Genève, Switzerland


Genève, Switzerland
Time filter
Source Type

Genoleta R.,University of Lausanne | Leignadier J.,University of Lausanne | Osteras M.,Fasteris SA | Farinelli L.,Fasteris SA | And 2 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2014

CD8aβ plays crucial roles in the thymic selection, differentiation, and activation of some, but not all, CD8+ T cells, whereas CD8aa does not. To investigate these roles, we produced mice that expressed transgene P14 T-cell receptor β (TCRβ) chain and CD8β or did not (WT and KO mice, respectively). The primary CD8+ T-cell response to acute lymphocytic choriomeningitis virus (LCMV) infection was predominantly Db/GP33 specific and CD8 independent in KO mice and was mostly CD8 dependent in WT mice. Cytotoxic T lymphocytes (CTL) from KO mice failed to mobilize intracellular Ca2+ and to kill via perforin/ granzyme. Their strong Fas/FasL-mediated cytotoxicity and IFN-γ responsewere signaled via a Ca2+-independent, PI3K-dependent pathway. This was also true for 15-20% of CD8-independent CTL found in WT mice. Conversely, the perforin/granzyme-mediated killing and IFN-γ response of CD8-dependent CTL were signaled via a Ca2+, p56lck , and nuclear factor of activated T cells-dependent pathway. Deep sequencing of millions of TCRa chain transcripts revealed that the TCR repertoires of preimmune CD8+ T cells were highly diverse, but those of LCMV Db/GP33-specific CTL, especially from KO mice, were narrow. The immune repertoires exhibited biased use of Va segments that encoded different complementary-determining region 1α (CDR1α) and CDR2α sequences. We suggest that TCR from WT CD8-independent T cells may engage MHC-peptide complexes in a manner unfavorable for efficient CD8 engagement and Ca2+ signaling but permissive for Ca 2+-independent, PI3K-dependent signaling. This duality of the CD8 compartment may provide organisms with broader protective immunity.

Gapp K.,University of Zürich | Jawaid A.,University of Zürich | Sarkies P.,Gurdon Institute | Bohacek J.,University of Zürich | And 6 more authors.
Nature Neuroscience | Year: 2014

Small non-coding RNAs (sncRNAs) are potential vectors at the interface between genes and environment. We found that traumatic stress in early life altered mouse microRNA (miRNA) expression, and behavioral and metabolic responses in the progeny. Injection of sperm RNAs from traumatized males into fertilized wild-type oocytes reproduced the behavioral and metabolic alterations in the resulting offspring. © 2014 Nature America, Inc. All rights reserved.

Riley R.,University of Ottawa | Charron P.,University of Ottawa | Idnurm A.,University of Missouri - Kansas City | Farinelli L.,FASTERIS S.A. | And 3 more authors.
New Phytologist | Year: 2014

Summary: Arbuscular mycorrhizal fungi (AMF) are important plant symbionts that have long been considered evolutionary anomalies because of their apparent long-term lack of sexuality, but recent explorations of available DNA sequence have challenged this notion by revealing the presence of homologues of fungal mating type-high-mobility group (MATA-HMG) and core meiotic genes in these organisms. To obtain more insights into the sexual potential of AMF, homologues of MATA-HMGs were sought in the transcriptome of three AMF isolates, and their functional and evolutionary trajectories were studied in genetically divergent strains of Rhizophagus irregularis using conventional and quantitative PCR procedures. Our analyses revealed the presence of at least 76 homologues of MATA-HMGs in R. irregularis isolates. None of these was found to be surrounded by genes generally found near other known fungal mating type loci, but here we report the presence of a 9-kb-long region in the AMF R. irregularis harbouring a total of four tandem-repeated MATA-HMGs; a feature that highlights a potentially elevated intragenomic diversity in this AMF species. The present study provides intriguing insights into the genome evolution of R. irregularis, and represents a stepping stone for understanding the potential of these fungi to undergo cryptic sex. See also the Commentary by Lee et al. © 2013 New Phytologist Trust.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.1.1-1 | Award Amount: 8.71M | Year: 2012

We propose a technology that will sit at the front-end of sequencing pipelines, present and future, and will significantly enhance the quality and throughput of DNA sequencing. Although much attention has been given to throughput/cost of the sequencing process itself, the same cannot be said for the preparation of samples. Identified bottlenecks are (1) sequencing technologies require days of upfront sample preparation which is further increased when sequencing selected parts of the genome; (2) genome assembly relies on computationally intensive comparisons to the reference genome because existing technologies produce short sequence reads; (3) it is difficult to begin with small amounts of sample material comprising micro-biopsies and single cells. The CELL-O-MATIC project will synergize efforts from SMEs, academics and large companies to address these bottlenecks by developing chip-based systems that process DNA from individual cells, ready for next generation high-throughput sequencing. Single cell analysis has numerous applications in systems biology but we will emphasize DNA isolation and sequencing from circulating tumor cells (CTC), which have a strong prognostic value in cancer management. A second innovation will be to develop methods that enable up to whole chromosome lengths of DNA to be contiguously mapped using nanofluidics. The inclusion of nanofluidics makes the project particularly distinctive and introduces European SMEs to an area that so far has been the domain of US companies. A modular prototype comprising, a chip, fluid and thermal control, sonication and optical detection will be developed. Samples prepared using CELL-O-MATIC technology will be benchmarked in a high throughput environment with samples prepared by existing methods. Finally, the information obtained from the CELL-O-MATIC processed sample material will be validated for its utility as an aid to clinical decision making.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2012.1.2-1 | Award Amount: 7.62M | Year: 2012

Hematological diseases are highly heterogeneous malignancies in the matter of the molecular mechanisms related to their development and progression. A considerable heterogeneity can be further observed within the same hematological disease at the inter-individual level, being reflected by different clinical outcomes and responses to treatment in different patients. Nowadays, the advent of high-throughput next generation sequencing (NGS) technologies that are revolutionizing genomics and transcriptomics by providing a single base resolution tool for a unified deep analysis of diseases complexity allows a fast and cost-efficient fine-scale assessment of the genetic variability hidden within cohorts of patients affected by the same leukemia. That being so, by potentially highlighting inter-individual differences that may play a role in the differential success of diverse therapeutic interventions, they promise to be crucial for selecting the most appropriate medical treatments. This project aims at developing a European Hematological/NGS platform of scientists for improving outcomes for therapeutic interventions on acute and chronic leukemias and at developing strategies to personalize treatments and tailor therapies to different stratified groups of leukemia patients, with the goal of optimizing their efficacy and safety through a deeper and deeper understanding of the influence of genetic alterations on leukemias pathogenesis and treatment response (i.e. personalized therapy). Moreover, the final aim will be the identification of novel prognostic biomarkers for acute and chronic leukemias, as well as of molecular biomarkers and/or genome-wide profiles for the assessment of minimal residual disease. The originality of this project is to perform systematic deep whole exome/transcriptome studies on well-clinically-characterized leukemia patients, by exploiting NGS technologies able to quickly produce data with a good cost-effectiveness and an unprecedented resolution.

Kaufmann K.,Wageningen University | Muino J.M.,Wageningen University | Osteras M.,Fasteris SA | Farinelli L.,Fasteris SA | And 3 more authors.
Nature Protocols | Year: 2010

Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNA amplification and purification. We also provide a guide for primary data analysis of ChIP-SEQ data. The complete protocol for ChIP-SEQ/ChIP-CHIP sample preparation starting from plant harvest takes 7 d. © 2010 Nature Publishing Group.

Wenner N.,University of Lausanne | Maes A.,University of Lausanne | Cotado-Sampayo M.,Fasteris SA | Lapouge K.,University of Lausanne
Environmental Microbiology | Year: 2014

Summary: The opportunistic pathogen Pseudomonas aeruginosaPAO1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. Here, we report the discovery and characterization of a novel small non-coding RNA: NrsZ (nitrogen-regulated sRNA). We show that under nitrogen limitation, NrsZ is induced by the NtrB/C two-component system, an important regulator of nitrogen assimilation and P.aeruginosa's swarming motility, in concert with the alternative sigma factor RpoN. Furthermore, we demonstrate that NrsZ modulates P.aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. This regulation takes place through the post-transcriptional control of rhlA, a gene essential for rhamnolipids synthesis. Interestingly, we also observed that NrsZ is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for NrsZ regulatory functions. © 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Genolet R.,University of Lausanne | Stevenson B.J.,University of Lausanne | Stevenson B.J.,Swiss Institute of Bioinformatics | Farinelli L.,Fasteris SA | And 2 more authors.
EMBO Journal | Year: 2012

Although the T-cell receptor αδ (TCRαδ) locus harbours large libraries of variable (TRAV) and junctional (TRAJ) gene segments, according to previous studies the TCRα chain repertoire is of limited diversity due to restrictions imposed by sequential coordinate TRAV-TRAJ recombinations. By sequencing tens of millions of TCRα chain transcripts from naive mouse CD8 + T cells, we observed a hugely diverse repertoire, comprising nearly all possible TRAV-TRAJ combinations. Our findings are not compatible with sequential coordinate gene recombination, but rather with a model in which contraction and DNA looping in the TCRαδ locus provide equal access to TRAV and TRAJ gene segments, similarly to that demonstrated for IgH gene recombination. Generation of the observed highly diverse TCRα chain repertoire necessitates deletion of failed attempts by thymic-positive selection and is essential for the formation of highly diverse TCRαβ repertoires, capable of providing good protective immunity. © 2012 European Molecular Biology Organization | All Rights Reserved.

Pelin A.,University of Ottawa | Selman M.,University of Ottawa | Aris-Brosou S.,University of Ottawa | Farinelli L.,FASTERIS S.A. | Corradi N.,University of Ottawa
Environmental Microbiology | Year: 2015

Nosema ceranae is a microsporidian pathogen whose infections have been associated with recent global declines in the populations of western honeybees (Apis mellifera). Despite the outstanding economic and ecological threat that N. ceranae may represent for honeybees worldwide, many aspects of its biology, including its mode of reproduction, propagation and ploidy, are either very unclear or unknown. In the present study, we set to gain knowledge in these biological aspects by re-sequencing the genome of eight isolates (i.e. a population of spores isolated from one single beehive) of this species harvested from eight geographically distant beehives, and by investigating their level of polymorphism. Consistent with previous analyses performed using single gene sequences, our analyses uncovered the presence of very high genetic diversity within each isolate, but also very little hive-specific polymorphism. Surprisingly, the nature, location and distribution of this genetic variation suggest that beehives around the globe are infected by a population of N. ceranae cells that may be polyploid (4n or more), and possibly clonal. Lastly, phylogenetic analyses based on genome-wide single-nucleotide polymorphism data extracted from these parasites and mitochondrial sequences from their hosts all failed to support the current geographical structure of our isolates. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Selman M.,University of Ottawa | Sak B.,Academy of Sciences of the Czech Republic | Kvac M.,Academy of Sciences of the Czech Republic | Farinelli L.,Fasteris S.A | And 2 more authors.
Eukaryotic Cell | Year: 2013

The genomes of microsporidia in the genus Encephalitozoon have been extensively studied for their minimalistic features, but they have seldom been used to investigate basic characteristics of the biology of these organisms, such as their ploidy or their mode of reproduction. In the present study, we aimed to tackle this issue by mapping Illumina sequence reads against the genomes of four strains of E. cuniculi. This approach, combined with more conventional molecular biology techniques, resulted in the identification of heterozygosity in all strains investigated, a typical signature of a diploid nuclear state. In sharp contrast with similar studies recently performed on a distant microsporidian lineage (Nematocida spp.), the level of heterozygosity that we identified across the E. cuniculi genomes was found to be extremely low. This reductive intraindividual genetic variation could result from the long-term propagation of these strains under laboratory conditions, but we propose that it could also reflect an intrinsic capacity of these vertebrate pathogens to self-reproduce. © 2013, American Society for Microbiology. All Rights Reserved.

Loading FASTERIS SA collaborators
Loading FASTERIS SA collaborators