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https://www.readbyqxmd.com/read/29222921/optimizing-rna-seq-studies-to-investigate-herbicide-resistance
#1
REVIEW
Darci A Giacomini, Todd Gaines, Roland Beffa, Patrick J Tranel
Transcriptomic profiling, specifically via RNA-seq, is becoming one of the more commonly used methods for investigating non-target site resistance (NTSR) to herbicides due to its high throughput capabilities and utility in organisms with little to no previous sequence information. A review of the weed science RNA-seq literature has revealed some basic principles behind generating quality data from these types of studies. First, studies that included more replicates per biotype and took steps to control for genetic background had significantly better control of false positives and, consequently, shorter lists of potential resistance genes to sift through...
December 9, 2017: Pest Management Science
https://www.readbyqxmd.com/read/29222807/long-non-coding-rna-expression-in-bladder-cancer
#2
REVIEW
Mohammad Taheri, Mir Davood Omrani, Soudeh Ghafouri-Fard
The advent of novel high-throughput sequencing methods has facilitated identification of non-coding RNAs with fundamental roles in cellular biological and pathological conditions. A group of these consisting of at least 200 nucleotides are called long non-coding RNAs (lncRNAs). Their participation in the pathogenesis of cancer has been highlighted in recent years. Bladder cancer, one of the most prevalent cancers worldwide, exhibits altered expression levels of several lncRNAs. Several in vitro and in vivo studies have assessed the effects of silencing RNAs on cancer cell phenotypes and in vivo tumor growth...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29222611/kiwifruit-svp2-controls-developmental-and-drought-stress-pathways
#3
Rongmei Wu, Tianchi Wang, Ben A W Warren, Susan J Thomson, Andrew C Allan, Richard C Macknight, Erika Varkonyi-Gasic
Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy...
December 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29222504/rnastructuromedb-a-genome-wide-database-for-rna-structural-inference
#4
Ryan J Andrews, Levi Baber, Walter N Moss
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222283/hereditary-thrombocytopenias-a-growing-list-of-disorders
#5
REVIEW
Patrizia Noris, Alessandro Pecci
The introduction of high throughput sequencing (HTS) techniques greatly improved the knowledge of inherited thrombocytopenias (ITs) over the last few years. A total of 33 different forms caused by molecular defects affecting at least 32 genes have been identified; along with the discovery of new disease-causing genes, pathogenetic mechanisms of thrombocytopenia have been better elucidated. Although the clinical picture of ITs is heterogeneous, bleeding has been long considered the major clinical problem for patients with IT...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222097/a-new-niche-for-anoxygenic-phototrophs-as-endoliths
#6
Daniel Roush, Estelle Couradeau, Brandon Guida, Susanne Neuer, Ferran Garcia-Pichel
Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. An ad hoc phylogenetic classification of these sequences allowed us to refine the assignments more stringently...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29222086/genome-wide-dna-methylation-profiling-using-the-methylation-dependent-restriction-enzyme-lpnpi
#7
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, Zeliha Ozgur, Anco Molijn, Wilfred van IJcken, Joop Laven, Joost Gribnau
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping...
December 8, 2017: Genome Research
https://www.readbyqxmd.com/read/29222063/evolutionary-dynamism-in-bryophytes-phylogenomic-inferences-confirm-rapid-radiation-in-the-moss-family-funariaceae
#8
Rafael Medina, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A Hedderson, Norman Wickett, Bernard Goffinet
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29221806/characterization-of-gene-alterations-following-editing-of-the-%C3%AE-globin-gene-locus-in-hematopoietic-stem-progenitor-cells
#9
Joseph Long, Megan D Hoban, Aaron R Cooper, Michael L Kaufman, Caroline Y Kuo, Beatriz Campo-Fernandez, Dianne Lumaquin, Roger P Hollis, Xiaoyan Wang, Donald B Kohn, Zulema Romero
The use of engineered nucleases combined with a homologous DNA donor template can result in targeted gene correction of the sickle cell disease mutation in hematopoietic stem and progenitor cells. However, because of the high homology between the adjacent human β- and δ-globin genes, off-target cleavage is observed at δ-globin when using some endonucleases targeted to the sickle mutation in β-globin. Introduction of multiple double-stranded breaks by endonucleases has the potential to induce intergenic alterations...
November 9, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29221193/steroidogenic-factor-1-hypermethylation-in-maternal-rat-blood-could-serve-as-a-biomarker-for-intrauterine-growth-retardation
#10
Dong-Mei Wu, Liang-Peng Ma, Gui-Li Song, Yong Long, Han-Xiao Liu, Yang Liu, Jie Ping
Intrauterine growth retardation (IUGR) is a common obstetric complication lacking an optimal method for prenatal screening. DNA methylation profile in maternal blood holds significant promise for prenatal screening. Here, we aimed to screen out potential IUGR biomarkers in maternal blood from the perspective of DNA methylation. The IUGR rat model was established by prenatal maternal undernutrition. High-throughput bisulfite sequencing of genomic DNA methylation followed by functional clustering analysis for differentially methylated region (DMR)-associated genes demonstrated that genes regulating transcription had the most significantly changed DNA methylation status in maternal blood with IUGR...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221171/proteogenomic-analysis-prioritises-functional-single-nucleotide-variants-in-cancer-samples
#11
Shiyong Ma, Ranjeeta Menon, Rebecca C Poulos, Jason W H Wong
Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221148/differently-expressed-long-noncoding-rnas-and-mrnas-in-tk6-cells-exposed-to-low-dose-hydroquinone
#12
Shaoyun Chen, Hairong Liang, Gonghua Hu, Hui Yang, Kairu Zhou, Longmei Xu, Jiaxian Liu, Bei Lai, Li Song, Hao Luo, Jianming Peng, Zhidong Liu, Yongmei Xiao, Wen Chen, Huanwen Tang
Previous studies have shown that long noncoding RNAs (lncRNAs) were related to human carcinogenesis and might be designated as diagnosis and prognosis biomarkers. Hydroquinone (HQ), as one of the metabolites of benzene, was closely relevant to occupational benzene poisoning and occupational leukemia. Using high-throughput sequencing technology, we investigated differences in lncRNA and mRNA expression profiles between experimental group (HQ 20 μmol/L) and control group (PBS). Compared to control group, a total of 65 lncRNAs and 186 mRNAs were previously identified to be aberrantly expressed more than two fold change in experimental group...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220646/dissecting-cell-type-composition-and-activity-dependent-transcriptional-state-in-mammalian-brains-by-massively-parallel-single-nucleus-rna-seq
#13
Peng Hu, Emily Fabyanic, Deborah Y Kwon, Sheng Tang, Zhaolan Zhou, Hao Wu
Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo...
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29220515/busco-applications-from-quality-assessments-to-gene-prediction-and-phylogenomics
#14
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220513/integrating-5hmc-and-gene-expression-data-to-infer-regulatory-mechanisms
#15
Cristina Mitrea, Priyanga Wijesinghe, Greg Dyson, Adéle Kruger, Douglas M Ruden, Sorin Draghici, Aliccia Bollig-Fischer
Motivation: Epigenetic mechanisms are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in an aggressive subtype known as triple negative breast cancer (TNBC). To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#16
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#17
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29218933/-research-progress-of-bixie
#18
REVIEW
Li-Xiang Dong, Jun Ni
The extract of ginkgo leaves showed positive effects on treatments of many diseases, and has been used clinically worldwide. Considering the fact that flavonoids are the main bioactive components in the extract of ginkgo leaves, it is very important to investigate the flavonoid biosynthesis in ginkgo leaves. In this paper, we first reviewed the research progress of flavonoid biosynthesis in different plants, and introduced the flavonoid biosynthesis related genes discovered in ginkgo. Then, several cases of ginkgo researches using high throughput sequencing technology were described in detail...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29217777/high-throughput-sequencing-in-acute-lymphoblastic-leukemia-reveals-clonal-architecture-of-central-nervous-system-and-bone-marrow-compartments
#19
Jack Bartram, Nick Goulden, Gary Wright, Stuart Adams, Tony Brooks, Darren Edwards, Sarah Inglott, Yasar Yousafzai, Mike Hubank, Christina Halsey
No abstract text is available yet for this article.
December 7, 2017: Haematologica
https://www.readbyqxmd.com/read/29217299/high-pd-l1-cd86-mfi-ratio-and-il-10-secretion-characterize-human-regulatory-dendritic-cells-generated-for-clinical-testing-in-organ-transplantation
#20
Alan F Zahorchak, Camila Macedo, David E Hamm, Lisa H Butterfield, Diana M Metes, Angus W Thomson
Human regulatory dendritic cells (DCreg) were generated from CD14 immunobead-purified or elutriated monocytes in the presence of vitamin D3 and IL-10. They exhibited similar, low levels of costimulatory CD80 and CD86, but comparatively high levels of co-inhibitory programed death ligand-1 (PD-L1) and IL-10 production compared to control immature DC (iDC). Following Toll-like receptor 4 ligation, unlike control iDC, DCreg resisted phenotypic and functional maturation and further upregulated PD-L1:CD86 expression...
September 14, 2017: Cellular Immunology
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