151 results match your criteria Gene Regulation and Systems Biology [Journal]


Model-based Evaluation of Gene Expression Changes in Response to Infection.

Gene Regul Syst Bio 2019 6;13:1177625019828350. Epub 2019 Feb 6.

School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA.

Since the development of high-density microarray technology in the late 1990s, global host gene expression changes in response to various stimuli have been extensively studied. More than a dozen peer-reviewed publications have investigated the effect of infection in various models since 2001. This review covers the transcriptional changes in macrophage models induced by various species and summarizes the resulting impact these studies have on our understanding of the host response to leishmaniasis in vitro. Read More

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http://dx.doi.org/10.1177/1177625019828350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376507PMC
February 2019

Transcriptomic Impacts of Rumen Epithelium Induced by Butyrate Infusion in Dairy Cattle in Dry Period.

Gene Regul Syst Bio 2018 9;12:1177625018774798. Epub 2018 May 9.

Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.

The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function. Read More

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http://dx.doi.org/10.1177/1177625018774798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954180PMC
May 2018
4 Reads

Linear-In-Flux-Expressions Methodology: Toward a Robust Mathematical Framework for Quantitative Systems Pharmacology Simulators.

Gene Regul Syst Bio 2017 26;11:1177625017711414. Epub 2017 Jul 26.

Translational Informatics Department, Sanofi US, Bridgewater, NJ, USA.

Quantitative Systems Pharmacology (QSP) modeling is increasingly used as a quantitative tool for advancing mechanistic hypotheses on the mechanism of action of a drug, and its pharmacological effect in relevant disease phenotypes, to enable linking the right drug to the right patient. Application of QSP models relies on creation of virtual populations for simulating scenarios of interest. Creation of virtual populations requires 2 important steps, namely, identification of a subset of model parameters that can be associated with a phenotype of disease and development of a sampling strategy from identified distributions of these parameters. Read More

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http://dx.doi.org/10.1177/1177625017711414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862386PMC
July 2017
5 Reads

A Quantitative Systems Pharmacology Platform to Investigate the Impact of Alirocumab and Cholesterol-Lowering Therapies on Lipid Profiles and Plaque Characteristics.

Gene Regul Syst Bio 2017 22;11:1177625017710941. Epub 2017 Jun 22.

Sanofi, Bridgewater, NJ, USA; Frankfurt Am Main, Germany, and Montpellier, France.

Reduction in low-density lipoprotein cholesterol (LDL-C) is associated with decreased risk for cardiovascular disease. Alirocumab, an antibody to proprotein convertase subtilisin/kexin type 9 (PCSK9), significantly reduces LDL-C. Here, we report development of a quantitative systems pharmacology (QSP) model integrating peripheral and liver cholesterol metabolism, as well as PCSK9 function, to examine the mechanisms of action of alirocumab and other lipid-lowering therapies, including statins. Read More

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http://dx.doi.org/10.1177/1177625017710941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484552PMC
June 2017
41 Reads

A Transcriptional Regulatory Role for the Membrane Type-1 Matrix Metalloproteinase in Carcinogen-Induced Inflammasome Gene Expression.

Gene Regul Syst Bio 2017 8;11:1177625017713996. Epub 2017 Jun 8.

Laboratoire d'Oncologie Moléculaire, Département de Chimie, Centre de recherche BIOMED, Université du Québec à Montréal, Montréal, QC, Canada.

Signal-transducing functions driven by the cytoplasmic domain of membrane type-1 matrix metalloproteinase (MT1-MMP) are believed to regulate many inflammation-associated cancer cell functions including migration, proliferation, and survival. Aside from upregulation of the inflammation biomarker cyclooxygenase-2 (COX-2) expression, MT1-MMP's role in relaying intracellular signals triggered by extracellular pro-inflammatory cues remains poorly understood. Here, we triggered inflammation in HT1080 fibrosarcoma cells with phorbol-12-myristate-13-acetate (PMA), an inducer of COX-2 and of MT1-MMP. Read More

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http://dx.doi.org/10.1177/1177625017713996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467917PMC
June 2017
21 Reads

Overexpression and Knockdown of Hypoxia-Inducible Factor 1 Disrupt the Expression of Steroidogenic Enzyme Genes and Early Embryonic Development in Zebrafish.

Gene Regul Syst Bio 2017 8;11:1177625017713193. Epub 2017 Jun 8.

State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong SAR.

Hypoxia is an important environmental stressor leading to endocrine disruption and reproductive impairment in fish. Although the hypoxia-inducible factor 1 (HIF-1) is known to regulate the transcription of various genes mediating oxygen homeostasis, its role in modulating steroidogenesis-related gene expression remains poorly understood. In this study, the regulatory effect of HIF-1 on the expression of 9 steroidogenic enzyme genes was investigated in zebrafish embryos using a "gain-of-function and loss-of-function" approach. Read More

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http://dx.doi.org/10.1177/1177625017713193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467919PMC
June 2017
6 Reads

Mechanistic Modelling of Drug-Induced Liver Injury: Investigating the Role of Innate Immune Responses.

Gene Regul Syst Bio 2017 30;11:1177625017696074. Epub 2017 May 30.

DILIsym Services, Inc., Research Triangle Park, NC, USA.

Drug-induced liver injury (DILI) remains an adverse event of significant concern for drug development and marketed drugs, and the field would benefit from better tools to identify liver liabilities early in development and/or to mitigate potential DILI risk in otherwise promising drugs. DILIsym software takes a quantitative systems toxicology approach to represent DILI in pre-clinical species and in humans for the mechanistic investigation of liver toxicity. In addition to multiple intrinsic mechanisms of hepatocyte toxicity (ie, oxidative stress, bile acid accumulation, mitochondrial dysfunction), DILIsym includes the interaction between hepatocytes and cells of the innate immune response in the amplification of liver injury and in liver regeneration. Read More

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http://dx.doi.org/10.1177/1177625017696074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459514PMC
May 2017
19 Reads

Effects of High-Fat Feeding on Skeletal Muscle Gene Expression in Diabetic Goto-Kakizaki Rats.

Gene Regul Syst Bio 2017 29;11:1177625017710009. Epub 2017 May 29.

Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA.

In the present report, we examined the responses of diabetic Goto-Kakizaki (GK) rats and control Wistar-Kyoto (WKY) rats fed either a standard chow or high-fat diet (HFD) from weaning to 20 weeks of age. This comparison included gene expression profiling of skeletal muscle using Affymetrix gene array chips. The expression profiling is interpreted within the context of a wide array of physiological measurements. Read More

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http://dx.doi.org/10.1177/1177625017710009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5457139PMC
May 2017
9 Reads

The Synergistic Role of Light-Feeding Phase Relations on Entraining Robust Circadian Rhythms in the Periphery.

Gene Regul Syst Bio 2017 20;11:1177625017702393. Epub 2017 Apr 20.

Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

The feeding and fasting cycles are strong behavioral signals that entrain biological rhythms of the periphery. The feeding rhythms synchronize the activities of the metabolic organs, such as liver, synergistically with the light/dark cycle primarily entraining the suprachiasmatic nucleus. The likely phase misalignment between the feeding rhythms and the light/dark cycles appears to induce circadian disruptions leading to multiple physiological abnormalities motivating the need to investigate the mechanisms behind joint light-feeding circadian entrainment of peripheral tissues. Read More

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http://dx.doi.org/10.1177/1177625017702393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404903PMC
April 2017
21 Reads

Time Course Expression Analysis of 1[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole Induction of Cytoprotection in Human Endothelial Cells.

Gene Regul Syst Bio 2017 7;11:1177625017701106. Epub 2017 Apr 7.

U.S. Army Institute of Surgical Research, San Antonio, TX, USA.

1[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), a synthetic derivative of oleanolic acid that exhibits antioxidant and anti-inflammatory activity in several animal and in vitro models, has been shown to be beneficial if given after injury. Although induction of heme oxygenase 1 appears to be a major effector of cytoprotection, the mechanism by which the overall effect is mediated is largely unknown. This study evaluated temporal gene expression profiles to better characterize the early transcriptional events and their relationship to the dynamics of the cytoprotective response in human umbilical vein endothelial cells (HUVEC) to CDDO-Im. Read More

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http://journals.sagepub.com/doi/10.1177/1177625017701106
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http://dx.doi.org/10.1177/1177625017701106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398299PMC
April 2017
4 Reads

Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.

Gene Regul Syst Bio 2017 15;11:1177625017696075. Epub 2017 Mar 15.

Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.

Drug-induced toxicity is a major public health concern that leads to patient morbidity and mortality. To address this problem, the Food and Drug Administration is working on the PredicTox initiative, a pilot research program on tyrosine kinase inhibitors, to build mechanistic and predictive models for drug-induced toxicity. This program involves integrating data acquired during preclinical studies and clinical trials within pharmaceutical company development programs that they have agreed to put in the public domain and in publicly available biological, pharmacological, and chemical databases. Read More

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http://dx.doi.org/10.1177/1177625017696075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398297PMC
March 2017
4 Reads

Graphical Modeling Meets Systems Pharmacology.

Gene Regul Syst Bio 2017 10;11:1177625017691937. Epub 2017 Mar 10.

The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Trento, Italy.

A main source of failures in systems projects (including systems pharmacology) is poor communication level and different expectations among the stakeholders. A common and not ambiguous language that is naturally comprehensible by all the involved players is a boost to success. We present bStyle, a modeling tool that adopts a graphical language close enough to cartoons to be a common media to exchange ideas and data and that it is at the same time formal enough to enable modeling, analysis, and dynamic simulations of a system. Read More

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http://dx.doi.org/10.1177/1177625017691937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398309PMC
March 2017
3 Reads

Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification.

Gene Regul Syst Bio 2017 12;11:1177625017690133. Epub 2017 Apr 12.

Cardiovascular and Metabolic Diseases, Pfizer Inc., USA.

Hepatic de-novo lipogenesis is a metabolic process implemented in the pathogenesis of type 2 diabetes. Clinically, the rate of this process can be ascertained by use of labeled acetate and stimulation by fructose administration. A systems pharmacology model of this process is desirable because it facilitates the description, analysis, and prediction of this experiment. Read More

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http://dx.doi.org/10.1177/1177625017690133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397296PMC
April 2017
4 Reads

Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.

Gene Regul Syst Bio 2016 13;10:105-110. Epub 2016 Dec 13.

Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.

We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Read More

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http://dx.doi.org/10.4137/GRSB.S40768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156548PMC
December 2016
9 Reads

Semi-Automated Curation Allows Causal Network Model Building for the Quantification of Age-Dependent Plaque Progression in ApoE Mouse.

Gene Regul Syst Bio 2016 6;10:95-103. Epub 2016 Nov 6.

Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.

The cellular and molecular mechanisms behind the process of atherosclerotic plaque destabilization are complex, and molecular data from aortic plaques are difficult to interpret. Biological network models may overcome these difficulties and precisely quantify the molecular mechanisms impacted during disease progression. The atherosclerosis plaque destabilization biological network model was constructed with the semiautomated curation pipeline, BELIEF. Read More

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http://dx.doi.org/10.4137/GRSB.S40031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100841PMC
November 2016
10 Reads
3 Citations

Dysregulation of Protein Kinase Gene Expression in NK Cells from Chronic Fatigue Syndrome/Myalgic Encephalomyelitis Patients.

Gene Regul Syst Bio 2016 28;10:85-93. Epub 2016 Aug 28.

School of Medical Science, Griffith University, QLD, Australia.; The National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, QLD, Australia.

Background: The etiology and pathomechanism of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) are unknown. However, natural killer (NK) cell dysfunction, in particular reduced NK cytotoxic activity, is a consistent finding in CFS/ME patients. Previous research has reported significant changes in intracellular mitogen-activated protein kinase pathways from isolated NK cells. Read More

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http://dx.doi.org/10.4137/GRSB.S40036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003121PMC
September 2016
17 Reads

DNA Microarray Highlights Nrf2-Mediated Neuron Protection Targeted by Wasabi-Derived Isothiocyanates in IMR-32 Cells.

Gene Regul Syst Bio 2016 11;10:73-83. Epub 2016 Aug 11.

The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.; Department of Food Sciences and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan.

6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC), 6-(methylthio)hexyl isothiocyanate (6-MTITC), and 4-(methylsulfinyl)butyl isothiocyanate (4-MSITC) are isothiocyanate (ITC) bioactive compounds from Japanese Wasabi. Previous in vivo studies highlighted the neuroprotective potential of ITCs since ITCs enhance the production of antioxidant-related enzymes. Thus, in this present study, a genome-wide DNA microarray analysis was designed to profile gene expression changes in a neuron cell line, IMR-32, stimulated by these ITCs. Read More

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http://dx.doi.org/10.4137/GRSB.S39440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982521PMC
August 2016
7 Reads

Endothelial Nitric Oxide Synthase (-786T>C) and Endothelin-1 (5665G>T) Gene Polymorphisms as Vascular Dysfunction Risk Factors in Sickle Cell Anemia.

Gene Regul Syst Bio 2016 28;10:67-72. Epub 2016 Jul 28.

Laboratório de Hematologia, Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz, FIOCRUZ, Salvador, Brasil.; Departamento de Analises Clínicas e Toxicologicas, Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brasil.

Sickle cell anemia (SCA) patients have vascular complications, and polymorphisms in endothelin-1 (ET-1) and endothelial nitric oxide synthase (eNOS) genes were associated with ET-1 and nitric oxide disturbance. We investigate the association of ET-1 5665G>T and eNOS -786T>C polymorphisms with soluble adhesion molecules (sVCAM-1 and sICAM-1), biochemical markers, and medical history. We studied 101 SCA patients; carriers of eNOS minor allele (C) had the highest levels of sVCAM-1, and carriers of ET-1 minor allele had more occurrence of acute chest syndrome (ACS). Read More

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http://dx.doi.org/10.4137/GRSB.S38276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966487PMC
August 2016
12 Reads

Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications.

Gene Regul Syst Bio 2016 12;10:51-66. Epub 2016 Jul 12.

Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies).

Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. Read More

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http://dx.doi.org/10.4137/GRSB.S39076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944831PMC
July 2016
19 Reads

Killer Cell Immunoglobulin-like Receptor Genotype and Haplotype Investigation of Natural Killer Cells from an Australian Population of Chronic Fatigue Syndrome/Myalgic Encephalomyelitis Patients.

Gene Regul Syst Bio 2016 19;10:43-9. Epub 2016 Jun 19.

National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.; School of Medical Science, Griffith University, Southport, QLD, Australia.

Killer cell immunoglobulin-like receptor (KIR) genes encode for activating and inhibitory surface receptors, which are correlated with the regulation of Natural Killer (NK) cell cytotoxic activity. Reduced NK cell cytotoxic activity has been consistently reported in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) patients, and KIR haplotypes and allelic polymorphism remain to be investigated. The aim of this article was to conduct a pilot study to examine KIR genotypes, haplotypes, and allelic polymorphism in CFS/ME patients and nonfatigued controls (NFCs). Read More

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http://dx.doi.org/10.4137/GRSB.S39861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913894PMC
June 2016
6 Reads

Integration of Telomere Length Dynamics into Systems Biology Framework: A Review.

Authors:
Lilit Nersisyan

Gene Regul Syst Bio 2016 16;10:35-42. Epub 2016 Jun 16.

Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Republic of Armenia.

Telomere length dynamics plays a crucial role in regulation of cellular processes and cell fate. In contrast to epidemiological studies revealing the association of telomere length with age, age-related diseases, and cancers, the role of telomeres in regulation of transcriptome and epigenome and the role of genomic variations in telomere lengthening are not extensively analyzed. This is explained by the fact that experimental assays for telomere length measurement are resource consuming, and there are very few studies where high-throughput genomics, transcriptomics, and/or epigenomics experiments have been coupled with telomere length measurements. Read More

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http://dx.doi.org/10.4137/GRSB.S39836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912229PMC
June 2016
6 Reads

Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome.

Gene Regul Syst Bio 2016 12;10:21-33. Epub 2016 Jun 12.

Biology Department, Clark University, Worcester, MA, USA.

A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). Read More

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http://dx.doi.org/10.4137/GRSB.S38462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907338PMC
June 2016
5 Reads
1 Citation

NEAT1 is Required for Survival of Breast Cancer Cells Through FUS and miR-548.

Gene Regul Syst Bio 2016 27;10(Suppl 1):11-7. Epub 2016 Apr 27.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.

Increasing evidence shows that long noncoding RNAs (lncRNAs) have important roles in the regulation of multiple cellular processes, including cell division, cell growth, and apoptosis, as well as cancer metastasis and neurological disease progression; however, the mechanism of how lncRNAs regulate these processes is not well established. In this study, we demonstrated that downregulating the expression of the lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in breast cancer cells inhibited cell growth and induced cell apoptosis. In addition, the RNA-binding protein fused in sarcoma/translocated in liposarcoma (FUS/TLS) physically interacted with NEAT1, and reducing the expression of FUS/TLS also induced cell apoptosis. Read More

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http://dx.doi.org/10.4137/GRSB.S29414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849421PMC
May 2016
21 Reads

Expression and Presence of OPG and RANKL mRNA and Protein in Human Periodontal Ligament with Orthodontic Force.

Gene Regul Syst Bio 2016 25;10:15-20. Epub 2016 Jan 25.

Master of Science Student, Pontificia Universidad Javeriana, Bogotá, Colombia.

Objective: The objective of this study is to investigate the expression and concentration of ligand receptor activator of NFkB (RANKL) and osteoprotegerin (OPG) in human periodontal ligament (hPDL) with orthodontic forces of different magnitudes.

Methods: Right premolars in 32 patients were loaded with 4oz or 7oz of orthodontic force for 7 days. Left first premolars were not loaded. Read More

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http://dx.doi.org/10.4137/GRSB.S35368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727488PMC
January 2016
6 Reads

Epigenetic Regulation of Tissue-Type Plasminogen Activator in Human Brain Tissue and Brain-Derived Cells.

Gene Regul Syst Bio 2016 24;10:9-13. Epub 2016 Jan 24.

Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

The serine protease tissue-type plasminogen activator (t-PA) is involved in both vital physiological brain processes, such as synaptic plasticity, and pathophysiological conditions, such as neurodegeneration and ischemic stroke. Recent data suggest that epigenetic mechanisms play an important role in the regulation of t-PA in human endothelial cells. However, there are limited data on epigenetic regulation of t-PA in human brain-derived cells. Read More

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http://dx.doi.org/10.4137/GRSB.S30241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727487PMC
January 2016
11 Reads

Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies.

Gene Regul Syst Bio 2016 18;10(Suppl 1):1-9. Epub 2016 Jan 18.

Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.

To isolate specific genomic regions that retain their molecular interactions, allowing direct identification of chromatin-bound molecules, we developed two locus-specific chromatin immunoprecipitation (locus-specific ChIP) technologies, insertional ChIP (iChIP) and engineered DNA-binding molecule-mediated ChIP (enChIP) using the clustered regularly interspaced short palindromic repeats (CRISPR) system or transcription activator-like (TAL) proteins. Essentially, a locus-specific ChIP consists of locus-tagging and affinity purification and can be combined with downstream analyses to identify molecules associated with the target genomic regions. In this review, we discuss the applications of locus-specific ChIP to analyze the genome functions, including transcription and epigenetic regulation. Read More

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http://dx.doi.org/10.4137/GRSB.S32520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718151PMC
January 2016
5 Reads

Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification.

Gene Regul Syst Bio 2016 21;10:1-8. Epub 2016 Jan 21.

Informatics Group, J. Craig Venter Institute, La Jolla, CA. USA.

Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Read More

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http://dx.doi.org/10.4137/GRSB.S35607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723047PMC
January 2016
5 Reads

tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins.

Gene Regul Syst Bio 2015 10;9:27-33. Epub 2015 Sep 10.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.

The advent of next-generation sequencing technologies has not only accelerated findings on various novel non-coding RNA (ncRNA) species but also led to the revision of the biological significance and versatility of fundamental RNA species with canonical function, such as transfer RNAs (tRNAs). Although tRNAs are best known as adapter components of translational machinery, recent studies suggest that tRNAs are not always end products but can further serve as a source for short ncRNAs. In many organisms, various tRNA-derived ncRNA species are produced from mature tRNAs or their precursor transcripts as functional molecules involved in various biological processes beyond translation. Read More

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http://dx.doi.org/10.4137/GRSB.S29411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567038PMC
September 2015
3 Reads

Effects of High Fat Feeding on Adipose Tissue Gene Expression in Diabetic Goto-Kakizaki Rats.

Gene Regul Syst Bio 2015 10;9:15-26. Epub 2015 Aug 10.

Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA. ; Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA. ; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.

Development and progression of type 2 diabetes is a complex interaction between genetics and environmental influences. High dietary fat is one environmental factor that is conducive to the development of insulin-resistant diabetes. In the present report, we compare the responses of lean poly-genic, diabetic Goto-Kakizaki (GK) rats to those of control Wistar-Kyoto (WKY) rats fed a high fat diet from weaning to 20 weeks of age. Read More

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http://dx.doi.org/10.4137/GRSB.S25172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4533846PMC
August 2015
12 Reads

p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo.

Gene Regul Syst Bio 2015 1;9:1-14. Epub 2015 Jun 1.

Department of Medicinal Chemistry, University Of Washington, Seattle, WA, USA.

The goal of the present study was to compare hepatic toxicogenomic signatures across in vitro and in vivo mouse models following exposure to acetaminophen (APAP) or its relatively nontoxic regioisomer 3'-hydroxyacetanilide (AMAP). Two different Affymetrix microarray platforms and one Agilent Oligonucleotide microarray were utilized. APAP and AMAP treatments resulted in significant and large changes in gene expression that were quite disparate, and likely related to their different toxicologic profiles. Read More

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http://dx.doi.org/10.4137/GRSB.S25388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454132PMC
June 2015
6 Reads

A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity.

Gene Regul Syst Bio 2014 18;8:141-7. Epub 2014 Dec 18.

Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.

Alteromonas macleodii AltDE1 is a deep sea protobacteria that is distinct from the surface isolates of the same species. This study was designed to elucidate the biological function of amad1_06475, a hypothetical protein of A. macleodii AltDE1. Read More

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http://dx.doi.org/10.4137/GRSB.S20802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271719PMC
January 2015
23 Reads
1 Citation

A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia.

Gene Regul Syst Bio 2014 8;8:127-39. Epub 2014 Dec 8.

Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan.

Microglia are resident mononuclear phagocytes that play a principal role in the maintenance of normal tissue homeostasis in the central nervous system (CNS). Microglia, rapidly activated in response to proinflammatory stimuli, are accumulated in brain lesions of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. The E26 transformation-specific (ETS) family transcription factor PU. Read More

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http://dx.doi.org/10.4137/GRSB.S19711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262374PMC
January 2015
4 Reads

Endothelin-1 but not Endothelial Nitric Oxide Synthase Gene Polymorphism is Associated with Sickle Cell Disease in Africa.

Gene Regul Syst Bio 2014 25;8:119-26. Epub 2014 May 25.

Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY, USA.

Sickle cell disease shows marked variability in severity and pathophysiology among individuals, probably linked to differential expression of various adhesion molecules. In this study, we investigated the differential distribution, genomic diversity and haplotype frequency of endothelial nitric oxide synthase (eNOS) and endothelin-1 (ET-1) polymorphisms, recently implicated as important in modification of disease severity. One hundred and forty five sickle cell disease patients (HbSS) and 244 adult and pediatric controls, without sickle cell disease (HbAA), were recruited from Mali. Read More

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http://dx.doi.org/10.4137/GRSB.S14836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051816PMC
June 2014
6 Reads

Species-Specific Regulation of t-PA and PAI-1 Gene Expression in Human and Rat Astrocytes.

Gene Regul Syst Bio 2014 8;8:113-8. Epub 2014 May 8.

Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

In recent years, the role and physiological regulation of the serine protease tissue-type plasminogen activator (t-PA) and its inhibitors, including plasminogen activator inhibitor type-1 (PAI-1), in the brain have received much attention. However, as studies focusing these issues are difficult to perform in humans, a great majority of the studies conducted to date have utilized rodent in vivo and/or in vitro models. In view of the species-specific structural differences present in both the t-PA and the PAI-1 promoters, we have compared the response of these genes in astrocytes of rat and human origin. Read More

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http://dx.doi.org/10.4137/GRSB.S13387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024051PMC
May 2014
6 Reads

Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity.

Gene Regul Syst Bio 2014 3;8:97-111. Epub 2014 Apr 3.

Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA.

Hepatic metabolic gene networks were studied in dairy cattle fed control (CON, 1.34 Mcal/kg) or higher energy (overfed (OVE), 1.62 Mcal/kg) diets during the last 45 days of pregnancy. Read More

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http://dx.doi.org/10.4137/GRSB.S14116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981572PMC
April 2014
9 Reads
8 Citations

DNA conformational transitions induced by supercoiling control transcription in chromatin.

Authors:
Andrey N Luchnik

Gene Regul Syst Bio 2014 12;8:89-96. Epub 2014 Mar 12.

Koltzov Institute of Developmental Biology, Moscow, Russia.

Regulation of transcription in eukaryotes is considered in the light of recent findings demonstrating the presence of negative and positive superhelical tension in chromatin. This tension induces conformational transitions in DNA duplex. Particularly, the transition into A-form renders DNA accessible and waylaying for initiation of transcription producing RNA molecules long known to belong to the A-conformation. Read More

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http://dx.doi.org/10.4137/GRSB.S13756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956857PMC
June 2014
3 Reads

Tissue-specific gene expression and regulation in liver and muscle following chronic corticosteroid administration.

Gene Regul Syst Bio 2014 10;8:75-87. Epub 2014 Mar 10.

Biomedical Engineering Department, Rutgers University, Piscataway, NJ, USA. ; Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ, USA.

Although corticosteroids (CSs) affect gene expression in multiple tissues, the array of genes that are regulated by these catabolic steroids is diverse, highly tissue specific, and depends on their functions in the tissue. Liver has many important functions in performing and regulating diverse metabolic processes. Muscle, in addition to its mechanical role, is critical in maintaining systemic energy homeostasis and accounts for about 80% of insulin-directed glucose disposal. Read More

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http://dx.doi.org/10.4137/GRSB.S13134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956809PMC
March 2014
17 Reads
3 Citations

Tetracycline derivative minocycline inhibits autophagy and inflammation in concanavalin-a-activated human hepatoma cells.

Gene Regul Syst Bio 2014 4;8:63-73. Epub 2014 Mar 4.

Laboratoire d'Oncologie Moléculaire, Département de Chimie, Université du Québec à Montréal, Québec, Canada.

Inhibition of soluble matrix metalloproteinase (MMP) activity is among the non-antibiotic cellular effects exerted by the anti-inflammatory tetracycline derivative minocycline. The impact of minocycline on the signal transduction functions of membrane-bound MMPs is however unknown. We assessed minocycline in a concanavalin-A (ConA)-activated human HepG2 hepatoma cell model, a condition known to increase the expression of membrane type-1 MMP (MT-MMP) and to trigger inflammatory and autophagy processes. Read More

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http://dx.doi.org/10.4137/GRSB.S13946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948715PMC
March 2014
8 Reads

Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™).

Gene Regul Syst Bio 2014 19;8:45-61. Epub 2014 Feb 19.

Philip Morris Research and Development, Neuchâtel, Switzerland.

Chronic obstructive pulmonary disease (COPD) is a respiratory disorder caused by extended exposure of the airways to noxious stimuli, principally cigarette smoke (CS). The mechanisms through which COPD develops are not fully understood, though it is believed that the disease process includes a genetic component, as not all smokers develop COPD. To investigate the mechanisms that lead to the development of COPD/emphysema, we measured whole genome gene expression and several COPD-relevant biological endpoints in mouse lung tissue after exposure to two CS doses for various lengths of time. Read More

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http://dx.doi.org/10.4137/GRSB.S13140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937248PMC
March 2014
7 Reads

Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.

Gene Regul Syst Bio 2014 20;8:33-43. Epub 2014 Jan 20.

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

Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. Read More

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http://dx.doi.org/10.4137/GRSB.S13612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921077PMC
February 2014
4 Reads

Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition.

Gene Regul Syst Bio 2014 8;8:17-32. Epub 2014 Jan 8.

Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA. ; Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA. ; Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, Illinois, USA.

Adipogenic/lipogenic transcriptional networks regulating intramuscular fat deposition (IMF) in response to weaning age and dietary starch level were studied. The longissimus muscle (LM) of beef steers on an early weaning (141 days age) plus high-starch diet (EWS) or a normal weaning (NW, 222 days age) plus starch creep-feed diet (CFS) was biopsied at 0 (EW), 25, 50, 96 (NW), 167, and 222 (pre-slaughter) days. Expression patterns of 35 target genes were studied. Read More

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http://dx.doi.org/10.4137/GRSB.S11782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894150PMC
February 2014
9 Reads
10 Citations

Innate immunity interactome dynamics.

Gene Regul Syst Bio 2014 Jan 6;8:1-15. Epub 2014 Jan 6.

Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan. ; Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.

Innate immune response involves protein-protein interactions, deoxyribonucleic acid (DNA)-protein interactions and signaling cascades. So far, thousands of protein-protein interactions have been curated as a static interaction map. However, protein-protein interactions involved in innate immune response are dynamic. Read More

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http://dx.doi.org/10.4137/GRSB.S12850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885269PMC
January 2014
5 Reads

Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases.

Gene Regul Syst Bio 2013 4;7:139-52. Epub 2013 Nov 4.

Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan.

Nuclear respiratory factor 1 (NRF1) serves as a transcription factor that activates the expression of a wide range of nuclear genes essential for mitochondrial biogenesis and function, including mitochondrial respiratory complex subunits, heme biosynthetic enzymes, and regulatory factors involved in the replication and transcription of mitochondrial DNA. Increasing evidence indicates that mitochondrial function is severely compromised in the brains of aging-related neurodegenerative diseases. To identify the comprehensive set of human NRF1 target genes potentially relevant to the pathogenesis of neurodegenerative diseases, we analyzed the NRF1 chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) dataset retrieved from the Encyclopedia of DNA Elements (ENCODE) project. Read More

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http://dx.doi.org/10.4137/GRSB.S13204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825669PMC
November 2013
4 Reads

CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells.

Gene Regul Syst Bio 2013 4;7:125-38. Epub 2013 Jul 4.

Department of Medicine, University of Toledo Medical Center, Toledo, USA.

Inter-individual variation in CCAAT/enhancer binding protein gamma (CEBPG) transcript expression in normal human bronchial epithelial cells (NBEC) is associated with predisposition to lung cancer. We hypothesize that this inter-individual variation is in part explained by cis-acting genetic variation in CEBPG. To test this hypothesis we measured transcript expression derived from each parental copy of CEBPG (ie, allele-specific expression; ASE). Read More

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http://dx.doi.org/10.4137/GRSB.S11879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712557PMC
July 2013
5 Reads

Dietary Lipid During Late-Pregnancy and Early-Lactation to Manipulate Metabolic and Inflammatory Gene Network Expression in Dairy Cattle Liver with a Focus on PPARs.

Gene Regul Syst Bio 2013 11;7:103-23. Epub 2013 Jun 11.

Mammalian NutriPhysioGenomics Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois, USA.

Polyunsaturated (PUFA) long-chain fatty acids (LCFAs) are more potent in eliciting molecular and tissue functional changes in monogastrics than saturated LCFA. From -21 through 10 days relative to parturition dairy cows were fed no supplemental LCFA (control), saturated LCFA (SFAT; mainly 16:0 and 18:0), or fish oil (FISH; high-PUFA). Twenty-seven genes were measured via quantitative RT-PCR in liver tissue on day -14 and day 10. Read More

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http://dx.doi.org/10.4137/GRSB.S12005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699062PMC
July 2013
10 Reads
2 Citations

Investigation of dmyc Promoter and Regulatory Regions.

Gene Regul Syst Bio 2013 15;7:85-102. Epub 2013 May 15.

Bio-Technopark Zurich, Molecular Biology Laboratory, Zurich, Switzerland. ; Institute of Molecular Life Sciences, University of Zurich-Irchel, Zurich, Switzerland.

Products of the myc gene family integrate extracellular signals by modulating a wide range of their targets involved in cellular biogenesis and metabolism; the purpose of this integration is to regulate cell death, proliferation, and differentiation. However, understanding the regulation of myc at the transcription level remains a challenge. We performed rapid amplification of dmyc cDNA ends (5' RACE) and mapped the transcription start site at P1 promoter, 18 base pairs upstream of the start of the known EST GM01143 and within the 5' UTR. Read More

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http://dx.doi.org/10.4137/GRSB.S10751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663572PMC
June 2013
4 Reads

Yin yang 1 and adipogenic gene network expression in longissimus muscle of beef cattle in response to nutritional management.

Gene Regul Syst Bio 2013 16;7:71-83. Epub 2013 Apr 16.

Mammalian NutriPhysioGenomics, University of Illinois, Urbana, USA. ; Department of Animal Sciences, University of Illinois, Urbana, USA.

Among 36 differentially-expressed genes during growth in longissimus muscle (LM) of Angus steers, Yin Yang 1 (YY1) had the most relationships with other genes including some associated with adipocyte differentiation. The objective of this study was to examine the effect of nutritional management on mRNA expression of YY1 along with its targets genes PPARG, GTF2B, KAT2B, IGFBP5 and STAT5B. Longissimus from Angus and Angus × Simmental steers (7 total/treatment) on early weaning plus high-starch (EWS), normal weaning plus starch creep feeding (NWS), or normal weaning without starch creep feeding (NWN) was biopsied at 0, 96, and 240 days on treatments. Read More

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http://dx.doi.org/10.4137/GRSB.S11783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653888PMC
May 2013
8 Reads
3 Citations

Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification.

Gene Regul Syst Bio 2013 26;7:57-70. Epub 2013 Mar 26.

Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, Maryland, United States of America.

Histone modification has emerged as a very important mechanism regulating the transcriptional status of the genome. Insulin-like growth factor 2 (IGF2) is a peptide hormone controlling various cellular processes, including proliferation and apoptosis. H19 gene is closely linked to IGF2 gene, and IGF2 and H19 are reciprocally regulated imprinted genes. Read More

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http://dx.doi.org/10.4137/GRSB.S11243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623616PMC
May 2013
5 Reads

A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms.

Gene Regul Syst Bio 2013 26;7:41-56. Epub 2013 Mar 26.

Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical, University, Noshio, Kiyose, Tokyo, Japan.

Interferon-gamma (IFNγ) plays a key role in macrophage activation, T helper and regulatory cell differentiation, defense against intracellular pathogens, tissue remodeling, and tumor surveillance. The diverse biological functions of IFNγ are mediated by direct activation of signal transducer and activator of transcription 1 (STAT1) as well as numerous downstream effector genes. Because a perturbation in STAT1 target gene networks is closely associated with development of autoimmune diseases and cancers, it is important to characterize the global picture of these networks. Read More

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http://dx.doi.org/10.4137/GRSB.S11433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623615PMC
May 2013
8 Reads

Global consensus theorem and self-organized criticality: unifying principles for understanding self-organization, swarm intelligence and mechanisms of carcinogenesis.

Authors:
Simon Rosenfeld

Gene Regul Syst Bio 2013 20;7:23-39. Epub 2013 Feb 20.

NIH, National Cancer Institute, Rockville, Maryland, USA.

Complex biological systems manifest a large variety of emergent phenomena among which prominent roles belong to self-organization and swarm intelligence. Generally, each level in a biological hierarchy possesses its own systemic properties and requires its own way of observation, conceptualization, and modeling. In this work, an attempt is made to outline general guiding principles in exploration of a wide range of seemingly dissimilar phenomena observed in large communities of individuals devoid of any personal intelligence and interacting with each other through simple stimulus-response rules. Read More

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http://dx.doi.org/10.4137/GRSB.S10885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583443PMC
March 2013
12 Reads