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Biological reaction network

Florian Böhrnsen, Henning Schliephake
Sites of implantation with compromised biology may be unable to achieve the required level of angiogenic and osteogenic regeneration. The specific function and contribution of different cell types to the formation of prevascularized, osteogenic networks in co-culture remains unclear. To determine how bone marrow-derived mesenchymal stromal cells (BMSCs) and endothelial cells (ECs) contribute to cellular proangiogenic differentiation, we analysed the differentiation of BMSCs and ECs in standardized monolayer, Transwell and co-cultures...
December 2, 2016: International Journal of Oral Science
Noushin Hadadi, Jasmin Hafner, Keng Cher Soh, Vassily Hatzimanikatis
Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great importance as it can deconvolute the overlapping catabolic/anabolic pathways resulting in the observed metabolic phenotype. The automated identification of atom transitions within a metabolic network is a very challenging task since the degree of complexity of metabolic networks dramatically increases when we transit from metabolite-level studies to atom-level studies...
November 29, 2016: Biotechnology Journal
Gil Speyer, Divya Mahendra, Hai J Tran, Jeff Kiefer, Stuart L Schreiber, Paul A Clemons, Harshil Dhruv, Michael Berens, Seungchan Kim
The effort to personalize treatment plans for cancer patients involves the identification of drug treatments that can effectively target the disease while minimizing the likelihood of adverse reactions. In this study, the gene-expression profile of 810 cancer cell lines and their response data to 368 small molecules from the Cancer Therapeutics Research Portal (CTRP) are analyzed to identify pathways with significant rewiring between genes, or differential gene dependency, between sensitive and non-sensitive cell lines...
2016: Pacific Symposium on Biocomputing
Robert W Smith, Britta Helwig, Adrie H Westphal, Eran Pel, Maximilian Hörner, Hannes M Beyer, Sophia L Samodelov, Wilfried Weber, Matias D Zurbriggen, Jan Willem Borst, Christian Fleck
BACKGROUND: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states...
November 25, 2016: BMC Systems Biology
Tommaso Pellegatta, Marco Saler, Viola Bonfanti, Giovanni Nicoletti, Angela Faga
Plastic surgery is transitioning from a fine craftsmanship to a regenerative science. In wound healing, the role of microorganisms is no longer considered to be just counteracting, but also promoting. Furthermore, host-microbe interactions are essential for numerous aspects of normal mammalian physiology, from metabolic activity to immune homeostasis. Each area of the human body hosts a unique microbial community, and the composition of microbiota is dependent on the host, age and the anatomical area, and it changes according to the characteristics of the microenvironment...
November 2016: Biomedical Reports
Ivan Kondofersky, Fabian J Theis, Christiane Fuchs
In systems biology, one is often interested in the communication patterns between several species, such as genes, enzymes or proteins. These patterns become more recognisable when temporal experiments are performed. This temporal communication can be structured by reaction networks such as gene regulatory networks or signalling pathways. Mathematical modelling of data arising from such networks can reveal important details, thus helping to understand the studied system. In many cases, however, corresponding models still deviate from the observed data...
December 2016: IET Systems Biology
Insiya Fidai, Christine Wachnowsky, J A Cowan
Ferredoxins are protein mediators of biological electron-transfer reactions and typically contain either [2Fe-2S] or [4Fe-4S] clusters. Two ferredoxin homologues have been identified in the human genome, Fdx1 and Fdx2, that share 43% identity and 69% similarity in protein sequence and both bind [2Fe-2S] clusters. Despite the high similarity, the two ferredoxins play very specific roles in distinct physiological pathways and cannot replace each other in function. Both eukaryotic and prokaryotic ferredoxins and homologues have been reported to receive their Fe-S cluster from scaffold/delivery proteins such as IscU, Isa, glutaredoxins, and Nfu...
November 23, 2016: Metallomics: Integrated Biometal Science
Sean Coffey, Michael J A Williams, L Vicky Phillips, Ivor F Galvin, Richard W Bunton, Gregory T Jones
Aortic valve stenosis (AS) is a major cause of morbidity and mortality, with no effective medical therapies. Investigation into the underlying biology of AS in humans is limited by difficulties in obtaining healthy valvular tissue for use as a control group. However, micro-ribonucleic acids (miRNAs) are stable in post-mortem tissue. We compared valve specimens from patients undergoing aortic valve replacement for AS to non-diseased cadaveric valves. We found 106 differentially expressed miRNAs (p < 0...
November 23, 2016: Scientific Reports
Mathias Foo, Rucha Sawlekar, Declan G Bates
BACKGROUND: Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours - ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic. RESULTS: In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry...
2016: Journal of Biological Engineering
Gioia Della Giustina, Stefano Giulitti, Laura Brigo, Michele Zanatta, Maximilian Tromayer, Robert Liska, Nicola Elvassore, Giovanna Brusatin
In this work, an engineered hydrogel system with a 2D and 3D tunable cross-linking degree is presented. A precise chemical design by the introduction of cross-linkable units, having reaction orthogonality, allows to control the network formation both in time and space and to selectively alter the hydrogel physical properties. Hydrogel chemistry has been tailored in order to produce spatially controlled stiffness changes and drive cell morphology through mechanical cues. Elastic modulus rises by more than double after photocross-linking, as shown by atomic force microscopy measurements...
November 17, 2016: Macromolecular Rapid Communications
Christian Cuba Samaniego, Giulia Giordano, Franco Blanchini, Elisa Franco
Oscillators are essential to fuel autonomous behaviours in molecular systems. Artificial oscillators built with programmable biological molecules such as DNA and RNA are generally easy to build and tune, and can serve as timers for biological computation and regulation. We describe a new artificial nucleic acid biochemical reaction network, and we demonstrate its capacity to exhibit oscillatory solutions. This network can be built in vitro using nucleic acids and three bacteriophage enzymes, and has the potential to be implemented in cells...
December 2017: Journal of Biological Dynamics
Peng Su, Shiwang Wen, Yuefeng Zhang, Yong Li, Yanzhao Xu, Yonggang Zhu, Huilai Lv, Fan Zhang, Mingbo Wang, Ziqiang Tian
Objective. Esophageal carcinoma (EC) is a frequently common malignancy of gastrointestinal cancer in the world. This study aims to screen key genes and pathways in EC and elucidate the mechanism of it. Methods. 5 microarray datasets of EC were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were screened by bioinformatics analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC...
2016: Gastroenterology Research and Practice
Carlene Perpetua P Arceo, Editha C Jose, Angelyn R Lao, Eduardo R Mendoza
This paper further develops the connection between Chemical Reaction Network Theory (CRNT) and Biochemical Systems Theory (BST) that we recently introduced [1]. We first use algebraic properties of kinetic sets to study the set of complex factorizable kinetics CFK(N) on a CRN, which shares many characteristics with its subset of mass action kinetics. In particular, we extend the Theorem of Feinberg-Horn [9] on the coincidence of the kinetic and stoichiometric subsets of a mass action system to CF kinetics, using the concept of span surjectivity...
November 4, 2016: Mathematical Biosciences
Eric T Sletten, Sai Kumar Ramadugu, Hien M Nguyen
The utilization of substoichiometric amounts of commercially available nickel(II) triflate as an activator in the reagent-controlled glycosylation reaction for the stereoselective construction of biologically relevant targets containing 1,2-cis-2-amino glycosidic linkages is reported. This straightforward and accessible methodology is mild, operationally simple and safe through catalytic activation by readily available Ni(OTf)2 in comparison to systems employing our previously in-house prepared Ni(4-F-PhCN)4(OTf)2...
November 29, 2016: Carbohydrate Research
Alida Palmisano, Judit Zámborszky, Cihan Oguz, Attila Csikász-Nagy
The cell division cycle is controlled by a complex regulatory network which ensures that the phases of the cell cycle are executed in the right order. This regulatory network receives signals from the environment, monitors the state of the DNA, and decides timings of cell cycle events. The underlying transcriptional and post-translational regulatory interactions lead to complex dynamical responses, such as the oscillations in the levels of cell cycle proteins driven by intertwined biochemical reactions. A cell moves between different phases of its cycle similar to a dynamical system switching between its steady states...
2017: Methods in Molecular Biology
M Tayahi, C Gharsallah, N Khamassy, H Fakhfakh, F Djilani-Khouadja
In Tunisia, potato virus Y (PVY) currently presents a significant threat to potato production, reducing tuber yield and quality. Three hundred and eighty-five potato samples (six different cultivars) collected in autumn 2007 from nine regions in Tunisia were tested for PVY infection by DAS-ELISA. The virus was detected in all regions surveyed, with an average incidence of 80.26%. Subsequently, a panel of 82 Tunisian PVY isolates (PVY-TN) was subjected to systematic biological, serological and molecular typing using immunocapture reverse-transcription polymerase chain reaction and a series of PVY(OC)- and PVY(N)-specific monoclonal antibodies...
October 17, 2016: Genetics and Molecular Research: GMR
Robert Clarke
Constructing, evaluating, and interpreting gene networks generally sits within the broader field of systems biology, which continues to emerge rapidly, particular with respect to its application to understanding the complexity of signaling in the context of cancer biology. For the purposes of this volume, we take a broad definition of systems biology. Considering an organism or disease within an organism as a system, systems biology is the study of the integrated and coordinated interactions of the network(s) of genes, their variants both natural and mutated (e...
2017: Methods in Molecular Biology
Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver Ernst Bläsing, Regine Fuchs, Thomas Ehrhardt, Christoph Wittmann
BACKGROUND: During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understanding of their metabolism and its regulation hampers the targeted development of desired plant phenotypes. In this regard, systems biology, in particular the integration of metabolic and regulatory networks, is promising to broaden our knowledge and to further explore the biotechnological potential of plants...
October 29, 2016: BMC Systems Biology
Anne Morgat, Thierry Lombardot, Kristian B Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
Rhea ( is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research...
October 26, 2016: Nucleic Acids Research
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
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