keyword
MENU ▼
Read by QxMD icon Read
search

deep sequence

keyword
https://www.readbyqxmd.com/read/28214735/rna-based-control-mechanisms-of-clostridium-difficile
#1
REVIEW
Olga Soutourina
Clostridium difficile (CD)-associated diarrhoea is currently the most prevalent nosocomial diarrhoea worldwide. Many characteristics of CD pathogenicity remain poorly understood. Recent data strongly indicate the importance of an RNA network for the control of gene expression in CD. More than 200 regulatory RNAs have been identified by deep sequencing and targeted approaches, including Hfq-dependent trans riboregulators, cis-antisense RNAs, CRISPR RNAs, and c-di-GMP-responsive riboswitches. These regulatory RNAs are involved in the control of major processes in the CD infection cycle, for example motility, biofilm formation, adhesion, sporulation, stress response, and defence against bacteriophages...
February 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28214361/identification-of-arabidopsis-genic-and-non-genic-promoters-by-paired-end-sequencing-of-tss-tags
#2
Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y Yamamoto
Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324,461 promoters that covered 79.7% (21,672/27,206) of protein-coding genes in the Arabidopsis genome. In addition, we identified intragenic, antisense, and Orphan promoters that were not associated with any gene models...
February 18, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28213872/capulavirus-and-grablovirus-two-new-genera-in-the-family-geminiviridae
#3
Arvind Varsani, Philippe Roumagnac, Marc Fuchs, Jesús Navas-Castillo, Enrique Moriones, Ali Idris, Rob W Briddon, Rafael Rivera-Bustamante, F Murilo Zerbini, Darren P Martin
Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus)...
February 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28213272/rev-erb-regulation-of-cholesterologenesis
#4
Sadichha Sitaula, Jinsong Zhang, Fernanda Ruiz, Thomas P Burris
REV-ERBα and REV-ERBβ are heme regulated nuclear receptors that are known to regulate metabolic pathways. We previously demonstrated that treatment of mice with synthetic REV-ERB agonists suppressed plasma cholesterol levels and the hepatic levels of the rate limiting enzyme in cholesterol biosynthesis (3-hydroxy-3-Mmethylglutaryl-CoA reductase). Here, we characterize the role of REV-ERB on the cholesterol biosynthetic pathway in greater detail. The REV-ERB agonist SR9009 reduced plasma cholesterol levels in both wild type C57Bl/6 and low density lipoprotein receptor (LDLR) null mice as well as reducing the expression of an array of genes within the cholesterol biosynthetic pathway...
February 14, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#5
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212285/transcriptomic-analysis-reveals-selective-metabolic-adaptation-of-streptococcus-suis-to-porcine-blood-and-cerebrospinal-fluid
#6
Anna Koczula, Michael Jarek, Christian Visscher, Peter Valentin-Weigand, Ralph Goethe, Jörg Willenborg
Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28211985/a-girl-with-developmental-delay-ataxia-cranial-nerve-palsies-severe-respiratory-problems-in-infancy-expanding-ndst1-syndrome
#7
Linlea Armstrong, Maja Tarailo-Graovac, Graham Sinclair, Kimberly I Seath, Wyeth W Wasserman, Colin J Ross, Clara D M van Karnebeek
NDST1 encodes an enzyme involved in the first steps in the synthesis of heparan sulfate chains, proteoglycans that are regulators found on the cell surface and in the extracellular matrix. Eight individuals homozygous for one of four family-specific missense mutations in the sulfotransferase domain of the enzyme have been described. They have intellectual disability. Some additionally had hypotonia, ataxia. seizures, and/or short stature, but none had history of respiratory problems. No humans with homozygous null mutations are known...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211848/host-specificity-of-symbiodinium-variants-revealed-by-an-its2-metahaplotype-approach
#8
Edward G Smith, Remi N Ketchum, John A Burt
Analysis of the widely used ITS region is confounded by the presence of intragenomic variants (IGVs). In Symbiodinium, the algal symbionts of reef building corals, deep-sequencing analyses are used to characterise communities within corals, yet these analyses largely overlook IGVs. Here we consider that distinct ITS2 sequences could represent IGVs rather than distinct symbiont types and argue that symbionts can be distinguished by their proportional composition of IGVs, described as their ITS2 metahaplotype...
February 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28210002/analytical-and-clinical-validation-of-a-novel-in-house-deep-sequencing-method-for-minimal-residual-disease-monitoring-in-a-phase-ii-trial-for-multiple-myeloma
#9
J Martinez-Lopez, B Sanchez-Vega, S Barrio, I Cuenca, Y Ruiz-Heredia, R Alonso, I Rapado, C Marin, M-T Cedena, B Paiva, N Puig, M-V Mateos, R Ayala, M-T Hernández, C Jimenez, L Rosiñol, R Martínez, A-I Teruel, N Gutiérrez, M-L Martin-Ramos, A Oriol, J Bargay, J Bladé, J San-Miguel, R Garcia-Sanz, J-J Lahuerta
Leukemia accepted article preview online, 17 February 2017. doi:10.1038/leu.2017.58.
February 17, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28209827/first-complete-genome-sequence-of-marinilactibacilluspiezotolerans-strain-15r-a-marine-lactobacillus-isolated-from-coal-bearing-sediment-2-0-kilometers-below-the-seafloor-determined-by-pacbio-single-molecule-real-time-technology
#10
Yuli Wei, Junwei Cao, Jiasong Fang, Chiaki Kato, Weicheng Cui
Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic lactobacillus isolated from deep marine subsurface sediment nearly 2 km below the seafloor in the northwestern Pacific. We report here the first whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908 bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences, with no identified plasmids.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28208788/next-generation%C3%A2-sequencing-based%C3%A2-ribomethseq%C3%A2-protocol%C3%A2-for%C3%A2-analysis%C3%A2-of%C3%A2-trna%C3%A2-2-o-methylation
#11
Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm, Yuri Motorin
Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations...
February 9, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208132/an-outbreak-of-acute-hepatitis-caused-by-genotype-ib-hepatitis-a-viruses-contaminating-the-water-supply-in-thailand
#12
Kriangsak Ruchusatsawat, Jongkonnee Wongpiyabovorn, Chonthicha Kawidam, Laddawan Thiemsing, Somchai Sangkitporn, Sayaka Yoshizaki, Masashi Tatsumi, Naokazu Takeda, Koji Ishii
BACKGROUND: In 2000, an outbreak of acute hepatitis A was reported in a province adjacent to Bangkok, Thailand. AIMS: To investigate the cause of the 2000 hepatitis A outbreaks in Thailand using molecular epidemiological analysis. METHODS: Serum and stool specimens were collected from patients who were clinically diagnosed with acute viral hepatitis. Water samples from drinking water and deep-drilled wells were also collected. These specimens were subjected to polymerase chain reaction (PCR) amplification and sequencing of the VP1/2A region of the hepatitis A virus (HAV) genome...
February 17, 2017: Intervirology
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#13
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28206693/plasmid-and-clonal-interference-during-post-horizontal-gene-transfer-evolution
#14
S Bedhomme, D Perez Pantoja, I G Bravo
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28205546/crispr-cpf1-mediated-dna-free-plant-genome-editing
#15
Hyeran Kim, Sang-Tae Kim, Jahee Ryu, Beum-Chang Kang, Jin-Soo Kim, Sang-Gyu Kim
Cpf1, a type V CRISPR effector, recognizes a thymidine-rich protospacer-adjacent motif and induces cohesive double-stranded breaks at the target site guided by a single CRISPR RNA (crRNA). Here we show that Cpf1 can be used as a tool for DNA-free editing of plant genomes. We describe the delivery of recombinant Cpf1 proteins with in vitro transcribed or chemically synthesized target-specific crRNAs into protoplasts isolated from soybean and wild tobacco. Designed crRNAs are unique and do not have similar sequences (≤3 mismatches) in the entire soybean reference genome...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28205307/segmentation-of-organs-at-risks-in-head-and-neck-ct-images-using-convolutional-neural-networks
#16
Bulat Ibragimov, Lei Xing
PURPOSE: Accurate segmentation of organs-at-risks (OARs) is the key step for efficient planning of radiation therapy for head and neck (HaN) cancer treatment. In the work, we proposed the first deep learning-based algorithm, for segmentation of OARs in HaN CT images, and compared its performance against state-of-the-art automated segmentation algorithms, commercial software, and interobserver variability. METHODS: Convolutional neural networks (CNNs)-a concept from the field of deep learning-were used to study consistent intensity patterns of OARs from training CT images and to segment the OAR in a previously unseen test CT image...
February 2017: Medical Physics
https://www.readbyqxmd.com/read/28203233/exo-mirexplorer-a-comprehensive-resource-for-exploring-and-comparatively-analyzing-exogenous-micrornas
#17
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202655/constraints-in-cancer-evolution
#18
REVIEW
Subramanian Venkatesan, Nicolai J Birkbak, Charles Swanton
Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28199404/loss-of-genes-related-to-nucleotide-excision-repair-ner-and-implications-for-reductive-genome-evolution-in-symbionts-of-deep-sea-vesicomyid-clams
#19
Shigeru Shimamura, Takashi Kaneko, Genki Ozawa, Mamiko Nishino Matsumoto, Takeru Koshiishi, Yoshihiro Takaki, Chiaki Kato, Ken Takai, Takao Yoshida, Katsunori Fujikura, James P Barry, Tadashi Maruyama
Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts)...
2017: PloS One
https://www.readbyqxmd.com/read/28198830/-final-common-pathway-of-human-cancer-immunotherapy-targeting-random-somatic-mutations
#20
REVIEW
Eric Tran, Paul F Robbins, Steven A Rosenberg
Effective clinical cancer immunotherapies, such as administration of the cytokine IL-2, adoptive cell transfer (ACT) and the recent success of blockade of the checkpoint modulators CTLA-4 and PD-1, have been developed without clear identification of the immunogenic targets expressed by human cancers in vivo. Immunotherapy of patients with cancer through the use of ACT with autologous lymphocytes has provided an opportunity to directly investigate the antigen recognition of lymphocytes that mediate cancer regression in humans...
February 15, 2017: Nature Immunology
keyword
keyword
84736
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"