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https://www.readbyqxmd.com/read/29453967/discovery-of-anti-viral-molecules-and-their-vital-functions-in-bombyx-mori
#1
REVIEW
Peng Lü, Ye Pan, Yanhua Yang, Feifei Zhu, Chengjun Li, Qin Yao, Keping Chen
The silkworm Bombyx mori (B. mori), a lepidopteran model organism, has become an important model for molecular biology researches with its genome completely sequenced. Silkworms confront different types of virus diseases, mainly including those caused by Bombyx mori nucleopolyhedrovirus (BmNPV), Bombyx mori densovirus type 1 (BmDNV-1), Bombyx mori bidesovirus (BmBDV) which was termed as Bombyx mori densovirus type 2 (BmDNV-2) or Bombyx mori parvo-like virus (BmPLV) before in sericulture. B. mori offers excellent models to study the molecular mechanisms of insect innate immune responses to viruses...
February 14, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29450149/human-and-mouse-microarrays-guided-expression-analysis-of-membrane-protein-trafficking-related-genes-in-mdck-cells-a-canine-epithelial-model-for-apical-and-basolateral-differential-protein-targeting
#2
Xiaofan Xu, Mingming Pan, Alexis E Gasiewicz, Rongzi Li, Shiu-Ming Kuo
MDCK cells are widely used to study the differential targeting of membrane transporters to apical and basolateral membrane but its canine origin limited the commercial tools available for the analysis of protein trafficking machinery. Because apical and basolateral membranes are only found in differentiated epithelial cells, genes critical for differential targeting may be specifically up-regulated upon MDCK cell differentiation. To search for these genes, a cross-species screening strategy was used. We first analyzed the human microarray data for protein trafficking-related genes that were up-regulated in colon carcinoma Caco2 cells upon differentiation...
June 2017: Biochimie Open
https://www.readbyqxmd.com/read/29447209/haplotype-based-genome-wide-association-study-identifies-loci-and-candidate-genes-for-milk-yield-in-holsteins
#3
Zhenliang Chen, Yunqiu Yao, Peipei Ma, Qishan Wang, Yuchun Pan
Since milk yield is a highly important economic trait in dairy cattle, the genome-wide association study (GWAS) is vital to explain the genetic architecture underlying milk yield and to perform marker-assisted selection (MAS). In this study, we adopted a haplotype-based empirical Bayesian GWAS to identify the loci and candidate genes for milk yield. A total of 1 092 Holstein cows were sequenced by using the genotyping by genome reducing and sequencing (GGRS) method. After filtering, 164 312 high-confidence SNPs and 13 476 haplotype blocks were identified to use for GWAS...
2018: PloS One
https://www.readbyqxmd.com/read/29445424/promoter-methylation-of-dna-damage-repair-ddr-genes-in-human-tumor-entities-rbbp8-ctip-is-almost-exclusively-methylated-in-bladder-cancer
#4
Jolein Mijnes, Jürgen Veeck, Nadine T Gaisa, Eduard Burghardt, Tim C de Ruijter, Sonja Gostek, Edgar Dahl, David Pfister, Sebastian C Schmid, Ruth Knüchel, Michael Rose
Background: Genome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers. Methods: Genome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29445130/comparative-genomic-inference-suggests-mixotrophic-lifestyle-for-thorarchaeota
#5
Yang Liu, Zhichao Zhou, Jie Pan, Brett J Baker, Ji-Dong Gu, Meng Li
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate...
February 14, 2018: ISME Journal
https://www.readbyqxmd.com/read/29441193/insights-into-the-roles-of-lncrnas-in-skeletal-and-dental-diseases
#6
REVIEW
Yuyu Li, Jiawei Zhang, Jie Pan, Xu Feng, Peipei Duan, Xing Yin, Yang Xu, Xin Wang, Shujuan Zou
Long noncoding RNAs (lncRNAs) are a class of non-protein-coding transcripts with the length longer than 200 nucleotides. Growing evidence suggests that lncRNAs, which were initially thought to be merely transcriptional "noise", participate in a wide repertoire of biological processes. It has been well established that lncRNAs not only play important roles in genomic regulation, transcription, posttranscriptional processes but are also implicated in the pathogenesis of human diseases including cardiovascular diseases, diabetes, neurodegenerative disorders, and cancer...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29440296/pim-kinases-are-a-potential-prognostic-biomarker-and-therapeutic-target-in-neuroblastoma
#7
Diede Brunen, Romy C de Vries, Cor Lieftink, Roderick L Beijersbergen, Rene Bernards
The majority of high-risk neuroblastoma patients are refractory to, or relapse on current treatment regimens, resulting in 5-year survival rates of less than 50%. This emphasizes the urgent need to identify novel therapeutic targets. Here, we report that high PIM kinase expression is correlated with poor overall survival. Treatment of neuroblastoma cell lines with the pan-PIM inhibitors AZD1208 or PIM-447 suppressed proliferation through inhibition of mTOR signaling. In a panel of neuroblastoma cell lines, we observed a marked binary response to PIM inhibition, suggesting that specific genetic lesions control responses to PIM inhibition...
February 13, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29440175/pan-cancer-molecular-classes-transcending-tumor-lineage-across-32-cancer-types-multiple-data-platforms-and-over-10-000-cases
#8
Chad J Creighton, Fengju Chen, Yiqun Zhang, Don L Gibbons, Benjamin Deneen, David Kwiatkowski, Michael Ittmann
PURPOSE: The Cancer Genome Atlas data resources represent an opportunity to explore commonalities across cancer types involving multiple molecular levels, but tumor lineage and histology can represent a barrier in moving beyond differences related to cancer type. EXPERIMENTAL DESIGN: On the basis of gene expression data, we classified 10224 cancers, representing 32 major types, into ten molecular-based "classes."  Molecular patterns representing tissue or histologic dominant effects were first removed computationally, with the resulting classes representing emergent themes across tumor lineages...
February 9, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29439659/validation-of-genotype-imputation-in-southeast-asian-populations-and-the-effect-of-single-nucleotide-polymorphism-annotation-on-imputation-outcome
#9
Worachart Lert-Itthiporn, Bhoom Suktitipat, Harald Grove, Anavaj Sakuntabhai, Prida Malasit, Nattaya Tangthawornchaikul, Fumihiko Matsuda, Prapat Suriyaphol
BACKGROUND: Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined. METHODS: This study was divided into two parts. In the first part, we applied imputation to genotyped SNPs from Southeast Asian populations from the Pan-Asian SNP database...
February 13, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29439654/prospective-study-on-human-fecal-carriage-of-enterobacteriaceae-possessing-mcr-1-and-mcr-2-genes-in-a-regional-hospital-in-hong-kong
#10
Wai-Sing Chan, Chun-Hang Au, Dona N Ho, Tsun-Leung Chan, Edmond Shiu-Kwan Ma, Bone Siu-Fai Tang
BACKGROUND: Human fecal carriage of Enterobacteriaceae possessing mobilized colistin resistance genes (mcr-1 and mcr-2) remains obscure in Hong Kong. As part of routine surveillance on emerging antibiotic resistance, we conducted a prospective study on this topic in a regional hospital in Hong Kong. METHODS: From October 31 to November 25, 2016, all fecal specimens submitted for routine analysis were included in this surveillance study. These comprised 672 consecutive routine fecal specimens collected from 616 individuals...
February 13, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29438172/gastric-carcinomas-with-lymphoid-stroma-an-evaluation-of-the-histopathologic-and-molecular-features
#11
Erika Hissong, Girish Ramrattan, Pan Zhang, Xi Kathy Zhou, Gloria Young, David S Klimstra, Jinru Shia, Helen Fernandes, Rhonda K Yantiss
Gastric carcinoma with lymphoid stroma is an uncommon variant enriched for mutually exclusive Epstein-Barr virus (EBV) positivity and mismatch repair (MMR) deficiency. We performed this study to evaluate molecular alterations in this morphologically homogeneous subtype and compare them with 295 conventional gastric cancers analyzed in The Cancer Genome Atlas study. We identified 31 study cases and subjected them to in situ hybridization for EBV-encoded RNAs and assessment for MMR status. Immunostains for PD-L1, β-catenin, and HER2 were performed; extracted DNA was sequenced with a Comprehensive Cancer Panel...
February 12, 2018: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29437112/whole-genome-sequence-of-human-rhinovirus-c47-isolated-from-an-adult-respiratory-illness-outbreak-in-butte-county-california-2017
#12
Chao-Yang Pan, Tasha Padilla, Shigeo Yagi, Linda S Lewis, Terry Fei Fan Ng, Rachel L Marine, William Allan Nix, Debra A Wadford
Here, we report the full coding sequence of rhinovirus C47 (RV-C47), obtained from a patient respiratory sample collected during an acute respiratory illness investigation in Butte County, California, in January 2017. This is the first whole-genome sequence of RV-C47 to be reported.
February 1, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29436707/the-molecular-pathology-of-cancer-from-pan-genomics-to-post-genomics
#13
REVIEW
David G Huntsman, Marc Ladanyi
As the cancer genomics of most major cancer types have been comprehensively catalogued over the past decade through a variety of national and international efforts, the delineation of cancer subtypes has been refined, and our understanding of critical cancer drivers and of the potentially targetable vulnerabilities they create has grown tremendously. The 2018 Annual Review Issue of The Journal of Pathology provides in-depth assessments of how these pan-genomic approaches have enabled advances in cancer classification, targeted therapy selection, and assessment of cancer progression, all of which are now genomically informed, using several cancer types as examples...
February 13, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29433445/comparative-genomic-analysis-reveals-the-evolution-and-environmental-adaptation-strategies-of-vibrios
#14
Heyu Lin, Min Yu, Xiaolei Wang, Xiao-Hua Zhang
BACKGROUND: Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29429564/genomic-comparison-between-members-of-the-salinibacteraceae-family-and-description-of-a-new-species-of-salinibacter-salinibacter-altiplanensis-sp-nov-isolated-from-high-altitude-hypersaline-environments-of-the-argentinian-altiplano
#15
Tomeu Viver, Luis Orellana, Pedro González-Torres, Sara Díaz, Mercedes Urdiain, María Eugenia Farías, Vladimir Benes, Peter Kaempfer, Azadeh Shahinpei, Mohammad Ali Amoozegar, Rudolf Amann, Josefa Antón, Konstantinos T Konstantinidis, Ramon Rosselló-Móra
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability...
January 31, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29427635/a-vibrio-owensii-strain-as-the-causative-agent-of-ahpnd-in-cultured-shrimp-litopenaeus-vannamei
#16
Liyuan Liu, Jinzhou Xiao, Mengmeng Zhang, Wanyu Zhu, Xiaoming Xia, Xilin Dai, Yingjie Pan, Shuling Yan, Yongjie Wang
The causative agent of shrimp AHPND was identified as specific Vibrio parahaemolyticus strains, which harbor a virulent plasmid that contains the toxic genes pirA and B (pirAB). Herein, a Vibrio bacterium was isolated from shrimp in Shanghai. This bacterium was identified as Vibrio owensii using 16S rRNA gene phylogeny, whole genome sequencing and comparative analysis. The V. owensii cells are rod-shape (1.86 ± 0.15 µm) with a single polar flagellum (4 µm). In addition, V. owensii form mauve colonies with jagged edges on CHROMagar plates...
February 7, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29426915/reference-gene-selection-for-rt-qpcr-analysis-in-harmonia-axyridis-a-global-invasive-lady-beetle
#17
Xiaowei Yang, Huipeng Pan, Ling Yuan, Xuguo Zhou
Harmonia axyridis is a voracious predator, a biological control agent, and one of the world most invasive insect species. The advent of next-generation sequencing platforms has propelled entomological research into the genomics and post-genomics era. Real-time quantitative PCR (RT-qPCR), a primary tool for gene expression analysis, is a core technique governs the genomic research. The selection of internal reference genes, however, can significantly impact the interpretation of RT-qPCR results. The overall goal of this study is to identify the reference genes in the highly invasive H...
February 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29420738/transcription-associated-mutation-promotes-rna-complexity-in-highly-expressed-genes-a-major-new-source-of-selectable-variation
#18
Shengkai Pan, Michael W Bruford, Yusong Wang, Zhenzhen Lin, Zhongru Gu, Xian Hou, Xuemei Deng, Andrew Dixon, Jennifer A Marshall Graves, Xiangjiang Zhan
Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces tenfold more isoforms than expected from the number of splice junctions in the genome...
February 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29420467/her-kinase-inhibition-in-patients-with-her2-and-her3-mutant-cancers
#19
David M Hyman, Sarina A Piha-Paul, Helen Won, Jordi Rodon, Cristina Saura, Geoffrey I Shapiro, Dejan Juric, David I Quinn, Victor Moreno, Bernard Doger, Ingrid A Mayer, Valentina Boni, Emiliano Calvo, Sherene Loi, Albert C Lockhart, Joseph P Erinjeri, Maurizio Scaltriti, Gary A Ulaner, Juber Patel, Jiabin Tang, Hannah Beer, S Duygu Selcuklu, Aphrothiti J Hanrahan, Nancy Bouvier, Myra Melcer, Rajmohan Murali, Alison M Schram, Lillian M Smyth, Komal Jhaveri, Bob T Li, Alexander Drilon, James J Harding, Gopa Iyer, Barry S Taylor, Michael F Berger, Richard E Cutler, Feng Xu, Anna Butturini, Lisa D Eli, Grace Mann, Cynthia Farrell, Alshad S Lalani, Richard P Bryce, Carlos L Arteaga, Funda Meric-Bernstam, José Baselga, David B Solit
Somatic mutations of ERBB2 and ERBB3 (which encode HER2 and HER3, respectively) are found in a wide range of cancers. Preclinical modelling suggests that a subset of these mutations lead to constitutive HER2 activation, but most remain biologically uncharacterized. Here we define the biological and therapeutic importance of known oncogenic HER2 and HER3 mutations and variants of unknown biological importance by conducting a multi-histology, genomically selected, 'basket' trial using the pan-HER kinase inhibitor neratinib (SUMMIT; clinicaltrials...
February 8, 2018: Nature
https://www.readbyqxmd.com/read/29419860/-performance-of-prenatal-screening-by-non-invasive-cell-free-fetal-dna-testing-for-women-with-various-indications
#20
Bin Zhang, Lingyan Pan, Huiyan Wang, Jianbing Liu, Beiyi Lu, Yingping Chen, Wei Long, Bin Yu
OBJECTIVE To assess the performance of non-invasive prenatal testing (NIPT) based on massive parallel sequencing. METHODS A total of 10 275 maternal blood samples were collected. Fetal chromosomal aneuploides were subjected to low coverage whole genome sequencing. Patients with high risks received further prenatal diagnosis. The outcome of all patients were followed up. RESULTS High-throughput sequencing detected 72 pregnancies with fetal autosomal chromosomal aneuploidy, including 57 cases of trisomy 21, 14 cases of trisomy 18, and 1 case of trisomy 13...
February 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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