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https://www.readbyqxmd.com/read/29334709/-molecular-epidemiological-study-of-human-coronavirus-oc43-in-shanghai-from-2009-2016
#1
Y J Yang, Y W Hu
Objective: To understand the epidemiological characteristics of Human coronavirus (HCoV), the patterns of emergence and circulation, and the genotype distribution of human coronavirus OC43 (HCoV-OC43) from November, 2009 to April, 2016 in Shanghai. Methods: A total of 6 059 respiratory specimens, including pharyngeal swab, sputum, nasopharyngeal aspirates and alveolar lavage fluid, as well as relative clinical data were collected from patients with acute respiratory infections from seven sentinel hospitals during November, 2009 to April, 2016 in Shanghai...
January 6, 2018: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/29334678/genome-evolution-analysis-of-recurrent-testicular-malignant-mesothelioma-by-whole-genome-sequencing
#2
Shigeng Zhang, Qi Zhang, Qing Sun, Jinlong Tang, Jimin Chen, Na Ji, Yichun Zheng, Francia Fang, Wanjun Lei, Pengpeng Li, Nan Zhang
BACKGROUND/AIMS: Malignant mesothelioma of the tunica vaginalis testis is a rare and lethal disease. The genomic characteristics and genetic changes of tumor cells during the progression of this disease are unknown. METHODS: we performed whole-genome sequencing of four successive tumor samples derived from surgery and a blood sample in a single patient. RESULTS: All tumors were found to have significant C-to-T and T-to-C mutations, and amplification of copy number in chromosomes 1 and 12 were notified in all tumor samples...
January 15, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29334603/multicenter-phase-ii-study-of-oxaliplatin-irinotecan-and-s-1-as-first-line-treatment-for-patients-with-recurrent-or-metastatic-biliary-tract-cancer
#3
Changhoon Yoo, Boram Han, Hyeong Su Kim, Kyu-Pyo Kim, Deokhoon Kim, Jae Ho Jeong, Jae-Lyun Lee, Tae Won Kim, Jung Han Kim, Dae Ro Choi, Hong Il Ha, Jinwon Seo, Heung-Moon Chang, Baek-Yeol Ryoo, Dae Young Zang
Purpose: Although gemcitabine plus cisplatin has been established as the standard first-line chemotherapy for patients with advanced biliary tract cancer (BTC), overall prognosis remains poor. We investigated the efficacy of a novel triplet combination of oxaliplatin, irinotecan, and S-1 (OIS) for advanced BTC. Materials and Methods: Chemotherapy-naive patients with histologically documented unresectable or metastatic BTC were eligible for this multicenter, single-arm phase II study...
January 8, 2018: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/29334593/reanalysis-of-clinical-whole-exome-sequence-data-yields-multiple-new-diagnoses-a-time-intensive-but-successful-strategy-highlights-the-benefits-of-data-sharing-and-international-collaborations
#4
(no author information available yet)
No abstract text is available yet for this article.
February 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29334500/overexpression-of-%C3%A2%C2%B5-opioid-receptors-in-peripheral-afferents-but-not-in-combination-with-enkephalin-decreases-neuropathic-pain-behavior-and-enhances-opioid-analgesia-in-mouse
#5
Amanda H Klein, Husam K Mohammad, Rabiah Ali, Brad Peper, Steven P Wilson, Srinivasa N Raja, Matthias Ringkamp, Sarah Sweitzer
BACKGROUND: The current study used recombinant herpes simplex virus type I to increase expression of µ-opiate receptors and the opioid ligand preproenkephalin in peripheral nerve fibers in a mouse model of neuropathic pain. It was predicted that viral vector delivery of a combination of genes encoding the µ-opioid receptor and preproenkephalin would attenuate neuropathic pain and enhance opioid analgesia. The behavioral effects would be paralleled by changes in response properties of primary afferent neurons...
January 15, 2018: Anesthesiology
https://www.readbyqxmd.com/read/29334476/biological-control-of-botrytis-cinerea-interactions-with-native-vineyard-yeasts-from-washington-state
#6
Xuefei Wang, Dean A Glawe, Elizabeth K Kramer, David M Weller, Patricia Ann Okubara
Native yeasts are of increasing interest to researchers, grape growers, and vintners because of their potential for biocontrol activity, and their contributions to the aroma, flavor and mouthfeel qualities of wines. To assess biocontrol activity, we tested 11 yeasts from Washington vineyards, representing isolates of Candida saitoana, Curvibasidium pallidicorallinum, Metschnikowia chrysoperlae, Metschnikowia pulcherrima, Meyerozyma guilliermondii, Saccharomyces cerevisiae and Wickerhamomyces anomalus, for ability to colonize 'Thompson Seedless' grape berries, inhibit the growth of Botrytis cinerea in vitro, and suppress disease symptoms on isolated berries...
January 15, 2018: Phytopathology
https://www.readbyqxmd.com/read/29334465/design-of-mini-nucleic-acid-probe-for-cooperative-binding-of-rna-repeated-transcript-associated-with-myotonic-dystrophy-type-1
#7
Wei-Che Hsieh, Raman Bahal, Shivaji Thadke, Kirti Bhatt, Krzysztof Sobczak, Charles A Thornton, Danith H Ly
Toxic RNAs containing expanded trinucleotide repeats are the cause of many neuromuscular disorders, one being myotonic dystrophy type 1 (DM1). DM1 is triggered by CTG-repeat expansion in the 3'-UTR of the DMPK gene, resulting in toxic-gain of RNA function through sequestration of MBNL1 protein, among others. Herein we report the development of a relatively short MPPNA probe, two triplet-repeats in length, containing terminal pyrene moieties, that is capable of binding rCUG-repeats in a sequence-specific and selective manner...
January 15, 2018: Biochemistry
https://www.readbyqxmd.com/read/29334409/climate-driven-mitochondrial-selection-a-test-in-australian-songbirds
#8
Annika Mae Lamb, Han Ming Gan, Chris Greening, Leo Joseph, Yin Peng Lee, Alejandra Morán-Ordóñez, Paul Sunnucks, Alexandra Pavlova
Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate-driven selection (i.e. associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages)...
January 15, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29334405/high-resolution-dental-mri-for-planning-palatal-graft-surgery-a-clinical-pilot-study
#9
Tim Hilgenfeld, Thorsten Kästel, Alexander Heil, Peter Rammelsberg, Sabine Heiland, Martin Bendszus, Franz Sebastian Schwindling
AIM: To evaluate whether high-resolution, non-contrast-enhanced dental MRI can be used for accurate determination of palatal-masticatory-mucosa-thickness (PMMT) and to locate the greater palatal artery (GPA). MATERIALS AND METHODS: In five volunteers (4 males, 1 female; mean age 30.2±0.4 years) two independent raters measured PMMT by use of dental MRI in 180 positions. For comparison, clinical bone sounding was performed. The GPA was identified in time-of-flight (TOF) angiography and MSVAT-SPACE-prototype sequence...
January 15, 2018: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/29334402/noninvasive-reconstruction-of-placental-methylome-from-maternal-plasma-dna-potential-for-prenatal-testing-and-monitoring
#10
Kun Sun, Fiona M F Lun, Tak Y Leung, Rossa W K Chiu, Y M Dennis Lo, Hao Sun
OBJECTIVE: During human pregnancy, the DNA methylation of placental tissue is highly relevant to the normal growth and development of the fetus, therefore methylomic analysis of the placental tissue possesses high research and clinical value in prenatal testing and monitoring. Thus our aim is to develop an approach for reconstruction of the placental methylome, which should be completely noninvasive and achieve high accuracy and resolution. RESULTS: We propose a novel size-based algorithm, FEMER, to noninvasively reconstruct the placental methylome by genomewide bisulfite sequencing and size-based analysis of maternal plasma DNA...
January 15, 2018: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29334382/a-de-novo-enzyme-catalyzes-a-life-sustaining-reaction-in-escherichia-coli
#11
Ann E Donnelly, Grant S Murphy, Katherine M Digianantonio, Michael H Hecht
Producing novel enzymes that are catalytically active in vitro and biologically functional in vivo is a key goal of synthetic biology. Here we describe Syn-F4, the first de novo protein that meets both criteria. Purified Syn-F4 hydrolyzes the siderophore ferric enterobactin, and expression of Syn-F4 allows an inviable strain of Escherichia coli to grow in iron-limited medium. These findings demonstrate that entirely new sequences can provide life-sustaining enzymatic functions in living organisms.
January 15, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29334379/highly-parallel-direct-rna-sequencing-on-an-array-of-nanopores
#12
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland, Michael Jordan, Jonah Ciccone, Sabrina Serra, Jemma Keenan, Samuel Martin, Luke McNeill, E Jayne Wallace, Lakmal Jayasinghe, Chris Wright, Javier Blasco, Stephen Young, Denise Brocklebank, Sissel Juul, James Clarke, Andrew J Heron, Daniel J Turner
Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29334364/compactness-of-viral-genomes-effect-of-disperse-and-localized-random-mutations
#13
Anže Lošdorfer Božič, Cristian Micheletti, Rudolf Podgornik, Luca Tubiana
Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic Virus in order to understand the observed sensitivity of the global compactness of their folds...
January 15, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29334293/dna-barcoding-for-species-identification-in-deep-sea-clams-mollusca-bivalvia-vesicomyidae
#14
Jun Liu, Haibin Zhang
Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species...
January 15, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29334255/ngs-based-methylation-profiling-differentiates-tcf3-hlf-and-tcf3-pbx1-positive-b-cell-acute-lymphoblastic-leukemia
#15
Priyadarshini Kachroo, Silke Szymczak, Femke-Anouska Heinsen, Michael Forster, Jörn Bethune, Georg Hemmrich-Stanisak, Lewis Baker, Martin Schrappe, Martin Stanulla, Andre Franke
AIM: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. MATERIALS & METHODS: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. RESULTS: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF...
January 15, 2018: Epigenomics
https://www.readbyqxmd.com/read/29334236/wb-mri-and-oncology-recent-major-advances
#16
Vassiliki Pasoglou, Nicolas Michoux, Ahmed Larbi, Van Nieuwenhove Sandy, Frédéric Lecouvet
Magnetic Resonance Imaging (MRI) is a very attractive approach for tumor detection and oncological staging with its absence of ionizing radiation, high soft tissue contrast and spatial resolution. Less than ten years ago the use of Whole Body MRI (WB-MRI) protocols was uncommon due to many limitations, such as the long acquisition times and limited availability. This decade has marked substantial progress in WB-MRI protocols. This very promising technique is rapidly arising from the research world and is becoming a commonly used exam for tumor detection, due to recent technological developments and validation of WB-MRI by multiple studies and consensus papers...
January 15, 2018: British Journal of Radiology
https://www.readbyqxmd.com/read/29334230/dna-methylation-changes-and-evolution-of-rna-based-duplication-in-sus-scrofa-based-on-a-two-step-strategy
#17
Chengchi Fang, Cheng Zou, Yuhua Fu, Jingxuan Li, Yao Li, Yunlong Ma, Shuhong Zhao, Changchun Li
AIM: This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS: A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS: A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits...
January 15, 2018: Epigenomics
https://www.readbyqxmd.com/read/29334224/diversity-oriented-approach-to-n-heterocyclic-compounds-from-%C3%AE-phenyl-%C3%AE-enamino-ester-via-a-mitsunobu-michael-reaction-sequence
#18
Hina P A Khan, Tushar Kanti Chakraborty
Herein we delineate a novel route for the diastereoselective construction of diversely substituted N-heterocyclic ring systems as valuable scaffolds for natural products and pharmaceuticals, starting from easily accessible prochiral α-phenyl-β-enamino ester. The reaction sequence relies on the unexplored reactivity of α-phenyl-β-enamino ester as a nucleophilic partner in Mitsunobu reaction to forge the N-tethered alkene-alcohol/thiol/amine intermediate which was subjected to intramolecular hetero-Michael addition reaction under mild conditions to furnish the respective N-heterocyclic compounds embedded with an exocyclic chiral center in high yields and excellent diastereoselectivities...
January 15, 2018: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29334217/characterization-of-an-hsp90-independent-interaction-between-the-co-chaperone-p23-and-the-transcription-factor-p53
#19
Huiwen Wu, Jashil Hyun, Maria A Martinez-Yamout, Sung Jean Park, Jane Dyson
The cancer-suppressing transcription factor p53 is regulated by a wide variety of cellular factors, including many chaperones. The DNA-binding domain (DBD) of p53 is known to interact with the chaperone Hsp90, but the role of other members of the chaperone network, including co-chaperones such as p23 is unknown. Using a combination of NMR titration, isothermal titration calorimetry, fluorescence anisotropy and native agarose gel electrophoresis, we have identified a direct interaction between the p53 DBD and the Hsp90 co-chaperone p23 that occurs in the absence of Hsp90...
January 15, 2018: Biochemistry
https://www.readbyqxmd.com/read/29334207/screening-for-causative-mutations-of-major-prolificacy-genes-in-iranian-fat-tailed-sheep
#20
Ramin Abdoli, Seyed Ziaeddin Mirhoseini, Navid Ghavi Hossein-Zadeh, Pouya Zamani
Background: The presence of different missense mutations in sheep breeds have shown that the bone morphogenetic protein receptor 1B (BMPR1B), bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) genes play a vital role in ovulation rate and prolificacy in ewes. Therefore, the present study aims to investigate BMPR1B, BMP15 and GDF9 gene mutations in prolific ewes of Iranian fat-tailed Lori-Bakhtiari sheep. MATERIALS AND METHODS: In the present experimental study, genomic DNA was extracted from whole blood of 10 prolific Lori-Bakhtiari ewes with at least two twinning records in the first four parities to identify point mutations of the BMPR1B, BMP15 and GDF9 genes, using DNA sequencing...
April 2018: International Journal of Fertility & Sterility
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