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Biological reaction network

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https://www.readbyqxmd.com/read/28719591/non-equilibrium-dissipative-supramolecular-materials-with-a-tunable-lifetime
#1
Marta Tena-Solsona, Benedikt Rieß, Raphael K Grötsch, Franziska C Löhrer, Caren Wanzke, Benjamin Käsdorf, Andreas R Bausch, Peter Müller-Buschbaum, Oliver Lieleg, Job Boekhoven
Many biological materials exist in non-equilibrium states driven by the irreversible consumption of high-energy molecules like ATP or GTP. These energy-dissipating structures are governed by kinetics and are thus endowed with unique properties including spatiotemporal control over their presence. Here we show man-made equivalents of materials driven by the consumption of high-energy molecules and explore their unique properties. A chemical reaction network converts dicarboxylates into metastable anhydrides driven by the irreversible consumption of carbodiimide fuels...
July 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28713985/microarray-expression-profiles-of-long-non-coding-rnas-in-germinal-center-like-diffuse-large-b-cell-lymphoma
#2
Hong-Yu Gao, Bin Wu, Wei Yan, Zi-Mu Gong, Qi Sun, Hui-Han Wang, Wei Yang
Long non-coding RNAs (lncRNAs) are continuously transcribed and are involved in various cellular activities. However, their contributions to the occurrence and development of germinal center B-cell (GCB)-like diffuse large B-cell lymphoma (DLBCL) remain largely unknown. We applied microarray technology to profile the expression of lncRNAs in two different GCB-DLBCL cell lines (OCI-ly1 and OCI-ly19) and normal B lymphocytes. We demonstrated that 21,539 lncRNAs were expressed in all of the samples analyzed...
July 14, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28713420/modeling-the-metabolism-of-arabidopsis-thaliana-application-of-network-decomposition-and-network-reduction-in-the-context-of-petri-nets
#3
Ina Koch, Joachim Nöthen, Enrico Schleiff
Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28712291/programming-cell-adhesion-for-on-chip-sequential-boolean-logic-functions
#4
Xiangmeng Qu, Shaopeng Wang, Zhilei Ge, Jianbang Wang, Guangbao Yao, Jiang Li, Xiaolei Zuo, Jiye Shi, Shiping Song, Lihua Wang, Li Li, Hao Pei, Chunhai Fan
Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in-vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely non-invasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28702565/identifying-the-common-genetic-networks-of-adr-adverse-drug-reaction-clusters-and-developing-an-adr-classification-model
#5
Youhyeon Hwang, Min Oh, Giup Jang, Taekeon Lee, Chihyun Park, Jaegyoon Ahn, Youngmi Yoon
Adverse drug reactions (ADRs) are one of the major concerns threatening public health and have resulted in failures in drug development. Thus, predicting ADRs and discovering the mechanisms underlying ADRs have become important tasks in pharmacovigilance. Identification of potential ADRs by computational approaches in the early stages would be advantageous in drug development. Here we propose a computational method that elucidates the action mechanisms of ADRs and predicts potential ADRs by utilizing ADR genes, drug features, and protein-protein interaction (PPI) networks...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28693282/identification-of-hub-genes-and-pathways-associated-with-bladder-cancer-based-on-co-expression-network-analysis
#6
Dong-Qing Zhang, Chang-Kuo Zhou, Shou-Zhen Chen, Yue Yang, Ben-Kang Shi
The aim of the present study was to identify hub genes and signaling pathways associated with bladder cancer (BC) utilizing centrality analysis and pathway enrichment analysis. The differentially expressed genes (DEGs) were screened from the ArrayExpress database between normal subjects and BC patients. Co-expression networks of BC were constructed using differentially co-expressed genes and links, and hub genes were investigated by degree centrality analysis of co-expression networks in BC. The enriched signaling pathways were investigated by Kyoto Encyclopedia of Genes and Genomes database analysis based on the DEGs...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28690829/a-simple-mathematical-approach-to-the-analysis-of-polypharmacology-and-polyspecificity-data
#7
Gerry Maggiora, Vijay Gokhale
There many possible types of drug-target interactions, because there are a surprising number of ways in which drugs and their targets can associate with one another.  These relationships are expressed as polypharmacology and polyspecificity.  Polypharmacology is the capability of a given drug to exhibit activity with respect to multiple drug targets, which are not necessarily in the same activity class. Adverse drug reactions ('side effects') are its principal manifestation, but polypharmacology is also playing a role in the repositioning of existing drugs for new therapeutic indications...
2017: F1000Research
https://www.readbyqxmd.com/read/28686462/a-logic-for-checking-the-probabilistic-steady-state-properties-of-reaction-networks
#8
Vincent Picard, Anne Siegel, Jérémie Bourdon
Designing probabilistic reaction models and determining their stochastic kinetic parameters are major issues in systems biology. To assist in the construction of reaction network models, we introduce a logic that allows one to express asymptotic properties about the steady-state stochastic dynamics of a reaction network. Basically, the formulas can express properties on expectancies, variances, and covariances. If a formula encoding for experimental observations on the system is not satisfiable, then the reaction network model can be rejected...
July 7, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28676416/noise-slows-the-rate-of-michaelis-menten-reactions
#9
J David Van Dyken
Microscopic randomness and the small volumes of living cells combine to generate random fluctuations in molecule concentrations called "noise". Here I investigate the effect of noise on biochemical reactions obeying Michaelis-Menten kinetics, concluding that substrate noise causes these reactions to slow. I derive a general expression for the time evolution of the joint probability density of chemical species in arbitrarily connected networks of non-linear chemical reactions in small volumes. This equation is a generalization of the chemical master equation (CME), a common tool for investigating stochastic chemical kinetics, extended to reaction networks occurring in small volumes, such as living cells...
July 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28676075/sgnesr-an-r-package-for-simulating-gene-expression-data-from-an-underlying-real-gene-network-structure-considering-delay-parameters
#10
Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
BACKGROUND: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles...
July 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28675379/non-steady-state-mass-action-dynamics-without-rate-constants-dynamics-of-coupled-reactions-using-chemical-potentials
#11
William Cannon, Scott Baker
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants...
July 4, 2017: Physical Biology
https://www.readbyqxmd.com/read/28671950/formal-reasoning-about-systems-biology-using-theorem-proving
#12
Adnan Rashid, Osman Hasan, Umair Siddique, Sofiène Tahar
System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of various diseases have been carried out by paper-and-pencil based proofs and simulations. However, these methods cannot provide an accurate analysis, which is a serious drawback for the safety-critical domain of human medicine. In order to overcome these limitations, we propose a framework to formally analyze biological networks and pathways...
2017: PloS One
https://www.readbyqxmd.com/read/28669884/determining-the-control-networks-regulating-stem-cell-lineages-in-colonic-crypts
#13
Jienian Yang, David E Axelrod, Natalia L Komarova
The question of stem cell control is at the center of our understanding of tissue functioning, both in healthy and cancerous conditions. It is well accepted that cellular fate decisions (such as divisions, differentiation, apoptosis) are orchestrated by a network of regulatory signals emitted by different cell populations in the lineage and the surrounding tissue. The exact regulatory network that governs stem cell lineages in a given tissue is usually unknown. Here we propose an algorithm to identify a set of candidate control networks that are compatible with (a) measured means and variances of cell populations in different compartments, (b) qualitative information on cell population dynamics, such as the existence of local controls and oscillatory reaction of the system to population size perturbations, and (c) statistics of correlations between cell numbers in different compartments...
June 29, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28656491/methods-of-model-reduction-for-large-scale-biological-systems-a-survey-of-current-methods-and-trends
#14
Thomas J Snowden, Piet H van der Graaf, Marcus J Tindall
Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity...
June 27, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28654912/identification-of-dysregulated-long-non-coding-rnas-micrornas-mrnas-in-tnm-i-stage-lung-adenocarcinoma
#15
Ziqiang Tian, Shiwang Wen, Yuefeng Zhang, Xinqiang Shi, Yonggang Zhu, Yanzhao Xu, Huilai Lv, Guiying Wang
Lung adenocarcinoma (LUAD) is the primary subtype in lung cancer, which is the leading cause of cancer-related death worldwide. This study aimed to investigate the aberrant expression profiling of long non-coding RNA (lncRNA) in TNM I stage (stage I) LUAD. The lncRNA/mRNA/miRNA expression profiling of stage I LUAD and adjacent non-tumor tissues from 4 patients were measured by RNA-sequencing. Total of 175 differentially expressed lncRNAs (DELs), 1321 differentially expressed mRNAs (DEMs) and 94 differentially expressed microRNAs (DEMIs) were identified in stage I LUAD...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28654904/digoxin-induced-anemia-among-patients-with-atrial-fibrillation-and-heart-failure-clinical-data-analysis-and-drug-gene-interaction-network
#16
Yubi Lin, Siqi He, Ruiling Feng, Zhe Xu, Wanqun Chen, Zifeng Huang, Yang Liu, Qianhuan Zhang, Bin Zhang, Kejian Wang, Shulin Wu
Digoxin is widely used to treat various heart conditions. In order to clarify the association between digoxin and anemia adverse reaction, we inspected case reports submitted to the FDA Adverse Event Reporting System (FAERS) between January 2004 and December 2015. These reports involved 75618 atrial fibrillation patients and 15699 heart failure patients. Compared to other therapies, digoxin treatment was significantly more likely to be concurrent with anemia adverse reaction among both atrial fibrillation patients (pooled OR = 1...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28654237/light-induced-proton-pumping-with-a-semiconductor-vision-for-photoproton-lateral-separation-and-robust-manipulation
#17
Hanna M Maltanava, Sergey K Poznyak, Daria V Andreeva, Marcela C Quevedo, Alexandre C Bastos, João Tedim, Mário G S Ferreira, Ekaterina V Skorb
Energy-transfer reactions are the key for living open systems, biological chemical networking, and the development of life-inspired nanoscale machineries. It is a challenge to find simple reliable synthetic chemical networks providing a localization of the time-dependent flux of matter. In this paper, we look to photocatalytic reaction on TiO2 from different angles, focusing on proton generation and introducing a reliable, minimal-reagent-consuming, stable inorganic light-promoted proton pump. Localized illumination was applied to a TiO2 surface in solution for reversible spatially controlled "inorganic photoproton" isometric cycling, the lateral separation of water-splitting reactions...
July 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#18
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
https://www.readbyqxmd.com/read/28640584/spectroscopic-evidence-for-a-h-bond-network-at-y356-located-at-the-subunit-interface-of-active-e-coli-ribonucleotide-reductase
#19
Thomas U Nick, Kanchana R Ravichandran, JoAnne Stubbe, Müge Kasanmascheff, Marina Bennati
The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y122·) cofactor that initiates radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y122· ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2). Experimental evidence exists for colinear and orthogonal PCET in α2 and β2, respectively...
July 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28628855/progress-in-programming-spatiotemporal-patterns-and-machine-assembly-in-cell-free-protein-expression-systems
#20
REVIEW
Alexandra M Tayar, Shirley S Daube, Roy H Bar-Ziv
Building biological systems outside the cell is an emerging interdisciplinary research field aimed to study design principles, and to emulate biological functions for technology. Reconstructing programmable cellular functions, from assembly of protein/nucleic-acid machines to spatially distributed systems, requires implementing minimal systems of molecular interactions encoded in genes, source-sink protein expression dynamics, and materials platforms for reaction-diffusion scenarios. Here, we first review how molecular turnover mechanisms, combined with nonlinear interactions and feedback in cell-free gene networks enable programmable dynamic expression patterns in various compartments...
June 16, 2017: Current Opinion in Chemical Biology
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