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Modeling gene regulation

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https://www.readbyqxmd.com/read/28822966/inhibitory-actions-of-the-nrg-1-erbb4-pathway-in-macrophages-during-tissue-fibrosis-in-heart-skin-and-lung
#1
Zarha Vermeulen, Anne-Sophie Hervent, Lindsey Dugaucquier, Leni Vandekerckhove, Miche Rombouts, Matthias Beyens, Dorien M Schrijvers, Guido R Y De Meyer, Stuart Maudsley, Gilles W De Keulenaer, Vincent Fm Segers
The neuregulin-1 (NRG-1)/ErbB system is an endothelium-controlled paracrine system modulating cardiac performance and adaptation. Recent studies indicate that NRG-1 has anti-fibrotic effects in the left ventricle (LV), which were explained by direct actions on cardiac fibroblasts. However, the NRG-1/ErbB system also regulates the function of macrophages. In this study, we hypothesized that the anti-fibrotic effect of NRG-1 in the heart is at least partially mediated through inhibitory effects on macrophages...
August 19, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28822934/ecotoxicological-effects-of-binary-mixtures-of-siduron-and-cd-on-mrna-expression-in-the-earthworm-eisenia-fetida
#2
Herman Uwizeyimana, Meie Wang, Weiping Chen, Kifayatullah Khan
This study aimed to investigate the eco-toxicological responses of earthworm (Eisenia fetida) exposed to combined siduron (herbicide) and cadmium (Cd). Eisenia fetida gene expressions including metallothionein (MT) and heat shock protein70 (Hsp70) were analyzed using real-time Polymerase Chain Reaction after individual and combined siduron (0.90, 1.80, 3.60 and 7.20μgcm(-2)) and Cd (0.225, 0.45, 0.90 and 1.80μgcm(-2)) sublethal exposures. Where, the nature of the toxicological interactions between siduron and Cd in inducing or suppressing MT and Hsp70 expression was determined by applying the Combination index (CI)-isobologram model...
August 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28822061/co-ultramicronized-palmitoylethanolamide-luteolin-facilitates-the-development-of-differentiating-and-undifferentiated-rat-oligodendrocyte-progenitor-cells
#3
Stephen D Skaper, Massimo Barbierato, Laura Facci, Mila Borri, Gabriella Contarini, Morena Zusso, Pietro Giusti
Oligodendrocytes, the myelin-producing cells of the central nervous system (CNS), have limited capability to bring about repair in chronic CNS neuroinflammatory demyelinating disorders such as multiple sclerosis (MS). MS lesions are characterized by a compromised pool of undifferentiated oligodendrocyte progenitor cells (OPCs) unable to mature into myelin-producing oligodendrocytes. An attractive strategy may be to replace lost OLs and/or promote their maturation. N-palmitoylethanolamine (PEA) is an endogenous fatty acid amide signaling molecule with anti-inflammatory and neuroprotective actions...
August 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28822016/in-situ-imaging-reveals-properties-of-purinergic-signalling-in-trigeminal-sensory-ganglia-in-vitro
#4
Arletta Nowodworska, Arn M J M van den Maagdenberg, Andrea Nistri, Elsa Fabbretti
Chronic pain is supported by sterile inflammation that induces sensitisation of sensory neurons to ambient stimuli including extracellular ATP acting on purinergic P2X receptors. The development of in vitro methods for drug screening would be useful to investigate cell crosstalk and plasticity mechanisms occurring during neuronal sensitisation and sterile neuroinflammation. Thus, we studied, at single-cell level, membrane pore dilation based on the uptake of a fluorescent probe following sustained ATP-gated P2X receptor function in neurons and non-neuronal cells of trigeminal ganglion cultures from wild-type (WT) and R192Q CaV2...
August 18, 2017: Purinergic Signalling
https://www.readbyqxmd.com/read/28821667/fibroblast-growth-factor-2-in-the-dorsomedial-striatum-is-a-novel-positive-regulator-of-alcohol-consumption
#5
Oren Even-Chen, Yossi Sadot-Sogrin, Ohad Shaham, Segev Barak
Repeated alcohol intake leads to mesostriatal neuroadaptations, resulting in drinking escalation and addiction phenotypes. Fibroblast growth factor 2 (FGF2) has been shown to interact with the mesostriatal dopaminergic system, and has been implicated in the actions of psychostimulants in the brain, and in several psychiatric disorders. Here, we report on a positive regulatory feedback loop of alcohol and FGF2 in rodent models. Specifically, we found that acute alcohol exposure (2.5 g/kg, i.p.) increased the mRNA expression of Fgf2 in the dorsal hippocampus, nucleus accumbens and dorsal striatum...
August 8, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28821632/transcriptomic-and-epigenetic-regulation-of-disuse-atrophy-and-the-return-to-activity-in-skeletal-muscle
#6
Andrew G Fisher, Robert A Seaborne, Thomas M Hughes, Alex Gutteridge, Claire Stewart, Judy M Coulson, Adam P Sharples, Jonathan C Jarvis
Physical inactivity and disuse are major contributors to age-related muscle loss. Denervation of skeletal muscle has been previously used as a model with which to investigate muscle atrophy following disuse. Although gene regulatory networks that control skeletal muscle atrophy after denervation have been established, the transcriptome in response to the recovery of muscle after disuse and the associated epigenetic mechanisms that may function to modulate gene expression during skeletal muscle atrophy or recovery have yet to be investigated...
August 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28821592/global-analysis-of-gene-expression-in-response-to-whole-chromosome-aneuploidy-in-hexaploid-wheat
#7
Ai Zhang, Ning Li, Lei Gong, Xiaowan Gou, Bin Wang, Xin Deng, Changping Li, Qianli Dong, Huakun Zhang, Bao Liu
Aneuploidy, a condition of unbalanced chromosome content, represents a large-effect mutation that bears significant relevancy to human health and microbe adaptation. As such, extensive studies of aneuploidy have been conducted in unicellular model organisms and cancer cells. Aneuploidy also frequently is associated with plant polyploidization, but its impact on gene expression and relevance to polyploid genome evolution/functional innovation remain largely unknown. Here, we used a panel of diverse types of whole-chromosome aneuploidy of hexaploid wheat, all under the common genetic background of cv...
August 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28821565/down-regulation-of-xiap-enhances-the-radiosensitivity-of-esophageal-cancer-cells-in-vivo-and-in-vitro
#8
Xin Wen, Xin-Rui Han, Shao-Hua Fan, Zi-Feng Zhang, Lu Chen, Gao Yi, Dong-Mei Wu, Jun Lu, Yuan-Lin Zheng
The study investigated the effects of XIAP gene silencing on the radiosensitivity of esophageal cancer (EC) cells. Western blotting was used to select EC cell lines with XIAP overexpression. Selected EC9706 and KYSE30 cell lines were both divided into four groups: the blank control group, the negative control (NC) group (transfected with pBSHH1), the siRNA-enhanced group (transfected with pBSHH1-XIAP1-siRNA), and the siRNA-decreased group (transfected with pBSHH1-XIAP2-siRNA). Expressions of XIAP were measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blotting, cell survival and viability by MTT assay and colony formation assay, and cell apoptosis by flow cytometry, respectively...
August 18, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28821448/cognitive-impairment-and-gene-expression-alterations-in-a-rodent-model-of-binge-eating-disorder
#9
A Chawla, Z A Cordner, G Boersma, T H Moran
Binge eating disorder (BED) is defined as recurrent, distressing over-consumption of palatable food (PF) in a short time period. Clinical studies suggest that individuals with BED may have impairments in cognitive processes, executive functioning, impulse control, and decision-making, which may play a role in sustaining binge eating behavior. These clinical reports, however, are limited and often conflicting. In this study, we used a limited access rat model of binge-like behavior in order to further explore the effects of binge eating on cognition...
August 15, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/28821316/obesity-and-fatty-liver-are-prevented-by-inhibition-of-the-aryl-hydrocarbon-receptor-in-both-female-and-male-mice
#10
Benjamin J Moyer, Itzel Y Rojas, Joanna S Kerley-Hamilton, Krishnamurthy V Nemani, Heidi W Trask, Carol S Ringelberg, Barjor Gimi, Eugene Demidenko, Craig R Tomlinson
Inhibition of the aryl hydrocarbon receptor (AHR) prevents Western diet-induced obesity and fatty liver in C57Bl/6J (B6) male mice. The AHR is a ligand-activated nuclear receptor that regulates genes involved in xenobiotic metabolism and T-cell differentiation. Here, we tested the hypothesis that AHR antagonism would also prevent obesity and fatty liver in female mice and that B6 mice (higher-affinity AHR) and congenic B6.D2 mice (lower-affinity AHR) would differentially respond to AHR inhibition. Female and male adult B6 and B6...
August 2017: Nutrition Research
https://www.readbyqxmd.com/read/28821297/differential-expression-of-osteopontin-and-osteoprotegerin-mrna-in-epicardial-adipose-tissue-between-patients-with-severe-coronary-artery-disease-and-aortic-valvular-stenosis-association-with-hdl-subclasses
#11
María Luna-Luna, David Cruz-Robles, Nydia Ávila-Vanzzini, Valentín Herrera-Alarcón, Jesús Martínez-Reding, Sergio Criales-Vera, Julio Sandoval-Zárate, Jesús Vargas-Barrón, Carlos Martínez-Sánchez, Armando Roberto Tovar-Palacio, José Manuel Fragoso, Elizabeth Carreón-Torres, Gilberto Vargas-Alarcón, Óscar Pérez-Méndez
BACKGROUND: Previous studies suggest a relationship of the epicardial adipose tissue (EAT) with progression and calcification of the atherosclerotic plaque; however, it is unknown if this tissue expresses genes that may participate on these processes and if the expression of these genes is regulated by high-density lipoprotein (HDL) subclasses. METHODS: To explore this possibility, we determined the mRNA expression by qPCR of a pro-calcifying gene (osteopontin (OPN)), and two anti-calcifying genes (osteoprotegerin (OPG) and osteonectin (ON)), in biopsies of EAT obtained from 15 patients with coronary artery disease (CAD) determined by angiography, and 15 patients with diagnostic of aortic valve stenosis but without CAD as control group...
August 18, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/28821270/calmodulin-like-protein-3-is-an-estrogen-receptor-alpha-coregulator-for-gene-expression-and-drug-response-in-a-snp-estrogen-and-serm-dependent-fashion
#12
Sisi Qin, James N Ingle, Mohan Liu, Jia Yu, D Lawrence Wickerham, Michiaki Kubo, Richard M Weinshilboum, Liewei Wang
BACKGROUND: We previously performed a case-control genome-wide association study in women treated with selective estrogen receptor modulators (SERMs) for breast cancer prevention and identified single nucleotide polymorphisms (SNPs) in ZNF423 as potential biomarkers for response to SERM therapy. The ZNF423rs9940645 SNP, which is approximately 200 bp away from the estrogen response elements, resulted in the SNP, estrogen, and SERM-dependent regulation of ZNF423 expression and, "downstream", that of BRCA1...
August 18, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28821015/extracting-replicable-associations-across-multiple-studies-empirical-bayes-algorithms-for-controlling-the-false-discovery-rate
#13
David Amar, Ron Shamir, Daniel Yekutieli
In almost every field in genomics, large-scale biomedical datasets are used to report associations. Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we propose a new method to allow joint analysis of multiple studies. Given a set of p-values obtained from each study, the goal is to identify associations that recur in at least k > 1 studies while controlling the false discovery rate. We propose several new algorithms that differ in how the study dependencies are modeled, and compare them and extant methods under various simulated scenarios...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820908/ribosomopathy-like-properties-of-murine-and-human-cancers
#14
Sucheta Kulkarni, James M Dolezal, Huabo Wang, Laura Jackson, Jie Lu, Brian P Frodey, Atinuke Dosunmu-Ogunbi, Youjun Li, Marc Fromherz, Audry Kang, Lucas Santana-Santos, Panayiotis V Benos, Edward V Prochownik
Ribosomopathies comprise a heterogeneous group of hematologic and developmental disorders, often characterized by bone marrow failure, skeletal and other developmental abnormalities and cancer predisposition. They are associated with mutations and/or haplo-insufficiencies of ribosomal proteins (RPs) and inefficient ribosomal RNA (rRNA) processing. The resulting ribosomal stress induces the canonical p19ARF/Mdm2/p53 tumor suppressor pathway leading to proliferative arrest and/or apoptosis. It has been proposed that this pathway is then inactivated during subsequent neoplastic evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28820499/choline-supplementation-normalizes-fetal-adiposity-and-reduces-lipogenic-gene-expression-in-a-mouse-model-of-maternal-obesity
#15
Chauntelle Jack-Roberts, Yaelle Joselit, Khatia Nanobashvili, Rachel Bretter, Olga V Malysheva, Marie A Caudill, Anjana Saxena, Kathleen Axen, Ahmed Gomaa, Xinyin Jiang
Maternal obesity increases fetal adiposity which may adversely affect metabolic health of the offspring. Choline regulates lipid metabolism and thus may influence adiposity. This study investigates the effect of maternal choline supplementation on fetal adiposity in a mouse model of maternal obesity. C57BL/6J mice were fed either a high-fat (HF) diet or a control (NF) diet and received either 25 mM choline supplemented (CS) or control untreated (CO) drinking water for 6 weeks before timed-mating and throughout gestation...
August 18, 2017: Nutrients
https://www.readbyqxmd.com/read/28820437/are-astrocytes-the-predominant-cell-type-for-activation-of-nrf2-in-aging-and-neurodegeneration
#16
REVIEW
Jeffrey R Liddell
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that regulates hundreds of antioxidant genes, and is activated in response to oxidative stress. Given that many neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease and multiple sclerosis are characterised by oxidative stress, Nrf2 is commonly activated in these diseases. Evidence demonstrates that Nrf2 activity is repressed in neurons in vitro, and only cultured astrocytes respond strongly to Nrf2 inducers, leading to the interpretation that Nrf2 signalling is largely restricted to astrocytes...
August 18, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#17
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819390/fluorofenidone-inhibits-the-proliferation-of-lung-adenocarcinoma-cells
#18
Zheng-Hao Deng, Jie Meng, Juan Tang, Gao-Yun Hu, Li-Jian Tao
Background: Lung carcinoma is the leading cause of malignant tumor related mortality in China in recent decades, and the development of new and effective therapies for patients with advanced lung carcinoma is needed. We recently found that fluorofenidone (FD), a newly developed pyridine compound, reduced the activation of Stat3 (Signal transducer and activator of transcription 3) in fibroblasts. Stat3 plays a crucial role in the development of lung cancer and may represent a new therapeutic target. In this study, we examined the effect of FD on human lung adenocarcinoma cells in vivo and in vitro...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819378/hif-is-not-essential-for-suppression-of-experimental-tumor-growth-by-mtor-inhibition
#19
Karl X Knaup, Regina Guenther, Johanna Stoeckert, Juliana M Monti, Kai-Uwe Eckardt, Michael S Wiesener
The Hypoxia Inducible Transcription Factor (HIF) is the master regulator of cellular response to hypoxic adaptation. Solid tumors inevitably harbour hypoxic regions with subsequent stabilization and activation of HIF and HIF target genes due to poor vascularization and rapid growth. The mammalian target of rapamycin (mTOR) is a global regulator of cellular growth and proliferation, which can also regulate HIF expression independantly of hypoxia via specific activation of cellular translation and transcription...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819320/genome-wide-identification-and-expression-analysis-of-e2-ubiquitin-conjugating-enzymes-in-tomato
#20
Bhaskar Sharma, Tarun Kumar Bhatt
The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme...
August 17, 2017: Scientific Reports
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