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Modeling gene regulation

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https://www.readbyqxmd.com/read/28454405/expression-of-b-cell-translocation-gene-2-is-associated-with-favorable-prognosis-in-hepatocellular-carcinoma-patients-and-sensitizes-irradiation-induced-hepatocellular-carcinoma-cell-apoptosis-in-vitro-and-in-nude-mice
#1
Yuanyuan Chen, Chuan Chen, Zhimin Zhang, He Xiao, Bijing Mao, Huan Huang, Chenchen Ding, Lin Lei, Hui Zhang, Jian Li, Mei Jiang, Ge Wang
B-cell translocation gene 2 (BTG2) proteins have been reported to be putative tumor suppressors in various cancer types. The present study first assessed BTG2 expression in 44 human liver cancer tissue specimens, then investigated BTG2 expression in the regulation of hepatocellular carcinoma (HCC) cell apoptosis with or without radiotherapy in vitro and in vivo. The results revealed that BTG2 protein expression was significantly reduced in HCC tissues, and associated with better survival for HCC patients (P=0...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454374/arsenic-trioxide-inhibits-tumor-induced-myeloid-derived-suppressor-cells-and-enhances-t-cell-activity
#2
Qingmin Gao, Jingwei Jiang, Zhaohui Chu, Hao Lin, Xinli Zhou, Xiaohua Liang
Myeloid-derived suppressor cells (MDSCs), one of the major orchestrators of the immunosuppressive network, are associated with immune suppression and considered a prime target for cancer immunotherapy. At present, various strategies have been explored to deplete and/or inactivate MDSCs in vivo. In this study, we investigated the effect of arsenic trioxide (ATO) on MDSCs derived from tumor-bearing mice. This study examined the in vitro and in vivo effects of ATO administration on MDSCs from C57/j mice bearing either the B16 or H22 tumor...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454114/estimating-the-effects-of-transcription-factors-binding-and-histone-modifications-on-gene-expression-levels-in-human-cells
#3
Lu-Qiang Zhang, Qian-Zhong Li
Transcription factors and histone modifications are vital for the regulation of gene expression. Hence, to estimate the effects of transcription factors binding and histone modifications on gene expression, we construct a statistical model for the genome-wide 15 transcription factors binding data, 10 histone modifications profiles and DNase-I hypersensitivity data in three mammalian. Remarkably, our results show POLR2A and H3K36me3 can highly and consistently predict gene expression in three cell lines. And H3K4me3, H3K27me3 and H3K9ac are more reliable predictors than other histone modifications in human embryonic stem cells...
April 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28453813/identification-and-allelic-dissection-uncover-roles-of-lncrnas-in-secondary-growth-of-populus-tomentosa
#4
Daling Zhou, Qingzhang Du, Jinhui Chen, Qingshi Wang, Deqiang Zhang
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation...
April 26, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28453775/deconvoluting-kinase-inhibitor-induced-cardiotoxicity
#5
Sarah D Lamore, Ernst Ahlberg, Scott Boyer, Michelle L Lamb, Maria P Hortigon-Vinagre, Victor Rodriguez, Godfrey L Smith, Johanna Sagemark, Lars Carlsson, Stephanie M Bates, Allison L Choy, Jonna Stålring, Clay W Scott, Matthew F Peters
Many drugs designed to inhibit kinases have their clinical utility limited by cardiotoxicity-related label warnings or prescribing restrictions. While this liability is widely recognized, designing safer kinase inhibitors (KI) requires knowledge of the causative kinase(s). Efforts to unravel the kinases have encountered pharmacology with nearly prohibitive complexity. At therapeutically relevant concentrations, KIs show promiscuity distributed across the kinome. Here, to overcome this complexity, 65 KIs with known kinome-scale polypharmacology profiles were assessed for effects on cardiomyocyte beating...
April 26, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28453771/interplay-between-ifn-%C3%AE-and-il-6-impacts-the-inflammatory-response-and-expression-of-interferon-regulated-genes-in-environmental-induced-autoimmunity
#6
David M Cauvi, Gabrielle Cauvi, Christopher B Toomey, Eric Jacquinet, K Michael Pollard
IFN-γ has been found to be robustly important to disease pathogenesis in both idiopathic and induced models of murine lupus. In transgenic mice, over production of IFN-γ in the skin results in an inflammatory response and autoimmunity. This suggests that localized exposure to environmental factors that induce autoimmunity may be associated with expression of an IFN-γ dependent inflammatory response. Using murine mercury-induced autoimmunity (mHgIA), the severity of inflammation and proinflammatory cytokine expression, including the cellular source of IFN-γ, were assessed at the site of subcutaneous exposure and in secondary lymphoid organs...
April 26, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28453658/androgen-receptor-agonists-increase-lean-mass-improve-cardiopulmonary-functions-and-extend-survival-in-preclinical-models-of-duchenne-muscular-dystrophy
#7
Suriyan Ponnusamy, Ryan D Sullivan, Dahui You, Nadeem Zafar, Chuan He Yang, Thirumagal Thiyagarajan, Daniel L Johnson, Maron L Barrett, Nikki J Koehler, Mayra Star, Erin J Stephenson, Dave Bridges, Stephania A Cormier, Lawrence M Pfeffer, Ramesh Narayanan
Duchenne muscular dystrophy (DMD) is a neuromuscular disease that predominantly affects boys as a result of mutation(s) in the dystrophin gene. DMD is characterized by musculoskeletal and cardiopulmonary complications, resulting in shorter life-span. Boys afflicted by DMD typically exhibit symptoms within 3-5 years of age and declining physical functions before attaining puberty. We hypothesized that rapidly deteriorating health of pre-pubertal boys with DMD could be due to diminished anabolic actions of androgens in muscle, and that intervention with an androgen receptor (AR) agonist will reverse musculoskeletal complications and extend survival...
April 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28453568/baicalin-inhibits-biofilm-formation-attenuates-the-quorum-sensing-controlled-virulence-and-enhances-pseudomonas-aeruginosa-clearance-in-a-mouse-peritoneal-implant-infection-model
#8
Jing Luo, Biying Dong, Ke Wang, Shuangqi Cai, Tangjuan Liu, Xiaojing Cheng, Danqing Lei, Yanling Chen, Yanan Li, Jinliang Kong, Yiqiang Chen
The quorum sensing (QS) circuit plays a role in the precise regulation of genes controlling virulence factors and biofilm formation in Pseudomonas aeruginosa. QS-controlled biofilm formation by Pseudomonas aeruginosa in clinical settings has remained controversial due to emerging drug resistance; therefore, screening diverse compounds for anti-biofilm or anti-QS activities is important. This study demonstrates the ability of sub-minimum inhibitory concentrations (sub-MICs) of baicalin, an active natural compound extracted from the traditional Chinese medicinal Scutellaria baicalensis, to inhibit the formation of Pseudomonas aeruginosa biofilms and enhance the bactericidal effects of various conventional antibiotics in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28453536/rtfa-controls-development-secondary-metabolism-and-virulence-in-aspergillus-fumigatus
#9
Ryan R Myers, Timothy D Smith, Sherine F Elsawa, Olivier Puel, Souraia Tadrist, Ana M Calvo
Invasive aspergillosis by Aspergillus fumigatus is a leading cause of infection-related mortality in immune-compromised patients. In order to discover potential genetic targets to control A. fumigatus infections we characterized rtfA, a gene encoding a putative RNA polymerase II transcription elongation factor-like protein. Our recent work has shown that the rtfA ortholog in the model fungus Aspergillus nidulans regulates morphogenesis and secondary metabolism. The present study on the opportunistic pathogen A...
2017: PloS One
https://www.readbyqxmd.com/read/28453302/variant-in-galnt3-gene-linked-with-reduced-coronary-artery-disease-risk-in-chinese-population
#10
Liwei Guo, Duan Li, Mengting Li, Lin Li, Yanmei Huang
AIM: Our previous study found expression of GALNT3 gene was reduced in coronary artery disease (CAD) patients, and it contributed to endothelial injury by regulating apoptosis and matrix metalloproteinase (MMP) expression. GALNT3 gene may be a potential target for future therapeutic intervention of CAD. However, none reports linking the GALNT3 gene to susceptibility of CAD. This study investigated the variant associations of GALNT3 gene and CAD. METHODS: Thirteen single nucleotide polymorphism (SNP) in and around the GALNT3 gene were tagged and analyzed in CAD patients (n = 1515) and control individuals (n = 5019), and the SNPs with CAD were tested with multiple logistic regression analysis in an additive genetic model (with one degree of freedom) after adjusting for age and sex...
April 28, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28449359/transcriptomic-responses-of-solanum-dulcamara-to-natural-and-simulated-herbivory
#11
Tobias Lortzing, Vivien Firtzlaff, Duy Nguyen, Ivo Rieu, Sandra Stelzer, Martina Schad, Jim Kallarackal, Anke Steppuhn
Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449155/mitochondrial-dysfunction-in-diabetic-cardiomyopathy-effect-of-mesenchymal-stem-cell-with-ppar-%C3%AE-agonist-or-exendin-4
#12
Mohamed Abd Elaziz Wassef, Ola M Tork, Laila A Rashed, Walaa Ibrahim, Heba Morsi, Dina Mohamed Mekawy Rabie
Therapy targeting mitochondria may provide novel ways to treat diabetes and its complications. Bone marrow-derived mesenchymal stem cells (MSCs), the peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists and exendin-4; an analog of glucagon-like peptide-1 have shown cardioprotective properties in many cardiac injury models. So, we evaluated their effects in diabetic cardiomyopathy (DCM) in relation to mitochondrial dysfunction. This work included seven groups of adult male albino rats: the control group, the non-treated diabetic group, and the treated diabetic groups: one group was treated with MSCs only, the second with pioglitazone only, the third with MSCs and pioglitazone, the forth with exendin-4 only and the fifth with MSCs and exendin-4...
April 27, 2017: Experimental and Clinical Endocrinology & Diabetes
https://www.readbyqxmd.com/read/28448946/oral-administration-of-methysticin-improves-cognitive-deficits-in-a-mouse-model-of-alzheimer-s-disease
#13
Athanassios Fragoulis, Stephanie Siegl, Markus Fendt, Sandra Jansen, Ulf Soppa, Lars-Ove Brandenburg, Thomas Pufe, Joachim Weis, Christoph Jan Wruck
INTRODUCTION: There is increasing evidence for the involvement of chronic inflammation and oxidative stress in the pathogenesis of Alzheimer's disease (AD). Nuclear factor erythroid 2-related factor 2 (Nrf2) is an anti-inflammatory transcription factor that regulates the oxidative stress defense. Our previous experiments demonstrated that kavalactones protect neuronal cells against Amyloid β (Aβ)-induced oxidative stress in vitro by Nrf2 pathway activation. Here, we tested an in vivo kavalactone treatment in a mouse model of AD...
April 19, 2017: Redox Biology
https://www.readbyqxmd.com/read/28448796/reconciling-epigenetic-memory-and-transcriptional-responsiveness
#14
Amanda G Fisher, Michael P H Stumpf, Matthias Merkenschlager
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448552/transcriptomic-analysis-of-the-hepatic-response-to-stress-in-the-red-cusk-eel-genypterus-chilensis-insights-into-lipid-metabolism-oxidative-stress-and-liver-steatosis
#15
Sebastian Naour, Brisa M Espinoza, Jorge E Aedo, Rodrigo Zuloaga, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Cristian Gallardo-Escarate, Alfredo Molina, Juan Antonio Valdés
Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress...
2017: PloS One
https://www.readbyqxmd.com/read/28448529/a-genome-wide-analysis-of-the-rna-guided-silencing-pathway-in-coffee-reveals-insights-into-its-regulatory-mechanisms
#16
Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antonio Chalfun-Junior
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover...
2017: PloS One
https://www.readbyqxmd.com/read/28447937/il17-factors-are-early-regulators-in-the-gut-epithelium-during-inflammatory-response-to-vibrio-in-the-sea-urchin-larva
#17
Katherine M Buckley, Eric Chun Hei Ho, Taku Hibino, Catherine S Schrankel, Nicholas W Schuh, Guizhi Wang, Jonathan Patrick Rast
IL17 cytokines are central mediators of mammalian immunity. In vertebrates, these factors derive from diverse cellular sources. Sea urchins share a molecular heritage with chordates that includes the IL17 system. Here, we characterize the role of epithelial expression of IL17 in the larval gut-associated immune response. The purple sea urchin genome encodes ten IL17 subfamilies (35 genes) and two IL17 receptors. Most of these subfamilies are conserved throughout echinoderms. Two IL17 subfamilies are sequentially strongly upregulated and attenuated in the gut epithelium in response to bacterial disturbance...
April 27, 2017: ELife
https://www.readbyqxmd.com/read/28447783/real-time-detection-reveals-responsive-co-transcriptional-formation-of-persistent-intramolecular-dna-and-intermolecular-dna-rna-hybrid-g-quadruplexes-stabilized-by-r-loop
#18
Yang Zhao, Jia-Yu Zhang, Zong-Yu Zhang, Tan-Jun Tong, Yu-Hua Hao, Zheng Tan
G-quadruplex (GQ) structures are implicated in important physiological and pathological processes. Millions of GQ-forming motifs are enriched near transcription start sites (TSSs) of animal genes. Transcription can induce formation of GQs which in turn regulates transcription. The kinetics of the formation and persistence of GQs in transcription is crucial for the role they play, but has not yet been explored. We established a method based on the fluorescence resonance energy transfer (FRET) technique to monitor in real-time the co-transcriptional formation and post-transcriptional persistence of GQs in DNA...
April 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28447737/17%C3%AE-estradiol-protects-against-doxorubicin-induced-cardiotoxicity-in-male-sprague-dawley-rats-by-regulating-nadph-oxidase-and-apoptosis-genes
#19
Xiao-Juan Zhang, Xiao-Qing Cao, Chun-Sheng Zhang, Zhuo Zhao
Doxorubicin (DOX) is one of the most effective chemotherapeutic agents for the treatment of a number of malignancies. However, its use is limited by serious cardiotoxic effects, for which there are currently no reliable pharmacologic therapies. Estrogen has exhibited protective effects against cardiac stressors in male and female animal models; however, its effects on DOX‑induced cardiotoxicity remain unknown. High mortality and morbidity rates have been observed in patients with cancer worldwide, and DOX is often administered to a greater number of men than women...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447571/neuroprotective-effects-of-betulin-in-pharmacological-and-transgenic-c-elegans-models-of-parkinson-s-disease
#20
Chia-Wen Tsai, Rong-Tzong Tsai, Shih-Ping Liu, Chang-Shi Chen, Min-Chen Tsai, Shao-Hsuan Chien, Huey-Shan Hung, Shinn-Zong Lin, Woei-Cherng Shyu, Ru-Huei Fu
Parkinson's disease (PD) is the second most common degenerative disorder of the central nervous system in the elderly.It is characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta, as well as by motor dysfunction. Although the causes of PD are not well understood, aggregation of α-synuclein (α-syn) in neurons contributes to this disease. Currently, therapeutics for PD provide satisfactory symptom relief, but not a cure. Treatment strategies include attempts to identify new drugs that will prevent or arrest the progressive course of PD by correcting disease-specific pathogenic process...
April 26, 2017: Cell Transplantation
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