1,028,466 results match your criteria RNA New York N.Y.[Journal]


Transformation of the Transcriptomic Profile of Mouse Periocular Mesenchyme During Formation of the Embryonic Cornea.

Invest Ophthalmol Vis Sci 2019 Feb;60(2):661-676

BioSciences Department, Rice University, Houston, Texas, United States.

Purpose: Defects in neural crest development are a major contributing factor in corneal dysgenesis, but little is known about the genetic landscape during corneal development. The purpose of this study was to provide a detailed transcriptome profile and evaluate changes in gene expression during mouse corneal development.

Methods: RNA sequencing was used to uncover the transcriptomic profile of periocular mesenchyme (pNC) isolated at embryonic day (E) 10. Read More

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http://dx.doi.org/10.1167/iovs.18-26018DOI Listing
February 2019

KLF4 Regulates Corneal Epithelial Cell Cycle Progression by Suppressing Canonical TGF-β Signaling and Upregulating CDK Inhibitors P16 and P27.

Invest Ophthalmol Vis Sci 2019 Feb;60(2):731-740

Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States.

Purpose: Krüppel-like factor 4 (KLF4) promotes corneal epithelial (CE) cell fate while suppressing mesenchymal properties. TGF-β plays a crucial role in cell differentiation and development, and if dysregulated, it induces epithelial-mesenchymal transition (EMT). As KLF4 and TGF-β regulate each other in a context-dependent manner, we evaluated the role of the crosstalk between KLF4 and TGF-β-signaling in CE homeostasis. Read More

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http://dx.doi.org/10.1167/iovs.18-26423DOI Listing
February 2019

Circular RNA biogenesis is decreased in postmortem cortical gray matter in schizophrenia and may alter the bioavailability of associated miRNA.

Neuropsychopharmacology 2019 Feb 20. Epub 2019 Feb 20.

School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.

Circular RNAs (circRNAs) are a covalently closed subclass of lncRNA molecules formed by back splicing of linear precursor RNA. These molecules are relatively stable and particularly abundant in the mammalian brain and therefore may participate in neural development and function. With the emergence of circRNAs activity in gene regulation, these molecules have been implicated in several biological processes, including synaptic plasticity, and we therefore suspect they may have a role in neurobehavioral disorders. Read More

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http://dx.doi.org/10.1038/s41386-019-0348-1DOI Listing
February 2019

The ubiquitin ligase KBTBD8 regulates PKM1 levels via Erk1/2 and Aurora A to ensure oocyte quality.

Aging (Albany NY) 2019 Feb 20. Epub 2019 Feb 20.

State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China.

Tight control of energy metabolism is essential for normal cell function and organism survival. PKM (pyruvate kinase, muscle) isoforms 1 and 2 originate from alternative splicing of PKM pre-mRNA. They are key enzymes in oxidative phosphorylation and aerobic glycolysis, respectively, and are essential for ATP generation. Read More

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http://dx.doi.org/10.18632/aging.101802DOI Listing
February 2019

Thermomorphogenesis.

Annu Rev Plant Biol 2019 Feb 20. Epub 2019 Feb 20.

School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; email:

When exposed to warmer, nonstressful average temperatures, some plant organs grow and develop at a faster rate without affecting their final dimensions. Other plant organs show specific changes in morphology or development in a response termed thermomorphogenesis. Selected coding and noncoding RNA, chromatin features, alternative splicing variants, and signaling proteins change their abundance, localization, and/or intrinsic activity to mediate thermomorphogenesis. Read More

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http://dx.doi.org/10.1146/annurev-arplant-050718-095919DOI Listing
February 2019

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.

Curr Protoc Bioinformatics 2019 Feb 20:e72. Epub 2019 Feb 20.

Aix-Marseille University, INSERM, Laboratory of Theory and Approaches of Genome Complexity (TAGC), Marseille, France.

Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. Read More

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http://doi.wiley.com/10.1002/cpbi.72
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http://dx.doi.org/10.1002/cpbi.72DOI Listing
February 2019
5 Reads

Chromatin-Associated RNA Sequencing (ChAR-seq).

Curr Protoc Mol Biol 2019 Feb 20:e87. Epub 2019 Feb 20.

Department of Biochemistry, Stanford University School of Medicine, Stanford, California.

RNA is a fundamental component of chromatin. Noncoding RNAs (ncRNAs) can associate with chromatin to influence gene expression and chromatin state; many also act at long distances from their transcriptional origin. Yet we know almost nothing about the functions or sites of action for most ncRNAs. Read More

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http://dx.doi.org/10.1002/cpmb.87DOI Listing
February 2019

Creating Cell and Animal Models of Human Disease by Genome Editing Using CRISPR/Cas9.

J Gene Med 2019 Feb 20:e3082. Epub 2019 Feb 20.

Department of Genetics, Shiraz University of Medical Science, Shiraz, Iran.

Aims: Set of unique sequences in bacterial genomes, responsible for protecting bacteria against bacteriophages, have been recently used for genetic manipulation of specific points in the genome. These system comprises of one RNA component and one enzyme component, known as CRISPR and Cas9, respectively. The present review focuses on the applications of the CRISPR/Cas9 technology in the development of cellular and animal models of human disease. Read More

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http://dx.doi.org/10.1002/jgm.3082DOI Listing
February 2019

Global gene expression changes reflecting pleiotropic effects of Irpex lacteus induced by low--intensity electromagnetic field.

Bioelectromagnetics 2019 Feb 20. Epub 2019 Feb 20.

School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China.

A polysaccharide of Irpex lacteus, a white-rot fungus with lignocellulose-degrading activities, has been used as a commercial medicine for nephritis treatment. Previously, a low-intensity electromagnetic field (LI-EMF) was found to increase the biomass and polysaccharide content of Irpex lacteus and induce twists on the cell surface. In this study, RNA-sequencing (RNA-seq) technology was used to analyze the underlying mechanism of LI-EMF's influence on Irpex lacteus. Read More

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http://dx.doi.org/10.1002/bem.22171DOI Listing
February 2019

Irradiation-induced osteocyte damage promotes HMGB1-mediated osteoclastogenesis in vitro.

J Cell Physiol 2019 Feb 20. Epub 2019 Feb 20.

Department of Radiation Health, Institute of Radiation Medicine, Fudan University, Shanghai, China.

Irradiation-induced bone loss is widely reported, especially in radiotherapy-induced osteoporosis. In addition to the mechanism of osteogenesis inhibition and osteoclastogenesis promotion, the regulation effect of osteocytes, which also send signals to modulate osteoclastogenesis, should be elucidated. In this study, the effect of irradiation on osteocyte and its accommodation to osteoclastogenesis via the release of high mobility group box 1 (HMGB1) was explored. Read More

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http://dx.doi.org/10.1002/jcp.28351DOI Listing
February 2019

Melatonin supplementation during in vitro maturation of oocyte enhances subsequent development of bovine cloned embryos.

J Cell Physiol 2019 Feb 20. Epub 2019 Feb 20.

Department of Basic Veterinary Sciences, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture, Yangling, Shaanxi, China.

Oocyte quality, which is directly related to reprogramming competence, is a major important limiting factor in animal cloning efficiency. Compared with oocytes matured in vivo, in vitro matured oocytes exhibit lower oocyte quality and reprogramming competence primarily because of their higher levels of reactive oxygen species. In this study, we investigate whether supplementing the oocyte maturation medium with melatonin, a free radical scavenger, could improve oocyte quality and reprogramming competence. Read More

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http://dx.doi.org/10.1002/jcp.28357DOI Listing
February 2019
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Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations.

PLoS One 2019 20;14(2):e0212449. Epub 2019 Feb 20.

Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy.

Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212449PLOS
February 2019

Kaposi's sarcoma-associated herpesvirus ORF57 protein protects viral transcripts from specific nuclear RNA decay pathways by preventing hMTR4 recruitment.

PLoS Pathog 2019 Feb 20;15(2):e1007596. Epub 2019 Feb 20.

Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas.

Nuclear RNAs are subject to a number of RNA decay pathways that serve quality control and regulatory functions. As a result, any virus that expresses its genes in the nucleus must have evolved mechanisms that avoid these pathways, but the how viruses evade nuclear RNA decay remains largely unknown. The multifunctional Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 (Mta) protein is required for the nuclear stability of viral transcripts. Read More

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http://dx.doi.org/10.1371/journal.ppat.1007596DOI Listing
February 2019

Nine-year distribution pattern of hepatitis C virus (HCV) genotypes in Southern Italy.

PLoS One 2019 20;14(2):e0212033. Epub 2019 Feb 20.

SSD Virology and Molecular Biology, Department of Diagnostic Area, Istituto Nazionale Tumori, Fondazione "G. Pascale", IRCCS Italia, Naples, Italy.

Introduction: It has been greatly described that different hepatitis C virus (HCV) genotypes are strictly correlated to various evolution, prognosis and response to therapy during the chronic liver disease. Aim of this study was to outline the changes in the epidemiology of Hepatitis C genotypes in Southern Italy regions from 2006 to 2014.

Material/methods: Prevalence of HCV genotypes was analyzed in 535 HCV-RNA positive patients with chronic Hepatitis C infection, selected during the period 2012-2014, and compared with our previous data, referred to periods 2006-2008 and 2009-2011. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212033PLOS
February 2019
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Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus.

PLoS Biol 2019 Feb 20;17(2):e3000142. Epub 2019 Feb 20.

Institute of Ecology and Evolution, University of Bern, Switzerland.

The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Read More

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http://dx.doi.org/10.1371/journal.pbio.3000142DOI Listing
February 2019

Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad.

J Neurophysiol 2019 Feb 20. Epub 2019 Feb 20.

Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, United States.

The functional state of denervated muscle is a critical factor in the ability to restore movement after injury- or disease-related paralysis. Here we used peripheral optogenetic stimulation and transcriptome profiling in the mouse whisker system to investigate the time course of changes in neuromuscular function following complete unilateral facial nerve transection. While most skeletal muscles rapidly lose functionality after lower motor neuron denervation, optogenetic muscle stimulation of the paralyzed whisker pad revealed sustained increases in the sensitivity, velocity, and amplitude of whisker movements, and reduced fatigability, starting 48 h after denervation. Read More

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http://dx.doi.org/10.1152/jn.00837.2018DOI Listing
February 2019

High glucose-induced ubiquitination of G6PD leads to the injury of podocytes.

FASEB J 2019 Feb 20:fj201801921R. Epub 2019 Feb 20.

Division of Endocrinology and Metabolism, Huashan Hospital, Fudan University, Shanghai, China.

Oxidative stress contributes substantially to podocyte injury, which plays an important role in the development of diabetic kidney disease. The mechanism of hyperglycemia-induced oxidative stress in podocytes is not fully understood. Glucose-6-phosphate dehydrogenase (G6PD) is critical in maintaining NADPH, which is an important cofactor for the antioxidant system. Read More

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http://dx.doi.org/10.1096/fj.201801921RDOI Listing
February 2019

The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality.

Arch Pathol Lab Med 2019 Feb 20. Epub 2019 Feb 20.

From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore);Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria);Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel);Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne);the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage);the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy);the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica);the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir);and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell).

Context.—: Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown.

Objective. Read More

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http://dx.doi.org/10.5858/arpa.2018-0172-OADOI Listing
February 2019

Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches.

J Integr Bioinform 2018 Dec 22. Epub 2018 Dec 22.

Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.

The advance of high-throughput RNA-Sequencing techniques enables researchers to analyze the complete gene activity in particular cells. From the insights of such analyses, researchers can identify disease-specific expression profiles, thus understand complex diseases like cancer, and eventually develop effective measures for diagnosis and treatment. The high dimensionality of gene expression data poses challenges to its computational analysis, which is addressed with measures of gene selection. Read More

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http://dx.doi.org/10.1515/jib-2018-0064DOI Listing
December 2018

Establishing CRISPR/Cas13a immune system conferring RNA virus resistance in both dicot and monocot plants.

Plant Biotechnol J 2019 Feb 20. Epub 2019 Feb 20.

Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.

Besides its powerful capability for genome editing, the clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) (CRISPR/Cas) systems, has been exploited to combat virus infection in eukaryotic organisms (Zaidi et al., 2016). By harnessing CRISPR/Cas system, its compelling inhibiting activities against DNA viruses (Ali et al. Read More

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http://dx.doi.org/10.1111/pbi.13095DOI Listing
February 2019

Entomological and virological surveillance for dengue virus in churches in Merida, Mexico.

Rev Inst Med Trop Sao Paulo 2019 Feb 14;61:e9. Epub 2019 Feb 14.

Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Laboratorio de Arbovirología, Mérida, Yucatán, México.

This study was designed to assess whether churches in endemic dengue districts in Merida, Mexico provide suitable breeding habitats for mosquitoes and are potential sites for dengue virus (DENV) transmission. Churches were inspected for immature and adult mosquitoes once every week from November 2015 to October 2016. A total of 10,997 immatures of five species were collected. Read More

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http://dx.doi.org/10.1590/S1678-9946201961009DOI Listing
February 2019

WAITING DAAS LIST MORTALITY IMPACT IN HCV CIRRHOTIC PATIENTS.

Arq Gastroenterol 2018 Oct-Dec;55(4):343-345

Universidade Estadual Paulista (UNESP), Faculdade de Medicina, Departamento de Clínica Médica, Botucatu, SP, Brasil.

Background: The infection for the hepatitis C virus (HCV) is a leading cause of liver-related morbidity and mortality through its evolution to liver cirrhosis, end-stage liver complications and hepatocellular carcinoma. Currently, the new drugs for the HCV infection, based on direct antiviral agents, have changed the outcomes in this setting.

Objective: To assess death incidence, during the wait for the treatment with the new drugs, and to analyze which independent variable (age, sex, ascite, HDA, albumin, α-fetoprotein, platelets and Meld score) had relation with death. Read More

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http://www.scielo.br/scielo.php?script=sci_arttext&pid=S
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http://dx.doi.org/10.1590/S0004-2803.201800000-76DOI Listing
May 2018
1 Read

Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW.

Mol Omics 2019 Feb 20. Epub 2019 Feb 20.

College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.

A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. Read More

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http://dx.doi.org/10.1039/c8mo00198gDOI Listing
February 2019

Ruxolitinib treatment reduces monocytic superoxide radical formation without affecting hydrogen peroxide formation or systemic oxidative nucleoside damage in myelofibrosis.

Leuk Lymphoma 2019 Feb 20:1-9. Epub 2019 Feb 20.

b Institute for Inflammation Research (IIR), Center for Rheumatology and Spine Diseases, Rigshospitalet, University of Copenhagen , Copenhagen , Denmark.

The role of excess reactive oxygen species (ROS) with consequent DNA/RNA damage is now recognized as a hallmark of cancer. In JAK2V617F mutated myeloproliferative neoplasms, ROS have been suggested to be important factors in disease initiation and progression. Ruxolitinib is the most widely used drug for myelofibrosis, because it improves symptom-score. Read More

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http://dx.doi.org/10.1080/10428194.2019.1579323DOI Listing
February 2019

Induction of Apoptosis in HeLa by Corn Small RNAs.

Nutr Cancer 2019 Feb 20:1-11. Epub 2019 Feb 20.

a Cancer and Translational Research Lab, Dr D. Y. Patil Biotechnology & Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth , Pune , India.

Insights in RNA biology have opened up a plethora of opportunities to explore the small regulatory RNAs from various natural and artificial sources. These small RNAs have been suggested to play a role too in tumor progression by either as oncogenic or tumor suppressor small RNAs. In this study, authors have attempted to evaluate the therapeutic potential of small RNAs fractionated from corn (Zea mays) upon growth and survival of HeLa. Read More

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https://www.tandfonline.com/doi/full/10.1080/01635581.2018.1
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http://dx.doi.org/10.1080/01635581.2018.1526307DOI Listing
February 2019
1 Read

Differentially expressed coding and noncoding RNAs in CoCl-induced cytotoxicity of C2C12 cells.

Epigenomics 2019 Feb 20. Epub 2019 Feb 20.

Guangzhou FitGene Biotechnology CO., LTD, Building D, 3 Ju Quan Road, Guangzhou 510663, PR China.

Aim: We aimed to explore potential regulators of coding and noncoding RNAs (ncRNAs) in Co(II) ion-induced myo cytotoxicity.

Materials & Methods: We confirmed the toxic effects of Co(II) on mouse skeletal C2C12 myotubes by CoCl, and performed the expression profiles of circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and mRNAs using microarray analysis. We constructed co-expression, competing endogenous RNA and cis/trans regulation networks for ncRNAs, and filtered 71 candidate circRNAs with coding potential. Read More

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http://dx.doi.org/10.2217/epi-2018-0087DOI Listing
February 2019

Circular RNA expression in exosomes derived from breast cancer cells and patients.

Epigenomics 2019 Feb 20. Epub 2019 Feb 20.

Center of Clinical Laboratory Science, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, PR China.

Aim: We aimed to explore the roles of circular RNAs (circRNAs) in breast cancer (BCa).

Materials & Methods: RNA was extracted from exosomes and BCa cells and analyzed using the RNA sequencing technique or microarray.

Results: Compared with controls, 1147 and 1195 circRNAs were dysregulated in exosomes from metastatic and localized BCa patients, respectively. Read More

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http://dx.doi.org/10.2217/epi-2018-0111DOI Listing
February 2019

Locality Sensitive Imputation for Single Cell RNA-Seq Data.

J Comput Biol 2019 Feb 20. Epub 2019 Feb 20.

Computer Science and Engineering Department, University of Connecticut, Storrs, Connecticut.

One of the most notable challenges in single cell RNA-Seq data analysis is the so called drop-out effect, where only a fraction of the transcriptome of each cell is captured. The random nature of dropouts, however, makes it possible to consider imputation methods as means of correcting for dropouts. In this article, we study some existing single cell RNA sequencing (scRNA-Seq) imputation methods and propose a novel iterative imputation approach based on efficiently computing highly similar cells. Read More

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http://dx.doi.org/10.1089/cmb.2018.0236DOI Listing
February 2019

The evolution of multiple-insecticide resistance in UK populations of tomato leafminer, Tuta absoluta.

Pest Manag Sci 2019 Feb 20. Epub 2019 Feb 20.

College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.

Background: The tomato leafminer, Tuta absoluta, is an economically important pest of tomatoes in Europe, Africa, Asia and South America. In the UK this species is controlled using an integrated pest management (IPM) programme which incorporates the insecticides spinosad and chlorantraniliprole. In response to UK grower concerns of loss of efficacy of these compounds at certain sites, insecticide bioassays were performed on five populations collected from four commercial glasshouses and potential mechanisms of resistance investigated. Read More

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http://dx.doi.org/10.1002/ps.5381DOI Listing
February 2019

Identification of atheroprone shear stress responsive regulatory elements in endothelial cells.

Cardiovasc Res 2019 Feb 20. Epub 2019 Feb 20.

Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149 Münster, Germany.

Aim: Oscillatory shear stress (OSS) is an atheroprone hemodynamic force that occurs in areas of vessel irregularities and is implicated in the pathogenesis of atherosclerosis. Changes in signaling and transcriptional program in response to OSS have been vigorously studied, however, the underlying changes in the chromatin landscape controlling transcription remain to be elucidated. Here, we investigated the changes in the regulatory element (RE) landscape of endothelial cells under atheroprone OSS conditions in an in vitro model. Read More

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http://dx.doi.org/10.1093/cvr/cvz027DOI Listing
February 2019
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Growth phase-specific changes in the composition of E. coli transcription complexes.

J Chromatogr B Analyt Technol Biomed Life Sci 2019 Jan 23;1109:155-165. Epub 2019 Jan 23.

Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States of America. Electronic address:

In E. coli, a single oligomeric enzyme transcribes the genomic DNA, while multiple auxiliary proteins and regulatory RNA interact with the core RNA polymerase (RP) during different stages of the transcription cycle to influence its function. In this work, using fast protein isolation techniques combined with mass spectrometry (MS) and immuno-analyses, we studied growth phase-specific changes in the composition of E. Read More

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http://dx.doi.org/10.1016/j.jchromb.2019.01.014DOI Listing
January 2019

mRNA and microRNA transcriptomics analyses in intermuscular bones of two carp species, rice flower carp (Cyprinus carpio var. Quanzhounensis) and Jian carp (Cyprinus carpio var. Jian).

Comp Biochem Physiol Part D Genomics Proteomics 2019 Jan 30;30:71-80. Epub 2019 Jan 30.

Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address:

The rice flower carp (Cyprinus carpio var. Quanzhounensis) is a bony fish (superclass Osteichthyes), with very soft bones that is a significant feature unlike the other carp species. In this study, we analyzed the mRNA and microRNA (miRNA) transcriptomes in the intermuscular bones of rice flower carp and Jian carp (Cyprinus carpio var. Read More

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http://dx.doi.org/10.1016/j.cbd.2019.01.013DOI Listing
January 2019

circRAPGEF5 Contributes to Papillary Thyroid Proliferation and Metastatis by Regulation miR-198/FGFR1.

Mol Ther Nucleic Acids 2019 Jan 15;14:609-616. Epub 2019 Jan 15.

Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, China. Electronic address:

The circular RNA RAPGEF5 (circRAPGEF5) is generated from five exons of the RAPGEF5 gene and abnormal expression in papillary thyroid cancer (PTC). However, whether circRAPGEF5 plays a role in PTC tumorigenesis remains unclear. The aim of the present study was to investigate the role of circRAPGEF5 in PTC. Read More

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http://dx.doi.org/10.1016/j.omtn.2019.01.003DOI Listing
January 2019

The travels of mRNAs in neurons: do they know where they are going?

Curr Opin Neurobiol 2019 Feb 18;57:110-116. Epub 2019 Feb 18.

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Janelia Research Campus, Ashburn, VA, USA. Electronic address:

Neurons are highly polarized cells that can extend processes far from the cell body. As such, transport of messenger RNAs serves as a set of blueprints for the synthesis of specific proteins at distal sites. RNA localization to dendrites and axons confers the ability to regulate translation with extraordinary precision in space and time. Read More

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http://dx.doi.org/10.1016/j.conb.2019.01.016DOI Listing
February 2019

LINC00152 facilitates tumorigenesis in esophageal squamous cell carcinoma via miR-153-3p/FYN axis.

Biomed Pharmacother 2019 Feb 19;112:108654. Epub 2019 Feb 19.

Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. Electronic address:

Long non-coding RNAs (LncRNAs) have been found to be associated with the biological behaviors of human cancers. LINC00152 is reported as an oncogene in many kinds of malignancies. However, the functions and mechanisms of LINC00152 involved in esophageal squamous cell carcinoma (ESCC) remain elusive. Read More

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http://dx.doi.org/10.1016/j.biopha.2019.108654DOI Listing
February 2019

Knockdown of lncRNA HOXD-AS1 suppresses proliferation, migration and invasion and enhances cisplatin sensitivity of glioma cells by sponging miR-204.

Biomed Pharmacother 2019 Feb 19;112:108633. Epub 2019 Feb 19.

Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, China. Electronic address:

Increasing evidence suggests the involvement of long noncoding RNAs (lncRNAs) in various biological process including cancer progression and drug resistance. LncRNA HOXD cluster antisense RNA 1 (HOXD-AS1) had been demonstrated to act as an oncogenic gene, contributing to the development and progression of several cancers. However, its functional role and molecular mechanism underlying glioma progression and cisplatin (DDP) resistance has not been well elucidated. Read More

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http://dx.doi.org/10.1016/j.biopha.2019.108633DOI Listing
February 2019

A TGFBR2/SMAD2/DNMT1/miR-145 negative regulatory loop is responsible for LPS-induced sepsis.

Biomed Pharmacother 2019 Feb 19;112:108626. Epub 2019 Feb 19.

Department of Intensive Medicine (ICU), Jining No.1 People's Hospital, No. 6, Jiankang Road, Jining 272000, China. Electronic address:

The critical roles of TGFBR2/Smad2 signaling have been established in LPS-induced sepsis, however, the underlying mechanisms by which TGFBR2/Smad2 signaling was regulated in LPS-induced sepsis are still confused. Here, miRNA-based on RNA-sequencing dataset revealed that miR-145 was significantly decreased in human umbilical vein endothelial cells (HUVECs) following LPS treatment. Bioinformatics, luciferase reporter and RNA immune co-precipitation (RIP) assays showed that miR-145 could directly target TGFBR2 and thus inactivated TGFBR2/Smad2 axis. Read More

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http://dx.doi.org/10.1016/j.biopha.2019.108626DOI Listing
February 2019

The role of m6A RNA methylation in cancer.

Biomed Pharmacother 2019 Feb 18;112:108613. Epub 2019 Feb 18.

Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. Electronic address:

N6-methyladenosine (m6A), the most abundant internal modification of RNA in eukaryotic cells, has gained increasing attention in recent years. The m6A modification affects multiple aspects of RNA metabolism, ranging from RNA processing, nuclear export, RNA translation to decay. Emerging evidence suggests that m6A methylation plays a critical role in cancer through various mechanisms. Read More

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http://dx.doi.org/10.1016/j.biopha.2019.108613DOI Listing
February 2019
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Network-pharmacology-based identification of caveolin-1 as a key target of Oldenlandia diffusa to suppress breast cancer metastasis.

Biomed Pharmacother 2019 Feb 20;112:108607. Epub 2019 Feb 20.

Integrative Research Laboratory of Breast Cancer, Discipline of Integrated Chinese and Western Medicine, the Research Center of Integrative Medicine, School of Basic Medical Sciences & the Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangdong Provincial Academy of Chinese Medical Sciences, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, China; Post-doctoral Research Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China. Electronic address:

Background: Breast cancer remains the most common female malignancy and metastasis is the leading cause of death in breast cancer patients. Oldenlandia diffusa has been empirically and extensively used as an adjuvant therapy for metastatic breast cancer patients in Traditional Chinese Medicine (TCM) with proven efficacy. However, its anti-metastasis mechanism has been poorly revealed. Read More

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http://dx.doi.org/10.1016/j.biopha.2019.108607DOI Listing
February 2019

Insight into bovine (Bos indicus) spermatozoal whole transcriptome profile.

Theriogenology 2019 Feb 12;129:8-13. Epub 2019 Feb 12.

Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India. Electronic address:

Mature spermatozoa harbor both coding and non-coding type of RNAs which regulates spermatogenesis, fertilization and early development. Characterization of bovine sperm transcriptome can provide more insight into the molecular mechanisms involved in these processes. Here, we have analyzed whole transcriptome profile of Bos indicus spermatozoa to access the global RNA expression. Read More

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http://dx.doi.org/10.1016/j.theriogenology.2019.01.037DOI Listing
February 2019

Regulation of chromatin remodeling through RNA polymerase II stalling in the immune system.

Mol Immunol 2019 Feb 19;108:75-80. Epub 2019 Feb 19.

Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China. Electronic address:

RNA polymerase II (Pol II) binds to promoter-proximal regions of inducible target genes that are controlled and not transcribed by several negative elongation factors, which is known as Pol II stalling. The occurrence of stalling is due to particular modification signatures and structural conformations of chromatin that affect Pol II elongation. The existence and physiological importance of Pol II stalling implies that there is a dynamic balance in chromatin regulation prior to endogenous or exogenous stimulation. Read More

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http://dx.doi.org/10.1016/j.molimm.2019.02.012DOI Listing
February 2019

Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis.

Cell Rep 2019 Feb;26(8):2241-2256.e4

Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. Electronic address:

We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S22111247193013
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http://dx.doi.org/10.1016/j.celrep.2019.01.095DOI Listing
February 2019
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eIF4A3 Phosphorylation by CDKs Affects NMD during the Cell Cycle.

Cell Rep 2019 Feb;26(8):2126-2139.e9

Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea. Electronic address:

Exon junction complexes (EJCs) loaded onto spliced mRNAs during splicing serve as molecular markers for various post-transcriptional gene-regulatory processes, including nonsense-mediated mRNA decay (NMD). Although the composition and structure of EJCs are well characterized, the mechanism regulating EJC deposition remains unknown. Here we find that threonine 163 (T163) within the RNA-binding motif of eIF4A3 (a core EJC component) is phosphorylated by cyclin-dependent protein kinases 1 and 2 in a cell cycle-dependent manner. Read More

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http://dx.doi.org/10.1016/j.celrep.2019.01.101DOI Listing
February 2019

RIG-I Selectively Discriminates against 5'-Monophosphate RNA.

Cell Rep 2019 Feb;26(8):2019-2027.e4

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA. Electronic address:

The innate immune sensor RIG-I must sensitively detect and respond to viral RNAs that enter the cytoplasm, while remaining unresponsive to the abundance of structurally similar RNAs that are the products of host metabolism. In the case of RIG-I, these viral and host targets differ by only a few atoms, and a molecular mechanism for such selective differentiation has remained elusive. Using a combination of quantitative biophysical and immunological studies, we show that RIG-I, which is normally activated by duplex RNAs containing a 5'-tri- or diphosphate (5'-ppp or 5'-pp RNAs), is actively antagonized by RNAs containing 5'-monophosphates (5'-p RNAs). Read More

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http://dx.doi.org/10.1016/j.celrep.2019.01.107DOI Listing
February 2019

Emerging Principles in Myelopoiesis at Homeostasis and during Infection and Inflammation.

Immunity 2019 Feb;50(2):288-301

Myeloid Cell Biology, LIMES Institute, University of Bonn, 53115 Bonn, Germany. Electronic address:

Myelopoiesis ensures the steady state of the myeloid cell compartment. Technological advances in fate mapping and genetic engineering, as well as the advent of single cell RNA-sequencing, have highlighted the heterogeneity of the hematopoietic system and revealed new concepts in myeloid cell ontogeny. These technologies are also shedding light on mechanisms of myelopoiesis at homeostasis and at different phases of infection and inflammation, illustrating important feedback loops between affected tissues and the bone marrow. Read More

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http://dx.doi.org/10.1016/j.immuni.2019.01.019DOI Listing
February 2019

NF90 regulation of immune factor expression in response to malaria antigens.

Cell Cycle 2019 Feb 20. Epub 2019 Feb 20.

a Laboratory of Genetics and Genomics , National Institute on Aging Intramural Research Program, National Institutes of Health , Baltimore , MD , US.

Nuclear factor 90 (NF90) is a dual DNA- and RNA-binding protein expressed ubiquitously in mammalian cells, including monocytes. Here, to elucidate the function of NF90 in the immune response, we analyzed systematically its influence on gene expression programs in the human monocytic cell line THP-1 expressing normal or reduced NF90 levels. RNA sequencing analysis revealed many mRNAs showing differential abundance in NF90-silenced cells, many of them encoding proteins implicated in the response to immune stimuli and malaria infection. Read More

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https://www.tandfonline.com/doi/full/10.1080/15384101.2019.1
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http://dx.doi.org/10.1080/15384101.2019.1580496DOI Listing
February 2019
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Treatment of Surface Plasmon Resonance (SPR) Background in Total Internal Reflection Ellipsometry: Characterization of RNA Polymerase II Film Formation.

Appl Spectrosc 2019 Feb 20:3702819826280. Epub 2019 Feb 20.

1 Department of Condensed Matter Physics, Masaryk University, Brno, Czech Republic.

To deal with the general problem of biomolecule specific binding analysis, we have applied the technique of difference spectra to the surface plasmon resonance (SPR)-enhanced total internal reflection ellipsometry measurement. We suggest a three-step treatment of the SPR background that can easily be integrated with the usual measurement routine. First, making use of the difference spectrum in ellipsometric angle Δ, single peak footprints of the topmost layer are obtained that facilitate its sensitive detection during film growth. Read More

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http://dx.doi.org/10.1177/0003702819826280DOI Listing
February 2019

Prognostic risk model construction and molecular marker identification in glioblastoma multiforme based on mRNA/microRNA/long non-coding RNA analysis using random survival forest method.

Authors:
H Wang D Liu J Yang

Neoplasma 2019 Feb 20. Epub 2019 Feb 20.

We aim to identify novel molecular signatures for prognosis prediction of glioblastoma multiforme (GBM). The expression and microarray data of GBM were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). Differentially expressed mRNAs, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) between GBM and normal samples were identified by differential expression analysis using Bayesian T-test. Read More

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http://dx.doi.org/10.4149/neo_2018_181008N746DOI Listing
February 2019

Zonula occludens-1 associated nucleic acid binding protein plays an invasion-promoting role in bladder cancer.

Authors:
X Xu K You B Wu

Neoplasma 2019 Feb 20. Epub 2019 Feb 20.

Cancer cell invasion is an important characteristic of malignant tumors. Cancer cells overcome the constraints of tight junctions (TJ) to invade other tissues, but less is known about the regulating role of tight junction on bladder cancer (BC) invasion. In order to identify the invasion-regulating function of tight junction component, we investigated the oncogenetic features of zonula occludens-1 associated nucleic acid binding protein (ZONAB), a TJ protein that is usually highly expressed in solid cancers. Read More

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http://dx.doi.org/10.4149/neo_2018_180725N530DOI Listing
February 2019

LncRNA SNHG16 promotes cell proliferation through miR-302a-3p/FGF19 axis in hepatocellular carcinoma.

Neoplasma 2019 Feb 20. Epub 2019 Feb 20.

Hepatocellular carcinoma (HCC) is the sixth common malignancies worldwide and the leading cause of death in Asian and African countries. Aberrant accumulation of lncRNAs is one of major causes of tumorigenesis in HCC. Small nucleolar RNA host gene 16 (SNHG16) is identified as an oncogene in multiple types of tumor. Read More

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http://dx.doi.org/10.4149/neo_2018_180720N504DOI Listing
February 2019
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