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Results: 75
Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.
Kathryn Holt, Johanna J Kenyon, Mohammad Hamidian, Mark B Schultz, Derek J Pickard, Gordon Dougan, Ruth Hall
Jun 25, 2018
The majority of Acinetobacter baumannii isolates that are multiply, extensively and pan-antibiotic resistant belong to two globally disseminated clones, GC1 and GC2, that were first noticed in the 1970s. Here, we investigated...
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
A Akay, T Di Domenico, KM Suen, A Nabih, GE Parada, M Larance, R Medhi, Berkyurek, X Zhang, CJ Wedeles, Rudolph, J Engelhardt, M Hemberg, P Ma, AI Lamond, JM Claycomb, Miska
Jul 16, 2017
Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis.
Christophe Lambing, Andrew J Tock, Stephanie D Topp, Kyuha Choi, Pallas C Kuo, Xiaohui Zhao, Kim Osman, James D Higgins, F Chris H Franklin, Ian R Henderson
Jan 13, 2020
Arabidopsis Arabidopsis Proteins Cell Cycle Proteins Chromatin Chromosomal Proteins Non-Histone Chromosomes Plant Crossing Over Genetic DNA Methylation DNA Transposable Elements Genome Plant Heterochromatin homologous recombination Meiosis Mutation Nucleosomes Saccharomyces cerevisiae Schizosaccharomyces SUPPRESSION Genetic
The transposable elements of the Drosophila melanogaster euchromatin
Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker
Jun 17, 2011
Mobile small RNAs regulate genome-wide DNA methylation.
Mathew G Lewsey, Thomas J Hardcastle, Charles W Melnyk, Attila Molnar, Adrián Valli, Mark A Urich, Joseph R Nery, David C Baulcombe, Joseph R Ecker
Jan 08, 2016
A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes.
Jorge de la Rosa, Julia Weber, Mathias Josef Friedrich, Yilong Li, Lena Rad, Hannes Ponstingl, Qi Liang, Sandra Bernaldo de Quirós, Imran Noorani, Emmanouil Metzakopian, Alexander Strong, Meng Amy Li, Aurora Astudillo, María Teresa Fernández-García, María Soledad Fernández-García, Gary J Hoffman, Rocío Fuente, George S Vassiliou, Roland Rad, Carlos López-Otín, Allan Bradley, Juan Cadiñanos
Oct 27, 2020
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional...
Animals Cell Line Cell Movement DNA Transposable Elements Epithelial Cells Gene Dosage Genes Tumor Suppressor Genetic Predisposition to Disease Humans Kaplan-Meier Estimate Male Mice Knockout Mice Transgenic Mutagenesis Insertional Mutation PTEN Phosphohydrolase Prostate Prostatic Neoplasms RNA Interference Signal Transduction
Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis.
Martin H Fabry, Federica A Falconio, Fadwa Joud, Emily K Lythgoe, Benjamin Czech, Gregory J Hannon
Jul 13, 2021
The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal...
D. melanogaster Drosophila Chromatin Chromosomes developmental biology embryogenesis epigenetics Gene Expression piRNA pathway transposable elements Animals Chromatin DNA Transposable Elements developmental biology Drosophila Drosophila Proteins Drosophila melanogaster Embryonic Development Epigenomics Female Gene Expression Germ Cells Heterochromatin Histones Male Maternal Inheritance RNA Small Interfering
Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress.
Pau Boher, Marçal Soler, Sandra Fernández-Piñán, Xènia Torrent, Sebastian Y Müller, Krystyna A Kelly, Olga Serra, Mercè Figueras
Dec 24, 2022
BACKGROUND: The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber)...
flowering Kh-domain Rna-binding Protein Potato Tuber Periderm Rna Regulation Rs2-interacting Kh Protein Arabidopsis Cell Nucleus DNA Transposable Elements Flowers Gene Expression Regulation Plant Gene Regulatory Networks Gene Silencing Plant Proteins Plant Tubers Plants Genetically Modified RNA Plant Solanum tuberosum Stress Physiological
Mechanism and Regulation of P Element Transposition
Drosophila P transposable elements THAP9 hybrid dysgenesis Animals DNA Transposable Elements Drosophila Proteins Drosophila melanogaster Gene Expression Regulation Gene Transfer Horizontal Germ Cells Histones hybridization Genetic Maternal Inheritance Protein Binding Protein Interaction Domains and Motifs Protein Transport RNA Splicing RNA Small Interfering selection Genetic Transposases Vertebrates
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions.
Kyuha Choi, Xiaohui Zhao, Andrew J Tock, Christophe Lambing, Charles J Underwood, Thomas J Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A Ziolkowski, Nataliya E Yelina, Ildoo Hwang, Robert A Martienssen, Ian R Henderson
Jun 04, 2018
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin...
Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements
SH Lewis, KA Quarles, Y Yang, M Tanguy, L Frezal, SA Smith, PP Sharma, R Cordaux, C Gilbert, I Giraud, DH Collins, PD Zamore, EA Miska, P Sarkies, FM Jiggins
Jan 09, 2018
Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival.
Mette T Christiansen, Rolf S Kaas, Roy R Chaudhuri, Mark A Holmes, Henrik Hasman, Frank M Aarestrup
Jul 15, 2014
Animals Anti-Bacterial Agents DNA Transposable Elements Gene Library Genes Essential Genome Genotype High-Throughput Screening Assays Humans Hydrogen-Ion Concentration Methicillin-Resistant Staphylococcus aureus Mutation Plasmids Sequence Analysis DNA Staphylococcal Infections Swine Virulence Factors
A track of the clones
Anne-Marie Lyne, David G Kent, Elisa Laurenti, Kerstin Cornils, Ingmar Glauche, Leïla Perié
Dec 17, 2018
Cell Lineage Cell Separation Cell Tracking Clinical Trials as Topic Clone Cells DNA barcoding Taxonomic DNA Transposable Elements Data Display Forecasting Genetic Markers Genetic Therapy Guidelines as Topic Hematopoiesis Models Biological Mosaicism Reproducibility of Results Research Design Stem Cells Virus Integration
Molecular Criteria for Defining the Naive Human Pluripotent State.
Thorold W Theunissen, Marc Friedli, Yupeng He, Evarist Planet, Ryan C O'Neil, Styliani Markoulaki, Julien Pontis, Haoyi Wang, Alexandra Iouranova, Michaël Imbeault, Julien Duc, Malkiel A Cohen, Katherine J Wert, Rosa Castanon, Zhuzhu Zhang, Yanmei Huang, Joseph R Nery, Jesse Drotar, Tenzin Lungjangwa, Didier Trono, Joseph R Ecker, Rudolf Jaenisch
Jul 07, 2016
DNA Methylation X chromosome reactivation Embryonic Stem Cells Imprinting mouse-human chimeras Pluripotency transposable elements Animals Blastocyst Cell Differentiation Cell Line Chimera Chromosomes Human X Cleavage Stage Ovum DNA Methylation DNA Transposable Elements DNA Mitochondrial Female Gene Expression Profiling Genome Human Genomic Imprinting Human Embryonic Stem Cells Humans Male Mice Mitochondria Morula Pluripotent Stem Cells Polymerase Chain Reaction Transcription Genetic
Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages.
Peter Sarkies, Murray E Selkirk, John T Jones, Vivian Blok, Thomas Boothby, Bob Goldstein, Ben Hanelt, Alex Ardila-Garcia, Naomi M Fast, Phillip M Schiffer, Christopher Kraus, Mark J Taylor, Georgios Koutsovoulos, Mark L Blaxter, Eric A Miska
Mar 20, 2015
Amino Acid Sequence Animals Base Sequence Biological Evolution Caenorhabditis elegans Caenorhabditis elegans Proteins DNA Methylation DNA Transposable Elements Drosophila melanogaster Gene Expression Regulation Humans MicroRNAs Molecular Sequence Data Nematoda Phylogeny RNA Small Interfering RNA-Dependent RNA Polymerase Ribonuclease III
The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.
Erik Hjerde, Marit Sjo Lorentzen, Matthew TG Holden, Kathy Seeger, Steinar Paulsen, Nathalie Bason, Carol Churcher, David Harris, Halina Norbertczak, Michael A Quail, Suzanne Sanders, Scott Thurston, Julian Parkhill, Nils Peder Willassen, Nicholas R Thomson
Sep 06, 2019
BACKGROUND: The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo. RESULTS: In total, 4...
The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification.
Pierre-Yves Helleboid, Moritz Heusel, Julien Duc, Cécile Piot, Christian W Thorball, Andrea Coluccio, Julien Pontis, Michaël Imbeault, Priscilla Turelli, Ruedi Aebersold, Didier Trono
Dec 12, 2019
Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin-inducing KAP1 as repressors of transposable elements...
A transposable element insertion is associated with an alternative life history strategy.
Alyssa Woronik, Kalle Tunström, Michael W Perry, Ramprasad Neethiraj, Constanti Stefanescu, Maria de la Paz Celorio-Mancera, Oskar Brattström, Jason Hill, Philipp Lehmann, Reijo Käkelä, Christopher W Wheat
Dec 22, 2020
Animals Butterflies CRISPR-Cas Systems Color DNA Transposable Elements Female Gene Editing Gene Expression Profiling Gene Expression Regulation Developmental Genetic Loci Homeodomain Proteins Life History Traits Male Pigmentation Pigments Biological Reproduction Sex Factors whole genome sequencing Wings Animal
Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation.
Daniel Gebert, Lena K Neubert, Catrin Lloyd, Jinghua Gui, Ruth Lehmann, Felipe Karam Teixeira
Jul 13, 2021
chromosome inversions flamenco Fruit fly Gene Silencing Germ Cells gypsy12 Heterochromatin POSITION-EFFECT VARIEGATION sterility transposable elements Animals Animals Genetically Modified Argonaute Proteins Chromosome Deletion Chromosomes Insect DNA Transposable Elements Drosophila Proteins Drosophila melanogaster evolution Molecular Female Fertility Gene Expression Regulation Developmental Multigene Family Ovary RNA Stability RNA Small Interfering
PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas.
Imran Noorani, Jorge de la Rosa, Yoon Ha Choi, Alexander Strong, Hannes Ponstingl, MS Vijayabaskar, Jusung Lee, Eunmin Lee, Angela Richard-Londt, Mathias Friedrich, Federica Furlanetto, Rocio Fuente, Ruby Banerjee, Fengtang Yang, Frances Law, Colin Watts, Roland Rad, George Vassiliou, Jong Kyoung Kim, Thomas Santarius, Sebastian Brandner, Allan Bradley
Aug 14, 2020
Glioma is the most common intrinsic brain tumor and also occurs in the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. However, the cooperative partners of EGFR driving gliomagenesis remain poorly...
O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli.
Connor Sharp, Christine Boinett, Amy Cain, Nicholas G Housden, Sandip Kumar, Keith Turner, Julian Parkhill, Colin Kleanthous
Aug 20, 2019
The outer membrane of Gram-negative bacteria presents a significant barrier for molecules entering the cell. Nevertheless, colicins, which are antimicrobial proteins secreted by Escherichia coli, can target other E. coli cells...
bacteriocins cell envelope enteric bacteria outer membrane Anti-Bacterial Agents Colicins DNA Transposable Elements Drug Resistance Bacterial Gene Silencing metabolism Microarray Analysis Microbial Sensitivity Tests Mutagenesis Insertional O Antigens Phenotype Sequence Analysis DNA Uropathogenic Escherichia coli
Ten things you should know about transposable elements.
Guillaume Bourque, Kathleen H Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L Levin, Todd S Macfarlan, Dixie L Mager, Cédric Feschotte
Dec 18, 2018
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and...
Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae.
Jyoti Verma, Satyabrata Bag, Bipasa Saha, Pawan Kumar, Tarini Shankar Ghosh, Mayanka Dayal, Tarosi Senapati, Seema Mehra, Prasanta Dey, Anbumani Desigamani, Dhirendra Kumar, Preety Rana, Bhoj Kumar, Tushar K Maiti, Naresh C Sharma, Rupak K Bhadra, Ankur Mutreja, G Balakrish Nair, Thandavarayan Ramamurthy, Bhabatosh Das
Jun 17, 2019
Antimicrobial resistance Cholera Genome mobile genetic elements Proteome Anti-Bacterial Agents Cholera Conjugation Genetic DNA Transposable Elements Diarrhea Drug Resistance Multiple Bacterial evolution Molecular Feces Gene Transfer Horizontal genetic variation Genome Bacterial Genomic Islands Humans Imipenem india Interspersed Repetitive Sequences Phenotype Plasmids Prophages Proteome Vibrio cholerae Vibrio cholerae O1 whole genome sequencing
Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells.
Kosuke Yusa, S Tamir Rashid, Helene Strick-Marchand, Ignacio Varela, Pei-Qi Liu, David E Paschon, Elena Miranda, Adriana Ordóñez, Nicholas RF Hannan, Foad J Rouhani, Sylvie Darche, Graeme Alexander, Stefan J Marciniak, Noemi Fusaki, Mamoru Hasegawa, Michael C Holmes, James P Di Santo, David A Lomas, Allan Bradley, Ludovic Vallier
Oct 22, 2020
Human induced pluripotent stem cells (iPSCs) represent a unique opportunity for regenerative medicine because they offer the prospect of generating unlimited quantities of cells for autologous transplantation, with potential...
Movement of transposable elements contributes to cichlid diversity.
Karen L Carleton, Matthew A Conte, Milan Malinsky, Sri Pratima Nandamuri, Benjamin A Sandkam, Joana I Meier, Salome Mwaiko, Ole Seehausen, Thomas D Kocher
Nov 09, 2020
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for...
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