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Hao Xu, Na Tong, Shaobin Huang, Waseem Hayat, Saima Fazal, Jianjun Li, Shuang Li, Jinwu Yan, Yongqing Zhang
The autotrophic removal of sulphate and nitrate in bioelectrochemical reactors was investigated at different external voltages (0.2, 0.4, 0.6, 0.8 and 1.0 V) under anaerobic conditions. Sulphate and nitrate removal, nitrite accumulation, reduction trend of nitrate and sulphate and microbial community structure were explored. Results indicate the highest removal efficiencies of nitrate and sulphate at 43.3 ± 2.8 and 7.1 ± 0.2 mg·l-1 ·d-1 when the voltage is 0.6 V. Moreover, nitrite accumulation decreases with increased voltage from 0...
June 15, 2018: Bioresource Technology
Lu Liu, Yu Feng, Alan McNally, Zhiyong Zong
Objectives: New Delhi MBL (NDM) is a type of carbapenemase; 20 variants of NDM have been identified to date. We have found a new variant of NDM, NDM-21, and describe it here. Methods: A carbapenem-resistant Escherichia coli was subjected to WGS using an Illumina X10 sequencer to identify the antimicrobial resistance genes and its ST. The gene encoding the new variant of NDM was cloned into E. coli DH5α, with blaNDM-5 being cloned as the control. Transformants were tested for susceptibility to carbapenems...
June 14, 2018: Journal of Antimicrobial Chemotherapy
Akila Subramaniam, William J Van Der Pol, Travis Ptacek, Elena Lobashevsky, Cherry Neely, Joseph R Biggio, Elliot J Lefkowitz, Casey D Morrow, Rodney K Edwards
OBJECTIVES: To evaluate if midtrimester maternal serum contains microbial DNA and whether it differs between women with spontaneous preterm birth (SPTB) and those delivering at term. STUDY DESIGN: In this retrospective case-control study, we identified 20 healthy nulliparas with SPTB at 24-33 weeks of a nonanomalous singleton in 2014. Each case was matched by race/ethnicity to a control delivering at 39-40 weeks. Serum samples, collected at 15-20 weeks and stored at -80C , were thawed and DNA extracted...
June 18, 2018: Journal of Maternal-fetal & Neonatal Medicine
Jazelyn M Salvador, Dame Loveliness T Apaga, Frederick C Delfin, Gayvelline C Calacal, Sheila Estacio Dennis, Maria Corazon A De Ungria
Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results...
June 8, 2018: Forensic Science International. Genetics
Boyang Qiu, Kait Al, Ana M Pena-Diaz, George S Athwal, Darren Drosdowech, Kenneth J Faber, Jeremy P Burton, David B O'Gorman
BACKGROUND: Advances in DNA sequencing technologies have made it possible to detect microbial genome sequences (microbiomes) within tissues once thought to be sterile. We used this approach to gain insights into the likely sources of Cutibacterium acnes (formerly Propionibacterium acnes) infections within the shoulder. METHODS: Tissue samples were collected from the skin, subcutaneous fat, anterior supraspinatus tendon, middle glenohumeral ligament, and humeral head cartilage of 23 patients (14 male and 9 female patients) during primary arthroplasty surgery...
June 13, 2018: Journal of Shoulder and Elbow Surgery
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Ratnam Wickneswari
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes...
June 15, 2018: Scientific Reports
Marc Teissier, Hélène Larroque, Christèle Robert-Granié
BACKGROUND: In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain the same fraction of genetic variance. However, ssGBLUP is not suitable for protein content, which is controlled by a major gene, i.e. α s 1 casein. This gene explains about 40% of the genetic variation in protein content. In this study, we evaluated the accuracy of genomic prediction using different genomic methods to include the effect of the α s 1 casein gene...
June 15, 2018: Genetics, Selection, Evolution: GSE
Xiangkun Li, Gaige Liu, Shuli Liu, Kaili Ma, Lingwei Meng
The volatile fatty acids (VFAs) accumulation pattern and microbial community succession were studied during excess sludge (ES) alkaline fermentation at pH of 10.0 with expanded granular sludge blanket reactor over 5 cyclers. Microbial community shifted conspicuously as ES suffered alkaline fermentation. Both VFAs and acid-producing bacteria increased rapidly during the first 8 days fermentation time, and they showed a quite positive correlation relationship. In addition, soluble chemical oxygen demand (SCOD) also dramatically increased during the first 8 days, which implied 8 day was the optimum sludge retention time (SRT) for ES alkaline fermentation and VFAs accumulation time...
June 12, 2018: Journal of Environmental Management
Arnold Bainomugisa, Tania Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben J Marais, Lachlan M Coin
A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99...
June 15, 2018: Microbial Genomics
Ruth E Timme, Hugh Rand, Maria Sanchez Leon, Maria Hoffmann, Errol Strain, Marc Allard, Dwayne Roberson, Joseph D Baugher
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions...
June 15, 2018: Microbial Genomics
Peng Wu, Guihao Zhang, Jie Zhao, Jiawei Chen, Yang Chen, Weina Huang, Jialei Zhong, Jiarong Zeng
Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be sterile has been overturned. Dysbiosis of the urinary microbiome has been revealed responsible for various urological disorders, including prostate cancer. The link between chronic inflammation, microbiome and solid tumors has been established for various neoplastic diseases. However, a detailed and comprehensive analysis of urinary microenvironment of bladder cancer has not been yet reported...
2018: Frontiers in Cellular and Infection Microbiology
Yanlu Qiao, Jiwen Liu, Meixun Zhao, Xiao-Hua Zhang
The mud sediments of the eastern China marginal seas (ECMS) are deposited under different hydrodynamic conditions with different organic matter sources. These events have been demonstrated to exert significant influences on microbial communities and biogeochemical processes in surface sediments. However, the extent to which such effects occur in subsurface microbial communities remains unclear. In this study, both horizontal and vertical (five sites, each for eight layers) distributions of bacterial abundance and community composition in mud deposits of the South Yellow Sea (SYS) and East China Sea (ECS) were investigated by quantitative PCR and Illumina sequencing of the 16S rRNA gene...
2018: Frontiers in Microbiology
Dieter M Tourlousse, Akiko Ohashi, Yuji Sekiguchi
Workflows for microbiome community profiling by high-throughput sequencing are prone to sample mix-ups and cross-contamination due to the complexity of the procedures and large number of samples typically analyzed in parallel. We employed synthetic 16S rRNA gene spike-in controls to establish a method for tracking of sample identity and detection of cross-contamination in microbiome community profiling assays based on 16S rRNA gene amplicon sequencing (16S-seq). Results demonstrated that combinatorial sample tracking mixes (STMs) can be reliably resolved by Illumina sequencing and faithfully represent their sample of origin...
June 14, 2018: Scientific Reports
Barbara Vona, Michaela A H Hofrichter, Jörg Schröder, Wafaa Shehata-Dieler, Indrajit Nanda, Thomas Haaf
OBJECTIVES: Despite recent advancements in diagnostic tools, the genomic landscape of hereditary hearing loss remains largely uncharacterized. One strategy to understand genome-wide aberrations includes the analysis of copy number variation that can be mapped using SNP-microarray technology. A growing collection of literature has begun to uncover the importance of copy number variation in hereditary hearing loss. This pilot study underpins a larger effort that involves the stage-wise analysis of hearing loss patients, many of whom have advanced to high-throughput sequencing analysis...
June 14, 2018: BMC Research Notes
Xiaoqi Liu, Yaqi Wu, Zequn Miao, Houbin Zhang, Bo Gong, Xianjun Zhu, Lulin Huang, Yi Shi, Fang Hao, Shi Ma, He Lin, Lejin Wang, Zhenglin Yang
PURPOSE: Congenital aniridia, a severe bilateral panocular visual disorder, is an autosomal dominantly inherited eye anomaly. Mutations in the paired box 6 gene (PAX6) have been shown to be responsible for congenital aniridia in most patients. The purpose of the present study was to report clinical features of a Chinese family with congenital aniridia and to screen novel genetic mutations for congenital aniridia. METHODS: All members of a three-generation family underwent comprehensive ophthalmic examination, and 8 of its 25 members were diagnosed with congenital aniridia...
June 14, 2018: Ophthalmic Genetics
Kamarul Zaman Zarkasi, Mardani Abdul Halim, Teh Faridah Nazari, Feizal Daud
This article contains data on the bacterial communities and its diversity associated with Anadara granosa . The A. granosa samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA Illumina sequencing approaches. A. granosa , a commercial blood cockles and popular seafoods, is fragile to the surrounding environments. Thus, our research focused to better understand the bacterial communities and it diversity in the A. granosa , as well as on the generation of a metagenomic library from A...
August 2018: Data in Brief
Zhaoqiang Qian, Ruoxin Zhang, Jinlong Zhou, Siqi Sun, Yuanyuan Di, Wei Ren, Yingfang Tian
The transcriptome sequencing data of valproic acid (VPA) model of autism and control rats are presented. VPA model of autism was induced by a single intraperitoneal injection of 600 mg/kg sodium valproic acid to female rats at day 12.5 post-conception, and the control rats were injected with saline. Male offspring of VPA- or saline-injected dams from different litters were sacrificed on PND 35 ( n = three rats/three litters/group). Prefrontal cortex was dissected from both hemispheres, and RNA was isolated...
June 2018: Data in Brief
Ton That Huu Dat, Georg Steinert, Nguyen Thi Kim Cuc, Hauke Smidt, Detmer Sipkema
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity...
2018: PeerJ
Zhe Xun, Qian Zhang, Tao Xu, Ning Chen, Feng Chen
Inflammatory bowel diseases (IBDs) are chronic, idiopathic, relapsing disorders of unclear etiology affecting millions of people worldwide. Aberrant interactions between the human microbiota and immune system in genetically susceptible populations underlie IBD pathogenesis. Despite extensive studies examining the involvement of the gut microbiota in IBD using culture-independent techniques, information is lacking regarding other human microbiome components relevant to IBD. Since accumulated knowledge has underscored the role of the oral microbiota in various systemic diseases, we hypothesized that dissonant oral microbial structure, composition, and function, and different community ecotypes are associated with IBD; and we explored potentially available oral indicators for predicting diseases...
2018: Frontiers in Microbiology
Venugopalan Cheriyath, Jaspreet Kaur, Anne Davenport, Ashjan Khalel, Nobel Chowdhury, Lalitha Gaddipati
BACKGROUND: Redox deregulations are ubiquitous in cancer cells. However, the role of mitochondrial redox deregulation in metastasis remains unclear. In breast cancer, upregulation of mitochondrial antiapoptotic protein G1P3 (IFI6) was associated with poor distance metastasis-free survival (DMFS). Therefore, we tested the hypothesis that G1P3-induced mitochondrial redox deregulation confers metastatic potentials in breast cancer cells. METHODS: Cell migration and invasion assays; confocal and immunofluorescence microscopy; and Illumina HumanHT-12 BeadChip to assess gene expression...
June 14, 2018: British Journal of Cancer
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