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Results: 16
Cardiac mitochondrial function depends on BUD23 mediated ribosome programming.
Matthew Baxter, Maria Voronkov, Toryn Poolman, Gina Galli, Christian Pinali, Laurence Goosey, Abigail Knight, Karolina Krakowiak, Robert Maidstone, Mudassar Iqbal, Min Zi, Sukhpal Prehar, Elizabeth J Cartwright, Julie Gibbs, Laura C Matthews, Antony D Adamson, Neil E Humphreys, Pedro Rebelo-Guiomar, Michal Minczuk, David A Bechtold, Andrew Loudon, David Ray
Mar 16, 2020
Efficient mitochondrial function is required in tissues with high energy demand such as the heart, and mitochondrial dysfunction is associated with cardiovascular disease. Expression of mitochondrial proteins is tightly...
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.
Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V Mello, Seoae Cho, Arang Rhie, Heebal Kim, Erich D Jarvis
Sep 28, 2022
BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete...
Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.
Strain 82T, a Gram-stain-positive, coagulase-negative staphylococcus was isolated from an air sample obtained from an industrial rabbit holding in Italy. It is phylogenetically closely related to the coagulase-negative species...
Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD.
Jeremiah Seni, Stephen E Mshana, Felician Msigwa, Shabani Iddi, Humphrey Mazigo, Julian Parkhill, Mark A Holmes, Gavin K Paterson
Aug 02, 2019
OBJECTIVES: Coagulase-negative staphylococci such as Staphylococcus cohnii are opportunistic pathogens of humans and animals. A multidrug-resistant isolate of S. cohnii subsp. urealyticus (073AN) was isolated from the nasal...
Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias
Haoxuan Liu, Ju Huang, Xiaoguang Sun, Jing Li, Yingwen Hu, Luyao Yu, Gianni Liti, Dacheng Tian, Laurence Hurst, Sihai Yang
Jan 01, 2018
GC-favouring gene conversion enables fixation of deleterious alleles, disturbs tests of natural selection and potentially explains both the evolution of recombination as well as the commonly reported intragenomic correlation...
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad Getz, Jared T Simpson, Mark B Gerstein, Li Ding, PCAWG Consortium
Oct 12, 2020
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the...
Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins.
Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias
Haoxuan Liu, Ju Huang, Xiaoguang Sun, Jing Li, Yingwen Hu, Luyao Yu, Gianni Liti, Dacheng Tian, Laurence Hurst, Sihai Yang
Jan 01, 2018
GC-favouring gene conversion enables fixation of deleterious alleles, disturbs tests of natural selection and potentially explains both the evolution of recombination as well as the commonly reported intragenomic correlation...
Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.
Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, Manasa Ramakrishna, Helen R Davies, Elli Papaemmanuil, Gunes Gundem, Adam Shlien, Niccolo Bolli, Sam Behjati, Patrick S Tarpey, Jyoti Nangalia, Charles E Massie, Adam P Butler, Jon W Teague, George S Vassiliou, Anthony R Green, Ming-Qing Du, Ashwin Unnikrishnan, John E Pimanda, Bin Tean Teh, Nikhil Munshi, Mel Greaves, Paresh Vyas, Adel K El-Naggar, Tom Santarius, V Peter Collins, Richard Grundy, Jack A Taylor, D Neil Hayes, David Malkin, ICGC Breast Cancer Group, ICGC Chronic Myeloid Disorders Group, ICGC Prostate Cancer Group, Christopher S Foster, Anne Y Warren, Hayley C Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Tapio Visakorpi, William B Isaacs, G Steven Bova, Adrienne M Flanagan, P Andrew Futreal, Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, Peter J Campbell
Nov 01, 2018
Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated...
cancer genome evolution evolutionary biology Genomics human Mitochondrial DNA mutational signature SEQUENCING Somatic mutation Animals Base Composition DNA DNA Replication DNA Mitochondrial DNA Neoplasm Data Mining evolution Molecular Genome Mitochondrial High-Throughput Nucleotide Sequencing Humans Mitochondria Mutation Neoplasms Polymorphism Single Nucleotide
The small RNA locus map for Chlamydomonas reinhardtii.
Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous...
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Konrad LM Rudolph, Bianca M Schmitt, Diego Villar, Robert J White, John C Marioni, Claudia Kutter, Duncan T Odom
May 31, 2016
Systematic bias in high-throughput sequencing data and its correction by BEADS.
Genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For example, sequencing data of total genomic DNA show significant, yet unexpected enrichments on promoters and...
Evolutionary and functional insights into Leishmania META1
BACKGROUND: Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear....
Amino Acid Sequence Bacterial Proteins Base Composition DNA Protozoan evolution Molecular Gene Transfer Horizontal Leishmania Models Molecular Molecular Sequence Data Mutagenesis Site-Directed Phylogeny Protein Structure Tertiary Protozoan Proteins selection Genetic Sequence Alignment Sequence Analysis DNA Virulence
GC content shapes mRNA storage and decay in human cells.
Maïté Courel, Yves Clément, Clémentine Bossevain, Dominika Foretek, Olivia Vidal Cruchez, Zhou Yi, Marianne Bénard, Marie-Noëlle Benassy, Michel Kress, Caroline Vindry, Michèle Ernoult-Lange, Christophe Antoniewski, Antonin Morillon, Patrick Brest, Arnaud Hubstenberger, Hugues Roest Crollius, Nancy Standart, Dominique Weil
Mar 09, 2020
mRNA translation and decay appear often intimately linked although the rules of this interplay are poorly understood. In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of...
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.
Christopher E Laumer, Harald Gruber-Vodicka, Michael G Hadfield, Vicki B Pearse, Ana Riesgo, John C Marioni, Gonzalo Giribet
Dec 19, 2019
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset...