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https://www.readbyqxmd.com/read/28732294/soil-bacterial-community-response-to-vegetation-succession-after-fencing-in-the-grassland-of-china
#1
Quanchao Zeng, Shaoshan An, Yang Liu
Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau...
July 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28732215/a-method-for-next-generation-sequencing-of-paired-diagnostic-and-remission-samples-to-detect-mitochondrial-dna-mutations-associated-with-leukemia
#2
Ilaria S Pagani, Chung H Kok, Verity A Saunders, Mark B Van der Hoek, Susan L Heatley, Anthony P Schwarer, Christopher N Hahn, Timothy P Hughes, Deborah L White, David M Ross
Somatic mitochondrial DNA (mtDNA) mutations have been identified in many human cancers, including leukemia. To identify somatic mutations, it is necessary to have a control tissue from the same individual for comparison. When patients with leukemia achieve remission, the remission peripheral blood may be a suitable and easily accessible control tissue, but this approach has not previously been applied to the study of mtDNA mutations. We have developed and validated a next-generation sequencing approach for the identification of leukemia-associated mtDNA mutations in 26 chronic myeloid leukemia patients at diagnosis using either nonhematopoietic or remission blood samples as the control...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28730685/tex15-a-dna-repair-gene-associated-with-prostate-cancer-risk-in-han-chinese
#3
Xiaoling Lin, Zhongzhong Chen, Peng Gao, Zhimei Gao, Haitao Chen, Jun Qi, Fang Liu, Dingwei Ye, Haowen Jiang, Rong Na, Hongjie Yu, Rong Shi, Daru Lu, Siqun Lilly Zheng, Zengnan Mo, Yinghao Sun, Qiang Ding, Jianfeng Xu
BACKGROUND: Both common and rare genetic variants may contribute to risk of developing prostate cancer. Genome-wide association studies (GWASs) have identified ∼100 independent, common variants associated with prostate cancer risk. However, little is known about the association of rare variants (minor allele frequency [MAF] <1%) in the genome with prostate cancer risk. METHODS: A two-stage study was used to test the association of rare, deleterious coding variants, annotated using predictive algorithms, with prostate cancer risk in Chinese men...
July 21, 2017: Prostate
https://www.readbyqxmd.com/read/28730541/increased-sequencing-depth-does-not-increase-captured-diversity-of-arbuscular-mycorrhizal-fungi
#4
Martti Vasar, Reidar Andreson, John Davison, Teele Jairus, Mari Moora, Maido Remm, J P W Young, Martin Zobel, Maarja Öpik
The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing...
July 20, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28730464/genome-wide-association-mapping-of-canopy-wilting-in-diverse-soybean-genotypes
#5
Avjinder S Kaler, Jeffery D Ray, William T Schapaugh, C Andy King, Larry C Purcell
Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and to confirm those loci with previously reported canopy wilting QTLs...
July 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28729889/differential-methylation-at-mhc-in-cd4-t-cells-is-associated-with-multiple-sclerosis-independently-of-hla-drb1
#6
Vicki E Maltby, Rodney A Lea, Katherine A Sanders, Nicole White, Miles C Benton, Rodney J Scott, Jeannette Lechner-Scott
BACKGROUND: Although many genetic variants have been associated with multiple sclerosis (MS) risk, they do not explain all the disease risk and there remains uncertainty as to how these variants contribute to disease. DNA methylation is an epigenetic mechanism that can influence gene expression and has the potential to mediate the effects of environmental factors on MS. In a previous study, we found a differentially methylation region (DMR) at MHC HLA-DRB1 that was associated within relapsing-remitting MS (RRMS) patients in CD4(+) T cells...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28729842/a-gene-based-analysis-of-acoustic-startle-latency
#7
Alicia K Smith, Tanja Jovanovic, Varun Kilaru, Adriana Lori, Lauren Gensler, Samuel S Lee, Seth Davin Norrholm, Nicholas Massa, Bruce Cuthbert, Bekh Bradley, Kerry J Ressler, Erica Duncan
Latency of the acoustic startle response is the time required from the presentation of startling auditory stimulus until the startle response is elicited and provides an index of neural processing speed. Latency is prolonged in subjects with schizophrenia compared to controls in some but not all studies and is 68-90% heritable in baseline startle trials. In order to determine the genetic association with latency as a potential inroad into genetically based vulnerability to psychosis, we conducted a gene-based study of latency followed by an independent replication study of significant gene findings with a single-nucleotide polymorphism (SNP)-based analysis of schizophrenia and control subjects...
2017: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/28729279/complete-genome-sequence-of-an-avian-metapneumovirus-subtype-a-strain-isolated-from-chicken-gallus-gallus-in-brazil
#8
Laís S Rizotto, Guilherme P Scagion, Tereza C Cardoso, Raphael M Simão, Leonardo C Caserta, Julia C Benassi, Lara B Keid, Trícia M F de S Oliveira, Rodrigo M Soares, Clarice W Arns, Steven Van Borm, Helena L Ferreira
We report here the complete genome sequence of an avian metapneumovirus (aMPV) isolated from a tracheal tissue sample of a commercial layer flock. The complete genome sequence of aMPV-A/chicken/Brazil-SP/669/2003 was obtained using MiSeq (Illumina, Inc.) sequencing. Phylogenetic analysis of the complete genome classified the isolate as avian metapneumovirus subtype A.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28729278/high-quality-genome-sequence-of-the-highly-resistant-bacterium-staphylococcus-haemolyticus-isolated-from-a-neonatal-bloodstream-infection
#9
Farideh Hosseinkhani, Mohammad Emaneini, Willem van Leeuwen
Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus, originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28728885/characterization-of-the-neuropeptidome-of-a-southern-ocean-decapod-the-antarctic-shrimp-chorismus-antarcticus-focusing-on-a-new-decapod-itp-like-peptide-belonging-to-the-chh-peptide-family
#10
Jean-Yves Toullec, Erwan Corre, Perrine Mandon, Marcelo Gonzalez-Aravena, Céline Ollivaux, Chi-Ying Lee
As part of the study of the resilience of Antarctic crustaceans to global warming, the shrimp Chorismus antarcticus was subjected to an analysis of global approach using the Next Generation Sequencing Illumina Hi-Seq platform. With this data a detailed study into the principal neuropeptides and neurohormones of this species have been undertaken. Total RNAs from whole animals were enriched with eyestalk extracts to ensure maximum sequencing depth of the different neurohormones and neuropeptides mainly expressed into the X organ-sinus gland complex, which is a major endocrine organ of their synthesis...
July 17, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28728852/for-publication-in-vitro-characteristics-of-an-atlantic-salmon-salmo-salarl-hind-gut-microbial-community-in-relation-to-different-dietary-treatments
#11
Kamarul Zaman Zarkasi, Richard S Taylor, Brett D Glencross, Guy C J Abell, Mark L Tamplin, John P Bowman
In this study, microbial community dynamics were assessed within a simple in vitro model system in order to understand those changes influenced by diet.The abundance and diversity of bacteria were monitored within different treatment slurries inoculated with salmon faecal samples in order to mimic the effects of dietary variables. A total of five complete diets and two ingredients (plant meal)were tested. The total viable counts (TVCs) and sequencing data revealed that there was very clear separation between the complete diets and the plant meal treatments, suggesting a dynamic response by the allochthonous bacteria to the treatments...
July 17, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28728593/high-throughput-sequencing-of-small-rnas-reveals-dynamic-micrornas-expression-of-lipid-metabolism-during-camellia-oleifera-and-c-meiocarpa-seed-natural-drying
#12
Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A El-Kassaby, Hui Chen
BACKGROUND: Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28728166/whole-genome-sequencing-revealed-novel-prognostic-biomarkers-and-promising-targets-for-therapy-of-ovarian-clear-cell-carcinoma
#13
Hiroaki Itamochi, Tetsuro Oishi, Nao Oumi, Satoshi Takeuchi, Kosuke Yoshihara, Mikio Mikami, Nobuo Yaegashi, Yasuhisa Terao, Kazuhiro Takehara, Kimio Ushijima, Hidemichi Watari, Daisuke Aoki, Tadashi Kimura, Toshiaki Nakamura, Yoshihito Yokoyama, Junzo Kigawa, Toru Sugiyama
BACKGROUND: Ovarian clear cell carcinoma (OCCC) is mostly resistant to standard chemotherapy that results in poor patient survival. To understand the genetic background of these tumours, we performed whole-genome sequencing of OCCC tumours. METHODS: Tumour tissue samples and matched blood samples were obtained from 55 Japanese women diagnosed with OCCC. Whole-genome sequencing was performed using the Illumina HiSeq platform according to standard protocols. RESULTS: Alterations to the switch/sucrose non-fermentable (SWI/SNF) subunit, the phosphatidylinositol-3-kinase (PI3K)/Akt signalling pathway, and the receptor tyrosine kinase (RTK)/Ras signalling pathway were found in 51%, 42%, and 29% of OCCC tumours, respectively...
July 20, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#14
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28727728/an-integrative-genomics-approach-identifies-novel-pathways-that-influence-candidaemia-susceptibility
#15
Vasiliki Matzaraki, Mark S Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D Johnson, Marije Oosting, Lude Franke, Sebo Withoff, John R Perfect, Leo A B Joosten, Bart Jan Kullberg, Frank L van de Veerdonk, Iris Jonkers, Yang Li, Cisca Wijmenga, Mihai G Netea, Vinod Kumar
Candidaemia is a bloodstream infection caused by Candida species that primarily affects specific groups of at-risk patients. Because only small candidaemia patient cohorts are available, classical genome wide association cannot be used to identify Candida susceptibility genes. Therefore, we have applied an integrative genomics approach to identify novel susceptibility genes and pathways for candidaemia. Candida-induced transcriptome changes in human primary leukocytes were assessed by RNA sequencing. Genetic susceptibility to candidaemia was assessed using the Illumina immunochip platform for genotyping of a cohort of 217 patients...
2017: PloS One
https://www.readbyqxmd.com/read/28727572/classical-swine-fever-virus-shimen-infection-increases-p53-signaling-to-promote-cell-cycle-arrest-in-porcine-alveolar-macrophages
#16
Pengbo Ning, Congxia Hu, Xuepeng Li, Yulu Zhou, Aoxue Hu, Ya Zhang, Lifang Gao, Cunmei Gong, Kangkang Guo, Xianghan Zhang, Yanming Zhang
Classical swine fever virus (CSFV) replicates in macrophages and causes persistent infection. Despite its role in disastrous economic losses in swine industries, the molecular mechanisms underlying its pathogenesis are poorly understood. The virus evades the neutralizing immune response, subverting the immune system to ensure its own survival and persistence.Our genome-wide analysis of porcine alveolar macrophage transcriptional responses to CSFV Shimen infection using the Solexa/Illumina digital gene expression system revealed that p53 pathway components and cell cycle molecules were differentially regulated during infection compared to controls...
July 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28727052/rapid-communication-subclinical-bovine-respiratory-disease-loci-and-pathogens-associated-with-lung-lesions-in-feedlot-cattle
#17
J N Kiser, T E Lawrence, M Neupane, C M Seabury, J F Taylor, J E Womack, H L Neibergs
Bovine respiratory disease (BRD) is an economically important disease of feedlot cattle that is caused by viral and bacterial pathogen members of the BRD complex. Many cases of subclinical BRD go untreated and are not detected until slaughter, when lung lesions are identified. The objectives of this study were to identify which BRD pathogens were associated with the presence of lung lesions at harvest and to identify genomic loci that were associated with susceptibility to lung lesions as defined by consolidation of the lung and/or the presence of fibrin tissue...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727016/genomewide-association-mapping-and-pathway-analysis-of-meat-tenderness-in-polled-nellore-cattle
#18
L M Castro, G J M Rosa, F B Lopes, L C A Regitano, A J M Rosa, C U Magnabosco
Brazil is one of the world's largest beef exporters, although the product has a low price due to quality issues. The meat exported by Brazil is considered medium and low quality by international buyers, mainly due to lack of tenderness. The predominant Zebu breeds (80% Nellore) are known for producing tougher beef than taurine breeds. Nonetheless, some studies have shown that there is substantial genetic variability for tenderness within the Nellore breed, although it is a difficult trait to improve by conventional selection methods...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28725665/data-on-haplotype-supported-immunoglobulin-germline-gene-inference
#19
Ufuk Kirik, Lennart Greiff, Fredrik Levander, Mats Ohlin
Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725556/de-novo-transcriptome-assembly-for-the-lung-of-the-ornamented-pygmy-frog-microhyla-fissipes
#20
Lusha Liu, Shouhong Wang, Lanying Zhao, Jianping Jiang
Microhyla fissipes, belonging to Neobatrachia, is a new model organism to study developmental biology, adaptive mechanisms from aquatic to terrestrial life, environmental toxicology, and human disease. M. fissipes use of lungs soon after hatching makes it extremely valuable for the study of lung function and development mechanisms. However, our knowledge of genes and pathways associated with lung development in M. fissipes is very limited. In this study, we conducted de novo transcriptome assembly for the lung of M...
September 2017: Genomics Data
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