The role of ubiquitin specific peptidase 15 (USP 15) in human glioblastoma

Glioblastoma (GBM) is the most common and most aggressive malignant primary brain tumour. Despite the aggressiveness of the applied therapy, the prognosis remains poor with a median survival to of about 15 months. It is important to identify new candidate genes that could have clinical application in this disease. Previous gene expression studies from human GBM samples in our laboratory, revealed Ubiquitin Specific Peptidase 15 (USP15) as a gene with low expression, significantly associated with genomic deletions of the chromosomal region encompassing the USP15 locus. USP15 belongs to the ubiquitin-specific protease (USPs) family of which the main role is the reversion of ubiquitination and thereby stabilization of substrates. Previously, USP15 has been suggested to have a tumour suppressor function via its substrates APC and Caspase 3. We established GBM cell lines that stably express USP15 wt or its catalytic mutant. USP15 expression impairs cell growth by inhibiting cell cycle progression. On the other hand USP15 depletion in GBM cell lines induces cell cycle progression and proliferation. In order to identify the molecular pathways in which USP15 is implicated we aimed to identify protein-binding partners in the GBM cell line LN-229 by Mass spectrometry. As a result we identified eight new proteins that interact with USP15. These proteins are involved in important cellular processes like cytokinesis, cell cycle, cellular migration, and apoptosis. Three of these protein interactions were confirmed by co-immunoprecipitation in four GBM cell lines LN-229, LN428, LN18, LN-Z308. One of the binding proteins is HECTD1 E3 ligase of which the murine homologue promotes the APC-Axin interaction to negatively regulate the Wnt pathway. USP15 can de-ubiquitinate HECTD1 in the LN229 cell line while its depletion led to decrease of HECTD1 in GBM cell lines suggesting stabilizing role for USP15. Moreover, HECTD1 stable expression in LN229 inhibits cell cycle, while its depletion induces cell cycle progression. These results suggest that the USP15-HECTD1 interaction might enhance the antiproliferative effect of HECTD1 in GBM cell lines. Using the TOPflash/FOPflash luciferase system we showed that HECTD1 and USP15 overexpression can attenuate WNT pathway activity, and decrease the Axin2 expression. These data indicate that this new protein interaction of USP15 with HECTD1 results in negative regulation of the WNT pathway in GBM cell lines. Further investigation of the regulation of this interaction or of the protein binding network of HECTD1 in GBM may allow the discovery of new therapeutic targets. Finally PTPIP51 and KIF15 are the other two identified protein partners of USP15. These two proteins are involved in cell proliferation and their depletion in LN-229 cell line led to induction of cell cycle progression. USP15 displays a stabilizing role for them. Hence, these results show that the tumour suppressive role of USP15 in GBM cell line via different molecular mechanisms indicating the multidimensional function of USP15. Résumé Le glioblastome (GBM) est la tumeur primaire la plus fréquente et la plus agressive du cervau caractérisée par une survie médiane d'environ à 15 mois. De précédant travaux effectués au sein de notre laboratoire portant sur l'étude de l'expression de gènes pour des échantillons humains de GBM ont montré que le gène Ubiquitin Specific Peptidase 15 (USP1S) était significativement associée à une délétion locales à 25% des cas. Initialement, les substrats protéiques APC et CaspaseS de USP15 ont conduit à considérer cette protéine comme un suppresseur de tumeur. USP15 appartient à la famille protèsse spécifique de l'ubiquitine (USPs) dont le rôle principal est la réversion de l'ubiquitination et la stabilisation de substrats. Par conséquent, nous avons établi des lignées de cellules de glioblastome qui expriment de manière stable USP15 ou bien son mutant catalytique. Ainsi, nous avons ainsi démontré que l'expression de l'USP15 empêche la croissance cellulaire en inhibant la progression du cycle cellulaire. Inversement, la suppression de l'expression du gène USP15 dans les lignées cellulaires de glioblastome induit la progression du cycle cellulaire et la prolifération. Afin d'identifier les voies moléculaires dans lesquelles sont impliquées USP15, nous avons cherché à identifier les partenaires de liaisons protéiques par spectrométrie de masse dans la lignée cellulaire LN-229. Ainsi, huit nouvelles protéines interagissant avec USP15 ont été identifiées dont la ligase E3 HECTD1. L'homologue murin de Hectdl favorise l'interaction APC-Axin en régulant négativement la voie de signalisation de Wnt. USP15 interagit en désubiquitinant HECTD1 dans la lignée cellulaire LN-229 et provoque ainsi l'atténuation de l'activité de cette voie de signalisation. En conclusion, HECTD1, en interagissant avec USP15, joue un rôle de suppresseur de tumeur dans les lignées cellulaire de GBM.

Regulation of bistable ICEclc transfer in pseudomonas knackmussii B13

L'élément génétique intégratif et conjugatif auto-transférable de 103 kb qui se trouve dans le génome de Pseudomonas knackmussii B13 (ICEc/c) confère la capacité de dégrader le 3-chlorobenzoate et le 2-aminophénol. L'élément ICE c/c peut être transféré par conjugaison de la souche B13 à diverses bêta- et gamma- protéobactéries. Seule une sous-population de 3 à 5% des cellules transfère l'élément, les cellules dites "compétentes pour le transfert". L'acquisition de la compétence pour le transfert est vraisemblablement la conséquence d'une régulation bistable, conduisant une partie des cellules au transfert de l'élément ICE c/c tandis que, dans les autres, l'élément reste quiescent et ne se transfère pas. À ce jour, les mécanismes et les acteurs moléculaires qui régulent l'activation bistable de l'élément sont restés inconnus. Mon travail de doctorat visait à identifier les éléments bistables du régulon de la compétence pour le transfert et d'analyser les fondements moléculaires de la bistabilité de l'élément ICE c/c chez P. knackmussii. Le premier chapitre introduit le thème du transfert génétique horizontal avec un accent particulier sur les éléments intégratifs et conjugatifs (ICE) et ICEcIc. L'état actuel des connaissances sur l'organisation génétique, la régulation, l'intégration et le transfert de différents modèles de ICEs est exposé en détail. En outre, je m'étends sur les phénomènes d'hétérogénéité et de bistabilité phénotyplques, qu'on peut distinguer dans une population isogénique dans des conditions de culture homogènes, et qui sont susceptibles de jouer un rôle dans le transfert de l'élément ICE c/c, dans la mesure où il ne s'active et n'est transférable que dans une très petite sous-population de cellules. Dans le chapitre 2, je présente une analyse globale des régions promotrices minimales des gènes appartenant au régulon de la compétence pour le transfert de l'élément ICE c/c. Nous avons étudié les caractéristiques d'expression des promoteurs et, s'ils s'avéraient bistables, leur activation dans le temps par comparaison avec le mutant lntB13. Pour ce faire, nous avons utilisé des fusions de promoteurs avec des gènes rapporteurs et testé l'expression bistable chez P. knackmussii par microscopie à épifluorescence. Pour six promoteurs présentant une expression bistable, nous avons employé de la microscopie temporelle pour déterminer la chronologie de leur expression par rapport à Pint et PinR. Parmi eux, nous avons identifié deux gènes exprimés précocement et trois gènes exprimés tardivement dans le processus d'acquisition de la compétence de transfert. Dans le chapitre 3, j'expose une analyse d'expression génétique pour l'un des groupes de gènes dont la transcription est la plus élevée dans la région conservée de ICE c/c, les gènes orf81655-orf68241 contenus dans une région de 14 kb. Nous montrons d'abord que cet opéron fait partie du même régulon bistable que intB13 et inrR et analysons les caractéristiques génétiques qui conduisent à une transcription élevée. Nous étudions les fonctions biologiques de ce groupe de gènes par des délétlons ciblées et montrons que certaines d'entre elles empêchent le transfert de l'élément. Nous approfondissons la caractérlsatlon de I'orf8l655 en construisant une fusion transcrlptionnelle avec le gène codant pour la protéine fluorescente verte (egfp) (en utilisant le système minl-Tn5). L'expression de Vorf81655 dans des cellules individuelles est comparée au signal mesuré par hybridation in situ en fluorescence (FISH) sur le ARN messager du gène. En utilisant FISH, des délétlons du promoteur et de l'analyse directe de transcription, nous avons localisé la région promotrice du groupe de gènes. En outre, nous avons utilisé des mutations dirigées pour comprendre la bistabilité de cette région promotrice, caractérisée par une transcription très élevée et une traduction lente de l'ARN messager.  Dans le chapitre 4, nous nous efforçons de comprendre comment la bistabilité est générée au sein du régulon te de l'élément ICE c/c. Pour ce faire, nous avons tenté de reconstituer une expression bistable, dans un hôte qui ne présente pas de bistabilité naturellement, à partir d'éléments génétiques individuels. L'hôte choisi est Pseudomonas putida dans lequel nous avons introduit une copie unique de Pint, PinR ou PaipA fusionnés à la egfp, construits qui permettent d'observer l'apparition de bistabilité. Nous avons ensuite construit différents assemblages de composants génétiques de l'élément ICE c/c, en nous concentrant sur la région parA-inrR. En effet, nous avons pu démontrer qu'une expression bistable apparaît dans P. putida grâce à ces éléments en l'absence de l'élément ICE c/c complet. À noter que la plupart des construits génétiques activent PaipA ou P|,,R, mais qu'un seul recrée la bistabilité de Pint, ce qui suggère que la région parA-inrR permet à la fois d'engendrer la bistabilité et d'opérer la transition entre les promoteurs précoces et les promoteurs tardifs du régulon de la bistabilité. Dans le chapitre 5, nous concluons sur une discussion de la pertinence de nos résultats et sur de futures perspectives de recherche. -- The 103-kb self-transmissible integrative and conjugative element (ICE) of Pseudomonas knackmussii B13 (ICEc/c) confers the capacity to degrade 3- chlorobenzoate and 2-aminophenol. ICEc/c can be conjugated from strain B13 to a variety of Beta- and Gammaproteobacteria. Interestingly, ICE c/c transfer is observed in a subpopulatlon of cells (3-5%) only, the so-called 'transfer competent' cells. The formation of transfer competence (tc) is thought to be the consequence of a 'bistable' decision, which forces those cells to follow the developmental path which leads to ICEc/c transfer, whereas in others ICE c/c remains silent and does not transfer. So far, the mechanisms and molecular partners generating this bistable transfer activation in cells of P. knackmussii B13 remain mostly unidentified. This thesis aimed at understanding the extent of the tc bistability regulon and to dissect the molecular basis of bistabillty formation of ICEc/c in P. knackmussii. The first chapter is a general Introduction on horizontal gene transfer (HGT) with particular emphasis on ICEs and ICE c/c. The emphasis is made on the current knowledge about the HGT gene organization, regulation and specific integration and transfer aspects of the different ICEs models. Furthermore, I focus on the phenomena of phenotypic heterogeneity and bistability (the property of two distinguishable phenotypes existing within an isogenic population under homogeneous conditions), which may play a particular role in ICEc/c behaviour, since ICE activation and transfer only occurs in a very small subpopulation of cells. In Chapter Two, I focus on a global analysis of the different core promoters that might belong to the ICEc/c tc pathway regulon. We studied both expression patterns of ICEc/c promoters and, once being identified as "bistable", their temporal activation compared to that of intB13. In order to do this, we used promoter reporter fusions and tested blstability expression in P. knackmussii using epifluorescence microscopy. For the 6 promoters that showed bistable expression, we used time-lapse microscopy to study the timing of promoter expression in comparison to that of P,,,t or PlnR. We could establish two "early" and 3 "late" phase promoters in the process of transfer competence. In Chapter Three, I focused my attention on analysis of gene expression of one of the most highly transcribed gene clusters in the conserved core region of ICEc/c, a 14-kb gene cluster formed by the genes orf81655-orf68241. First we showed that this operon is part of the same bistability 'regulon' as intB13 and inrR, and analysed the genetic features that lead to high transcription. We studied the potential biological function of this cluster for ICE c/c by making specific gene deletions, showing that some interrupt ICEc/c transfer. We further analysed the orfdl655 promoter by constructing transcriptional egfp fusion reporter strains using the miniTn5 delivery system. Expression of the orf81655 promoter in single cells was compared to signals measured by Fluorescence In Situ Hybridization (FISH) on orfSl655 mRNA. We localized the promoter region of the gene cluster using FISH, promoter deletions, and by direct transcript analysis. We further used site-directed mutagenesis to understand the bistability character of the promoter region and the extremely high transcription but low translation from this mRNA. In Chapter Four, we set out to understand how bistability is generated in the tc pathway of ICEc/c. For this we tried rebuilding bistable expression from ICEc/c individual gene components in a host, which normally does not display bistability. As host we used P. putida without ICEc/c but with a single copy Pint-, PlnR- or PalpA- egfp fusion that enabled us to verify bistability formation. Subsequently, we built different assemblages of ICEc/c gene components, focusing on the parA-inrR region. Indeed, we found that bistable expression can be build from those components in P. putida without ICEc/c. Interestingly, most genetic constructs activated PaipA or PlnR, but only one resulted in bistable activation of PinT. This suggests that the parA-inrR region acts as a bistability "generator", but also as a bistability "relay" from early to late promoters in the tc pathway hierarchy. In the final fifth chapter, we conclude with a discussion of the relevance of the present thesis and the resulting perspectives for future studies.

Schistosoma mansoni and HIV acquisition in fishing communities of Lake Victoria, Uganda: a nested case-control study.

OBJECTIVE: It has been suggested that Schistosoma mansoni, which is endemic in African fishing communities, might increase susceptibility to human immunodeficiency virus (HIV) acquisition. If confirmed, this would be of great public health importance in these high HIV-risk communities. This study was undertaken to determine whether S. mansoni infection is a risk factor for HIV infection among the fishing communities of Lake Victoria, Uganda. We conducted a matched case-control study, nested within a prospective HIV incidence cohort, including 50 HIV seroconverters (cases) and 150 controls during 2009-2011. METHODS: S. mansoni infection prior to HIV seroconversion was determined by measuring serum circulating anodic antigen (CAA) in stored serum. HIV testing was carried out using the Determine rapid test and infection confirmed by enzyme-linked immunosorbent assays. RESULTS: About 49% of cases and 52% of controls had S. mansoni infection prior to HIV seroconversion (or at the time of a similar study visit, for controls): odds ratio, adjusting for ethnicity, religion, marital status, education, occupation, frequency of alcohol consumption in previous 3 months, number of sexual partners while drunk, duration of stay in the community, and history of schistosomiasis treatment in the past 2 years was 1.23 (95% CI 0.3-5.7) P = 0.79. S. mansoni infections were chronic (with little change in status between enrolment and HIV seroconversion), and there was no difference in median CAA concentration between cases and controls. CONCLUSIONS: These results do not support the hypothesis that S. mansoni infection promotes HIV acquisition.

Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening.

This paper contains a joint ESHG/ASHG position document with recommendations regarding responsible innovation in prenatal screening with non-invasive prenatal testing (NIPT). By virtue of its greater accuracy and safety with respect to prenatal screening for common autosomal aneuploidies, NIPT has the potential of helping the practice better achieve its aim of facilitating autonomous reproductive choices, provided that balanced pretest information and non-directive counseling are available as part of the screening offer. Depending on the health-care setting, different scenarios for NIPT-based screening for common autosomal aneuploidies are possible. The trade-offs involved in these scenarios should be assessed in light of the aim of screening, the balance of benefits and burdens for pregnant women and their partners and considerations of cost-effectiveness and justice. With improving screening technologies and decreasing costs of sequencing and analysis, it will become possible in the near future to significantly expand the scope of prenatal screening beyond common autosomal aneuploidies. Commercial providers have already begun expanding their tests to include sex-chromosomal abnormalities and microdeletions. However, multiple false positives may undermine the main achievement of NIPT in the context of prenatal screening: the significant reduction of the invasive testing rate. This document argues for a cautious expansion of the scope of prenatal screening to serious congenital and childhood disorders, only following sound validation studies and a comprehensive evaluation of all relevant aspects. A further core message of this document is that in countries where prenatal screening is offered as a public health programme, governments and public health authorities should adopt an active role to ensure the responsible innovation of prenatal screening on the basis of ethical principles. Crucial elements are the quality of the screening process as a whole (including non-laboratory aspects such as information and counseling), education of professionals, systematic evaluation of all aspects of prenatal screening, development of better evaluation tools in the light of the aim of the practice, accountability to all stakeholders including children born from screened pregnancies and persons living with the conditions targeted in prenatal screening and promotion of equity of access.

Hepatitis C Virus Awareness Among Men Who Have Sex With Men in Southwest Switzerland.

BACKGROUND: In Switzerland, the incidence of hepatitis C virus (HCV) infection in HIV-positive men who have sex with men (MSM) rose 18-fold between 1998 and 2011. We aimed to evaluate transmission risk factors, awareness, and seroprevalence of HCV among MSM in southwest Switzerland. METHODS: From 1st June 2011 to 31st August 2012, trained health care professionals invited individuals attending (1) MSM screening clinics and (2) indoor and outdoor meeting areas to complete an anonymous questionnaire. Consenting participants were rapid tested for HCV (OraQuick HCV Rapid Antibody Test). RESULTS: Of 918 MSM approached, 654 agreed to participate, most of whom (536, 82%) were enrolled via MSM screening clinics. Of 654 participants, 21 (3.2%) disclosed being HIV positive; 140 (21%) had unknown HIV status. In the preceding 12 months, 357 (55%) of 654 participants reported unprotected anal intercourse (UAI) and 321 (49%) of 654 participants reported UAI with partners of different/unknown HIV status. Not HIV serosorting was reported more frequently among HIV-positive individuals (76%, P < 0.001). Three hundred two participants (46%) were aware of HCV, awareness being higher among clinic than meeting area participants (49% vs. 33%, P = 0.04). One individual (of 654; 0.2%), with a negative HIV test result 18 months previously was newly diagnosed as being HCV positive on rapid testing. CONCLUSIONS: In this sample of predominantly HIV-negative MSM, half the participants were aware of HCV and HCV seroprevalence was low. However, high rates of UAI and of UAI without HIV serosorting were reported. Given the increasing incidence of HCV among HIV-positive men, we propose that HCV counseling should be offered to MSM regardless of HIV status, with testing offered to those at high risk.

Protein pocket and ligand shape comparison and its application in virtual screening.

Understanding molecular recognition is one major requirement for drug discovery and design. Physicochemical and shape complementarity between two binding partners is the driving force during complex formation. In this study, the impact of shape within this process is analyzed. Protein binding pockets and co-crystallized ligands are represented by normalized principal moments of inertia ratios (NPRs). The corresponding descriptor space is triangular, with its corners occupied by spherical, discoid, and elongated shapes. An analysis of a selected set of sc-PDB complexes suggests that pockets and bound ligands avoid spherical shapes, which are, however, prevalent in small unoccupied pockets. Furthermore, a direct shape comparison confirms previous studies that on average only one third of a pocket is filled by its bound ligand, supplemented by a 50 % subpocket coverage. In this study, we found that shape complementary is expressed by low pairwise shape distances in NPR space, short distances between the centers-of-mass, and small deviations in the angle between the first principal ellipsoid axes. Furthermore, it is assessed how different binding pocket parameters are related to bioactivity and binding efficiency of the co-crystallized ligand. In addition, the performance of different shape and size parameters of pockets and ligands is evaluated in a virtual screening scenario performed on four representative targets.

t(15;21) translocations leading to the concurrent downregulation of RUNX1 and its transcription factor partner genes SIN3A and TCF12 in myeloid disorders.

Through a combined approach integrating RNA-Seq, SNP-array, FISH and PCR techniques, we identified two novel t(15;21) translocations leading to the inactivation of RUNX1 and its partners SIN3A and TCF12. One is a complex t(15;21)(q24;q22), with both breakpoints mapped at the nucleotide level, joining RUNX1 to SIN3A and UBL7-AS1 in a patient with myelodysplasia. The other is a recurrent t(15;21)(q21;q22), juxtaposing RUNX1 and TCF12, with an opposite transcriptional orientation, in three myeloid leukemia cases. Since our transcriptome analysis indicated a significant number of differentially expressed genes associated with both translocations, we speculate an important pathogenetic role for these alterations involving RUNX1.

Cost-effectivness in a DRG system for two-step exchange of infected total joint arthroplasty

The costs related to the treatment of infected total joint arthroplasties represent an ever groving burden to the society. Different patient-adapted therapeutic options like débridement and retention, 1- or 2-step exchange can be used. If a 2-step exchange is used we have to consider short (2-4 weeks) or long (>4-6 weeks) interval treatment. The Swiss DRG (Diagnose related Groups) determines the reimboursement the hopsital receives for the treatment of an infected total arthroplasty. The review assesses the cost-effectiveness of hospitalisation practices linked to surgical treatment in the two-stage exchange of a prosthetic-joint infection. The aim of this retrospectiv study is to compare the economical impact between a short (2 to 4 weeks) versus a long (6 weeks and above) interval during a two-satge procedure to determine the financial impact. Retrospectiv study of the patients with a two-stage procedure for a hip or knee prosthetic joint infection at CHUV hospital Lausanne (Switzerland) between 2012 and 2013. The review analyses the correlation between the interval length and the length of the hospital stay as well as with the costs and revenues per hospital stay. In average there is a loss of 40′000 Euro per hospitalisation for the treatment of prosthetic joint infection. Revenues never cover all the costs, even with a short interval procedure. This economical loss increases with the length of the hospital stay if a long-term intervall is choosen. The review explores potential for improvement in reimbourement practices and hospitalisation practices in the current Swiss healthcare setting. There should be alternative setups to decrease the burden of medical costs by a) increase the reimboursment for the treatment of infected total joints or by b) splitting the hospital stay with partners (rapid transfer after first operation from center hospital to level 2 hospital and retransfer for second operation to center) in order to increase revenues.

Interactome analysis reveals that FAM161A, deficient in recessive retinitis pigmentosa, is a component of the Golgi-centrosomal network.

Defects in FAM161A, a protein of unknown function localized at the cilium of retinal photoreceptor cells, cause retinitis pigmentosa, a form of hereditary blindness. By using different fragments of this protein as baits to screen cDNA libraries of human and bovine retinas, we defined a yeast two-hybrid-based FAM161A interactome, identifying 53 bona fide partners. In addition to statistically significant enrichment in ciliary proteins, as expected, this interactome revealed a substantial bias towards proteins from the Golgi apparatus, the centrosome and the microtubule network. Validation of interaction with key partners by co-immunoprecipitation and proximity ligation assay confirmed that FAM161A is a member of the recently recognized Golgi-centrosomal interactome, a network of proteins interconnecting Golgi maintenance, intracellular transport and centrosome organization. Notable FAM161A interactors included AKAP9, FIP3, GOLGA3, KIFC3, KLC2, PDE4DIP, NIN and TRIP11. Furthermore, analysis of FAM161A localization during the cell cycle revealed that this protein followed the centrosome during all stages of mitosis, likely reflecting a specific compartmentalization related to its role at the ciliary basal body during the G0 phase. Altogether, these findings suggest that FAM161A's activities are probably not limited to ciliary tasks but also extend to more general cellular functions, highlighting possible novel mechanisms for the molecular pathology of retinal disease.

Conflict over multiple-partner mating between males and females of the polygynandrous common lizards.

The optimal number of mate partners for females rarely coincides with that for males, leading to a potential sexual conflict over multiple-partner mating. This suggests that the population sex ratio may affect multiple-partner mating and thus multiple paternity. We investigate the relationship between multiple paternity and the population sex ratio in the polygynandrous common lizard (Lacerta vivipara). In six populations the adult sex ratio was biased toward males, and in another six populations the adult sex ratio was biased toward females, the latter corresponding to the average adult sex ratio encountered in natural populations. In males the frequency and the degree of polygyny were lower in male-biased populations, as expected if competition among males determines polygyny. In females the frequency of polyandry was not different between treatments, and polyandrous females produced larger clutches, suggesting that polyandry might be adaptive. However, in male-biased populations females suffered from reduced reproductive success compared to female-biased populations, and the number of mate partners increased with female body size in polyandrous females. Polyandrous females of male-biased populations showed disproportionately more mating scars, indicating that polyandrous females of male-biased populations had more interactions with males and suggesting that the degree of multiple paternity is controlled by male sexual harassment. Our results thus imply that polyandry may be hierarchically controlled, with females controlling when to mate with multiple partners and male sexual harassment being a proximate determinant of the degree of multiple paternity. The results are also consistent with a sexual conflict in which male behaviors are harmful to females.

Pre-existing astrocytes form functional perisynaptic processes on neurons generated in the adult hippocampus.

The adult dentate gyrus produces new neurons that morphologically and functionally integrate into the hippocampal network. In the adult brain, most excitatory synapses are ensheathed by astrocytic perisynaptic processes that regulate synaptic structure and function. However, these processes are formed during embryonic or early postnatal development and it is unknown whether astrocytes can also ensheathe synapses of neurons born during adulthood and, if so, whether they play a role in their synaptic transmission. Here, we used a combination of serial-section immuno-electron microscopy, confocal microscopy, and electrophysiology to examine the formation of perisynaptic processes on adult-born neurons. We found that the afferent and efferent synapses of newborn neurons are ensheathed by astrocytic processes, irrespective of the age of the neurons or the size of their synapses. The quantification of gliogenesis and the distribution of astrocytic processes on synapses formed by adult-born neurons suggest that the majority of these processes are recruited from pre-existing astrocytes. Furthermore, the inhibition of astrocytic glutamate re-uptake significantly reduced postsynaptic currents and increased paired-pulse facilitation in adult-born neurons, suggesting that perisynaptic processes modulate synaptic transmission on these cells. Finally, some processes were found intercalated between newly formed dendritic spines and potential presynaptic partners, suggesting that they may also play a structural role in the connectivity of new spines. Together, these results indicate that pre-existing astrocytes remodel their processes to ensheathe synapses of adult-born neurons and participate to the functional and structural integration of these cells into the hippocampal network.

Phenotypical analysis of mice deficient for the channel activating protease CAP2

Channel activating proteases (CAP) are membrane-bound serine proteases that have been identified as in vitro activators of the epithelial sodium channel (ENaC). Two of them are mainly studied in the laboratory. CAP1/Prss8 was previously shown implicated in colonic sodium homeostasis in vivo. In the first part of this thesis, we generated and characterized mice deficient for CAP2/Tmprss4. The mice are healthy and viable, and they do not show any obvious phenotype. We investigated ENaC activity and expression under regular and sodium- deficient diet, and we could demonstrate that CAP2 is not a major regulator of sodium homeostasis in vivo. We next studied whether CAP2 is implicated in potassium homeostasis. We detected a strong gender-dependency when CAP2 knock-out mice were put under a potassium-deficient diet. We showed in male mice an implication of CAP2 in the regulation of the colonic H+, K+- ATPase, and we propose an implication of membrane-associated progesterone receptors and their binding partners, as well as a possible cleavage-mediated glucocorticoid receptor signalling. We studied the possible interaction between CAPI and CAP2 by generating and characterizing two different mouse study groups, displaying different hypomorphic mutations in the CAPI gene, and deficient for CAP2. We demonstrate that balanced expression of CAPI and CAP2 is required for maintainance of skin integrity and for normal placental development. As CAPI knock-out embryos die due to a placental failure, the additional combined deletion of CAP2 resulted in survival until birth. We could evidence that CAPI and CAP2 are implicated in the same signalling pathway as proposed in cancer studies at the level of the placenta, implicating integrin a5, ERK, AKT, E- and N-cadherin. Furthermore, we investigated whether CAPI is implicated in the pathogenesis and susceptibility to experimental chronic colitis in a mutant rat model. By giving CAPI mutant rats Dextran sodium sulfate, we induced chronic inflammation of the colon, and we highlighted the protective role of CAPI at the histopathological and clinical levels. In conclusion, we showed that CAP2 is not a major regulator of ENaC-mediated sodium homeostasis in vivo, but rather a regulator of potassium homeostasis in a gender-dependent manner implicating the colonic H+, K+-ATPase, membrane progesterone receptors, and the glucocorticoid receptor. We have investigated whether CAPI and CAP2 interact at the functional level, and we show that a balanced expression of CAPI and CAP2 is required in the skin, but also in the placenta. Imbalanced expression of CAPI and CAP2 leads to impaired EMT-associated signalling. We have studied whether CAPI is implicated in the pathogenesis and susceptibility to chronic colitis, and we demonstrated the protective role of CAPI in distal colon. -- Les protéases activatrices de canal (CAP) sont des protéases à serine attachées à la membrane qui ont été identifiées comme activateurs in vitro du canal sodique épithélial (ENaC). Deux de ces protéases sont principalement étudiées dans le laboratoire. CAP1/Prss8 a été identifié préalablement comme impliqué dans l'homéostasie du sodium in vivo au niveau du côlon. Dans la première partie de cette thèse, nous avons généré et caractérisé des souris déficientes pour CAP2/Tmprss4. Les souris sont en bonne santé et viables, et elles ne présentent pas de phénotype visible. Nous avons étudié l'activité et l'expression d'ENaC sous diète normale et déficiente en sodium, et nous avons démontré que CAP2 n'est pas un régulateur essentiel de l'homéostasie sodique in vivo. Nous avons ensuite étudié si CAP2 est impliqué dans l'homéostasie du potassium. Nous avons détecté une forte dépendance du sexe lorsque les souris knock-out pour CAP2 étaient placées sous diète déficiente en potassium. Nous avons démontré dans les souris mâles une implication de CAP2 dans la régulation de la H+, K+- ATPase colonique, des récepteurs membranaires à la progestérone et de leur partenaires de liaison, ainsi que dans la possible signalisation médiée par le clivage du récepteur aux glucocorticoïdes. Nous avons étudié l'interaction possible entre CAPI et CAP2 en générant et en caractérisant deux groupes d'étude de souris différents, porteurs de différentes mutations hypomorphiques dans le gène de CAPI, et déficients pour CAP2. Nous avons pu montrer qu'une expression équilibrée de CAPI et CAP2 est requise pour le maintien de l'intégrité de la peau et pour le développement normal du placenta. Les embryons knock-out pour CAPI meurent suite à une défaillance placentaire, et la délétion additionnelle et combinée de CAP2 permet la survie jusqu'à la naissance. Nous supposons que CAPI et CAP2 sont impliqués dans la même voie de signalisation au niveau du placenta que celle proposée dans les études de cancer, impliquant l'intégrine a5, ERK, AKT, E- et N-cadhérine. De plus, nous avons étudié si CAPI est impliqué dans la pathogenèse et la susceptibilité de colite chronique expérimentale dans un modèle de rat mutant. En administrant aux rats mutants pour CAPI du Dextran sodium sulfate, nous avons induit une inflammation chronique du côlon, et nous avons pu mettre en évidence le rôle protecteur de CAPI au niveau histopathologique et au niveau clinique. En conclusion, nous avons démontré que CAP2 n'est pas un régulateur essentiel de l'homéostasie sodique médiée par ENaC in vivo, mais plutôt de l'homéostasie potassique d'une manière dépendante du sexe et impliquant la H+, K+-ATPase colonique, les récepteurs membranaires à la progestérone et le récepteur aux glucocorticoïdes. Nous avons étudié si CAPI et CAP2 interagissent au niveau fonctionnel, et nous avons montré qu'une expression équilibrée entre CAPI et CAP2 est requise dans la peau et le placenta. L'expression déséquilibrée de CAPI et CAP2 mène à une altération de la signalisation associée à l'EMT. Nous avons étudié si CAPI est impliqué dans la pathogenèse et la susceptibilité de colite chronique expérimentale, et nous avons démontré le rôle protecteur de CAPI dans le côlon distal.

Role of Munc18c in SNARE-mediated exocytosis

Background: The SNARE (Soluble N-ethylmaleimide-sensitive factor Attachment protein Receptors) and SM (Sec1/Munc18) family of proteins form the core machinery that drives the fusion of vesicles in different membrane trafficking steps. They are highly conserved, implying a similar mode of binding and function. In vertebrates, Munc18a is essential for neuronal exocytosis. It binds to its partner syntaxin1a (Syx1a) at both its N-peptide and closed conformation, and thereby inhibits SNARE complex formation in vitro. By contrast, its close homolog Munc18c is thought to interact with only the N-peptide of its partner Syx4. Moreover, different effects of Munc18c on SNARE complex formation have been reported, suggesting that the two Munc18/Syx pairs act differently. Objective: The aim of the present study was to investigate whether the mechanism of action of Munc18c indeed deviates from that of Munc18a by using sensitive biochemical and biophysical methods. Results: I found that Munc18c does have a similar binding mode as Munc18a and interacts tightly with Syx4 at both the N-peptide and closed conformation. Moreover, I established, through a novel assay, that Munc18c inhibits SNARE complex assembly, with both the binding sites contributing to inhibition, similar to Munc18a. However, there were several subtle differences between the two Munc18/Syx pairs. Munc18a exerted stronger inhibition than Munc18c. Also their respective Syx partners were found to differ in the rate of binding to SNAP25, suggesting that the equilibrium of their open and closed conformations is different. Moreover, Munc18a was found to interact with Syx 1, 2, 3 but not 4, while Munc18c bound to Syx 2, 4 and 1 but not 3. By comparing the kinetics of interaction of Syx with either Munc18 or SNAP25, I found that the block of SNARE complex assembly by Munc18 is effective on a shorter time scale, but SNAP25 eventually binds to Syx resulting in SNARE complex formation. Nevertheless, these findings do not explain how Syx can escape the tight grip of Munc18, suggesting that other proteins or mechanisms are needed for this step. I also discovered that Munc18 is able to bind on the surface of the SNARE core complex; however, this observation needs to be tested more rigorously. Conclusion: Munc18c was found to be similar to Munc18a in its mode of binding to Syx and inhibition of SNARE complex assembly. However, differences in kinetics and interaction specificities were observed between the different Munc18/Syx pairs. -- Contexte : Les familles des protéines SNARE (Soluble N-ethylmaleimide-sensitive factor At- tachment protein Receptors) et SM (Sec1/Munc18) forment le coeur de la machinerie chargée de la fusion vésiculaire au cours des différentes étapes du trafic intracellulaire. Elles sont très conservées, suggérant un mode d'interaction et des fonctions semblables. Chez les Verté- brés, Munc18a est essentielle à l'exocytose neuronale. Elle se lie à sa partenaire d'interaction syntaxin1a (Syx1a) à la fois via un peptide N-terminal et la conformation fermée de celle-ci, inhibant ainsi la formation du complexe SNARE in vitro. Son homologue proche Munc18c au contraire, est supposée interagir seulement avec le peptide N-terminal de sa partenaire Syx4. En outre, différents effets de Munc18c sur la formation du complexe SNARE ont été décrits, suggérant que les deux paires Munc18/Syx fonctionnent différemment. Objectif : Le but de cette étude est de tester si les mécanismes de fonctionnement de Munc18c diffèrent vraiment de ceux de Munc18a par le biais de méthodes biochimiques et biophysiques très précises. Résultats : J'ai pu démontrer que Munc18c se comporte en effet de façon semblable à Munc18a, et interagit étroitement avec Syx4 à ses deux sites de liaison. J'ai pu de surcroît montrer par une nouvelle méthode que Munc18c inhibe l'assemblage du complexe SNARE en impliquant ces deux sites de liaison, comme le fait Munc18a. il existe cependant de subtiles différences entre les deux paires Munc18/Syx : Munc18a exerce une inhibition plus forte que Munc18c ; leurs Syx partenaires diffèrent également dans leur degré de liaison à SNAP25, ce qui suggère un équilibre different de leurs conformations ouverte et fermée. De plus, Munc18a interagit avec Syx 1, 2 et 3 mais pas Syx 4, alors que Munc18c se lie à Syx 2, 4 et 1 mais pas Syx 3. En comparant les cinétiques d'interaction de Syx avec Munc18 ou SNAP25, j'ai découvert que le blocage par Munc18 de l'assemblage du complexe SNARE est effectif de façon brève, bien que SNAP25 finisse par se lier à Syx et aboutir ainsi à la formation du complexe SNARE. Ces découvertes n'expliquent cependant pas comment Syx parvient à échapper à la solide emprise de Munc18, et suggèrent ainsi l'intervention nécessaire d'autres protéines ou mécanismes à cette étape. J'ai également découvert que Munc18 peut se lier à la surface de la partie centrale du complexe SNARE - cette observation reste à être testée de façon plus stringente. Conclusion : Il a pu être établi que Munc18c est semblable à Munc18a quant à son mode de liaison à Syx et d'inhibition de l'assemblage du complexe SNARE. Des différences de cinétique et de spécificité d'interaction entre les diverses paires Munc18/Syx ont cependant été identifiées.

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.