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High-Throughput Sequencing

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https://www.readbyqxmd.com/read/27921175/molecular-characterization-of-a-new-soybean-infecting-member-of-the-genus-nepovirus-identified-by-high-throughput-sequencing
#1
Tuba Yasmin, Berlin D Nelson, Houston A Hobbs, Nancy K McCoppin, Kris N Lambert, Leslie L Domier
The complete nucleotide sequence of a new soybean-infecting member of the genus Nepovirus (provisionally named "soybean latent spherical virus" [SLSV]) was identified by high-throughput sequencing of RNAs from soybean leaf samples from North Dakota, USA. The sequences of RNAs 1 (8,190 nt) and 2 (5,788 nt) were completed by rapid amplification of cDNA ends. Each contained a single long open reading frame and a 3' nontranslated region of greater than 1,500 nt. The predicted amino acid sequences of the two ORFs were most closely related to nepoviruses in subgroup C...
December 5, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27921137/vertical-profiles-of-water-and-sediment-denitrifiers-in-two-plateau-freshwater-lakes
#2
Guozhu Mao, Ling Chen, Yuyin Yang, Zhen Wu, Tianli Tong, Yong Liu, Shuguang Xie
The present study investigated the abundance, richness, diversity, and community composition of denitrifiers (based on nirS and nosZ genes) in the stratified water columns and sediments in eutrophic Dianchi Lake and mesotrophic Erhai Lake using quantitative PCR assay and high-throughput sequencing analysis. Both nirS- and nosZ denitrifiers were detected in waters of these two lakes. Surface water showed higher nosZ gene density than bottom water, and Dianchi Lake waters had larger nirS gene abundance than Erhai Lake waters...
December 6, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27920783/genomic-tools-in-pearl-millet-breeding-for-drought-tolerance-status-and-prospects
#3
REVIEW
Desalegn D Serba, Rattan S Yadav
Pearl millet [Penisetum glaucum (L) R. Br.] is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by 100s of genes and significantly influenced by the environment...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27920770/the-use-of-transposon-insertion-sequencing-to-interrogate-the-core-functional-genome-of-the-legume-symbiont-rhizobium-leguminosarum
#4
Benjamin J Perry, Mir S Akter, Christopher K Yost
The free-living legume symbiont Rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. Discovery based research into the genetics and physiology of R. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. Transposon insertion sequencing (INSeq) facilitates high-throughput forward genetic screening at a genomic scale to identify individual genes required for growth in a specific environment...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920086/a-role-for-mitotic-bookmarking-of-sox2-in-pluripotency-and-differentiation
#5
Cédric Deluz, Elias T Friman, Daniel Strebinger, Alexander Benke, Mahé Raccaud, Andrea Callegari, Marion Leleu, Suliana Manley, David M Suter
Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains...
December 5, 2016: Genes & Development
https://www.readbyqxmd.com/read/27918973/long-term-effects-of-cupric-oxide-nanoparticles-cuo-nps-on-the-performance-microbial-community-and-enzymatic-activity-of-activated-sludge-in-a-sequencing-batch-reactor
#6
Sen Wang, Zhiwei Li, Mengchun Gao, Zonglian She, Bingrui Ma, Liang Guo, Dong Zheng, Yangguo Zhao, Chunji Jin, Xuejiao Wang, Feng Gao
The long-term effects of cupric oxide nanoparticles (CuO NPs) on the performance, microbial activity and microbial community of activated sludge were investigated in a sequencing batch reactor (SBR). The SBR performance had no evident change at 0-10 mg/L CuO NPs, whereas the CuO NPs concentration at 30-60 mg/L affected the COD, NH4(+)-N and soluble orthophosphate (SOP) removal, nitrogen and phosphorus removal rate and microbial enzymatic activity of activated sludge. Some CuO NPs might be absorbed on the surface of activated sludge or penetrate the microbial cytomembrane into the microbial cell interior of activated sludge...
December 2, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#7
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27918488/transcriptome-profiling-analysis-of-wolf-spider-pardosa-pseudoannulata-araneae-lycosidae-after-cadmium-exposure
#8
Chang-Chun Li, Yong Wang, Guo-Yuan Li, Yue-Li Yun, Yu-Jun Dai, Jian Chen, Yu Peng
Pardosa pseudoannulata is one of the most common wandering spiders in agricultural fields and a potentially good bioindicator for heavy metal contamination. However, little is known about the mechanisms by which spiders respond to heavy metals at the molecular level. In the present study, high-throughput transcriptome sequencing was employed to characterize the de novo transcriptome of the spiders and to identify differentially expressed genes (DEGs) after cadmium exposure. We obtained 60,489 assembled unigenes, 18,773 of which were annotated in the public databases...
December 3, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#9
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27918147/genome-analysis-of-a-hyper-acetone-butanol-ethanol-abe-producing-clostridium-acetobutylicum-bkm19
#10
Changhee Cho, Donghui Choe, Yu-Sin Jang, Kyung-Jin Kim, Won Jun Kim, Byung-Kwan Cho, E Terry Papoutsakis, George N Bennett, Do Young Seung, Sang Yup Lee
We previously reported development of a hyper acetone-butanol-ethanol (ABE) producing Clostridium acetobutylicum BKM19 strain capable of producing 30.5% more total solvent by random mutagenesis of its parental strain PJC4BK, which is a buk mutant C. acetobutylicum ATCC 824 strain. Here BKM19 and PJC4BK strains were re-sequenced by a high-throughput sequencing technique to understand the mutations responsible for enhanced solvent production. In comparison with the C. acetobutylicum PJC4BK, 13 single nucleotide variants (SNVs), 1 deletion and 1 back mutation SNV were identified in the C...
December 5, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27917931/metagenomic-profiling-of-historic-colorado-front-range-flood-impact-on-distribution-of-riverine-antibiotic-resistance-genes
#11
Emily Garner, Joshua S Wallace, Gustavo Arango Argoty, Caitlin Wilkinson, Nicole Fahrenfeld, Lenwood S Heath, Liqing Zhang, Mazdak Arabi, Diana S Aga, Amy Pruden
Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917186/expression-level-of-the-dreb2-type-gene-identified-with-amplifluor-snp-markers-correlates-with-performance-and-tolerance-to-dehydration-in-bread-wheat-cultivars-from-northern-kazakhstan
#12
Yuri Shavrukov, Aibek Zhumalin, Dauren Serikbay, Makpal Botayeva, Ainur Otemisova, Aiman Absattarova, Grigoriy Sereda, Sergey Sereda, Vladimir Shvidchenko, Arysgul Turbekova, Satyvaldy Jatayev, Sergiy Lopato, Kathleen Soole, Peter Langridge
A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27916419/comparative-transcriptomics-analyses-of-the-different-growth-states-of-multidrug-resistant-acinetobacter-baumannii
#13
Shuai Li, Haitao Li, Tianjie Qi, Xixin Yan, Boli Wang, Jitao Guan, Yu Li
Multidrug-resistant (MDR) Acinetobacter baumannii is an important bacterial pathogen commonly associated with hospital acquired infections. A. baumannii can remain viable and hence virulent in the environment for a long period of time due primarily to its ability to form biofilms. A total of 459 cases of MDR A. baumannii our hospital collected from March 2014 to March 2015 were examined in this study, and a representative isolate selected for high-throughput mRNA sequencing and comparison of gene expression profiles under the biofilm and exponential growth conditions...
December 1, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#14
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27915330/mechanism-of-sex-determination-in-humans-insights-from-disorders-of-sex-development
#15
Anu Bashamboo, Ken McElreavey
In this review we will consider the gene mutations responsible for the non-syndromic forms of disorders of sex development (DSD) and how recent genetic findings are providing insights into the mechanism of sex determination. High-throughput sequencing technologies are having a major impact on our understanding of the genetic basis of rare human disorders, including DSD. The study of human DSD is progressively revealing subtle differences in the genetics of the sex-determining system between the mouse and the human...
December 3, 2016: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/27915285/depth-dependent-influence-of-different-land-use-systems-on-bacterial-biogeography
#16
Brent J Seuradge, Maren Oelbermann, Josh D Neufeld
Despite progress in understanding microbial biogeography of surface soils, few studies have investigated depth-dependent distributions of terrestrial microorganisms in subsoils. We leveraged high-throughput sequencing of 16S rRNA genes obtained from soils collected from the RARE: Charitable Research Reserve (Cambridge, Ontario, Canada) to assess the influence of depth on bacterial communities across various land-use types. Although bacterial communities were strongly influenced by depth across all sites, the magnitude of this influence was variable and demonstrated that land-use attributes also played a significant role in shaping soil bacterial communities...
December 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27914786/evaluating-the-feasibility-of-ratio-control-strategy-for-achieving-partial-nitritation-in-a-continuous-floccular-sludge-reactor-experimental-demonstration
#17
Wenru Liu, Dianhai Yang
To investigate the applicability of ratio control strategy to other systems, a continuous floccular sludge reactor was used in this study. It was found that nitrite accumulation was barely detected throughout 70days' investigation, being the average concentration in the effluent of 0.7±0.4mg/L. Batch experiments indicated that low dissolved oxygen (DO<0.3mg·L(-1)) greatly repressed the ammonium oxidizing bacteria (AOB) but only slightly inhibited the nitrite oxidizing bacteria (NOB). However, high-throughput sequencing revealed that the ratio of abundance between Nitrospira and Nitrosomonas, being the dominant NOB and AOB respectively, was considerably low (1...
November 25, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27914278/fdstools-a-software-package-for-analysis-of-massively-parallel-sequencing-data-with-the-ability-to-recognise-and-correct-str-stutter-and-other-pcr-or-sequencing-noise
#18
Jerry Hoogenboom, Kristiaan J van der Gaag, Rick H de Leeuw, Titia Sijen, Peter de Knijff, Jeroen F J Laros
Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions...
November 27, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27914072/identifying-bacterial-immune-evasion-proteins-using-phage-display
#19
Cindy Fevre, Lisette Scheepmaker, Pieter-Jan Haas
Methods aimed at identification of immune evasion proteins are mainly rely on in silico prediction of sequence, structural homology to known evasion proteins or use a proteomics driven approach. Although proven successful these methods are limited by a low efficiency and or lack of functional identification. Here we describe a high-throughput genomic strategy to functionally identify bacterial immune evasion proteins using phage display technology. Genomic bacterial DNA is randomly fragmented and ligated into a phage display vector that is used to create a phage display library expressing bacterial secreted and membrane bound proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913675/motility-and-adhesion-through-type-iv-pili-in-gram-positive-bacteria
#20
REVIEW
Kurt H Piepenbrink, Eric J Sundberg
Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria...
December 15, 2016: Biochemical Society Transactions
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