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https://www.readbyqxmd.com/read/28432095/mushroom-emergence-detected-by-combining-spore-trapping-with-molecular-techniques
#1
Carles Castaño, Jonàs Oliva, Juan Martínez de Aragón, Josu G Alday, Javier Parladé, Joan Pera, José Antonio Bonet
Obtaining reliable and representative mushroom production data requires time-consuming sampling schemes. In this paper, we assessed a simple methodology to detect mushroom emergence by trapping the fungal spores of the fruiting body community in plots where mushroom production was determined weekly. We compared the performance of filter paper traps with that of funnel traps and combined these spore trapping methods with species-specific quantitative real-time PCR and Illumina MiSeq to determine the spore abundance...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431497/effect-of-ensiled-mulberry-leaves-and-sun-dried-mulberry-fruit-pomace-on-the-fecal-bacterial-community-composition-in-finishing-steers
#2
Yan Li, Qingxiang Meng, Bo Zhou, Zhenming Zhou
BACKGROUND: Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community...
April 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28431359/reconstruction-of-microbial-community-structures-as-evidences-for-soil-redox-coupled-reductive-dechlorination-of-pcp-in-a-mangrove-soil
#3
Yan Xu, Yan He, Xianjin Tang, Philip C Brookes, Jianming Xu
The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics...
April 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28431310/characterization-of-bacterial-communities-of-donkey-milk-by-high-throughput-sequencing
#4
Maria de Los Dolores Soto Del Rio, Alessandra Dalmasso, Tiziana Civera, Maria Teresa Bottero
The interest in donkey milk (DM) is growing because of its functional properties and nutritional value, especially for children with allergies and food intolerances. However, most of the available reports of DM microbiota are based on culture-dependent methods to investigate food safety issues and the presence of lactic acid bacteria (LAB). The aim of this study was to determine the composition of DM bacterial communities using a high-throughput sequencing (HTS) approach. Bulk milk samples from Italian donkey dairy farms from two consecutive years were analysed using the MiSeq Illumina platform...
March 30, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28429823/changes-in-the-gut-microbiome-of-the-chinese-mitten-crab-eriocheir-sinensis-in-response-to-white-spot-syndrome-virus-wssv-infection
#5
Z F Ding, M J Cao, X S Zhu, G H Xu, R L Wang
Intestinal microorganisms play important roles in maintaining host health, but their functions in aquatic animal hosts have yet to be fully elucidated. The Chinese mitten crab, Eriocheir sinensis, is one such example. We attempted to identify the shift of gut microbiota that occurred in response to infection of white spot syndrome virus (WSSV), an emerging viral pathogen in the crab aquaculture industry. The microbiota may exert some control over aspects of the viral pathogenesis. We investigated the changes in composition and structure of the crab gut microbiome during various WSSV infection stages of 6 h post-infection (hpi) and 48 hpi, using a 16S rRNA approach on the MiSeq Illumina sequencing platform...
April 21, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28428148/plasma-ctdna-analysis-for-detection-of-the-egfr-t790m-mutation-in-patients-with-advanced-non-small-cell-lung-cancer
#6
Suzanne Jenkins, James C-H Yang, Suresh S Ramalingam, Karen Yu, Sabina Patel, Susie Weston, Rachel Hodge, Mireille Cantarini, Pasi A Jänne, Tetsuya Mitsudomi, Glenwood D Goss
INTRODUCTION: Tumor biopsies for detecting epidermal growth factor receptor mutations (EGFRm) in advanced non-small cell lung cancer (NSCLC) are invasive, costly and not always feasible for patients with late-stage disease. The clinical utility of the cobas(®) EGFR Mutation Test v2 with plasma samples from patients with NSCLC at disease progression following previous EGFR-tyrosine kinase inhibitor (TKI) therapy was investigated to determine osimertinib treatment eligibility. METHODS: Matched tumor tissue and plasma samples from patients screened for AURA extension and AURA2 phase II studies were tested for EGFRm using tissue- and plasma-based cobas(®) EGFR Mutation Tests v2...
April 17, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28423512/kinase-analysis-of-penile-squamous-cell-carcinoma-on-multiple-platforms-to-identify-potential-therapeutic-targets
#7
Eddy S Yang, Christopher D Willey, Amitkumar Mehta, Michael R Crowley, David K Crossman, Dongquan Chen, Joshua C Anderson, Gurudatta Naik, Deborah L Della Manna, Tiffiny S Cooper, Guru Sonpavde
Penile squamous cell carcinoma (PSCC) is an orphan malignancy with poorly understood biology and suboptimal systemic therapy. Given that kinases may be drivers and readily actionable, we performed comprehensive multiplatform analysis of kinases in PSCC tumor and normal tissue. Fresh frozen tumors were collected from 11 patients with PSCC. After macrodissection to demarcate tumor from normal tissue, the samples underwent multiplatform analysis of kinases. Next Generation Sequencing (NGS) of 517 kinase genes was performed using Agilent Kinome capture and run on the Illumina MiSeq at PE150bp...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#8
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419064/the-application-of-next-generation-sequencing-for-mutation-detection-in-autosomal-dominant-hereditary-hearing-impairment
#9
Nicolas Gürtler, Benno Röthlisberger, Katja Ludin, Christoph Schlegel, Anil K Lalwani
OBJECTIVE: Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. PATIENTS: Two Swiss families with autosomal-dominant hereditary hearing impairment. INTERVENTION: Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library...
April 17, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28417591/effective-mosquito-and-arbovirus-surveillance-using-metabarcoding
#10
J Batovska, S E Lynch, N O I Cogan, K Brown, J M Darbro, E A Kho, M J Blacket
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernise vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding'. The aim of our study was to establish a metabarcoding protocol to characterise pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28417435/lachnospiraceae-shift-in-the-microbial-community-of-mice-faecal-sample-effects-on-water-immersion-restraint-stress
#11
Shiyin Li, Zelin Wang, Yun Yang, Sha Yang, Chenchen Yao, Kaiyun Liu, Sixin Cui, Quanming Zou, Hongwu Sun, Gang Guo
Stress, including both psychological and physical stimulation, can cause changes in the microbiota and mucosal function of the gastrointestinal system. There are few research studies available about the faecal microbiota changes after stress, such as water immersion restraint stress (WIRS). Therefore, in this study, we focused on analysing the composition changes of faecal microbiota in WIRS mice. The WIRS model, in which Blab/c mice were immersed in 21 ± 2 °C water for 4 h each day for 14 days, was established...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28417259/comparison-between-magnetic-bead-and-qpcr-library-normalisation-methods-for-forensic-mps-genotyping
#12
Bhavik Mehta, Samantha Venables, Paul Roffey
Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample...
April 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28410439/responses-of-bacterial-communities-to-cuo-nanoparticles-in-activated-sludge-system
#13
Xiaohui Wang, Jing Li, Rui Liu, Reti Hai, Dexun Zou, Xiaobiao Zhu, Nan Luo
The main objectives of this study were to investigate the influence of copper oxide nanoparticles (CuO NPs) on wastewater nutrient removal, bacterial community and molecular ecological network in activated sludge. The results showed that long-term exposure to 1 mg/L CuO NPs induced an increase of effluent concentrations of ammonia and total phosphorus, which was consistent with the inhibition of enzyme activities of ammonia monooxygenase, nitrite oxidoreductase, exopolyphosphatase and polyphosphate in the presence of CuO NPs...
April 14, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28410368/comprehensive-bioinformatics-analysis-of-mycoplasma-pneumoniae-genomes-to-investigate-underlying-population-structure-and-type-specific-determinants
#14
Maureen H Diaz, Heta P Desai, Shatavia S Morrison, Alvaro J Benitez, Bernard J Wolff, Jason Caravas, Timothy D Read, Deborah Dean, Jonas M Winchell
Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs...
2017: PloS One
https://www.readbyqxmd.com/read/28408641/gastroparesis-and-lipid-metabolism-associated-dysbiosis-in-wistar-kyoto-rats
#15
Julie E Dalziel, Karl Fraser, Wayne Young, Catherine M Lloyd-West, Shalome A Bassett, Nicole C Roy
Altered gastric accommodation and intestinal morphology suggests impaired gastrointestinal (GI) transit may occur in the Wistar Kyoto (WKY) rat strain, as common in stress-associated functional GI disorders. Because changes in GI transit can alter microbiota composition, we investigated whether these are altered in WKY rats compared with the resilient Sprague Dawley (SD) rats under basal conditions, and characterized plasma lipid and metabolite differences. Bead transit was tracked by X-ray imaging to monitor: gastric emptying (GE; 4 h), small intestine (SI) transit (9 h) and large intestine transit (12 h)...
April 13, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28407967/molecular-characterization-of-an-unauthorized-genetically-modified-bacillus-subtilis-production-strain-identified-in-a-vitamin-b2-feed-additive
#16
Valentina Paracchini, Mauro Petrillo, Ralf Reiting, Alexandre Angers-Loustau, Daniela Wahler, Andrea Stolz, Birgit Schönig, Anastasia Matthies, Joachim Bendiek, Dominik M Meinel, Sven Pecoraro, Ulrich Busch, Alex Patak, Joachim Kreysa, Lutz Grohmann
Many food and feed additives result from fermentation of genetically modified (GM) microorganisms. For vitamin B2 (riboflavin), GM Bacillus subtilis production strains have been developed and are often used. The presence of neither the GM strain nor its recombinant DNA is allowed for fermentation products placed on the EU market as food or feed additive. A vitamin B2 product (80% feed grade) imported from China was analysed. Viable B. subtilis cells were identified and DNAs of two bacterial isolates (LHL and LGL) were subjected to three whole genome sequencing (WGS) runs with different devices (MiSeq, 454 or HiSeq system)...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28407078/inulin-with-different-degrees-of-polymerization-modulates-composition-of-intestinal-microbiota-in-mice
#17
Limeng Zhu, Song Qin, Shixiang Zhai, Yonglin Gao, Lili Li
The study aimed to analyse the global influences of dietary inulin with different degrees of polymerization (DP) on intestinal microbial communities. 6-week-old male C57BL/6J mice were treated with fructo-oligosaccharides (FOS) and inulin for 6 weeks. Fecal samples were obtained at time point 0 and 6th week. 16S rRNA sequence analysis was used to measure intestinal microbiota performed on Illumina MiSeq platform. Influences of dietary inulin on intestinal microbiota were more complex effects than bifidogenic effects, relative abundance of butyrate-producing bacteria increased after interventions...
April 12, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28405600/longitudinal-analysis-of-the-intestinal-microbiota-in-liver-transplantation
#18
Karin Kato, Miki Nagao, Kentaro Miyamoto, Kentaro Oka, Motomichi Takahashi, Masaki Yamamoto, Yasufumi Matsumura, Toshimi Kaido, Shinji Uemoto, Satoshi Ichiyama
BACKGROUND: Increasing evidence suggests that the intestinal microbiota plays an important role in liver diseases. However, the dynamics of the intestinal microbiota during liver transplantation (LT) and its potential role in clinical course remain unknown. METHODS: We prospectively analyzed the intestinal microbiota of 38 patients who underwent LT in Kyoto University Hospital. We characterized the microbial compositions of fecal specimens from LT patients using a metagenomics approach by an Illumina MiSeq platform...
April 2017: Transplantation Direct
https://www.readbyqxmd.com/read/28405400/microbe-biogeography-tracks-water-masses-in-a-dynamic-oceanic-frontal-system
#19
Anni Djurhuus, Philipp H Boersch-Supan, Svein-Ole Mikalsen, Alex D Rogers
Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance-decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28404012/a-non-endoscopic-device-to-sample-the-oesophageal-microbiota-a-case-control-study
#20
Daffolyn R Fels Elliott, Alan W Walker, Maria O'Donovan, Julian Parkhill, Rebecca C Fitzgerald
BACKGROUND: The strongest risk factor for oesophageal adenocarcinoma is reflux disease, and the rising incidence of this coincides with the eradication of Helicobacter pylori, both of which might alter the oesophageal microbiota. We aimed to profile the microbiota at different stages of Barrett's carcinogenesis and investigate the Cytosponge as a minimally invasive tool for sampling the oesophageal microbiota. METHODS: In this case-control study, 16S rRNA gene amplicon sequencing was done on 210 oesophageal samples from 86 patients representing the Barrett's oesophagus progression sequence (normal squamous controls [n=20], non-dysplastic [n=24] and dysplastic Barrett's oesophagus [n=23], and oesophageal adenocarcinoma [n=19]), relevant negative controls, and replicates on the Illumina MiSeq platform...
January 2017: Lancet. Gastroenterology & Hepatology
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