BISTRO

#13205 : Optimisation of freeze and conservation method of peripherical blood mononucleated cells

The provision of human biological material collected, processed and stored under optimal conditions is crucial to ensure the quality of research carried out downstream. These optimal conditions must b...

#13204 : Early transcriptional signature of T-cell memory after dengue vaccination

Dengue virus (DENV) induces strong T and B cell responses upon infection. However, there is currently neither vaccine nor specific treatment against DENV, which is spreading worldwide causing 400 mill...

#13196 : Chikungunya virus adaptation to a low temperature in a French population Ae. albopictus

The chikungunya virus (CHIKV) is an emerging mosquito-borne virus which has widely spread around the world in the last two decades. The virus is transmitted between human hosts by Aedes mosquitoes, in...

#13174 : Characterization of Yolk Sac Derived Progenitors in the Fetal Liver

Erythromyeloid progenitors (EMPs) originate from the yolk sac during early mouse development and migrate to the fetal liver via the circulation where they undergo massive expansion and differentiation...

#13146 : Intégration d'outils bioinformatique dans Galaxy pour identification bactérienne

Intégration d'outils bio-informatique dans Galaxy pour identification bactérienne...

#13141 : 3D PATH

Complex chronic diseases are caused by the accumulation of genetic, microbial and lifestyle factors. The number and complexity of such factors makes prediction of pathogenesis and therapy particularly...

#13128 : Remettre les servers Genolist comme LegioList, TuberclListe, Colibri etc en service

The servers like LegioList are used by my group and many groups around the world working on Legionella pathogenesis since its establishment in 2004. This server has provided us with an important reser...

#13125 : Move of the DISCO-BAC server VM to the new DSI infrastructure

DISCO-Bac (http://disco-bac.web.pasteur.fr/), a Web server, is a part of a recent publication https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3932-y (Co-authored by former Hub member...

#13116 : Targeted search of specific commensals in 16S databases

Bacteria analysis of fecal samples by 16S sequencing has provided a wealth of information for the distribution of bacterial species in both health and disease conditions. When looking at bacterial com...

#13081 : Hamper cell-to-cell variation to enhance drug-mediated killing

Without new treatment development tuberculosis could cause about 70 million deaths by 2050, mostly due to the spread of multidrug-resistant strains. The standard drug regimen still builds on the first...

#13078 : Determination of the transcriptome controlled by the two-component system BvrR/BvrS using dominant positive and negative BvrR mutants

Our project is focused on the intracellular life of Brucella abortus, the causative agent of bovine brucellosis. B. abortus is a facultative extracellular-intracellular pathogen that upon infection of...

#13043 : Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing

Disruption of GABAergic inhibitory circuits is one of the common alteration responsible for several psychiatric developmental disorders. Gephyrin (GPHN) is the common and main molecular organizer of i...

#12997 : Identifying subpopulation-specific signatures of tuberculosis persistence for enhanced diagnostics.

Microbes are prone to rapid changes and they can either exploit or countervail their variation in a context-dependent manner. To this purpose, both genetic diversity and non-genetic phenotypic variati...

#12996 : Analyse transcriptionnelle du cellules cancéreuse intestinal vs normales après co-culture avec la bactérie associée au cancer Streptococcus gallolyticus

Streptococcus gallolyticus sous espèce gallolyticus, autrefois dénommée Streptococcus bovis biotype I, est une bactérie de la flore intestinale qui constitue une cause émergente de septicémies et d’en...

#12992 : Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil

Burkholderia ambifaria bacteria are uiquituos microorganisms present in different environmental sources. Particularly these bacteria have been found to be frequently isolated from rhizospheric soils o...

#12991 : Role of RNA primary and secondary structure in non-homologous recombination

Enteroviruses are known to recombine a lot during the replication cycle. A lot of viruses produce defective genomes, which are generated by the polymerase skipping several nucleotides and thus, formin...

#12988 : LGP2 binds PACT to regulate RIG-I- and MDA5-mediated antiviral response

We need an independent statistician to confirm that appropriate statistical tests were used to analyze the data in your manuscript for the final revision of our manuscript in Science Signaling (Manus...

#12987 : Afribiota-Neuro

Globally one out of four children under 5 years is affected by linear growth delay (stunting). This syndrome has severe long-term sequelae including increased risk of illness and mortality and delayed...

#12963 : Gene expression and its regulation during and after inpatient detoxification of cocaine: a link to relapse?

Cocaine is the most widely used illicit stimulant in Europe1, with a recent increase in use in the French general population. Cocaine addiction (CocAdd) is recognised as a public health priority world...

#12929 : Single nucleotide polymorphisms and genome organization in members of the genus Yersinia

Members of the genus Yersinia include environmental as well as pathogenic bacteria. Pathogenic species (Y. pestis, Y. pseudotuberculosis and Y. enterocolitica) have historically been targets for resea...

#12920 : Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)

Dans notre laboratoire nous nous intéressons à la conception et construction de banques d’anticorps simple chaine issus du répertoire immunitaire des alpagas. Ces banques immunes, sont constituées d’u...

#12913 : Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur

The project aims at developing (1) a database dedicated to the storage and statistical analysis of Collaborative Cross based data and (2) implement genetic analysis tools based on rqtl2 for the identi...

#12901 : crispr.pasteur.fr

crispr.pasteur.fr is a website providing resources to visualize CRISPR screen data and design CRISPR experiments in bacteria...

#12897 : Comparative genomics of Listeria monocytogenes isolates

There exists a broad biodiversity inside the Listeria monocytogenes species, which can be summarized by the existence of evolutionary lineages and more than 100 clonal complexes (CCs or clones) based ...

#12891 : Identification d’une mémoire épigénomique à Streptococcus pneumoniae

Les modifications de la chromatine, au niveau de l’ADN ou des histones, jouent un rôle fondamental dans la régulation de l’expression des gènes chez les eucaryotes, en contrôlant l’accès de la machine...

#12853 : Impact des contraintes biomécanistiques sur la dynamique des macro-ouverture induits par l'EDIN de Staphylococcus aureus.

Several bacterial pathogens compromise the barrier function of endothelia by triggering the opening of transendothelial cell macroaperture (TEM) tunnels as large as several micrometres in width. This ...

#12833 : Training project for bacterial ChIP-seq Analysis on Streptococcus agalactiae

Streptococcus agalactiae (GBS) is a commensal gram-positive bacteria which asymptomatically colonize the genital and intestinal tract of healthy women. However, GBS is the leading cause of bacterial i...

#12775 : Determination of host response elicited by different Salmonella lifestyles

A number of mammalian cell types are susceptible to Salmonella Typhimurium infection, including epithelial cells, fibroblasts and macrophages. It has recently been demonstrated that Salmonella display...

#12771 : Tissue-resident stromal cell heterogeneity

Stromal cells are essential during organ morphogenesis and for the maintenance of tissue homeostasis. In addition, increasing evidence indicates that stromal cells play a role in certain type of chron...

#12767 : Comparative genomics of Helicobacter pylori bismuth resistant strains

Helicobacter pylori is a Gram-negative pathogen whose infection results in various gastric diseases including gastric cancer in Humans. Current drug therapy against the bacteria involves a combination...

#12765 : Viral Host Range Databank

Bacteriophages infect bacteria. One bacteriophage can infect several strains. Around the world, many labs have performed spot tests to determine the host range of bacteriophages but this information i...

#12674 : DNMT orthologs in Leishmania

Looking for DNMT (DNA methyltransferase) orthologs in Leishmania which could be potential targets of epigenetic inhibitors active against the parasite....

#12670 : Genome-wide interactions between HP1g and RNA.

The three HP1 proteins (Heterochromatin Protein 1 alpha, -beta, -gamma) are epigenetic markers of heterochromatin, the condensed, repressed form of chromatin. They are typically known to associate to ...

#12647 : Sequence analysis of Mycobacterium marinum mutants

Nous souhaitons analyser les séquences de sept mutant de Mycobacterium marinum générées par l’utilisation de concentrations croissante d’un antibiotique candidat dont nous ne connaissons pas la cible....

#12641 : Functional interactomics of SKAP2

The SRC Kinase Adaptor Phosphoprotein 2 (SKAP2), a broadly expressed protein with some higher expression in haematological lineages recruiting protein partners to specific subcellular domains, plays a...

#12627 : Role of small non coding RNAs in the adaptive response to oxidative stress in pathogenic Leptospira

Pathogen leptospires are responsible for the zoonotic disease leptospirosis. This neglected but emerging infectious disease has a worldwide distribution and affects people from developing countries, m...

#12619 : Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar

This project is integrated in the analysis of the gut ecosystem of children implicated in the AFRIBIOTA project, a translational project performed within a consortium of researchers and medical doctor...

#12618 : Cellular plasticity during mammary gland development

The development of the mammary gland occurs in five distinct phases: embryogenesis, puberty, pregnancy, lactation, and involution. Due to its extraordinary regenerative capacity, the mammary epitheliu...

#12591 : Rainfalls and water contamination in Antananarivo over 25 years

Concerns are growing over urban drinking-water quality due to an inefficient management infrastructure in most low-income countries. Outbreaks of waterborne were linked to extreme climatic events, des...

#12571 : Role of the Topoisomerase 1 and Guanine quadruplexes as transcriptional regulators

DNA Topoisomerase 1 (Top1) is a major regulator of gene expression with great impact on genome stability. Similarly, Guanine quadruplexes (G4) have recently emerged as critical elements for transcript...

#12502 : Toxin induced dephosphorylation of H3S10

During infection with bacteria, secretion of toxin induces histone modifications in the host cell. One such modification is dephosphorylation of histone H3 on serine 10. We have characterized this mod...

#12497 : Genome annotation of sequenced bacteria of the Culture Collection of the Pasteur Institut

The CRBIP, Centre de Ressources Biologiques de l’Institut Pasteur, is a structure created in 2001 that encompasses the Pasteurian culture collections: the CIP (bacteria collection), the PCC (cyanobact...

#12401 : Comparison of matrices of antibody gene usage

Our goal is to have a bioinformatic tool that performs the 2 x 2 comparison of matrices of numbers in matrix batches. Each matrix corresponds to the use of gene fragments (V or J) to create a re-arran...

#12288 : High content screening of mitochondrial morphology defects in mitochondrial genetic diseases

Mitochondria are double-membrane bound organelles that are essential in every tissue of the body. They are metabolic hubs and signalling platforms that are deeply integrated into cellular homeostasis....

#12261 : Identification of eukaryotic 5'UTRs

Identification of alternative 5'UTR in an eukaryotic transcripts...

#12260 : Pasteur MLST: Institut Pasteur genomic taxonomy database of microbial strains

- The Institut Pasteur genomic taxonomy database of microbial strains (“Pasteur MLST”) is a free, publicly-accessible resource that hosts nucleotide sequence-based definitions of microbial strains, al...

#12257 : Analysis of neuronal population dynamics in rodents during virtual navigation

To study the neuronal mechanisms underlying the generation of distinct memories, it is necessary to perform experiments in which the sensory elements of the environment are under the precise control o...

#12246 : functional enrichment of RNA processing factors associated with proteins of influenza viruses

A protein-protein interaction screen has been done beween viral proteins of influenza A viruses and a library of about 100 human factors invovled in RNA processing through RNA exonucleases activity. 2...

#12231 : Identification of immune response signatures that correlate with therapeutic responses to TNF inhibitors using machine-learning algorithms

Anti-TNF therapy has revolutionized treatment of many chronic inflammatory diseases, including rheumatoid arthritis, Crohn’s disease and spondyloarthritis (SpA). However, clinical efficacy of TNF-inhi...

#12220 : The Flemmingsome: the proteome of intact cytokinetic midbodies

The central part of the intercellular bridge connecting the two daughter cells during cytokinesis is a highly dense structure named the Midbody first described by Flemming in 1891. Work in the past te...

#12193 : Automated merging of CSV documents.

We want to automatize the merging of CSV document for data analysis purposes. We've already discussed it with Gael Millot....

#12128 : Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets

Despite the worldwide importance of malaria due to Plasmodium vivax, there is currently almost no data on the molecular responses of the Anopheles mosquito vectors to this parasite species. Understa...

#12107 : Ecological evolution in Klebsiella

In this project we study ecological diversification of Klebsiella pneumoniae and closely related species. Using comparative genomics we want to identify the pattern of genome adaptation to different e...

#12106 : An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe

As a result of combined climate change and globalization (increased flow of travelers and goods), the distribution of the mosquito Aedes albopictus is expanding significantly outside tropical regions....

#12069 : Heterogeneity of tissue resident stromal cells

Tissue resident stromal cells form the scaffold of all organs. In addition, they provide signals for proper positioning, survival and interaction of a number of other cell types, such as immune cells....

#12068 : Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa

We are involved, in collboration with the WHO, in the SaMARA which aims at detecting the emergence of antimalarial drug resistance in Africa. Samples (dried blood spots) are collected from the Nantio...

#12049 : Understanding the pathways of small RNA production during Meiotic Silencing by Unpaired DNA (MSUD) in the fungus Neurospora crassa

The canonical (“textbook”) process of DNA homology search and recognition is initiated by DNA double-strand breaks and is mediated by the universally conserved recombinases of the RecA family. Using t...

#12041 : Characterization of Yolk Sac Derived Progenitors in the Fetal Liver

Erythromyeloid progenitors (EMPs) originate from the yolk sac during early mouse development and migrate to the fetal liver via the circulation where they undergo massive expansion and differentiation...

#12018 : Assessing the integrations of viral sequences into the genomes of Aedes albopictus and Aedes aegypti

Aedes albopictus is an important vector for transmitting arboviruses, such as Dengue, Chikungunya, West Nile or Zika viruses. Its worldwide distribution due to its high ability to adapt to variable en...

#11988 : Phage infection dynamics in the gut of gnotobiotic mice

Taking advantage of a murine model of controlled microbiota composed of 12 strains, we evaluated the activity of a cocktail of three virulent bacteriophages to target a murine Escherichia coli strain ...

#11975 : Analyse d’expression de gènes de la réponse immune par voies fonctionnelles

Ce projet a pour but de réaliser une analyse par voies fonctionnelles d’environ 600 gènes impliqués dans la réponse immunitaire chez l’homme avec une attention particulière vis-à-vis des gènes impliqu...

#11966 : Dynamic and integrative multidimensional OMICs analysis of the cellular senescence fate

Cellular senescence is a complex stress response that durable (yet not irreversibly) arrests cell proliferation and is accompanied by widespread changes in chromatin structure, metabolism and gene exp...

#11936 : Dissecting Peptidoglycan pathways in human near-haploid cells

It has been found that specific fragments of the peptidoglycan (PG), namely the Muramyl-triDAP (MTP) and Muramyl-dipeptide (MDP) are specifically recognized by the innate immune receptors Nod1 and Nod...

#11931 : High-throuput nanobodies (VHH) screening and sequencing

Alpacas belong to the family of camelids, which has the peculiarity to produce two kinds of antibodies: conventional antibodies made of heavy and light chains and particular single chain antibodies ma...

#11885 : Development of a Software tool to integrate Bottomp-up, Middle-down and Top-down proteomics data

The aim of the project is to develop a powerful software tool to integrate MS data for the visualization of the protein coverage and mapping of Post Translational Modifications (PTMs). Even if some to...

#11805 : Implémentation d’un algorithme rapide de génotypage cgMLST

Le génotypage MLST (Multi-Locus Sequence Typing) est une technique standard qui permet une caractérisation génotypique précise et reproductible des souches bactériennes. Elle consiste à déterminer la ...

#11793 : ChIP-seq analysis of the majour regulator of GBS virulence

Streptococcus agalactiae (GBS) is a gram positive-bacteria which asymptomatically colonize the genital and intestinal tract of healthy women, although the leading cause of bacterial invasive infection...

#11691 : Fusion proteins in mammals and yeasts

Membrane fusion is an essential process in all forms of life, and fusion proteins are responsible of catalysing this reaction by forcing the two membranes against each other by undergoing a fusogenic ...

#11681 : Genetic traits involved in the regulation of NK cell and ILC homeostasis and NK cell-mediated anti-tumor functions

This project aims at identifying novel genetic traits that regulate the anti-tumor activities of NK cells and homeostasis of NK cells and other ILC using an unique mouse resource, the Collaborative Cross (CC). CC is a panel of recombinant inbred mice derived from randomized breeding of eight laboratory inbred strains combining high genetic diversity with the advantage of inbred mouse strains. We have identified CC strains that diverge in their anti-tumor immune responses and are characterizing ...

#11642 : Defining Shigella-targeting of human lamina propria mononuclear cells using CyTOF technology

Invasion of human intestinal epithelial cells by Shigella flexneri is secondary to the delivery of bacterial effectors into the host cell cytoplasm via a type III secretion system (T3SS). By using a beta-lactamase reporter tool we observed that in contrast to the epithelium, human lymphocytes are mainly targeted by injection of T3SS effectors not resulting in subsequent cell invasion (Pinaud et al., 2017). Furthermore, we observed that the targeting process, in form of successful injection of ef...

#11593 : Search for non-annotated transcripts in zebrafish lymphocytes

With collaborators in Cambridge, we performed single-cell sequencing of various types of zebrafish lymphocytes. However, standard mapping misses many interesting genes, which are not properly annotated yet in the zebrafish genome. The aim of this project would be to provide a simple way to BLAST for given sequences, from nonannotated genes, in this dataset....

#11514 : Exploring immunological mechanisms of human graft-verus-host disease after hematopoietic stem cell transplantation

Hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematologic malignancies. The main therapeutic benefit derives both from the ability to treat patients with intensive chemotherapy and from a potent graft-versus-leukemia (GVL) effect mediated by donor T lymphocytes. Unfortunately, in some patients, donor T cells also attack host normal tissues, giving rise to graft-versus-host disease (GVHD). GVHD prevalence is between 40-80% depending on patient and transplantat...

#11491 : MOODel: Modeling Mood Disorders

Mood disorders such as bipolar and major depressive illnesses are among the most severe psychiatric disorders. They have high prevalence and chronic course, and are associated with significant mental and somatic comorbidities and high personal and societal costs (lost productivity and increased medical expenses). Patients with bipolar disorder (BD), for example, exhibit a reduced lifespan compared with the general population, a finding that cannot only be explained by high suicide risk, reduced ...

#11317 : Role of ATM in EBV latency

Ataxia-telangiectasia (AT) is an autosomal recessive disorder characterized by a biallelic mutation of the Ataxia Telangiectasia Mutated (ATM) gene. The ATM protein is involved in a very large number of cellular functions (over 700 substrates), mainly DNA repair, cell cycle regulation, mitochondrial and oxidative metabolism, as well as regulation of gene expression. The majority of hematological malignancies occurring in AT patients are non-Hodgkin's B lymphomas and Hodgkin's lymphomas. The ass...

#11315 : Next Generation Surveillance of Salmonella and Shigella infections

Whole genome sequencing is revolutionizing the surveillance of foodborne and waterborne bacterial pathogens. The speed with which public health laboratories obtain information after the onset of symptoms and the regular sharing of this information between public health laboratories and epidemiologists are critical for the successful use of information to detect outbreaks early and to identify their source. For this purpose, this project aims at providing the most relevant bacterial genomic infor...

#11308 : Transcriptome of epithelial cells challenged with different serotypes of S. pneumoniae

The project is to identify differentially modified genes and pathways in epithelia cells when challenged with Streptococcus pneumoniae serotypes. S. pneumoniae has >90 different serotypes designated as either “carrier” or “invasive”. Some serotypes of S. pneumoniae are naturally carried within the nasopharynx (carrier), or are opportunistic serotypes that escape the nasopharynx causing disease within the host (invasive). In the case of a carrier serotype, the host is able to clear/con...

#11305 : Modulation of neutrophil cytosolic proteome in GCSF-treated patients. Impact of sample treatment

Neutrophils are the most abundant immune cells circulating in the blood and recruited to infectious sites. Neutrophil survival is a critical aspect for their study in vitro. We propose to study the impact of anoxia and GCSF treatment on neutrophil cytosolic protein abundance...

#11290 : Analyse statistique d'interactions protéine-protéine

Réalisation d'un interactome entre des protéines de mammifères et une protéine bactérienne de virulence....

#11226 : Extracting spatiotemporal gene expression activity from live biological tissues

In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy...

#11221 : State and parameter inference for stochastic models of gene expression

Quantitatively understanding the stochastic dynamics of gene expression requires measurements at the level of single cells. A common approach to follow the expression of genes in single cells and in real time is to make use of fluorescent reporter proteins and to record the cells' fluorescence by microscopy. However, this provides only an indirect readout of the biological processes that are of interest such as the regulation mechanisms at the promoter. A possible way to uncover the unobservable...

#11123 : Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome

The human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome (a developmental disease affecting the olfactory system), has been identified in 1991 by positional cloning. It is located on the X chromosome short arm (at Xp22.3), close to the STS gene and close to the boundary of the pseudoautosomal region (common to the X and Y sex chromosomes). Since then, orthologous genes have been identified in all animal species (including invertebrates), except in the mouse, rat, a...

#11075 : characterization of RNA virus populations from untargeted NGS in natural infections samples

There is a wide variation in both animal and human risk and outcome of infection, generally encompassing asymptomatic, to more severe and sometimes lethal cases. Dengue virus, a re-emerging arbovirus is a great examples of this, as it lead to a very wide spectrum of disease severity. Genetic variation associated with intrahost populations has been postulated to influence viral fitness and disease pathogenesis. This project aims to characterize the complexity of viral populations in samples fro...

#11074 : Evaluation de la représentativité génétique d'un pool de souches

Objectives: Our objective was, through whole genome sequencing, to establish a comprehensive repertoire of the non-synonymous polymorphisms (natural polymorphisms and/or mutations of resistance) in genes involved in resistance to azoles and echinocandins. Methods: Two collections of C. albicans clinical isolates were used. The first one consists of 151 epidemiologically-unrelated strains susceptible to antifungal agents. The second one consists of 9 isolates resistant to fluconazole and 1 to f...

#10966 : Analysis of methylation for HIV patients with co-infections

It has been shown that methylation can act as a kind of memory of the immune system. For patients with co-infections, it is of particular importance to know when to begin an anti-retroviral therapy, especially if they are already infected with tuberculosis. The goal of this study is to find hyper or hypo methylated loci related to the reaction of HIV patients (co-infected or not) to different kind of treatments....

#10958 : BD-CheM - Development of a chemical database to store structural and physico-chemistry data

The purpose of this short project is to develop a database that can efficiently store millions of unique molecular compounds along with some of their already calculated properties. The database named BD-CheM should be able to deal with extensive sets of data: millions of compounds and several hundreds of molecular properties. The import of new data should deal with the detection of molecule uniqueness to prevent data redundancy and with multiple sources of molecular compounds to keep track of th...

#10948 : Insight into the Immune System: A bioresource and data-sharing platform to study chronic inflammatory diseases (IsIShare)

Chronic inflammatory systemic diseases (CIDs) are a burden to humans because of life-long debilitating illness, increased mortality and high therapy costs. CIDs’ increasing prevalence in western countries has indeed placed them at the third rank of morbi-mortality causes. Unfortunately, available treatments are poorly targeted and non-curative. That is partly linked to a complex and largely ununderstood pathophysiology. Genetic susceptibility clearly plays a role. Genes linked to the immune sy...

#10940 : CRC related Dysbiosis

Analyasis of environemntal factors in the occurenc eof CRC by comparing normal colonosopcy and CRC patients in two categories : sporadic (average risk) and constitutional gene mutated individuals (very high risk) for CRC...

#10939 : Microbiota dysbiosis in human colon cancer

Colon cancer (CRC) is frequent, of bad prognosis, whilst the cost continues to increase. Environmental factors play a role in the majority of sporadic CRC cases. All members of a family share common environment factors and gene determinants. In about 5% of CRC, dominant role of gene is identified as Lynch Syndrome (LS) with mutation in DNA mismatch repair (MMR) genes. Considering the high lifetime risk of developing carcinomas in these individuals, it is relevant to study whether modifiable life...

#10938 : Implication du plasmide pKOBEG dans le génome d'Escherechia coli 55989

Le plasmide pKOBEG est un plasmide de recombinaison classique utilisé pour faire de la mutagénèse chez les bactéries et particulièrement chez Escherichia coli. Cependant, nous avons pu constater que le plasmide lui-même engendrait des modifications au sein de la souche Escherichia coli 55989 entéroaggrégative. Afin de déterminer l'étendue des modifications du à ce plasmide dans une souche wild type, nous avons séquencé le génome de nos souches WT et en présence du plasmide ainsi q...

#10937 : Physical Contact between human and non human primates in Southeastern Cameroon

Non human primates are an important reservoir for zoonotic disease. Here we analyze in Cameroon how human activities in the forest influence contact with non human primates to better understand processes of emergence....

#10934 : Mechanisms of phage resistance in Vibrio cholerae O1 biotype classic

phage phiVC8 is a lytic phage for Vibrio cholerae 01 biotype classic. This phage has a narrow host range and we are interested to undersatand why. We have selected several mutants of the Vibrio strain resistant to the phage. Resistance could be due to several mechanisms that we want to uunderstand...

#10928 : DNA encapsulation of human resources for research projects on immune system and inflammatory diseases

Freezing is the most commonly used method for storing DNA extracts. However, that method is non-practical and expensive, since requiring freezers and back-up generators for storage, and specific conditions/reagents for transport. In addition, even when adequate procedures are followed, the frozen extracts integrity might suffer from repeated freeze-thaw cycles or residual microorganism activity. The Institut Pasteur’s ICAReB platform hosts the biological collection related to the CoSImmGEn c...

#10921 : Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae

The goal of this project is to study the strategies undertaken by Gram negative bacteria to respond to sub-lethal antibiotic stress. We previously established that low doses of antibiotics that do not affect bacterial growth still induce stress responses in bacteria and suggest that understanding the mechanisms underlying these stress responses can prime strategies to increase antibiotic treatment efficiency. In this project, we will address consequences of stress responses and pathways activate...

#10920 : Phylogenetic analysis of HHD-PDZ containing proteins

Harmonin Homology Domains (HHD) are protein-protein interaction domains primarily identified in a few proteins involved in earing and vision. Only six HHD-containing proteins encompassing 9 HHD domains have been identified so far in mammals. Four of these proteins are neuronal and also contain PDZ domains, exhibiting different HHD-PDZ modular organisations. This project aims at 1) searching orthologs with HHD domains, 2) establishing the phylogenetic tree of HHD-containing proteins and 3) unders...

#10913 : Finding and Predicting CRISPR-Cas9 Efficiency

CRISPR-Cas systems provide immunity to bacteria and archaea. One of the reasons these systems have attracted so much attention in the past few years is due to the discovery of nucleases among the Cas proteins that are guided by small RNAs to bind and degrade homologous DNA. The introduction of breaks in DNA that can be repaired either in a controlled or uncontrolled manner now is a widely used method to introduce mutations in genomes. We are interested in probing the CRISPR-Cas system efficienc...

#10906 : Identification of APOBEC3 mutations in cancer genoms

The APOBEC3 proteins (APOBEC3A-H) are single-stranded DNA (ssDNA) cytidine deaminases (CDAs). Those proteins were first tied to innate immunity as antiviral restriction factors as cytidine deamination to uridine results in hypermutation of viral genomes. However APOBEC3 mutațional signature was recently identified in cancer genomes, suggesting a causal role of APOBEC3 proteins in cancer onset. Accordingly, we demonstrated that both APOBEC3A and APOEC3B proteins can elicit somatic mutations on ...

#10896 : Prediction of Congenital Infection in Tunisian Pregnant Women

Congenital infections are considered to be as a public health problem. It can affect the unborn fetus and newborn infants and may cause perinatal morbidity and lifelong handicaps. They are generally caused by viruses, bacteria and/or parasites when primary infection occurs during the first months of pregnancy or through the time of delivery. Cytomegalovirus (CMV) infections are major contributors to prenatal and infant morbidity and mortality. In countries with relatively low socio-economic lev...

#10895 : CNF-domain containing toxin family

Alterations of the cellular proteome over time due to spontaneous or enzymatic deamidation of glutamine (Gln) and asparagine (Asn) residues is a probable source of aging-related diseases. In particular, deamidation of a conserved glutamine in all GTPases of the Ras superfamily that are essential for cellular GTP turnover, confers to these molecular switches gain-of-function properties that can stimulate oncogenic signaling pathways. The CNF1 toxin produced by pathogenic Escherichia coli, a preva...

#10893 : Impact of gut microbiota on lipid metabolism

We have shown that chronic stress impact gut microbiota and leads also to metabolomic abnormalitites . We want here to decipher whether particular gut bacterial species could be directly link to the metabolism differences we observed....

#10841 : Duplications in bacteriophage genomes.

We recently reported an unusual homologous intra genomic recombination event within the the tail fiber genes of one bacteriophage and shown that is event is conserved in several other tail fiber genes from bacteriophages of the public database. Now, we aim at recording the frequency of this event and its position in the all available bacteriophages genomes....

#10840 : Identification of Ago2-bound nuclear transcripts and genomic loci in adult zebrafish neural stem cells

Adult neurogenesis is the process by which adult neural stem cells (NSCs) produce new neuronal and glial cells throughout an animal life. Studies in vertebrates have unveiled the crucial importance of this phenomenon for neural tissue homeostasis and proper brain function. Fundamentally, this process is a balance between maintaining a quiescent NSC pool and recruiting them into the neurogenesis cascade. Using the adult zebrafish anterior brain (telencephalon) as a model, we aim at deciphering th...

#10825 : Characterization of the role of Argonaute proteins in regulating germline gene expression at the transcriptional and the post-transcriptional levels.

This research project focuses on the characterization of the role of small RNAs and their associated Argonaute proteins in transcriptional and post-transcriptional regulation of germline gene expression. Using the nematode C. elegans, we have recently showed that one of the germline-expressed Argonaute protein, CSR-1, promotes germline transcription. However, CSR-1 also possess an endonucleolytic activity that might participate in post-transcriptional silencing. Therefore, two possible functions...

#10791 : Mapping of Enhancers from transcriptome data

Enhancers of transcription are regulatory sequences enabling gene expression from a distance. The landscape of active enhancers is cell-type specific and provides extensive information on the transcription factors at play. Currently, enhancers are mostly mapped based on the histone modifications positioned on their DNA sequence. This type of data is abundantly available for tumor-derived tissue culture cells, but difficult to obtain when the biological material has a limited availability. As an ...

#10781 : Analysis of IFITM RNA levels in vraious cell types and tissues

The interferon-induced transmembrane (IFITM) proteins protect cells from diverse virus infections, including Influenza, HIV and Zika viruses, by inhibiting virus-cell fusion. We showed that IFITM proteins act additively in both productively infected cells and uninfected target cells to inhibit HIV-1 spread, potentially conferring these proteins with greater breadth and potency against enveloped viruses. We also reported that amino-terminal mutants of IFITM3 preventing ubiquitination or endocytos...

#10757 : Evolutionary approach to protein thermal stability

Phylogenetic analysis of protein families to find mutations that increase their thermal stability and expression levels in a cost- and labor-effective way....

#10712 : VCF filtering script

A partir de fichier VCF appliquer un certain nombre de filtre et retourner un fichier VCF...

#10700 : Genomic determinants for initiation and length of natural antisense transcripts in a compact eukaryotic genome and phylogenetic analysis of related Entamoeba species

Entamoeba histolytica is a protozoan parasite and an amitochondriate pathogenic amoeba, which causes amoebiasis (dysentery and liver abscess) in humans. In addition to E. histolytica several species infect the human intestine although these do not cause disease and include in most of cases E. dispar and ocassionnally E. moshkovskii. A phylogenetically close Entamoeba, E. invadens infecting snails, is used as cellular model for Entamoeba cyst formation.

Supported by the National Agenc...

#10674 : Channels in metagenomics data

We would like to have a detailed picture of the presence (or not) of several types of ion channels in some metagenomic data....

#10570 : Phylogenetic analysis of insect-specific flaviviruses

Mosquitoes are vectors for flaviviruses such as dengue virus or Zika virus that cause a substantial public health burden worldwide. These vectors are also infected with insect-specific flaviviruses that can only replicate in mosquitoes and are unable to replicate in cells of vertebrate organisms, such as humans. Many of them were discovered and sequenced in the last few decades. Despite several studies on their phylogenetic analysis to date, the analysis should be regularly updated. Therefore,...

#10540 : Characterization of a Salmonella mutant carrying a single amino-acid substitution in the stress sigma factor RpoS

The RpoS/σS sigma subunit of RNA polymerase is the master regulator of the general stress response in many Gram-negative bacteria. σS also contributes to virulence and biofilm formation of the human pathogen Salmonella enterica serovar Typhimurium. We have used RNA-sequencing to unravel the σS-dependent transcriptome in S. Typhimurium ATCC14028. These studies have revealed a major effect of σS on the remodelling of metabolism and membrane functions, and have highlighted the importance of d...

#10508 : Genotype to phenotype analysis of immune responses in chronic inflammatory diseases

Chronic inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, spondyloarthritis (SpA) and psoriasis cause significant morbidity and are a substantial burden for the affected individuals and the society. An important obstacle to early diagnosis and the development of more specific and effective therapies is the very limited understanding of the pathogenesis of these diseases. In the past years genome-wide association studies have identified many genes that were not known...

#10502 : The resurgence of a neglected disease, Yellow fever: from jungle to urban environments

Yellow fever virus (YFV), a Flavivirus transmitted by mosquitoes causes a severe hemorrhagic fever in humans. Despite the availability of a safe and effective vaccine (17D), YFV is still a public health problem in tropical Africa and South America. In the Americas, the massive campaign of mosquito control during the first half of the 20th century led to the eradication of Aedes aegypti from most American countries, and as a consequence, urban outbreaks of YF were no longer observed. However, the...

#10357 : Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar and the impact during the switch from tOPV to bOPV

Poliomyelitis has been a major public health concern and currently, efforts are being made towards eradicating wild poliovirus type 2 (WPV2). A global switch from trivalent oral poliovirus vaccine (tOPV) to bivalent oral poliovirus vaccine (bOPV without PV2) has taken place in countries, like Madagascar, where epidemics of recombinant type 2 pathogenic circulating vaccine-derived polioviruses (cVDPVs) were reported in the last decade. This occurs when low polio vaccine coverage and high populati...

#10344 : Amélioration des techniques permettant la détection de poliovirus dans l'environnement.

Les poliovirus sont les agents étiologiques de la poliomyélite, une maladie qui fait l’objet d’un programme mondial d’éradication conduit par l’OMS dans lequel sont impliqués l’Institut Pasteur de Paris et de nombreux laboratoires du réseau international des instituts Pasteur. Les poliovirus se répliquent principalement dans l’intestin des sujets infectés et sont excrétés dans les selles. Ils peuvent ainsi être retrouvés dans des échantillons d’eaux usées. La surveil...

#10343 : Détection et assemblage d’entérovirus dans des échantillons cliniques et environnementaux

PARTIE 1: Résolution des problèmes liés à l’assemblage de novo de génomes recombinants présents sous forme de mélanges dans les échantillons cliniques et environnementaux La recombinaison génétique est un phénomène très fréquent chez les entérovirus. Celle-ci consiste en la génération de génomes chimériques constitués par l’assemblage de séquences génétiques provenant de différents génomes parentaux. La présence dans des échantillons cliniques ou environementaux...

#10315 : De novo sequencing and analysis of three unassigned species of non tuberculous mycobacteria.

In recent years, the number of non-tuberculous mycobacteria (NTM) isolated from clinical specimens has increased greatly, due to opportunistic infections accompanying immunosuppression, but also as a result of improved culture and identification techniques. It becomes increasingly clear that NTM, or at least some of them, might be responsible for difficult-to-treat infections in immunocompetent hosts. In this respect, we have undertaken a study aimed at characterizing NTM that were isolated f...

#10297 : viral evolution around Ebola Treatment Center in Macenta

Samples were collected in the field from infected patients admited in Ebola treatment Center of Macenta (ETC Guinea). Deep sequencing was performed in order to look for majority and minority variants. The aim of this study is to compare quasispecies of patients who survived and those who died and also to get detailed description of EBOV evolution in an ETC to identify phylogenetic clusters or transmission chain....

#10209 : identification of sRNA in Leptospira biflexa and influence of a putative Hfq on the transcriptome

In a previous project (collaboration with PF2 and C3BI) , we determined the transcriptome landscape of the pathogen Leptospira interrogans (Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppée JY, Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M. Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans.Front Cell Infect Microbiol. 2017 Jan 19;7:10.). In the present project, we performed RNA-seq with the PF2 on the sa...

#10143 : AIMyc: Analysis of the Impact of antibiotics, antifungals on the Mycobiome of allogeneic stem cell recipients.

Patients undergoing hematopoietic stem cell transplant (HSCT) are known to be at risk of invasive candidiasis despite antifungal prophylaxis with Candida dissemination occurring from the gut mycobiome to the bloodstream. These patients are given antifungal drugs, antibiotics known to impact growth and favor the selection of some intrinsically resistant fungal species. The AIMyc project proposes to depict the impact of antifungal, antibiotics treatments on the diversity of species within the myc...

#9762 : Trichosporon asahii NGS analysis

Trichosporon asahii is a yeast responsible of human invasive infection worldwide. Actually, no genotyping method is available to determine relationship between clinical isolates. At the NRCMA we have more than 40 clinical isolates and 2 collection strains associated with clinical data. Thanks to P2M facility, whole genome for 33 isolates was sequenced. The aim of this project is to study the genetic diversity of Trichosporon asahii and the potential relationship with clinical and/or phenotypic d...

#9635 : Assembly of insect virus genome

Mosquitoes of the Anopheles gambiae complex display strong preference for human blood- meals and are major malaria vectors in Africa. However, their interaction with viruses or role in arbovirus transmission during epidemics has been little examined, with the exception of O’nyong-nyong virus, closely related to Chikungunya virus. We have recently identified two novel insect RNA viruses, a Dicistrovirus and a Cypovirus, found in laboratory colonies of An. gambiae taxa using small-RNA deep seq...

#9210 : Effects of expanded-spectrum cephalosporins ( ceftriaxone or céfotaxime) on the human gut Mycobiome

The gastrointestinal tract of humans is colonized by hundreds of microbial species, - bacteria, archaebacterial, fungi, protozoa and viruses -, collectively named the gut microbiome. The intestinal commensal bacteria have an important role in metabolic processes and contribute to colonization resistance against intestinal pathogens. Fungi are usually considered to be a minor component of the global microbiome. However, the mycobiome (fungal component of the entire microbiome) has been in fact l...

#8806 : Characterizaion of the microbiome of lab colonies of Aedes aegypti

The goal of the project is to determine if there are differences in the midgut microbiome of our lab colonies of Aedes aegypti. We frequently observe various phenotypic differences between different colonies of mosquitoes and it is a recurring question whether these phenotypic differences are a result of differences in the microbiome. We will sequence the microbiome of 6 representative established lab colonies that have been collected from geographically diverse areas and compare the bacterial ...

#8788 : Super-resolution imaging and reconstructions of human cell chromosome architecture

Chromosomes are arranged non-randomly in the 3D space of cellular nuclei. This architecture is important to key biological processes including gene expression and DNA repair, but remains poorly understood in detail. Genome-wide chromosome conformation capture (Hi-C) is currently the most powerful experimental technique to probe chromosomal structures. However, this technique does not directly provide a description of high-resolution chromosomal configurations in individual cells and remains blin...

#8727 : Functional interactions between HP1 proteins and RNA.

The three HP1 proteins (Heterochromatin Protein 1 alpha, -beta, -gamma) are epigenetic markers of heterochromatin, the condensed, repressed form of chromatin. They are typically known to associate to the di-/tri-methylated lysine 9 of histone H3 (H3-K9me2/3), a repressive histone mark, HP1s are therefore linked to chromatin silencing. But on the other hand, HP1s are also linked to activated transcription, for example HP1g has been shown to localize within the body of coding genes in correlation ...

#8657 : Biomarqueurs d’identification précoce du sepsis aux urgences (BIPS)

Rationnel. Le mode de présentation clinique du sepsis est très polymorphe. Chez les patients septiques consultants dans les services des urgences, la présence d’une hyperthermie ou d’autres critères du syndrome de réponse inflammatoire systémique (SIRS) n’est pas suffisante pour aider au diagnostic de sepsis. De nombreux efforts de recherche ont abouti à la proposition d’innombrables biomarqueurs de sepsis essentiellement étudiés en soins intensifs. Même si cer...

#8565 : Multi-traits GWAS in Malaria

Malaria is a complex disease resulting in more than 700,000 deaths per year, most notably among under 5-year olds in sub–Saharan Africa. Malaria is caused by several Plasmodium spp. parasites of which P. falciparum is responsible for the majority of deaths worldwide. Parasites are inoculated by infectious mosquitoes during their bloodmeal. Subsequent development of the parasite within the liver leads to the blood stage infection, where parasites replicate within red blood cells leadin...

#8543 : the role of host defense in female genital tract infection by Chlamydia trachomatis

The present work is to systematically investigate the role of TLRs and NODs in the host defense during C. trachomatis infection using KO animals. The inflammatory cytokines and bacterial burden will be measured using Bio-Plex ELISA kit. C3BI will provide help in the data analysis....

#8528 : Comparing V-J gene usage for specific antibody generation

Notre but est de trouver un test statistique capable de dire si deux matrices de nombres sont différents. Ces matrices correspondent à l’utilisation de fragments de gènes (V ou J) pour créer un gène ré-arrangé (V-J) codant pour un anticorps de spécificité particulière. Ici nous avons représenté pour chaque gène V la famille de gène J utilisé (parmi J1, J2, J3, J4). Le nombre correspondant au nombre d’occurrences que nous avons trouvé après séquençage du répertoire d’ant...

#8521 : Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia

Extended spectrum β-lactamase (ESBL) genes encode resistance to penicillins and cephalosporins and can be horizontally transferred among Enterobacteriaceae. More than 60% of healthy humans living in southeast Asia are faecal carriers of ESBL-producing Enterobacteriaceae (ESBL-PE), compared to <10% in Western Europe, suggesting diverse exposure routes. In Cambodia, meat and fish consumption is high and food safety is poorly enforced. Thus, we hypothesized that meat and fish ...

#8494 : NOXO1 interacting partners in intestinal epithelial cells under inflammatory and infectious conditions

Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (or NOX) are a unique family of enzymes dedicated to the production of reactive oxygen species (ROS) such as superoxide anion (O^.-₂) and hydrogen peroxide (H₂O₂) (1). This family includes NOX1-5, DUOX1 and DUOX2 and has been defined on the basis of its members’ structural homology with gp91^PHOX (now renamed NOX2), the catalytic core of the phagocyte NADP...

#8491 : Investigating developmental defects of a C. trachomatis mutant strain

Invasion of epithelial cells by the obligate intracellular bacterium Chlamydia trachomatis results in its enclosure inside a membrane-bound compartment termed an inclusion. The bacterium quickly begins manipulating interactions between host intracellular trafficking and the inclusion interface, diverging from the endocytic pathway and escaping lysosomal fusion. We have isolated a mutant strain that shows several developmental defects. The C3BI will contribute to the statistical analys...

#8453 : Heritability of the melatonin synthesis pathway in Autism Spectrum Disorders

Autism Spectrum Disorders (ASD) are heterogeneous neurodevelopmental disorders with a complex genetic architecture. They are characterized by impaired social communication, stereotyped behaviors and restricted interests and are frequently associated with comorbidities such as intellectual disability, epilepsy and severe sleep disorders. Hyperserotonemia and low melatonin levels are among the most replicated endophenotypes reported in ASD, but the genetic causes of such alterations remain largely...

#8392 : Transcriptional profile of Nod2+ neurons upon MDP signaling

I am interested in gut-brain axis and specifically how a bacterial metabolite, MDP, can be sensed directly by neurons....

#8364 : Assess possible correlations between enteric viruses found in sewage waste water and healthy Roma children in Romania in the period 2016-2017

Enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Among them, polioviruses (PVs) are the etiologic agent of paralytic poliomyelitis, a disease characterised by acute flaccid paralysis due to the destruction of motor neurons following PV replication. Thanks to the high coverage rate within the different contries, the WHO European region was certified polio-free m...

#8363 : Analyse génomique de corynebacterie

Vérification et cartographie de génomes de corynebacteries modifiés. Recherche de suppresseurs à partir de délétions de gènes de kinase (pknA; pknB ...)...

#8340 : Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato by in peri-urban forests of France

Lyme borreliosis is the most common tick-borne disease in the northern hemisphere. In Europe, it is transmitted by Ixodes ticks that carries bacteria belonging to the Borrelia burgdorferi sensu lato complex. Our study was focused on peri-urban forests of Île-de-France. These forests are frequented by many visitors and the risk of exposure to tick bites is high. One of them, the Sénart forest, is located 30 km south of Paris (in the Île-de-France region) and has a large numbe...

#8328 : Experimental evolution of Chikungunya and Zika viruses’ strains to study emerging variants.

Chikungunya and Zika viruses have recently extended to previously disease free areas. In addition, their high mutations rates and fast replication lead to the emergence of new strains potentially able to disseminate in these new territories, through the apparition of novel characteristics. The African (MR-766) and American (PRVABC-59) Zika strains, and the La Reunion Island and Caribbean Chikungunya strains, were passaged several times in mammalian or mosquito cells only or alternatively in o...

#8318 : Salmonella CRISPR database

CRISPR polymorphism is a powerful tool  to subtype Salmonella strains and is now used in routine for epidemiological investigations. The aim of this project is to transfer and upgrade a published and worldwide used webtool to extract the spacer content from fasta sequences or paired-end reads....

#8302 : Metabolic characterization of ILCs under homeostatic or stress conditions

Innate lymphoid cells (ILCs) are the most recently identified components of the innate immune system. ILCs colonize different tissue sites and react promptly to microenvironmental perturbations. Due to their high plasticity, ILCs can shape their functional output in response to local cues. As such, ILCs play roles under homeostatic conditions and in the context of infection, chronic inflammation, metabolic diseases and cancer. Diverse ILC subsets (NK cells, ILC2) have been shown to regulate...

#8290 : Common and phylogenetically widespread coding for peptides by bacterial small RNAs – Follow up of a project regarding its journal review

Following a collaboration started a few years ago between a postdoc of the System Biology team (Robin Friedman) and Olivia Doppelt-Azeroual, a publication is in review in the journal Genome Biology. One of the reviewers made comments regarding the database and web interface implemented by Olivia at the time and after a brainstorm on the review, the first author (Robin) needs to make a few modifications on the database. This modification requires Olivia's intervention to update the database a...

#8263 : Performing Gene Ontology Analysis on RNAseq data in Aedes aegypti

Our team studies interactions between arboviruses and Aedes aegypti mosquitoes. We recently generated RNAseq data to analyse the response of the mosquito to virus infection. We would now like to analyse that data using Gene Ontology to find pathways or processes that are activated upon infection....

#8239 : INNOV DIAG HPV VALOEXPRESS

Molecular markers of cervix lesions linked to HPV infections....

#8232 : Looking for the SNPs in evolved Corynebacterium diphtheriae genomes

Searching and annotating SNPs in evolved Corynebacterium diphtheriae genomes...

#8227 : TB drugs and host response

Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (MTB), is the deadliest disease due to a single infectious agent. Despite considerable efforts to fight the disease, TB remains a major public health problem. Even more worrying for the future, multidrug resistant (MDR) strains of MTB are continually emerging and about 10% of people with MDR-TB have extensively drug-resistant TB (XDR-TB). Drug-sensitive TB can be cured by a 6-month treatment using 4 antibiotics, but MDR-TB...

#8217 : Evaluation of the GO annotation of the Leishmania donovani genome

We are generating massive amounts of omics data for Leishmania donovani. Anna Zukhova enabled to use the BiNGO module of Cytoskape to perform and visualize our GO enrichment analyses. We would like to continue our collaboration and ask Anna's help to assess the current state of GO annotation of the Leishmania genome and if possible to complete it using domain searches or ortholog mapping from other genomes, including L. major, T. bruce or model organisms such as yeast. We expect that improveme...

#8202 : Transcriptomic analysis of blood cells from ebola infected patients

Blood cells were collected in the field from patients admited in the Ebola treatment center of Macenta (Guinea). After red cells lysis, blood cells were frozen and RNA was extracted after the shipment of samples in France. Despite poor RNA quality, Affimetrix chips have been performed and transcriptomic data are available. The aim of this study is to compare the transcriptomic data from patients who survived and those who died and also to perform a kinetic analysis of the infection in the two gr...

#8130 : Genomic analysis of catheter-related Escherichia coli infection

Escherichia coli is one of the major bacterial pathogens that are responsible for numerous nosocomial infections. While most of the E. coli infections are rather related to colonisation of the urinary...

#8125 : Lipid-binding domains in Vaccinia virus proteins

Our lab is interested in the assembly of the inner viral membrane of Vaccinia virus and what are the molecular regulators (proteins and lipids) playing a role in this complex and unique process of virion morphogenesis....

#8117 : Histone Methyltransferase and Demethylase in Leishmania

I would like to retrieve all HMT and HDM in Leishmania...

#8094 : ModeMood: Modeling Mood Disorders

Mood disorders such as bipolar and major depressive disorders affects 2-5% of the population worldwide. They are relapsing, major psychiatric illnesses with poorly understood neurobiology, typically incomplete treatment responses, and often unsatisfactory clinical outcomes, with a high risk of premature mortality due to suicide and clinical comorbidities. Its complex manifestations include marked disturbances of emotional regulation, sensory-perception as well as major changes in mood, thinking,...

#8067 : Bioinformatic analysis of the adenylate cyclase CyaA toxin

The adenylate cyclase (CyaA) produced by B. pertussis, the causative agent of whooping cough, is one of the major virulence factors of this organism. CyaA plays an important role in the early stages of respiratory tract colonization by B. pertussis. This toxin uses an original intoxication mechanism: secreted by the virulent bacteria, it is able to invade eukaryotic target cells through a unique but poorly understood mechanism that involves a direct translocation of the catalytic domain across t...

#8002 : Genetic profile of patients with dyslexia

Background: Dyslexia is characterized by difficulty with learning to read fluently and with accurate comprehension despite normal intelligence. It affects 5–10% of school-age children. Familial studies repeatedly showed that first-degree relatives of affected individuals have a 30–50% risk of developing the disorder. Twin studies showed that heritability was approximately 50% with a higher concordance rate for monozygotic twins compared to dizygotic twins. Although genetic f...

#8001 : Characterization of an RNA binding protein of Listeria monocytogenes

We are analyzing a Listeria protein secreted in the supernatant. From cells transfected with this protein, after crosslinking, we have isolated RNA and found the protein in the RNA fraction. In addition, the protein binds several splicing factors in RNA dependent manner. Furthemore, the protein localizes to the nucleus. In this project, we have isolated the protein from the supernatant and from bacterial extract after growth in BHI. We have extracted the RNA from the supernatant fraction contain...

#7990 : MacSyDBCapsule

Extracellular capsules constitute the outermost layer of some bacteria and establish the first contact between the cell and its environment. They are major virulence factors involved, amongst other, in antibiotic tolerance and immune escape. Bacterial capsules are also known to mediate unspecific cell-to-cell interactions between and across species and affect population structure and dynamics. Despite the great number of studies characterizing capsule diversity and their role during infection in...

#7968 : Extraction of sequence information from published genomes of commensal bacteria

The microbiota of the gastrointestinal tract is a diverse mixture different species and strains of bacteria. We aim to identify regions of dissimilarity between two different bacterial strains to be able to quantitate their relative abundance and thus obtain information about their ability to cohabitate a common environment. In addition, we are interested in assessing the surface localised protein repertoir of specific species through a combination bioinformatic analysis and proteomics....

#7965 : Statistical analysis of PI survey for the scientific direction

Statistical analysis of PI survey for the scientific direction...

#7964 : Identification de SNP entre 2 souches bactériennes

Identification de SNP entre 2 souches bactériennes la souche sauvage et le révertant (Pseudomonas aeruginosa)...

#7930 : Gene expression profiling in Kupffer cells

The liver is the biggest internal organ that is responsible for metabolism, detoxification and the defense between the host and the external environment. Thus the liver is also an immune organ, which constantly confronts conflicting demands of immunity against pathogens and tolerance to antigens metabolized locally and bacteria products derived from the gut. In homeostasis, many mechanisms ensure suppression of immune response in the liver, which include low expression levels of MHC molecules in...

#7917 : Recombination among enteroviruses

Notre objectif est d'étudier comment la recombinaison génétique génère de la diversité au sein des écosystèmes d'entérovirus....

#7901 : Automatic detection of antibiotic resistance genes

Linked with the project #7283 managed by Thomas Bigot, this proposal aims to detect antibiotic resistance genes in whole-genome sequence data of the bacteria deposited and stored at CIP. The CARD library (http://arpcard.mcmaster.ca) would be used to screen for common acquired resistance genes. Detection of point mutations in house-keeping genes and/or transporters would require specific queries from a fasta file continuously implemented by myself....

#7841 : Research of SNPs to explain the non virulent phenotype of a mutant of L. interrogans serovar Manilae L495 affecting the expression of a protein not involved in virulence

We are studying mutants of L. interrogans obtained after random mutagenesis (M58) along with complemented mutant strain (C5M58), constructed using a secondary random mutagenesis. The M58 mutant was found non virulent in gerbils and mice, but the C5M58 strain showing restored expression of the protein, is also non virulent. We have another mutant strain (M1901) in the same gene that retained its virulence, which is the expected phenotype. We are interested in findings SNPs present in bot...

#7836 : Graphical representation of co-expressed genes in various datasets

We have identified a candidate gene associated with increased resistance to a pathogen. This gene is poorly annotated in public databases. To get insight into its function we are focusing on genes that are co-expressed with this candidate gene in various datasets, including microarray collection on various mouse tissues or in a given tissue across inbred strains of mice. Indeed, coexpression is one of the central idea in gene expression analysis. The 'Guilt by association' principle states that ...

#7834 : Role of PerR-regulated oxidative stress response in pathogen Leptospira virulence

Pathogen leptospires are responsible for the zoonotic disease leptospirosis. This neglected but emerging infectious disease has a worldwide distribution and affects people from developing countries, mostly under tropical areas. The clinical manifestations of this infection range from a febrile state to a severe life-threatening form characterized by multiple organ hemorrhages. More than one million cases of leptospirosis are currently reported annually in the word, with 10% of mortality. Duri...

#7829 : Discovery of non-annotated transcripts in RNAseq data from Aedes Aegypti

The genome of the yellow fever mosquito (Aedes Aegypti) is not fully annoyed, and this project aims at discovering novel transcripts using RNAseq data....

#7820 : Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome

Because of their increasing incidence, dramatic severity, lack of treatment or vaccine, complicated diagnosis, misreading of the pathogenesis, and need for a maximum containment, Viral Hemorrhagic Fevers (VHF) constitute a major public health problem. There is therefore an urgent need to further study VHF to understand the pathogenesis of the severe disease and the host responses involved in their control or in the dramatic damages. Among VHF, Lassa fever (LF) is probably the most worrying one b...

#7810 : Quantitative temporal analysis of cellular proteins regulated by HBV in primary human hepatocytes

Despite effective prevention against HBV infection, 300 million people worldwide are chronic HBV carriers, of whom 25% will die of liver cirrhosis or hepatocellular carcinoma (HCC). Current treatments for chronic hepatitis B (CHB) are inefficient to completely clear the virus and liver cancer is a lethal disease, thus representing an area of highly unmet medical need. Viral persistence is due to the maintenance, in the nuclei of infected cells, of the viral nuclear DNA : the cccDNA that is no...

#7789 : Caractéristiques génomiques de souches d’Escherichia coli productrices de BLSE associées à un portage persistant après un voyage en zone tropicale

Nous avons pu montrer grâce au projet de recherche clinique VOYAG’R (PHRC AOR 11101- IP Pr S. Matheron) que les voyages dans une zone tropicale constituaient un risque d’acquérir une Entérobactérie multi-résistante (EMR). Pendant 15 mois, la présence d’EMR a été recherchée chez 574 sujets avant et après leur voyage en zone tropicale. Les voyageurs porteurs au retour étaient suivis sur une période de 12 mois (1, 2, 3, 6 et 12 mois ou jusqu’à négativation). Au cours de leur s...

#7757 : Comparative analysis of transcriptomic and proteomic data to study RNA and protein expression regulation during RVFV infection in mice.

In order to study a differential regulation of RNA and protein expression level during Rift valley fever virus (RVFV) infection in a murine model, we want to compare transcriptomic and proteomic analysis.  ...

#7750 : Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages

Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages.  Scientific context During the course of cutaneous or visceral disease in humans or experimental animal models, the resolution of leishmanial infections or the control of parasite growth is dependent on appropriate innate and adaptive immune responses developed by the parasitized host. Leishmania largely evad...

#7721 : Comparative analysis of gene expression pattern between samples of tumor and normal mice tissue

The post-translational modification by SUMO is an essential regulatory mechanism of protein function that is involved in most challenges faced by eukaryotic cells. Gene expression is particularly regulated by sumoylation as many SUMO substrates are transcription factors and chromatin-associated proteins, including histones. The emerging paradigm for the proposed work is that sumoylation controls multiple aspects of chromatin structure and function in response to external cues. According to this ...

#7704 : Comparative analysis of gene expression in different human cell clones

The post-translational modification by SUMO is an essential regulatory mechanism of protein function that is involved in most challenges faced by eukaryotic cells. Gene expression is particularly regulated by sumoylation as many SUMO substrates are transcription factors and chromatin-associated proteins, including histones. The emerging paradigm for the proposed work is that sumoylation controls multiple aspects of chromatin structure and function in response to external cues. According to this ...

#7631 : Differentiation of Shigella species from Escherichia coli by MALDI-TOF mass spectrometry

Shigella species and E. coli are very closely related bacteria belonging to the Enterobacteriaceae family. Phenotypically they are very similar and genotypically they could be considered the same species. The differentiation of Shigella species from E. coli is a significant diagnostic challenge for the clinical microbiology laboratories. They increasingly use maldi-tof mass spectrometry-based microbial identification systems but the latter are currently not...

#7608 : Single cell analysis of HIV-specific CD4+ T cell differentiation

HIV infects and depletes CD4+ T cells, leading to a progressive loss of adaptive immune responses and ultimately to AIDS. In addition, HIV preferentially targets HIV-specific CD4+ T cells, resulting in an attrition of the very cells that should orchestrate the antiviral immune response. Due to this preferential depletion, HIV-specific CD4+ T cells are few and remain incompletely characterized. The emergence of single cell technologies opens the opportunity for an in depth analysis of the rare sp...

#7607 : JASS: an online tool for the joint analysis of GWAS summary statistics

In recent years, large genome-wide association studies (GWAS) have been successful in identifying thousands of significant genetic associations for multiple traits and diseases1. In the course of this endeavor, sample size has proven to be the key factor for identifying new variants. For example, GWAS of body mass index (BMI), now including up to 350,000 individuals from more than 100 cohorts, have been able to identify genetic variant that explain as low as 0.02% of BMI variance2. While standar...

#7596 : Immune control of the gut microbiota and lifespan of A. stephensi.

Anopheles mosquitoes are the vectors of Plasmodium parasites, the etiological agents of malaria in humans. In Anopheles gambiae, a major vector in Africa, parasite transmission is largely under genetic control. We have previously shown that a gene family is implicated in the immune control of the parasite in this vector. The response of the family members is pathogen-specific, with one controlling P. falciparum infection and the other controlling rodent parasites. Recently, the genome of Anophel...

#7528 : Characterization of the specific TCR repertoire preferentially expressed in spontaneously controlled HIV infection

The rare patients who spontaneously control HIV replication in the absence of therapy show signs of a particularly efficient cellular immune response. To identify the molecular determinants underlying this response, we characterized the TCR repertoire directed at the most immunodominant CD4 epitope in HIV-1 capsid, Gag293. HIV Controllers from the ANRS CO21 CODEX cohort showed a highly skewed TCR repertoire characterized by a predominance of the TRAV24 and TRBV2 variable gene families. Controlle...

#7437 : Utilize mouse models to study infection by HIV-1

We previously showed that humanized immune system (HIS) mice generated in Balb/c Rag2^-/-γ_c^-/- SIRP^NOD (BRGS) recipients are susceptible to HIV-1 infection (X4 and R5 isolates) and maintain circulating HIV-1 in the plasma, resulting in a dramatic depletion of human CD4⁺ T cells. We also characterized features of HIV physiopathology in this model. Human thymocyte subsets developing in the thymus of HIS mice appear phenotypically normal,...

#7429 : A novel MacSyFinder module for detection of bacterial capsule systems on the future Galaxy platform.

Extracellular capsules constitute the outermost layer of some bacteria and establish the first contact between the cell and its environment. They are major virulence factors involved, amongst other, in antibiotic tolerance and immune escape. Bacterial capsules are also known to mediate unspecific cell-to-cell interactions between and across species and affect population structure and dynamics. Despite the great number of studies characterizing capsule diversity and their role during infection in...

#7427 : Add unit tests to IntegronFinder

Integrons drive the spread of antibiotic resistance genes in bacterial populations. While their role is widely known (integron+antibiotic+resistance in PubMed gives > 1700 hits), there was no software available to identify integrons and their different components. We have made integronFinder (with Bertrand Néron) for this (Cury, NAR, 16). We would like to make improvements to IntegronFinder:

• Unit tests to facilitate the development of the tool. Especially since Jean Cury (the m...
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  Project keyword
  Tool Development
  Project organism
  Bacteria
  Manager

  • Bertrand NÉRON
  Operators

  • Bertrand NÉRON
  • Amandine PERRIN

#7419 : Development of a new web interface for ARIA

The ARIA (Ambiguous Restraints for Iterative Assignment) software, developed at the Structural Bioinformatics Unit, automatizes the treatment of NMR data and protein structure calculation by molecular dynamics simulation. To enhance the visibility of the software, it is necessary to develop a new web interface where users will be able to easily manage their data, perform calculations and analyze the results of the ARIA calculations....

#7413 : In silico analyses of a novel LincRNA potentially involved in type I IFN response

We study the regulation of type I interferon (IFN) response in humans and in particular the functioning of a key negative feedback regulator, USP18. A recent article reported on a predicted 897nt-long LincRNA (long intergenic non coding RNA) that may target USP18. We have collected information for this LincRNA (genomic locus, putative transcript variants, sequence similarities with USP18 RNA, predicted ORFs, homologies with other genes, etc). To draw a guideline for wet lab experiments, we ne...

#7409 : Development of top-down proteomics for clinical microbiology

Rapid and accurate identification of microorganisms is a prerequisite for appropriate patient care and infection control. In the last decade, Mass Spectrometry (MS) has revolutionized the field of clinical microbiology with the introduction of MALDI-TOF for rapid microbial identification. However, MALDI-TOF MS suffers from important limitations. Some bacteria remain difficult to identify, either because they do not give a specific profile or because the database lacks the appropriate referenc...

#7331 : Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae.

Thanks to RNA-Seq experiments we identified  a new orphan DNA methylase (not associated with a restriction enzyme) that is highly upregulated in the presence of low concentrations of aminoglycosides in V. cholerae. The results allow us to consider a differential DNA methylation profile depending on the environment (with or without antibiotics), which can possibly correspond to a novel epigenetic control of the response....

#7283 : Detection of virulence Genes and genes of interest in Bacillus cereus

Bacillus cereus is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and more serious infections. Moreover, emerging B. cereus strains that cause anthrax-like disease have been isolated in Cameroon and Côte d’Ivoire. These strains are particular, because although they belong to the B. cereus species genetically speaking, they harbor two plasmids, pBCXO1 and pBCOX2, that are very ...

#7277 : optimisation d\'un programme sous R

Nous avons créer un programme sous R pur l'analyse non supervisé de fichier de cytométrie et nous avons besoin d'aide pour optimiser ce programme. Nous avons également besoin de conseils pour optimiser le clustering. Nous avons déjà rencontré Hugo Varet....

#7213 : Activation of plasmacytoïd dendritic cells by arenaviruses : transcriptomic analysis

Lassa virus (LASV) is an arenavirus causing hemorrhagic fever in human. 300 000 to 500 000 cases of LASV infection are reported every year in western Africa, including 5 000 to 6 000 deaths. LASV is highly pathogenic, and no vaccine or treatment is available in endemic areas. LASV pathogenesis mechanisms are not well documented, and further investigations are needed to understand viral and immunological factors involved during infection. As previously shown by studies conducted on patients a...

#7198 : Genomic analysis of bacterial evolution

We are interested to look at evolution of bacteria in presence of bacteriophages within the gastrointestinal tract of animals.    ...

#7188 : Genomic differences of the same strains preserved in different culture collections

Bacterial strains used for quality control (e. g. fertility and viability controls) are recommended in different ISO norms. Each strain is at least deposited in two different collections. So, equivalent strains are found in different collections. Their preservation is generally performed by freeze-drying. As control strains, they are much distributed, thereby, new freeze-dried batches have been done in the course of time. The subm...

#7143 : Modeling mitochondrial metabolism dormant Cryptococcus neoformans

Cryptococcus neoformans is a ubiquitous yeast present in the environment that is able to interact closely with numerous organisms including amoeba, paramecium or nematodes. The interaction with these organisms shaped its virulence with acquisition of infectious properties as a consequence especially in mammals . The ability to survive nutrient starvation, oxidative stress, desiccation, both in the environment and during infection, indicates a high level of physiological and metabolic ...

#7142 : Development of a web application and new functionalities for the maintenance and curation of iPPI-DB

A new version of the iPPI-DB, a manually curated database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundred modulators of protein-protein interactions.

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