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https://www.readbyqxmd.com/read/29738614/proteomic-and-cellular-localisation-studies-suggest-non-tight-junction-cytoplasmic-and-nuclear-roles-for-occludin-in-astrocytes
#1
S V Morgan, C J Garwood, L Jennings, J E Simpson, L M Castelli, P R Heath, S R Mihaylov, I Vazquez Villasenor, T C Minshull, P G Ince, M J Dickman, G M Hautbergue, S B Wharton
Occludin is a component of tight junctions, which are essential structural components of the blood brain barrier. However, occludin is expressed in cells without tight junctions, implying additional functions. We determined the expression and localisation of occludin in astrocytes in cell culture and in human brain tissue, and sought novel binding partners using a proteomic approach. Expression was investigated by immunocytochemistry and immunoblotting in the 1321N1 astrocytoma cell line and ScienCell human primary astrocytes, and by immunohistochemistry in human autopsy brain tissue...
May 8, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29724161/transcriptional-profiling-of-swine-mammary-gland-during-the-transition-from-colostrogenesis-to-lactogenesis-using-rna-sequencing
#2
V Palombo, J J Loor, M D'Andrea, M Vailati-Riboni, K Shahzad, U Krogh, P K Theil
BACKGROUND: Colostrum and milk are essential sources of antibodies and nutrients for the neonate, playing a key role in their survival and growth. Slight abnormalities in the timing of colostrogenesis/lactogenesis potentially threaten piglet survival. To further delineate the genes and transcription regulators implicated in the control of the transition from colostrogenesis to lactogenesis, we applied RNA-seq analysis of swine mammary gland tissue from late-gestation to farrowing. Three 2nd parity sows were used for mammary tissue biopsies on days 14, 10, 6 and 2 before (-) parturition and on day 1 after (+) parturition...
May 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29703432/antiviral-activity-safety-and-tolerability-of-multiple-ascending-doses-of-elbasvir-or-grazoprevir-in-participants-infected-with-hepatitis-c-virus-genotype-1-or-3
#3
Wendy W Yeh, Iain P Fraser, Patricia Jumes, Amelia Petry, Inge De Lepeleire, Martine Robberechts, Christina Reitmann, Kristien Van Dyck, Xiaobi Huang, Zifang Guo, Deborah Panebianco, Robert B Nachbar, Edward O'Mara, John A Wagner, Joan R Butterton, Frank J Dutko, Valentin Moiseev, Zhanna Kobalava, Andreas Hüser, Sorin Visan, Christian Schwabe, Edward Gane, Serghei Popa, Nelea Ghicavii, Markus Uhle, Frank Wagner
PURPOSE: Elbasvir (MK-8742) and grazoprevir (MK-5172; Merck & Co, Inc, Kenilworth, New Jersey) are hepatitis C virus (HCV)-specific inhibitors of the nonstructural protein 5A phosphoprotein and the nonstructural protein 3/4A protease, respectively. The aims of these studies were to evaluate the antiviral activity and safety of different doses of elbasvir or grazoprevir each administered as monotherapy to participants infected with either HCV genotype (GT) 1 or GT3. METHODS: These 2 double-blind, randomized, placebo-controlled, sequential-panel, multiple ascending dose studies were conducted to assess the safety and pharmacodynamics of 5 days of once-daily elbasvir or 7 days of once-daily grazoprevir in adult male participants chronically infected with either HCV GT1 or GT3...
April 24, 2018: Clinical Therapeutics
https://www.readbyqxmd.com/read/29680649/an-initiator-codon-mutation-in-sde2-causes-recessive-embryonic-lethality-in-holstein-cattle
#4
Sébastien Fritz, Chris Hoze, Emmanuelle Rebours, Anne Barbat, Méline Bizard, Amanda Chamberlain, Clémentine Escouflaire, Christy Vander Jagt, Mekki Boussaha, Cécile Grohs, Aurélie Allais-Bonnet, Maëlle Philippe, Amélie Vallée, Yves Amigues, Benjamin J Hayes, Didier Boichard, Aurélien Capitan
Researching depletions in homozygous genotypes for specific haplotypes among the large cohorts of animals genotyped for genomic selection is a very efficient strategy to map recessive lethal mutations. In this study, by analyzing real or imputed Illumina BovineSNP50 (Illumina Inc., San Diego, CA) genotypes from more than 250,000 Holstein animals, we identified a new locus called HH6 showing significant negative effects on conception rate and nonreturn rate at 56 d in at-risk versus control mating. We fine-mapped this locus in a 1...
April 18, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29665022/streamd-advanced-analysis-of-molecular-dynamics-using-r
#5
Maximilian J Dombrowsky, Sven Jager, Benjamin Schiller, Benjamin E Mayer, Sebastian Stammler, Kay Hamacher
Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD, the first interface between Gromacs trajectory files and the statistical language R. The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root-mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph-based analysis methods as the java library Stream leads to both: improved speed and analysis depth...
April 17, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29618007/subphenotype-meta-analysis-of-testicular-cancer-genome-wide-association-study-data-suggests-a-role-for-rbfox-family-genes-in-cryptorchidism-susceptibility
#6
Yanping Wang, Dione R Gray, Alan K Robbins, Erin L Crowgey, Stephen J Chanock, Mark H Greene, Katherine A McGlynn, Katherine Nathanson, Clare Turnbull, Zhaoming Wang, Marcella Devoto, Julia Spencer Barthold
STUDY QUESTION: Can subphenotype analysis of genome-wide association study (GWAS) data from subjects with testicular germ cell tumor (TGCT) provide insight into cryptorchidism (undescended testis, UDT) susceptibility? SUMMARY ANSWER: Suggestive intragenic GWAS signals common to UDT, TGCT case-case and TGCT case-control analyses occur in genes encoding RBFOX RNA-binding proteins (RBPs) and their neurodevelopmental targets. WHAT IS KNOWN ALREADY: UDT is a strong risk factor for TGCT, but while genetic risk factors for TGCT are well-known, genetic susceptibility to UDT is poorly understood and appears to be more complex...
March 29, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29546367/the-molecular-characterisation-of-mitochondrial-dna-deficient-oocytes-using-a-pig-model
#7
Te-Sha Tsai, Sonika Tyagi, Justin C St John
STUDY QUESTION: What are the molecular differences between mitochondrial DNA (mtDNA)-deficient and mtDNA-normal oocytes and how does mitochondrial supplementation alter these? SUMMARY ANSWER: Changes to DNA methylation in a 5' cytosine-phosphate-guanine 3' (CpG) island in the mtDNA-specific replication factor (DNA polymerase gamma (POLG)) of mtDNA-deficient oocytes mediates an increase in mtDNA copy number by the 2-cell stage that positively modulates the expression of nuclear genes, which affect cellular and metabolic processes, following autologous mitochondrial supplementation...
March 13, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29516485/enrichment-of-methylated-peptides-using-an-antibody-free-approach-for-global-methylproteomics-analysis
#8
Keyun Wang, Mingliang Ye
Protein methylation is receiving increasing attention for its important role in regulating diverse biological processes, including epigenetic regulation of gene transcription, RNA processing, DNA damage repair, and signal transduction. Proteome level analysis of protein methylation requires the enrichment of various forms of methylated peptides. Unfortunately, immunoaffinity purification can only enrich a subset of them due to the lack of pan-specific antibodies. Chromatography-based methods, however, can enrich methylated peptides in a global manner...
February 21, 2018: Current Protocols in Protein Science
https://www.readbyqxmd.com/read/29512114/poliovirus-replicon-rna-generation-transfection-packaging-and-quantitation-of-replication
#9
Ekaterina G Viktorova, Sunil Khattar, Siba Samal, George A Belov
Poliovirus is a prototype member of the Enterovirus genus of the Picornaviridae family of small positive strand RNA viruses, which include important human and animal pathogens. Quantitative assessment of viral replication is very important for investigation of the virus biology and the development of anti-viral strategies. The poliovirus genome structure allows replacement of structural genes with a reporter protein, such as a luciferase or a fluorescent protein, whose signals can be detected and quantified in vivo, thus permitting observation of replication kinetics in live cells...
February 22, 2018: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/29512113/porcine-reproductive-and-respiratory-syndrome-virus-propagation-and-quantification
#10
Zexu Ma, Liping Yang, Yan-Jin Zhang
Porcine reproductive and respiratory syndrome virus (PRRSV) is a member of the family Arteriviridae, order Nidovirale. PRRSV is an enveloped, single-stranded, positive-sense RNA virus with a genome around 15 kb in length. For propagation of PRRSV in vitro, the MARC-145 cell line is the most often used in a laboratory setting. Infectious cDNA clones of many PRRSV strains have been established, from which these viruses can be recovered. PRRSV titration is generally done in MARC-145 cells. PRRSV RNA copy numbers can be assessed by reverse transcription and real-time PCR...
February 22, 2018: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/29475804/tenofovir-alafenamide-plus-emtricitabine-versus-abacavir-plus-lamivudine-for-treatment-of-virologically-suppressed-hiv-1-infected-adults-a-randomised-double-blind-active-controlled-non-inferiority-phase-3-trial
#11
Alan Winston, Frank A Post, Edwin DeJesus, Daniel Podzamczer, Giovanni Di Perri, Vicente Estrada, François Raffi, Peter Ruane, Paula Peyrani, Gordon Crofoot, Patrick W G Mallon, Francesco Castelli, Mingjin Yan, Stephanie Cox, Moupali Das, Andrew Cheng, Martin S Rhee
BACKGROUND: Abacavir and tenofovir alafenamide offer reduced bone toxicity compared with tenofovir disoproxil fumarate. We aimed to compare safety and efficacy of tenofovir alafenamide plus emtricitabine with that of abacavir plus lamivudine. METHODS: In this randomised, double-blind, active-controlled, non-inferiority phase 3 trial, HIV-1-positive adults (≥18 years) were screened at 79 sites in 11 countries in North America and Europe. Eligible participants were virologically suppressed (HIV-1 RNA <50 copies per mL) and on a stable three-drug regimen containing abacavir plus lamivudine...
April 2018: Lancet HIV
https://www.readbyqxmd.com/read/29416641/-pd-l1-cd274-and-pd-l2-pdcd1lg2-promoter-methylation-is-associated-with-hpv-infection-and-transcriptional-repression-in-head-and-neck-squamous-cell-carcinomas
#12
Alina Franzen, Timo J Vogt, Tim Müller, Jörn Dietrich, Andreas Schröck, Carsten Golletz, Peter Brossart, Friedrich Bootz, Jennifer Landsberg, Glen Kristiansen, Dimo Dietrich
Background: DNA methylation of the immune checkpoint gene PD-L1 has recently been shown to be associated with PD-L1 mRNA expression in various malignancies. This study aimed to investigate the association of PD-L1 and PD-L2 methylation with mRNA expression, immune cell infitration, protein expression and human papilloma virus (HPV) infection in head and neck squamous cell carcinoma (HNSCC) patients. Results: DNA methylation of PD-L1 and PD-L2 correlates inversely with mRNA expression ( PD-L1 : p ≤ 0...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29363650/microrna-profiling-of-transgenic-mice-with-myocardial-overexpression-of-nucleolin
#13
Qing-Lan Lyu, Bi-Mei Jiang, Bin Zhou, Li Sun, Zhong-Yi Tong, Yuan-Bin Li, Yu-Ting Tang, Hui Sun, Mei-Dong Liu, Xian-Zhong Xiao
BACKGROUND: Nucleolin (NCL) is the most abundant RNA-binding protein in the cell nucleolus and plays an important role in chromatin stability, ribosome assembly, ribosomal RNA maturation, ribosomal DNA transcription, nucleocytoplasmic transport, and regulation of RNA stability and translation efficiency. In addition to its anti-apoptotic properties, the underlying mechanisms associated with NCL-related roles in different cellular processes remain unclear. In this study, the effect of NCL on microRNA (miRNA) expression was evaluated by generating transgenic mice with myocardial overexpression of NCL and by analyzing microarrays of mature and precursor miRNAs from mice...
February 5, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29357110/hybridization-histochemistry-of-neural-transcripts
#14
W Scott Young, June Song, Éva Mezey
This unit presents protocols to locate RNA transcripts in tissues. Numerous approaches are detailed, including those that use radiolabeled or colorimetric probes. Also, the probes may be modified oligodeoxynucleotides, singly or in pairs, as well as ribonucleic acids. High sensitivity and specificity are obtained, especially with sets of oligodeoxynucleotide pairs. © 2018 by John Wiley & Sons, Inc.
January 22, 2018: Current Protocols in Neuroscience
https://www.readbyqxmd.com/read/29344612/association-of-disease-severity-with-skin-microbiome-and-filaggrin-gene-mutations-in-adult-atopic-dermatitis
#15
Maja-Lisa Clausen, Tove Agner, Berit Lilje, Sofie M Edslev, Thor Bech Johannesen, Paal Skytt Andersen
Importance: Skin microbiome correlates with disease severity for lesional and nonlesional skin, indicating a global influence of atopic dermatitis (AD). A relation between skin microbiome and filaggrin gene (FLG) mutations proposes a possible association between skin microbiome and host genetics. Objectives: To assess skin and nasal microbiome diversity and composition in patients with AD and compare with healthy controls, and to investigate the microbiome in relation to disease severity and FLG mutations in patients with AD...
January 17, 2018: JAMA Dermatology
https://www.readbyqxmd.com/read/29337374/pooled-lentiviral-delivery-genetic-screens
#16
Federica Piccioni, Scott T Younger, David E Root
Pooled cell-based screens of mammalian genetic perturbations enable systematic large-scale, even genome-scale, evaluation of gene function. Pooled screens introduce genetic perturbations into a cell population through viral transduction such that each cell integrates into its DNA a single or small number of library perturbations with barcodes identifying the perturbations. One then selects and physically isolates the subset of cells that exhibit the phenotype of interest. Sequencing the barcodes in the hit cells reveals which genes favored or inhibited the hit phenotype...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29337373/making-use-of-cancer-genomic-databases
#17
Chad J Creighton
The vast amounts of genomic data now deposited in public repositories represent rich resources for cancer researchers. Large-scale genomics initiatives such as The Cancer Genome Atlas have made available data from multiple molecular profiling platforms (e.g., somatic mutation, RNA and protein expression, and DNA methylation) for the same set of over 10,000 human tumors. There has been much collective effort toward providing user-friendly software tools for biologists lacking computational skills to ask questions of large-scale genomic datasets...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29337370/modulating-gene-expression-in-epstein-barr-virus-ebv-positive-b-cell-lines-with-crispra-and-crispri
#18
Liang Wei Wang, Stephen J Trudeau, Chong Wang, Catherine Gerdt, Sizun Jiang, Bo Zhao, Benjamin E Gewurz
Epstein-Barr virus (EBV) transforms small resting primary B cells into large lymphoblastoid cells which are able to grow and survive in vitro indefinitely. These cells represent a model for oncogenesis. In this unit, variants of conventional clustered regularly interspaced short palindromic repeats (CRISPR), namely the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) methods, are discussed in the context of gene regulation at genomic DNA promoter and enhancer elements. Lymphoblastoid B cell lines (LCLs) stably expressing nuclease-deficient Cas9 (dCas9)-VP64 (Cas9 associated with CRISPRa) or dCas9-KRAB (Cas9 associated with CRISPRi) are transduced with lentivirus that encodes a single guide RNA (sgRNA) that targets a specific gene locus...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29315667/collision-free-poisson-motion-planning-in-ultra-high-dimensional-molecular-conformation-spaces
#19
Rasmus Fonseca, Dominik Budday, Henry van den Bedem
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra-high dimensional configuration spaces, and the requirement to avoid (self-) collisions, which results in low acceptance rates...
May 5, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29286106/integrative-analysis-of-long-non-coding-rnas-and-messenger-rna-expression-profiles-in-systemic-lupus-erythematosus
#20
Qing Luo, Xue Li, Chuxin Xu, Lulu Zeng, Jianqing Ye, Yang Guo, Zikun Huang, Junming Li
Thousands of long noncoding RNAs (lncRNAs) have been reported and represent an important subset of pervasive genes associated with a broad range of biological functions. Abnormal expression levels of lncRNAs have been demonstrated in multiple types of human disease. However, the role of lncRNAs in systemic lupus erythematosus (SLE) remains poorly understood. In the present study, the expression patterns of lncRNAs and messenger RNAs (mRNAs) were investigated in peripheral blood mononuclear cells (PBMCs) in SLE using Human lncRNA Array v3...
March 2018: Molecular Medicine Reports
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