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  • genetics
  • One exciting aspect of this study is that it provides a proof-of-principle for how engineering a specific metabolic pathway in the liver can affect the whole body adiposity and response to a high-fat diet," said Karen Reue, a UCLA professor of human genetics and an author of the study. (technologynetworks.com)
  • Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. (plantcell.org)
  • This represents a unique and valuable approach to the study of complex networks using quantitative genetics. (plantcell.org)
  • In this context, studies in pigs can have a dual purpose: first, to study the genetics of food, i.e., how the genotype of the animal influences the FA content and profile of meat and, secondly, as an animal model for nutrigenomic studies or for human metabolic diseases. (biomedcentral.com)
  • enzyme
  • Arita constructed a database for atomic tracing based on substrate-product relationship extracted from known enzyme reactions [ 4 , 5 ], where possible pathways can be found as combinations of established substrate-product relationships. (omicsonline.org)
  • We now believe there is a specific enzyme critical to the reverse pathway that can be deleted without impairing normal function. (technologynetworks.com)
  • The novelty in the approach utilized to generate SteatoNet is the definition of model parameters as a mathematical formalism based on reaction reversibility r, the distribution of the metabolic influx f into alternative pathways, the total influx φI and the ratio between bound and free enzyme, w. (nih.gov)
  • Specifically, genetic manipulation of a secondary metabolic enzyme led to altered free-running rhythms. (plantcell.org)
  • Specifically, using an experimentally refined stoichiometric model for Saccharomyces cerevisiae, we computed a three-dimensional matrix of epistatic interactions between any two enzyme gene deletions, with respect to all metabolic flux phenotypes. (nih.gov)
  • A biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. (nih.gov)
  • We present an analysis of one of the mechanisms by which metabolic regulation occurs: enzyme inhibition and activation by small molecules. (biomedcentral.com)
  • In contrast, although the role of enzyme inhibition and activation in individual pathways has been studied and modelled in some detail, genome-scale analyses of enzyme inhibition and activation networks have been lacking to date. (biomedcentral.com)
  • It has been proposed that this property is biologically useful and actively selected for by evolution[ 15 ], though other studies have questioned whether this is a real feature of metabolic networks[ 16 ], and have suggested that the topology simply derives from the way in which new enzyme functions evolve. (biomedcentral.com)
  • biological
  • Genostar, a developer of bioinformatics software that enables biologists and bioinformaticians to expertly mine and analyze diverse biological data, today announced that Merial, a world leader in animal health, has purchased its IOGMA(R) 3.4 Metabolic Pathway Builder software. (technologynetworks.com)
  • A systems biology library of objects corresponding to biological entities was utilised to compile the SteatoNet (Steatosis Network) in a systematic workflow (Fig. 1) to form a closed multi-pathway metabolic network (Fig. 2). (nih.gov)
  • These fascinating new techniques provide a powerful tool for setting scientific hypotheses and linking cellular pathways to biological mechanism. (intechopen.com)
  • Treatment strategies to combat metabolic dysfunction and associated pathologies have been hampered by our lack of understanding regarding the biological causes of these clinical conditions and our incomplete understanding regarding the effects of estrogens and the tissue-specific functions and molecular actions of its receptors. (springer.com)
  • There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size. (nih.gov)
  • The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems. (nih.gov)
  • While metabolic cycles in yeast colonies were already very well known and associated to the alternation of 'reductive' and 'oxidative' phases , in this case the relevant feature of the observed cycles was their independence of any specific biological function of the involved gene products. (nih.gov)
  • Discovering refinements to biological networks, such as metabolic pathways. (salford.ac.uk)
  • The ability to perform quantitative studies using isotope tracers and metabolic flux analysis (MFA) is critical for detecting pathway bottlenecks and elucidating network regulation in biological systems, especially those that have been engineered to alter their native metabolic capacities. (nih.gov)
  • Proteins
  • Strain SB22 T has all the proteins for complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. (standardsingenomics.org)
  • Treatment of SB caused regulation of 20 proteins such as heat shock-related 70 kDa protein 2 (hsp70), LIM domain protein CLP-36, copine I, peroxiredoxin-2, coronin-1 B and cytoplasmic dynein intermediate chain 2C.The regulation of SB on protein levels was confirmed by Western blotting.The signal cascades network induced by SB after its binding with integrin α2β1 was predicted. (nih.gov)
  • The signal cascades network of SB after binding with integrin α2β1 might include regulation of intracellular Ca²+ level, cytoskeleton-related proteins such as coronin-1B and cytoskeleton structure of platelets. (nih.gov)
  • regulation
  • SteatoNet: the first integrated human metabolic model with multi-layered regulation to investigate liver-associated pathologies. (nih.gov)
  • Objects were compiled to feature two novel hepatic modelling aspects: the interaction of hepatic metabolic pathways with extra-hepatic tissues and the inclusion of transcriptional and post-transcriptional regulation. (nih.gov)
  • SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and transcriptional and post-translational regulatory factors are represented in the hepatic, adipose, macrophage, peripheral tissue and pancreatic compartments with inter-tissue connectivity via the blood. (nih.gov)
  • To do so, a model must provide reliable descriptions of key system properties-in particular, the network of metabolic pathways and their dynamic regulation. (pnnl.gov)
  • The researches found that modeling cellular regulation with cybernetic control laws provides an efficient route to describing the complex dynamic behavior of S. oneidensis MR-1 particularly when considering large-scale metabolic networks. (pnnl.gov)
  • The approaches and results reported could influence future efforts in understanding metabolic diseases and the role of biochemical regulation in the cell. (nih.gov)
  • I am trying to engage these two drivers in designing projects to foster the diverse interests of individual members of my group, ranging from evolution of pathways to mechanisms of gene regulation, and to capitalize on the diverse training backgrounds in the group, ranging from molecular biology to physics. (carnegiescience.edu)
  • prediction
  • Prediction accuracy (AUC) average overall network sizes of unsupervised and supervised methods on knockout, knockdown, multifactorial and average data generated by GeneNetWeaver and extracted fromE. (nih.gov)
  • Prediction of global features in real-world networks. (nih.gov)
  • b) To study whether the prediction is robust with respect to the chosen threshold, we depict the relative mean-squared error (defined as in Figure 2) averaged over the whole data-set of real-world networks as it depends on the threshold. (nih.gov)
  • experimentally
  • ascomyceticus was constructed based on the latest reported metabolic model of S. coelicolor A3(2) and validated experimentally. (biomedcentral.com)
  • In this use, L-HCM predicted experimentally determined dynamic metabolic shifts, a capability well beyond the scope of constraint-based modeling approaches. (pnnl.gov)
  • homeostasis
  • Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. (biomedcentral.com)
  • Given the importance of C. albicans as an emerging eukaryotic model, very little is known regarding the genetic networks that control size homeostasis in this opportunistic yeast. (g3journal.org)
  • Computational Biology
  • We present here a software tool designed to support computational biology studies where Markovian dynamics takes place and MFPTs between initial and single or multiple final states in network-like systems are used. (nih.gov)
  • Mechanism
  • The identification of the mechanism could provide a future target for drugs that would attack tumors relying upon the reverse pathway for sustenance and growth. (technologynetworks.com)
  • degradation
  • The new pathway, however, allowed for fat degradation even when the body was full. (technologynetworks.com)
  • XylS is the positive regulator of the inducible Pm promoter, originating from Pseudomonas putida, where the system controls a biochemical pathway involved in degradation of aromatic hydrocarbons, which also act as inducers. (nih.gov)
  • coli
  • Rational strain development of E. coli achieved by metabolic engineering strategies has provided new processes for efficiently biotechnological production of various high-value chemical building blocks. (mendeley.com)
  • Compared to previous reviews, this review focuses on recent advances in metabolic engineering of the industrial model bacteria E. coli that lead to efficient recombinant biocatalysts for the production of high-value organic acids like succinic acid, lactic acid, 3-hydroxypropanoic acid and glucaric acid as well as alcohols like 1,3-propanediol, xylitol, mannitol, and glycerol with the discussion of the future research in this area. (mendeley.com)
  • algorithm
  • We first compare the accuracy of the predictions with an exact algorithm on small random metabolic networks. (nih.gov)
  • We also verify that the predictions of the algorithm match closely those of Monte Carlo based methods in the case of the Red Blood Cell metabolic network. (nih.gov)
  • We extracted the largest strongly connected component (LSCC) of each network using a classical algorithm . (nih.gov)
  • syndrome
  • A metabolically translational feature of the thesis in a heterogeneous population confers a significant increase in the risk of CRC incidence with metabolic syndrome (MetS). (bl.uk)
  • reaction
  • BRP-dependent and CFB networks are generated by network expansion from seed compounds via balanced reaction pattern (BRP) and via simple cleavage/formation of chemical bonds, respectively. (omicsonline.org)
  • However, only a few tools provide functions to compare two groups of metabolic networks which are usually limited to the reaction level, not the pathway level. (hku.hk)
  • Some of these pathways cannot be identified by other tools which only consider reaction level or do not take into account possible mutations among species. (hku.hk)
  • The advantage of genome-scale studies is that they may identify emergent properties of the system that are not obvious at the reaction, or even pathway, level. (biomedcentral.com)
  • methods
  • However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. (plantcell.org)
  • Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. (nih.gov)
  • 200) and average (over all sizes of networks), SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods.For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. (nih.gov)
  • approach
  • Concept of network expansion, a term introduced by Heinrich's group, is generalized and a previous approach by Hatzimanikatis and his colleagues for generation of BRP-dependent network equivalent is re-defined in the context of network expansion. (omicsonline.org)
  • We call such an approach for exploring pathways binary relationship approach. (omicsonline.org)
  • This approach is unique in that it is able to model metabolic dynamics. (pnnl.gov)
  • However, it is rarely considered to which degree the results obtained for one particular network class can be extrapolated to real-world networks.Our results confirm and extend previous findings regarding the synchronization properties of neural networks.Our approach provides a method to estimate global properties of under-sampled networks in good approximation. (nih.gov)
  • Our approach provides a method to estimate global properties of under-sampled networks in good approximation. (nih.gov)
  • distributions
  • For example, the power-law distributions of node connectivities in social networks have been derived from dynamical network evolution models ( 8 ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ - 17 ). (pnas.org)
  • mutation
  • A new study from an international team of researchers is the first to identify a rarely-seen type of DNA mutation as the cause of an inherited metabolic disorder. (technologynetworks.com)
  • The problem also captures the mutation in pathways and derives a measure (p-value and e-score) for evaluating the confident of the pathways. (hku.hk)
  • simulate
  • They used the Lumped Hybrid Cybernetic Model (L-HCM), developed by Purdue researchers Dr. Hyun-Seob Song and Dr. Doraiswami Ramkrishna, to predict and simulate the metabolic dynamics of Shewanella oneidensis MR-1 during aerobic growth in a bioreactor. (pnnl.gov)
  • Statistical
  • These models are aimed at replicating specific statistical features encountered in real-world networks. (nih.gov)
  • In particular, we consider the statistical constraints which the respective construction scheme imposes on the generated networks. (nih.gov)
  • After having identified the most variable networks, we address the issue of which constraints are common to all network classes and are thus suitable candidates for being generic statistical laws of complex networks. (nih.gov)
  • Finally, we demonstrate on three different data sets (C. elegans neuronal network, R. prowazekii metabolic network, and a network of synonyms extracted from Roget's Thesaurus) that real-world networks have statistical relations compatible with those obtained using regression models. (nih.gov)
  • High values point toward a general statistical law for all networks. (nih.gov)
  • The statistics of the real-world networks lie in the data cloud, suggesting that those relations correspond to relevant statistical laws of complex networks. (nih.gov)
  • Biomarkers
  • The aim of this thesis was to identify potential metabolic biomarkers of CRC patients using 'Metabonomics' based on proton nuclear magnetic resonance (1H NMR) spectroscopy. (bl.uk)
  • transcriptional
  • Recent studies revealed that global regulatory factors such as the cAMP receptor protein (Crp) and the carbon storage regulator (Csr) system are part of a large network of transcriptional and posttranscriptional control strategies adjusting metabolic changes and virulence in response to temperature, ion and nutrient availability. (nih.gov)
  • experimental
  • The successful constructing and experimental validation of the metabolic model of S. hygroscopicus var. (biomedcentral.com)
  • Experimental results show that DMPFinder is able to identify pathways that are critical for the first group to exhibit a certain phenotype which is absent in the other group. (hku.hk)
  • The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network. (nih.gov)
  • 10 networks were generated for each size and experimental condition. (nih.gov)