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https://www.readbyqxmd.com/read/28108659/yamat-seq-an-efficient-method-for-high-throughput-sequencing-of-mature-transfer-rnas
#1
Megumi Shigematsu, Shozo Honda, Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos, Yohei Kirino
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28107348/predicting-length-of-stay-among-patients-discharged-from-the-emergency-department-using-an-accelerated-failure-time-model
#2
Chung-Hsien Chaou, Hsiu-Hsi Chen, Shu-Hui Chang, Petrus Tang, Shin-Liang Pan, Amy Ming-Fang Yen, Te-Fa Chiu
BACKGROUND: Emergency department (ED) crowding continues to be an important health care issue in modern countries. Among the many crucial quality indicators for monitoring the throughput process, a patient's length of stay (LOS) is considered the most important one since it is both the cause and the result of ED crowding. The aim of this study is to identify and quantify the influence of different patient-related or diagnostic activities-related factors on the ED LOS of discharged patients...
2017: PloS One
https://www.readbyqxmd.com/read/28106300/expression-profiles-analysis-and-functional-characterization-of-microrna-660-in-skeletal-muscle-differentiation
#3
Binglin Yue, Jiyao Wu, Yanhuan Wang, Chunlei Zhang, Xingtang Fang, Hong Chen
MicroRNA are a series of small non-coding RNAs that have emerged as critical regulators of skeletal muscle development. Here, we concentrated on the function of miR-660 during bovine skeletal myogenesis from our previous high-throughput sequencing results, then analyzed its expression profiles and characterized related functional roles. Overexpression of miR-660 significantly attenuated myogenic differentiation of C2C12 cells, whereas miR-660 inhibition enhanced C2C12 differentiation. Dual-Luciferase Reporter Assay went for demonstrating that miR-660 directly targeted the 3'-UTR of Rho guanine nucleotide exchange factor 12(ARHGEF-12)...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#4
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28096402/establishment-of-expression-state-boundaries-by-rif1-and-taz1-in-fission-yeast
#5
Tea Toteva, Bethany Mason, Yutaka Kanoh, Peter Brøgger, Daniel Green, Janne Verhein-Hansen, Hisao Masai, Geneviève Thon
The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28093921/microbial-genomics-and-antimicrobial-susceptibility-testing
#6
W Michael Dunne, Magali Jaillard, Olivier Rochas, Alex van Belkum
Antimicrobial susceptibility testing is key in modern clinical microbiology. With pandemic emergence of (multi-)antibiotic resistance, methods to detect and quantify resistance of clinically important bacterial species are imperative. Historically, antimicrobial susceptibility testing (AST) was mostly performed using methods relying on bacterial growth. Such methods may be time-consuming and more rapid alternatives have been actively sought for. Areas covered: Among the new AST methods there are many that focus on detection of causal resistance genes and/or gene mutations...
January 17, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#7
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#8
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28091735/comprehensive-assessment-of-peripheral-blood-tcr%C3%AE-repertoire-in-infectious-mononucleosis-and-chronic-active-ebv-infection-patients
#9
Shenglin Liu, Qian Zhang, Dongli Huang, Wenli Zhang, Fengluan Zhong, Jia Feng, Xueru Chen, Qingxiang Meng, Xiaofan Chen, Wei Zhang, Hongyu Zhang
Epstein-Barr virus (EBV) primary infection is usually asymptomatic, but it sometimes progresses to infectious mononucleosis (IM). Occasionally, some people develop chronic active EBV infection (CAEBV) with underlying immunodeficiency, which belongs to a continuous spectrum of EBV-associated lymphoproliferative disorders (EBV(+) LPD) with heterogeneous clinical presentations and high mortality. It has been well established that T cell-mediated immune response plays a critical role in the disease evolution of EBV infection...
January 14, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28079877/genome-wide-transposon-screening-and-quantitative-insertion-site-sequencing-for-cancer-gene-discovery-in-mice
#10
Mathias J Friedrich, Lena Rad, Iraad F Bronner, Alexander Strong, Wei Wang, Julia Weber, Matthew Mayho, Hannes Ponstingl, Thomas Engleitner, Carolyn Grove, Anja Pfaus, Dieter Saur, Juan Cadiñanos, Michael A Quail, George S Vassiliou, Pentao Liu, Allan Bradley, Roland Rad
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28076445/emerging-bordetella-pertussis-strains-induce-enhanced-signaling-of-human-pattern-recognition-receptors-tlr2-nod2-and-secretion-of-il-10-by-dendritic-cells
#11
Elise S Hovingh, Marjolein van Gent, Hendrik-Jan Hamstra, Marc Demkes, Frits R Mooi, Elena Pinelli
Vaccines against pertussis have been available for more than 60 years. Nonetheless, this highly contagious disease is reemerging even in countries with high vaccination coverage. Genetic changes of Bordetella pertussis over time have been suggested to contribute to the resurgence of pertussis, as these changes may favor escape from vaccine-induced immunity. Nonetheless, studies on the effects of these bacterial changes on the immune response are limited. Here, we characterize innate immune recognition and activation by a collection of genetically diverse B...
2017: PloS One
https://www.readbyqxmd.com/read/28071894/noninvasive-monitoring-of-blood-glucose-with-raman-spectroscopy
#12
Rishikesh Pandey, Santosh Kumar Paidi, Tulio A Valdez, Chi Zhang, Nicolas Spegazzini, Ramachandra Rao Dasari, Ishan Barman
The successful development of a noninvasive blood glucose sensor that can operate reliably over sustained periods of time has been a much sought after but elusive goal in diabetes management. Since diabetes has no well-established cure, control of elevated glucose levels is critical for avoiding severe secondary health complications in multiple organs including the retina, kidney and vasculature. While fingerstick testing continues to be the mainstay of blood glucose detection, advances in electrochemical sensing-based minimally invasive approaches have opened the door for alternate methods that would considerably improve the quality of life for people with diabetes...
January 10, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28067089/metabolomic-applications-in-radiation-biodosimetry-exploring-radiation-effects-through-small-molecules
#13
Evan L Pannkuk, Albert J Fornace, Evagelia C Laiakis
PURPOSE: Exposure of the general population to ionizing radiation has increased in the past decades, primarily due to long distance travel and medical procedures. On the other hand, accidental exposures, nuclear accidents, and elevated threats of terrorism with the potential detonation of a radiological dispersal device or improvised nuclear device in a major city, all have led to increased needs for rapid biodosimetry and assessment of exposure to different radiation qualities and scenarios...
January 9, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/28065270/functional-study-of-the-vitamin-k-cycle-enzymes-in-live-cells
#14
J-K Tie, D W Stafford
Vitamin K-dependent carboxylation, an essential posttranslational modification catalyzed by gamma-glutamyl carboxylase, is required for the biological functions of proteins that control blood coagulation, vascular calcification, bone metabolism, and other important physiological processes. Concomitant with carboxylation, reduced vitamin K (KH2) is oxidized to vitamin K epoxide (KO). KO must be recycled back to KH2 by the enzymes vitamin K epoxide reductase and vitamin K reductase in a pathway known as the vitamin K cycle...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#15
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
https://www.readbyqxmd.com/read/28059958/future-technologies-for-monitoring-hiv-drug-resistance-and-cure
#16
Urvi M Parikh, Kevin McCormick, Gert van Zyl, John W Mellors
PURPOSE OF REVIEW: Sensitive, scalable and affordable assays are critically needed for monitoring the success of interventions for preventing, treating and attempting to cure HIV infection. This review evaluates current and emerging technologies that are applicable for both surveillance of HIV drug resistance (HIVDR) and characterization of HIV reservoirs that persist despite antiretroviral therapy and are obstacles to curing HIV infection. RECENT FINDINGS: Next-generation sequencing (NGS) has the potential to be adapted into high-throughput, cost-efficient approaches for HIVDR surveillance and monitoring during continued scale-up of antiretroviral therapy and rollout of preexposure prophylaxis...
January 5, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28056744/nucleotide-second-messenger-signaling-as-a-target-for-the-control-of-bacterial-biofilm-formation
#17
Alberto J Martín-Rodríguez, Ute Römling
Bacterial biofilm formation and associated phenotypes are the major cause of chronic infection in humans. The major regulator of biofilm formation in Gram-negative and Gram-positive bacteria are nucleotide-based second messenger signaling pathways. Nucleotide-based signaling is a ubiquitous signal transduction mechanism in all domains of life that relay changes in the extracellular or intracellular milieu to protein or RNA effectors, leading to adaptive physiological responses. To date, six bona fide nucleotide signaling pathways, (p)ppGpp, cAMP, cGMP, c-di-AMP, c-di-GMP and cGAMP, have been characterized with respect to basic pathway modules and phenotypic and physiological output...
January 5, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28052134/assessment-of-common-and-emerging-bioinformatics-pipelines-for-targeted-metagenomics
#18
Léa Siegwald, Hélène Touzet, Yves Lemoine, David Hot, Christophe Audebert, Ségolène Caboche
Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results...
2017: PloS One
https://www.readbyqxmd.com/read/28051309/chemical-modifications-to-rna-a-new-layer-of-gene-expression-regulation
#19
Jinghui Song, Chengqi Yi
The first chemical modification to RNA was discovered nearly 60 years ago; to date, more than 100 chemically distinct modifications have been identified in cellular RNA. With the recent development of novel chemical and/or biochemical methods, dynamic modifications to RNA have been identified in the transcriptome, including N(6)-methyladenosine (m(6)A), inosine (I), 5-methylcytosine (m(5)C), pseudouridine (Ψ), 5-hydroxymethylcytosine (hm(5)C), and N(1)-methyladenosine (m(1)A). Collectively, the multitude of RNA modifications are termed epitranscriptome, leading to the emerging field of epitranscriptomics...
January 12, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28050688/high-prevalences-and-a-wide-genetic-diversity-of-simian-retroviruses-in-non-human-primate-bushmeat-in-rural-areas-of-the-democratic-republic-of-congo
#20
Ahuka-Mundeke Steve, Ayouba Ahidjo, Mbala-Kingebeni Placide, Foncelle Caroline, Mubonga Mukulumanya, Ndimbo-Kumugo Simon-Pierre, Lunguya-Metila Octavie, Mbenzo-Abokome Valentin, Muyembe-Tamfum Jean-Jacques, Delaporte Eric, Peeters Martine
Like the majority of emerging infectious diseases, HIV and HTLV are of zoonotic origin. Here we assess the risk of cross-species transmissions of their simian counterparts, SIV and STLV, from non-human primates (NHP) to humans in the Democratic Republic of Congo (DRC). A total of 331 samples, derived from NHP bushmeat, were collected as dried blood spots (DBS, n = 283) or as tissue samples (n = 36) at remote forest sites mainly in northern and eastern DRC. SIV antibody prevalences in DBS were estimated with a novel high throughput immunoassay with antigens representing the actual known diversity of HIV/SIV lineages...
January 3, 2017: EcoHealth
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