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High-Throughput Sequencing

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https://www.readbyqxmd.com/read/29774870/radiomics-in-gliomas-a-promising-assistance-for-glioma-clinical-research
#1
Yueshuang Leng, Xiaoyi Wang, Weihua Liao, Ya Cao
Gliomas are the most common brain primary tumors worldwide, which is the earliest sequenced cancer gene in the Cancer Genome Atlas (TCGA) project. The World Health Organization Classification Update of Central Nervous System (CNS) Tumors 2016 highlights that glioma is the first tumor classified based on both of the molecular markers and histology. Radiomics is an extraction approach for high-throughput data which collects the quantitative image information appearing. Combined imaging data with genomics and proteomics, radiomics show promising prediction for cancer diagnosis, treatment, and prognosis...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774834/human-endophthalmitis-caused-by-pseudorabies-virus-infection-china-2017
#2
Jing-Wen Ai, Shan-Shan Weng, Qi Cheng, Peng Cui, Yong-Jun Li, Hong-Long Wu, Yi-Min Zhu, Bin Xu, Wen-Hong Zhang
We report human endophthalmitis caused by pseudorabies virus infection after exposure to sewage on a hog farm in China. High-throughput sequencing and real-time PCR of vitreous humor showed pseudorabies virus sequences. This case showed that pseudorabies virus might infect humans after direct contact with contaminants.
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774828/bilberry-pomace-in-rabbit-nutrition-effects-on-growth-performance-apparent-digestibility-caecal-traits-bacterial-community-and-antioxidant-status
#3
S Dabbou, I Ferrocino, A Kovitvadhi, S Bergagna, D Dezzuto, A Schiavone, L Cocolin, F Gai, V Santoro, L Gasco
Agricultural by-products could be used as alternative raw materials in rabbit nutrition as they have been found to be highly nutritious and low cost feeding sources. The aim of this study was to estimate the nutritive value and potential use of bilberry pomace (BP) for growing rabbits. A total of 144 Grimaud rabbits (35 days old) were allotted to four groups and fed with a diet containing increasing level of BP: BP0 (basal diet), BP5, BP10 and BP15 containing 0, 50, 100 and 150 g/kg respectively. Growth trial lasted 48 days; apparent digestibility was evaluated, starting at 46 days of age, over 4 consecutive days...
May 18, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29774508/the-bacterial-and-archaeal-community-structures-and-methanogenic-potential-of-the-cecal-microbiota-of-goats-fed-with-hay-and-high-grain-diets
#4
Wei Jin, Yin Li, Yanfen Cheng, Shengyong Mao, Weiyun Zhu
The cecum plays an important role in the feed fermentation of ruminants. However, information is very limited regarding the cecal microbiota and their methane production. In the present study, the cecal content from twelve local Chinese goats, fed with either a hay diet (0% grain) or a high-grain diet (71.5% grain), were used to investigate the bacterial and archaeal community and their methanogenic potential. Microbial community analysis was determined using high-throughput sequencing of 16S rRNA genes and real-time PCR, and the methanogenesis potential was assessed by in vitro fermentation with ground corn or hay as substrates...
May 17, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29774020/high-diversity-of-myocyanophage-in-various-aquatic-environments-revealed-by-high-throughput-sequencing-of-major-capsid-protein-gene-with-a-new-set-of-primers
#5
Weiguo Hou, Shang Wang, Brandon R Briggs, Gaoyuan Li, Wei Xie, Hailiang Dong
Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29772800/identification-and-expression-of-mirnas-related-to-female-flower-induction-in-walnut-juglans-regia-l
#6
Li Zhou, Shaowen Quan, Hang Xu, Li Ma, Jianxin Niu
Flower induction is an essential stage in walnut ( Juglans regia L.) trees, directly affecting yield, yield stability, fruit quality and commodity value. The objective of this study was to identify miRNAs related to female flower induction via high-throughput sequencing and bioinformatics analysis. A total of 123 miRNAs were identified including 51 known miRNAs and 72 novel miRNAs. Differential expression was observed in 19 of the known miRNAs and 34 of the novel miRNAs. Twelve miRNAs were confirmed by RT-qPCR...
May 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29772771/a-novel-hepadnavirus-identified-in-an-immunocompromised-domestic-cat-in-australia
#7
Mahdis Aghazadeh, Mang Shi, Vanessa R Barrs, Alicia J McLuckie, Scott A Lindsay, Barbara Jameson, Bronte Hampson, Edward C Holmes, Julia A Beatty
High-throughput transcriptome sequencing allows for the unbiased detection of viruses in host tissues. The application of this technique to immunosuppressed animals facilitates the detection of viruses that might otherwise be excluded or contained in immunocompetent individuals. To identify potential viral pathogens infecting domestic cats we performed high-throughput transcriptome sequencing of tissues from cats infected with feline immunodeficiency virus (FIV). A novel member of the Hepadnaviridae , tentatively named domestic cat hepadnavirus, was discovered in a lymphoma sample and its complete 3187 bp genome characterized...
May 17, 2018: Viruses
https://www.readbyqxmd.com/read/29772753/dietary-polysaccharide-from-enteromorpha-clathrata-modulates-gut-microbiota-and-promotes-the-growth-of-akkermansia-muciniphila-bifidobacterium-spp-and-lactobacillus-spp
#8
Qingsen Shang, Ya Wang, Lin Pan, Qingfeng Niu, Chao Li, Hao Jiang, Chao Cai, Jiejie Hao, Guoyun Li, Guangli Yu
Recently, accumulating evidence has suggested that Enteromorpha clathrata polysaccharide (ECP) could contribute to the treatment of diseases. However, as a promising candidate for marine drug development, although ECP has been extensively studied, less consideration has been given to exploring its effect on gut microbiota. In this light, given the critical role of gut microbiota in health and disease, we investigated here the effect of ECP on gut microbiota using 16S rRNA high-throughput sequencing. As revealed by bioinformatic analyses, ECP considerably changed the structure of the gut microbiota and significantly promoted the growth of probiotic bacteria in C57BL/6J mice...
May 17, 2018: Marine Drugs
https://www.readbyqxmd.com/read/29772600/an-accurate-bacterial-dna-quantification-assay-for-hts-library-preparation-of-human-biological-samples
#9
Sarah Seashols-Williams, Raquel Green, Denise Wohlfahrt, Angela Brand, Antonio Limjuco Tan-Torres, Francy Nogales, J Paul Brooks, Baneshwar Singh
Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS)...
May 17, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29772310/recombination-activity-of-human-rag2-mutations-and-correlation-with-the-clinical-phenotype
#10
Irit Tirosh, Yasuhiro Yamazaki, Francesco Frugoni, Francesca A Ververs, Eric J Allenspach, Yu Zhang, Siobhan Burns, Waleed Al-Herz, Lenora Noroski, Jolan E Walter, Andrew R Gennery, Mirjam van der Burg, Luigi D Notarangelo, Yu Nee Lee
BACKGROUND: Mutations in the Recombinase Activating Gene 1 and 2 (RAG1, RAG2) are associated with a broad range of clinical and immunological phenotypes in humans. OBJECTIVE: Using a flow cytometry-based assay, we aimed to measure the recombinase activity of naturally occurring RAG2 mutant proteins, and to correlate results with the severity of the clinical and immunological phenotype. METHODS: Abelson virus-transformed Rag2-/- pro-B cells engineered to contain an inverted GFP cassette flanked by recombination signal sequences (RSS) were transduced with retroviruses encoding either wild-type or 41 naturally occurring RAG2 variants...
May 14, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29772236/identification-and-characterization-of-circular-rnas-in-rapid-atrial-pacing-dog-atrial-tissue
#11
Wenfeng Shangguan, Xue Liang, Wen Shi, Tong Liu, Manman Wang, Guangping Li
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29771995/correction-investigation-of-the-fungal-community-structures-of-imported-wheat-using-high-throughput-sequencing-technology
#12
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pone.0171894.].
2018: PloS One
https://www.readbyqxmd.com/read/29771965/evaluation-of-commercial-dna-and-rna-extraction-methods-for-high-throughput-sequencing-of-ffpe-samples
#13
Stine H Kresse, Heidi M Namløs, Susanne Lorenz, Jeanne-Marie Berner, Ola Myklebost, Bodil Bjerkehagen, Leonardo A Meza-Zepeda
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors...
2018: PloS One
https://www.readbyqxmd.com/read/29771371/allele-phasing-greatly-improves-the-phylogenetic-utility-of-ultraconserved-elements
#14
Tobias Andermann, Alexandre M Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C Faircloth, Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies...
May 15, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#15
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29770143/a-census-of-tandemly-repeated-polymorphic-loci-in-genic-regions-through-the-comparative-integration-of-human-genome-assemblies
#16
Loredana M Genovese, Filippo Geraci, Lucia Corrado, Eleonora Mangano, Romina D'Aurizio, Roberta Bordoni, Marco Severgnini, Giovanni Manzini, Gianluca De Bellis, Sandra D'Alfonso, Marco Pellegrini
Polymorphic Tandem Repeat (PTR) is a common form of polymorphism in the human genome. A PTR consists in a variation found in an individual (or in a population) of the number of repeating units of a Tandem Repeat (TR) locus of the genome with respect to the reference genome. Several phenotypic traits and diseases have been discovered to be strongly associated with or caused by specific PTR loci. PTR are further distinguished in two main classes: Short Tandem Repeats (STR) when the repeating unit has size up to 6 base pairs, and Variable Number Tandem Repeats (VNTR) for repeating units of size above 6 base pairs...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29769540/different-clusters-of-candidatus-methanoperedens-nitroreducens-like-archaea-as-revealed-by-high-throughput-sequencing-with-new-primers
#17
Sai Xu, Chen Cai, Jianhua Guo, Wenjing Lu, Zhiguo Yuan, Shihu Hu
The newly discovered Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769381/tosr-mediated-regulation-of-adhesins-and-biofilm-formation-in-uropathogenic-escherichia-coli
#18
Courtney L Luterbach, Valerie S Forsyth, Michael D Engstrom, Harry L T Mobley
Uropathogenic Escherichia coli strains utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (<u>t</u>ype <u>o</u>ne <u>s</u>ecretion <u>A</u>) is a nonfimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29768437/oral-health-status-in-historic-population-macroscopic-and-metagenomic-evidence
#19
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Elodie Cabot, Pierre Chevet, Eric Crubézy, Ludovic Orlando, Rémi Esclassan, Catherine Thèves
Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked...
2018: PloS One
https://www.readbyqxmd.com/read/29768432/the-ecology-of-the-drosophila-yeast-mutualism-in-wineries
#20
Allison S Quan, Michael B Eisen
The fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit...
2018: PloS One
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