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Biological reaction network

Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
Emanuele Mauri, Alessandro Sacchetti, Filippo Rossi
The use of polymers as biomaterials has provided significant advantages in therapeutic applications. In particular, the possibility to modify and functionalize polymer chains with compounds that are able to improve biocompatibility, mechanical properties, or cell viability allows the design of novel materials to meet new challenges in the biomedical field. With the polymer functionalization strategies, click chemistry is a powerful tool to improve cell-compatibility and drug delivery properties of polymeric devices...
October 7, 2016: Journal of Visualized Experiments: JoVE
Gaspar Morgado, Daniel Gerngross, Tania M Roberts, Sven Panke
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity...
October 19, 2016: Advances in Biochemical Engineering/biotechnology
Laura Arroyo, Ricard Carreras, Daniel Valent, Raquel Peña, Eva Mainau, Antonio Velarde, Josefa Sabrià, Anna Bassols
Chemical neurotransmitters (NT) are principal actors in all neuronal networks of animals. The central nervous system plays an important role in stress susceptibility and organizes the response to a stressful situation through the interaction of the dopaminergic and the serotonergic pathways, leading to the activation of the hypothalamus-pituitary-adrenal axis (HPA). This study was designed to investigate: a) the effects of stressful handling of pigs at the slaughterhouse on the neurotransmitter profile in four brain areas: amygdala, prefrontal cortex (PFC), hippocampus and hypothalamus, and b) whether the alterations in the brain NT profile after stressful handling were associated with fear, determined by the tonic immobility (TI) test...
October 11, 2016: Physiology & Behavior
Matthew A Richards, Thomas J Lie, Juan Zhang, Stephen W Ragsdale, John A Leigh, Nathan D Price
: Hydrogenotrophic methanogenesis occurs in multiple environments ranging from the intestinal tracts of animals to anaerobic sediments and hot springs. Energy conservation in hydrogenotrophic methanogens was long a mystery; only within the last decade, it was reported that net energy conservation for growth depends on electron bifurcation. In this work we focus on Methanococcus maripaludis, a well-studied hydrogenotrophic marine methanogen. To better understand hydrogenotrophic methanogenesis and compare it with methylotrophic methanogenesis that utilizes oxidative phosphorylation rather than electron bifurcation, we have built iMR539, a genome scale metabolic reconstruction that accounts for 539 of the 1722 protein-coding genes of M...
October 10, 2016: Journal of Bacteriology
Elizabeth Gross, Brent Davis, Kenneth L Ho, Daniel J Bates, Heather A Harrington
Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation and model selection. These are all optimization problems, well known to be challenging due to nonlinearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data are available. Here, we consider polynomial models (e.g. mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry...
October 2016: Journal of the Royal Society, Interface
Atsushi Mochizuki
Modern biology has provided many examples of large networks describing the interactions between multiple species of bio-molecules. It is believed that the dynamics of molecular activities based on such networks are the origin of biological functions. On the other hand, we have a limited understanding for dynamics of molecular activity based on networks. To overcome this problem, we have developed two structural theories, by which the important aspects of the dynamical properties of the system are determined only from information on the network structure, without assuming other quantitative details...
2016: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
C Kohn, J M Klemens, C Kascholke, N S Murthy, J Kohn, M Brandenburger, M C Hacker
Toward a new generation of improved nerve guidance conduits (NGCs), novel biomaterials are required to address pressing clinical shortcomings in peripheral nerve regeneration (PNR) and to promote biological performance. A dual-component hydrogel system formed by cross-linking reaction between maleic anhydride groups in an oligomeric building block for cross-linking of free amine functionalities in partially hydrolyzed collagen is formulated for continuous processing and NGC fabrication. The influence of the gelation base is optimized for processing from a double syringe delivery system with a static mixer...
October 18, 2016: Biomaterials Science
Breland G Oscar, Weimin Liu, Nikita D Rozanov, Chong Fang
Proton transfer reactions are functionally important in numerous chemical and biological processes. To unravel proton scavengers in action with atomistic details, we studied excited-state proton transfer (ESPT) from photoacid pyranine to the weak base acetate in methanol using transient absorption and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). Proton transfer is inhibited in neat methanol, but coherent proton motions and the formation of a charge-separated state occur on the sub-picosecond (sub-ps) timescale, accompanied by chromophore solvation wherein the longitudinal relaxation time of methanol (∼9 ps) dominates...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Ying Huang, Meng-Yao Li, Peng Wu, Zhi-Sheng Xu, Feng Que, Feng Wang, Ai-Sheng Xiong
BACKGROUND: Transmitted by the whitefly Bemisia tabaci, tomato yellow leaf curly virus (TYLCV) has posed serious threats to plant growth and development. Plant innate immune systems against various threats involve WRKY Group III transcription factors (TFs). This group participates as a major component of biological processes in plants. RESULTS: In this study, 6 WRKY Group III TFs (SolyWRKY41, SolyWRKY42, SolyWRKY53, SolyWRKY54, SolyWRKY80, and SolyWRKY81) were identified, and these TFs responded to TYLCV infection...
October 7, 2016: BMC Genomics
Rebecca B Price, Stephanie Lane, Kathleen Gates, Thomas E Kraynak, Michelle S Horner, Michael E Thase, Greg J Siegle
BACKGROUND: There is well-known heterogeneity in affective mechanisms in depression that may extend to positive affect. We used data-driven parsing of neural connectivity to reveal subgroups present across depressed and healthy individuals during positive processing, informing targets for mechanistic intervention. METHODS: Ninety-two individuals (68 depressed patients, 24 never-depressed control subjects) completed a sustained positive mood induction during functional magnetic resonance imaging...
July 5, 2016: Biological Psychiatry
X Qiao, J H Wu, R B Wu, R Su, C Li, Y J Zhang, R J Wang, Y H Zhao, Y X Fan, W G Zhang, J Q Li
The mammalian hair follicle (HF) is a unique, highly regenerative organ with a distinct developmental cycle. Cashmere goat (Capra hircus) HFs can be divided into two categories based on structure and development time: primary and secondary follicles. To identify differentially expressed genes (DEGs) in the primary and secondary HFs of cashmere goats, the RNA sequencing of six individuals from Arbas, Inner Mongolia, was performed. A total of 617 DEGs were identified; 297 were upregulated while 320 were downregulated...
September 2, 2016: Genetics and Molecular Research: GMR
Z Z Liu, S T Cui, B Tang, Z Z Wang, Z X Luan
The aim of this study was to screen for key biomarkers of osteosarcoma (OS) by tracking altered modules. Protein-protein interaction (PPI) networks of OS and normal groups were constructed and re-weighted using the Pearson correlation coefficient (PCC), respectively. The condition-specific modules were explored from OS and normal PPI networks using a clique-merging algorithm. Altered modules were identified by a maximum weight bipartite-matching method. The important biological pathways in OS were identified by a pathway-enrichment analysis using genes from disrupted modules...
August 26, 2016: Genetics and Molecular Research: GMR
Jianting Xu, Changyong E, Yongfang Yao, Shuangchun Ren, Guoqing Wang, Haofan Jin
Gastric cancer (GC) is one of the most common types of cancer of the digestive tract. Invasion of tumor cells into surrounding tissue and metastasis are among the most significant checkpoints in tumor progression. It is known that matrix metalloproteinases (MMPs) are involved in these processes; however, knowledge of their molecular interaction networks is still limited. Investigation of these networks could provide a more comprehensive picture of the function of MMPs in tumorigenesis. Furthermore, it could be used to develop new approaches to targeted anticancer therapy...
October 2016: Oncology Letters
A Ronca, S Ronca, G Forte, S Zeppetelli, A Gloria, R De Santis, L Ambrosio
A vinyl-terminated Polycaprolactone has been developed for tissue engineering applications using a one-step synthesis and functionalization method based on Ring Opening Polymerization (ROP) of ԑ-caprolactone, with Hydroxyl Ethyl Vinyl Ether (HEVE) acting both as the initiator of ROP and as photo-curable functional group. The proposed method employs a catalyst based on Al, instead of the most popular Tin(II) 2-ethylhexanoate, to reduce the cytotoxicity. Following the synthesis of the vinyl-terminated polycaprolactone, its reaction with Fumaryl Chloride (FuCl) results in a divinyl-fumarate polycaprolactone (VPCLF)...
September 30, 2016: Journal of Tissue Engineering and Regenerative Medicine
Jianxia Cui, Laurel J Ng, Vladislav Volman
Mild traumatic brain injury (mTBI) often results in neurobehavioral aberrations such as impaired attention and increased reaction time. Diffusion imaging and post mortem analysis studies suggest that mTBI primarily affects myelinated axons in white matter tracts. In particular, corpus callosum, mediating inter-hemispheric information exchange, has been shown to be affected in mTBI. Yet little is known about the mechanisms linking the injury of myelinated callosal axons to the neurobehavioral sequelae of mTBI...
September 28, 2016: Journal of Neurophysiology
Sergey N Semenov, Lewis J Kraft, Alar Ainla, Mengxia Zhao, Mostafa Baghbanzadeh, Victoria E Campbell, Kyungtae Kang, Jerome M Fox, George M Whitesides
Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood...
2016: Nature
Ricardo Andrade, Martin Wannagat, Cecilia C Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V Milreu, Leen Stougie, Marie-France Sagot
BACKGROUND: What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux...
2016: Algorithms for Molecular Biology: AMB
Christoph Hold, Sonja Billerbeck, Sven Panke
Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design...
2016: Nature Communications
Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen
MOTIVATION: Gap filling for the reconstruction of metabolic networks is to restore the connectivity of metabolites via finding high-confidence reactions that could be missed in target organism. Current methods for gap filling either fall into the network topology or have limited capability in finding missing reactions that are indirectly related to dead-end metabolites but of biological importance to the target model. RESULTS: We present an automated dead-end filling (DEF) approach, which is derived from the wisdom of endosymbiosis theory, to fill gaps by finding the most efficient dead-end utilization paths in a constructed quasi-endosymbiosis model...
September 26, 2016: Bioinformatics
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