Search results for " genomi"
showing 10 items of 572 documents
A complete set of nascent transcription rates for yeast genes
2010
The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) a…
Annotation of microsporidian genomes using transcriptional signals
2012
EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-asso…
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…
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…
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…
Genomic analysis of anadromous brown trout (Salmo trutta) reveals new insights into connectivity patterns and population divergence
2018
Master's thesis Aquatic Ecology BIO500 - University of Agder 2018 A large body of studies on brown trout genetics currently exists. However, fewer of these studies have been conducted on anadromous brown trout (sea trout) and have been limited to only a few genetic markers like allozymes, mtDNA or microsatellites. Here we analyzed population structure and connectivity in sea trout applying a modern genomic approach, analyzing 503 single nucleotide polymorphic variants (SNP’s) by next generation sequencing. We studied four streams along the Skagerrak coast and found an overall significant population structure (FST = 0.0161; P<0.01) which further seemed to constitute of three genetically dist…
Kopepoder langs Skagerrakkysten - En oversikt basert på morfologisk og molekylærgenetisk identifisering
2018
Masteroppgave akvatisk økologi BIO500 - Universitetet i Agder 2018 Konfidensiell til / confidential until 01.07.2023
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…
Effect of somatic cell count level on functional longevity in Valle del Belice dairy sheep assessed using survival analysis.
2009
The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 103 cells/mL, wer…