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Gene Regulation and Systems Biology

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https://www.readbyqxmd.com/read/28469414/the-synergistic-role-of-light-feeding-phase-relations-on-entraining-robust-circadian-rhythms-in-the-periphery
#1
Seul-A Bae, Ioannis P Androulakis
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...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28469413/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
#2
James A Bynum, Xinyu Wang, Salomon A Stavchansky, Phillip D Bowman
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...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28469412/use-of-biomedical-ontologies-for-integration-of-biological-knowledge-for-learning-and-prediction-of-adverse-drug-reactions
#3
REVIEW
Shadia Zaman, Sirarat Sarntivijai, Darrell R Abernethy
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...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28469411/graphical-modeling-meets-systems-pharmacology
#4
Rosario Lombardo, Corrado Priami
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...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28469410/modeling-fructose-load-induced-hepatic-de-novo-lipogenesis-by-model-simplification
#5
Richard J Allen, Cynthia J Musante
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. Due to the multiple enzymes involved in de-novo lipogenesis, and the limited data, it is desirable to use single functional expressions to encapsulate the flux between multiple enzymes...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28008225/identifying-cell-type-specific-transcription-factors-by-integrating-chip-seq-and-eqtl-data-application-to-monocyte-gene-regulation
#6
Mudra Choudhury, Stephen A Ramsey
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. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27840576/semi-automated-curation-allows-causal-network-model-building-for-the-quantification-of-age-dependent-plaque-progression-in-apoe-mouse
#7
Justyna Szostak, Florian Martin, Marja Talikka, Manuel C Peitsch, Julia Hoeng
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. Cellular and molecular mechanisms promoting plaque destabilization or rupture were captured in the network model...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27594784/dysregulation-of-protein-kinase-gene-expression-in-nk-cells-from-chronic-fatigue-syndrome-myalgic-encephalomyelitis-patients
#8
Anu Chacko, Donald R Staines, Samantha C Johnston, Sonya M Marshall-Gradisnik
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. The purpose of this present investigation was to examine whether protein kinase genes have a role in abnormal NK cell intracellular signaling in CFS/ME...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27547033/dna-microarray-highlights-nrf2-mediated-neuron-protection-targeted-by-wasabi-derived-isothiocyanates-in-imr-32-cells
#9
Phoebe Zapanta Trio, Satoru Fujisaki, Shunsuke Tanigawa, Ayami Hisanaga, Kozue Sakao, De-Xing Hou
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...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27486304/endothelial-nitric-oxide-synthase-786t-c-and-endothelin-1-5665g-t-gene-polymorphisms-as-vascular-dysfunction-risk-factors-in-sickle-cell-anemia
#10
Wendell Vilas-Boas, Camylla V B Figueiredo, Thassila N Pitanga, Magda O S Carvalho, Rayra P Santiago, Sânzio S Santana, Caroline C Guarda, Angela M D Zanette, Bruno A V Cerqueira, Marilda S Gonçalves
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)...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27429547/community-reviewed-biological-network-models-for-toxicology-and-drug-discovery-applications
#11
Aishwarya Alex Namasivayam, Alejandro Ferreiro Morales, Ángela María Fajardo Lacave, Aravind Tallam, Borislav Simovic, David Garrido Alfaro, Dheeraj Reddy Bobbili, Florian Martin, Ganna Androsova, Irina Shvydchenko, Jennifer Park, Jorge Val Calvo, Julia Hoeng, Manuel C Peitsch, Manuel González Vélez Racero, Maria Biryukov, Marja Talikka, Modesto Berraquero Pérez, Neha Rohatgi, Noberto Díaz-Díaz, Rajesh Mandarapu, Rubén Amián Ruiz, Sergey Davidyan, Shaman Narayanasamy, Stéphanie Boué, Svetlana Guryanova, Susana Martínez Arbas, Swapna Menon, Yang Xiang
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. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27346947/killer-cell-immunoglobulin-like-receptor-genotype-and-haplotype-investigation-of-natural-killer-cells-from-an-australian-population-of-chronic-fatigue-syndrome-myalgic-encephalomyelitis-patients
#12
T K Huth, E W Brenu, D R Staines, S M Marshall-Gradisnik
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)...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27346946/integration-of-telomere-length-dynamics-into-systems-biology-framework-a-review
#13
REVIEW
Lilit Nersisyan
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...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27330274/nucleotide-interdependency-in-transcription-factor-binding-sites-in-the-drosophila-genome
#14
Jacqueline M Dresch, Rowan G Zellers, Daniel K Bork, Robert A Drewell
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). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/27147820/neat1-is-required-for-survival-of-breast-cancer-cells-through-fus-and-mir-548
#15
Hao Ke, Limin Zhao, Xu Feng, Haibo Xu, Li Zou, Qin Yang, Xiaosan Su, Lingtao Peng, Baowei Jiao
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...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/26823650/expression-and-presence-of-opg-and-rankl-mrna-and-protein-in-human-periodontal-ligament-with-orthodontic-force
#16
Liliana Otero, Dabeiba Adriana García, Liseth Wilches-Buitrago
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. After 7 days, premolars were extracted for treatment as indicated. OPG and RANKL mRNA expressions were measured by quantitative reverse transcription polymerase chain reaction (qRT-PCR), and ELISA was used to assess OPG and RANKL protein concentration in compression and tension sides of PDL...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/26823649/epigenetic-regulation-of-tissue-type-plasminogen-activator-in-human-brain-tissue-and-brain-derived-cells
#17
Martina Olsson, Karin Hultman, Sylvie Dunoyer-Geindre, Maurice A Curtis, Richard L M Faull, Egbert K O Kruithof, Christina Jern
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. We demonstrate that treatment of cultured human neurons and human astrocytes with the histone deacetylase inhibitors trichostatin A (TSA) and MS-275 resulted in a two- to threefold increase in t-PA mRNA and protein expression levels...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/26819551/biochemical-analysis-of-genome-functions-using-locus-specific-chromatin-immunoprecipitation-technologies
#18
REVIEW
Toshitsugu Fujita, Hodaka Fujii
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...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/26819550/transcriptomic-sequencing-reveals-a-set-of-unique-genes-activated-by-butyrate-induced-histone-modification
#19
Cong-Jun Li, Robert W Li, Ransom L Baldwin, Le Ann Blomberg, Sitao Wu, Weizhong Li
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...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/26401098/trna-derived-short-non-coding-rna-as-interacting-partners-of-argonaute-proteins
#20
REVIEW
Megumi Shigematsu, Yohei Kirino
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...
2015: Gene Regulation and Systems Biology
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