Search results for "Transcriptome"
showing 10 items of 610 documents
Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries.
2010
For certain food products, postharvest controlled stresses or treatments with specific elicitors are applied to induce desired physical/chemical changes and/or to positively affect phytochemical content. This is the case of wine grapes where both strategies, singularly applied or coupled, can be used to modulate berry composition and, as a consequence, affect wine quality traits. Since the knowledge of the effects of these postharvest treatments on berry metabolism and the regulation of gene expression is very limited, a large-scale transcriptome analysis has been carried out, using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries subjected to deh…
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing
2021
The alignment of reads to a transcriptome is an important initial step in a variety of bioinformatics RNA-seq pipelines. As traditional alignment-based tools suffer from high runtimes, alternative, alignment-free methods have recently gained increasing importance. We present a novel approach to the detection of local similarities between transcriptomes and RNA-seq reads based on context-aware minhashing. We introduce RNACache, a three-step processing pipeline consisting of minhashing of k-mers, match-based (online) filtering, and coverage-based filtering in order to identify truly expressed transcript isoforms. Our performance evaluation shows that RNACache produces transcriptomic mappings …
The Medicago truncatula hypermycorrhizal B9 mutant displays an altered response to phosphate and is more susceptible to Aphanomyces euteiches.
2014
SPE IPM; National audience; Inorganic phosphate (Pi) plays a key role in the development of arbuscular mycorrhizal (AM) symbiosis, which is favoured when Pi is limiting in the environment. We have characterized the Medicago truncatula hypermycorrhizal B9 mutant for its response to limiting (P/10) and replete (P2) Pi. On P2, mycorrhization was significantly higher in B9 plants than in wild-type (WT). The B9 mutant displayed hallmarks of Pi-limited plants, including higher levels of anthocyanins and lower concentrations of Pi in shoots than WT plants. Transcriptome analyses of roots of WT and B9 plants cultivated on P2 or on P/10 confirmed the Pi-limited profile of the mutant on P2 and highli…
Genetic determinisms, evolution and detection of non-target-site based resistance to herbicides inhibiting acetolactate-synthase in rye-grass (Lolium…
2016
The aim of this study is to unravel the genetic determinism of non-target-site resistance (NTSR) to herbicides inhibiting acetolactate-synthase (ALS) in the major weed rye-grass (Lolium sp.), and to estimate the feasibility of NTSR diagnosis based on genetic data. On the one hand, this work contributes to the understanding of the processes driving the evolution of NTSR to herbicides, and on the other hand it lays the foundations for the development of a diagnosis tool to identify NTSR to ALS inhibiting herbicides. - Using a quantitative transcriptome sequencing approach, we showed that NTSR evolve by recurrent selection of higher and higher constitutive expression levels of genes involved i…
Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes
2019
γδ T lymphocytes represent ∼1% of human peripheral blood mononuclear cells and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current single-cell RNA sequencing (scRNA-seq) studies do not identify γδ T lymphocytes because their transcriptomes at the single-cell level are unknown. Here we show that high-resolution clustering of large scRNA-seq datasets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their T cell receptor (TCR)Vδ1 and TCRVδ2 subsets in large datasets from complex cell mixtures. In t -distributed stochastic neighbor embedding plots from blood and tumor sa…
The multiple facets of Cajal-Retzius neurons.
2021
ABSTRACTCajal-Retzius neurons (CRs) are among the first-born neurons in the developing cortex of reptiles, birds and mammals, including humans. The peculiarity of CRs lies in the fact they are initially embedded into the immature neuronal network before being almost completely eliminated by cell death at the end of cortical development. CRs are best known for controlling the migration of glutamatergic neurons and the formation of cortical layers through the secretion of the glycoprotein reelin. However, they have been shown to play numerous additional key roles at many steps of cortical development, spanning from patterning and sizing functional areas to synaptogenesis. The use of genetic l…
Characterization and role of nitric oxide production in Arabidopsis thaliana defense responses induced by oligogalacturonides
2011
Nitric oxide (NO) regulates a wide range of plant processes from development toenvironmental adaptation. In this study, NO production and its effects were investigated in aplant-pathogen context. The production of NO following Arabidopsis treatment witholigogalacturonides (OGs), an endogenous elicitor of plant defense, was assessed using the NOsensitive probe 4, 5-diamino fluorescein diacetate. Pharmacological and genetic approaches wereused to analyze NO enzymatic sources and its role in the Arabidopsis thaliana /Botrytis cinereainteraction. We showed that NO production involves both a L-arginine- and a nitrate reductase(NR)-pathways. OGs-induced NO production was Ca2+-dependent and modula…
The antennal transcriptome of a moth
2010
International audience
Role of nitric oxide in tumor development. Role of HSF1 in development of zebrafish embryos in non heat-shocked conditions
2014
The use of animal models has led to the discovery of important mechanisms of biology development in general, and tumor development in particular, to establish and develop new treatments. The Zebrafish (Danio rerio) is increasingly used nowadays as part of this research because of its many advantages such as the transparency of the larvae, and the high homology with human. Several approaches have been developed in this fish, as the gene-knockdown in order to identify the role of a protein in the development, or the tumor transplantation of mammalian cells to study anti-tumor treatments response.It is in one of these two contexts that we studied the role of nitric oxide in tumor development i…
Towards a cell-specific expression atlas of arbuscular mycorrhizal roots in the model legume Medicago truncatula
2007
International audience