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High-Throughput Sequencing

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https://www.readbyqxmd.com/read/28330331/identification-and-quantification-of-novel-rna-isoforms-in-horn-cancer-of-bos-indicus-by-comprehensive-rna-seq
#1
Subhash J Jakhesara, Prakash G Koringa, Neelam M Nathani, Chaitanya G Joshi
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329687/impact-of-dietary-interventions-on-noncoding-rna-networks-and-mrnas-encoding-chromatin-related-factors
#2
Christopher D Green, Yi Huang, Xiaoyang Dou, Liu Yang, Yong Liu, Jing-Dong J Han
Dietary interventions dramatically affect metabolic disease and lifespan in various aging models. Here, we profiled liver microRNA (miRNA), coding, and long non-coding RNA (lncRNA) expression by high-throughput deep sequencing in mice across multiple energy intake and expenditure interventions. Strikingly, three dietary intervention network design patterns were uncovered: (1) lifespan-extending interventions largely repressed the expression of miRNAs, lncRNAs, and transposable elements; (2) protein-coding mRNAs with expression positively correlated with long lifespan are highly targeted by miRNAs; and (3) miRNA-targeting interactions mainly target chromatin-related functions...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328985/construction-and-evaluation-of-a-high-density-snp-array-for-the-pacific-oyster-crassostrea-gigas
#3
Haigang Qi, Kai Song, Chunyan Li, Wei Wang, Busu Li, Li Li, Guofan Zhang
Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology...
2017: PloS One
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#4
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327636/high-throughput-amplicon-sequencing-and-stream-benthic-bacteria-identifying-the-best-taxonomic-level-for-multiple-stressor-research
#5
R K Salis, A Bruder, J J Piggott, T C Summerfield, C D Matthaei
Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity)...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327635/the-evolutionary-and-phylogeographic-history-of-woolly-mammoths-a-comprehensive-mitogenomic-analysis
#6
Dan Chang, Michael Knapp, Jacob Enk, Sebastian Lippold, Martin Kircher, Adrian Lister, Ross D E MacPhee, Christopher Widga, Paul Czechowski, Robert Sommer, Emily Hodges, Nikolaus Stümpel, Ian Barnes, Love Dalén, Anatoly Derevianko, Mietje Germonpré, Alexandra Hillebrand-Voiculescu, Silviu Constantin, Tatyana Kuznetsova, Dick Mol, Thomas Rathgeber, Wilfried Rosendahl, Alexey N Tikhonov, Eske Willerslev, Greg Hannon, Carles Lalueza-Fox, Ulrich Joger, Hendrik Poinar, Michael Hofreiter, Beth Shapiro
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327113/low-cell-number-single-tube-amplification-sta-of-total-rna-revealed-transcriptome-changes-from-pluripotency-to-endothelium
#7
Yi-Hsuan Lee, Ya-Wen Hsueh, Yao-Hung Peng, Kung-Chao Chang, Kuen-Jer Tsai, H Sunny Sun, Ih-Jen Su, Po-Min Chiang
BACKGROUND: In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28326079/differences-in-ureolytic-bacterial-composition-between-the-rumen-digesta-and-rumen-wall-based-on-urec-gene-classification
#8
Di Jin, Shengguo Zhao, Nan Zheng, Dengpan Bu, Yves Beckers, Stuart E Denman, Christopher S McSweeney, Jiaqi Wang
Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen of dairy cows using high-throughput sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28325976/arthropod-and-oligochaete-assemblages-from-grasslands-of-the-southern-kenai-peninsula-alaska
#9
Matthew L Bowser, John M Morton, John Delton Hanson, Dawn R Magness, Mallory Okuly
BACKGROUND: By the end of this century, the potential climate-biome of the southern Kenai Peninsula is forecasted to change from transitional boreal forest to prairie and grasslands, a scenario that may already be playing out in the Caribou Hills region. Here, spruce (Picea × lutzii Little [glauca × sitchensis]) forests were heavily thinned by an outbreak of the spruce bark beetle (Dendroctonus rufipennis (Kirby, 1837)) and replaced by the native but invasive grass species, Calamagrostis canadensis (Michx...
2017: Biodiversity Data Journal
https://www.readbyqxmd.com/read/28325876/comprehensive-and-quantitative-mapping-of-rna-protein-interactions-across-a-transcribed-eukaryotic-genome
#10
Richard She, Anupam K Chakravarty, Curtis J Layton, Lauren M Chircus, Johan O L Andreasson, Nandita Damaraju, Peter L McMahon, Jason D Buenrostro, Daniel F Jarosz, William J Greenleaf
RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28324826/nitrogen-removal-by-the-enhanced-floating-treatment-wetlands-from-the-secondary-effluent
#11
Lei Gao, Weili Zhou, Jungchen Huang, Shengbing He, Yijia Yan, Wenying Zhu, Suqing Wu, Xu Zhang
Three novel floating treatment wetlands, including autotrophic enhanced floating treatment wetland (AEFTW), heterotrophic enhanced floating treatment wetland (HEFTW) and enhanced floating treatment wetland (EFTW) were developed to remove nitrogen from the secondary effluent. Results showed that the analogously excellent nitrogen removal performance was achieved in AEFTW and HEFTW. About 89.4% of the total nitrogen (TN) was removed from AEFTW at a low S/N of 0.9 and 88.5% from HEFTW at a low C/N of 3.5 when the hydraulic retention time (HRT) was 1d in summer...
March 9, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28324256/legacy-effects-of-simulated-short-term-climate-change-on-ammonia-oxidisers-denitrifiers-and-nitrous-oxide-emissions-in-an-acid-soil
#12
Xiaoya Xu, Xiaorui Liu, Yong Li, Yu Ran, Yapeng Liu, Qichun Zhang, Zheng Li, Yan He, Jianming Xu, Hongjie Di
Although the effect of simulated climate change on nitrous oxide (N2O) emissions and on associated microbial communities has been reported, it is not well understood if these effects are short-lived or long-lasting. Here, we conducted a field study to determine the interactive effects of simulated warmer and drier conditions on nitrifier and denitrifier communities and N2O emissions in an acidic soil and the longevity of the effects. A warmer (+2.3 °C) and drier climate (-7.4% soil moisture content) was created with greenhouses...
March 21, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28322270/huntington-s-disease-blood-and-brain-show-a-common-gene-expression-pattern-and-share-an-immune-signature-with-alzheimer-s-disease
#13
Davina J Hensman Moss, Michael D Flower, Kitty K Lo, James R C Miller, Gert-Jan B van Ommen, Peter A C 't Hoen, Timothy C Stone, Amelia Guinee, Douglas R Langbehn, Lesley Jones, Vincent Plagnol, Willeke M C van Roon-Mom, Peter Holmans, Sarah J Tabrizi
There is widespread transcriptional dysregulation in Huntington's disease (HD) brain, but analysis is inevitably limited by advanced disease and postmortem changes. However, mutant HTT is ubiquitously expressed and acts systemically, meaning blood, which is readily available and contains cells that are dysfunctional in HD, could act as a surrogate for brain tissue. We conducted an RNA-Seq transcriptomic analysis using whole blood from two HD cohorts, and performed gene set enrichment analysis using public databases and weighted correlation network analysis modules from HD and control brain datasets...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321050/alteration-of-gut-microbial-community-after-n-n-dimethylformamide-exposure
#14
Man Zhang, Min Zheng, Zhijun Wu, Mingyue Guan, Shuai Liu, Wenjin Zhao, Juan Cheng
N,N-Dimethylformamide (DMF), a solvent commonly used in factories, can induce liver toxicities, including hepatitis, fibrosis, cirrhosis and hepatoma. It is well known that the gut microbial community plays a role in the metabolism of many toxic substance and in liver regeneration. However, the effect of DMF on rat gut microbial community is poorly understood. The gut microbiotas in control rats and rats exposed to DMF were characterized by high-throughput sequencing of the bacterial 16S rRNA gene. The levels of biochemical parameters in the serum of rats, including cholesterol, bile acid, alanine aminotransferase (ALT), and aspartate aminotransferase (AST), were evaluated...
2017: Journal of Toxicological Sciences
https://www.readbyqxmd.com/read/28320778/the-epitranscriptome-of-noncoding-rnas-in-cancer
#15
REVIEW
Manel Esteller, Pier Paolo Pandolfi
The activity of RNA is controlled by different types of post-transcriptional modifications, such as the addition of methyl groups and other chemical and structural changes, that have been recently described in human cells by high-throughput sequencing. Herein, we will discuss how the so-called epitranscriptome is disrupted in cancer and what the contribution of its writers, readers, and erasers to the process of cellular transformation is, particularly focusing on the epigenetic modifications of ncRNAs.Significance: Chemical modifications of RNA play a central role in the control of messenger and ncRNA activity and, thus, are tightly regulated in cells...
March 20, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28320620/effect-of-fe-0-addition-on-volatile-fatty-acids-evolution-on-anaerobic-digestion-at-high-organic-loading-rates
#16
Xin Kong, Shuyao Yu, Shuang Xu, Wen Fang, Jianguo Liu, Huan Li
Excessive acidification frequently occurs in the anaerobic digestion of the organic fraction of municipal solid waste (OFMSW) at high organic loading rates (OLR), due to the accumulation of non-acetic volatile fatty acids (VFA). In this study, the performance of Fe(0) in enhancing various VFA production and metabolism was investigated. The butyric acid concentration in a high OLR reactor with Fe(0) addition decreased from 7200 to 0mg/L after a short lag phase, and the total VFA (TVFA) concentration also decreased substantially...
March 17, 2017: Waste Management
https://www.readbyqxmd.com/read/28320326/lw-fqzip-2-a-parallelized-reference-based-compression-of-fastq-files
#17
Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun, Zexuan Zhu
BACKGROUND: The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing volume of raw data outpaces the decreasing disk cost and the storage of huge sequencing data has become a bottleneck of downstream analyses. Data compression is considered as a solution to reduce the dependency on storage. Efficient sequencing data compression methods are highly demanded...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28319716/multiple-stressors-in-sediments-impact-adjacent-hard-substrate-habitats-and-across-biological-domains
#18
Jasmin C Lawes, Katherine A Dafforn, Graeme F Clark, Mark V Brown, Emma L Johnston
Coastal systems are increasingly impacted by human activities. While the direct effects of individual contaminants have been investigated, the potential for multiple contaminants to impact adjacent hard substrate habitats is poorly understood. Sediment-bound contaminants pose a risk to water column organisms through resuspension and the fluxing of dissolved nutrients and metals. This study experimentally manipulated contaminated coastal sediments in mesocosms with additions of a common fertiliser to investigate the impact on both bacterial biofilms and macrofouling communities on nearby hard substrates...
March 16, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28319085/synergistic-drug-combinations-for-cancer-identified-in-a-crispr-screen-for-pairwise-genetic-interactions
#19
Kyuho Han, Edwin E Jeng, Gaelen T Hess, David W Morgens, Amy Li, Michael C Bassik
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs...
March 20, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28318230/label-free-discovery-array-platform-for-the-characterization-of-glycan-binding-proteins-and-glycoproteins
#20
Christopher John Gray, Antonio Sánchez-Ruiz, Ivana Šardzíková, Yassir A Ahmed, Rebecca Louise Miller, Juana E Reyes Martinez, Edward Pallister, Kun Huang, Peter Both, Mirja Hartmann, Hannah N Roberts, Robert Šardzik, Santanu Mandal, Jeremy E Turnbull, Claire E Eyers, Sabine L Flitsch
The identification of carbohydrate-protein interactions is central to our understanding of the roles of cell-surface carbohydrates (the glycocalyx), fundamental for cell-recognition events. Therefore there is a need for fast high-throughput biochemical tools to capture the complexity of these biological interactions. Here we describe a rapid method for qualitative label-free detection of carbohydrate-protein interactions on arrays of simple synthetic glycans, more com-plex natural glycosaminoglycans (GAG) and lectins/carbohydrate binding proteins using MALDI-ToF mass spectrometry...
March 20, 2017: Analytical Chemistry
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