Search results for "Transcriptome"
showing 10 items of 610 documents
Induction of Chromosome Instability by Activation of Yes-Associated Protein and Forkhead Box M1 in Liver Cancer
2016
Background & Aims Many different types of cancer cells have chromosome instability. The hippo pathway leads to phosphorylation of the transcriptional activator yes-associated protein 1 (YAP1, YAP), which regulates proliferation and has been associated with the development of liver cancer. We investigated the effects of hippo signaling via YAP on chromosome stability and hepatocarcinogenesis in humans and mice. Methods We analyzed transcriptome data from 242 patients with hepatocellular carcinoma (HCC) to search for gene signatures associated with chromosomal instability (CIN); we investigated associations with overall survival time and cancer recurrence using Kaplan–Meier curves. We analyze…
Human Upcyte Hepatocytes: Characterization of the Hepatic Phenotype and Evaluation for Acute and Long-Term Hepatotoxicity Routine Testing
2016
The capacity of human hepatic cell-based models to predict hepatotoxicity depends on the functional performance of cells. The major limitations of human hepatocytes include the scarce availability and rapid loss of the hepatic phenotype. Hepatoma cells are readily available and easy to handle, but are metabolically poor compared with hepatocytes. Recently developed human upcyte hepatocytes offer the advantage of combining many features of primary hepatocytes with the unlimited availability of hepatoma cells. We analyzed the phenotype of upcyte hepatocytes comparatively with HepG2 cells and adult primary human hepatocytes to characterize their functional features as a differentiated hepatic …
Bacterial antisense RNAs are mainly the product of transcriptional noise
2015
Most of the antisense transcripts in bacteria are the product of transcriptional noise derived from spurious promoters.
CENTENARIANS TRANSCRIPTOME IS UNIQUE AND REVEALS A ROLE OF BCL-XL IN SUCCESSFUL AGING
2017
Centenarians not only enjoy an extraordinary aging, but also show a compression of morbidity. We identified 1721 mRNAs differentially expressed by PMBCs from centenarians when compared with septuagenarians and young people. Sub-network analysis led us to identify Bcl-xL as an important gene up-regulated in centenarians. We found that centenarians display lower plasma cytochrome C levels, higher mitochondrial membrane potential and also less cellular damage accumulation. Immune function is significantly impaired in septuagenarians compared with young people whereas centenarians maintain it. To further ascertain the functional role of Bcl-xL in cellular aging, we found in transduced lymphocyt…
Functional Genomics in Wine Yeast: DNA Arrays and Next Generation Sequencing
2017
Since their very beginning, DNA array and next-generation sequencing technologies have been used with Saccharomyces cerevisiae cells. In the last 7 years, an increasing number of studies have focused on the study of wine strains and winemaking. The uncovering of the genomic features of these strains and expression profiles under the different stressful conditions that they have to deal with have contributed significantly to the knowledge of how this amazing microorganism can convert grape must into a drink that has enormously influenced mankind for 7000 years.This review presents a synopsis of DNA array and next-generation sequencing (NGS) technologies and focus mainly in their use in study…
Microbiome-assisted carrion preservation aids larval development in a burying beetle
2018
Significance Ephemeral diets such as carrion are high-quality resources that are susceptible to microbial spoilage. Carrion-feeding insects that breed on decaying carcasses must overcome challenges arising from competing microbes. Here we report that a carrion-feeding burying beetle preserves carcasses by regulating its microbial growth, resulting in changes in its biochemical properties including the reduction of toxic polyamines associated with putrefaction and nutrient loss. The beetle’s microbial symbionts form a biofilm-like matrix on carcasses, which is important for optimal larval development. The beetles and their microbiome thus coordinate a specialized adaptive strategy of carrion…
Viable But Not Culturable (VBNC) state of Brettanomyces bruxellensis in wine: New insights on molecular basis of VBNC behaviour using a transcriptomi…
2016
International audience; The spoilage potential of Brettanomyces bruxellensis in wine is strongly connected with the aptitude of this yeast to enter in a Viable But Non Culturable (VBNC) state when exposed to the harsh wine conditions. In this work, we characterized the VBNC behaviour of seven strains of B. bruxellensis representing a regional intraspecific biodiversity, reporting conclusive evidence for the assessment of VBNC as a strain-dependent character. The VBNC behaviour was monitored by fluorescein diacetate staining/flow cytometry for eleven days after addition of 0.4, 0.6, 0.8, 1 and 1.2 mg/L of molecular SO2 (entrance in the VBNC state) and after SO2 removal (exit from the VBNC st…
The ‘Shellome’ of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization
2021
Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are focused predominantly on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we hav…
Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut.
2018
International audience; Candida albicans is part of the human gastrointestinal (GI) microbiota. To better understand how C. albicans efficiently establishes GI colonisation, we competitively challenged growth of 572 signature-tagged strains (~10% genome coverage), each conditionally overexpressing a single gene, in the murine gut. We identified CRZ2, a transcription factor whose overexpression and deletion respectively increased and decreased early GI colonisation. Using clues from genome-wide expression and gene-set enrichment analyses, we found that the optimal activity of Crz2p occurs under hypoxia at 37°C, as evidenced by both phenotypic and transcriptomic analyses following CRZ2 geneti…
The developmental proteome of Drosophila melanogaster
2017
Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison wi…