identificadas, evidenciando a importância desta classe de proteínas no processo estudado. / Control of tumor cell proliferation is an objective that has been pursued for decades, with modest or no success in the majority of the cases. Among the several kinds of tumors that develop in humans, some gliomas are considered the most fatal, due to the lack of alternatives for effective treatment. Anti-tumor agents, such as glucocorticoids (GC) or all-trans retinoic acid (ATRA) are used in combination with other drugs in some glioma cases. However, besides being very known molecules, their anti-tumor mechanism is not completely understood. In order to address this problem, our laboratory decided to isolate and characterize genes regulated by these agents, using cellular models, such as the C6 and ST1 rat glioma cell lines and the T98G and A172 human glioma models. The C6 cell line is fully transformed and tumoral in culture and responds to GC or ATRA treatment, showing growth inhibition and cell flattening. The ST1 variant is hyper-responsive to the treatment with GC and, apparently, more responsive to the treatment with ATRA, when compared to C6. Upon treatment with these agents, it undergoes a complete tumoral to normal phenotypic reversion, characterized by an increase in doubling time, decrease of saturation density in culture, recovery of dependence of serum factors for proliferation and anchorage for colony formation, besides inhability to form tumors in nude mice and morphological changes. Here we present the efforts undertaken towards better understanding of the molecular changes induced by ATRA in ST1 cells. Aiming at the correlation of the data obtained from a rat model with human models, all the studies were performed in parallel with the T98G human glioma cell model. To this end, two study methodologies were applied: a) proteomic analysis through bidimensional electrophoresis coupled to MALDI-TOF identification, to generate protein expression profiles in the presence and absence of ATRA, allowing comparison and identification of proteins modulated in the process; b) construction of plasmid and retroviral vectors to overexpress or block the expression of a serine protease inhibitor (serpinb6), previously described in the laboratory as being potentially involved in the process of tumoral to normal phenotypic reversion promoted by ATRA in ST1. The proteomics approach allowed the identification of seven proteins potentially regulated by ATRA in ST1, such as the proteins involved in cell proliferation (c-Fos and SCGF), cytoskeleton organization (actin and tubulin), cellular stress (GRP78 and Hsc70) and the tumor related protein TCTP, classically repressed in tumoral to normal reversions, and related to the three groups of proteins mentioned above. By using plasmid and retroviral vectors it was possible to obtain recombinant cell populations over-expressing serpinb6. The phenotype analysis of these populations indicated that serpinb6 can also have cell protection effects in ST1, which would classify it together with GRP78 and Hsc70 as an anti-stress protein highlighting the importance of this protein class in the process studied.
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Etude par génomique fonctionnelle des conséquences de la surexpression de TRIB1 et FKBP11 dans les lymphocytes B au cours du lupus érythémateux systémique / Study by functional genomics of TRIB1 and FKBP11 overexpression in B cells during systemicSimoni, Léa 23 October 2015 (has links)
Le lupus érythémateux systémique est une maladie autoimmune systémique caractérisée par des lésions multiviscérales et la production d’autoanticorps (ex : anticorps anti-ADN double brin (db)) par les lymphocytes B (LB), qui jouent un rôle central dans la physiopathologie lupique. L’étiologie du lupus est à la fois environnementale et génétique. Dans le but d’identifier des anomalies génétiques intrinsèques aux LB, le laboratoire a réalisé une analyse transcriptomique sur les LB de patients lupiques en phase quiescente et a montré une surexpression des gènes TRIB1 et FKBP11 comparé aux sujets sains.Afin d’étudier les conséquences de la surexpression de ces gènes sur la fonction des LB et le développement d’une autoimmunité, nous avons généré une lignée murine conditionnelle spécifique, surexprimant Trib1 dans les LB à partir du stade précoce pro-préB et une lignée murine transgénique surexprimant Fkbp11 de façon ubiquitaire. La surexpression de Trib1 ne modifie pas l’homéostasie lymphocytaire mais induit une diminution de la production de certaines Ig : 1) les IgG1 dans le sérum à l’état basal et après une stimulation de LB in vitro ; 2) les IgM anti-OVA (Ovalbumine) après immunisation in vivo avec de l’OVA ; 3) les IgM anti-ADNdb dans le cas d’une immunisation par le LPS. Cette anomalie de la production des Ig semble provenir d’un défaut de sécrétion. De plus nous avons généré une lignée cellulaire B surexprimant Trib1 qui nous a permis de confirmer le phénotype et d’identifier des partenaires potentiels de Trib1 par technique de protéomique. La surexpression du gène Fkbp11, est, quant à elle, suffisante à induire des signes de la maladie lupique chez la souris âgée de 8 mois, tels qu’une rupture de tolérance (caractérisée par la production d’autoanticorps) et une initiation de la différenciation plasmocytaire. En conclusion, Trib1 pourrait exercer un rôle d’immunosupresseur et sa surexpression dans les LB lupiques pourrait constituer un nouveau mécanisme de régulation des LB pendant la phase de rémission du lupus, alors que Fkbp11 semble contribuer à la pathologie lupique. La description de ces deux nouvelles voies biologiques pourrait mener à une meilleure compréhension de la maladie et conduire à de potentielles applications thérapeutiques. / Systemic Lupus Erythematosous (SLE) is an autoimmune disease characterized by an inflammation of various tissues and a high production of autoantibodies (autoAb) (for example: anti-double-stranded(ds)DNA) by B cells, central actors in the physiopathology of lupus. The etiology of SLE includes both genetics and environmental factors. Looking for B cell genetic abnormalities during lupus, our B cell microarray analysis in quiescent SLE patients pointed to the overexpression of TRIB1 and FKBP11 compared to B cells from healthy controls.In order to study the consequences of these expression deregulations on B cell function and autoimmunity development, we generated a B-cell specific Trib1-KI mouse line, overexpressing Trib1 in B cells, starting from a very immature stage (pro-pre B) and a transgenic mouse overexpressing Fkbp11 ubiquitously. Trib1 overexpression induces a normal B cell homeostasis but a decrease in the production of some immunoglobulins (Ig): 1) IgG1 subclass in the serum, at a basal level and after an in vitro stimulation of splenic B cells; 2) Anti-OVA (Ovalbumine) IgM after immunization in vivo with OVA; 3) Anti-dsDNA IgM after immunization with LPS. This abnormal production of Ig seems to be linked to a defect in Ig secretion process. In addition, we developed a murine B cell line overexpressing Trib1 that let us to confirm the Ig production deficiency and to identify potential Trib1’s partners in B cells. In contrast, Fkbp11 overexpression, leads to some features of lupus disease in 8-month-aged-mice, including a tolerance breakdown (characterized by autoantibody production) and the initiation of plasma cell differentiation. In conclusion, Trib1 could exert an immunosuppressive role and its overexpression in SLE could constitute a new mechanism of B cell regulation during remission phases, whereas Fkbp11 seems rather to contribute to lupus physiopathology. Thus, the description of these two biological pathways could bring new insights into the comprehension of lupus disease and could also potentially lead to the development of new therapeutic applications.
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Functional proteomics : Generation and analysis of cDNA-encoded proteinsGräslund, Susanne January 2002 (has links)
No description available.
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On Transcriptome SequencingKlevebring, Daniel January 2009 (has links)
This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci. / QC 20100723
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A recombineering pipeline for functional genomics applied to Caenorhabditis elegansSarov, Mihail 19 February 2007 (has links) (PDF)
Genome sequencing and annotation projects define the complete sets of RNA and protein components for living systems. They also present the challenge to generate functional information for thousands of previously uncharacterized genes. Protein tagging with fluorescent or affinity tags provides a generic way to describe protein expression and localization patterns and protein-protein interactions. The genome wide application of this approach in Saccharomyces cerevisiae has resulted in a comprehensive picture of the core proteome of a simple, well-studied model system. Extending these studies to more complex, multicellular model organisms, would allow us to place protein function onto a 4 dimensional space-time map, and will improve our understanding of the complex processes of development and differentiation. This will require efficient protein tagging methods and new high performance tags. Here we present a generic protein tagging approach for the model nematode Caenorhabditis elegans. The method is based on recombination mediated DNA engineering of genomic BAC clones into tagged transgenes for integrative transformation. C.elegans offers unique advantages for function discovery through protein tagging: compact and a well annotated genome, combined with a simple and well-understood anatomy and pattern of development. However, the methods for protein tagging in C.elegans have so far been inefficient and largely dependent on artificial cDNA based constructs, which can lack important regulatory elements. In contrast, our approach combines the advantages of authentic regulation with a new application of recombineering, which is simple, fast and efficient. For the first time we apply liquid culture cloning for multiple recombineering steps. This is particularly important when high throughput applications are considered, as it offers significant advantages in scale up and automation. We show that the BAC derived transgenes can be used for stable, integrative transformation in C. elegans. We show that the tagged transgene can take over the function of its endogenous counterpart. Using florescent reporter, we reproduce known and document new expression patterns. The second part of the thesis describes a project that we undertook to develop improved double affinity cassettes for protein purification. We evaluated the performance of 5 new double tag combinations in vitro and in mammalian culture cells. All of the new cassettes performed well and present a valuable tool for protein interaction studies in higher model systems.
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Functional proteomics : Generation and analysis of cDNA-encoded proteinsGräslund, Susanne January 2002 (has links)
No description available.
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Ribosome display for selection and evolution of affibody moleculesGrimm, Sebastian January 2011 (has links)
Affinity proteins are invaluable tools in biotechnological and medical applications. This thesis is about combinatorial protein engineering principles for the generation of novel affinity proteins to purify mouse immunoglobulin, detect a potential cancer marker protein or inhibit a cell proliferation pathway. In a first study, ribosome display was for the first time applied to the selection of so-called affibody molecules, including the design of a ribosome display gene cassette, initial test enrichment experiments and the selection of binders against murine IgG1. One of the selected binders (ZMAB25) showed a highly selective binding profile to murine IgG1, which was exploited in the recovery of two different mouse monoclonal IgG1 antibodies from a bovine immunoglobulin-containing background. Ribosome display was further applied to the selection of affibody molecules binding to SATB1, a suggested marker protein for metastasizing adenocarcinoma. The study also included the selection of VHH antibody fragments from a naïve gene repertoire displayed on phage. Binders from both classes of protein scaffolds could be isolated that selectively recognized SATB1 but not its close homologue SATB2, and were used to detect endogenous SATB1 in Jurkat cells by immunofluorescence microscopy. The well-established phage display technology was used to select affibody molecules binding to H-Ras and Raf-1, both involved in the mitogen-activated protein kinase (MAPK) pathway and playing a central role in the control of cell proliferation, survival and differentiation. An isolated affibody molecule denoted ZRAF322 was found to selectively bind to Raf-1 and inhibit the interaction between H-Ras and Raf-1 in vitro. In a continued effort, ribosome display was applied to the affinity maturation of the ZRAF322 variant in a novel approach, based on repetitive cycles of diversification by error-prone PCR of the entire affibody gene and ribosome display selection, mimicking the principles of natural evolution. The method involved a monitoring of the progress of evolution and variants of ZRAF322 with 13- to 26-fold improved affinities were obtained, that contained different combinations of single or double amino acid substitutions in either previously randomized or framework positions. Implications of the substitutions for binder stability and selectivity were also investigated, showing that a higher affinity could be associated with a lower thermal melting point and that affinity-improved variants showed uncompromised binding selectivity to the hRaf-1 target. / QC 20110506
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