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https://www.readbyqxmd.com/read/28346953/lennox-gastaut-syndrome-a-state-of-the-art-review
#1
Mario Mastrangelo
Lennox-Gastaut syndrome (LGS) is a severe age-dependent epileptic encephalopathy usually with onset between 1 and 8 years of age. Functional neuroimaging studies recently introduced the concept of Lennox-Gastaut as "secondary network epilepsy" resulting from dysfunctions of a complex system involving both cortical and subcortical structures (default-mode network, corticoreticular connections, and thalamus). These dysfunctions are produced by different disorders including hypoxic-ischemic encephalopathies, meningoencephalitis, cortical malformations, neurocutaneous disorders, or tumors...
March 27, 2017: Neuropediatrics
https://www.readbyqxmd.com/read/28346710/the-arabidopsis-thiamin-deficient-mutant-pale-green1-lacks-thiamin-monophosphate-phosphatase-of-the-vitamin-b1-biosynthesis-pathway
#2
Wei-Yu Hsieh, Jo-Chien Liao, Hsin-Tzu Wang, Tzu-Huan Hung, Ching-Chih Tseng, Tsui-Yun Chung, Ming-Hsiun Hsieh
Thiamin diphosphate (TPP, vitamin B1) is an essential coenzyme present in all organisms. Animals obtain TPP from their diets, but plants synthesize TPP de novo. We isolated and characterized an Arabidopsis pale green1 (pale1) mutant that contained higher concentrations of thiamin monophosphate (TMP) and less thiamin and TPP than the wild type. Supplementation with thiamin, but not the thiazole and pyrimidine precursors, rescued the mutant phenotype, indicating that the pale1 mutant is a thiamin-deficient mutant...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346477/disruption-of-sorcs2-reveals-differences-in-the-regulation-of-stereociliary-bundle-formation-between-hair-cell-types-in-the-inner-ear
#3
Andrew Forge, Ruth R Taylor, Sally J Dawson, Michael Lovett, Daniel J Jagger
Behavioural anomalies suggesting an inner ear disorder were observed in a colony of transgenic mice. Affected animals were profoundly deaf. Severe hair bundle defects were identified in all outer and inner hair cells (OHC, IHC) in the cochlea and in hair cells of vestibular macular organs, but hair cells in cristae were essentially unaffected. Evidence suggested the disorder was likely due to gene disruption by a randomly inserted transgene construct. Whole-genome sequencing identified interruption of the SorCS2 (Sortilin-related VPS-10 domain containing protein) locus...
March 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28346448/a-footprint-of-desiccation-tolerance-in-the-genome-of-xerophyta-viscosa
#4
Maria-Cecília D Costa, Mariana A S Artur, Julio Maia, Eef Jonkheer, Martijn F L Derks, Harm Nijveen, Brett Williams, Sagadevan G Mundree, José M Jiménez-Gómez, Thamara Hesselink, Elio G W M Schijlen, Wilco Ligterink, Melvin J Oliver, Jill M Farrant, Henk W M Hilhorst
Desiccation tolerance is common in seeds and various other organisms, but only a few angiosperm species possess vegetative desiccation tolerance. These 'resurrection species' may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance, we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration...
March 27, 2017: Nature Plants
https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#5
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345639/genomic-characterization-of-nontuberculous-mycobacteria
#6
Tarcisio Fedrizzi, Conor J Meehan, Antonella Grottola, Elisabetta Giacobazzi, Giulia Fregni Serpini, Sara Tagliazucchi, Anna Fabio, Clotilde Bettua, Roberto Bertorelli, Veronica De Sanctis, Fabio Rumpianesi, Monica Pecorari, Olivier Jousson, Enrico Tortoli, Nicola Segata
Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345240/prenatal-dna-sequencing-clinical-counseling-and-diagnostic-laboratory-considerations
#7
Ahmad N Abou Tayoun, Nancy B Spinner, Heidi L Rehm, Robert C Green, Diana W Bianchi
Clinical diagnostic laboratories are producing next generation sequencing (NGS)-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history and the physical examination is only indirectly available via prenatal sonography...
March 27, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28344890/suppression-of-indoleamine-2-3-dioxygenase-1-expression-by-promoter-hypermethylation-in-er-positive-breast-cancer
#8
Dyah L Dewi, Soumya R Mohapatra, Saioa Blanco Cabañes, Isabell Adam, Luis F Somarribas Patterson, Bianca Berdel, Masroor Kahloon, Loreen Thürmann, Stefanie Loth, Katharina Heilmann, Dieter Weichenhan, Oliver Mücke, Ines Heiland, Pauline Wimberger, Jan Dominik Kuhlmann, Karl-Heinz Kellner, Sarah Schott, Christoph Plass, Michael Platten, Clarissa Gerhäuser, Saskia Trump, Christiane A Opitz
Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. As the response of breast cancer to immune checkpoint inhibitors may be limited, a better understanding of the expression of additional targetable immunomodulatory pathways is of importance. We therefore investigated the regulation of IDO1 expression in different breast cancer subtypes. We identified estrogen receptor α (ER) as a negative regulator of IDO1 expression...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344774/the-dockstore-enabling-modular-community-focused-sharing-of-docker-based-genomics-tools-and-workflows
#9
Brian D O'Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing...
2017: F1000Research
https://www.readbyqxmd.com/read/28344519/assessment-of-repli-g-multiple-displacement-whole-genome-amplification-wga-techniques-for-metagenomic-applications
#10
Sofia Ahsanuddin, Ebrahim Afshinnekoo, Jorge Gandara, Mustafa Hakyemezoğlu, Daniela Bezdan, Samuel Minot, Nick Greenfield, Christopher E Mason
Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28344109/phylogenomic-proximity-and-metabolic-discrepancy-of-methanosarcina-mazei-go1-across-methanosarcinal-genomes
#11
M Bharathi, P Chellapandi
Methanosarcina mazei Go1 is a heterotrophic methanogenic archaean contributing a significant role in global methane cycling and biomethanation process. Phylogenomic relatedness and metabolic discrepancy of this genome were described herein by comparing its whole genome sequence, intergenomic distance, genome function, synteny homologs and origin of replication, and marker genes with very closely related genomes, Methanosarcina acetivorans and Methanosarcina barkeri. Phylogenomic analysis of this study revealed that genome functional feature and metabolic core of M...
March 23, 2017: Bio Systems
https://www.readbyqxmd.com/read/28344011/the-epidemiology-pathogenesis-transmission-diagnosis-and-management-of-multidrug-resistant-extensively-drug-resistant-and-incurable-tuberculosis
#12
REVIEW
Keertan Dheda, Tawanda Gumbo, Gary Maartens, Kelly E Dooley, Ruth McNerney, Megan Murray, Jennifer Furin, Edward A Nardell, Leslie London, Erica Lessem, Grant Theron, Paul van Helden, Stefan Niemann, Matthias Merker, David Dowdy, Annelies Van Rie, Gilman K H Siu, Jotam G Pasipanodya, Camilla Rodrigues, Taane G Clark, Frik A Sirgel, Aliasgar Esmail, Hsien-Ho Lin, Sachin R Atre, H Simon Schaaf, Kwok Chiu Chang, Christoph Lange, Payam Nahid, Zarir F Udwadia, C Robert Horsburgh, Gavin J Churchyard, Dick Menzies, Anneke C Hesseling, Eric Nuermberger, Helen McIlleron, Kevin P Fennelly, Eric Goemaere, Ernesto Jaramillo, Marcus Low, Carolina Morán Jara, Nesri Padayatchi, Robin M Warren
Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis)...
March 15, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28343239/improved-full-length-killer-cell-immunoglobulin-like-receptor-transcript-discovery-in-mauritian-cynomolgus-macaques
#13
Trent M Prall, Michael E Graham, Julie A Karl, Roger W Wiseman, Adam J Ericsen, Muthuswamy Raveendran, R Alan Harris, Donna M Muzny, Richard A Gibbs, Jeffrey Rogers, David H O'Connor
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS)...
March 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28343122/genetic-and-epigenetic-variation-of-transposable-elements-in-arabidopsis
#14
REVIEW
Charles J Underwood, Ian R Henderson, Robert A Martienssen
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation...
March 23, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28343068/the-role-of-trail-in-fatigue-induced-by-repeated-stress-from-radiotherapy
#15
Li Rebekah Feng, Simeng Suy, Sean P Collins, Leorey N Saligan
Fatigue is one of the most common and debilitating side effects of cancer and cancer treatment, and yet its etiology remains elusive. The goal of this study is to understand the role of chronic inflammation in fatigue following repeated stress from radiotherapy. Fatigue and non-fatigue categories were assessed using ≥ 3-point change in Functional Assessment of Cancer Therapy-Fatigue questionnaire (FACT-F) administered to participants at baseline/before radiotherapy and one year post-radiotherapy. Whole genome microarray and cytokine multiplex panel were used to examine fatigue-related transcriptome and serum cytokine changes, respectively...
March 20, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28342926/causes-and-clinical-features-of-infertile-men-with-non-obstructive-azoospermia-and-histopathological-diagnosis-of-hypospermatogenesis
#16
Yu-Sheng Cheng, Chun-Wun Lu, Tsung-Yen Lin, Pei-Yu Lin, Yung-Ming Lin
OBJECTIVE: To analyze the causes and the clinical features of infertile men with non-obstructive azoospermia (NOA) and hypospermatogenesis (HS). METHODS: This retrospective cohort study included 100 patients with NOA and HS and eight patients with obstructive azoospermia and normal spermatogenesis. The severity of HS was subdivided into three groups (mild, moderate, and severe) based on spermatogenic score. Data of history, physical findings, serum hormone profiles, genetic studies and sperm retrieval rate (SRR) were collected...
March 22, 2017: Urology
https://www.readbyqxmd.com/read/28341732/novel-recurrent-chromosomal-aberrations-detected-in-clonal-plasma-cells-of-light-chain-amyloidosis-patients-show-potential-adverse-prognostic-effect-first-results-from-a-genome-wide-copy-number-array-analysis
#17
Martin Granzow, Ute Hegenbart, Katrin Hinderhofer, Dirk Hose, Anja Seckinger, Tilmann Bochtler, Kari Hemminki, Hartmut Goldschmidt, Stefan O Schönland, Anna Jauch
Immunoglobulin light chain amyloidosis is a rare plasma cell dyscrasia characterized by deposition of abnormal amyloid fibrils in multiple organs impairing their function. In the largest cohort studied up to now of 118 CD138-purified plasma cell samples from previously untreated immunoglobulin light chain amyloidosis patients, we assessed in parallel copy number alterations using high-density copy number arrays and interphase fluorescence in situ hybridization. We used fluorescence in situ hybridization probes for the IgH translocations t(11;14), t(4;14), and t(14;16) or any other IgH rearrangement as well as numerical aberrations of the chromosome loci 1q21, 8p21, 5p15/5q35, 11q22...
March 24, 2017: Haematologica
https://www.readbyqxmd.com/read/28341681/chromosome-encoded-hemolysin-phospholipase-and-collagenase-contribute-to-virulence-for-fish-in-plasmidless-isolates-of-photobacterium-damselae-subsp-damselae
#18
Ana Vences, Amable J Rivas, Manuel L Lemos, Matthias Husmann, Carlos R Osorio
Photobacterium damselae subsp. damselae is a pathogen of marine animals including fish of importance in aquaculture. The virulence plasmid pPHDD1, characteristic of highly hemolytic isolates, encodes the hemolysins damselysin (Dly) and phobalysin (PhlyP). Strains lacking pPHDD1 constitute the vast majority of the isolates from fish outbreaks, but genetic studies to identify virulence factors in plasmidless strains are scarce. Here we show that the chromosome-I encoded hemolysin PhlyC plays a role in virulence and cell toxicity in pPHDD1-negative isolates of this pathogen...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28341546/co-circulation-of-two-usutu-virus-strains-in-northern-italy-between-2009-and-2014
#19
Mattia Calzolari, Chiara Chiapponi, Paolo Bonilauri, Davide Lelli, Laura Baioni, Ilaria Barbieri, Antonio Lavazza, Stefano Pongolini, Michele Dottori, Ana Moreno
Usutu virus is an arbovirus closely related to West Nile virus (genus Flavivirus), which circulates between mosquitoes and wild birds. This virus has been increasingly reported in Europe, raising concerns for its possible pathogenic potential for wild birds and humans. This study reports the whole genome sequences of 15 strains of USUV, isolated between 2010 and 2014 from mosquitoes and wild birds in the course of West Nile virus surveillance in the Emilia-Romagna and Lombardy regions of Northern Italy. Both whole and 656 partial genome sequences, obtained from isolated viruses and field samples (mosquitoes and wild birds), were analyzed to describe the temporal and geographical spread of USUV in the surveyed area...
March 21, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28341545/novel-putative-bluetongue-virus-in-healthy-goats-from-sardinia-italy
#20
Giovanni Savini, Giantonella Puggioni, Giorgio Meloni, Maurilia Marcacci, Marco Di Domenico, Angela Maria Rocchigiani, Massimo Spedicato, Annalisa Oggiano, Daniela Manunta, Liana Teodori, Alessandra Leone, Ottavio Portanti, Francesca Cito, Annamaria Conte, Massimiliano Orsini, Cesare Cammà, Paolo Calistri, Armando Giovannini, Alessio Lorusso
In recent years, novel Bluetongue virus (BTV) serotypes have been isolated and/or sequenced by researchers within the field. During Bluetongue surveillance activities, we identified a putative novel BTV serotype in healthy goats from Sardinia, Italy. RNAs purified from blood and serum samples were positive for BTV by a generic real time RT-PCR and c-ELISA, respectively, whereas genotyping and serotyping were unsuccessful. By NGS, the whole genome sequence was obtained from two blood samples (BTV-X ITL2015 strains 34200 and 33531)...
March 21, 2017: Infection, Genetics and Evolution
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