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https://www.readbyqxmd.com/read/29656136/streptococcous-gallolyticus-subsp-pasteurianus-meningitis-complicated-by-venous-sinus-thrombosis-a-case-report
#1
Martin Wardle, Andre Mu, Steven Y C Tong
We describe a case of Streptococcus gallolyticus subsp pasteurianus meningitis, unusually occurring in a splenectomised patient and complicated by cerebral venous thrombosis. Following presentation with meningism and diagnosis and management of S. gallolyticus meningitis, the patient represented with a further four days of fevers and subsequently developed left sided paresthesias. Cerebral imaging revealed venous thrombus in the right frontal cortical veins and left sigmoid sinus. The patient recovered following four weeks of intravenous ceftriaxone and anticoagulation with enoxaparin and then warfarin...
April 12, 2018: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29655603/new-technologies-to-uncover-the-molecular-basis-of-disorders-of-sex-development
#2
REVIEW
Hayk Barseghyan, Emmanuèle C Délot, Eric Vilain
The elegant developmental biology experiments conducted in the 1940s by French physiologist Alfred Jost demonstrated that the sexual phenotype of a mammalian embryo depended whether the embryonic gonad develops into a testis or not. In humans, anomalies in the processes that regulate development of chromosomal, gonadal or anatomic sex result in a spectrum of conditions termed Disorders/Differences of Sex Development (DSD). Each of these conditions is rare, and understanding of their genetic etiology is still incomplete...
April 12, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29655579/hungarian-tick-borne-encephalitis-viruses-isolated-from-a-0-5-ha-focus-are-closely-related-to-finnish-strains
#3
László Egyed, Zsuzsanna Rónai, Ádám Dán
Four tick-borne encephalitis virus strains were isolated from a small 0.5-ha focus over a six-year-long period (2011-2016) in Hungary. Two strains with identical genomes were isolated from Ixodes ricinus and Haemaphysalis concinna two months apart, which shows that the virus had not evolved separately in these tick species. Whole-genome sequencing of the virus revealed that the isolates differed from each other in 4 amino acids and 9 nucleotides. The calculated substitution rates indicated that the speed of genome evolution differs from habitat to habitat, and continuously changes even within the same focus...
April 7, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29653190/evaluation-of-whole-genome-sequencing-and-software-tools-for-drug-susceptibility-testing-of-mycobacterium-tuberculosis
#4
Janko van Beek, Marjo Haanperä, Pieter W Smit, Silja Mentula, Hanna Soini
OBJECTIVES: Culture-based assays are currently the gold standard for drug susceptibility testing (DST) for Mycobacterium tuberculosis. They provide good sensitivity and specificity, but are time-consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture based assays for drug susceptibility testing of M. tuberculosis. METHODS: M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n=211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first line drug susceptibilities...
April 10, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29653001/-genetic-analysis-of-two-fetuses-with-congenital-heart-defects-and-3q-microdeletion
#5
Wei Long, Jiandong Gu, Jun Ouyang, Saiyu Jia, Bin Zhang, Jianbin Liu, Bin Yu
OBJECTIVE: To determine the nature of genomic copy number variations (CNVs) in two fetuses with congenital heart defects (CHD) and explore the correlation between 3q microdeletions and CHD. METHODS: Genomic DNA was extracted from fetal umbilical cord tissue, and chromosome copy number variations were detected by low coverage whole genome sequencing. RESULTS: Both fetuses had microdeletions of the long arm of chromosome 3. Fetus 1 had ventricular septal defect, cleft lip and palate, and a 1...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29652800/full-genome-sequencing-reveals-new-southern-african-territories-genotypes-bringing-us-closer-to-understanding-true-variability-of-foot-and-mouth-disease-virus-in-africa
#6
Lidia Lasecka-Dykes, Caroline F Wright, Antonello Di Nardo, Grace Logan, Valerie Mioulet, Terry Jackson, Tobias J Tuthill, Nick J Knowles, Donald P King
Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that poses a constant burden on farmers in endemic regions and threatens the livestock industries in disease-free countries. Despite the increased number of publicly available whole genome sequences, FMDV data are biased by the opportunistic nature of sampling. Since whole genomic sequences of Southern African Territories (SAT) are particularly underrepresented, this study sequenced 34 isolates from eastern and southern Africa...
April 13, 2018: Viruses
https://www.readbyqxmd.com/read/29651704/hdac9-polymorphism-alters-blood-gene-expression-in-patients-with-large-vessel-atherosclerotic-stroke
#7
Natasha Shroff, Bradley P Ander, Xinhua Zhan, Boryana Stamova, DaZhi Liu, Heather Hull, Farah R Hamade, Cheryl Dykstra-Aiello, Kwan Ng, Frank R Sharp, Glen C Jickling
The histone deacetylase 9 (HDAC9) polymorphism rs2107595 is associated with an increased risk for large vessel atherosclerotic stroke (LVAS). In humans, there remains a need to better understand this HDAC9 polymorphism's contribution to large vessel stroke. In this pilot study, we evaluated whether the HDAC9 polymorphism rs2107595 is associated with differences in leukocyte gene expression in patients with LVAS. HDAC9 SNP rs2107595 was genotyped in 155 patients (43 LVAS and 112 vascular risk factor controls)...
April 13, 2018: Translational Stroke Research
https://www.readbyqxmd.com/read/29651137/publisher-correction-identification-and-characterization-of-the-novel-colonization-factor-cs30-based-on-whole-genome-sequencing-in-enterotoxigenic-escherichia-coli-etec
#8
Astrid von Mentzer, Joshua Tobias, Gudrun Wiklund, Stefan Nordqvist, Martin Aslett, Gordon Dougan, Åsa Sjöling, Ann-Mari Svennerholm
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29650961/identification-of-rare-sequence-variation-underlying-heritable-pulmonary-arterial-hypertension
#9
Stefan Gräf, Matthias Haimel, Marta Bleda, Charaka Hadinnapola, Laura Southgate, Wei Li, Joshua Hodgson, Bin Liu, Richard M Salmon, Mark Southwood, Rajiv D Machado, Jennifer M Martin, Carmen M Treacy, Katherine Yates, Louise C Daugherty, Olga Shamardina, Deborah Whitehorn, Simon Holden, Micheala Aldred, Harm J Bogaard, Colin Church, Gerry Coghlan, Robin Condliffe, Paul A Corris, Cesare Danesino, Mélanie Eyries, Henning Gall, Stefano Ghio, Hossein-Ardeschir Ghofrani, J Simon R Gibbs, Barbara Girerd, Arjan C Houweling, Luke Howard, Marc Humbert, David G Kiely, Gabor Kovacs, Robert V MacKenzie Ross, Shahin Moledina, David Montani, Michael Newnham, Andrea Olschewski, Horst Olschewski, Andrew J Peacock, Joanna Pepke-Zaba, Inga Prokopenko, Christopher J Rhodes, Laura Scelsi, Werner Seeger, Florent Soubrier, Dan F Stein, Jay Suntharalingam, Emilia M Swietlik, Mark R Toshner, David A van Heel, Anton Vonk Noordegraaf, Quinten Waisfisz, John Wharton, Stephen J Wort, Willem H Ouwehand, Nicole Soranzo, Allan Lawrie, Paul D Upton, Martin R Wilkins, Richard C Trembath, Nicholas W Morrell
Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis. Deleterious variation within components of the transforming growth factor-β pathway, particularly the bone morphogenetic protein type 2 receptor (BMPR2), underlies most heritable forms of PAH. To identify the missing heritability we perform whole-genome sequencing in 1038 PAH index cases and 6385 PAH-negative control subjects. Case-control analyses reveal significant overrepresentation of rare variants in ATP13A3, AQP1 and SOX17, and provide independent validation of a critical role for GDF2 in PAH...
April 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29650777/-mll-leukemia-induction-by-t-9-11-chromosomal-translocation-in-human-hematopoietic-stem-cells-using-genome-editing
#10
Corina Schneidawind, Johan Jeong, Dominik Schneidawind, In-Suk Kim, Jesús Duque-Afonso, Stephen Hon Kit Wong, Masayuki Iwasaki, Erin H Breese, James L Zehnder, Matthew Porteus, Michael L Cleary
Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here, we used transcription activator-like effector nucleases to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells...
April 24, 2018: Blood Advances
https://www.readbyqxmd.com/read/29650582/draft-genome-sequences-of-12-clinical-and-environmental-methicillin-resistant-staphylococcus-pseudintermedius-strains-isolated-from-a-veterinary-teaching-hospital-in-washington-state
#11
Devendra H Shah, Lisa P Jones, Narayan Paul, Margaret A Davis
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a globally emergent multidrug-resistant pathogen of dogs associated with nosocomial transmission in dogs and with potential zoonotic impacts. Here, we report the draft whole-genome sequences of 12 hospital-associated MRSP strains and their resistance genotypes and phenotypes.
April 12, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29650580/high-quality-whole-genome-sequences-for-59-historical-shigella-strains-generated-with-pacbio-sequencing
#12
Justin Kim, Rebecca L Lindsey, Lisley Garcia-Toledo, Vladimir N Loparev, Lori A Rowe, Dhwani Batra, Phalasy Juieng, Devon Stoneburg, Haley Martin, Kristen Knipe, Peyton Smith, Nancy Strockbine
Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical Shigella strains that represent the four species and a variety of serotypes.
April 12, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29650572/draft-whole-genome-sequence-of-the-fluorene-degrading-sphingobium-sp-strain-lb126-isolated-from-polycyclic-aromatic-hydrocarbon-contaminated-soil
#13
Floriana Augelletti, Julien Tremblay, Spiros N Agathos, Ben Stenuit
We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium sp. strain LB126. The genes involved in the upper biodegradation pathway of fluorene are located on a plasmid, and the lower pathway that generates tricarboxylic acid cycle intermediates is initiated by the meta -cleavage of protocatechuic acid that is chromosomally encoded.
April 12, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29650569/whole-genome-sequences-of-cronobacter-sakazakii-isolates-obtained-from-foods-of-plant-origin-and-dried-food-manufacturing-environments
#14
Hyein Jang, Nicole Addy, Laura Ewing, Junia Jean-Gilles Beaubrun, YouYoung Lee, JungHa Woo, Flavia Negrete, Samantha Finkelstein, Ben D Tall, Angelika Lehner, Athmanya Eshwar, Gopal R Gopinath
Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from foods of plant origin and dried-food manufacturing facilities. Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb and 3,977 to 4,256 gene-coding sequences with G+C contents of ∼57.0%.
April 12, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29650553/enduring-epigenetic-landmarks-define-the-cancer-microenvironment
#15
Ruth Pidsley, Mitchell G Lawrence, Elena Zotenko, Birunthi Niranjan, Aaron Statham, Jenny Song, Roman M Chabanon, Wenjia Qu, Hong Wang, Michelle Richards, Shalima S Nair, Nicola J Armstrong, Hieu T Nim, Melissa Papargiris, Preetika Balanathan, Hugh French, Timothy Peters, Sam Norden, Andrew Ryan, John Pedersen, James Kench, Roger J Daly, Lisa G Horvath, Phillip Stricker, Mark Frydenberg, Renea A Taylor, Clare Stirzaker, Gail P Risbridger, Susan J Clark
The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs)...
April 12, 2018: Genome Research
https://www.readbyqxmd.com/read/29650458/matching-algorithms-for-assigning-orthologs-after-genome-duplication-events
#16
Guillaume Fertin, Falk Hüffner, Christian Komusiewicz, Manuel Sorge
In this paper, we introduce and analyze two graph-based models for assigning orthologs in the presence of whole-genome duplications, using similarity information between pairs of genes. The common feature of our two models is that genes of the first genome may be assigned two orthologs from the second genome, which has undergone a whole-genome duplication. Additionally, our models incorporate the new notion of duplication bonus, a parameter that reflects how assigning two orthologs to a given gene should be rewarded or penalized...
March 14, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29649963/whole-genome-sequence-of-the-orchid-anthracnose-pathogen-colletotrichum-orchidophilum
#17
Riccardo Baroncelli, Serenella Sukno, Sabrina Sarrocco, Giovanni Cafà, Gaetan Le Floch, Michael R Thon
Colletotrichum orchidophilum is a plant pathogenic fungus infecting a wide range of plant species belonging to the family Orchidaceae. Besides its economic impact, C. orchidophilum has been used in recent years in evolutionary studies as it represents the closest related species to the C. acutatum species complex. Here we present the first draft whole-genome sequence of C. orchidophilum IMI 309357, providing a resource for future research on anthracnose of Orchidaceae and other hosts.
April 12, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29649618/preimplantation-high-resolution-hla-sequencing-using-next-generation-sequencing
#18
Maryam Rafati, Mohammad Mahdi Akhondi, Mohammad Reza Sadeghi, Seyedeh Zahra Tara, Saeed Reza Ghaffari
Hematopoietic Stem Cell Transplantation (HSCT) is the only therapeutic option in a number of heritable hematologic disorders as well as hematologic cancers. Many parents and families fail to find an HLA-identical donor for their affected family member. In such cases, conceiving for a savior baby remains the only option especially in countries without access to national registries. By means of Next Generation Sequencing (NGS) techniques, in a single experiment on single cell products of IVF, a healthy HLA-identical embryo can be implanted in the uterus of a concerned mother...
April 9, 2018: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/29649616/subgenome-assignment-in-allopolyploids-challenges-and-future-directions
#19
REVIEW
Patrick P Edger, Michael R McKain, Kevin A Bird, Robert VanBuren
Whole genome duplications (WGDs), also known as polyploid events, have played a crucial role in the evolutionary success of angiosperms across recent and ancient timescales. A recurrent observation from the analysis of allopolyploids is that one of the parental subgenomes is generally more dominant, referred to as 'subgenome dominance', based on higher gene content and expression patterns. Subgenome dominance has far reaching implications to research areas ranging from crop improvement efforts to evolutionary and ecological studies...
April 9, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29649588/characterization-of-oxa-258-enzymes-and-axyabm-efflux-pump-from-achromobacter-ruhlandii
#20
Mariana Papalia, Germán Traglia, Melina Ruggiero, Marisa Almuzara, Carlos Vay, Gabriel Gutkind, Soledad María Ramírez, Marcela Radice
OBJECTIVES: The aim of this study was to characterize OXA-258 variants and other features that may contribute to the carbapenem resistant in Achromobacter ruhlandii. METHODS: Kinetic parameters for purified OXA-258a and OXA-258b were determined measuring the rate of hydrolysis of a representative group of antibiotics. Whole-genome shotgun sequencing was performed on A. ruhlandii 38 (producing OXA-258a) and A. ruhlandii 319 (producing OXA-258b) and in silico analysis of antimicrobial resistant determinants was conducted...
April 9, 2018: Journal of Global Antimicrobial Resistance
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