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Ahmed Farghaly, Sophie Le Roux, Pascal Peu, Patrick Dabert, Ahmed Tawfik
The aim of this study is to highlight the robustness and potentials of the anaerobic baffled reactor (ABR) configuration on keeping the microbial richness and diversity after starvation period of 7 days. The module at steady state operating conditions provided an average volumetric hydrogen production (VHP) of 0.2±0.08 and 0.423±0.5 l/d in the 1st and last compartment (C4). The VHP was gradually decreased from 0.2 to 0.003 l/d and from 0.423 to 0.1 l/d in compartments (C1 and C4) respectively during feed less period...
March 20, 2018: Environmental Technology
Haitao Huang, Huaqiang Tan, Dongmei Xu, Yi Tang, Yisong Niu, Yunsong Lai, Manman Tie, Huanxiu Li
Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean...
March 19, 2018: Scientific Reports
Johannes Birtel, Tobias Eisenberger, Martin Gliem, Philipp L Müller, Philipp Herrmann, Christian Betz, Diana Zahnleiter, Christine Neuhaus, Steffen Lenzner, Frank G Holz, Elisabeth Mangold, Hanno J Bolz, Peter Charbel Issa
Macular and cone/cone-rod dystrophies (MD/CCRD) demonstrate a broad genetic and phenotypic heterogeneity, with retinal alterations solely or predominantly involving the central retina. Targeted next-generation sequencing (NGS) is an efficient diagnostic tool for identifying mutations in patient with retinitis pigmentosa, which shows similar genetic heterogeneity. To detect the genetic causes of disease in patients with MD/CCRD, we implemented a two-tier procedure consisting of Sanger sequencing and targeted NGS including genes associated with clinically overlapping conditions...
March 19, 2018: Scientific Reports
Lucie Ravella, Marc Barritault, Pierre-Paul Bringuier, Lara Chalabreysse, Françoise Thivolet-Bejui, Jean-Michel Maury, Michaël Duruisseaux, Marie Brevet
Multiple lung carcinomas are 5 to 11,5% of lung carcinomas. The distinction between primary lung carcinomas from carcinomas with intrapulmonary metastasis is essential for optimal patient management. The histopathological analysis is very useful but it has to be completed by genotypic assessment using molecular biology (NGS). Molecular biology can also identify genetic alterations with therapeutic implications. We present the case of a patient with a history of surgery for multiple lung carcinomas diagnosed from 2013 to 2017...
March 16, 2018: Annales de Pathologie
John A Handley, Si Hong Park, Sun Ae Kim, Steven C Ricke
Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR)...
2018: Frontiers in Microbiology
Yu Xia, Xianghua Wen, Bing Zhang, Yunfeng Yang
Understanding diversity and assembly patterns of microbial communities in activated sludge (AS) is pivotal for addressing fundamental ecological questions and wastewater treatment engineering. Recent applications of molecular methods especially next generation sequencing (NGS) have led to the explosion of information about AS community diversity, including the identification of uncultured taxa, and characterization of low-abundance but environmentally important populations such as antibiotic resistant bacteria and pathogens...
March 15, 2018: Biotechnology Advances
Stefan A Boers, Saskia D Hiltemann, Andrew P Stubbs, Ruud Jansen, John P Hays
Microbiota profiling has the potential to greatly impact on routine clinical diagnostics by detecting DNA derived from live, fastidious, and dead bacterial cells present within clinical samples. Such results could potentially be used to benefit patients by influencing antibiotic prescribing practices or to generate new classical-based diagnostic methods, e.g., culture or PCR. However, technical flaws in 16S rRNA gene next-generation sequencing (NGS) protocols, together with the requirement for access to bioinformatics, currently hinder the introduction of microbiota analysis into clinical diagnostics...
March 16, 2018: European Journal of Clinical Microbiology & Infectious Diseases
P T Tassios, J Moran-Gilad
No abstract text is available yet for this article.
April 2018: Clinical Microbiology and Infection
Judy F C Chow, William S B Yeung, Vivian C Y Lee, Estella Y L Lau, Ernest H Y Ng
OBJECTIVES: To evaluate the applicability of a commonly used next generation sequencing workflow in detecting unbalanced meiotic segregation products for reciprocal translocation and inversion carriers. STUDY DESIGN: All preimplantation genetic testing treatment cycles performed for reciprocal translocation or inversion carriers from 2012 to April 2017 were included. Three hundreds and forty-two archived whole genome amplified DNA, which had previously analyzed by array comparative genomic hybridization (aCGH), were retrospectively analyzed by next generation sequencing (NGS)...
March 9, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Qin Xiang, Yuping Liu, Xuefeng Zou, Bingbing Hu, Yujie Qiang, Danmei Yu, Wei Yin, Changguo Chen
In this work, g-C3N4@GO gel-like hybrid is obtained by assembling intentionally exfoliated g-C3N4 sheets on graphene oxide (GO) sheets under a hydrothermal condition. A specific N-doping process is firstly designed by heating the g-C3N4@GO interlaced hybrid in vacuum to form nitrogen-doped graphene nanosheets (NGS) with high level of pyridinic-N (56.0%) and edge-rich defect structure. The prepared NGS exhibited a great electrocatalysis for oxygen reduction reaction (ORR) in terms of the activity, durability, methanol tolerance, and the reaction kinetics...
March 16, 2018: ACS Applied Materials & Interfaces
Stephan Bartels, Akinyele Adisa, Timothy Aladelusi, Juliana Lemound, Angelika Stucki-Koch, Sami Hussein, Hans Kreipe, Christian Hartmann, Ulrich Lehmann, Kais Hussein
The aim of this study was to evaluate the mutation profile of BRAF wild-type craniopharyngiomas and ameloblastomas. Pre-screening by immunohistochemistry and pyrosequencing for identifying BRAF wild-type tumors was performed on archived specimens of ameloblastic tumors (n = 20) and craniopharyngiomas (n = 62). Subsequently, 19 BRAF wild-type tumors (nine ameloblastic tumors and ten craniopharyngiomas) were analyzed further using next-generation sequencing (NGS) targeting hot spot mutations of 22 cancer-related genes...
March 15, 2018: Virchows Archiv: An International Journal of Pathology
Ewa Heyduk, Tomasz Heyduk
Promoter escape involves breaking of the favourable contacts between RNA polymerase (RNAP) and the promoter to allow transition to an elongation complex. The sequence of DNA template that is transcribed during promoter escape (ITS; Initially Transcribed Sequence) can affect promoter escape by mechanisms that are not yet fully understood. We employed a highly parallel strategy utilizing Next Generation Sequencing (NGS) to collect data on escape properties of thousands of ITS variants. We show that ITS controls promoter escape through a combination of position-dependent effects (most prominently, sequence-directed RNAP pausing), and position-independent effects derived from sequence encoded physical properties of the template (for example, RNA/DNA duplex stability)...
March 13, 2018: Nucleic Acids Research
Abinaya Manivannan, Jin-Hee Kim, Eun-Young Yang, Yul-Kyun Ahn, Eun-Su Lee, Sena Choi, Do-Sun Kim
Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding...
2018: BioMed Research International
Júlia Perera-Bel, Barbara Hutter, Christoph Heining, Annalen Bleckmann, Martina Fröhlich, Stefan Fröhling, Hanno Glimm, Benedikt Brors, Tim Beißbarth
BACKGROUND: A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene-drug interactions complicates the task of assigning clinical significance to genomic variants. METHODS: Here we present a method that automatically matches patient-specific genomic alterations to treatment options...
March 15, 2018: Genome Medicine
He Chen, Jiacheng Yao, Yusi Fu, Yuhong Pang, Jianbin Wang, Yanyi Huang
The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically labeling adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing...
March 15, 2018: ACS Applied Materials & Interfaces
V Jung-Schroers, M Adamek, S Harris, H Syakuri, A Jung, I Irnazarow, D Steinhagen
The effect of dietary β-glucan on the bacterial community in the gut of common carp (Cyprinus carpio) was examined after oral application of Aeromonas hydrophila. Carp received either feed supplemented with 1% MacroGard® , a β-1,3/1,6-glucan, or a β-glucan-free diet. Fourteen days after feeding, half of the carp from each group were intubated with 109 colony-forming units (CFU) of a pathogenic strain of A. hydrophila. Gut samples were taken 12 hr to 7 days after application and analysed using microbiological and molecular biological techniques (NGS, RT-PCR-DGGE)...
March 15, 2018: Journal of Fish Diseases
Yanchun Ma, Kun Chen, Zhenhua Yang, Ming Guan
Lung cancer is the most common type of malignancy to metastasize to the brain, with the median survival time of patients being 6-11 months. In the present study, the aim was to compare the actionable gene mutation profiles of primary lung adenocarcinoma (LC) samples and LC brain metastasis (LCBM) samples through targeted sequencing. Next generation sequencing (NGS) of 13 formalin-fixed, paraffin-embedded LC samples and 15 LCBM samples was performed using a customized OncoAim™ cancer panel and OncoAim™ RNA fusion panel on the MiSeq platform...
April 2018: Oncology Letters
Yan Hao, Dawei Chen, Zhiguo Zhang, Ping Zhou, Yunxia Cao, Zhaolian Wei, Xiaofeng Xu, Beili Chen, Weiwei Zou, Mingrong Lv, Dongmei Ji, Xiaojin He
Hearing loss may place a heavy burden on the patient and patient's family. Given the high incidence of hearing loss among newborns and the huge cost of treatment and care (including cochlear implantation), prenatal diagnosis is strongly recommended. Termination of the fetus may be considered as an extreme outcome to the discovery of a potential deaf fetus, and therefore preimplantation genetic diagnosis has become an important option for avoiding the birth of affected children without facing the risk of abortion following prenatal diagnosis...
April 2018: Oncology Letters
R W W Brouwer, M C G N van den Hout, C E M Kockx, E Brosens, B Eussen, A de Klein, F Sleutels, W F J van IJcken
Motivation: PCR-based DNA enrichment followed by massively parallel sequencing is a straightforward and cost effective method to sequence genes up to high depth. The full potential of amplicon based sequencing assays is currently not achieved as analysis methods do not take into account the source amplicons of the detected variants. Tracking the source amplicons has the potential to identify systematic biases, enhance variant calling and improve the designs of future assays. Results: We present Nimbus, a software suite for the analysis of amplicon based sequencing data...
March 10, 2018: Bioinformatics
Zehra Aycan, Şenay Savaş-Erdeve, Semra Çetinkaya, Erdal Kurnaz, Melikşah Keskin, Nursel Muratoğlu Şahin, Elvan Bayramoğlu, Gülay Ceylaner
OBJECTIVE: Little is known about the genetic cause of idiopathic central precocious puberty (CPP). The aim of this clinical study was to determine the rate of MKRN3 mutation in cases of familial idiopathic central precocious puberty. METHODS: Potential sequence variations in the maternally imprinted MKRN3 gene were evaluated in 19 participants from 10 families using next-generation sequencing (NGS) analysis. RESULTS: In the whole group, the novel heterozygous mutation NM_005664...
February 28, 2018: Journal of Clinical Research in Pediatric Endocrinology
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