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https://www.readbyqxmd.com/read/29332039/alzheimer-s-disease-rs11767557-variant-regulates-epha1-gene-expression-specifically-in-human-whole-blood
#1
Guiyou Liu, Yan Zhang, Longcai Wang, Jianyong Xu, Xiaoyun Chen, Yunjuan Bao, Yang Hu, Shuilin Jin, Rui Tian, Weiyang Bai, Wenyang Zhou, Tao Wang, Zhifa Han, Jian Zong, Qinghua Jiang
Large-scale genome-wide association studies have reported EPHA1 rs11767557 variant to be associated with Alzheimer's disease (AD) risk in the European population. However, it is still unclear how this variant functionally contributes to the underlying disease pathogenesis. The rs11767557 variant is located approximately 3 kb upstream of EPHA1 gene. We think that rs11767557 may modify the expression of nearby genes such as EPHA1 and further cause AD risk. Until now, the potential association between rs11767557 and the expression of nearby genes has not been reported in previous studies...
2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29331684/reprogramming-neurodegeneration-in-the-big-data-era
#2
REVIEW
Lujia Zhou, Patrik Verstreken
Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331671/the-molecular-characteristics-of-avian-influenza-viruses-h9n2-derived-from-air-samples-in-live-poultry-markets
#3
Yanheng Wu, Jinsi Lin, Shuhuan Yang, Ying Xie, Man Wang, Xueqin Chen, Yayang Zhu, Le Luo, Wuyang Shi
OBJECTIVE: To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. METHODS: Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing...
January 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#4
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29327207/phenotypic-and-functional-characteristics-of-human-schwann-cells-as-revealed-by-cell-based-assays-and-rna-seq
#5
Paula V Monje, David Sant, Gaofeng Wang
This study comprehensively addresses the phenotype, function, and whole transcriptome of primary human and rodent Schwann cells (SCs) and highlights key species-specific features beyond the expected donor variability that account for the differential ability of human SCs to proliferate, differentiate, and interact with axons in vitro. Contrary to rat SCs, human SCs were insensitive to mitogenic factors other than neuregulin and presented phenotypic variants at various stages of differentiation, along with a mixture of proliferating and senescent cells, under optimal growth-promoting conditions...
January 11, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29326229/genomic-understanding-of-an-infectious-brain-disease-from-the-desert
#6
Leandro F Moreno, Abdalla A O Ahmed, Balázs Brankovics, Christina A Cuomo, Steph B J Menken, Saad J Taj-Aldeen, Hani Faidah, J Benjamin Stielow, Marcus de M Teixeira, Francesc X Prenafeta-Boldú, Vania A Vicente, Sybren de Hoog
Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper we describe the whole genome re-sequencing of two Rhinocladiella mackenziei strains from patients in Saudi Arabia and Qatar...
January 11, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29325576/reanalysis-of-chinese-treponema-pallidum-samples-all-chinese-samples-cluster-with-ss14-like-group-of-syphilis-causing-treponemes
#7
Michal Strouhal, Jan Oppelt, Lenka Mikalová, Natasha Arora, Kay Nieselt, Fernando González-Candelas, David Šmajs
OBJECTIVE: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget...
January 11, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29324680/phylogenetic-analysis-and-characterization-of-a-sporadic-isolate-of-equine-influenza-a-h3n8-from-an-unvaccinated-horse-in-2015
#8
Chithra C Sreenivasan, Sunayana S Jandhyala, Sisi Luo, Ben M Hause, Milton Thomas, David E B Knudsen, Pamela Leslie-Steen, Travis Clement, Stephanie E Reedy, Thomas M Chambers, Jane Christopher-Hennings, Eric Nelson, Dan Wang, Radhey S Kaushik, Feng Li
Equine influenza, caused by the H3N8 subtype, is a highly contagious respiratory disease affecting equid populations worldwide and has led to serious epidemics and transboundary pandemics. This study describes the phylogenetic characterization and replication kinetics of recently-isolated H3N8 virus from a nasal swab obtained from a sporadic case of natural infection in an unvaccinated horse from Montana, USA. The nasal swab tested positive for equine influenza by Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR)...
January 11, 2018: Viruses
https://www.readbyqxmd.com/read/29321570/transfer-of-a-bla-ctx-m-1-carrying-plasmid-between-different-escherichia-coli-strains-within-the-human-gut-explored-by-whole-genome-sequencing-analyses
#9
Per Kristian Knudsen, Karianne Wiger Gammelsrud, Kristian Alfsnes, Martin Steinbakk, Tore G Abrahamsen, Fredrik Müller, Jon Bohlin
Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320986/revealing-alzheimer-s-disease-genes-spectrum-in-the-whole-genome-by-machine-learning
#10
Xiaoyan Huang, Hankui Liu, Xinming Li, Liping Guan, Jiankang Li, Laurent Christian Asker M Tellier, Huanming Yang, Jian Wang, Jianguo Zhang
BACKGROUND: Alzheimer's disease (AD) is an important, progressive neurodegenerative disease, with a complex genetic architecture. A key goal of biomedical research is to seek out disease risk genes, and to elucidate the function of these risk genes in the development of disease. For this purpose, expanding the AD-associated gene set is necessary. In past research, the prediction methods for AD related genes has been limited in their exploration of the target genome regions. We here present a genome-wide method for AD candidate genes predictions...
January 10, 2018: BMC Neurology
https://www.readbyqxmd.com/read/29320538/germline-and-somatic-variant-identification-using-bgiseq-500-and-hiseq-x-ten-whole-genome-sequencing
#11
Ann-Marie Patch, Katia Nones, Stephen H Kazakoff, Felicity Newell, Scott Wood, Conrad Leonard, Oliver Holmes, Qinying Xu, Venkateswar Addala, Jenette Creaney, Bruce W Robinson, Shujin Fu, Chunyu Geng, Tong Li, Wenwei Zhang, Xinming Liang, Junhua Rao, Jiahao Wang, Mingyu Tian, Yonggang Zhao, Fei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V Pearson, Nicola Waddell
Technological innovation and increased affordability have contributed to the widespread adoption of genome sequencing technologies in biomedical research. In particular large cancer research consortia have embraced next generation sequencing, and have used the technology to define the somatic mutation landscape of multiple cancer types. These studies have primarily utilised the Illumina HiSeq platforms. In this study we performed whole genome sequencing of three malignant pleural mesothelioma and matched normal samples using a new platform, the BGISEQ-500, and compared the results obtained with Illumina HiSeq X Ten...
2018: PloS One
https://www.readbyqxmd.com/read/29319231/temporal-and-spatial-expression-of-insulin-like-peptide-insl5a-and-insl5b-paralog-genes-during-the-embryogenesis-of-danio-rerio
#12
Massimo Venditti, Aldo Donizetti, Marcella Fiengo, Chiara Fasano, Alessandra Santillo, Francesco Aniello, Sergio Minucci
Relaxin (RLN) and insulin (INSL)-like peptides are member of the INSL/RLN superfamily, which are encoded by seven genes in humans and can activate the G-protein coupled receptor RXFP 1-4. These peptides evolved from a common ancestor, RLN3-like gene. Two rounds of whole genome duplication (WGD) in early vertebrate evolution, together with an additional WGD in the teleost lineage, caused an expansion of RLN genes set in the genome of Danio rerio. In particular, six RLN genes are present: a single copy of rln and insl3 genes, and two paralogs for the rln3 gene (rln3a and rln3b), and the insl5 gene (insl5a and insl5b)...
January 10, 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/29317534/linking-secondary-metabolites-to-gene-clusters-through-genome-sequencing-of-six-diverse-aspergillus-species
#13
Inge Kjærbølling, Tammi C Vesth, Jens C Frisvad, Jane L Nybo, Sebastian Theobald, Alan Kuo, Paul Bowyer, Yudai Matsuda, Stephen Mondo, Ellen K Lyhne, Martin E Kogle, Alicia Clum, Anna Lipzen, Asaf Salamov, Chew Yee Ngan, Chris Daum, Jennifer Chiniquy, Kerrie Barry, Kurt LaButti, Sajeet Haridas, Blake A Simmons, Jon K Magnuson, Uffe H Mortensen, Thomas O Larsen, Igor V Grigoriev, Scott E Baker, Mikael R Andersen
The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29317533/the-social-genome-of-friends-and-schoolmates-in-the-national-longitudinal-study-of-adolescent-to-adult-health
#14
Benjamin W Domingue, Daniel W Belsky, Jason M Fletcher, Dalton Conley, Jason D Boardman, Kathleen Mullan Harris
Humans tend to form social relationships with others who resemble them. Whether this sorting of like with like arises from historical patterns of migration, meso-level social structures in modern society, or individual-level selection of similar peers remains unsettled. Recent research has evaluated the possibility that unobserved genotypes may play an important role in the creation of homophilous relationships. We extend this work by using data from 5,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine genetic similarities among pairs of friends...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29317018/outbreak-of-salmonella-bovismorbificans-associated-with-the-consumption-of-uncooked-ham-products-the-netherlands-2016-to-2017
#15
Diederik Brandwagt, Cees van den Wijngaard, Anna Dolores Tulen, Annemieke Christine Mulder, Agnetha Hofhuis, Rianne Jacobs, Max Heck, Anjo Verbruggen, Hans van den Kerkhof, Ife Slegers-Fitz-James, Lapo Mughini-Gras, Eelco Franz
In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S...
January 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29316495/vdr-and-gc-gene-polymorphisms-modulate-the-risk-of-lumbar-disc-degeneration-in-iran
#16
Sohail Mashayekhi, Alia Saberi, Zivar Salehi, Gelareh Biazar, Roghayeh Mehrdel
OBJECTIVE: Lumbar disc degeneration (LDD) occurs commonly in humans. Vitamin D metabolic and signaling pathway plays a significant role in intervertebral disc degeneration. The aim of this study was to evaluate the influence of the genetic polymorphism in the two key genes of 1,25-(OH)2-D3 pathway, VDR (vitamin D receptor) and GC (group-specific component), in LDD development. PATIENTS AND METHODS: Two single-nucleotide polymorphisms, VDR rs2228570 (FokI) and GC rs7041, were genotyped in 180 patients with LDD and 230 healthy individuals...
December 29, 2017: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/29312578/integrated-analysis-of-chromosome-copy-number-variation-and-gene-expression-in-cervical-carcinoma
#17
Deng Yan, Song Yi, Wang Chi Chiu, Liu Gui Qin, Wong Hoi Kin, Chung Tony Kwok Hung, Han Linxiao, Choy Kwong Wai, Sui Yi, Yang Tao, Tang Tao
Objective: This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Methods: Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K)...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310579/gene-trait-matching-across-the-bifidobacterium-longum-pan-genome-reveals-considerable-diversity-in-carbohydrate-catabolism-among-human-infant-strains
#18
Silvia Arboleya, Francesca Bottacini, Mary O'Connell-Motherway, C Anthony Ryan, R Paul Ross, Douwe van Sinderen, Catherine Stanton
BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29306352/porcine-commensal-escherichia-coli-a-reservoir-for-class-1-integrons-associated-with-is26
#19
Cameron J Reid, Ethan R Wyrsch, Piklu Roy Chowdhury, Tiziana Zingali, Michael Liu, Aaron E Darling, Toni A Chapman, Steven P Djordjevic
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia...
December 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29305654/spontaneous-regression-of-neuroblastoma
#20
REVIEW
Garrett M Brodeur
Neuroblastomas are characterized by heterogeneous clinical behavior, from spontaneous regression or differentiation into a benign ganglioneuroma, to relentless progression despite aggressive, multimodality therapy. Indeed, neuroblastoma is unique among human cancers in terms of its propensity to undergo spontaneous regression. The strongest evidence for this comes from the mass screening studies conducted in Japan, North America and Europe and it is most evident in infants with stage 4S disease. This propensity is associated with a pattern of genomic change characterized by whole chromosome gains rather than segmental chromosome changes but the mechanism(s) underlying spontaneous regression are currently a matter of speculation...
January 5, 2018: Cell and Tissue Research
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