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Anantharaman Ramani, Yongxun Wong, Si Zhen Tan, Bing Hong Shue, Christopher Syn
The ability to predict bio-geographic ancestry can be valuable to generate investigative leads towards solving crimes. Ancestry informative marker (AIM) sets include large numbers of SNPs to predict an ancestral population. Massively parallel sequencing has enabled forensic laboratories to genotype a large number of such markers in a single assay. Illumina's ForenSeq DNA Signature Kit includes the ancestry informative SNPs reported by Kidd et al. In this study, the ancestry prediction capabilities of the ForenSeq kit through sequencing on the MiSeq FGx were evaluated in 1030 unrelated Singapore population samples of Chinese, Malay and Indian origin...
August 15, 2017: Forensic Science International. Genetics
Ping Wang, Zhisheng Yu, Jihong Zhao, Hongxun Zhang
Microbial communities of sludge samples from a full-scale anaerobic digestion (AD) fed with primary sludge (PS) and excess sludge (ES) were analyzed using qPCR and MiSeq. The results showed that the microbial composition of digested sludge remained relatively stable but was partially changed by microbial immigration from feeding sludge. The dominant archaea in the digested sludge were largely the same as those in the feeding sludge, but their abundances differed markedly. The dominant fungal genera in the digested sludge were different from those in PS but were similar to those in ES...
September 28, 2017: Bioresource Technology
Hyun Min Jang, Young Beom Kim, Sangki Choi, Yunho Lee, Seung Gu Shin, Tatsuya Unno, Young Mo Kim
The wide use of antibiotics in aquaculture for prophylactic and therapeutic purposes can potentially lead to the prevalence of antibiotic resistance genes (ARGs). This study reports for the first time the profile of ARGs from effluents of coastal aquaculture located in South Jeolla province and Jeju Island, South Korea. Using quantitative PCR (qPCR), twenty-two ARGs encoding tetracycline resistance (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetBP), sulfonamide resistance (sul1, sul2), quinolone resistance (qnrD, qnrS, aac(6')-Ib-cr), β-lactams resistance (blaTEM, blaCTX, blaSHV), macrolide resistance (ermC), florfenicol resistance (floR) and multidrug resistance (oqxA) and a class 1 integrons-integrase gene (intI1) were quantified...
October 12, 2017: Environmental Pollution
Xiumei Jiang, Wenfei Wang, Yongmei Yang, Lutao Du, Xiaoyun Yang, Lili Wang, Guixi Zheng, Weili Duan, Rui Wang, Xin Zhang, Lishui Wang, Xiaoyang Chen, Chuanxin Wang
Circulating microRNAs (miRNAs) are emerging as novel noninvasive biomarkers for prediction of lymph node metastasis (LNM) in cancer. The aim of this study was to identify serum miRNA signatures for prediction and prognosis of LNM in gastric cancer (GC). MiSeq sequencing was performed for an initial screening of serum miRNAs in 10 GC patients with LNM, 10 patients without LNM and 10 healthy controls. Reverse transcription quantitative real-time PCR was applied to confirm concentration of candidate miRNAs using a training cohort (n = 279) and a validation cohort (n = 180)...
September 12, 2017: Oncotarget
J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
Daria Liamina, Wladimir Sibirnyj, Anna Khokhlova, Viacheslav Saenko, Eugenia Rastorgueva, Aleksandr Fomin, Yury Saenko
In our study, we estimate an effect from chromosome aberrations and genome mutations on changes in microRNA expression profiles in cancer cell lines demonstrating different radiosensitivity. Here, cell viability and microRNA spectrum have been estimated 1, 4, and 24 h after irradiation. MiSeq high-throughput sequencing system (Illumina, San Diego, CA, USA) is employed to perform microRNA spectrum estimation. In the K562 cell line, the number of expressed microRNAs in chromosomes demonstrates a more pronounced variation...
October 13, 2017: Cancers
Tomasz Jagielski, Jan Gawor, Zofia Bakuła, Karolina Zuchniewicz, Iwona Żak, Robert Gromadka
BACKGROUND: The complex cell wall structure of algae often precludes efficient extraction of their genetic material. The purpose of this study was to design a next-generation sequencing-suitable DNA isolation method for unicellular, achlorophyllous, yeast-like microalgae of the genus Prototheca, the only known plant pathogens of both humans and animals. The effectiveness of the newly proposed scheme was compared with five other, previously described methods, commonly used for DNA isolation from plants and/or yeasts, available either as laboratory-developed, in-house assays, based on liquid nitrogen grinding or different enzymatic digestion, or as commercially manufactured kits...
2017: Plant Methods
Emily McGovern, Matthew S McCabe, Paul Cormican, Milka Popova, Kate Keogh, Alan K Kelly, David A Kenny, Sinead M Waters
Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal's compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals...
October 12, 2017: Scientific Reports
Akhikun Nahar, Anthony L Baker, Michael A Charleston, John P Bowman, Margaret L Britz
Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of two novel sub-Antarctic Williamsia species, designated strains 1135 and 1138. The estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb, respectively. This genome sequence information will aid in understanding the lipid metabolic pathways of cold-tolerant Williamsia species.
October 12, 2017: Genome Announcements
Xiai Yang, Liangliang Liu, Jing Chen, Aiping Xiao
In order to investigate the influence of aflatoxin B1 (AFB1) on intestinal bacterial flora, 24 Kunming mice (KM mice) were randomly placed into four groups, which were labeled as control, low-dose, medium-dose, and high-dose groups. They were fed intragastrically with 0.4 mL of 0 mg/L, 2.5 mg/L, 4 mg/L, or 10 mg/L of AFB1 solutions, twice a day for 2 months. The hypervariable region V3 + V4 on 16S rDNA of intestinal bacterial flora was sequenced by the use of a high-flux sequencing system on a Miseq Illumina platform; then, the obtained sequences were analyzed...
October 12, 2017: Toxins
K Adamberg, K Kolk, M Jaagura, R Vilu, S Adamberg
The metabolic activity of colon microbiota is specifically affected by fibres with various monomer compositions, degree of polymerisation and branching. The supply of a variety of dietary fibres assures the diversity of gut microbial communities considered important for the well-being of the host. The aim of this study was to compare the impact of different oligo- and polysaccharides (galacto- and fructooligosaccharides, resistant starch, levan, inulin, arabinogalactan, xylan, pectin and chitin), and a glycoprotein mucin on the growth and metabolism of faecal microbiota in vitro by using isothermal microcalorimetry (IMC)...
October 12, 2017: Beneficial Microbes
Yo-Jin Shiau, Yuanfeng Cai, Yu-Te Lin, Zhongjun Jia, Chih-Yu Chiu
Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions...
October 11, 2017: Microbial Ecology
Jamie K Lemon, Pavel P Khil, Karen M Frank, John P Dekker
Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. Here, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection...
October 11, 2017: Journal of Clinical Microbiology
Alfred J Arulandhu, Martijn Staats, Rico Hagelaar, Marleen M Voorhuijzen, Theo W Prins, Ingrid Scholtens, Adalberto Costessi, Danny Duijsings, François Rechenmann, Frédéric B Gaspar, Maria Teresa Barreto Crespo, Arne Holst-Jensen, Matthew Birck, Malcolm Burns, Edward Haynes, Rupert Hochegger, Alexander Klingl, Lisa Lundberg, Chiara Natale, Hauke Niekamp, Elena Perri, Alessandra Barbante, Jean-Philippe Rosec, Ralf Seyfarth, Tereza Sovová, Christoff Van Moorleghem, Saskia van Ruth, Tamara Peelen, Esther Kok
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories...
October 1, 2017: GigaScience
Haiyan Pei, Hangzhou Xu, Jingjing Wang, Yan Jin, Hong-Di Xiao, Chunxia Ma, Jiongming Sun, Hongmin Li
This is the first study to systematically investigate the microbial community structure in cyanobacteria-laden drinking water sludge generated by different types of coagulants (including AlCl3, FeCl3, and polymeric aluminium ferric chloride (PAFC)) using Illumina 16S rRNA gene MiSeq sequencing. Results show that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, and Planctomycetes were the most dominant phyla in sludge, and because of the toxicity of high Al and Fe level in AlCl3 and FeCl3 sludges, respectively, the PAFC sludge exhibited greater microbial richness than that in AlCl3 and FeCl3 sludges...
October 10, 2017: Environmental Science & Technology
Zhihui Yang, Mark Mammel, Efstathia Papafragkou, Kaoru Hida, Christopher A Elkins, Michael Kulka
Next generation sequencing (NGS) holds promise as a single application for both detection and sequence identification of foodborne viruses; however, technical challenges remain due to anticipated low quantities of virus in contaminated food. In this study, with a focus on data analysis using several bioinformatics tools, we applied NGS toward amplification-independent detection and identification of norovirus at low copy (<10(3) copies) or within multiple strains from produce. Celery samples were inoculated with human norovirus (stool suspension) either as a single norovirus strain, a mixture of strains (GII...
August 3, 2017: International Journal of Food Microbiology
Pavol Sulo, Dana Szabóová, Peter Bielik, Silvia Poláková, Katarína Šoltys, Katarína Jatzová, Tomáš Szemes
The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters...
June 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Yuan Zhang, Yifan Ping, Ruyu Zhou, Juan Wang, Guangdong Zhang
This study aims to explore the water quality of dental unit waterlines (DUWLs) and the diversity of microbial communities in DUWLs. Water samples from 33 dental chair units (DCUs) were collected, diluted and then spread on sterilized R2A plate for incubation. Subsequently, the microbial colony-forming units per milliliter (CFU/ml) were recorded by an automatic colony analyzer. Total DNA extracted from the rest of the samples was tested on the Illumina MiSeq PE300 platform. T-test and Kruskal-Wallis rank test were adopted for statistical analysis...
October 5, 2017: Journal of Infection and Public Health
Kaori Morishima, Tomohiro Suzuki, Mineaki Aizawa
We developed 13 polymorphic microsatellite loci of the Japanese land leech (Haemadipsa japonica; Haemadipsidea) using an Illumina MiSeq sequencing approach. A total of 42,064 nuclear DNA contigs were filtered for microsatellite motifs, of among 30,873 simple sequence repeat loci were identified. From these sequences, we selected 30 primer sets, and 13 of these loci were successfully amplified. Polymorphism of the 13 loci was tested using 16 individuals sampled from sixteen populations across Japan. The number of alleles and polymorphism information content varied from 5 to 17 and 0...
October 5, 2017: Parasitology International
Gunilla Högnäs, Kati Kivinummi, Heini M L Kallio, Reija Hieta, Pekka Ruusuvuori, Antti Koskenalho, Juha Kesseli, Teuvo L J Tammela, Jarno Riikonen, Joanna Ilvesaro, Saara Kares, Pasi P Hirvikoski, Marita Laurila, Tuomas Mirtti, Matti Nykter, Paula M Kujala, Tapio Visakorpi, Teemu Tolonen, G Steven Bova
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied...
October 3, 2017: American Journal of Surgical Pathology
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