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High throughput sequencing

Shuo Zhang, Jiali Chang, Wei Liu, Yiran Pan, Kangping Cui, Xi Chen, Peng Liang, Xiaoyuan Zhang, Qing Wu, Yong Qiu, Xia Huang
Based on the new syntrophic methanogenesis route via direct interspecies electron transfer (DIET), a novel bioaugmentation method by adding exoelectrogenic Geobacter species to accelerate methanogenesis was developed in this study. Geobacter sulfurreducens PCA, type exoelectrogenic strain of Geobacter species was chosen for the research. To clarify the effect of G. sulfurreducens on methanogenesis, batch tests of CH4 production were carried out. Acetate, the most typical precursor of methanogenesis was chosen as the substrate of batch tests...
June 12, 2018: Science of the Total Environment
Justus Hardegen, Adriel Latorre-Pérez, Cristina Vilanova, Thomas Günther, Manuel Porcar, Olaf Luschnig, Claudia Simeonov, Christian Abendroth
In this work, liquid and solid fractions of grass biomass were used as co-substrates for anaerobic co-digestion of sewage sludge. The input of grass biomass was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based cell counting and full-length 16S rRNA gene high-throughput sequencing, proving for the first time the suitability of nanopore-based portable sequencers as a monitoring tool for anaerobic digestion systems. In both cases co-fermentation resulted in an increased number of bacteria and methanogenic archaea...
June 6, 2018: Bioresource Technology
Weihua Zhou, Yibin Zhang, Yayue Zeng, Minyuan Peng, Hui Li, Shuming Sun, Bianying Ma, Yanpeng Wang, Mao Ye, Jing Liu
Multiple myeloma (MM) is a malignant plasma cell disease and is considered incurable. Annexin A2 (ANXA2) is closely related to the proliferation and adhesion of MM. Using protein-SELEX, we performed a screen for aptamers that bind GST-ANXA2 from a library, and GST protein was used for negative selection. The enrichment of the ssDNA pool was monitored by filter-binding assay during selection. After nine rounds of screening and high-throughput sequencing, we obtained six candidate aptamers that bind to the ANXA2 protein...
June 12, 2018: Biochimie
Jiadi Sun, Pei Zhu, Xiumei Wang, Jian Ji, Jean de Dieu Habimana, Jingdong Shao, Hongtao Lei, Yinzhi Zhang, Xiulan Sun
Lipopolysaccharide (LPS), a characteristic component of the outer membrane of Gram-negative bacteria, can be used as an effective biomarker to detect bacterial contamination. Here, we reported a 293/hTLR4A-MD2-CD14 cell-based fluorescent biosensor to detect and identify LPS, which is carried out in a 96-well microplate with nondestructive, user-friendly and high efficiency. The promoter sequence of the critical signaling pathway gene ZC3H12A (encoding MCPIP1 protein) and Enhanced Green Fluorescence Protein (EGFP) were combined to construct a recombinant plasmid, which was transferred into 293/hTLR4A-MD2-CD14 cells through lipid-mediated, DNA-transfection way...
June 15, 2018: Journal of Agricultural and Food Chemistry
Sergey V Prykhozhij, Charlotte Fuller, Shelby L Steele, Chansey J Veinotte, Babak Razaghi, Johane M Robitaille, Christopher R McMaster, Adam Shlien, David Malkin, Jason N Berman
We have optimized point mutation knock-ins into zebrafish genomic sites using clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 reagents and single-stranded oligodeoxynucleotides. The efficiency of knock-ins was assessed by a novel application of allele-specific polymerase chain reaction and confirmed by high-throughput sequencing. Anti-sense asymmetric oligo design was found to be the most successful optimization strategy. However, cut site proximity to the mutation and phosphorothioate oligo modifications also greatly improved knock-in efficiency...
June 14, 2018: Nucleic Acids Research
Tobias Moser
This review addresses the advances of our molecular understanding of hearing and how this benefits the hearing impaired. Classical biochemical methods usually fall short in contributing to the analysis of the molecular mechanisms of hearing e. g. in the cochlea, the auditory part of the inner ear, due to the scarcity of the cells of interest. Genetics, molecular cell biology, and physiology, on the other hand, have elucidated the intricate molecular and cellular mechanisms that bring about the outstanding performance of the auditory system...
March 2018: Laryngo- Rhino- Otologie
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
C F Wright, M Parker, A M Lucassen
PURPOSE: Accidental discovery of misattributed parentage is an age-old problem in clinical medicine, but the ability to detect it routinely has increased recently as a result of high-throughput DNA sequencing technologies coupled with family sequencing studies. Problems arise at the clinical-research boundary, where policies and consent forms guaranteeing nondisclosure may conflict with standard clinical care. METHODS: To examine the challenges of managing misattributed parentage within hybrid translational research studies, we used a case study of a developmentally delayed child with a candidate variant found through a large-scale trio genome sequencing study in which data from unrelated samples were routinely excluded...
June 14, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
David López-Escardó, Jordi Paps, Colomban de Vargas, Ramon Massana, Iñaki Ruiz-Trillo, Javier Del Campo
Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations...
June 14, 2018: Scientific Reports
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
Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro
Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory) based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS), Genome-Wide Association Studies (GWAS), Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective...
June 14, 2018: High-throughput
Jian Zhang, Haiting Chai, Song Guo, Huaping Guo, Yanling Li
Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins...
June 14, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Liping Wu, Huawei Liu, Jorge Abad, Ronald D French, Ruhui Li
The complete genome of a Sweet potato vein clearing virus (SPVCV) isolate infecting a quarantined sweet potato accession from Fiji was determined. Sequence comparisons revealed the highest nucleotide sequence identity of 94.6% with that of the SPVCV type species, an isolate from the Dominican Republic. The virus was mechanically transmitted to Nicotiana bigelovii plants.
June 14, 2018: Genome Announcements
Katherine L Pogrebniak, Christina N Curtis
High-throughput sequencing can be used to measure changes in tumor composition across space and time. Specifically, comparisons of pre- and post-treatment samples can reveal the underlying clonal dynamics and resistance mechanisms. Here, we discuss evidence for distinct modes of tumor evolution and their implications for therapeutic strategies. In addition, we consider the utility of spatial tissue sampling schemes, single-cell analysis, and circulating tumor DNA to track tumor evolution and the emergence of resistance, as well as approaches that seek to forestall resistance by targeting tumor evolution...
June 11, 2018: Trends in Genetics: TIG
J A Michel-Macarty, M A Murillo-Escobar, R M López-Gutiérrez, C Cruz-Hernández, L Cardoza-Avendaño
BACKGROUND AND OBJECTIVES: Currently, telemedicine is levered upon the improvement in communication network technology such as Body Area Sensor Networks (BASN) to provided biomedicine solutions. Nevertheless, information security is an important issue since biomedical data is exchanged through insecure channels, which exposes private information that can be intercepted by malicious intruder. Therefore, secure communication protocols for multiuser networks in telemedicine applications are a big challenge...
August 2018: Computer Methods and Programs in Biomedicine
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
Yanxin Zhang, Linhai Wang, Yuan Gao, Donghua Li, Jingyin Yu, Rong Zhou, Xiurong Zhang
BACKGROUND: As an important oil crop, growth habit of sesame (Sesamum indicum L.) is naturally indeterminate, which brings about asynchronous maturity of capsules and causes loss of yield. RESULTS: The genetic basis of determinate growth habit in sesame was investigated by classical genetic analysis through multiple populations, results revealed that it was controlled by an unique recessive gene. The genotyping by sequencing (GBS) approach was employed for high-throughput SNP identification and genotyping in the F2 population, then a high density bin map was constructed, the map was 1086...
June 14, 2018: BMC Genetics
Baekgyu Kim, V Narry Kim
CLIP-seq (crosslinking immunoprecipitation and sequencing) is widely used to map the binding sites of a protein of interest on the transcriptome, and generally employs UV to induce the covalent bonds between protein and RNA, which allows stringent washing. However, dsRNA is inefficiently crosslinked by UV, making it difficult to study the interactions between dsRNA binding proteins and their substrates. A dsRNA endoribonuclease DROSHA initiates the maturation of microRNA (miRNA) by cleaving primary miRNA (pri-miRNA)...
June 11, 2018: Methods: a Companion to Methods in Enzymology
Wei Xing, Jin-Long Li, Desheng Li, Jincui Hu, Shi-Hai Deng, Yuwei Cui, Hong Yao
Combined heterotrophic and autotrophic denitrification (HAD) is a sustainable and practical method for removing nitrate from organic-limited wastewater. However, the active microorganisms responsible for denitrification in wastewater treatment have not been clearly identified. In this study, a combined micro-electrolysis, heterotrophic, and autotrophic denitrification (CEHAD) process was established. DNA-based stable isotope probing was employed to identify the active denitrifiers in reactors fed either 13 C-labeled inorganic or organic carbon source...
June 14, 2018: Environmental Science & Technology
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
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