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Duplexed direct RNA sequencing protocol using polyadenylation and polyuridylation.
Microbiol Resour Announc
January 2025
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.
Oxford Nanopore Technologies provides multiplexing options for DNA and cDNA sequencing, but not for direct RNA sequencing. Here we describe a duplexing approach and validate it by simultaneously sequencing the rRNA from wild type and knockout that have differential rRNA modifications, successfully demultiplexing the data using bioinformatics approaches.
View Article and Find Full Text PDFMathematical model linking telomeres to senescence in Saccharomyces cerevisiae reveals cell lineage versus population dynamics.
Nat Commun
January 2025
Sorbonne Université, CNRS, Laboratory of Computational and Quantitative Biology, LCQB, Paris, France.
Telomere shortening ultimately causes replicative senescence. However, identifying the mechanisms driving replicative senescence in cell populations is challenging due to the heterogeneity of telomere lengths and the asynchrony of senescence onset. Here, we present a mathematical model of telomere shortening and replicative senescence in Saccharomyces cerevisiae which is quantitatively calibrated and validated using data of telomerase-deficient single cells.
View Article and Find Full Text PDFSynthesis of Headful Packaging Phages Through Yeast Transformation-Associated Recombination.
Viruses
December 2024
School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
De novo synthesis of phage genomes enables flexible genome modification and simplification. This study explores the synthetic genome assembly of phage vB_PaeS_SCUT-S4 (S4), a 42,932 bp headful packaging phage, which encapsidates a terminally redundant, double-stranded DNA genome exceeding unit length. We demonstrate that using the yeast TAR approach, the S4 genome can be assembled and rebooted from a unit-length genome plus a minimal 60 bp terminal redundant sequence.
View Article and Find Full Text PDFEnhanced Tolerance to Antifungals as a General Feature of Rho Mutants in Yeast Species: Implications to Positive Selection of Respiratory Deficiency.
Microorganisms
January 2025
Centre for Bioscience, Manchester Metropolitan University, John Dalton Building, Chester Street, Manchester M1 5GD, UK.
Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). Strains without mtDNA (known as rho mutants or petite mutants) are respiration-deficient and require fermentable carbon sources (such as glucose) for their metabolism. However, they are compromised in many aspects of fitness and competitiveness.
View Article and Find Full Text PDFMechanisms of RCD-1 pore formation and membrane bending.
Nat Commun
January 2025
Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, PR China.
Regulator of cell death-1 (RCD-1) governs the heteroallelic expression of RCD-1-1 and RCD-1-2, a pair of fungal gasdermin (GSDM)-like proteins, which prevent cytoplasmic mixing during allorecognition and safeguard against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (e.g., senescence plasmids) by effecting a form of cytolytic cell death.
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