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Regulatory network

Steffen Schulz, Jens Haueisen, Karl-Juergen Bär, Andreas Voss

 The new interdisciplinary field of network physiology is getting more and more into the focus of interest in medicine. The autonomic nervous system (ANS) dysfunction is well described in schizophrenia (SZO). However, the linear and nonlinear coupling between the ANS and central nervous system (CNS) is only partly addressed until now. This coupling can be assumed as a feedback-feedforward network, reacting with flexible and adaptive responses to internal and external factors.
 For the first time, in this study, we investigated linear and nonlinear short-term central-cardiorespiratory couplings of 17 patients suffering from paranoid schizophrenia (SZO) in comparison to 17 age-gender matched healthy subjects (CON) analyzing heart rate (HR), respiration (RESP) and the power of frontal EEG activity (PEEG)...
June 22, 2018: Physiological Measurement
Louis Anthony Tony Cox
Sufficiently high and prolonged inhalation exposures to some respirable elongated mineral particles (REMPs), notably including amphibole asbestos fibers, can increase risk of inflammation-mediated diseases including malignant mesothelioma, pleural diseases, fibrosis, and lung cancer. Chronic inflammation involves ongoing activation of the NLRP3 inflammasome, which enables immune cells to produce potent proinflammatory cytokines IL-1β and IL-18. Reactive oxygen species (ROS) (in particular, mitochondrial ROS) contribute to NRLP3 activation via a well-elucidated mechanism involving oxidation of reduced thioredoxin and association of thioredoxin-interacting protein with NLRP3...
June 19, 2018: Toxicology and Applied Pharmacology
Vikas U Kapase, Asha A Nesamma, Pannaga P Jutur
Optimizing the production of the high-value renewables such as OMEGAs through pathway engineering requires an in-depth understanding of the structure-function relationship of genes involved in the OMEGA biosynthetic pathways. In this preliminary study, our rationale is to identify and characterize the ∼221 putative genes involved in production of OMEGAs using bioinformatic analysis from the Streptophyte (plants), Chlorophyte (green algae), Rhodophyta (red algae), and Bacillariophyta (diatoms) lineages based on their phylogenomic profiling, conserved motif/domain organization and physico-chemical properties...
June 22, 2018: Preparative Biochemistry & Biotechnology
Ahmed A Moustafa, Hogyoung Kim, Rasha S Albeltagy, Ola H El-Habit, Asim B Abdel-Mageed
MicroRNAs (miRNAs) are a small functional non-coding RNAs that post-transcriptionally regulate gene expression through mRNA degradation or translational repression. miRNAs are key regulatory components of various cellular networks. Current evidence support that multiple mammalian genome-encoded miRNAs impact the cellular biology, including proliferation, apoptosis, differentiation, and tumorigenesis, by targeting specific subsets of mRNAs. This minireview is focused on the current themes underlying the interactions between miRNAs and their mRNA targets and pathways in prostate tumorigenesis and progression, and their potential clinical utility as biomarkers for prostate cancer...
June 2018: Experimental Biology and Medicine
Jordan K Villa, Yichi Su, Lydia M Contreras, Ming C Hammond
In bacteria and archaea, small RNAs (sRNAs) regulate complex networks through antisense interactions with target mRNAs in trans, and riboswitches regulate gene expression in cis based on the ability to bind small-molecule ligands. Although our understanding and characterization of these two important regulatory RNA classes is far from complete, these RNA-based mechanisms have proven useful for a wide variety of synthetic biology applications. Besides classic and contemporary applications in the realm of metabolic engineering and orthogonal gene control, this review also covers newer applications of regulatory RNAs as biosensors, logic gates, and tools to determine RNA-RNA interactions...
May 2018: Microbiology Spectrum
Anupam Kumar, Subhashree Nayak, Pankaj Pathak, Suvendu Purkait, Prit Benny Malgulawar, Mehar Chand Sharma, Vaishali Suri, Arijit Mukhopadhyay, Ashish Suri, Chitra Sarkar
INTRODUCTION: Although role of individual microRNAs (miRNAs) in the pathogenesis of gliomas has been well studied, their role as a clustered remains unexplored in gliomas. METHODS: In this study, we performed the expression analysis of miR-379/miR-656 miRNA-cluster (C14MC) in oligodendrogliomas (ODGs) and also investigated the mechanism underlying modulation of this cluster. RESULTS: We identified significant downregulation of majority of the miRNAs from this cluster in ODGs...
June 21, 2018: Journal of Neuro-oncology
Z Yang, H M Yang, D Q Gong, S P Rose, V Pirgozliev, X S Chen, Z Y Wang
Dietary methionine (Met) restriction produces a coordinated series of transcriptional responses in the liver that limits growth performance and amino acid metabolism. Methyl donor supplementation with betaine (Bet) may protect against this disturbance and affect the molecular basis of gene regulation. However, a lack of genetic information remains an obstacle to understand the mechanisms underlying the relationship between Met and Bet supplementation and its effects on genetic mechanisms. The goal of this study was to identify the effects of dietary supplementation of Met and Bet on growth performance, transcriptomic gene expression, and epigenetic mechanisms in geese on a Met-deficient diet...
June 20, 2018: Poultry Science
Ping Zhu, Nan Ge, Dongyan Liu, Fan Yang, Kai Zhang, Jintao Guo, Xiang Liu, Sheng Wang, Guoxin Wang, Siyu Sun
The incidence of pancreatic cancer is increasing annually in Asia as a whole. Pancreatic cancer ranks sixth in terms of incidence of all malignant tumors. Circular RNA (circRNA) is a type of non-coding RNA which forms a covalently closed continuous loop. CircRNA is extensively expressed in the cytoplasm, and is markedly conservative and stable. MicroRNA (miR)-378a-3p and human (hsa)_circ_0006215 were detected using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in tissue and cells...
July 2018: Oncology Letters
Yan Wang, Yuanyuan Zhang, Lei Wang
Circadian clock and senescence have been shown to tightly intertwined with each other in numerous eukaryotes, but the regulation of circadian oscillator on triggering leaf senescence, and vice versa, remains largely unknown in higher plants. Very recently, circadian system and leaf senescence were found to be highly interconnected in higher plants. Circadian clock was shown to regulate leaf senescence through a few cross signaling pathways including age-dependent, plant hormone mediated, and dark induced manners to trigger the onset of leaf senescence...
2018: Frontiers in Plant Science
Timothy Tapscott, Ju-Sim Kim, Matthew A Crawford, Liam Fitzsimmons, Lin Liu, Jessica Jones-Carson, Andrés Vázquez-Torres
The repressive activity of ancestral histone-like proteins helps integrate transcription of foreign genes with discrepant AT content into existing regulatory networks. Our investigations indicate that the AT-rich discriminator region located between the -10 promoter element and the transcription start site of the regulatory gene ssrA plays a distinct role in the balanced expression of the Salmonella pathogenicity island-2 (SPI2) type III secretion system. The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally, whereas the alarmone guanosine tetraphosphate (ppGpp) relieves the negative regulation imposed by the AT-rich ssrA discriminator region...
June 21, 2018: Scientific Reports
Carolin Rommel, Stephan Rösner, Achim Lother, Margareta Barg, Martin Schwaderer, Ralf Gilsbach, Timo Bömicke, Tilman Schnick, Sandra Mayer, Sophia Doll, Michael Hesse, Oliver Kretz, Brigitte Stiller, Franz-Josef Neumann, Matthias Mann, Markus Krane, Bernd K Fleischmann, Ursula Ravens, Lutz Hein
<u>Rationale:</u> Structural and electrophysiological remodeling of the atria are recognized consequences of sustained atrial arrhythmias, such as atrial fibrillation (AF). The identification of underlying key molecules and signaling pathways has been challenging due to the changing cell type composition during structural remodeling of the atria. <u>Objective:</u> Thus, the aims of our study were (1) to search for transcription factors and downstream target genes, which are involved in atrial structural remodeling, (2) to characterize the significance of the transcription factor ETV1 in atrial remodeling and arrhythmia and (3) to identify ETV1-dependent gene regulatory networks in atrial cardiac myocytes...
June 21, 2018: Circulation Research
Haihai Liang, Xiaoguang Zhao, Chengyu Wang, Jian Sun, Yingzhun Chen, Guoyuan Wang, Lei Fang, Rui Yang, Mengxue Yu, Yunyan Gu, Hongli Shan
BACKGROUND: A deeper mechanistic understanding of epithelial-to-mesenchymal transition (EMT) regulation is needed to improve current anti-metastasis strategies in ovarian cancer (OvCa). This study was designed to investigate the role of lncRNAs in EMT regulation during process of invasion-metastasis in serous OvCa to improve current anti-metastasis strategies for OvCa. METHODS: We systematically analyzes high-throughput gene expression profiles of both lncRNAs and protein-coding genes in OvCa samples with integrated epithelial (iE) subtype and integrated mesenchymal (iM) subtype labels...
June 21, 2018: Molecular Cancer
R A Bellmore, J E Compton, J R Brooks, E W Fox, R A Hill, D J Sobota, D J Thornbrugh, M H Weber
Ecological and human health impairments related to excess nitrogen (N) in streams and rivers remain widespread in the United States (U.S.) despite recent efforts to reduce N pollution. Many studies have quantified the relationship between N loads to streams in terms of N mass and N inputs to watersheds; however, N concentrations, rather than loads, are more closely related to impacts on human health and aquatic life. Additionally, concentrations, rather than loads, trigger regulatory responses. In this study, we examined how N concentrations are related to N inputs to watersheds (atmospheric deposition, synthetic fertilizer, manure applied to agricultural land, cultivated biological N fixation, and point sources), land cover characteristics, and stream network characteristics, including stream size and the extent of lakes and reservoirs...
October 15, 2018: Science of the Total Environment
Nancy Adriana Espinoza-Sánchez, Jennifer Enciso, Rosana Pelayo, Ezequiel M Fuentes-Pananá
Breast cancer is a complex disease exhibiting extensive inter- and intra-tumor heterogeneity. Inflammation is a well-known driver of cancer progression, often attributed to immune cells infiltrating the tumor stroma. However, tumor cells themselves are capable to secrete a variety of inflammatory molecules, of which we understand very little about their role in intra-clonal communication. We recently reported the capacity of triple negative cell lines to induce a cancer stem cell (CSC)-like phenotype and invasion properties into luminal cells, a mechanism mediated by pro-inflammatory cytokines that up-regulated the CXCL12/CXCR4/CXCR7 chemokine signaling axis...
June 1, 2018: Oncotarget
Weiqing Li, Xugang Zhang, Zhitian Li, Fusheng Jiang, Hongwei Zhao, Bo Wei
The aim of the present study was to identify genes with similar function to that of matrix metalloproteinases (MMPs) in invasive lung adenocarcinoma (AC) and to screen the transcription factors that regulate MMPs. The gene expression dataset GSE2514, including 20 invasive lung AC samples and 19 adjacent normal lung samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using the limma package in R. Genes with similar function to MMPs were identified by K-means clustering...
July 2018: Oncology Letters
Tania Islam, Rezanur Rahman, Esra Gov, Beste Turanli, Gizem Gulfidan, Anwarul Haque, Kazım Yalçın Arga, Nurul Haque Mollah
The head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world, but robust biomarkers and diagnostics are still not available. This study provides in-depth insights from systems biology analyses to identify molecular biomarker signatures to inform systematic drug targeting in HNSCC. Gene expression profiles from tumors and normal tissues of 22 patients with histological confirmation of nonmetastatic HNSCC were subjected to integrative analyses with genome-scale biomolecular networks (i...
June 2018: Omics: a Journal of Integrative Biology
Hai-Ping Zhao, Ping Liu, Chang-Min Xu, Guang-Wen Li, Li Gao, Yu-Min Luo
OBJECTIVE: To identify the differentially expressed microRNAs (miRNAs) profiles of yang and yin syndromes in patients with acute ischemic stroke, and to provide the molecular basis of the classififi cation of these two syndrome types in acute ischemic stroke patients. METHODS: A microarray assay was performed to assess the expression pattern of miRNAs in the lymphocyte of acute ischemic stroke patients. Target genes for the deregulated miRNAs were predicated using the online bioinformatic algorithms and functional annotation via Kyoto encyclopedia of genes and genomes pathway analysis for miRNAs predicted targets was carried out...
June 20, 2018: Chinese Journal of Integrative Medicine
Xiaojian Zhou, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinshen Liu, Yulan Zou, Zixia Liu, Feng Wen
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B...
June 20, 2018: Functional & Integrative Genomics
Thomas B Barton-Owen, David E K Ferrier, Ildikó M L Somorjai
The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates...
June 20, 2018: Scientific Reports
Chang Chen, Jian Gao, Tie-Shan Wang, Cong Guo, Yu-Jing Yan, Chao-Yi Mao, Li-Wei Gu, Yang Yang, Zhong-Feng Li, An Liu
Emodin is a natural anthraquinone derivative that is present in various herbal preparations. The pharmacological effects of emodin include anticancer, hepatoprotective, anti-inflammatory, antioxidant and even antimicrobial activities. However, emodin also has been reported to induce hepatotoxicity, nephrotoxicity, genotoxicity and reproductive toxicity. The mechanism of emodin's adverse effects is complicated and currently not well understood. This study aimed to establish a cell metabonomic method to investigate the toxicity of emodin and explore its potential mechanism and relevant targets...
June 20, 2018: Scientific Reports
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