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High-Throughput Sequencing

Jing Li, Shuwen Xue, Chunqiu He, Huixia Qi, Fulin Chen, Yanling Ma
Pseudomonas aeruginosa DN1 strain and Bacillus subtilis QHQ110 strain were chosen as rhamnolipid and lipopeptide producer respectively, to evaluate the efficiency of exogenous inoculants on enhancing oil recovery (EOR) and to explore the relationship between injected bacteria and indigenous bacterial community dynamics in long-term filed pilot of Hujianshan low permeability water-flooded reservoir for 26 months. Core-flooding tests showed that the oil displacement efficiency increased by 18.46% with addition of exogenous consortia...
March 20, 2018: World Journal of Microbiology & Biotechnology
Chun-Mei Wang, Xue-Lu Yang, Ming-Hui Liu, Bao-Hua Cheng, Jing Chen, Bo Bai
miRNAs regulate a variety of biological processes through pairing-based regulation of gene expression at the 3' end of the noncoding region of the target miRNA. miRNAs were found to be abnormally expressed in ischemia/reperfusion injury models. High-throughput sequencing is a recently developed method for sequencing miRNAs and has been widely used in the analysis of miRNAs. In this study, ischemia/reperfusion injury models were intracerebroventricularly injected with 50 μg/kg apelin-13. High-throughput sequencing showed that 357 known miRNAs were differentially expressed among rat models, among which 78 changed to > 2-fold or < 0...
February 2018: Neural Regeneration Research
Jamie R Wood
Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts...
March 20, 2018: Parasitology
Michael A Schmidt, Eric M Simmons, Carolyn S Wei, Hyunsoo Park, Martin D Eastgate
An efficient, concise enantioselective total synthesis of the potent antitumor antibiotic (+)-duocarmycin SA is described. The invented route is based on a disconnection strategy that was devised to facilitate rapid and efficient synthesis of key core compounds to enable preclinical structure-activity relationship investigations. The key tricycle core was constructed with a highly enantioselective indole hydrogenation to set the stereocenter and a subsequent hitherto unexplored vicarious, nucleophilic-substitution/cyclization sequence to effectively forge a final indole ring...
March 20, 2018: Journal of Organic Chemistry
Luanfeng Hou, Qingping Wu, Qihui Gu, Qin Zhou, Jumei Zhang
Aniline has aroused general concern owing to its strong toxicity and widespread distribution in water and soil. In the present study, the bacterial community composition before and after aniline acclimation was investigated. High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the structure of the bacterial community during the aniline acclimation period. Bacillus, Lactococcus, and Enterococcus were the dominant bacteria in biologically activated carbon before acclimation. However, the proportions of Pseudomonas, Thermomonas, and Acinetobacter increased significantly and several new bacterial taxa appeared after aniline acclimation, indicating that aniline acclimation had a strong impact on the bacterial community structure of biological activated carbon samples...
March 19, 2018: Current Microbiology
Isabelle Laforest-Lapointe, Marie-Claire Arrieta
Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health...
March 2018: MSystems
Jingjiang Pi, Jie Liu, Tao Zhuang, Lin Zhang, Huimin Sun, Xiaoli Chen, Qian Zhao, Yashu Kuang, Sheng Peng, Xiaohui Zhou, Zuoren Yu, Ting Tao, Brian Tomlinson, Paul Chan, Ying Tian, Huimin Fan, Zhongmin Liu, Xiangjian Zheng, Edward Morrisey, Yuzhen Zhang
Rationale: Angiogenesis is critical for embryonic development and microRNAs fine-tune this process, but the underlying mechanisms remain incompletely understood. Methods: Endothelial cell (EC) specific miR302-367 line was used as gain-of-function and anti-miRs as loss-of-function models to investigate the effects of miR302-367 on developmental angiogenesis with embryonic hindbrain vasculature as an in vivo model and fibrin gel beads and tube formation assay as in vitro models. Cell migration was evaluated by Boyden chamber and scratch wound healing assay and cell proliferation by cell count, MTT assay, Ki67 immunostaining and PI cell cycle analysis...
2018: Theranostics
V S Sundar, Chun-Chieh Fan, Dominic Holland, Anders M Dale
With the availability of high-throughput sequencing data, identification of genetic causal variants accurately requires the efficient incorporation of function annotation data into the optimization routine. This motivates the need for development of novel methods for genome wide association studies with special focus on fine-mapping capabilities. A penalty function method that is simple to implement and capable of integrating functional annotation information into the estimation procedure, is proposed in this work...
2018: Frontiers in Genetics
V Pillonel, D Juskevicius, C K Y Ng, A Bodmer, A Zettl, D Jucker, S Dirnhofer, A Tzankov
Nodal marginal zone lymphoma (NMZL) is a rare small B-cell lymphoma lacking disease-defining phenotype and precise diagnostic markers. To better understand the mutational landscape of NMZL, particularly in comparison to other nodal small B-cell lymphomas, we performed whole-exome sequencing, targeted high-throughput sequencing, and array-comparative genomic hybridization on a retrospective series. Our study identified for the first time recurrent, diagnostically useful, and potentially therapeutically relevant BRAF mutations in NMZL...
February 28, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Dragos Ciocan, Vinciane Rebours, Cosmin Sebastian Voican, Laura Wrzosek, Virginie Puchois, Anne-Marie Cassard, Gabriel Perlemuter
Excessive alcohol consumption leads to severe alcoholic hepatitis (sAH) or chronic alcoholic pancreatitis (CAP) only in a subset of patients. We aimed to characterize the intestinal microbiota profiles of alcoholic patients according to the presence and nature of the complications observed: sAH or CAP. Eighty two alcoholic patients were included according to their complications: CAP (N = 24), sAH (N = 13) or no complications (alcoholic controls, AC, N = 45). We analyzed the intestinal microbiota by high-throughput sequencing...
March 19, 2018: Scientific Reports
Xiaole Tong, Mujeeb Ur Rehman, Shucheng Huang, Xiong Jiang, Hui Zhang, Jia KuiLi
Tibial dyschondroplasia (TD) is a common skeletal problem of avian species. The cause and etiology of this disorder is still not clear. The intestinal bacterial community is a complex ecosystem and plays very important role in healthy life of human and animals. Many researchers have made the connection between diseases and alteration of gut microbiota. However, little is know about the role of gut microbiota in TD. The objective of this study was to explore the diversity and composition of small and large intestinal bacterial communities of TD chickens...
March 16, 2018: Microbial Pathogenesis
Aaron M Walsh, Fiona Crispie, Orla O'Sullivan, Laura Finnegan, Marcus J Claesson, Paul D Cotter
BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species...
March 20, 2018: Microbiome
Zhi-Hui Zou, Dong Liu, Hong-Dong Li, Dan-Ping Zhu, Yu He, Ting Hou, Jia-Lin Yu
BACKGROUND: To explore the influences of prenatal antibiotic exposure, the intensity of prenatal and postnatal antibiotic exposure on gut microbiota of preterm infants and whether gut microbiota and drug resistant strains in the neonatal intensive care unit (NICU) over a defined period are related. METHODS: Among 28 preterm infants, there were two groups, the PAT (prenatal antibiotic therapy) group (12 cases), and the PAF (prenatal antibiotic free) group (12 cases)...
March 19, 2018: Annals of Clinical Microbiology and Antimicrobials
Yiling Li, Bin He, Jiejun Gao, Qian S Liu, Runzeng Liu, Guangbo Qu, Jianbo Shi, Ligang Hu, Guibin Jiang
The neurotoxic effects of methylmercury (MeHg) have been intensively studied. However, the molecular mechanisms responsible for the neurotoxicity of MeHg are not fully understood. To decipher these mechanisms, proteomic and high-throughput mRNA sequencing (RNA-seq) technique were utilized, comprehensively evaluating the cellular responses of human neuroblastoma SK-N-SH cells to MeHg exposure. Proteomic results revealed that MeHg exposure interfered with RNA splicing via splicesome, along with the known molecular mechanisms of mercury-related neurotoxicity (e...
March 16, 2018: Environmental Pollution
Jun Gu, Qin Yang, Yu Liu
The conventional biological processes for municipal wastewater are facing the challenges of high energy consumption and production of excessive sludge. To address these two emerging issues, this study demonstrated the feasibility to integrate mainstream anammox into an A-2B process for municipal wastewater treatment towards energy-efficient operation with reduced sludge production. In the proposed A-2B process, an anaerobic fixed bed reactor (AFBR) served as A-stage for COD capture, an anammox moving bed biofilm reactor (MBBR) was employed as B2-stage, which received effluent containing nitrite from a sequencing batch reactor (SBR) at B1-stage...
February 21, 2018: Water Research
Valentine Svensson, Sarah A Teichmann, Oliver Stegle
Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.
March 19, 2018: Nature Methods
Sara L Revolinski, L Silvia Munoz-Price
New studies have been published regarding the epidemiology of Clostridium difficile in topics such as asymptomatic C. difficile colonization, community-associated C. difficile infection, environmental contamination outside healthcare settings, animal colonization, and the interactions between C. difficile and the gut microbiome. In addition to summarizing these findings, this review offers a perspective on the potential impact of high-throughput sequencing and other potential techniques on the prevention of C...
March 19, 2018: Infection Control and Hospital Epidemiology
Ye Chen, SuNing Chen, Jian Zhang, YangMin Wang, Zhengping Jia, Xin Zhang, Xiao Han, Xiuquan Guo, XiaoDi Sun, Chen Shao, Ji Wang, Tian Lan
The current study aimed to identify a comprehensive expression-profile of microRNAs (miRNAs) in expressed prostatic secretion (EPS) collected from healthy men and patients with CP/CPPS (Chronic prostatitis/Chronic pelvic pain syndrome). After clinical screening of 382 participants, 60 healthy men and 59 IIIA CP/CPPS patients with significant pelvic-pain were included into this study from March 2012 to December 2014. High-throughput sequencing was employed to identify characteristic expression-profile of EPS-miRNAs...
February 23, 2018: Oncotarget
Andrew S Fister, Lena Landherr, Siela N Maximova, Mark J Guiltinan
Theobroma cacao , the source of cocoa, suffers significant losses to a variety of pathogens resulting in reduced incomes for millions of farmers in developing countries. Development of disease resistant cacao varieties is an essential strategy to combat this threat, but is limited by sources of genetic resistance and the slow generation time of this tropical tree crop. In this study, we present the first application of genome editing technology in cacao, using Agrobacterium-mediated transient transformation to introduce CRISPR/Cas9 components into cacao leaves and cotyledon cells...
2018: Frontiers in Plant Science
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
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