Search results for "genomics"
showing 10 items of 1255 documents
Melatonin induces transcriptional regulation of Bim by FoxO3a in HepG2 cells
2012
Background: Melatonin induces apoptosis in many different cancer cell lines, including hepatocellular carcinoma cells. However, the responsible pathways have not been clearly elucidated. A member of the forkhead transcription factors' family, FoxO3a, has been implicated in the expression of the proapoptotic protein Bim (a Bcl-2-interacting mediator of cell death). In this study, we used human HepG2 liver cancer cells as an in vitro model to investigate whether melatonin treatment induces Bim through regulation by the transcription factor FoxO3a. Methods: Cytotoxicity of melatonin was compared in HepG2 hepatoblastoma cells and primary human hepatocytes. Proapoptotic Bim expression was analys…
TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay
2018
Chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique to understand transcriptional regulation. However, ChIP is currently limited by the requirement of large amount of starting material. This renders studying rare cell populations very challenging, or even impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high-quality datasets from low cell numbers. The method relies on Tn5 transposon activity to fragment the chromatin that is immunoprecipitated, thus circumventing the need for sonication or MNAse digestion to fragment. Furthermore, Tn5 adds the sequencing adapto…
The Norway spruce genome sequence and conifer genome evolution
2013
Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinu…
Functional genomics of Lactobacillus casei establishment in the gut
2014
International audience; Although the composition of the gut microbiota and its symbiotic contribution to key host physiological functions are well established, little is known as yet about the bacterial factors that account for this symbiosis. We selected Lactobacillus casei as a model microorganism to proceed to genomewide identification of the functions required for a symbiont to establish colonization in the gut. As a result of our recent development of a transposon-mutagenesis tool that overcomes the barrier that had prevented L. casei random mutagenesis, we developed a signature-tagged mutagenesis approach combining whole-genome reverse genetics using a set of tagged transposons and in…
What is in a lichen? A metagenomic approach to reconstruct the holo-genome of Umbilicaria pustulata
2019
AbstractLichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are generally poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis – the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) – were assemble…
Extremophilic taxa predominate in a microbial community of photovoltaic panels in a tropical region
2021
ABSTRACT Photovoltaic panels can be colonized by a highly diverse microbial diversity, despite life-threatening conditions. Although they are distributed worldwide, the microorganisms living on their surfaces have never been profiled in tropical regions using 16S rRNA high-throughput sequencing and PICRUst metagenome prediction of functional content. In this work, we investigated photovoltaic panels from two cities in southeast Brazil, Sorocaba and Itatiba, using these bioinformatics approach. Results showed that, despite significant differences in microbial diversity (p < 0.001), the taxonomic profile was very similar for both photovoltaic panels, dominated mainly by Proteobacteria,…
Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa.
2016
The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell-forming tissue, the mantle. This so-called ‘calcifying matrix’ is a complex mixture of proteins, glycoproteins and polysaccharides that is assembled and occluded within the mineral phase during the calcification process. Better molecular-level characterization of the substances that regulate nacre formation is still required. Notable advances in expressed tag sequencing of freshwater mussels, such as Elliptio complanata and Villosa lienosa , provide a pre-requisite to further characterize bivalve nacre proteins by a proteomic approach. In this…
Identifying and validating the presence of guanine-quadruplexes (G4) within the blood fluke parasite schistosoma mansoni
2021
Schistosomiasis is a neglected tropical disease that currently affects over 250 million individuals worldwide. In the absence of an immunoprophylactic vaccine and the recognition that mono-chemotherapeutic control of schistosomiasis by praziquantel has limitations, new strategies for managing disease burden are urgently needed. A better understanding of schistosome biology could identify previously undocumented areas suitable for the development of novel interventions. Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within the Schistosoma mansoni genome. We find that G4 are present in both intragenic and intergenic regi…
Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.)
2015
Published version of an article from the journal:Genome Biology and Evolution. Available from the publisher: http.//dx.doi.org/1093/gbe/evv093 How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35% in the North Sea to 7% within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci…
Relationship between beta lactoglobulin and subclinical mastitis in Valle del Belice sheep breed
2010
The objective of the following research was to determine the effect of LGB genotypes on subclinical mastitis in Valle del Belice dairy sheep. Ewes were classified as affected or not by subclinical mastitis within a lactation based on i) a positive culture in one of the test-days and ii) more than 750,000 somatic cells. Generalized linear mixed models were fitted to assess the significance of LGB genotypes on MTB and MTC. The LGB genotypes significantly affected MTB (p=0.0387), and showed a tendency on MTC (p=0.1104). Least square means showed that in the analysis for MTB, individuals with genotypes BB and AB had a higher frequency of subclinical mastitis. Moreover, the least square differen…