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Biological reaction network

Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
Jie Wang, Hao-Long Zeng, Hongying Du, Zeyuan Liu, Ji Cheng, Taotao Liu, Ting Hu, Ghulam Mustafa Kamal, Xihai Li, Huili Liu, Fuqiang Xu
Metabolomics generate a profile of small molecules from cellular/tissue metabolism, which could directly reflect the mechanisms of complex networks of biochemical reactions. Traditional metabolomics methods, such as OPLS-DA, PLS-DA are mainly used for binary class discrimination. Multiple groups are always involved in the biological system, especially for brain research. Multiple brain regions are involved in the neuronal study of brain metabolic dysfunctions such as alcoholism, Alzheimer's disease, etc. In the current study, 10 different brain regions were utilized for comparative studies between alcohol preferring and non-preferring rats, male and female rats respectively...
March 1, 2018: Talanta
S Jimena Mora, Emmanuel Odella, Gary F Moore, Devens Gust, Thomas A Moore, Ana L Moore
Artificial photosynthetic constructs can in principle operate more efficiently than natural photosynthesis because they can be rationally designed to optimize solar energy conversion for meeting human demands rather than the multiple needs of an organism competing for growth and reproduction in a complex ecosystem. The artificial photosynthetic constructs described in this Account consist primarily of covalently linked synthetic chromophores, electron donors and acceptors, and proton donors and acceptors that carry out the light absorption, electron transfer, and proton-coupled electron transfer (PCET) processes characteristic of photosynthetic cells...
January 8, 2018: Accounts of Chemical Research
Ping Ouyang, Bode Lin, Jinlin Du, Haiyan Pan, Haibing Yu, Rongwei He, Zhigang Huang
Our preview studies showed TPI gene which encodes the Triosephosphate isomerase was overexpressed in human gastric cancer (GC) tissues. However, the potential molecular mechanisms how TPI influences the GC development is not clear. Here, we performed global gene expression profiling for TPI knockdown using microarrays in human GC cell line MGC-803 cells. The differentially expressed genes (DEGs) were identified using reverse transcription-quantitative polymerase chain reaction analysis. Then the DEGs were analyzed by an online software WebGestalt to perform the functional analysis, pathway analysis and network analysis...
January 4, 2018: Gene
Wei-Guo Ma, Jie Wang, Xiang-Wei Bu, Hong-Hong Zhang, Jian-Ping Zhang, Xiao-Xu Zhang, Yu-Xi He, Da-Li Wang, Zheng-Ju Zhang, Feng-Xian Meng
OBJECTIVE: To observe the effects of Polygonum cuspidatum (PC) on adenosine 5'-monophosphateactivated protein kinase (AMPK), forkhead box O3α (FOXO3α), Toll-like receptor-4 (TLR4), NACHT, LRR and PYD domains-containing protein 3 (NLRP3), and monocyte chemoattractant protein-1 (MCP-1) expression in a rat model of uric acid-induced renal damage and to determine the molecular mechanism. METHODS: A rat model of uric acid-induced renal damage was established, and rats were randomly divided into a model group, a positive drug group, and high-, medium-, and low-dose Chinese medicine (CM) PC groups (n=12 per group)...
December 28, 2017: Chinese Journal of Integrative Medicine
Ilmo E Hassinen
SIGNIFICANCE: NAD+ and NADP+ are important co-substrates in redox reactions and participate in regulatory networks operating in adjustment of metabolic pathways. Moreover, NAD+ is a co-substrate in post-translational modification of proteins and is involved in DNA repair. NADPH is indispensable for reductive syntheses and the redox chemistry involved in attaining and maintaining correct protein conformation. Recent Advances: Within a pair of decades, a wealth of information has been gathered on NAD(H)+/NADP(H) redox imaging, regulatory role of redox potential in assembly of spatial protein structures and the role of ADP-ribosylation of regulatory proteins affecting both gene expression and metabolism...
December 28, 2017: Antioxidants & Redox Signaling
Antonio González-Sánchez, Ciro A Cubillas, Fabiola Miranda, Araceli Dávalos, Alejandro García-de Los Santos
Copper (Cu) is an essential micronutrient for all aerobic forms of life. Its oxidation states (Cu+ /Cu2+ ) make this metal an important cofactor of enzymes catalyzing redox reactions in essential biological processes. In gram-negative bacteria, Cu uptake is an unexplored component of a finely regulated trafficking network, mediated by protein-protein interactions that deliver Cu to target proteins and efflux surplus metal to avoid toxicity. Rhizobium etliCFN42 is a facultative symbiotic diazotroph that must ensure its appropriate Cu supply for living either free in the soil or as an intracellular symbiont of leguminous plants...
December 27, 2017: MicrobiologyOpen
Adugna Abdi Woldesemayat, Peter Van Heusden, Bongani K Ndimba, Alan Christoffels
BACKGROUND: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait...
December 22, 2017: BMC Genetics
Ting Wang, Petr Plecháč
Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks...
December 21, 2017: Journal of Chemical Physics
Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek, Kourosh Zarringhalam
BACKGROUND: Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers...
December 19, 2017: BMC Bioinformatics
Edmund Kozieł, Józef J Bujarski, Katarzyna Otulak
Prune dwarf virus (PDV) is one of the members of Bromoviridae family, genus Ilarvirus. Host components that participate in the regulation of viral replication or cell-to-cell movement via plasmodesmata are still unknown. In contrast, viral infections caused by some other Bromoviridae members are well characterized. Bromoviridae can be distinguished based on localization of their replication process in infected cells, cell-to-cell movement mechanisms, and plant-specific response reactions. Depending upon the genus, "genome activation" and viral replication are linked to various membranous structures ranging from endoplasmic reticulum, to tonoplast...
December 16, 2017: International Journal of Molecular Sciences
Lin Jin, Yuanyuan Li, Xinrong Zhou, Huiping Yuan
The aim of the present study was to reveal the role of long noncoding RNAs (lncRNAs) in the regulation of the pathogenesis of optineurin (OPTN)-silenced cells. The microarray data set GSE12452 was re-annotated using the non-coding RNA function annotation server to identify differentially expressed lncRNAs. Weighted correlation network analysis was used to construct an lncRNA-lncRNA co-expression network and identify co-expression modules. Three OPTN small interfering RNAs (siRNAs) were transiently transfected into HeLa cells...
February 2018: International Journal of Molecular Medicine
Josep M Ribó, David Hochberg, Joaquim Crusats, Zoubir El-Hachemi, Albert Moyano
Recent reports on both theoretical simulations and on the physical chemistry basis of spontaneous mirror symmetry breaking (SMSB), that is, asymmetric synthesis in the absence of any chiral polarizations other than those arising from the chiral recognition between enantiomers, strongly suggest that the same nonlinear dynamics acting during the crucial stages of abiotic chemical evolution leading to the formation and selection of instructed polymers and replicators, would have led to the homochirality of instructed polymers...
December 2017: Journal of the Royal Society, Interface
Zixiang Xu, Jibin Sun, Qiaqing Wu, Dunming Zhu
Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry...
December 11, 2017: Scientific Reports
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
Thao N D Pham, Bethany E Perez White, Huiping Zhao, Fariborz Mortazavi, Debra A Tonetti
BACKGROUND: Despite recent advances in the diagnosis and treatment of breast cancer, metastasis remains the main cause of death. Since migration of tumor cells is considered a prerequisite for tumor cell invasion and metastasis, a pressing goal in tumor biology has been to elucidate factors regulating their migratory activity. Protein kinase C alpha (PKCα) is a serine-threonine protein kinase implicated in cancer metastasis and associated with poor prognosis in breast cancer patients...
December 7, 2017: BMC Cancer
Gilles Gnacadja
Pharmacology, the study of interactions between biological processes and therapeutic agents, is traditionally presented as consisting of two subdisciplines: pharmacokinetics, which is about the distribution and metabolism of drugs in organisms, and pharmacodynamics, which is about the organisms' response to drugs. In discovery-stage pharmacology however, one primary concern is what we call pharmacostatics, the characterization of equilibrium parameters and states of core interactions of physiologic and therapeutic interest...
December 6, 2017: Bulletin of Mathematical Biology
Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Miguel A Rodríguez, Suvi Aivio, Travis H Stracker, Oscar Yanes, Alexandre Perera-Lluna
Metabolomics experiments identify metabolites whose abundance varies as the conditions under study change. Pathway enrichment tools help in the identification of key metabolic processes and in building a plausible biological explanation for these variations. Although several methods are available for pathway enrichment using experimental evidence, metabolomics does not yet have a comprehensive overview in a network layout at multiple molecular levels. We propose a novel pathway enrichment procedure for analysing summary metabolomics data based on sub-network analysis in a graph representation of a reference database...
2017: PloS One
Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F Sbalzarini
Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation of the most efficient partial-propensity methods for simulating exact stochastic chemical kinetics. pSSAlib can import models encoded in Systems Biology Markup Language, supports time delays in chemical reactions, and stochastic spatiotemporal reaction-diffusion systems. It also provides tools for statistical analysis of simulation results and supports multiple output formats...
December 4, 2017: PLoS Computational Biology
C T Watson, A T Cohain, R S Griffin, Y Chun, A Grishin, H Hacyznska, G E Hoffman, N D Beckmann, H Shah, P Dawson, A Henning, R Wood, A W Burks, S M Jones, D Y M Leung, S Sicherer, H A Sampson, A J Sharp, E E Schadt, S Bunyavanich
Mechanisms driving acute food allergic reactions have not been fully characterized. We profile the dynamic transcriptome of acute peanut allergic reactions using serial peripheral blood samples obtained from 19 children before, during, and after randomized, double-blind, placebo-controlled oral challenges to peanut. We identify genes with changes in expression triggered by peanut, but not placebo, during acute peanut allergic reactions. Network analysis reveals that these genes comprise coexpression networks for acute-phase response and pro-inflammatory processes...
December 5, 2017: Nature Communications
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