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Modeling and Robustness Analysis of Biochemical Networks of Glycerol Metabolism by Klebsiella Pneumoniae
[chapter]
2009
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
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Glycerol bioconversion to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae (K. pneumoniae) can be characterized by an intricate network of interactions among biochemical fluxes, metabolic compounds, key ...
To determine the most reasonable metabolic network from all possible ones, we establish a quantitative definition of biological robustness and undertake parameter identification and robustness analysis ...
and Discussions Metabolic network of glycerol enzyme-catalytic dissimilation by K. pneumoniae includes some uncertain factors since the transport mechanisms of glycerol and 1,3-PD across the cell membrane ...
doi:10.1007/978-3-642-02466-5_44
fatcat:5hwh45lvxza6vpzmjonrx4qd44
Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae
2009
Computational biology and chemistry
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Flux balance analysis (FBA) is an effective tool in the analysis of metabolic network. ...
In this work, we propose two nonlinear bilevel programming models on anaerobic glycerol metabolism in Klebsiella pneumoniae (K. pneumoniae) for 1,3-propanediol (1,3-PD) production. ...
Acknowledgements This research is supported by National Natural Science Foundation of China (No. 10671126) and National Basic Research Program of China (No. 2007AA02Z208). ...
doi:10.1016/j.compbiolchem.2008.06.005
pmid:18804419
fatcat:b5dthfb6vfbb3l4lafra7j5fge
Contemplating 3-Hydroxypropionic Acid Biosynthesis in Klebsiella pneumoniae
2015
Indian Journal of Microbiology
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Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, here we advocate protocols for overproducing 3-HP in K. pneumoniae. ...
To surmount this problem, this review aims to portray a picture of 3-HP biosynthesis, involving 3-HP-synthesizing strains, biochemical attributes, metabolic pathways and key enzymes. ...
Klebsiella pneumoniae and Glycerol Dissimilation Among 3-HP-synthesizing strains, Klebsiella pneumoniae is of great attractiveness due to its biochemical attributes, including remarkable capacity to metabolize ...
doi:10.1007/s12088-015-0513-0
pmid:25805899
pmcid:PMC4363255
fatcat:csonomlqvngwdamsefp3i3q7ze
Metabolic Changes in Klebsiella oxytoca in Response to Low Oxidoreduction Potential, as Revealed by Comparative Proteomic Profiling Integrated with Flux Balance Analysis
2014
Applied and Environmental Microbiology
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As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. ...
Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis. ...
The working model was Klebsiella oxytoca. ...
doi:10.1128/aem.03327-13
pmid:24584239
pmcid:PMC3993281
fatcat:iwpkq37bjjbofnndphxojicqge
Identification and robustness analysis of nonlinear hybrid dynamical system of genetic regulation in continuous culture
2017
Journal of Industrial and Management Optimization
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Numerical results indicate that the most likely transmembrane mode of transport is active transport coupling with passive diffusion for glycerol and 1,3-propanediol. 2010 Mathematics Subject Classification ...
A novel quantitative definition of biological robustness is proposed to characterize the system's resilience when system parameters were perturbed. ...
Over the past years, a number of models have been proposed to describe the bio-dissimilation process of glycerol to 1,3-PD by Klebsiella pneumoniae (K. pneumoniae). ...
doi:10.3934/jimo.2018168
fatcat:gqeq4e3tjrcudb7anyqhccjw7m
Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1
2020
PLoS ONE
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These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil. ...
We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization ...
Ricardo Kruger and Dr. Sonia Maria de Freitas (head and former head of Molecular Biology Department of Universidade de Brasília) for all the support for developing research in the department. ...
doi:10.1371/journal.pone.0243739
pmid:33351813
pmcid:PMC7755216
fatcat:gsjffcc3qfejraiy7rthyavssy
Cofactor Engineering Enhances the Physiological Function of an Industrial Strain
[chapter]
2011
Progress in Molecular and Environmental Bioengineering - From Analysis and Modeling to Technology Applications
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By inactivating aldehyde dehydrogenase (ALDH) in Klebsiella pneumonia, an enzyme that competes with 1,3-PD oxidoreductase for NADH, the final titer, the productivity of 1,3-PD and the yield of 1,3-PD relative ...
(e.g. the intracellular energy charge and the interior redox potential and intracellular pH) on the phenotype, based on an accurate analysis of the metabolic network structure. ...
Cofactor Engineering Enhances the Physiological Function of an Industrial Strain, Progress in Molecular and Environmental Bioengineering -From Analysis and Modeling to Technology Applications, Prof. ...
doi:10.5772/18249
fatcat:armdwcmjrzddrp6yxadz7b6nlu
Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
2014
Metabolic Engineering
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In this study, we extended this analysis for non-native compounds by using an integrated approach through heterologous pathway integration and growth-coupled metabolite production design. ...
The production of 75% of the current drug molecules and 35% of all chemicals could be achieved through bioprocessing (Arundel and Sawaya, 2009) . ...
Funding for this work was provided by the Novo Nordisk Foundation. ...
doi:10.1016/j.ymben.2014.07.009
pmid:25080239
fatcat:ylnnzwxpizadjab7pz5qydq6xm
Advances in industrial microbiome based on microbial consortium for biorefinery
2017
Bioresources and Bioprocessing
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Comparison of 1,3-propanediol production by mixed and pure cultures were then introduced, and interaction relationships between cells in microbial consortium were summarized. ...
One of the important targets of industrial biotechnology is using cheap biomass resources. The traditional strategy is microbial fermentations with single strain. ...
Metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organism, but also to capture growth parameters and composition of simple bacterial ...
doi:10.1186/s40643-017-0141-0
pmid:28251041
pmcid:PMC5306255
fatcat:nhhfdy76wnghfeija2t4rz3o7e
Industrial biotechnology: Tools and applications
2009
Biotechnology Journal
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A Ab bb br re ev vi ia at ti io on ns s: : ISPR, in situ product removal; MFA, metabolic flux analysis; 1 1, ,3 3--P PD D, 1,3-propanediol ...
Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. ...
In another study, the metabolic network of glycerol metabolism in K. pneumoniae was extended, and elementary flux modes (EFM) analysis incorporating oxygen regulatory systems was carried out for 1,3-PD ...
doi:10.1002/biot.200900127
pmid:19844915
fatcat:4wjc2x4eibdg5d3hdvzcuucj7m
Industrial biotechnology: Tools and applications
2015
Biotechnology Advances
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A Ab bb br re ev vi ia at ti io on ns s: : ISPR, in situ product removal; MFA, metabolic flux analysis; 1 1, ,3 3--P PD D, 1,3-propanediol ...
Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. ...
In another study, the metabolic network of glycerol metabolism in K. pneumoniae was extended, and elementary flux modes (EFM) analysis incorporating oxygen regulatory systems was carried out for 1,3-PD ...
doi:10.1016/j.biotechadv.2015.10.012
pmid:26598053
fatcat:lkv7wjbikjbw5g5bba7fpyjs6m
A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products
2022
Fermentation
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This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted ...
upgrading of sugar crop products/by-products. ...
One study reported using elementary mode analysis with clustering to examine the M. succiniciproducens metabolic networks and predicted that overexpression of the zwf gene would increase succinic acid ...
doi:10.3390/fermentation8050216
fatcat:3jbhwdrhtfe6fj7qbtavs6eeyi
Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage
2012
PLoS ONE
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Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. ...
The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. ...
Designed and performed the computations with ME-matrix: IT RMTF. ...
doi:10.1371/journal.pone.0045635
pmid:23029152
pmcid:PMC3461016
fatcat:umwo6aegezej7l3vxwjkzikfvm
Metabolic Design and Control for Production in Prokaryotes
[chapter]
2011
Comprehensive Biotechnology
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Synopsis Prokaryotic life on earth is manifested by its diversity and omnipresence. ...
Major drivers of this trend include recombinant DNA technology, high throughput characterization of macromolecular cellular components, quantitative modeling for metabolic engineering, targeted combinatorial ...
The applications of genome--scale models span beyond metabolic engineering into the realms of bacterial evolution, network analysis, phenotypic behavior, biological discovery and synthetic biology. ...
doi:10.1016/b978-0-08-088504-9.00031-3
fatcat:t37oxhcgpraaxo5btrqhilaina
Mammalian Cell Culture Process for Monoclonal Antibody Production: Nonlinear Modelling and Parameter Estimation
2015
BioMed Research International
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By using a dynamical model of such kind of processes, an optimization-based technique for estimation of kinetic parameters in the model of mammalian cell culture process is developed. ...
The nonlinearity of these processes and the absence of suitable instrumentation require an enhanced modelling effort and modern kinetic parameter estimation strategies. ...
Most of the reported works were focused on the process of glycerol fermentation by Klebsiella pneumoniae in batch, fed-batch, and continuous cultures [37] [38] [39] [40] [41] . Shen et al. ...
doi:10.1155/2015/598721
pmid:25685797
pmcid:PMC4313526
fatcat:izvjmb4k6zf6jexcaatqefblca
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