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https://www.readbyqxmd.com/read/27926536/a-minimal-titration-model-of-the-mammalian-dynamical-heat-shock-response
#1
Aude Sivéry, Emmanuel Courtade, Quentin Thommen
Environmental stress, such as oxidative or heat stress, induces the activation of the heat shock response (HSR) and leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular chaperones to maintain cellular proteostasis. Controlled by highly intricate regulatory mechanisms, having stress-induced activation and feedback regulations with multiple partners, the HSR is still incompletely understood. In this context, we propose a minimal molecular model for the gene regulatory network of the HSR that reproduces quantitatively different heat shock experiments both on heat shock factor 1 (HSF1) and HSPs activities...
December 7, 2016: Physical Biology
https://www.readbyqxmd.com/read/27925325/inflammation-oxidative-stress-and-apoptosis-cascade-implication-in-bisphenol-a-induced-liver-fibrosis-in-male-rats
#2
Sahar El-Sayed Elswefy, Fatma Rizk Abdallah, Hebatallah Husseini Atteia, Alaa Samir Wahba, Rehab Abdallah Hasan
Bisphenol A (BPA) is a key monomer in the production of plastics. It has been shown to be hepatotoxic. Inflammation and oxidative stress are closely linked with liver fibrosis, the major contributing factor to hepatic failure. Therefore, the aim of this study was to evaluate the impact of chronic exposure to BPA on the development of hepatic fibrosis in male rats and to determine the cross-talk between the hepatic cytokine network, oxidative stress and apoptosis. For this purpose, 30 male Wistar albino rats were divided into three equal groups as follows: the first group was given no treatment (normal control group); the second group was given corn oil once daily by oral gavage for 8 weeks (vehicle control group); and the third group received BPA (50 mg/kg body weight/day, p...
December 7, 2016: International Journal of Experimental Pathology
https://www.readbyqxmd.com/read/27925216/light-regulation-of-alternative-pre-mrna-splicing-in-plants
#3
Hangxiao Zhang, Chentao Lin, Lianfeng Gu
Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27924948/foxa1-gata3-and-ppar%C3%A9-cooperate-to-drive-luminal-subtype-in-bladder-cancer-a-molecular-analysis-of-established-human-cell-lines
#4
Joshua I Warrick, Vonn Walter, Hironobu Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany L Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka I Kawasawa, Matthew Kaag, Wansong Guo, Jay D Raman, Joo-Seop Park, David J DeGraff
Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924512/computational-analysis-reveals-microrna-mrna-regulatory-network-in-esophageal-squamous-cell-carcinoma
#5
Jie Zhao, Bi-Cheng Zhang, Li-Fang Yu, Wei-Xing Wang, Yong Zhao, Zhi-Guo Rao
MicroRNAs (miRNAs) are known to regulate post-transcriptional gene expression. They are involved in carcinogenesis and tumor progression. The aim of this study was to explore the microRNA-mRNA regulatory network in esophageal squamous cell carcinoma (ESCC) using comprehensive computational approaches. In this study we have selected a total of 11 miRNAs from one previously reported study in ESCC. The mRNA targets of these miRNAs were predicted using various algorithms. The expression profiles of these mRNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples...
December 2016: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/27924475/determination-of-anti-mir-association-with-mirna-argonaute-complexes-in-vivo
#6
Dimitrios G Zisoulis
Aberrant expression of microRNAs (miRNAs) has been causatively linked to multiple disease pathologies while pharmacological inhibition of overexpressed miRNAs by modified oligonucleotides, termed anti-miRs, has been shown to ameliorate the disease phenotype. Anti-miRs are also widely used in academia to define miRNA-mediated regulation of gene networks in vitro and in vivo. Here, we describe a methodology that allows the determination of the physical association of miRNA inhibitors and their targets in the context of the Argonaute complex in vivo, providing unprecedented insight into the physiological interactions of anti-miRs and the miRNA machinery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924281/causality-analysis-detects-the-regulatory-role-of-maternal-effect-genes-in-the-early-drosophila-embryo
#7
Zara Ghodsi, Xu Huang, Hossein Hassani
In developmental studies, inferring regulatory interactions of segmentation genetic network play a vital role in unveiling the mechanism of pattern formation. As such, there exists an opportune demand for theoretical developments and new mathematical models which can result in a more accurate illustration of this genetic network. Accordingly, this paper seeks to extract the meaningful regulatory role of the maternal effect genes using a variety of causality detection techniques and to explore whether these methods can suggest a new analytical view to the gene regulatory networks...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27924190/network-analysis-of-human-post-mortem-microarrays-reveals-novel-genes-micrornas-and-mechanistic-scenarios-of-potential-importance-in-fighting-huntington-s-disease
#8
Sreedevi Chandrasekaran, Danail Bonchev
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924044/plamom-a-comprehensive-database-compiles-plant-mobile-macromolecules
#9
Daogang Guan, Bin Yan, Christoph Thieme, Jingmin Hua, Hailong Zhu, Kenneth R Boheler, Zhongying Zhao, Friedrich Kragler, Yiji Xia, Shoudong Zhang
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924033/chipbase-v2-0-decoding-transcriptional-regulatory-networks-of-non-coding-rnas-and-protein-coding-genes-from-chip-seq-data
#10
Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924014/the-string-database-in-2017-quality-controlled-protein-protein-association-networks-made-broadly-accessible
#11
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J Jensen, Christian von Mering
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923923/antiviral-innate-immune-response-interferes-with-the-formation-of-replication-associated-membrane-structures-induced-by-a-positive-strand-rna-virus
#12
Diede Oudshoorn, Barbara van der Hoeven, Ronald W A L Limpens, Corrine Beugeling, Eric J Snijder, Montserrat Bárcena, Marjolein Kikkert
: Infection with nidoviruses like corona- and arteriviruses induces a reticulovesicular network of interconnected endoplasmic reticulum (ER)-derived double-membrane vesicles (DMVs) and other membrane structures. This network is thought to accommodate the viral replication machinery and protect it from innate immune detection. We hypothesized that the innate immune response has tools to counteract the formation of these virus-induced replication organelles in order to inhibit virus replication...
December 6, 2016: MBio
https://www.readbyqxmd.com/read/27923919/quorum-sensing-coordinates-cooperative-expression-of-pyruvate-metabolism-genes-to-maintain-a-sustainable-environment-for-population-stability
#13
Lisa A Hawver, Jennifer M Giulietti, James D Baleja, Wai-Leung Ng
: Quorum sensing (QS) is a microbial cell-cell communication system that regulates gene expression in response to population density to coordinate collective behaviors. Yet, the role of QS in resolving the stresses caused by the accumulation of toxic metabolic by-products at high cell density is not well defined. In response to cell density, QS could be involved in reprogramming of the metabolic network to maintain population stability. Using unbiased metabolomics, we discovered that Vibrio cholerae mutants genetically locked in a low cell density (LCD) QS state are unable to alter the pyruvate flux to convert fermentable carbon sources into neutral acetoin and 2,3-butanediol molecules to offset organic acid production...
December 6, 2016: MBio
https://www.readbyqxmd.com/read/27923776/establishment-of-expression-in-the-shortroot-scarecrow-transcriptional-cascade-through-opposing-activities-of-both-activators-and-repressors
#14
Erin E Sparks, Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H Hennacy, Jingyuan Zhang, Gina Turco, Jalean J Petricka, Jessica Foret, Alexander J Hartemink, Raluca Gordân, Molly Megraw, Siobhan M Brady, Philip N Benfey
Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT...
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27923654/zeb1-is-neither-sufficient-nor-required-for-epithelial-mesenchymal-transition-in-ls174t-colorectal-cancer-cells
#15
Sabine Jägle, Annika Dertmann, Monika Schrempp, Andreas Hecht
Epithelial-mesenchymal transition (EMT) is implicated in metastases formation and acquired therapy resistance in several tumor entities. The two transcription factors SNAIL1 and ZEB1 are thought to be master regulators of EMT and to form a core regulatory network required for EMT-associated transcriptional reprogramming. Yet, inducible EMT models show the sequential upregulation first of SNAIL1 and only subsequently of ZEB1. Therefore, SNAIL1 and ZEB1 might be differentially needed for the onset and propagation of EMT...
December 3, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27923621/transcriptomic-analysis-of-gene-expression-profiles-of-stomach-carcinoma-reveal-abnormal-expression-of-mitotic-components
#16
Hongfei Tong, Jisheng Wang, Hui Chen, Zhaohong Wang, Henwei Fan, Zhonglin Ni
AIMS: In order to explore the etiology of gastric cancer on global gene expression level, we developed advanced bioinformatic analysis to investigate the variations of global gene expression and the interactions among them. MAIN METHODS: We downloaded the dataset GSE63288 from Gene Expression Omnibus (GEO) database which included 22 human gastric cancer and 22 healthy control samples. We identified the differential expression genes, and explored the Gene ontology (GO) and pathways of the differentially expressed genes...
December 3, 2016: Life Sciences
https://www.readbyqxmd.com/read/27923592/developments-in-targeted-therapy-in-melanoma
#17
REVIEW
V C Amann, E Ramelyte, S Thurneysen, R Pitocco, N Bentele-Jaberg, S M Goldinger, R Dummer, J Mangana
Melanomas are disease entities driven in part by the mitogen activated protein kinase (MAPK) pathway. The TCGA network recently defined four genetic subtypes based on the most prevalent significantly mutated genes, including mutant BRAF, mutant RAS (N/H/K), mutant NF1, and Triple wild-type melanoma (harboring none of the aforementioned mutations, but instead includes KIT, GNA and GNAQ mutations). The successful development of kinase inhibitors marked a milestone in the treatment of metastatic melanoma. Combination treatment with a BRAF- and MEK-inhibitor is the current standard of care for inoperable stage IIIC/IV BRAF-mutated melanoma...
November 5, 2016: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/27923364/pcan-phenotype-consensus-analysis-to-support-disease-gene-association
#18
Patrice Godard, Matthew Page
BACKGROUND: Bridging genotype and phenotype is a fundamental biomedical challenge that underlies more effective target discovery and patient-tailored therapy. Approaches that can flexibly and intuitively, integrate known gene-phenotype associations in the context of molecular signaling networks are vital to effectively prioritize and biologically interpret genes underlying disease traits of interest. RESULTS: We describe Phenotype Consensus Analysis (PCAN); a method to assess the consensus semantic similarity of phenotypes in a candidate gene's signaling neighborhood...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27923054/fused-regression-for-multi-source-gene-regulatory-network-inference
#19
Kari Y Lam, Zachary M Westrick, Christian L Müller, Lionel Christiaen, Richard Bonneau
Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms) and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922823/slm35-links-mitochondrial-stress-response-and-longevity-through-tor-signaling-pathway
#20
Jose L Aguilar-Lopez, Raymond Laboy, Fabiola Jaimes-Miranda, Erika Garay, Alexander DeLuna, Soledad Funes
In most eukaryotic cells mitochondria are essential organelles involved in a great variety of cellular functions. One of the physiological processes linked to mitochondria is aging, a gradual process of damage accumulation that eventually promotes cell death. Aging depends on a balance between mitochondrial biogenesis, function and degradation. It has been previously shown that Tor1, Sch9 and Ras2 are activated in response to nutrient availability and regulate cell growth and division. A deficiency in any of these genes promotes lifespan extension and cell protection during oxidative and heat shock stress...
December 2, 2016: Aging
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