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https://www.readbyqxmd.com/read/28239402/high-cholesterol-diet-does-not-alter-gut-microbiota-composition-in-mice
#1
Lidiya G Dimova, Nikola Zlatkov, Henkjan J Verkade, Bernt Eric Uhlin, Uwe J F Tietge
INTRODUCTION: Western diet containing both saturated fat and cholesterol impairs cardio-metabolic health partly by modulating diversity and function of the microbiota. While diet containing only high fat has comparable effects, it is unclear how diets only enriched in cholesterol impact the microbiota. Therefore, we aimed to characterize the response of host and microbiota to a high cholesterol (HC) diet in mice susceptible to cardio-metabolic disease. METHODS: LDLR knockout mice received either 1...
2017: Nutrition & Metabolism
https://www.readbyqxmd.com/read/28239315/single-fecal-microbiota-transplantation-failed-to-change-intestinal-microbiota-and-had-limited-effectiveness-against-ulcerative-colitis-in-japanese-patients
#2
Shinta Mizuno, Kosaku Nanki, Katsuyoshi Matsuoka, Keiichiro Saigusa, Keiko Ono, Mari Arai, Shinya Sugimoto, Hiroki Kiyohara, Moeko Nakashima, Kozue Takeshita, Makoto Naganuma, Wataru Suda, Masahira Hattori, Takanori Kanai
BACKGROUND/AIMS: Recent developments in analytical techniques including next-generation sequencing have clarified the correlation between intestinal microbiota and inflammatory bowel disease. Fecal microbiota transplantation (FMT) for patients with ulcerative colitis (UC) is proposed as a potential approach to resolving their dysbiosis; however, its safety and efficacy have not been confirmed. This single-arm, open-label, non-randomized study aimed to evaluate the safety and efficacy of FMT for Japanese patients with UC as the first registered clinical trial in Japan...
January 2017: Intestinal Research
https://www.readbyqxmd.com/read/28239231/genome-wide-discovery-of-dna-polymorphisms-in-mei-prunus-mume-sieb-et-zucc-an-ornamental-woody-plant-with-contrasting-tree-architecture-and-their-functional-relevance-for-weeping-trait
#3
Jie Zhang, Kai Zhao, Dan Hou, Junhuo Cai, Qixiang Zhang, Tangren Cheng, Huitang Pan, Weiru Yang
Next-generation sequencing technologies provide opportunities to ascertain the genetic basis of phenotypic differences, even in the closely related cultivars via detection of large amount of DNA polymorphisms. In this study, we performed whole-genome re-sequencing of two mei cultivars with contrasting tree architecture. 75.87 million 100 bp pair-end reads were generated, with 92 % coverage of the genome. Re-sequencing data of two former upright mei cultivars were applied for detecting DNA polymorphisms, since we were more interested in variations conferring weeping trait...
2017: Plant Molecular Biology Reporter
https://www.readbyqxmd.com/read/28238875/the-genomic-and-biological-characterization-of-citrullus-lanatus-cryptic-virus-infecting-watermelon-in-china
#4
Min Xin, Mengji Cao, Wenwen Liu, Yingdang Ren, Chuantao Lu, Xifeng Wang
A dsRNA virus was detected in the watermelon (Citrullus lanatus) samples collected from Kaifeng, Henan province, China through the use of next generation sequencing of small RNAs. The complete genome of this virus is comprised of dsRNA-1 (1603 nt) and dsRNA-2 (1466 nt), both of which are single open reading frames and potentially encode a 54.2kDa RNA-dependent RNA polymerase (RdRp) and a 45.9kDa coat protein (CP), respectively. The RdRp and CP share the highest amino acid identities 85.3% and 75.4% with citrullus lanatus cryptic virus (CiLCV), respectively...
February 23, 2017: Virus Research
https://www.readbyqxmd.com/read/28238063/functional-germline-variants-in-driver-genes-of-breast-cancer
#5
Stella Göhler, Miguel Inacio Da Silva Filho, Robert Johansson, Kerstin Enquist-Olsson, Roger Henriksson, Kari Hemminki, Per Lenner, Asta Försti
PURPOSE: Germline mutations in tumour suppressor genes cause various cancers. These genes are also somatically mutated in sporadic tumours. We hypothesized that there may also be cancer-related germline variants in the genes commonly mutated in sporadic breast tumours. METHODS: After excluding the well-characterized breast cancer (BC) genes, we screened 15 novel genes consistently classified as BC driver genes in next-generation sequencing approaches for single nucleotide polymorphisms (SNPs)...
February 25, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28237902/ultrasensitive-and-selective-electrochemical-biosensor-for-detection-of-mercury-ii-ions-by-nicking-endonuclease-assisted-target-recycling-and-hybridization-chain-reaction-signal-amplification
#6
Minqiang Hong, Mengyan Wang, Jing Wang, Xueqin Xu, Zhenyu Lin
In this paper, a novel and signal-on electrochemical biosensor based on Hg(2+)- triggered nicking endonuclease-assisted target recycling and hybridization chain reaction (HCR) amplification tactics was developed for sensitive and selective detection of Hg(2+). The hairpin-shaped capture probe A (PA) contained a specific sequence which was recognized by nicking endonuclease (NEase). In the presence of Hg(2+), probe B (PB) hybridized with PA to form stand-up duplex DNA strands via the Hg(2+) mediated thymine-Hg(2+)-thymine (T-Hg(2+)-T) structure, which automatically triggered NEase to selectively digest duplex region from the recognition sites, spontaneously dissociating PB and Hg(2+) and leaving the remnant initiators...
February 22, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28236503/y-and-w-chromosome-assemblies-approaches-and-discoveries
#7
REVIEW
Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova
Hundreds of vertebrate genomes have been sequenced and assembled to date. However, most sequencing projects have ignored the sex chromosomes unique to the heterogametic sex - Y and W - that are known as sex-limited chromosomes (SLCs). Indeed, haploid and repetitive Y chromosomes in species with male heterogamety (XY), and W chromosomes in species with female heterogamety (ZW), are difficult to sequence and assemble. Nevertheless, obtaining their sequences is important for understanding the intricacies of vertebrate genome function and evolution...
February 21, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28236292/the-role-of-genomics-in-common-variable-immunodeficiency-disorders
#8
REVIEW
Anne-Kathrin Kienzler, Chantal E Hargreaves, Smita Y Patel
The advent of next generation sequencing (NGS) and 'omic' technologies has revolutionised the field of genetics and its implementation in healthcare has the potential to realise precision medicine. Primary immunodeficiencies (PID) are a group of rare diseases which have benefitted from NGS, with a massive increase in causative genes identified in the past few years. Common Variable Immunodeficiency Disorders (CVID) are a heterogeneous form of PID and the most common form of antibody failure in children and adults...
February 25, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28235842/acquired-mutations-associated-with-ibrutinib-resistance-in-waldenstrom-macroglobulinemia
#9
Lian Xu, Nicholas Tsakmaklis, Guang Yang, Jiaji G Chen, Xia Liu, Maria Demos, Amanda Kofides, Christopher J Patterson, Kirsten Meid, Joshua Gustine, Toni Dubeau, M Lia Palomba, Ranjana Advani, Jorge J Castillo, Richard R Furman, Zachary R Hunter, Steven P Treon
Ibrutinib produces high response rates and durable remissions in Waldenstrom's Macroglobulinemia (WM) that are impacted by MYD88 and CXCR4(WHIM) mutations. Disease progression can develop on ibrutinib, though the molecular basis remains to be clarified. We sequenced sorted CD19(+) lymphoplasmacytic cells from 6 WM patients who progressed after achieving major responses on ibrutinib using Sanger, TA cloning and sequencing, and highly sensitive and specific AS-PCR assays that we developed for BTK mutations. AS-PCR assays were used to screen patients with and without progressive disease on ibrutinib, and ibrutinib-naïve disease...
February 24, 2017: Blood
https://www.readbyqxmd.com/read/28235734/a-novel-electrochemiluminescence-biosensor-for-the-detection-of-micrornas-based-on-a-dna-functionalized-nitrogen-doped-carbon-quantum-dots-as-signal-enhancers
#10
Qiao Liu, Cheng Ma, Xing-Pei Liu, Yu-Pin Wei, Chang-Jie Mao, Jun-Jie Zhu
An ultrasensitive electrochemiluminescence (ECL) biosensor for the detection of microRNA was developed based on nicking enzymes Nb.BbvCI mediated signal amplification (NESA). First, the hairpin probe1-N-CQDs with assistant probe and microRNA (miRNA) formed Y junction structure which was cleaved with the addition of nicking enzymes Nb.BbvCI to release miRNA and assistant probe. Subsequently, the released miRNA and assistant probe can initiate the next recycling process. The generation of numerous intermediate sequences nitrogen doped carbon quantum dots-DNA (N-CQDs-DNA) can further hybridize with hairpin probe2 immobilized on GO/Au composite modified electrode surface, the initial ECL intensity was enhanced...
February 17, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28235609/massive-parallel-insertion-site-sequencing-of-an-arrayed-sinorhizobium-meliloti-signature-tagged-mini-tn-5-transposon-mutant-library
#11
Javier Serrania, Tobias Johner, Oliver Rupp, Alexander Goesmann, Anke Becker
Transposon mutagenesis in conjunction with identification of genomic transposon insertion sites is a powerful tool for gene function studies. We have implemented a protocol for parallel determination of transposon insertion sites by Illumina sequencing involving a hierarchical barcoding method that allowed for tracking back insertion sites to individual clones of an arrayed signature-tagged transposon mutant library. This protocol was applied to further characterize a signature-tagged mini-Tn 5 mutant library comprising about 12,000 mutants of the symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti (Pobigaylo et al...
February 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28231512/the-impact-of-third-generation-genomic-technologies-on-plant-genome-assembly
#12
REVIEW
Wen-Biao Jiao, Korbinian Schneeberger
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies...
February 20, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28231340/the-widely-used-nicotiana-benthamiana-16c-line-has-an-unusual-t-dna-integration-pattern-including-a-transposon-sequence
#13
Joshua G Philips, Fatima Naim, Michał T Lorenc, Kevin J Dudley, Roger P Hellens, Peter M Waterhouse
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site...
2017: PloS One
https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#14
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28230858/ngs-based-transcriptome-profiling-reveals-biomarkers-for-companion-diagnostics-of-the-tgf-%C3%AE-receptor-blocker-galunisertib-in-hcc
#15
Yuan Cao, Rahul Agarwal, Francesco Dituri, Luigi Lupo, Paolo Trerotoli, Serena Mancarella, Peter Winter, Gianluigi Giannelli
Transforming growth factor-beta (TGF-β) signaling has gained extensive interest in hepatocellular carcinoma (HCC). The small molecule kinase inhibitor galunisertib, targeting the TGF-β receptor I (TGF-βRI), blocks HCC progression in preclinical models and shows promising effects in ongoing clinical trials. As the drug is not similarly effective in all patients, this study was aimed at identifying new companion diagnostics biomarkers for patient stratification. Next-generation sequencing-based massive analysis of cDNA ends was used to investigate the transcriptome of an invasive HCC cell line responses to TGF-β1 and galunisertib...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230760/bioinformatics-approaches-for-fetal-dna-fraction-estimation-in-noninvasive-prenatal-testing
#16
REVIEW
Xianlu Laura Peng, Peiyong Jiang
The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28230645/clinical-scale-rapid-autologous-bk-virus-specific-t-cell-line-generation-from-kidney-transplant-recipients-with-active-viremia-for-adoptive-immunotherapy
#17
Caroline Lamarche, Julie Orio, Victoria Georges-Tobar, Thomas Pincez, Mathieu Goupil, Amina Dahmani, Cedric Carli C, Ann Brasey, Lambert Busque, Jean-Sébastien Delisle
BACKGROUND: Polyomavirus-associated nephropathy (PVAN) following BK virus reactivation in kidney transplant recipients (KTR) can compromise graft survival. Lowering immunosuppression is the only established approach to prevent or treat PVAN but nonspecifically increasing host immune competence also augments rejection risk. Ex vivo T cell stimulation/expansion offers the possibility to generate BK-specific T cell lines for adoptive immunotherapy. The objective of this study was to develop and characterize a clinical scale protocol to generate BK-specific T cell lines from viremic KTR...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28230642/strategies-to-obtain-diverse-and-specific-human-monoclonal-antibodies-from-transgenic-animals
#18
Marianne Brüggemann, Michael J Osborn, Biao Ma, Roland Buelow
Techniques to obtain large quantities of antigen-specific monoclonal antibodies, mAbs, were first established in the 1970s when Georges Köhler and César Milstein immortalized antibody-producing mouse B-lymphocytes by fusion with myeloma cells (http://www.whatisbiotechnology.org/exhibitions/milstein). Combined with the expression of human antibodies in transgenic animals, this technique allowed upon immunization the generation of highly specific fully human mAbs for therapeutic applications. Apart from being extremely beneficial, mAbs are a huge success commercially...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28230599/a-targeted-next-generation-genetic-sequencing-study-on-tetralogy-of-fallot-combined-with-cleft-lip-and-palate
#19
Lin Liu, Haisong Bu, Yifeng Yang, Zhiping Tan, Fei Zhang, Shijun Hu, Tianli Zhao
BACKGROUND: Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS: The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28230180/assessment-of-chicken-carcass-microbiome-responses-during-processing-in-the-presence-of-commercial-antimicrobials-using-a-next-generation-sequencing-approach
#20
Sun Ae Kim, Si Hong Park, Sang In Lee, Casey M Owens, Steven C Ricke
The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence...
February 23, 2017: Scientific Reports
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