The Experts below are selected from a list of 841881 Experts worldwide ranked by ideXlab platform
Hans V Westerhoff - One of the best experts on this subject based on the ideXlab platform.
-
(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-Expression Regulation: marrying control engineering with metabolic control analysis.
BMC systems biology, 2013Co-Authors: Vincent Fromion, Hans V WesterhoffAbstract:Background Metabolic control analysis (MCA) and supply–demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic Regulation. Supply–demand theory has not yet considered gene-Expression Regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-Expression Regulation would be involved, but designed different ways in which Regulation could be organized, with the potential of causing adaptation to be perfect.
-
(Im) Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-Expression Regulation: marrying control engineering with metabolic control analysis
BMC Systems Biology, 2013Co-Authors: Fei He, Vincent Fromion, Hans V WesterhoffAbstract:Background: Metabolic control analysis (MCA) and supply-demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic Regulation. Supply-demand theory has not yet considered gene-Expression Regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-Expression Regulation would be involved, but designed different ways in which Regulation could be organized, with the potential of causing adaptation to be perfect. Results: This study integrates control engineering and classical MCA augmented with supply-demand theory and HCA. Because gene-Expression Regulation involves time integration, it is identified as a natural instantiation of the 'integral control' (or near integral control) known in control engineering. This study then focuses on robustness against and adaptation to perturbations of process activities in the network, which could result from environmental perturbations, mutations or slow noise. It is shown however that this type of 'integral control' should rarely be expected to lead to the 'perfect adaptation': although the gene-Expression Regulation increases the robustness of important metabolite concentrations, it rarely makes them infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero order in the concentration of the protein, which may be rare biologically for cells growing steadily. Conclusions: A proposed new framework integrating the methodologies of control engineering and metabolic and hierarchical control analysis, improves the understanding of biological systems that are regulated both metabolically and by gene Expression. In particular, the new approach enables one to address the issue whether the intracellular biochemical networks that have been and are being identified by genomics and systems biology, correspond to the 'perfect' regulatory structures designed by control engineering vis-a-vis optimal functions such as robustness. To the extent that they are not, the analyses suggest how they may become so and this in turn should facilitate synthetic biology and metabolic engineering.
Vincent Fromion - One of the best experts on this subject based on the ideXlab platform.
-
(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-Expression Regulation: marrying control engineering with metabolic control analysis.
BMC systems biology, 2013Co-Authors: Vincent Fromion, Hans V WesterhoffAbstract:Background Metabolic control analysis (MCA) and supply–demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic Regulation. Supply–demand theory has not yet considered gene-Expression Regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-Expression Regulation would be involved, but designed different ways in which Regulation could be organized, with the potential of causing adaptation to be perfect.
-
(Im) Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-Expression Regulation: marrying control engineering with metabolic control analysis
BMC Systems Biology, 2013Co-Authors: Fei He, Vincent Fromion, Hans V WesterhoffAbstract:Background: Metabolic control analysis (MCA) and supply-demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic Regulation. Supply-demand theory has not yet considered gene-Expression Regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-Expression Regulation would be involved, but designed different ways in which Regulation could be organized, with the potential of causing adaptation to be perfect. Results: This study integrates control engineering and classical MCA augmented with supply-demand theory and HCA. Because gene-Expression Regulation involves time integration, it is identified as a natural instantiation of the 'integral control' (or near integral control) known in control engineering. This study then focuses on robustness against and adaptation to perturbations of process activities in the network, which could result from environmental perturbations, mutations or slow noise. It is shown however that this type of 'integral control' should rarely be expected to lead to the 'perfect adaptation': although the gene-Expression Regulation increases the robustness of important metabolite concentrations, it rarely makes them infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero order in the concentration of the protein, which may be rare biologically for cells growing steadily. Conclusions: A proposed new framework integrating the methodologies of control engineering and metabolic and hierarchical control analysis, improves the understanding of biological systems that are regulated both metabolically and by gene Expression. In particular, the new approach enables one to address the issue whether the intracellular biochemical networks that have been and are being identified by genomics and systems biology, correspond to the 'perfect' regulatory structures designed by control engineering vis-a-vis optimal functions such as robustness. To the extent that they are not, the analyses suggest how they may become so and this in turn should facilitate synthetic biology and metabolic engineering.
Fei He - One of the best experts on this subject based on the ideXlab platform.
-
(Im) Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-Expression Regulation: marrying control engineering with metabolic control analysis
BMC Systems Biology, 2013Co-Authors: Fei He, Vincent Fromion, Hans V WesterhoffAbstract:Background: Metabolic control analysis (MCA) and supply-demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic Regulation. Supply-demand theory has not yet considered gene-Expression Regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-Expression Regulation would be involved, but designed different ways in which Regulation could be organized, with the potential of causing adaptation to be perfect. Results: This study integrates control engineering and classical MCA augmented with supply-demand theory and HCA. Because gene-Expression Regulation involves time integration, it is identified as a natural instantiation of the 'integral control' (or near integral control) known in control engineering. This study then focuses on robustness against and adaptation to perturbations of process activities in the network, which could result from environmental perturbations, mutations or slow noise. It is shown however that this type of 'integral control' should rarely be expected to lead to the 'perfect adaptation': although the gene-Expression Regulation increases the robustness of important metabolite concentrations, it rarely makes them infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero order in the concentration of the protein, which may be rare biologically for cells growing steadily. Conclusions: A proposed new framework integrating the methodologies of control engineering and metabolic and hierarchical control analysis, improves the understanding of biological systems that are regulated both metabolically and by gene Expression. In particular, the new approach enables one to address the issue whether the intracellular biochemical networks that have been and are being identified by genomics and systems biology, correspond to the 'perfect' regulatory structures designed by control engineering vis-a-vis optimal functions such as robustness. To the extent that they are not, the analyses suggest how they may become so and this in turn should facilitate synthetic biology and metabolic engineering.
Huang Xin-xiang - One of the best experts on this subject based on the ideXlab platform.
-
Analysis of Genes Expression Regulation controlled by luxS/AI-2 in Salmonella enterica serovar Typhi
Journal of Jiangsu University, 2011Co-Authors: Huang Xin-xiangAbstract:Objective: To elucidate the influence of LuxS on gene Expression Regulation of Salmonella enterica serovar Typhi(S.Typhi) at mid-log phase in the presence of glucose.Methods: The luxS deleted mutant of S.Typhi was prepared by the homologous recombination mediated by suicide plasmid;the differences of growth and motility between wild-type(WT) and mutant were compared;luminescence assays were performed in WT and mutant at different growth phases in the presence and absence of glucose with reporter strain Vibrio harveyi BB170;the difference of gene Expression profiles between the WT and the luxS mutant at mid-log phage in the presence of glucose was investigated by genomic microarray assay;qRT-PCR was performed to validate the results of microarray assay.Results: The luxS deleted mutant of S.Typhi was constructed successfully;luxS gene had effect on the bacterial motility but not on the bacterial growth;the luminescence of WT was higher at any growth phases in the presence of glucose than in its absence and reached the maximum at mid-log phase in the presence of glucose,while the mutant did not produce luminescence in both the presence and absence of glucose at any growth phases;gene Expression profiles analysis revealed that Expression of 47 and 27 genes were induced and decreased,respectively,in the luxS mutant at mid-log phases in the presence of glucose.The results of qRT-PCR are similar with that of genomic assay.Conclusion: The luxS gene of S.Typhi was involved in the synthesis of AI-2 and played a vital role in genes Expression Regulation at mid-log phase.
-
Influence of Hfq on gene Expression Regulation of Salmonella enterica serovar Typhi at earlier stage of hyperosmotic stress
Journal of Jiangsu University, 2010Co-Authors: Huang Xin-xiangAbstract:Objective:To explore the influence of Hfq on gene Expression Regulation of S.enterica serovar Typhi at early-stage of hyperosmotic stress.Methods:The hfq deleted mutant of S.enterica serovar Typhi was prepared by homologous recombination mediated by suicide plasmid;the difference of gene Expression profiles between the wild strain and the hfq mutant at early-stage of hyperosmotic stress was investigated by genomic assay;qRT-PCR was performed to validate the results of microarray assay. Results:The hfq deleted mutant of S.enterica serovar Typhi was constructed successfully;gene Expression profiles analysis revealed that Expression of 62 genes and 32 genes were induced and decreased respectively in the hfq mutant at earlier stage of hyperosmotic stress.The results of qRT-PCR were consistent with the results of genomic assay. Conclusion:Hfq of S.enterica serovar Typhi can serve as an important factor to regulate gene Expression in response to hyperosmotic stress.
Gregory M. Miller - One of the best experts on this subject based on the ideXlab platform.
-
Advances in tryptophan hydroxylase-2 gene Expression Regulation: New insights into serotonin–stress interaction and clinical implications†‡
American Journal of Medical Genetics, 2012Co-Authors: Guo-lin Chen, Gregory M. MillerAbstract:Serotonin (5-HT) modulates the stress response by interacting with the hormonal hypothalamic-pituitary-adrenal (HPA) axis and neuronal sympathetic nervous system (SNS). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in 5-HT biosynthesis, and the recent identification of a second, neuron-specific TPH isoform (TPH2) opened up a new area of research. While TPH2 genetic variance has been linked to numerous behavioral traits and disorders, findings on TPH2 gene Expression have not only reinforced, but also provided new insights into, the long-recognized but not yet fully understood 5-HT-stress interaction. In this review, we summarize advances in TPH2 Expression Regulation and its relevance to the stress response and clinical implications. Particularly, based on findings on rhesus monkey TPH2 genetics and other relevant literature, we propose that: 1) upon activation of adrenal cortisol secretion, the cortisol surge induces TPH2 Expression and de novo 5-HT synthesis; 2) the induced 5-HT in turn inhibits cortisol secretion by modulating the adrenal sensitivity to ACTH via the suprachiasmatic nuclei (SCN)-SNS-adrenal system, such that it contributes to the feedback inhibition of cortisol production; 3) basal TPH2 Expression or 5-HT synthesis, as well as early-life experience, influence basal cortisol primarily via the hormonal HPA axis; and 4) 5′- and 3′-regulatory polymorphisms of TPH2 may differentially influence the stress response, presumably due to their differential roles in gene Expression Regulation. Our increasing knowledge of TPH2 Expression Regulation not only helps us better understand the 5-HT-stress interaction and the pathophysiology of neuropsychiatric disorders, but also provides new strategies for the treatment of stress-associated diseases.
-
Advances in tryptophan hydroxylase-2 gene Expression Regulation: new insights into serotonin-stress interaction and clinical implications.
American journal of medical genetics. Part B Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 2012Co-Authors: Guo-lin Chen, Gregory M. MillerAbstract:Serotonin (5-HT) modulates the stress response by interacting with the hormonal hypothalamic-pituitary-adrenal (HPA) axis and neuronal sympathetic nervous system (SNS). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in 5-HT biosynthesis, and the recent identification of a second, neuron-specific TPH isoform (TPH2) opened up a new area of research. While TPH2 genetic variance has been linked to numerous behavioral traits and disorders, findings on TPH2 gene Expression have not only reinforced, but also provided new insights into, the long-recognized but not yet fully understood 5-HT-stress interaction. In this review, we summarize advances in TPH2 Expression Regulation and its relevance to the stress response and clinical implications. Particularly, based on findings on rhesus monkey TPH2 genetics and other relevant literature, we propose that: (i) upon activation of adrenal cortisol secretion, the cortisol surge induces TPH2 Expression and de novo 5-HT synthesis; (ii) the induced 5-HT in turn inhibits cortisol secretion by modulating the adrenal sensitivity to ACTH via the suprachiasmatic nuclei (SCN)-SNS-adrenal system, such that it contributes to the feedback inhibition of cortisol production; (iii) basal TPH2 Expression or 5-HT synthesis, as well as early-life experience, influence basal cortisol primarily via the hormonal HPA axis; and (iv) 5'- and 3'-regulatory polymorphisms of TPH2 may differentially influence the stress response, presumably due to their differential roles in gene Expression Regulation. Our increasing knowledge of TPH2 Expression Regulation not only helps us better understand the 5-HT-stress interaction and the pathophysiology of neuropsychiatric disorders, but also provides new strategies for the treatment of stress-associated diseases.
