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High throughput sequencing

Xiao Fang Du, Ying Bin Li, Fang Liu, Xiao Lin Su, Qi Li
Soil micro-food web, as a part of the detritus food webs, directly or indirectly participates in nutrient cycling by feeding on substrate and microorganisms and consequently influences the functions of terrestrial ecosystems. Here, we reviewed the research progress of soil micro-food web in recent years by focusing on its composition, structure and ecological function in soil ecosystem. The important roles of soil micro-food web in driving carbon (C) and nitrogen (N) transformation, organic matter decomposition and plant growth were reviewed through the description of energy channel and trophic cascade effects of soil micro-food web...
February 2018: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
Jinlong Jian, Wei Wei, Guowei Yin, Aubryanna Hettinghouse, Chuanju Liu, Yongxiang Shi
p204, a murine member of the interferon-inducible p200 protein family, and its human analogue, IFI16, have been shown to function as tumor suppressors in vitro, but the molecular events involved, in particular in vivo, remain unclear. Herein we induced the Lewis Lung carcinoma (LLC) murine model of human lung cancer in p204 null mice (KO) and their control littermates (WT). We compared the transcriptome in spleen from WT and p204 KO mice using a high-throughput RNA-sequencing array. A total 30.02 Gb of clean data were obtained, and overall Q30% was greater than 90...
April 24, 2018: Scientific Reports
Nicole Ludwig, Tobias Fehlmann, Valentina Galata, Andre Franke, Christina Backes, Eckart Meese, Andreas Keller
BACKGROUND: Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. METHODS: Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data...
April 24, 2018: Clinical Chemistry
Se-Hoon Lee, Boram Lee, Joon Ho Shim, Kwang Woo Lee, Jae Won Yun, Sook-Young Kim, Tae-You Kim, Yeul Hong Kim, Young Hyeh Ko, Hyun Cheol Chung, Chang Sik Yu, Jeeyun Lee, Sun Young Rha, Tae Won Kim, Kyung Hae Jung, Seock-Ah Im, Hyeong-Gon Moon, Sukki Cho, Jin Hyoung Kang, Jihun Kim, Sang Kyum Kim, Han Suk Ryu, Sang Yun Ha, Jong Il Kim, Yeun-Jun Chung, Cheolmin Kim, Hyung-Lae Kim, Woong-Yang Park, Dong-Young Noh, Keunchil Park
Purpose: With the emergence of next-generation sequencing (NGS) technology, profiling a wide range of genomic alterations has become a possibility resulting in improved implementation of targeted cancer therapy. In Asian populations, the prevalence and spectrum of clinically actionable genetic alterations has not yet been determined because of a lack of studies examining high-throughput cancer genomic data. Materials and Methods: To address this issue, 1,071 tumor samples were collected from five major cancer institutes in Korea and analyzed using targeted NGS at a centralized laboratory...
April 23, 2018: Cancer Research and Treatment: Official Journal of Korean Cancer Association
Idan Gabdank, Esther T Chan, Jean M Davidson, Jason A Hilton, Carrie A Davis, Ulugbek K Baymuradov, Aditi Narayanan, Kathrina C Onate, Keenan Graham, Stuart R Miyasato, Timothy R Dreszer, J Seth Strattan, Otto Jolanki, Forrest Y Tanaka, Benjamin C Hitz, Cricket A Sloan, J Michael Cherry
January 1, 2018: Database: the Journal of Biological Databases and Curation
Siamak Zamani Dadaneh, Mingyuan Zhou, Xiaoning Qian
Motivation: Rapid adoption of high-throughput sequencing technologies has enabled better understanding of genome-wide molecular profile changes associated with phenotypic differences in biomedical studies. Often, these changes are due to multiple interacting factors. Existing methods are mostly considering differential expression across two conditions studying one main factor without considering other confounding factors. In addition, they are often coupled with essential sophisticated ad-hoc pre-processing steps such as normalization, restricting their adaptability to general experimental setups...
April 24, 2018: Bioinformatics
Tae Woong Whon, Won-Hyong Chung, Mi Young Lim, Eun-Ji Song, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jin-Woo Bae, Young-Do Nam
High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1-4), Illumina MiSeq (V1-3, V3-4 and V4), and PacBio (V1-9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets...
April 24, 2018: Scientific Data
Varsha Mathur, Javier Del Campo, Martin Kolisko, Patrick J Keeling
Apicomplexans are a group of obligate intracellular parasites, but their retention of a relict non-photosynthetic plastid reveals that they evolved from free-living photosynthetic ancestors. The closest relatives of apicomplexans include photosynthetic chromerid algae (e.g., Chromera and Vitrella), non-photosynthetic colpodellid predators (e.g., Colpodella), and several environmental clades collectively called Apicomplexan-Related Lineages (ARLs). Here we investigate the global distribution and inferred ecology of the ARLs by expansively searching for apicomplexan-related plastid small ribosomal subunit (SSU) genes in large-scale high-throughput bacterial amplicon surveys...
April 24, 2018: Environmental Microbiology
Markus Hippich, Alexandra Oleynik, Komal Jain, Christiane Winkler, Ricardo C Ferreira, Ezio Bonifacio, Anette-Gabriele Ziegler, Thomas Briese
No abstract text is available yet for this article.
April 23, 2018: Acta Diabetologica
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects...
2018: Computational and Structural Biotechnology Journal
Ruibo Sun, Wenyan Li, Wenxu Dong, Yinping Tian, Chunsheng Hu, Binbin Liu
Tillage can strongly affect the long-term productivity of an agricultural system by altering the composition and spatial distribution of nutrients and microbial communities. The impact of tillage methods on the vertical distribution of soil microbial communities is not well understood, and the correlation between microbial communities and soil nutrients vertical distributions is also not clear. In the present study, we investigated the effects of conventional plowing tillage (CT: moldboard plowing), reduced tillage (RT: rotary tillage), and no tillage (NT) on the composition of bacterial and fungal communities within the soil profile (0-5, 5-10, 10-20, and 20-30 cm) using high-throughput sequencing of the microbial 16S/ITS gene...
2018: Frontiers in Microbiology
Jin-Long Cui, Vinod Vijayakumar, Gang Zhang
Endophytic fungi are an integral part and even seen as host organs of plant, influencing physiology, ecology, and development of host plants. However, little is known about micro-ecosystems and functional interactions of endophytic fungi in root-parasitic interactions of Cynomorium songaricum and its host Nitraria tangutorum . Here, distribution and dynamics of endophytic fungi were objectively investigated in their associations with C. songaricum and N. tangutorum based on mycobiome studies using high-throughput sequencing...
2018: Frontiers in Microbiology
May Salem Al-Nbaheen
Down syndrome (DS) is a genetic disorder appeared due to the presence of trisomy in chromosome 21 in the G-group of the acrocentric region. DS is also known as non-Mendelian inheritance, due to the lack of Mendel's laws. The disorder in children is identified through clinical symptoms and chromosomal analysis and till now there are no biochemical and molecular analyses. Presently, whole exome sequencing (WES) has largely contributed in identifying the new disease-causing genes and represented a significant breakthrough in the field of human genetics and this technique uses high throughput sequencing technologies to determine the arrangement of DNA base pairs specifying the protein coding regions of an individual's genome...
March 2018: Saudi Journal of Biological Sciences
Milka Koupenova, Eric Mick, Heather A Corkrey, Tianxiao Huan, Lauren Clancy, Ravi Shah, Emelia J Benjamin, Daniel Levy, Evelyn A Kurt-Jones, Kahraman Tanriverdi, Jane E Freedman
Viral infections associate with disease risk and select families of viruses encode miRNAs that control an efficient viral cycle. The association of viral miRNA expression with disease in a large human population has not been previously explored. We sequenced plasma RNA from 40 participants of the Framingham Heart Study (FHS, Offspring Cohort, Visit 8) and identified 3 viral miRNAs from 3 different human Herpesviridae. These miRNAs were mostly related to viral latency and have not been previously detected in human plasma...
April 23, 2018: Scientific Reports
Chuan Li, Jianzhi Zhang
A fitness landscape (FL) describes the genotype-fitness relationship in a given environment. To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently. Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments. Although genotype-by-environment interaction is abundantly detected, its pattern is so simple that we can transform an existing FL to that in a new environment with fitness measures of only a few genotypes in the new environment...
April 23, 2018: Nature Ecology & Evolution
Weihua Huang, Yajuan Zhu, Wenjuan Wu, Xuan Li, Delin Zhang, Ping Yin, Jirong Huang
Chloroplast biogenesis and development are highly complex processes requiring interaction between plastid and nuclear genomic products. Using a high-throughput screen for chloroplast biogenesis suppressors in Arabidopsis thaliana, we identified a suppressor of thf1 (sot5) that displays virescent and serrated leaves. Further characterization revealed that sot5 mutants are defective in leaf adaxial and abaxial polarity, and act as enhancer of asymmetric leaves2. Map-based cloning identified SOT5 as a gene previously named EMB2279 that encodes a plastid-targeted pentatricopeptide repeat (PPR) protein with 11 PPR motifs...
April 23, 2018: Plant Physiology
Tian Huang, Xifeng Wang, Run Si, Hao Chi, Binyue Han, Haitang Han, Gengsheng Cao, Yaofeng Zhao
Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2...
April 23, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Kyle P Eagen
Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops...
April 20, 2018: Trends in Biochemical Sciences
Ana C Borsanelli, David F Lappin, Lorenzo Viora, David Bennett, Iveraldo S Dutra, Bernd W Brandt, Marcello P Riggio
Periodontitis is an infectious polymicrobial, immuno-inflammatory disease of multifactorial aetiology that has an impact on the health, production and welfare of ruminants. The objective of the present study was to determine the microbial profiles present in the gingival sulcus of cattle considered periodontally healthy and in the periodontal pocket of animals with periodontitis lesions using high-throughput bacterial 16S rRNA gene sequencing. Subgingival biofilm samples were collected from 40 cattle with periodontitis and 38 periodontally healthy animals...
May 2018: Veterinary Microbiology
Chunyan Li, Yueling Sun, Zhenlei Yue, Mingyan Huang, Jinming Wang, Xi Chen, Xuejiao An, Hailian Zang, Dapeng Li, Ning Hou
The immobilization of organonitrile-degrading bacteria via the addition of biofilm-forming bacteria represents a promising technology for the treatment of organonitrile-containing wastewater, but biofilm-forming bacteria simply mixed with degrading bacteria may reduce the biodegradation efficiency. Nitrile hydratase and amidase genes, which play critical roles in organonitriles degradation, were cloned and transformed into the biofilm-forming bacterium Bacillus subtilis N4 to construct a recombinant bacterium B...
April 10, 2018: Journal of Hazardous Materials
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