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https://www.readbyqxmd.com/read/28736575/identification-of-bifurcation-transitions-in-biological-regulatory-networks-using-answer-set-programming
#1
Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé
BACKGROUND: Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject to different competing transitions, potentially leading the system to different attractors. This paper focusses on the formal identification of states and transitions that are crucial for preserving or pre-empting the reachability of a given behaviour. METHODS: In the context of non-deterministic automata networks, we propose a static identification of so-called bifurcations, i...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28733488/identification-of-optimal-strategies-for-state-transition-of-complex-biological-networks
#2
REVIEW
Meichen Yuan, Weirong Hong, Pu Li
Complex biological networks typically contain numerous parameters, and determining feasible strategies for state transition by parameter perturbation is not a trivial task. In the present study, based on dynamical and structural analyses of the biological network, we optimized strategies for controlling variables in a two-node gene regulatory network and a T-cell large granular lymphocyte signaling network associated with blood cancer by using an efficient dynamic optimization method. Optimization revealed the critical value for each decision variable to steer the system from an undesired state into a desired attractor...
July 21, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28733351/multi-cellular-transcriptional-analysis-of-mammalian-heart-regeneration
#3
Gregory A Quaife-Ryan, Choon Boon Sim, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Mirana Ramialison, Assam El-Osta, James E Hudson, Enzo R Porrello
Background -The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time...
July 21, 2017: Circulation
https://www.readbyqxmd.com/read/28733120/employing-decomposable-partially-observable-markov-decision-processes-to-control-gene-regulatory-networks
#4
Utku Erdogdu, Faruk Polat, Reda Alhajj
OBJECTIVE: Formulate the induction and control of gene regulatory networks (GRNs) from gene expression data using Partially Observable Markov Decision Processes (POMDPs). METHODS AND MATERIAL: Different approaches exist to model GRNs; they are mostly simulated as mathematical models that represent relationships between genes. Actually, it has been realized that biological functions at the cellular level are controlled by genes; thus, by controlling the behavior of genes, it is possible to regulate these biological functions...
July 18, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28731857/cytomcs-a-multiple-maximum-common-subgraph-detection-tool-for-cytoscape
#5
Simon J Larsen, Jan Baumbach
Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28729650/large-scale-analysis-of-drug-side-effects-via-complex-regulatory-modules-composed-of-micrornas-transcription-factors-and-gene-sets
#6
Xiaodong Jia, Qing Jin, Xiangqiong Liu, Xiusen Bian, Yunfeng Wang, Lei Liu, Hongzhe Ma, Fujian Tan, Mingliang Gu, Xiujie Chen
Identifying the occurrence mechanism of drug-induced side effects (SEs) is critical for design of drug target and new drug development. The expression of genes in biological processes is regulated by transcription factors(TFs) and/or microRNAs. Most of previous studies were focused on a single level of gene or gene sets, while studies about regulatory relationships of TFs, miRNAs and biological processes are very rare. Discovering the complex regulating relations among TFs, gene sets and miRNAs will be helpful for researchers to get a more comprehensive understanding about the mechanism of side reaction...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729025/following-micrornas-through-the-cancer-metastatic-cascade
#7
Eleonora Grisard, Milena S Nicoloso
Approximately a decade ago the first MicroRNAs (MiRNAs) participating in cancer metastasis were identified and metastmiRs were initially only a handful. Since those first reports, MiRNA research has explosively thrived, mainly due to their revolutionary mechanism of action and the hope of having at hand a novel tool to control cancer aggressiveness. This has ultimately led to delineate an almost impenetrable regulatory network: hundreds of MiRNAs transversally dominating every aspect of normal and cancer biology, each MiRNA having hundreds of targets and context-dependent activity...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28727484/construction-and-analysis-of-circular-rna-molecular-regulatory-networks-in-liver-cancer
#8
Shuangchun Ren, Zhuoyuan Xin, Yinyan Xu, Jianting Xu, Guoqing Wang
Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we employed a systems biology approach to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network...
July 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28727145/transcriptional-control-of-photosynthetic-capacity-conservation-and-divergence-from-arabidopsis-to-rice
#9
REVIEW
Peng Wang, Ross-William Hendron, Steven Kelly
1 I. 1 II. 2 III. 5 IV. 10 12 References 12 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression...
July 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#10
Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Repoila Francis, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis...
July 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723574/proteomic-analysis-of-the-human-tankyrase-protein-interaction-network-reveals-its-role-in-pexophagy
#11
Xu Li, Han Han, Mao-Tian Zhou, Bing Yang, Albert Paul Ta, Nan Li, Junjie Chen, Wenqi Wang
Tankyrase 1 (TNKS) and tankyrase 2 (TNKS2) belong to the poly(ADP-ribose) polymerase family of proteins, which use nicotinamide adenine dinucleotide to modify substrate proteins with ADP-ribose modifications. Emerging evidence has revealed the pathological relevance of TNKS and TNKS2, and identified these two enzymes as potential drug targets. However, the cellular functions and regulatory mechanisms of TNKS/2 are still largely unknown. Through a proteomic analysis, we defined the protein-protein interaction network for human TNKS/2 and revealed more than 100 high-confidence interacting proteins with numerous biological functions in this network...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28719625/differences-of-immune-disorders-between-alzheimer-s-disease-and-breast-cancer-based-on-transcriptional-regulation
#12
Wei Kong, Xiaoyang Mou, Jin Deng, Benteng Di, Ruxing Zhong, Shuaiqun Wang, Yang Yang, Weiming Zeng
Although chronic inflammation and immune disorders are of great importance to the pathogenesis of both dementia and cancer, the pathophysiological mechanisms are not clearly understood. In recent years, growing epidemiological evidence and meta-analysis data suggest an inverse association between Alzheimer's disease (AD), which is the most common form of dementia, and cancer. It has been revealed that some common genes and biological processes play opposite roles in AD and cancer; however, the biological immune mechanism for the inverse association is not clearly defined...
2017: PloS One
https://www.readbyqxmd.com/read/28714412/regulation-mechanism-of-micrornas-in-non-small-cell-lung-cancer
#13
Feng-Yun Gong, Tao Bai, Ding-Yu Zhang, Chao-Lin Huang, Jing Lv, Jing-Li Wang, Xu-Dong Hu, Juan Wang, Wei Liu
MicroRNAs are small non-coding RNAs with regulatory biological activity, by modulating target genes on epigenetic, transcriptional, post-transciptional and translational levels. Hundreds of reports indicated that miRNAs play important roles in non-small cell lung cancer (NSCLC). Actually, microRNAs are both regulation targets and regulators targeting effector genes. This article reviewed multifaceted role of microRNAs associated to NSCLC, not only targeting to but also targeted by tumor related genes, to help us understand microRNAs related complex regulation networks...
July 14, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28713898/identification-of-potential-biomarkers-and-therapeutic-targets-for-human-iga-nephropathy-and-hypertensive-nephropathy-by-bioinformatics-analysis
#14
Yingchun Cui, Shengmao Liu, Wenpeng Cui, Dan Gao, Wenhua Zhou, Ping Luo
In order to further elucidate the potential correlations and treatments of IgA nephropathy (IgAN) and hypertensive nephropathy (HT), bioinformatics analysis of IgAN and HT was performed. The mRNA expression profiles of human renal biopsy samples from patients with IgAN, patients with HT and pre‑transplant healthy living controls (LD) were downloaded from the Gene Expression Omnibus database. Then, the differentially expressed genes (DEGs) were identified and functions of DEGs were analyzed. Finally, the regulatory networks containing DEGs and related‑transcription factors (TFs) were constructed using Cytoscape software...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713244/regulatory-roles-of-long-non-coding-rnas-in-the-central-nervous-system-and-associated-neurodegenerative-diseases
#15
REVIEW
Zhenzhen Quan, Da Zheng, Hong Qing
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28710380/biological-analysis-of-cancer-specific-micrornas-on-function-modeling-in-osteosarcoma
#16
Hao Wang, Min Tang, Liping Ou, Mengyi Hou, Tianyu Feng, Yu-E Huang, Yaqian Jin, Heng Zhang, Guowei Zuo
Osteosarcoma (OS) is the most common bone tumor characterized with a high risk of amputation and malignant morbidity among teenagers and adolescents. However, relevant pathogenic/biological mechanisms underlying OS-genesis remains to be ambiguous. The aim of this study was to elucidate functional relationship about microRNAs-mRNAs networks and to identify potential molecular markers via a computational method. Gene expression profile (GSE70415) was recruited from Gene Expression Omnibus. 3856 differentially expressed genes and 250 significantly expressed microRNAs were identified by using GCBI...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710369/the-adipokine-leptin-modulates-adventitial-pericyte-functions-by-autocrine-and-paracrine-signalling
#17
Federica Riu, Sadie C Slater, Eva Jover Garcia, Iker Rodriguez-Arabaolaza, Valeria Alvino, Elisa Avolio, Giuseppe Mangialardi, Andrea Cordaro, Simon Satchell, Carlo Zebele, Andrea Caporali, Gianni Angelini, Paolo Madeddu
Transplantation of adventitial pericytes (APCs) improves recovery from tissue ischemia in preclinical animal models by still unknown mechanisms. This study investigates the role of the adipokine leptin (LEP) in the regulation of human APC biological functions. Transcriptomic analysis of APCs showed components of the LEP signalling pathway are modulated by hypoxia. Kinetic studies indicate cultured APCs release high amounts of immunoreactive LEP following exposure to hypoxia, continuing upon return to normoxia...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710010/local-network-component-analysis-for-quantifying-transcription-factor-activities
#18
Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu, Luonan Chen
Transcription factors (TFs) could regulate physiological transitions or determine stable phenotypic diversity. The accurate estimation on TF regulatory signals or functional activities is of great significance to guide biological experiments or elucidate molecular mechanisms, but still remains challenging. Traditional methods identify TF regulatory signals at the population level, which masks heterogeneous regulation mechanisms in individuals or subgroups, thus resulting in inaccurate analyses. Here, we propose a novel computational framework, namely Local Network Component Analysis (LNCA), to exploit data heterogeneity and automatically quantify accurate transcription factor activity (TFA) in practical terms, through integrating the partitioned expression sets (i...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28707296/ebp1-regulates-myogenic-differentiation-of-myoblast-cells-via-smad2-3-signaling-pathway
#19
Minli Yu, Huan Wang, Zhen Liu, Yinglin Lu, Debing Yu, Dongfeng Li, Wenxing Du
Regulation of skeletal muscle development requires many of the regulatory networks that are fundamental to developmental myogenesis. ErbB3 binding protein-1 (Ebp1) is involved in the control of myoblasts development in chicken. However, the expression and biological functions of Ebp1 in the progress of myogenesis are unclear. This study focused on determining the effect of Ebp1 on myogenic proliferation and differentiation using a primary myoblasts culture model. Ebp1 was found to upregulate in proliferating myoblasts and decrease at the early stage of myogenic differentiation...
July 13, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/28705115/microrna-21-versus-microrna-34-lung-cancer-promoting-and-inhibitory-micrornas-analysed-in-silico-and-in-vitro-and-their-clinical-impact
#20
Meik Kunz, Claudia Göttlich, Thorsten Walles, Sarah Nietzer, Gudrun Dandekar, Thomas Dandekar
MicroRNAs are well-known strong RNA regulators modulating whole functional units in complex signaling networks. Regarding clinical application, they have potential as biomarkers for prognosis, diagnosis, and therapy. In this review, we focus on two microRNAs centrally involved in lung cancer progression. MicroRNA-21 promotes and microRNA-34 inhibits cancer progression. We elucidate here involved pathways and imbed these antagonistic microRNAs in a network of interactions, stressing their cancer microRNA biology, followed by experimental and bioinformatics analysis of such microRNAs and their targets...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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