We report the complete genome sequence of ITTG R7, a nitrogen-fixing bacterium isolated from nodules of plants growing naturally in Chiapas, Mexico. The genome is distributed in four replicons comprising one 4.31-Mbp chromosome, one 1,933-Kb chromid, and two plasmids of 436 and 455 Kb.
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http://dx.doi.org/10.1128/MRA.01251-20 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037.
is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), alongside and (. CH can progress to myeloid malignancies including chronic monomyelocytic leukemia (CMML) and is also strongly associated with inflammatory cardiovascular disease and all-cause mortality in humans. DNMT3A and TET2 regulate DNA methylation and demethylation pathways, respectively, and loss-of-function mutations in these genes reduce DNA methylation in heterochromatin, allowing derepression of silenced elements in heterochromatin.
View Article and Find Full Text PDFPLoS One
January 2025
Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom.
Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prior studies of primary prostate cancer tumour genetics revealed extensive inter and intra-patient genomic tumour heterogeneity. Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data.
View Article and Find Full Text PDFPLoS One
January 2025
Département des Sciences Naturelles, Institut des Sciences de la Forêt Tempérée (ISFORT), Université du Québec en Outaouais (UQO), Ripon, Canada.
Forests face an escalating threat from the increasing frequency of extreme drought events driven by climate change. To address this challenge, it is crucial to understand how widely distributed species of economic or ecological importance may respond to drought stress. In this study, we examined the transcriptome of white spruce (Picea glauca (Moench) Voss) to identify key genes and metabolic pathways involved in the species' response to water stress.
View Article and Find Full Text PDFPLoS One
January 2025
College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.
Porcine epidemic diarrhea virus (PEDV) is a significant pathogen affecting swine, causing severe economic losses worldwide. This study explores the regulatory role of miRNA-328-3p to ZO-1 expression and its impact on PEDV proliferation via the PLC-β1-PKC pathway in IPEC-J2 cells. We found that miRNA-328-3p can target ZO-1, influencing its expression and subsequently affecting the integrity of tight junctions in the cells.
View Article and Find Full Text PDFBioinformatics
January 2025
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States.
Motivation: Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.
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