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https://www.readbyqxmd.com/read/28241675/-association-between-single-nucleotide-polymorphismsin-human-heat-shock-protein-70-gene-and-susceptibility-to-noise-induced-hearing-loss
#1
Y H Li, G S Chen, J Jiao, W H Zhou, H Wu, G Z Gu, H L Zhang, Y X Zheng, S F Yu
Objective: To investigate the association between the single nucleotide polymorphisms (SNPs) at rs1043618, rs2075800, and rs2763979 in human heat shock protein 70 (HSP70) gene and susceptibility to noise-induced hearing loss (NIHL) . Methods: A case-control study was performed, and 5 934 workers exposed to noise in an iron and steel plant in Henan, China, who underwent physical examination from 2006 to 2015, were enrolled as study subjects. According to the criteria of binaural average high - frequency (3000, 4000, and 6000 Hz) hearing threshold≥40 dB (HL) and monauralaverage speech-frequency (500, 1000, 2000 Hz) hearing threshold≥26 dB (HL) on the basis of binauralhigh frequency loss measured by pure tone audiometry, as well as the exclusion of NIHL, a total of 286 workers were enrolled as hearing loss group; after the adjustment for sex, type of work, age (difference≤5 years) , and working years of noise exposure (difference ≤2 years) , 286 workers were enrolled as control group...
December 20, 2016: Chinese Journal of Industrial Hygiene and Occupational Diseases
https://www.readbyqxmd.com/read/28241508/accelerators-sparking-innovation-and-transdisciplinary-team-science-in-disparities-research
#2
Carol R Horowitz, Khader Shameer, Janice Gabrilove, Ashish Atreja, Peggy Shepard, Crispin N Goytia, Geoffrey W Smith, Joel Dudley, Rachel Manning, Nina A Bickell, Maida P Galvez
Development and implementation of effective, sustainable, and scalable interventions that advance equity could be propelled by innovative and inclusive partnerships. Readied catalytic frameworks that foster communication, collaboration, a shared vision, and transformative translational research across scientific and non-scientific divides are needed to foster rapid generation of novel solutions to address and ultimately eliminate disparities. To achieve this, we transformed and expanded a community-academic board into a translational science board with members from public, academic and private sectors...
February 23, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28241446/dna-methylation-status-of-pax1-and-znf582-in-esophageal-squamous-cell-carcinoma
#3
Jin Huang, Guo Wang, Jie Tang, Wei Zhuang, Li-Ping Wang, Yu-Ligh Liou, Ying-Zi Liu, Hong-Hao Zhou, Yuan-Shan Zhu
Hypermethylation of specific gene promoters is an important mechanism of carcinogenesis. A high frequency of promoter methylation of PAX1 and ZNF582 genes has been detected in cervical cancer. In the present study, we investigated the methylation status of PAX1 and ZNF582 genes in esophageal squamous cell carcinoma (ESCC) tissues. Tumor and paracancerous tissues were obtained from 14 ESCC patients. Genomic DNA was extracted from both tumor and paracancerous tissues, and the concentration of DNA were determined...
February 22, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28241430/the-importance-of-endophenotypes-to-evaluate-the-relationship-between-genotype-and-external-phenotype
#4
REVIEW
Marinus F W Te Pas, Ole Madsen, Mario P L Calus, Mari A Smits
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment...
February 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28241413/a-cross-species-gene-expression-marker-based-genetic-map-and-qtl-analysis-in-bambara-groundnut
#5
Hui Hui Chai, Wai Kuan Ho, Neil Graham, Sean May, Festo Massawe, Sean Mayes
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip...
February 22, 2017: Genes
https://www.readbyqxmd.com/read/28241310/editing-vegfr2-blocks-vegf-induced-activation-of-akt-and-tube-formation
#6
Xionggao Huang, Guohong Zhou, Wenyi Wu, Gaoen Ma, Patricia A D'Amore, Shizuo Mukai, Hetian Lei
Purpose: Vascular endothelial growth factor receptor 2 (VEGFR2) plays a key role in VEGF-induced angiogenesis. The goal of this project was to test the hypothesis that editing genomic VEGFR2 loci using the technology of clustered regularly interspaced palindromic repeats (CRISPR)-associated DNA endonuclease (Cas)9 in Streptococcus pyogenes (SpCas9) was able to block VEGF-induced activation of Akt and tube formation. Methods: Four 20 nucleotides for synthesizing single-guide RNAs based on human genomic VEGFR2 exon 3 loci were selected and cloned into a lentiCRISPR v2 vector, respectively...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28241173/jak1-genomic-alteration-associated-with-exceptional-response-to-siltuximab-in-cutaneous-castleman-disease
#7
Maulik Patel, Sadakatsu Ikeda, Susan R Pilat, Razelle Kurzrock
Importance: Castleman disease (CD) is an ultrarare, interleukin-6 (IL-6)-driven lymphoproliferative disorder whose underlying molecular alterations are unknown. Siltuximab (anti-IL-6 antibody) is approved for treatment of this disease. To our knowledge, genomic sequencing of CD has not been reported. Objective: To investigate and identify molecular aberration(s) that help explain the exceptional response to siltuximab in a patient with cutaneous CD. Design, Setting, and Participants: This case study examines data from comprehensive genomic profiling (using targeted next-generation sequencing) of tissue from a patient with cutaneous CD who demonstrated an exceptional response to siltuximab treated at a National Cancer Institute-designated Comprehensive Cancer Center...
February 22, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28241139/transcription-control-by-the-enl-yeats-domain-in-acute-leukaemia
#8
Michael A Erb, Thomas G Scott, Bin E Li, Huafeng Xie, Joshiawa Paulk, Hyuk-Soo Seo, Amanda Souza, Justin M Roberts, Shiva Dastjerdi, Dennis L Buckley, Neville E Sanjana, Ophir Shalem, Behnam Nabet, Rhamy Zeid, Nana K Offei-Addo, Sirano Dhe-Paganon, Feng Zhang, Stuart H Orkin, Georg E Winter, James E Bradner
Recurrent chromosomal translocations producing a chimaeric MLL oncogene give rise to a highly aggressive acute leukaemia associated with poor clinical outcome. The preferential involvement of chromatin-associated factors as MLL fusion partners belies a dependency on transcription control. Despite recent progress made in targeting chromatin regulators in cancer, available therapies for this well-characterized disease remain inadequate, prompting the need to identify new targets for therapeutic intervention. Here, using unbiased CRISPR-Cas9 technology to perform a genome-scale loss-of-function screen in an MLL-AF4-positive acute leukaemia cell line, we identify ENL as an unrecognized gene that is specifically required for proliferation in vitro and in vivo...
March 1, 2017: Nature
https://www.readbyqxmd.com/read/28241135/an-atlas-of-human-long-non-coding-rnas-with-accurate-5-ends
#9
Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J L Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A Medvedeva, Alison C Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O Daub, Michiel J L de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters...
March 1, 2017: Nature
https://www.readbyqxmd.com/read/28241097/the-gmfwl1-fw2-2-like-nodulation-gene-encodes-a-plasma-membrane-microdomain-associated-protein
#10
Zhenzhen Qiao, Laurent Brechenmacher, Benjamin Smith, Gregory W Strout, William Mangin, Christopher Taylor, Scott D Russell, Gary Stacey, Marc Libault
The soybean gene GmFWL1 (FW2.2-like1) belongs to a plant-specific family that includes the tomato FW2-2 and the maize CNR1 genes, two regulators of plant development. In soybean, GmFWL1 is specifically expressed in root hair cells in response to rhizobia and in nodules. Silencing of GmFWL1 expression significantly reduced nodule numbers supporting its role during soybean nodulation. While the biological role of GmFWL1 has been described, its molecular function and, more generally, the molecular function of plant FW2...
February 27, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28241077/%C3%AE-amanitin-resistance-in-drosophila-melanogaster-a-genome-wide-association-approach
#11
Chelsea L Mitchell, Catrina E Latuszek, Kara R Vogel, Ian M Greenlund, Rebecca E Hobmeier, Olivia K Ingram, Shannon R Dufek, Jared L Pecore, Felicia R Nip, Zachary J Johnson, Xiaohui Ji, Hairong Wei, Oliver Gailing, Thomas Werner
We investigated the mechanisms of mushroom toxin resistance in the Drosophila Genetic Reference Panel (DGRP) fly lines, using genome-wide association studies (GWAS). While Drosophila melanogaster avoids mushrooms in nature, some lines are surprisingly resistant to α-amanitin-a toxin found solely in mushrooms. This resistance may represent a pre-adaptation, which might enable this species to invade the mushroom niche in the future. Although our previous microarray study had strongly suggested that pesticide-metabolizing detoxification genes confer α-amanitin resistance in a Taiwanese D...
2017: PloS One
https://www.readbyqxmd.com/read/28241071/structure-of-a-pentameric-virion-associated-fiber-with-a-potential-role-in-orsay-virus-entry-to-host-cells
#12
Yanlin Fan, Yusong R Guo, Wang Yuan, Ying Zhou, Matthew V Holt, Tao Wang, Borries Demeler, Nicolas L Young, Weiwei Zhong, Yizhi J Tao
Despite the wide use of Caenorhabditis elegans as a model organism, the first virus naturally infecting this organism was not discovered until six years ago. The Orsay virus and its related nematode viruses have a positive-sense RNA genome, encoding three proteins: CP, RdRP, and a novel δ protein that shares no homology with any other proteins. δ can be expressed either as a free δ or a CP-δ fusion protein by ribosomal frameshift, but the structure and function of both δ and CP-δ remain unknown. Using a combination of electron microscopy, X-ray crystallography, computational and biophysical analyses, here we show that the Orsay δ protein forms a ~420-Å long, pentameric fiber with an N-terminal α-helical bundle, a β-stranded filament in the middle, and a C-terminal head domain...
February 27, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28241056/the-complete-chloroplast-genome-sequences-of-lychnis-wilfordii-and-silene-capitata-and-comparative-analyses-with-other-caryophyllaceae-genomes
#13
Jong-Soo Kang, Byoung Yoon Lee, Myounghai Kwak
The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications...
2017: PloS One
https://www.readbyqxmd.com/read/28241055/autopolyploidy-genome-duplication-preserves-other-ancient-genome-duplications-in-atlantic-salmon-salmo-salar
#14
Kris A Christensen, William S Davidson
Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity...
2017: PloS One
https://www.readbyqxmd.com/read/28241049/expression-of-cd133-and-cd44-in-glioblastoma-stem-cells-correlates-with-cell-proliferation-phenotype-stability-and-intra-tumor-heterogeneity
#15
Daniel V Brown, Gulay Filiz, Paul M Daniel, Frédéric Hollande, Sebastian Dworkin, Stephanie Amiridis, Nicole Kountouri, Wayne Ng, Andrew P Morokoff, Theo Mantamadiotis
Glioblastoma (GBM) is a heterogeneous tumor of the brain with a poor prognosis due to recurrence and drug resistance following therapy. Genome-wide profiling has revealed the existence of distinct GBM molecular subtypes that respond differently to aggressive therapies. Despite this, molecular subtype does not predict recurrence or drug resistance and overall survival is similar across subtypes. One of the key features contributing to tumor recurrence and resistance to therapy is proposed to be an underlying subpopulation of resistant glioma stem cells (GSC)...
2017: PloS One
https://www.readbyqxmd.com/read/28241006/identification-and-validation-of-single-nucleotide-polymorphic-markers-linked-to-ug99-stem-rust-resistance-in-spring-wheat
#16
Long-Xi Yu, Shiaoman Chao, Ravi P Singh, Mark E Sorrells
Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT)...
2017: PloS One
https://www.readbyqxmd.com/read/28240985/a-palb2-interacting-domain-in-rnf168-couples-homologous-recombination-to-dna-break-induced-chromatin-ubiquitylation
#17
Martijn S Luijsterburg, Dimitris Typas, Marie-Christine Caron, Wouter W Wiegant, Diana van den Heuvel, Rick A Boonen, Anthony M Couturier, Leon H Mullenders, Jean-Yves Masson, Haico van Attikum
DNA double-strand breaks (DSB) elicit a ubiquitylation cascade that controls DNA repair pathway choice. This cascade involves the ubiquitylation of histone H2A by the RNF168 ligase and the subsequent recruitment of RIF1, which suppresses homologous recombination (HR) in G1 cells. The RIF1-dependent suppression is relieved in S/G2 cells, allowing PALB2-driven HR to occur. With the inhibitory impact of RIF1 relieved, it remains unclear how RNF168-induced ubiquitylation influences HR. Here, we uncover that RNF168 links the HR machinery to H2A ubiquitylation in S/G2 cells...
February 27, 2017: ELife
https://www.readbyqxmd.com/read/28240958/comparison-of-the-diagnostic-performance-of-bacterial-culture-of-nasopharyngeal-swab-and-bronchoalveolar-lavage-fluid-samples-obtained-from-calves-with-bovine-respiratory-disease
#18
Sarah F Capik, Brad J White, Brian V Lubbers, Michael D Apley, Keith D DeDonder, Robert L Larson, Greg P Harhay, Carol G Chitko-McKown, Dayna M Harhay, Ted S Kalbfleisch, Gennie Schuller, Michael L Clawson
OBJECTIVE To compare predictive values, extent of agreement, and gamithromycin susceptibility between bacterial culture results of nasopharyngeal swab (NPS) and bronchoalveolar lavage fluid (BALF) samples obtained from calves with bovine respiratory disease (BRD). ANIMALS 28 beef calves with clinical BRD. PROCEDURES Pooled bilateral NPS samples and BALF samples were obtained for bacterial culture from calves immediately before and at various times during the 5 days after gamithromycin (6 mg/kg, SC, once) administration...
March 2017: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/28240957/evaluation-of-gene-expression-and-dna-copy-number-profiles-of-adipose-tissue-derived-stromal-cells-and-consecutive-neurosphere-like-cells-generated-from-dogs-with-naturally-occurring-spinal-cord-injury
#19
Ji-Hey Lim, Sehwon Koh, Rachael Thomas, Matthew Breen, Natasha J Olby
OBJECTIVE To evaluate gene expression and DNA copy number in adipose tissue-derived stromal cells (ADSCs) and in ADSC-derived neurosphere-like cell clusters (ADSC-NSCs) generated from tissues of chronically paraplegic dogs. ANIMALS 14 client-owned paraplegic dogs. PROCEDURES Dorsal subcutaneous adipose tissue (< 1 cm(3)) was collected under general anesthesia; ADSCs were isolated and cultured. Third-passage ADSCs were cultured in neural cell induction medium to generate ADSC-NSCs. Relative gene expression of mesenchymal cell surface marker CD90 and neural progenitor marker nestin was assessed in ADSCs and ADSC-NSCs from 3 dogs by quantitative real-time PCR assay; expression of these and various neural lineage genes was evaluated for the same dogs by reverse transcription PCR assay...
March 2017: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/28240912/domain-targeted-metabolomics-delineates-the-heterocycle-assembly-steps-of-colibactin-biosynthesis
#20
Eric Trautman, Alan R Healy, Emilee Shine, Seth B Herzon, Jason M Crawford
Modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) comprise giant multidomain enzymes responsible for the "assembly line" biosynthesis of many genetically-encoded small molecules. Site-directed mutagenesis, protein biochemical, and structural studies have focused on elucidating the catalytic mechanisms of individual multidomain proteins and protein domains within these megasynthases. Probing their functions at the cellular level typically has invoked the complete deletion (or overexpression) of multidomain-encoding genes or combinations of genes and comparing those mutants to a control pathway...
February 27, 2017: Journal of the American Chemical Society
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