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https://www.readbyqxmd.com/read/29779865/gmf-as-an-actin-network-remodeling-factor
#1
REVIEW
Bruce L Goode, Meredith O Sweeney, Julian A Eskin
Glia maturation factor (GMF) has recently been established as a regulator of the actin cytoskeleton with a unique role in remodeling actin network architecture. Conserved from yeast to mammals, GMF is one of five members of the ADF-H family of actin regulatory proteins, which includes ADF/cofilin, Abp1/Drebrin, Twinfilin, and Coactosin. GMF does not bind actin, but instead binds the Arp2/3 complex with high affinity. Through this association, GMF catalyzes the debranching of actin filament networks and inhibits actin nucleation by Arp2/3 complex...
May 18, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29777200/a-map-of-the-pgc-1%C3%AE-and-nt-pgc-1%C3%AE-regulated-transcriptional-network-in-brown-adipose-tissue
#2
Ji Suk Chang, Sujoy Ghosh, Susan Newman, J Michael Salbaum
Transcriptional coactivator PGC-1α and its splice variant NT-PGC-1α play crucial roles in regulating cold-induced thermogenesis in brown adipose tissue (BAT). PGC-1α and NT-PGC-1α are highly induced by cold in BAT and subsequently bind to and coactivate many transcription factors to regulate expression of genes involved in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis. To identify the complete repertoire of PGC-1α and NT-PGC-1α target genes in BAT, we analyzed genome-wide DNA-binding and gene expression profiles...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29775459/on-the-role-of-sparseness-in-the-evolution-of-modularity-in-gene-regulatory-networks
#3
Carlos Espinosa-Soto
Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology...
May 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29769331/temporal-transcriptional-logic-of-dynamic-regulatory-networks-underlying-nitrogen-signaling-and-use-in-plants
#4
Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D Brooks, Angelo V Pasquino, Sophie Léran, Shipra Mittal, Tara M Rock, Molly B Edwards, Grace J Kim, Sandrine Ruffel, W Richard McCombie, Dennis Shasha, Gloria M Coruzzi
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our "just-in-time" analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to "prune" the network to 155 TFs and 608 targets...
May 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29768444/ensemble-methods-for-stochastic-networks-with-special-reference-to-the-biological-clock-of-neurospora-crassa
#5
C Caranica, A Al-Omari, Z Deng, J Griffith, R Nilsen, L Mao, J Arnold, H-B Schüttler
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data...
2018: PloS One
https://www.readbyqxmd.com/read/29765519/long-noncoding-rnas-are-associated-with-metabolic-and-cellular-processes-in-the-jejunum-mucosa-of-pre-weaning-calves-in-response-to-different-diets
#6
Rosemarie Weikard, Frieder Hadlich, Harald M Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel, Christa Kuehn
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764727/the-spring-of-systems-biology-driven-breeding
#7
REVIEW
Jérémy Lavarenne, Soazig Guyomarc'h, Christophe Sallaud, Pascal Gantet, Mikaël Lucas
Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network...
May 12, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29764374/direct-measurement-of-pervasive-weak-repression-by-micrornas-and-their-role-at-the-network-level
#8
Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E Zhang, Chung-I Wu
BACKGROUND: A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. RESULTS: To measure miRNA repression directly, we inhibited transcript synthesis in Drosophila larvae and collected time-course data on mRNA abundance, the decline of which reflects transcript degradation...
May 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29761430/gas-chromatography-mass-spectrometry-based-13-c-labeling-studies-in-plant-metabolomics
#9
Valéria F Lima, Leonardo Perez de Souza, Thomas C R Williams, Alisdair R Fernie, Danilo M Daloso
Stable-isotope labeling analysis has been used to discover new metabolic pathways and their key regulatory points in a wide range of organisms. Given the complexity of the plant metabolic network, this analysis provides information complementary to that obtained from metabolite profiling that can be used to understand how plants cope with adverse conditions, and how metabolism varies between different cells, tissues, and organs. Here we describe the experimental procedures from sample harvesting and extraction to mass spectral analysis and interpretation that allow the researcher to perform 13 C-labeling experiments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761061/transcriptomic-studies-reveal-a-key-metabolic-pathway-contributing-to-a-well-maintained-photosynthetic-system-under-drought-stress-in-foxtail-millet-setaria-italica-l
#10
Weiping Shi, Jingye Cheng, Xiaojie Wen, Jixiang Wang, Guanyan Shi, Jiayan Yao, Liyuan Hou, Qian Sun, Peng Xiang, Xiangyang Yuan, Shuqi Dong, Pingyi Guo, Jie Guo
Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet ( Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents...
2018: PeerJ
https://www.readbyqxmd.com/read/29760686/the-transcriptional-regulator-tfb-rf1-activates-transcription-of-a-putative-abc-transporter-in-pyrococcus-furiosus
#11
Robert Reichelt, Katharina M A Ruperti, Martina Kreuzer, Stefan Dexl, Michael Thomm, Winfried Hausner
Transcription factor B recruiting factor 1 (TFB-RF1; PF1088) is a transcription regulator which activates transcription on archaeal promoters containing weak TFB recognition elements (BRE) by recruiting TFB to the promoter. The mechanism of activation is described in detail, but nothing is known about the biological function of this protein in Pyrococcus furiosus . The protein is located in an operon structure together with the hypothetical gene pf1089 and western blot as well as end-point RT-PCR experiments revealed an extremely low expression rate of both proteins...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29760609/identification-of-potential-crucial-genes-and-construction-of-microrna-mrna-negative-regulatory-networks-in-osteosarcoma
#12
Yue Pan, Lingyun Lu, Junquan Chen, Yong Zhong, Zhehao Dai
Background: This study aimed to identify potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma by comprehensive bioinformatics analysis. Methods: Data of gene expression profiles (GSE28424) and miRNA expression profiles (GSE28423) were downloaded from GEO database. The differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by R Bioconductor packages. Functional and enrichment analyses of selected genes were performed using DAVID database...
2018: Hereditas
https://www.readbyqxmd.com/read/29760555/comprehensive-analysis-of-a-long-noncoding-rna-associated-competing-endogenous-rna-network-in-colorectal-cancer
#13
Qiaowei Fan, Bingrong Liu
Purpose: This study was aimed to develop a lncRNA-associated competing endogenous RNA (ceRNA) network to provide further understanding of the ceRNA regulatory mechanism and pathogenesis in colorectal cancer (CRC). Patients and methods: Expression profiles of mRNAs, lncRNAs, and miRNAs, and clinical information for CRC patients were obtained from The Cancer Genome Atlas. The differentially expressed mRNAs, lncRNAs, and miRNAs (referred to as "DEmRNAs", "DElncRNAs", and "DEmiRNAs", respectively) were screened out between 539 CRC samples and 11 normal samples...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29760208/rpon-dependent-direct-regulation-of-quorum-sensing-and-the-type-vi-secretion-system-in-pseudomonas-aeruginosa-pao1
#14
Xiaolong Shao, Xiaoning Zhang, Yingchao Zhang, Miao Zhu, Pan Yang, Jian Yuan, Yingpeng Xie, Tianhong Zhou, Wei Wang, Sheng Chen, Haihua Liang, Xin Deng
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, particularly those with cystic fibrosis. As a global regulator, RpoN controls a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa To further gain insights into the direct targets of RpoN in vivo , the present study focused on identifying the direct targets of RpoN regulation in QS and the type VI secretion system (T6SS). We performed a chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) assay that identified 1,068 binding sites of RpoN, mostly including metabolic genes, a group of genes in QS ( lasI , rhlI and pqsR ) and the T6SS ( hcpA and hcpB )...
May 14, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29759817/enhancer-logic-and-mechanics-in-development-and-disease
#15
REVIEW
Ryan Rickels, Ali Shilatifard
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health...
May 11, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29759552/the-emerging-co-regulatory-role-of-long-noncoding-rnas-in-epithelial-mesenchymal-transition-and-the-warburg-effect-in-aggressive-tumors
#16
REVIEW
Qian Hua, Baoming Mi, Gang Huang
Malignant tumor cells have several unique characteristics, and their ability to undergo epithelial-mesenchymal transition (EMT) is a molecular gateway to invasive behavior. Rapid proliferation and increased invasiveness during EMT enhance aberrant glucose metabolism in tumor cells. Meanwhile, aerobic glycolysis provides energy, biosynthesis precursors, and an appropriate microenvironment to facilitate EMT. Reciprocal crosstalk between the processes synergistically contributes to malignant cancer behaviors, but the regulatory mechanisms underlying this interaction remain unclear...
June 2018: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29758769/modulation-of-dynamic-modes-by-interplay-between-positive-and-negative-feedback-loops-in-gene-regulatory-networks
#17
Liu-Suo Wang, Ning-Xi Li, Jing-Jia Chen, Xiao-Peng Zhang, Feng Liu, Wei Wang
A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758668/gene-regulatory-and-signaling-networks-exhibit-distinct-topological-distributions-of-motifs
#18
Gustavo Rodrigues Ferreira, Helder Imoto Nakaya, Luciano da Fontoura Costa
The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29755323/environmental-enrichment-prevents-transcriptional-disturbances-induced-by-alpha-synuclein-overexpression
#19
Zinah Wassouf, Thomas Hentrich, Sebastian Samer, Carola Rotermund, Philipp J Kahle, Ingrid Ehrlich, Olaf Riess, Nicolas Casadei, Julia M Schulze-Hentrich
Onset and progression of neurodegenerative disorders, including synucleinopathies such as Parkinson's disease, have been associated with various environmental factors. A highly compelling association from a therapeutic point of view has been found between a physically active lifestyle and a significantly reduced risk for Parkinson's disease. Mimicking such conditions in animal models by promoting physical activity, social interactions, and novel surroundings yields in a so-called enriched environment known to enhance adult neurogenesis, increase synaptic plasticity, and decelerate neuronal loss...
2018: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29755291/transcription-factor-co-expression-networks-of-adipose-rna-seq-data-reveal-regulatory-mechanisms-of-obesity
#20
Ruta Skinkyte-Juskiene, Lisette J A Kogelman, Haja N Kadarmideen
Background: Transcription Factors (TFs) control actuation of genes in the genome and are key mediators of complex processes such as obesity. Master Regulators (MRs) are the genes at the top of a regulation hierarchy which regulate other genes. Objective: To elucidate clusters of highly co-expressed TFs (modules), involved pathways, highly inter-connected TFs (hub-TFs) and MRs leading to obesity and leanness, using porcine model for human obesity. Methods: We identified 817 expressed TFs in RNA-Sequencing dataset representing extreme degrees of obesity (DO; lean, obese)...
May 2018: Current Genomics
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