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https://www.readbyqxmd.com/read/29149178/drivers-of-genetic-diversity-in-secondary-metabolic-gene-clusters-within-a-fungal-species
#1
Abigail L Lind, Jennifer H Wisecaver, Catarina Lameiras, Philipp Wiemann, Jonathan M Palmer, Nancy P Keller, Fernando Rodrigues, Gustavo H Goldman, Antonis Rokas
Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence...
November 17, 2017: PLoS Biology
https://www.readbyqxmd.com/read/29148374/pathogenic-elizabethkingia-miricola-infection-in-cultured-black-spotted-frogs-china-2016
#2
Ruixue Hu, Junfa Yuan, Yin Meng, Zhe Wang, Zemao Gu
Multiregional outbreaks of meningitis-like disease caused by Elizabethkingia miricola were confirmed in black-spotted frog farms in China in 2016. Whole-genome sequencing revealed that this amphibian E. miricola strain is closely related to human clinical isolates. Our findings indicate that E. miricola can be epizootic and may pose a threat to humans.
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29147625/a-transcriptomic-insight-into-the-impacts-of-mast-cells-in-lung-breast-and-colon-cancers
#3
Eun-A Ko, Kenton M Sanders, Tong Zhou
To date, the exact impact of mast cells in tumor microenvironment is still controversial because of inconsistency in observations regarding the relationship between mast cell infiltrates and cancer development and prognosis. The discrepancies in previous studies have motivated us to examine the roles of mast cells in cancer pathology from different perspectives. Here, we investigated the impact of mast cells on transcriptomic profiles in the tissue microenvironment. Mice carrying the W-sh mutation in c-kit (Kit(W-sh) ) are deficient in mast cell production and were used to assess the influence of mast cells on gene expression...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29146476/mutation-screening-of-the-glis3-gene-in-a-cohort-of-592-chinese-patients-with-congenital-hypothyroidism
#4
Chunyun Fu, Shiyu Luo, Xigui Long, Yingfeng Li, Shangyang She, Xuehua Hu, Meizhen Mo, Zhanghong Wang, Yuhua Chen, Chun He, Jiasun Su, Yue Zhang, Fei Lin, Bobo Xie, Qifei Li, Shaoke Chen
OBJECTIVES: Defects in the human GLI-similar 3 (GLIS3) gene are reported to be a rare cause of congenital hypothyroidism (CH) and neonatal diabetes. The aim of this study was to examine the prevalence of GLIS3 mutation among CH patients in the Guangxi Zhuang Autonomous Region of China and to define the relationships between GLIS3 genotypes and clinical phenotypes. METHODS: Blood samples were collected from 592 patients with CH in Guangxi Zhuang Autonomous Region, China, and genomic DNA was extracted from peripheral blood leukocytes...
November 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29145861/hybrid-de-novo-genome-assembly-and-centromere-characterization-of-the-gray-mouse-lemur-microcebus-murinus
#5
Peter A Larsen, R Alan Harris, Yue Liu, Shwetha C Murali, C Ryan Campbell, Adam D Brown, Beth A Sullivan, Jennifer Shelton, Susan J Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C Durand, Muhammad S Shamim, Erez Lieberman Aiden, Donna M Muzny, Richard A Gibbs, Anne D Yoder, Jeffrey Rogers, Kim C Worley
BACKGROUND: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29145783/ntp-niehs-global-contributions-to-toxicologic-pathology
#6
Robert Sills, Amy Brix, Mark Cesta, Sheba R Churchill, Michelle C Cora, Darlene Dixon, Michael Dykstra, Gordon Flake, Ron Herbert, Ramesh Kovi, Kyathanahalli Janardhan, Angela King-Herbert, David Malarkey, Arun Pandiri, Greg Travlos, Cynthia Willson, Susan A Elmore
National Toxicology Program (NTP) pathologists are engaged in important initiatives that have significant global impact. These initiatives build on its leadership in pathology peer review and publications in the areas of toxicologic pathology, clinical pathology, and laboratory animal medicine. Over the past decade, NTP/National Institute of Environmental Health Sciences research initiatives have focused on cancer and noncancer hazard identification, with the goal of understanding cellular and molecular mechanisms of disease...
January 1, 2017: Toxicologic Pathology
https://www.readbyqxmd.com/read/29145608/medreaders-a-database-for-transcription-factors-that-bind-to-methylated-dna
#7
Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29144536/isolation-and-whole-genome-sequencing-of-fetal-cells-from-maternal-blood-towards-the-ultimate-non-invasive-prenatal-testing
#8
Fang Chen, Ping Liu, Ying Gu, Zhu Zhu, Amulya Nanisetti, Zhangzhang Lan, Zhiwei Huang, Sophie Jia Liu, Xiongbin Kang, Yuqing Deng, Liqiong Luo, Dan Jiang, Yong Qiu, Jianchang Pan, Jun Xia, Ken Xiong, Chao Liu, Lin Xie, Qianyu Shi, Jing Li, Xiuqing Zhang, Wei Wang, Snezana Drmanac, Hui Jiang, Radoje Drmanac, Xun Xu
OBJECTIVE: To develop a methodology of isolating fetal cells from maternal blood and use deep sequencing demonstrating the promise for more complete and accurate genetic screening compared to other non-invasive prenatal testing (NIPT). METHODS: Here in this study, we developed a double negative selection (DNS) procedure to unbiasedly enrich fetal cells. After validated by short tandem repeat (STR), the isolated CFCs were subjected to deep whole genome sequencing analysis (WGS)...
November 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29143419/long-non-coding-rna-rp11-380d23-2-drives-distal-proximal-patterning-of-the-lung-by-regulating-pitx2-expression
#9
Poulomi Banerjee, Harshini Surendran, Kapil Bharti, Kaoru Morishita, Anurag Varshney, Rajarshi Pal
Early lung development is a tightly orchestrated process encompassing (a) formation of definitive endoderm, (b) anteriorization of definitive endoderm followed by (c) specification and maturation of both proximal and distal lung precursors. Several reports detailing the interaction of genes and proteins during lung development are available; however, studies reporting the role(s) of long non-coding RNAs (lncRNA) in lung morphogenesis are limited. To investigate this, we tailored a protocol for differentiation of human induced pluripotent stem cells into distal and proximal lung progenitors to mimic in vivo lung development...
November 16, 2017: Stem Cells
https://www.readbyqxmd.com/read/29142125/emergence-of-double-and-triple-gene-reassortant-g1p-8-rotaviruses-possessing-a-ds-1-like-backbone-post-rotavirus-vaccine-introduction-in-malawi
#10
Khuzwayo C Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E Tate, Umesh D Parashar, Robert S Heyderman, Neil French, Nigel A Cunliffe, Iturriza-Gomara Miren
To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunisation programmes. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix™) into its immunisation schedule in 2012. Utilising a surveillance platform of hospitalised rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 - 2012) and after (2013 - 2014) vaccine introduction. Analysis of whole genomes obtained through next generation sequencing revealed that all randomly-selected pre-vaccine G1P[8] strains sequenced (n=32) possessed a Wa-like genetic constellation, whereas post-vaccine G1P[8] strains (n=18) had a DS-1-like constellation...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#11
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29134693/microglia-from-offspring-of-dams-with-allergic-asthma-exhibit-epigenomic-alterations-in-genes-dysregulated-in-autism
#12
Annie Vogel Ciernia, Milo Careaga, Janine M LaSalle, Paul Ashwood
Dysregulation in immune responses during pregnancy increases the risk of a having a child with an autism spectrum disorder (ASD). Asthma is one of the most common chronic diseases among pregnant women, and symptoms often worsen during pregnancy. We recently developed a mouse model of maternal allergic asthma (MAA) that induces changes in sociability, repetitive, and perseverative behaviors in the offspring. Since epigenetic changes help a static genome adapt to the maternal environment, activation of the immune system may epigenetically alter fetal microglia, the brain's resident immune cells...
November 14, 2017: Glia
https://www.readbyqxmd.com/read/29133946/whole-genomic-analysis-of-two-potential-recombinant-strains-within-human-mastadenovirus-species-c-previously-found-in-beijing-china
#13
Naiying Mao, Zhen Zhu, Pierre Rivailler, Meng Chen, Qin Fan, Fang Huang, Wenbo Xu
Human mastadenovirus species C (HAdV-C) are the most common etiologic agents of respiratory disease in young children and are frequently detected worldwide including China. Two recombinant HAdV-C strains (BJ04 and BJ09) were isolated from infants with acute respiratory infection (ARI) in Beijing in 2012-2013. The whole genome sequences (WGS) of BJ04 and BJ09 were generated and compared to other 35 HAdV-C WGSs publicly available. Phylogenetic analyses showed that the BJ04 strain might be the result of three homologous recombination events involving the parental strains JX173086 (HAdV-1), NC_001405 (HAdV-2) and LC068718 (HAdV-6), whereas BJ09 viral genome might be made of genetic elements from JX173083 (HAdV-1), KF268199 (HAdV-5), and KR699642 (strain CBJ113)...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29129848/significance-of-functional-disease-causal-susceptible-variants-identified-by-whole-genome-analyses-for-the-understanding-of-human-diseases
#14
Yuki Hitomi, Katsushi Tokunaga
Human genome variation may cause differences in traits and disease risks. Disease-causal/susceptible genes and variants for both common and rare diseases can be detected by comprehensive whole-genome analyses, such as whole-genome sequencing (WGS), using next-generation sequencing (NGS) technology and genome-wide association studies (GWAS). Here, in addition to the application of an NGS as a whole-genome analysis method, we summarize approaches for the identification of functional disease-causal/susceptible variants from abundant genetic variants in the human genome and methods for evaluating their functional effects in human diseases, using an NGS and in silico and in vitro functional analyses...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/29128545/massive-parallel-sequencing-of-mitochondrial-dna-genomes-from-mother-child-pairs-using-the-ion-torrent-personal-genome-machine-pgm
#15
Ke Ma, Xueying Zhao, Hui Li, Yu Cao, Wei Li, Jian Ouyang, Lu Xie, Wenbin Liu
Mitochondrial genome analysis is a potent tool in forensic practice and in the understanding of human phylogeny in the maternal lineage. With the development of molecular biology and bioinformatics techniques, high-throughput sequencing has enabled mtDNA analysis during whole genome sequencing, which provides more comprehensive information and raises the power of discrimination. In this study, peripheral blood samples were taken from 194 mother-offspring pairs and sequenced by Ion Torrent Personal Genome Machine and obtained high-coverage mitochondrial sequencing data, demonstrating the mutation levels at each position in the mitochondrial DNA (mtDNA) between maternally related pairs...
November 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29127343/global-phylogenetic-analysis-of-escherichia-coli-and-plasmids-carrying-the-mcr-1-gene-indicates-bacterial-diversity-but-plasmid-restriction
#16
Sébastien Matamoros, Jarne M van Hattem, Maris S Arcilla, Niels Willemse, Damian C Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D de Jong, Constance Schultsz
To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126393/genomic-characterisation-of-clinical-and-environmental-pseudomonas-putida-group-strains-and-determination-of-their-role-in-the-transfer-of-antimicrobial-resistance-genes-to-pseudomonas-aeruginosa
#17
Silke Peter, Philipp Oberhettinger, Leonard Schuele, Ariane Dinkelacker, Wichard Vogel, Daniela Dörfel, Daniela Bezdan, Stephan Ossowski, Matthias Marschal, Jan Liese, Matthias Willmann
BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that P. putida functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between P...
November 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29126233/endothelin-1-promotes-human-germinal-vesicle-stage-oocyte-maturation-by-downregulating-connexin-26-expression-in-cumulus-cells
#18
Long Cui, Jiajie Shen, Li Fang, Xiaodan Mao, Hanzhi Wang, Yinghui Ye
STUDY QUESTION: Does endothelin-1 (ET-1) promote human oocyte maturation and by what mechanism? SUMMARY ANSWER: Addition of ET-1 to the medium in which human germinal vesicle (GV)-stage immature oocytes are cultured enhances the GV breakdown (GVBD) rate; the resumption of meiosis may be initiated by ET-1 downregulating the expression of connexin-26 (Cx26) in cumulus cells via endothelin receptor type B (ETRB), leading to decreased cAMP levels in the oocyte. WHAT IS KNOWN ALREADY: The paracrine factor ET-1 is secreted by ovarian somatic cells in pre-ovulatory follicles and regulates oocyte maturation in mice...
November 8, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29126206/the-incidence-and-origin-of-segmental-aneuploidy-in-human-oocytes-and-preimplantation-embryos
#19
D Babariya, E Fragouli, S Alfarawati, K Spath, D Wells
STUDY QUESTION: What is the incidence, origin and clinical significance of segmental aneuploidy in human oocytes and preimplantation embryos? SUMMARY ANSWER: Segmental aneuploidy occurs at a considerable frequency in preimplantation embryos with a majority being mitotic in origin. WHAT IS KNOWN ALREADY: In recent years, accurate techniques for the detection of aneuploidy in single cells have been developed. Research using such methods has confirmed that aneuploidy is a common feature of human oocytes and preimplantation embryos...
November 8, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29125517/genetic-epidemiology-of-neural-tube-defects
#20
Philip J Lupo, A J Agopian, Heidi Castillo, Jonathan Castillo, Gerald H Clayton, Nienke P Dosa, Betsy Hopson, David B Joseph, Brandon G Rocque, William O Walker, John S Wiener, Laura E Mitchell
It has been estimated that 60-70% of neural tube defects (NTDs) have a genetic component, but few causative genes have been identified. The lack of information on genes associated with non-syndromic NTDs in humans is especially notable as the "genomic revolution" has led to new tools (e.g., genome-wide genotyping arrays, next-generation sequencing) that are helping to elucidate the full spectrum of genetic variation (from common to rare) contributing to complex traits, including structural birth defects. However, the application of modern genomic approaches to the study of NTDs has lagged behind that of some other common structural birth defects...
October 20, 2017: Journal of Pediatric Rehabilitation Medicine
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