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https://www.readbyqxmd.com/read/28345796/establishing-nucleosome-architecture-and-stability-at-promoters-roles-of-pioneer-transcription-factors-and-the-rsc-chromatin-remodeler
#1
REVIEW
Slawomir Kubik, Maria Jessica Bruzzone, David Shore
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS)...
March 27, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28345652/synergistic-infection-of-bryv-and-pemv-2-increases-the-accumulations-of-both-bryv-and-bryv-derived-sirnas-in-nicotiana-benthamiana
#2
Cui-Ji Zhou, Xiao-Yan Zhang, Song-Yu Liu, Ying Wang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han
Viral synergism is caused by co-infection of two unrelated viruses, leading to more severe symptoms or increased titres of one or both viruses. Synergistic infection of phloem-restricted poleroviruses and umbraviruses has destructive effects on crop plants. The mechanism underlying this synergy remains elusive. In our study, synergism was observed in co-infections of a polerovirus Brassica yellows virus (BrYV) and an umbravirus Pea enation mosaic virus 2 (PEMV 2) on Nicotiana benthamiana, which led to (1) increased titres of BrYV, (2) appearance of severe symptoms, (3) gain of mechanical transmission capacity of BrYV, (4) broader distribution of BrYV to non-vascular tissues...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345060/genome-reduction-and-microbe-host-interactions-drive-adaptation-of-a-sulfur-oxidizing-bacterium-associated-with-a-cold-seep-sponge
#3
Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding, Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed "Gsub") may represent a new deep-sea SOB group...
March 2017: MSystems
https://www.readbyqxmd.com/read/28343981/global-epidemiology-of-hcv-subtypes-and-resistance-associated-substitutions-evaluated-by-sequencing-based-subtype-analyses
#4
Tania Welzel, Neeru Bhardwaj, Charlotte Hedskog, Krishna Chodavarapu, Gregory Camus, John McNally, Diana Brainard, Michael D Miller, Hongmei Mo, Evguenia Svarovskaia, Ira Jacobson, Stefan Zeuzem, Kosh Agarwal
BACKGROUND & AIMS: Hepatitis C virus (HCV) is highly variable with 7 genotypes and 67 subtypes characterized to date. HCV genotype (GT) and subtype, and presence of resistance associated substitutions (RASs) represent the key viral determinants for the selection of direct-acting antiviral (DAA) treatment regimens. However, currently available HCV genotyping assays have limitations in differentiating between HCV subtypes and RAS prevalence in different subtypes is largely undefined. METHODS: In this study, we compared HCV GT and subtypes with INNO-LiPA 2...
March 23, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28343630/de-novo-truncating-mutations-in-the-last-and-penultimate-exons-of-ppm1d-cause-an-intellectual-disability-syndrome
#5
Sandra Jansen, Sinje Geuer, Rolph Pfundt, Rachel Brough, Priyanka Ghongane, Johanna C Herkert, Elysa J Marco, Marjolein H Willemsen, Tjitske Kleefstra, Mark Hannibal, Joseph T Shieh, Sally Ann Lynch, Frances Flinter, David R FitzPatrick, Alice Gardham, Birgitta Bernhard, Nicola Ragge, Ruth Newbury-Ecob, Raphael Bernier, Malin Kvarnung, E A Helena Magnusson, Marja W Wessels, Marjon A van Slegtenhorst, Kristin G Monaghan, Petra de Vries, Joris A Veltman, Christopher J Lord, Lisenka E L M Vissers, Bert B A de Vries
Intellectual disability (ID) is a highly heterogeneous disorder involving at least 600 genes, yet a genetic diagnosis remains elusive in ∼35%-40% of individuals with moderate to severe ID. Recent meta-analyses statistically analyzing de novo mutations in >7,000 individuals with neurodevelopmental disorders highlighted mutations in PPM1D as a possible cause of ID. PPM1D is a type 2C phosphatase that functions as a negative regulator of cellular stress-response pathways by mediating a feedback loop of p38-p53 signaling, thereby contributing to growth inhibition and suppression of stress-induced apoptosis...
March 18, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343148/de-novo-mutations-in-cbl-causing-early-onset-paediatric-moyamoya-angiopathy
#6
Stéphanie Guey, Lou Grangeon, Francis Brunelle, Françoise Bergametti, Jeanne Amiel, Stanislas Lyonnet, Audrey Delaforge, Minh Arnould, Béatrice Desnous, Céline Bellesme, Dominique Hervé, Jan C Schwitalla, Markus Kraemer, Elisabeth Tournier-Lasserve, Manoelle Kossorotoff
BACKGROUND: Moyamoya angiopathy (MMA) is characterised by a progressive stenosis of the terminal part of the internal carotid arteries and the development of abnormal collateral deep vessels. Its pathophysiology is unknown. MMA can be the sole manifestation of the disease (moyamoya disease) or be associated with various conditions (moyamoya syndrome) including some Mendelian diseases. We aimed to investigate the genetic basis of moyamoya using a whole exome sequencing (WES) approach conducted in sporadic cases without any overt symptom suggestive of a known Mendelian moyamoya syndrome...
March 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28342885/high-throughput-identification-of-mirnas-of-taenia-ovis-a-cestode-threatening-sheep-industry
#7
Yadong Zheng
Taenia ovis is a tapeworm that is mainly transmitted between dogs and sheep or goats and has an adverse effect on sheep industry. miRNAs are short regulatory non-coding RNAs, involved in parasite development and growth as well as parasite infection. The miRNA profile of T. ovis remains to be established. Herein, 33 known miRNAs belonging to 23 different families were identified in T. ovis metacestodes using deep sequencing approach. Of them, expression of some miRNAs such as tov-miR-10 and -let-7 was absolutely predominant...
March 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28340599/dna-methylation-changes-at-infertility-genes-in-newborn-twins-conceived-by-in-vitro-fertilisation
#8
Juan E Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D Spector, Richard Saffery, Jeffrey M Craig, Jordana T Bell
BACKGROUND: The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome. METHODS: We investigated the links between IVF and DNA methylation patterns in whole cord blood cells (n = 98) and cord blood mononuclear cells (n = 82) from newborn twins using genome-wide methylated DNA immunoprecipitation coupled with deep sequencing...
March 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#9
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28338896/rapid-evolution-of-microrna-loci-in-the-brown-algae
#10
J Mark Cock, Fuli Liu, Delin Duan, Simon Bourdareau, Agnieszka Lipinska, Susana M Coelho, James E Tarver
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on analysis of a single species, the filamentous brown alga Ectocarpus sp. Here we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families...
March 3, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28337682/three-members-of-opisthomonorcheides-parukhin-1966-digenea-monorchiidae-from-carangid-fishes-perciformes-from-indonesia-with-a-review-of-the-genus
#11
Rodney A Bray, Harry W Palm, Scott C Cutmore, Thomas H Cribb
Three species of Opisthomonorcheides Parukhin, 1966 are reported for the first time from Indonesian waters: O. pampi (Wang, 1982) Liu, Peng, Gao, Fu, Wu, Lu, Gao & Xiao, 2010 and O. ovacutus (Mamaev, 1970) Machida, 2011 from Parastromateus niger (Bloch), and O. decapteri Parukhin, 1966 from Atule mate (Cuvier). Both O. pampi and O. ovacutus can now be considered widespread in the Indo-Pacific region, with earlier records of these species being from Fujian Province, China and Penang, Malaysia, respectively. We redescribe O...
March 23, 2017: Systematic Parasitology
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#12
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28336607/genome-sequence-of-human-rhinovirus-a22-strain-lancaster-2015
#13
Kate V Atkinson, Lisa A Bishop, Glenn Rhodes, Nicolas Salez, Neil R McEwan, Matthew J Hegarty, Julie Robey, Nicola Harding, Simon Wetherell, Robert M Lauder, Roger W Pickup, Mark Wilkinson, Derek Gatherer
The genome of human rhinovirus A22 (HRV-A22) was assembled by deep sequencing RNA samples from nasopharyngeal swabs. The assembled genome is 8.7% divergent from the HRV-A22 reference strain over its full length, and it is only the second full-length genome sequence for HRV-A22. The new strain is designated strain HRV-A22/Lancaster/2015.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#14
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28335448/a-community-multi-omics-approach-towards-the-assessment-of-surface-water-quality-in-an-urban-river-system
#15
David J Beale, Avinash V Karpe, Warish Ahmed, Stephen Cook, Paul D Morrison, Christopher Staley, Michael J Sadowsky, Enzo A Palombo
A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5-V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem...
March 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#16
Haoyang Zeng, David K Gifford
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334821/in-vivo-cleavage-specificity-of-trypanosoma-brucei-editosome-endonucleases
#17
Jason Carnes, Suzanne McDermott, Atashi Anupama, Brian G Oliver, D Noah Sather, Kenneth Stuart
RNA editing is an essential post-transcriptional process that creates functional mitochondrial mRNAs in Kinetoplastids. Multiprotein editosomes catalyze pre-mRNA cleavage, uridine (U) insertion or deletion, and ligation as specified by guide RNAs. Three functionally and compositionally distinct editosomes differ by the mutually exclusive presence of the KREN1, KREN2 or KREN3 endonuclease and their associated partner proteins. Because endonuclease cleavage is a likely point of regulation for RNA editing, we elucidated endonuclease specificity in vivo...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334209/comparative-study-of-chemosensory-organs-of-shrimp-from-hydrothermal-vent-and-coastal-environments
#18
Magali Zbinden, Camille Berthod, Nicolas Montagné, Julia Machon, Nelly Léger, Thomas Chertemps, Nicolas Rabet, Bruce Shillito, Juliette Ravaux
The detection of chemical signals is involved in a variety of crustacean behaviors, such as social interactions, search and evaluation of food and navigation in the environment. At hydrothermal vents, endemic shrimp may use the chemical signature of vent fluids to locate active edifices, however little is known on their sensory perception in these remote deep-sea habitats. Here, we present the first comparative description of the sensilla on the antennules and antennae of 4 hydrothermal vent shrimp (Rimicaris exoculata, Mirocaris fortunata, Chorocaris chacei, and Alvinocaris markensis) and of a closely related coastal shrimp (Palaemon elegans)...
February 22, 2017: Chemical Senses
https://www.readbyqxmd.com/read/28334114/biren-predicting-enhancers-with-a-deep-learning-based-model-using-the-dna-sequence-alone
#19
Bite Yang, Feng Liu, Chao Ren, Zhangyi Ouyang, Ziwei Xie, Xiaochen Bo, Wenjie Shu
Motivation: Enhancer elements are noncoding stretches of DNA that play key roles in controlling gene expression programmes. Despite major efforts to develop accurate enhancer prediction methods, identifying enhancer sequences continues to be a challenge in the annotation of mammalian genomes. One of the major issues is the lack of large, sufficiently comprehensive and experimentally validated enhancers for humans or other species. Thus, the development of computational methods based on limited experimentally validated enhancers and deciphering the transcriptional regulatory code encoded in the enhancer sequences is urgent...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334071/on-the-design-and-prospects-of-direct-rna-sequencing
#20
Georgi K Marinov
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets...
February 17, 2017: Briefings in Functional Genomics
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