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Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Mee K Lee, Mohd Saberi Mohamad, Yee Wen Choon, Kauthar Mohd Daud, Nurul Athirah Nasarudin, Mohd Arfian Ismail, Zuwairie Ibrahim, Suhaimi Napis, Richard O Sinnott
2020 Journal of Integrative Bioinformatics  
In this paper, PSOMOMA was compared with CSMOMA and ABCMOMA for maximizing the production of succinic acid in E. coli.  ...  However, the metabolic networks are too complex that cause problem in identifying near-optimal knockout genes/reactions for maximizing the metabolite's production.  ...  Acknowledgements We would like to thank the Ministry of Education Malaysia for supporting this re-search by the Fundamental Research Grant Scheme -Malaysia's Research Star Award -FRGS-MRSA (grant number  ... 
doi:10.1515/jib-2019-0073 pmid:32374287 pmcid:PMC7734505 fatcat:kjewmcypifgrjaoast57rx7bwa


Mei Jing Liew, Abdul Hakim Mohamed Salleh, Mohd Saberi Mohamad, Yee Wen Choon, Safaai Deris, Azurah A Samah, Hairudin Abdul Majid
2016 Jurnal Teknologi  
By performing an experiment on Escherichia coli, the results indicate that the proposed hybrid algorithm of Particle Swarm Optimization and Flux Balance Analysis is able to obtain optimal gene deletions  ...  Metabolic engineering of microorganism is widely used to enhance the production of metabolites that is useful in food additives, pharmaceutical, supplements, cosmetics, and polymer materials.  ...  Acknowledgement We would like to thank the Universiti Teknologi Malaysia for supporting this research through a GUP research grant (Grant number: Q.J130000.2528.12H12) and FRGS research grant (Grant number  ... 
doi:10.11113/jt.v78.10040 fatcat:mazqotnpc5ffndwkprzrr6qxwa

Reconstruction and analysis of genome-scale metabolic models of industrial Escherichia coli strains [article]

Patricia Alvarez
2019 Figshare  
These models and strategies will be of great value for identifying products of biotechnological interest.  ...  Here we present and perform a diversity of strategies, including Possibilistic Flux Analysis, for validation of 9 industrially relevant Escherichia coli constraint-based models.  ...  In this work, the approach will be developed for a variety of industrially relevant strains of a canonical species, Escherichia coli, and particularized for a reference strain, Escherichia coli Nissle  ... 
doi:10.6084/m9.figshare.9820688.v1 fatcat:3vi7ukstkratpkkmap4ugxlnfy

Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli

Rishi Jain, Ranjan Srivastava
2009 BMC Systems Biology  
In addition, the genome-scale metabolic model of E. coli is the most comprehensive model at this time.  ...  Escherichia coli/MS2 was used as the host-pathogen model system as MS2 is easy to work with, harmless to humans, but shares many features with eukaryotic viruses.  ...  Acknowledgements Support for this work was provided by NIH Grant 1R03LM009753-01.  ... 
doi:10.1186/1752-0509-3-121 pmid:20042079 pmcid:PMC2813233 fatcat:u7vqo4p67zehxcijvh763o2z5i

Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd

Yier Ma, Takeyuki Tamura
2021 Frontiers in Bioinformatics  
We applied the proposed method DynCubeProd to iJO1366, which is a genome-scale constraint-based model of Escherichia coli.  ...  In addition, under the anaerobic condition of iJO1366, DynCubeProd could obtain the reaction deletion strategies for almost 40% of the target metabolites that the elementary flux vector-based method, which  ...  We applied the proposed method DynCubeProd to iJO1366, which is a genome-scale constraint-based model of Escherichia coli .  ... 
doi:10.3389/fbinf.2021.716112 fatcat:ttjrm3j6ovfpxaosx5as5uee64

RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George, Corey M. Hudson
2019 BMC Bioinformatics  
Brute-force determination of the optimal pathways to efficient production of a target chemical in a chassis organism is computationally intractable.  ...  With this comprehensive suite of features RetSynth exceeds any open-source software or webservice currently available for identifying optimal pathways for target production.  ...  International, Inc., for the U.S.  ... 
doi:10.1186/s12859-019-3025-9 fatcat:utjedecjmnekffjjikwe5vobv4

OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites

Honglei Liu, Yanda Li, Xiaowo Wang
2014 Quantitative Biology  
We compared OP-Synthetic with several state-of-the-art computational approaches on the problems of succinate overproduction and Nacetylneuraminic acid synthetic pathway optimization in Escherichia coli  ...  These methods seek to find genetic manipulations that maximally couple the desired metabolites with the cellular growth objective.  ...  In principle, a lower OUT_ms bound makes the program to search for a higher production rate for the desired metabolite but with the cost of lower biomass production rate.  ... 
doi:10.1007/s40484-014-0033-7 fatcat:htkrmu3dkbhe3dcenohufwibli

A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli

Ana Patrícia Lima, Vítor Baixinho, Daniel Machado, Isabel Rocha
2016 IFAC-PapersOnLine  
Hereby we analyse and compare the most used and complete kinetic models available for the central carbon metabolism of E. coli.  ...  Hereby we analyse and compare the most used and complete kinetic models available for the central carbon metabolism of E. coli.  ...  This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684  ... 
doi:10.1016/j.ifacol.2016.12.137 fatcat:exlmet5xrfat3cwzdezk7cbdfm

Metabolic systems analysis to advance algal biotechnology

Brian J. Schmidt, Xiefan Lin-Schmidt, Austin Chamberlin, Kourosh Salehi-Ashtiani, Jason A. Papin
2010 Biotechnology Journal  
Optimization of lycopene production in E. coli Alper et al. [50] investigated gene knockout methods to further optimize an industrial E. coli strain for the production of lycopene.  ...  Comparisons will facilitate selecting an optimal species as a starting point for biofuel production.  ... 
doi:10.1002/biot.201000129 pmid:20665641 fatcat:qrqi2dq54rbqziupu3azyh37ca

Improved Metaheuristic Algorithms for Metabolic Network Optimization

K Mohd Daud, Z Zakaria, R Hassan, M S Mohamad, Z Ali Shah
2019 IOP Conference Series: Materials Science and Engineering  
In metabolic engineering, the problem of identifying near-optimal reactions knockout that can optimize the production rate of desired metabolites are hindered by the complexity of the metabolic networks  ...  These algorithms are tested on succinic acid production in Escherichia coli. The comparative performances are measured based on production rate, growth rate, and computational time.  ...  Acknowledgements This work was financially supported by FRGS, Vot No: 4F973 from Ministry of Education (MOHE), and also RUG, Vot No: 16H73 from Universiti Teknologi Malaysia.  ... 
doi:10.1088/1757-899x/551/1/012065 fatcat:xleyolz2yzguhbdrjrz7trdlzm

Extending knowledge of Escherichia coli metabolism by modeling and experiment

Eberhard O Voit, Monica Riley
2003 Genome Biology  
Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and  ...  One of the challenges for 'post-genomic' biology is the integration of data from many different sources.  ...  [2] sheds light on some of these issues with a combination of two methods, one for measuring gene expression and one for detecting proteins in E. coli cells. In contrast, Reed et al.  ... 
doi:10.1186/gb-2003-4-11-235 pmid:14611652 pmcid:PMC329109 fatcat:wckb5wtonrd5hou6mptvn3nzy4

Improved Bioactive Metabolite Production by Saccharopolyspora halotolerans VSM-2 Using Response Surface Methodology and Unstructured Kinetic Modelling

Ushakiranmayi Managamuri, Muvva Vijayalakshmi, Mani Deepa Indupalli, Venkat Siva Rama Krishna Ganduri, Satish Babu Rajulapati, Sudhakar Poda
2018 Pharmacognosy Journal  
This study targets to optimize and analyse the interactive effects of process variables for improved bioactive metabolite production using RSM and unstructured kinetic modelling by S. halotolerans VSM  ...  Unstructured models provided a better approximation of kinetic profiles for bioactive metabolite production by S. halotolerans VSM 2.  ...  ACKNOWLEDGEMENT The first author U.K.M is grateful to University grants commission (U.G.C), New Delhi, Government of India, for providing financial assistance.  ... 
doi:10.5530/pj.2018.5.142 fatcat:wmwrmra6rrch7i3gkhqkuzneu4

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

Hyun-Seob Song, Jaques Reifman, Anders Wallqvist, Néstor V. Torres
2014 PLoS ONE  
In contrast to other approaches, our method was able to provide quantitative predictions for both model organisms under a variety of conditions.  ...  In case studies of wild-type Saccharomyces cerevisiae, and wild-type and mutant Escherichia coli strains, our method achieved high prediction accuracy, as gauged by correlation coefficients and sums of  ...  Department of Defense. This paper has been approved for public release with unlimited distribution. Author Contributions Conceived and designed the experiments: HSS JR AW.  ... 
doi:10.1371/journal.pone.0112524 pmid:25397773 pmcid:PMC4232356 fatcat:oz4lkucg3nbppibfcfuimxtree


2021 Asian Journal of Pharmaceutical and Clinical Research  
Cultural conditions for production of antimicrobials were optimized by "one variable at a time" method.  ...  Production of the antimicrobial metabolite has been optimized for the inoculum density, aeration, temperature, pH as well as carbon, and nitrogen sources.  ...  Determination of optimum conditions for production of antimicrobial metabolites To determine the optimum conditions for production of antimicrobial metabolite, one variable at a time method was used and  ... 
doi:10.22159/ajpcr.2021.v14i1.40187 fatcat:jo6qkubus5glzpfeyiw5cpyfki

Determination of growth-coupling strategies and their underlying principles [article]

Tobias Benedikt Alter, Lars M. Blank, Birgitta Elisabeth Ebert
2018 bioRxiv   pre-print
Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance.  ...  Impeding the balancing of cofactors and protons in the absence of target production was the underlying principle of all other strategies and further increased the GC strength of the aforementioned strategies  ...  The color code relates to Figure 9 .Figure EV1 . 9EV1 Comparison of the rank of GC target products of the E. coli iAF1260 core model in the energy hierarchy of metabolites of GC mutants and the wild-type  ... 
doi:10.1101/258996 fatcat:5nl7ivtnvnbkndyrblvbdo3ag4
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