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https://www.readbyqxmd.com/read/29775788/complete-genome-sequence-of-achromobacter-spanius-type-strain-dsm-23806t-a-pathogen-isolated-from-human-blood
#1
Gengmi Li, Li Yang, Tao Zhang, Xiaojiao Guo, Jian Qin, Yingjiang Cao, Qianhua Yang, Shumei You, Guoliang Yuan, Xianqi Wan, Jing Luo, Zhaoxiang Li, Lei Gao, Ying Liu, Kaifeng Jiang, Jiakui Zheng
OBJECTIVES: Achromobacter spanius is a new described, non-fermenting Gram-negative and coccoid pathogen that isolated from patient blood. In order to investigate the pathogenesis of this strain in genomic level, whole genome sequencing was carried out on this strain. METHODS: In this study, complete genome of the type strain of this species DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: Complete genome of DSM 23806T consists of one circular DNA chromosome of 6,425,783bp with a GC content of 64...
May 15, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29775755/whole-genome-sequencing-and-bioinformatics-analysis-of-two-egyptian-genomes
#2
Mahmoud ElHefnawi, Sungwon Jeon, Youngjune Bhak, Asmaa ElFiky, Ahmed Horaiz, JeHoon Jun, Hyunho Kim, Jong Bhak
We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775428/the-involvement-of-human-monogenic-cardiomyopathy-genes-in-experimental-polygenic-cardiac-hypertrophy
#3
Priscilla R Prestes, Francine Z Marques, Guillermo Lopez-Campos, Paul Lewandowski, Lea M D Delbridge, Fadi J Charchar, Stephen B Harrap
Hypertrophic cardiomyopathy thickens heart muscles reducing functionality and increasing risk of cardiac disease and morbidity. Genetic factors are involved, but their contribution is poorly understood. We used the hypertrophic heart rat (HHR), a unique normotensive polygenic model of cardiac hypertrophy and heart failure to investigate the role of genes associated with monogenic human cardiomyopathy. We selected 42 genes involved in monogenic human cardiomyopathies to study: 1) DNA variants, by sequencing the whole-genome of 13-week old HHR and age-matched normal heart rat (NHR), its genetic control strain; 2) mRNA expression, by targeted RNA-sequencing in left ventricles of HHR and NHR at five ages (2-days old, 4-, 13-, 33- and 50-weeks old) compared to human idiopathic dilated data; and 3) microRNA expression, with rat microRNA microarrays in left ventricles of 2-days old HHR and age-matched NHR...
May 18, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29774212/alkaline-peptone-water-based-enrichment-method-for-mcr-3-from-acute-diarrheic-outpatient-gut-samples
#4
Qiaoling Sun, Yanyan Hu, Hongwei Zhou, Lingbin Shu, Hanyu Wang, Zixian Huang, Rong Zhang
A third plasmid-mediated colistin resistance gene, mcr-3 , is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2 , and mcr-3 using polymerase chain reaction (PCR)-based assays...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29773854/genome-wide-haplotype-association-analysis-of-primary-biliary-cholangitis-risk-in-japanese
#5
Cindy Im, Yadav Sapkota, Wonjong Moon, Minae Kawashima, Minoru Nakamura, Katsushi Tokunaga, Yutaka Yasui
Primary biliary cholangitis (PBC) susceptibility loci have largely been discovered through single SNP association testing. In this study, we report genic haplotype patterns associated with PBC risk genome-wide in two Japanese cohorts. Among the 74 genic PBC risk haplotype candidates we detected with a novel methodological approach in a discovery cohort of 1,937 Japanese, nearly two-thirds were replicated (49 haplotypes, Bonferroni-corrected P < 6.8 × 10-4 ) in an independent Japanese cohort (N = 949)...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773831/dnajc17-is-localized-in-nuclear-speckles-and-interacts-with-splicing-machinery-components
#6
A Pascarella, G Ferrandino, S C Credendino, C Moccia, F D'Angelo, B Miranda, C D'Ambrosio, P Bielli, O Spadaro, M Ceccarelli, A Scaloni, C Sette, M De Felice, G De Vita, E Amendola
DNAJC17 is a heat shock protein (HSP40) family member, identified in mouse as susceptibility gene for congenital hypothyroidism. DNAJC17 knockout mouse embryos die prior to implantation. In humans, germline homozygous mutations in DNAJC17 have been found in syndromic retinal dystrophy patients, while heterozygous mutations represent candidate pathogenic events for myeloproliferative disorders. Despite widespread expression and involvement in human diseases, DNAJC17 function is still poorly understood. Herein, we have investigated its function through high-throughput transcriptomic and proteomic approaches...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773658/detecting-quantifying-and-discriminating-the-mechanism-of-mosaic-chromosomal-aneuploidies-using-mad-seq
#7
Yu Kong, Esther R Berko, Anthony Marckette, Shahina B Maqbool, Claudia A Simões-Pires, David F Kronn, Qian K Ye, Masako Suzuki, Adam Auton, John Greally
Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe the mosaic aneuploidy detection by massively-parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins, and how the MADSEQ analytical approach can be applied to exome or whole genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29772771/a-novel-hepadnavirus-identified-in-an-immunocompromised-domestic-cat-in-australia
#8
Mahdis Aghazadeh, Mang Shi, Vanessa R Barrs, Alicia J McLuckie, Scott A Lindsay, Barbara Jameson, Bronte Hampson, Edward C Holmes, Julia A Beatty
High-throughput transcriptome sequencing allows for the unbiased detection of viruses in host tissues. The application of this technique to immunosuppressed animals facilitates the detection of viruses that might otherwise be excluded or contained in immunocompetent individuals. To identify potential viral pathogens infecting domestic cats we performed high-throughput transcriptome sequencing of tissues from cats infected with feline immunodeficiency virus (FIV). A novel member of the Hepadnaviridae , tentatively named domestic cat hepadnavirus, was discovered in a lymphoma sample and its complete 3187 bp genome characterized...
May 17, 2018: Viruses
https://www.readbyqxmd.com/read/29772399/characterization-of-a-g10p-14-rotavirus-strain-from-a-diarrheic-child-in-thailand-evidence-for-bovine-to-human-zoonotic-transmission
#9
Ratana Tacharoenmuang, Satoshi Komoto, Ratigorn Guntapong, Tomihiko Ide, Phakapun Singchai, Sompong Upachai, Saori Fukuda, Yumika Yoshida, Takayuki Murata, Tetsushi Yoshikawa, Kriangsak Ruchusatsawat, Kazushi Motomura, Naokazu Takeda, Somchai Sangkitporn, Koki Taniguchi
An unusual rotavirus strain, DB2015-066 with the G10P[14] genotype (RVA/Human-wt/THA/dB2015-066/2015/G10P[14]), was detected in a stool sample from a child hospitalized with acute gastroenteritis in Thailand. Here, we sequenced and characterized the full-genome of the strain DB2015-066. On whole genomic analysis, strain DB2015-066 was shown to have a unique genotype constellation: G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The backbone genes of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) are commonly found in rotavirus strains from artiodactyls such as cattle...
May 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29771541/plasmodial-kinase-inhibitors-license-to-cure
#10
Diego Gonzalez Cabrera, André Horatscheck, Colin Rylott Wilson, Gregory S Basarab, Charles J Eyermann, Kelly Chibale
Advances in the genetics, function and stage-specificity of Plasmodium kinases has driven robust efforts to identify targets for the design of antimalarial therapies. Reverse genomics following phenotypic screening against Plasmodia or related parasites has uncovered vulnerable kinase targets including PI4K, PKG and GSK-3, an approach bolstered by access to human disease-directed kinase libraries. Alternatively, screening compound libraries against Plasmodium kinases has successfully led to inhibitors with antiplasmodial activity...
May 17, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29769347/avian-influenza-viruses-in-wild-birds-virus-evolution-in-a-multi-host-ecosystem
#11
Divya Venkatesh, Marjolein J Poen, Theo M Bestebroer, Rachel D Scheuer, Oanh Vuong, Mzia Chkhaidze, Anna Machablishvili, Jimsher Mamuchadze, Levan Ninua, Nadia B Fedorova, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, David E Wentworth, Divya Kriti, Jayeeta Dutta, Harm van Bakel, Anita Puranik, Marek J Slomka, Steve Essen, Ian H Brown, Ron A M Fouchier, Nicola S Lewis
Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter or stage. The Republic of Georgia is located at the intersection of three migratory flyways: Central Asian Flyway, East Asian/East African Flyway and Black Sea/Mediterranean Flyway. For six consecutive years (2010-2016), we collected AIV samples from various duck and gull species that breed, migrate and overwinter in Georgia...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29768498/genomic-variants-in-an-inbred-mouse-model-predict-mania-like-behaviors
#12
Michael C Saul, Sharon A Stevenson, Changjiu Zhao, Terri M Driessen, Brian E Eisinger, Stephen C Gammie
Contemporary rodent models for bipolar disorders split the bipolar spectrum into complimentary behavioral endophenotypes representing mania and depression. Widely accepted mania models typically utilize single gene transgenics or pharmacological manipulations, but inbred rodent strains show great potential as mania models. Their acceptance is often limited by the lack of genotypic data needed to establish construct validity. In this study, we used a unique strategy to inexpensively explore and confirm population allele differences in naturally occurring candidate variants in a manic rodent strain, the Madison (MSN) mouse strain...
2018: PloS One
https://www.readbyqxmd.com/read/29768213/mirnas-that-induce-human-cardiomyocyte-proliferation-converge-on-the-hippo-pathway
#13
Marta Diez-Cuñado, Ke Wei, Paul J Bushway, Mano R Maurya, Ranjan Perera, Shankar Subramaniam, Pilar Ruiz-Lozano, Mark Mercola
Understanding the mechanisms that control human cardiomyocyte proliferation might be applicable to regenerative medicine. We screened a whole genome collection of human miRNAs, identifying 96 to be capable of increasing proliferation (DNA synthesis and cytokinesis) of human iPSC-derived cardiomyocytes. Chemical screening and computational approaches indicated that most of these miRNAs (67) target different components of the Hippo pathway and that their activity depends on the nuclear translocation of the Hippo transcriptional effector YAP...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29765361/biodiversity-of-environmental-leptospira-improving-identification-and-revisiting-the-diagnosis
#14
Roman Thibeaux, Dominique Girault, Emilie Bierque, Marie-Estelle Soupé-Gilbert, Anna Rettinger, Anthony Douyère, Michael Meyer, Gregorio Iraola, Mathieu Picardeau, Cyrille Goarant
Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been a growing interest in understanding the environmental lifestyle of Leptospira . However, Leptospira isolation from complex environmental samples is difficult and time-consuming and few tools are available to identify Leptospira isolates at the species level. Here, we propose a polyphasic isolation and identification scheme, which might prove useful to recover and identify environmental isolates and select those to be submitted to whole-genome sequencing...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29764365/towards-pan-genome-read-alignment-to-improve-variation-calling
#15
Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764212/the-clinical-application-of-single-sperm-based-snp-haplotyping-for-pgd-of-osteogenesis-imperfecta
#16
Linjun Chen, Zhenyu Diao, Zhipeng Xu, Jianjun Zhou, Guijun Yan, Haixiang Sun
Osteogenesis imperfecta (OI) is a genetically heterogeneous disorder, presenting either autosomal dominant, autosomal recessive or X-linked inheritance patterns. The majority of OI cases are autosomal dominant and are caused by heterozygous mutations in either the COL1A1 or COL1A2 gene. In these dominant disorders, allele dropout (ADO) can lead to misdiagnosis in preimplantation genetic diagnosis (PGD). Polymorphic markers linked to the mutated genes have been used to establish haplotypes for identifying ADO and ensuring the accuracy of PGD...
May 15, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29763432/distinctive-types-of-postzygotic-single-nucleotide-mosaicisms-in-healthy-individuals-revealed-by-genome-wide-profiling-of-multiple-organs
#17
August Yue Huang, Xiaoxu Yang, Sheng Wang, Xianing Zheng, Qixi Wu, Adam Yongxin Ye, Liping Wei
Postzygotic single-nucleotide mosaicisms (pSNMs) have been extensively studied in tumors and are known to play critical roles in tumorigenesis. However, the patterns and origin of pSNMs in normal organs of healthy humans remain largely unknown. Using whole-genome sequencing and ultra-deep amplicon re-sequencing, we identified and validated 164 pSNMs from 27 postmortem organ samples obtained from five healthy donors. The mutant allele fractions ranged from 1.0% to 29.7%. Inter- and intra-organ comparison revealed two distinctive types of pSNMs, with about half originating during early embryogenesis (embryonic pSNMs) and the remaining more likely to result from clonal expansion events that had occurred more recently (clonal expansion pSNMs)...
May 15, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29762926/genetic-complexity-of-mitral-valve-prolapse-revealed-by-clinical-and-genetic-evaluation-of-a-large-family
#18
Gloria T Haskell, Brian C Jensen, Cecile Skrzynia, Thelsa Pulikkotil, Christian R Tilley, Yurong Lu, Daniel S Marchuk, Leigh Ann Samsa, Kirk C Wilhelmsen, Ethan Lange, Cam Patterson, James P Evans, Jonathan S Berg
BACKGROUND: A genetic component to familial mitral valve prolapse (MVP) has been proposed for decades. Despite this, very few genes have been linked to MVP. Herein is described a four-generation pedigree with numerous individuals affected with severe MVP, some at strikingly young ages. METHODS: A detailed clinical evaluation performed on all affected family members demonstrated a spectrum of MVP morphologies and associated phenotypes. RESULTS: Linkage analysis failed to identify strong candidate loci, but revealed significant regions, which were investigated further using whole-exome sequencing of one of the severely affected family members...
September 2017: Journal of Heart Valve Disease
https://www.readbyqxmd.com/read/29761890/glucocorticoid-receptor-gene-variants-and-lower-expression-of-nr3c1-are-associated-with-cocaine-use
#19
Andrea B Schote, Kristina Jäger, Sara L Kroll, Matthias Vonmoos, Lea M Hulka, Katrin H Preller, Jobst Meyer, Edna Grünblatt, Boris B Quednow
Animal and cross-sectional human studies suggest that chronic cocaine use is associated with altered responsivity of the hypothalamic-pituitary-adrenal axis to stress. Moreover, increased susceptibility to stress has been proposed as an important factor for development, maintenance and relapse of cocaine addiction. As the glucocorticoid receptor gene (NR3C1) mediates genomic effects of the stress hormone cortisol, we investigated NR3C1 expression and the association of NR3C1 genotypes with cocaine use, addiction and comorbid psychiatric symptoms in 126 chronic cocaine users and 98 stimulant-naïve healthy controls...
May 15, 2018: Addiction Biology
https://www.readbyqxmd.com/read/29755435/analysis-of-phylogenetic-variation-of-stenotrophomonas-maltophilia-reveals-human-specific-branches
#20
Joerg Steinmann, Uwe Mamat, Ebrahim M Abda, Lisa Kirchhoff, Wolfgang R Streit, Ulrich E Schaible, Stefan Niemann, Thomas A Kohl
Stenotrophomonas maltophilia is a non-fermenting Gram-negative bacterium that is ubiquitous in the environment. In humans, this opportunistic multi-drug-resistant pathogen is responsible for a plethora of healthcare-associated infections. Here, we utilized a whole genome sequencing (WGS)-based phylogenomic core single nucleotide polymorphism (SNP) approach to characterize S. maltophilia subgroups, their potential association with human infection, and to detect any possible transmission events. In total, 89 isolates (67 clinical and 22 environmental) from Germany were sequenced...
2018: Frontiers in Microbiology
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