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https://www.readbyqxmd.com/read/29455464/disparities-in-second-generation-dna-metabarcoding-results-exposed-with-accessible-and-repeatable-workflows
#1
Timothy J Divoll, Veronica A Brown, Jeff Kinne, Gary F McCracken, Joy M O'Keefe
Different second-generation sequencing technologies may have taxon-specific biases when DNA metabarcoding prey in predator feces. Our major objective was to examine differences in prey recovery from bat guano across two different sequencing workflows using the same fecal DNA extracts. We compared results between the Ion Torrent PGM and the Illumina MiSeq with similar library preparations and the same analysis pipeline. We focus on repeatability and provide an R Notebook in an effort toward transparency for future methodological improvements...
February 17, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29455240/taxonomic-structure-and-function-of-seed-inhabiting-bacterial-microbiota-from-common-reed-phragmites-australis-and-narrowleaf-cattail-typha-angustifolia-l
#2
Ting Gao, Xian-Yang Shi
The present study investigated the endophytic bacterial communities in the seeds of mature, natural common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.). Additionally, seed endophytic bacterial communities were compared with rhizospheric and root endophytic bacterial communities using Illumina-based sequencing. Seed endophytic bacterial communities were dominated by Proteobacteria (reed, 41.24%; cattail, 45.51%), followed by Bacteroidetes (reed, 12.01%; cattail, 10.41%), Planctomycetes (reed, 10...
February 17, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29455155/newly-designed-11-gene-panel-reveals-first-case-of-hereditary-amyloidosis-captured-by-massive-parallel-sequencing
#3
Zuzana Chyra Kufova, Tereza Sevcikova, Jaroslav Januska, Petr Vojta, Arpad Boday, Pavla Vanickova, Jana Filipova, Katerina Growkova, Tomas Jelinek, Marian Hajduch, Roman Hajek
AIMS: Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance...
February 17, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29453765/statistical-assessment-of-dna-extraction-methodology-for-culture-independent-analysis-of-microbial-community-associated-with-diverse-environmental-samples
#4
Rishi Mahajan, Sampan Attri, Kavita Sharma, Niharika Singh, Deepika Sharma, Gunjan Goel
Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food...
February 16, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29453220/identification-of-novel-fusion-transcripts-in-multiple-myeloma
#5
Mingxuan Lin, Peak Ling Lee, Lily Chiu, Constance Chua, Kenneth H K Ban, Adeline H F Lin, Zit Liang Chan, Tae-Hoon Chung, Benedict Yan, Wee-Joo Chng
AIMS: Multiple myeloma (MM) is a heterogeneous disease characterised by genetically complex abnormalities. The classical mutational spectrum includes recurrent chromosomal aberrations and gene-level mutations. Recurrent translocations involving the IGH gene such as t(11;14), t(4;14) and t(14;16) are well known. However, the presence of complex genetic abnormalities raises the possibility that fusions other than the recurrent IGH translocations exist. We therefore employed a targeted RNA-sequencing panel to identify novel putative fusions in a local cohort of MM...
February 16, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29453107/body-fluid-identification-using-a-targeted-mrna-massively-parallel-sequencing-approach-results-of-a-euroforgen-ednap-collaborative-exercise
#6
S Ingold, G Dørum, E Hanson, A Berti, W Branicki, P Brito, P Elsmore, K B Gettings, F Giangasparo, T E Gross, S Hansen, E N Hanssen, M-L Kampmann, M Kayser, F-X Laurent, N Morling, A Mosquera-Miguel, W Parson, C Phillips, M J Porto, E Pośpiech, A D Roeder, P M Schneider, K Schulze Johann, C R Steffen, D Syndercombe-Court, M Trautmann, M van den Berge, K J van der Gaag, J Vannier, V Verdoliva, A Vidaki, C Xavier, J Ballantyne, C Haas
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols...
January 31, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29452334/seed-2-a-user-friendly-platform-for-amplicon-high-throughput-sequencing-data-analyses
#7
Tomáš Vetrovský, Petr Baldrian, Daniel Morais, Bonnie Berger
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29451918/manipulation-of-the-rhizosphere-microbial-community-through-application-of-a-new-bio-organic-fertilizer-improves-watermelon-quality-and-health
#8
Jia Zhao, Jiang Liu, Hong Liang, Jing Huang, Zhe Chen, Yuanjun Nie, Changbiao Wang, Yuguo Wang
Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community...
2018: PloS One
https://www.readbyqxmd.com/read/29451882/de-novo-transcriptomic-analysis-of-leaf-and-fruit-tissue-of-cornus-officinalis-using-illumina-platform
#9
Dian-Yun Hou, Lin-Chun Shi, Meng-Meng Yang, Jiong Li, Shuang Zhou, Hong-Xiao Zhang, Hua-Wei Xu
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization...
2018: PloS One
https://www.readbyqxmd.com/read/29451060/cord-blood-buffy-coat-dna-methylation-is-comparable-to-whole-cord-blood-methylation
#10
John Dou, Rebecca J Schmidt, Kelly S Benke, Craig Newschaffer, Irva Hertz-Picciotto, Lisa A Croen, Ana-Maria Iosif, Janine M LaSalle, M Daniele Fallin, Kelly M Bakulski
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples...
February 16, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29449781/whole-genome-sequencing-of-multidrug-resistant-salmonella-enterica-serovar-typhimurium-isolated-from-humans-and-poultry-in-burkina-faso
#11
Assèta Kagambèga, Taru Lienemann, Jonathan G Frye, Nicolas Barro, Kaisa Haukka
Background: Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods: Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method...
2018: Tropical Medicine and Health
https://www.readbyqxmd.com/read/29449400/complete-genome-sequence-of-rice-hoja-blanca-tenuivirus-isolated-from-a-susceptible-rice-cultivar-in-colombia
#12
Jenyfer Jimenez, Monica Carvajal-Yepes, Ana Maria Leiva, Maribel Cruz, Luz Elena Romero, Carmen A Bolaños, Ivan Lozano, Wilmer J Cuellar
We describe here the complete genome of Rice hoja blanca tenuivirus The sequenced isolate was obtained by insect vector transmission from a symptomatic rice sample grown in Colombia. Sequence data from the four RNA components were obtained by deep sequencing (Illumina), and infections were confirmed by enzyme-linked immunosorbent assay and Sanger sequencing.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449382/complete-genome-sequence-of-escherichia-coli-ml35
#13
Angeline Casale, Stephanie Clark, Melissa Grasso, Marta Kryschuk, Lukas Ritzer, Madyson Trudeau, Laura E Williams
We report here the complete genome sequence of Escherichia coli strain ML35. We assembled PacBio reads into a single closed contig with 169× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp sequence with 50.8% GC content.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449381/complete-genome-sequence-of-pseudomonas-sp-strain-nc02-isolated-from-soil
#14
Joseph Cerra, Hailey Donohue, Alexander Kral, Molly Oser, Laura Rostkowski, Luke Zappia, Laura E Williams
We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil in eastern Massachusetts. We assembled PacBio reads into a single closed contig with 132× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449378/complete-genome-sequences-of-six-listeria-monocytogenes-sequence-type-9-isolates-from-meat-processing-plants-in-norway
#15
Annette Fagerlund, Solveig Langsrud, Birgitte Moen, Even Heir, Trond Møretrø
Listeria monocytogenes is a foodborne pathogen that causes the often-fatal disease listeriosis. We present here the complete genome sequences of six L. monocytogenes isolates of sequence type 9 (ST9) collected from two different meat processing facilities in Norway. The genomes were assembled using Illumina and Nanopore sequencing data.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29448118/calcium-channel-blockers-as-drug-repurposing-candidates-for-gestational-diabetes-mining-large-scale-genomic-and-electronic-health-records-data-to-repurpose-medications
#16
Jeffery A Goldstein, Lisa A Bastarache, Joshua C Denny, Dan M Roden, Jill M Pulley, David M Aronoff
New therapeutic approaches are needed for gestational diabetes mellitus (GDM), but must show safety and efficacy in a historically understudied population. We studied associations between electronic medical record (EMR) phenotypes and genetic variants to uncover drugs currently considered safe in pregnancy that could treat or prevent GDM. We identified 129 systemically active drugs considered safe in pregnancy targeting the proteins produced from 196 genes. We tested for associations between GDM and/or type 2 diabetes (DM2) and 306 SNPs in 130 genes represented on the Illumina Infinium Human Exome Bead Chip (DM2 was included due to shared pathophysiological features with GDM)...
February 12, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29446852/isolation-of-crithidia-spp-from-lesions-of-immunocompetent-patients-with-suspected-cutaneous-leishmaniasis-in-iran
#17
Nafiseh Ghobakhloo, Mohammad Hossei Motazedian, S Naderi, Ebrahimi Sepideh
OBJECTIVE: Leishmania major has been considered as the main etiological agent of cutaneous leishmaniasis in Iran. However, there are recent reports about existence of Crithidia spp in cutaneous lesions in southern Iran. Therefore, this study was designed to decipher some morphological, biological, and molecular aspects of this phenomenon. METHODS: Clinical isolates were obtained from 167 patients with cutaneous ulcers. A set of specific primers based on GAPDH (Glyceraldehyde-3-Phosphate Dehydrogenase) gene were used to distinguish between Crithidia and Leishmania genera...
February 15, 2018: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/29445422/sleeping-beauty-transposon-integrates-into-non-ta-dinucleotides
#18
Yabin Guo, Yin Zhang, Kaishun Hu
Background: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29444297/draft-genomes-of-two-blister-beetles-genus-hycleus-harvested-for-the-potent-blistering-agent-cantharidin
#19
Yuan-Ming Wu, Jiang Li, Xiang-Sheng Chen
Background: Commonly known as blister beetles or Spanish fly, there are more than 1,500 species in the Meloidae family (Hexapoda: Coleoptera: Tenebrionoidea) that produce the potent defensive blistering agent cantharidin. Cantharidin and its derivatives have been used to treat cancers, such as liver, stomach, lung and esophageal cancers. Hycleus cichorii and Hycleus phaleratus are the most commercially important blister beetles in China due to their ability to biosynthesize this potent vesicant...
February 10, 2018: GigaScience
https://www.readbyqxmd.com/read/29444253/hiv-1-genotypic-resistance-testing-using-the-vela-automated-next-generation-sequencing-platform
#20
Stéphanie Raymond, Florence Nicot, Romain Carcenac, Caroline Lefebvre, Nicolas Jeanne, Karine Saune, Pierre Delobel, Jacques Izopet
Objectives: To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods: Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples...
February 12, 2018: Journal of Antimicrobial Chemotherapy
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