Search results for "genomics"
showing 10 items of 1255 documents
Photostability and Photoreactivity in Biomolecules: Quantum Chemistry of Nucleic Acid Base Monomers and Dimers
2008
The great potentials of high-level ab initio methods, in particular, the CASPT2//CASSCF protocol, are fully illustrated through: (i) the study of ultrafast energy relaxation in DNA/RNA base monomers, (ii) the intrinsic population mechanism of the lowest triplet state, and (iii) how bioexcimers can be considered as precursors of charge transfer and photoinduced reactivity. In order to describe these processes properly, the presence of conical intersections (CIs) and the topology of the involved pathways have to be determined correctly. Thus, in theoretical calculations the dynamic electronic correlation has to be considered. The accessibility of the CIs (or the seam of CIs) becomes crucial t…
Appendix D. Pairwise Pearson correlation coefficients between the commercial and ecological traits considered in the meta-analysis.
2016
Pairwise Pearson correlation coefficients between the commercial and ecological traits considered in the meta-analysis.
Additional file 2: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic bioma…
2019
Table S1 Pairwise comparison of the gene expression of normal and tumor tissue using negative binomial generalized log-linear model and correction for false discovery rate (FDR). (TXT 2100 kb)
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
2018
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…
The contribution of epistasis to the architecture of fitness in an RNA virus
2004
4 pages, 2 figures.-- PMID: 15492220 [PubMed].-- PMCID: PMC524436.-- Additional information (Suppl. table S1: Relevant information about each single- and double-nucleotide substitution mutant created) available at: http://www.pnas.org/content/101/43/15376/suppl/DC1
Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled…
2017
Dysbalance in gut microbiota has been linked to increased microbial translocation, leading to chronic inflammation in HIV-patients, even under effective HAART. Moreover, microbial translocation is associated with insufficient reconstitution of CD4+T cells, and contributes to the pathogenesis of immunologic non-response. In a double-blind, randomised, placebo-controlled trial, we recently showed that, compared to placebo, 12 weeks treatment with probiotic Saccharomyces boulardii significantly reduced plasma levels of bacterial translocation (Lipopolysaccharide-binding protein or LBP) and systemic inflammation (IL-6) in 44 HIV virologically suppressed patients, half of whom (n = 22) had immun…
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
2021
Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among…
A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechan…
2021
[EN] Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,0…
Receiver-operating characteristic curves for somatic cell scores and California mastitis test in Valle del Belice dairy sheep.
2013
Using receiver-operating characteristic (ROC) curve methodology this study was designed to assess the diagnostic effectiveness of somatic cell count (SCC) and the California mastitis test (CMT) in Valle del Belice sheep, and to propose and evaluate threshold values for those tests that would optimally discriminate between healthy and infected udders. Milk samples (n = 1357) were collected from 684 sheep in four flocks. The prevalence of infection, as determined by positive bacterial culture was 0.36, 87.7% of which were minor and 12.3% major pathogens. Of the culture negative samples, 83.7% had an SCC < 500,000/mL and 97.4% had <1,000,000 cells/mL. When the associations between SC score (SC…
Genetic variants linked to myopic macular degeneration in persons with high myopia: CREAM Consortium.
2019
Purpose: To evaluate the roles of known myopia-associated genetic variants for development of myopic macular degeneration (MMD) in individuals with high myopia (HM), using case-control studies from the Consortium of Refractive Error and Myopia (CREAM). Methods: A candidate gene approach tested 50 myopia-associated loci for association with HM and MMD, using meta-analyses of case-control studies comprising subjects of European and Asian ancestry aged 30 to 80 years from 10 studies. Fifty loci with the strongest associations with myopia were chosen from a previous published GWAS study. Highly myopic (spherical equivalent [SE] ≤ -5.0 diopters [D]) cases with MMD (N = 348), and two sets of cont…