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https://www.readbyqxmd.com/read/29156774/micrornas-as-predictors-for-cns-relapse-of-systemic-diffuse-large-b-cell-lymphoma
#1
Nir Pillar, Osnat Bairey, Neta Goldschmidt, Yakov Fellig, Yevgenia Rosenblat, Itchak Shehtman, Danielle Haguel, Pia Raanani, Noam Shomron, Tali Siegal
Systemic diffuse large B-cell lymphoma (DLBCL) is a potentially curable disease using current regimen of immunochemotherapy. Central nervous system (CNS) relapse is a complication that occurs in approximately 5% of DLBCL patients and is associated with a high fatality rate. Early identification of molecular markers for CNS involvement may serve for the highly needed accurate stratification of patients into risk groups regarding CNS relapse. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at the post-transcriptional level and are known to be involved in DLBCL pathophysiology...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156628/-differentially-expressed-trna-derived-small-rnas-co-sediment-primarily-with-non-polysomal-fractions-in-drosophila
#2
Çağdaş Göktaş, Hatice Yiğit, Mehmet İlyas Coşacak, Bünyamin Akgül
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0-1 and 7-8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5'ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29156510/isolation-and-characterization-of-a-novel-broad-host-range-bacteriophage-infecting-salmonella-enterica-subsp-enterica-for-biocontrol-and-rapid-detection
#3
In Young Choi, Ju-Hoon Lee, Hye-Jin Kim, Mi-Kyung Park
Bacteriophages have gained substantial attention as biocontrol and bio-recognition agents, substituting antibodies. In this study, a Salmonella Enteritidis-specific bacteriophage, KFS-SE1, was isolated, identified, and characterized. This Siphoviridae phage infects S. Enteritidis with high specificity. This phage is highly stable under various pH (5-11), temperature (4-60°C), and organic solvent conditions. The KFS-SE1 genome consists of 59,715-bp with 73 predicted open reading frames and 57.14% GC content; it has a complete set of genes required for phage reconstruction...
November 21, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29156057/prgdb-3-0-a-comprehensive-platform-for-prediction-and-analysis-of-plant-disease-resistance-genes
#4
Cristina M O Cruz, Andreu Paytuvi-Gallart, Antimo Di Donato, Vicky Sundesha, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria R Ercolano
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155959/the-discovery-potential-of-rna-processing-profiles
#5
Amadís Pagès, Ivan Dotu, Joan Pallarès-Albanell, Eulàlia Martí, Roderic Guigó, Eduardo Eyras
Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155880/molecular-characterization-of-novel-mosquito-borne-rickettsia-spp-from-mosquitoes-collected-at-the-demilitarized-zone-of-the-republic-of-korea
#6
Alice N Maina, Terry A Klein, Heung-Chul Kim, Sung-Tae Chong, Yu Yang, Kristin Mullins, Ju Jiang, Heidi St John, Richard G Jarman, Jun Hang, Allen L Richards
Rickettsiae are associated with a diverse range of invertebrate hosts. Of these, mosquitoes could emerge as one of the most important vectors because of their ability to transmit significant numbers of pathogens and parasites throughout the world. Recent studies have implicated Anopheles gambiae as a potential vector of Rickettsia felis. Herein we report that a metagenome sequencing study identified rickettsial sequence reads in culicine mosquitoes from the Republic of Korea. The detected rickettsiae were characterized by a genus-specific quantitative real-time PCR assay and sequencing of rrs, gltA, 17kDa, ompB, and sca4 genes...
2017: PloS One
https://www.readbyqxmd.com/read/29155867/spectrum-of-pathogen-and-model-specific-histopathologies-in-mouse-models-of-acute-pneumonia
#7
Kristina Dietert, Birgitt Gutbier, Sandra M Wienhold, Katrin Reppe, Xiaohui Jiang, Ling Yao, Catherine Chaput, Jan Naujoks, Markus Brack, Alexandra Kupke, Christin Peteranderl, Stephan Becker, Carolin von Lachner, Nelli Baal, Hortense Slevogt, Andreas C Hocke, Martin Witzenrath, Bastian Opitz, Susanne Herold, Holger Hackstein, Leif E Sander, Norbert Suttorp, Achim D Gruber
Pneumonia may be caused by a wide range of pathogens and is considered the most common infectious cause of death in humans. Murine acute lung infection models mirror human pathologies in many aspects and contribute to our understanding of the disease and the development of novel treatment strategies. Despite progress in other fields of tissue imaging, histopathology remains the most conclusive and practical read out tool for the descriptive and semiquantitative evaluation of mouse pneumonia and therapeutic interventions...
2017: PloS One
https://www.readbyqxmd.com/read/29155823/development-and-preliminary-evaluation-of-a-multiplexed-amplification-and-next-generation-sequencing-method-for-viral-hemorrhagic-fever-diagnostics
#8
Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche
BACKGROUND: We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. METHODOLOGY: An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform...
November 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155600/recommended-reading-from-boston-university-school-of-medicine-pulmonary-and-critical-care-medicine-fellows
#9
Eric D Abston, Stephanie M Hon, Andrew Berical, Christine L Reardon
No abstract text is available yet for this article.
November 20, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29155332/unusual-features-of-the-large-linear-plasmid-psa3239-from-streptomyces-aureofaciens-ccm-3239
#10
Erik Mingyar, Renata Novakova, Renata Knirschova, Lubomira Feckova, Carmen Bekeova, Jan Kormanec
We previously identified the aur1 gene cluster, responsible for the production of the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Pulse-field gel electrophoresis showed a single, 241kb linear plasmid, pSA3239, in this strain, and several approaches confirmed the presence of the aur1 cluster in this plasmid. We report here the nucleotide sequence of this 241,076-bp plasmid. pSA3239 contains an unprecedentedly small (13bp) telomeric sequence CCCGCGGAGCGGG, which is identical to the conserved Palindrome I sequence involved in the priming of end-patching replication...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29155284/the-dynamic-evolution-of-drosophila-innubila-nudivirus
#11
Tom Hill, Robert L Unckless
Viruses coevolve with their hosts to overcome host resistance and gain the upper hand in the evolutionary arms race. Drosophila innubila nudivirus (DiNV) is a double stranded DNA virus, closely related to Oryctes rhinoceros nudivirus (OrNV) and Kallithea virus. DiNV is the first DNA virus found to naturally infect Drosophila and therefore has the potential to be developed as a model for DNA virus immune defense and host/virus coevolution within its well-studied host system. Here we sequence and annotate the genome of DiNV and identify signatures of adaptation, revealing clues for genes involved in host-parasite coevolution...
November 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29155138/hpv16-e5-is-produced-from-an-hpv16-early-mrna-spliced-from-sd226-to-sa3358
#12
Kersti Nilsson, Christopher Norberg, Ann-Kristin Mossberg, Stefan Schwartz
The HPV16 E5 open reading frame (ORF) is present on the majority of all alternatively spliced HPV16 mRNAs, but it is currently unknown how well it is translated into E5 protein. To identify HPV16 mRNAs that are efficiently translated into E5, we have generated cDNA plasmids expressing individual, alternatively spliced HPV16 mRNAs with the potential to produce E5. By replacing the E5 ORF with sLuc, we could quantitate sLuc and determine how well each cDNA was translated. Our results showed that the upstream E1 and E7 AUGs inhibited translation of the E5 ORF and revealed that only one HPV16 mRNA produced high levels of E5...
November 16, 2017: Virus Research
https://www.readbyqxmd.com/read/29155131/human-lung-epithelial-cell-cultures-for-analysis-of-inhaled-toxicants-lessons-learned-and-future-directions
#13
REVIEW
Pieter S Hiemstra, Gwendolynn Grootaers, Anne M van der Does, Cyrille A M Krul, Ingeborg M Kooter
The epithelium that covers the conducting airways and alveoli is a primary target for inhaled toxic substances, and therefore a focus in inhalation toxicology. The increasing concern about the use of animal models has stimulated the development of in vitro cell culture models for analysis of the biological effects of inhaled toxicants. However, the validity of the current in vitro models and their acceptance by regulatory authorities as an alternative to animal models is a reason for concern, and requires a critical review...
November 15, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29155031/the-involvement-of-suppressor-of-cytokine-signaling-6-socs6-in-immune-response-of-chinese-mitten-crab-eriocheir-sinensis
#14
Chen Qu, Qingsong Xu, Mengmeng Lu, Feifei Wang, Zhaoqun Liu, Dongyang Liu, Wen Yang, Qilin Yi, Lingling Wang, Linsheng Song
Suppressor of cytokine signaling (SOCS) is a family of cytokine-inducible negative regulators of cytokine signaling and it plays a crucial role in various physiological processes. In the present study, the full-length cDNA of a SOCS (designated as EsSOCS6) was cloned from Chinese mitten crab Eriocheir sinensis. The open reading frame of EsSOCS6 cDNA was of 1266 bp, which encoded a polypeptide of 421 amino acid residues. There were two typically conserved SOCS family domains in EsSOCS6, including a central Src homology 2 (SH2) domain and a C-terminal SOCS box...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29155009/thresholds-for-sine-wave-corrugations-defined-by-binocular-disparity-in-random-dot-stereograms-factor-analysis-of-individual-differences-revealstwo-stereoscopic-mechanisms-tuned-for-spatial-frequency
#15
David H Peterzell, Ignacio Serrano-Pedraza, Michael Widdall, Jenny C A Read
Threshold functions for sinusoidal depth corrugations typically reach their minimum (highest sensitivity) at spatial frequencies of 0.2-0.4 cycles/degree (cpd), with lower thresholds for horizontal than vertical corrugations at low spatial frequencies. To elucidate spatial frequency and orientation tuning of stereoscopic mechanisms, we measured the disparity sensitivity functions, and used factor analytic techniques to estimate the existence of independent underlying stereo channels. The data set (N=30 individuals) was for horizontal and vertical corrugations of spatial frequencies ranging from 0...
November 15, 2017: Vision Research
https://www.readbyqxmd.com/read/29154906/increase-in-taxonomic-assignment-efficiency-of-viral-reads-in-metagenomic-studies
#16
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
November 14, 2017: Virus Research
https://www.readbyqxmd.com/read/29154899/combining-diagnostic-methods-for-antimicrobial-susceptibility-testing-a-comparative-approach
#17
Sylvia Natalie Kłodzińska, Petra Alexandra Priemel, Thomas Rades, Hanne Mørck Nielsen
BACKGROUND: The minimum inhibitory concentration (MIC) is a measure of antimicrobial susceptibility testing (AST) of a given antibiotic, but provides insufficient information when bacterial killing is crucial, e.g. when treating immunocompromised patients. In these cases, the minimum bactericidal concentration (MBC) is a more reliable measure of antibiotic activity. Here, we aim to demonstrate and recommend combinations of methods for MIC and MBC measurements. We also aim to emphasize the importance of uniform protocols for these procedures including the time point for reading MIC results, which the authors suggest to be 20h...
November 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29154795/vision-improvement-in-pilots-with-presbyopia-following-perceptual-learning
#18
Anna Sterkin, Yuval Levy, Russell Pokroy, Maria Lev, Liora Levian, Ravid Doron, Oren Yehezkel, Moshe Fried, Yael Frenkel-Nir, Barak Gordon, Uri Polat
Israeli Air Force (IAF) pilots continue flying combat missions after the symptoms of natural near-vision deterioration, termed presbyopia, begin to be noticeable. Because modern pilots rely on the displays of the aircraft control and performance instruments, near visual acuity (VA) is essential in the cockpit. We aimed to apply a method previously shown to improve visual performance of presbyopes, and test whether presbyopic IAF pilots can overcome the limitation imposed by presbyopia. Participants were selected by the IAF aeromedical unit as having at least initial presbyopia and trained using a structured personalized perceptual learning method (GlassesOff application), based on detecting briefly presented low-contrast Gabor stimuli, under the conditions of spatial and temporal constraints, from a distance of 40 cm...
November 14, 2017: Vision Research
https://www.readbyqxmd.com/read/29154654/variety-in-parental-use-of-want-relates-to-subsequent-growth-in-children-s-theory-of-mind
#19
Ted Ruffman, Aastha Puri, Olivia Galloway, Japher Su, Mele Taumoepeau
In 2 cross-lagged, longitudinal studies we contrasted parental talk about want in a single context versus multiple contexts. Study 1 examined thirty-two 2 year olds, with mothers describing pictures to children. Mothers could use want in zero, one, or multiple contexts. Children whose mothers used want in multiple contexts experienced a significantly larger gain in mental state terms over a 6-month period. Study 2 examined 50 preschoolers, measuring theory of mind (ToM) with tasks and mental state terms, then had parents intervene by reading booklets in which want was used in 1 or multiple contexts...
November 20, 2017: Developmental Psychology
https://www.readbyqxmd.com/read/29154645/center-based-early-care-and-education-and-children-s-school-readiness-do-impacts-vary-by-neighborhood-poverty
#20
Taryn W Morrissey, Katie Vinopal
Neighborhoods provide resources that may affect children's achievement or moderate the influences of other developmental contexts, such as early care and education (ECE). Using a sample (N ≈ 12,430) from the 2010-2011 Early Childhood Longitudinal Study-Kindergarten Cohort, merged with census tract-level poverty data from the 2008-2012 American Community Survey, this article examines associations between center-based ECE participation, neighborhood poverty, and children's academic skills and behavior at kindergarten entry...
November 20, 2017: Developmental Psychology
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