Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83-94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007910 | PMC |
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199471 | PLOS |
Congenital disorders of glycosylation (CDG) comprise a class of inborn errors of metabolism resulting from pathogenic variants in genes coding for enzymes involved in the asparagine-linked glycosylation of proteins. Unexpectedly to date, no CDG has been described for , encoding the alpha-1,2-glucosyltransferase catalyzing the final step of lipid-linked oligosaccharide biosynthesis. Genome-wide association studies (GWAS) of human traits in the UK Biobank revealed significant SNP associations with short sleep duration, reduced napping frequency, later sleep timing and evening diurnal preference as well as cardiac traits at a genomic locus containing a pair of paralogous enzymes and .
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LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal.
Wheat is an essential staple food, and its production and grain quality are affected by extreme temperature events. These effects are even more relevant considering the increasing food demand for a growing world population and the predicted augmented frequency of heat waves. This study investigated the impact of simulated heat wave (HW) conditions imposed during grain filling on starch granule characteristics, endosperm ultrastructure, and transcriptomic modulation of genes involved in starch synthesis and degradation.
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December 2024
Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.
An in-depth analysis of susceptibility factors modifying the penetrance of rare Leber hereditary optic neuropathy-causing mutations in respiratory complex I genes encoded in mitochondrial deoxyribonucleic acid has not been performed. To bridge this gap, we conducted a review of the literature on rare mutations associated with LHON, selected those with substantial evidence of pathogenicity, and performed an in-depth analysis of the various pedigrees. Examining the influences that modify the penetrance of the classical mutations associated with this disease may offer insights into susceptibility factors in individuals carrying the rare mutations.
View Article and Find Full Text PDFG3 (Bethesda)
December 2024
Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1.
The release of heavy metals from industrial, agricultural, and mining activities poses significant risks to aquatic ecosystems by degrading water quality and generating reactive oxygen species (ROS) that can damage DNA in aquatic organisms. Daphnia is a widespread keystone species in freshwater ecosystems that is routinely exposed to a range of anthropogenic and natural stressors. With a fully sequenced genome, a well-understood life history and ecology, and an extensive library of responses to toxicity, Daphnia serves as an ideal model organism for studying the impact of environmental stressors on genomic stability.
View Article and Find Full Text PDFAm J Med Genet A
December 2024
Department of Internal Medicine, Amsterdam University Medical Center, Amsterdam, The Netherlands.
Osteogenesis imperfecta (OI) is a rare disease, hallmarked by bone fragility, multiple fractures, and deformities, and is commonly caused by pathogenic variants in the genes encoding type I collagen. Type II OI is the most severe form and is lethal in the perinatal period. Here, we report recurrence of perinatal lethal OI in two fetuses due to parental mosaicism for a deep intronic pathogenic variant at c.
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