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Watson for genomics

Michael A Hardigan, Thomas J Poorten, Charlotte B Acharya, Glenn S Cole, Kim E Hummer, Nahla Bassil, Patrick P Edger, Steven J Knapp
Garden strawberry ( × Duchesne ex Rozier) arose from spontaneous hybridization of distinct octoploid species 300 yr ago. Since its discovery in the 1700s, migration and selection restructured the genetic diversity of early hybrids to produce elite fruit-bearing groups. Breeders' understanding of the genetic architecture of domesticated populations is incomplete. To resolve the impacts of domestication on strawberry genetic diversity, we analyzed genome-wide DNA profiles of 1300 octoploid individuals (1814-present), including wild species, historic varieties, and the University of California germplasm collection...
November 2018: Plant Genome
Ruoting Yang, Daniel Watson, Joshua Williams, Raina Kumar, Ross Campbell, Uma Mudunuri, Rasha Hammamieh, Marti Jett
BACKGROUND: Network medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype. Furthermore, investigating the time dimension of disease progression from a network perspective is key to gaining key insights to the disease process and to identify diagnostic or therapeutic targets. Existing platforms are ineffective to modularize the large complex systems into subgroups and consolidate heterogeneous data to web-based interactive animation...
November 29, 2018: BMC Bioinformatics
Tim Regan, Mark W Barnett, Dominik R Laetsch, Stephen J Bush, David Wragg, Giles E Budge, Fiona Highet, Benjamin Dainat, Joachim R de Miranda, Mick Watson, Mark Blaxter, Tom C Freeman
The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee...
November 26, 2018: Nature Communications
Shantanu Kundu, Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Devkant Singha, Iftikar Rahaman, Avas Pakrashi, Kailash Chandra
The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR)...
November 26, 2018: Scientific Reports
Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J McGrew, Alan L Archibald, Helen M Sang, Ross D Houston, C Bruce Whitelaw, Mick Watson
The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food...
November 26, 2018: Genome Biology
Eduardo Gorab
Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences...
November 23, 2018: Cells
Kota Itahashi, Shunsuke Kondo, Takashi Kubo, Yutaka Fujiwara, Mamoru Kato, Hitoshi Ichikawa, Takahiko Koyama, Reitaro Tokumasu, Jia Xu, Claudia S Huettner, Vanessa V Michelini, Laxmi Parida, Takashi Kohno, Noboru Yamamoto
Background: Oncologists increasingly rely on clinical genome sequencing to pursue effective, molecularly targeted therapies. This study assesses the validity and utility of the artificial intelligence Watson for Genomics (WfG) for analyzing clinical sequencing results. Methods: This study identified patients with solid tumors who participated in in-house genome sequencing projects at a single cancer specialty hospital between April 2013 and October 2016. Targeted genome sequencing results of these patients' tumors, previously analyzed by multidisciplinary specialists at the hospital, were reanalyzed by WfG...
2018: Frontiers in Medicine
Kay Boulton, Matthew J Nolan, Zhiguang Wu, Androniki Psifidi, Valentina Riggio, Kimberley Harman, Stephen C Bishop, Pete Kaiser, Mitchell S Abrahamsen, Rachel Hawken, Kellie A Watson, Fiona M Tomley, Damer P Blake, David A Hume
BACKGROUND: Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there are commercial incentives to breed chickens with greater resistance to this important production disease. To identify phenotypic biomarkers that are associated with the production impacts of coccidiosis, and to assess their covariance and heritability, 942 Cobb500 commercial broilers were subjected to a defined challenge with Eimeria tenella (Houghton)...
November 21, 2018: Genetics, Selection, Evolution: GSE
Ann-Kathrin Schneider, Christof M Niemeyer
The evolution of DNA microarray technology has led to sophisticated DNA chips that are being used as routine tools for fundamental and applied genome research such as genotyping and expression profiling. Owing to their capability for highly parallel, site-directed immobilization of complementary nucleic acids through canonical Watson-Crick base-pairing, however, DNA surfaces can as well be used for the assembly of complex surface architectures comprised of non-nucleic acid compounds, such as proteins or colloidal materials...
November 15, 2018: Angewandte Chemie
Simon Haile, Richard D Corbett, Steve Bilobram, Morgan H Bye, Heather Kirk, Pawan Pandoh, Eva Trinh, Tina MacLeod, Helen McDonald, Miruna Bala, Diane Miller, Karen Novik, Robin J Coope, Richard A Moore, Yongjun Zhao, Andrew J Mungall, Yussanne Ma, Rob A Holt, Steven J Jones, Marco A Marra
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome...
November 12, 2018: Nucleic Acids Research
Robert D Stewart, Marc Auffret, Timothy J Snelling, Rainer Roehe, Mick Watson
Motivation: Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously, to enable identification and functional characterisation. Results: Here we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree...
November 10, 2018: Bioinformatics
John Lindo, Randall Haas, Courtney Hofman, Mario Apata, Mauricio Moraga, Ricardo A Verdugo, James T Watson, Carlos Viviano Llave, David Witonsky, Cynthia Beall, Christina Warinner, John Novembre, Mark Aldenderfer, Anna Di Rienzo
The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact...
November 2018: Science Advances
François Le Loarer, Daniel Pissaloux, Sarah Watson, Catherine Godfraind, Louise Galmiche-Rolland, Karen Silva, Laetitia Mayeur, Antoine Italiano, Audrey Michot, Gaëlle Pierron, Alexandre Vasiljevic, Dominique Ranchère-Vince, Jean Michel Coindre, Franck Tirode
CIC-fused sarcomas represent an emerging family of tumors, for long connected to the Ewing family group of tumors, but underlined by distinct CIC fusions with different partners. 3' Fusion partners include DUX4, FOXO4, and, as recently emphasized, NUTM1. In this study, we report the clinicopathologic and molecular features of a series of 6 CIC-NUTM1 sarcomas. Mean age at diagnosis was 6 years (2 to 27 y), and 4 patients were male individuals. Primary tumors were located in the central nervous system (n=3), paravertebral soft tissue and epidural spaces (n=1, each), and lung (n=1)...
November 6, 2018: American Journal of Surgical Pathology
Yun Ding, Aaron M Fleming, Cynthia J Burrows
Genomes provide a platform for storage of chemical information that must be stable under the context in which an organism thrives. The 2'-deoxyguanosine (G) nucleotide has the potential to provide additional chemical information beyond its Watson-Crick base-pairing capacity. Sequences with four or more runs of three G nucleotides each are potential G-quadruplex forming sequences (PQSs) that can adopt G-quadruplex folds. Herein, we analyzed sequenced genomes from the NCBI database to determine the PQS densities of the genome sequences...
October 24, 2018: Scientific Reports
Andrew M Collins, Corey T Watson
Discussion of the antibody repertoire usually emphasizes diversity, but a conspicuous feature of the light chain repertoire is its lack of diversity. The diversity of reported allelic variants of germline light chain genes is also limited, even in well-studied species. In this review, the implications of this lack of diversity are considered. We explore germline and rearranged light chain genes in a variety of species, with a particular focus on human and mouse genes. The importance of the number, organization and orientation of the genes for the control of repertoire development is discussed, and we consider how primary rearrangements and receptor editing together shape the expressed light chain repertoire...
2018: Frontiers in Immunology
Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayon, S Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M Luscombe, James Briscoe
Neural induction in vertebrates generates a CNS that extends the rostral-caudal length of the body. The prevailing view is that neural cells are initially induced with anterior (forebrain) identity; caudalizing signals then convert a proportion to posterior fates (spinal cord). To test this model, we used chromatin accessibility to define how cells adopt region-specific neural fates. Together with genetic and biochemical perturbations, this identified a developmental time window in which genome-wide chromatin-remodeling events preconfigure epiblast cells for neural induction...
November 1, 2018: Cell
Tao Guo, Yi-Li Feng, Jing-Jing Xiao, Qian Liu, Xiu-Na Sun, Ji-Feng Xiang, Na Kong, Si-Cheng Liu, Guo-Qiao Chen, Yue Wang, Meng-Meng Dong, Zhen Cai, Hui Lin, Xiu-Jun Cai, An-Yong Xie
BACKGROUND: Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA double strand breaks may be repaired preferentially by accurate NHEJ. RESULTS: In the repair of two adjacent double strand breaks induced by paired Cas9-gRNAs at 71 genome sites, accurate NHEJ accounts for about 50% of NHEJ events. This paired Cas9-gRNA approach underestimates the level of accurate NHEJ due to frequent + 1 templated insertions, which can be avoided by the predefined Watson/Crick orientation of protospacer adjacent motifs (PAMs)...
October 19, 2018: Genome Biology
Anna Motnenko, Chih-Chao Liang, Di Yang, David Lopez-Martinez, Yasunaga Yoshikawa, Bao Zhan, Katherine E Ward, Jiayang Tian, Wilhelm Haas, Paolo Spingardi, Benedikt M Kessler, Skirmantas Kriaucionis, Steven P Gygi, Martin A Cohn
The Fanconi Anemia (FA) pathway is important for repairing interstrand crosslinks (ICLs) between the Watson-Crick strands of the DNA double helix. An initial and essential stage in the repair process is the detection of the ICL. Here, we report the identification of UHRF2, a paralogue of UHRF1, as an ICL sensor protein. UHRF2 is recruited to ICLs in the genome within seconds of their appearance. We show that UHRF2 cooperates with UHRF1, to ensure recruitment of FANCD2 to ICLs. A direct protein-protein interaction is formed between UHRF1 and UHRF2, and between either UHRF1 and UHRF2, and FANCD2...
October 2018: PLoS Genetics
Edgar A Rivera-Muñoz, Laura V Milko, Steven M Harrison, Danielle R Azzariti, C Lisa Kurtz, Kristy Lee, Jessica L Mester, Meredith A Weaver, Erin Currey, William Craigen, Charis Eng, Birgit Funke, Madhuri Hegde, Ray E Hershberger, Rong Mao, Robert D Steiner, Lisa M Vincent, Christa L Martin, Sharon E Plon, Erin Ramos, Heidi L Rehm, Michael Watson, Jonathan S Berg
Genome-scale sequencing creates vast amounts of genomic data, increasing the challenge of clinical sequence variant interpretation. The demand for high-quality interpretation requires multiple specialties to join forces to accelerate the interpretation of sequence variant pathogenicity. With over 600 international members including clinicians, researchers, and laboratory diagnosticians, the Clinical Genome Resource (ClinGen), funded by the National Institutes of Health, is forming expert groups to systematically evaluate variants in clinically relevant genes...
November 2018: Human Mutation
Laura M Thornton, Melissa A Munn-Chernoff, Jessica H Baker, Anders Juréus, Richard Parker, Anjali K Henders, Janne T Larsen, Liselotte Petersen, Hunna J Watson, Zeynep Yilmaz, Katherine M Kirk, Scott Gordon, Virpi M Leppä, Felicity C Martin, David C Whiteman, Catherine M Olsen, Thomas M Werge, Nancy L Pedersen, Walter Kaye, Andrew W Bergen, Katherine A Halmi, Michael Strober, Allan S Kaplan, D Blake Woodside, James Mitchell, Craig L Johnson, Harry Brandt, Steven Crawford, L John Horwood, Joseph M Boden, John F Pearson, Laramie E Duncan, Jakob Grove, Manuel Mattheisen, Jennifer Jordan, Martin A Kennedy, Andreas Birgegård, Paul Lichtenstein, Claes Norring, Tracey D Wade, Grant W Montgomery, Nicholas G Martin, Mikael Landén, Preben Bo Mortensen, Patrick F Sullivan, Cynthia M Bulik
BACKGROUND: Genetic factors contribute to anorexia nervosa (AN); and the first genome-wide significant locus has been identified. We describe methods and procedures for the Anorexia Nervosa Genetics Initiative (ANGI), an international collaboration designed to rapidly recruit 13,000 individuals with AN and ancestrally matched controls. We present sample characteristics and the utility of an online eating disorder diagnostic questionnaire suitable for large-scale genetic and population research...
November 2018: Contemporary Clinical Trials
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