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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.  ...  Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of metabolites.  ...  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

Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization

Govind Nair, Christian Jungreuthmayer, Jürgen Zanghellini
2017 BMC Bioinformatics  
Finally, we use PSOMCS to predict knockouts satisfying multiple objectives in a genome-scale metabolic model of E. coli and compare it with OptKnock and RobustKnock.  ...  Our solution (PSOMCS) is to use particle swarm optimization (PSO) along with the direct calculation of cMCSs from the stoichiometric matrix to obtain optimal designs satisfying multiple objectives.  ...  Acknowledgements We thank David A. Peña Navarro for providing the reduced E. coli iAF1260 model growing anaerobically on glucose.  ... 
doi:10.1186/s12859-017-1483-5 pmid:28143607 pmcid:PMC5286819 fatcat:qku7lv4rvfcezhatahvnhirfzu

In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment

Mei Yen Man, Mohd Saberi Mohamad, Yee Wen Choon, Mohd Arfian Ismail
2021 Journal of Integrative Bioinformatics  
and lactate production rates in Escherichia coli (E. coli).  ...  As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate  ...  Figure 5 : 5 Figure 5: Metabolic pathway of Escherichia coli for lactate.  ... 
doi:10.1515/jib-2020-0037 pmid:34348418 pmcid:PMC8573224 fatcat:unp4frm6o5bojcg47ilhkublpi

Role of Filamentous Phage SW1 in Regulating the Lateral Flagella of Shewanella piezotolerans Strain WP3 at Low Temperatures

Huahua Jian, Xiang Xiao, Fengping Wang
2013 Applied and Environmental Microbiology  
WP3ΔSW1 was shown to have a higher production of lateral flagella than WP3 and enhanced swarming motility when cultivated on solid agar plates.  ...  The phage SW1 is shown to have a significant influence on the swarming ability of the host and thus may play an important role in adjusting the fitness of the cells in the deep-sea environment.  ...  Labeled controls and test samples were quantitatively adjusted based on the efficiency of the Cy dye incorporation and mixed with 30 l of hybridization solution (50% formamide, 1ϫ hybridization buffer;  ... 
doi:10.1128/aem.01675-13 pmid:24038680 pmcid:PMC3811541 fatcat:djc2lst23zewhocgukdtvpgmh4

COPASI and its applications in biotechnology

Frank T. Bergmann, Stefan Hoops, Brian Klahn, Ursula Kummer, Pedro Mendes, Jürgen Pahle, Sven Sahle
2017 Journal of Biotechnology  
A B S T R A C T COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields.  ...  It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages.  ...  Marina Kaiser is acknowledged for literature digging. Finally, we would like to acknowledge the members of the COPASI user forum for their active support.  ... 
doi:10.1016/j.jbiotec.2017.06.1200 pmid:28655634 pmcid:PMC5623632 fatcat:uebyrccn6rfhpnrj4sx6o3dmai

The use of differential evolution algorithm for solving chemical engineering problems

Elena Niculina Dragoi, Silvia Curteanu
2016 Reviews in chemical engineering  
Optimization is an important aspect in the chemical engineering area, especially when striving to obtain the best results with a minimum of consumed resources and a minimum of additional by-products.  ...  AbstractDifferential evolution (DE), belonging to the evolutionary algorithm class, is a simple and powerful optimizer with great potential for solving different types of synthetic and real-life problems  ...  DE, a real value EA, and a fully informed particle swarm (FIPS).  ... 
doi:10.1515/revce-2015-0042 fatcat:6ljdjoiozbddxcmklcom2irlxq

Kinetic models in industrial biotechnology – Improving cell factory performance

Joachim Almquist, Marija Cvijovic, Vassily Hatzimanikatis, Jens Nielsen, Mats Jirstrand
2014 Metabolic Engineering  
One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models.  ...  They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design  ...  Acknowledgments This work has been supported by the EU Framework VII project SYSINBIO -Systems Biology as a Driver for Industrial Biotechnology (call FP7-KBBE-2007-1).  ... 
doi:10.1016/j.ymben.2014.03.007 pmid:24747045 fatcat:7nankknr4batfkyvrgzx5mpl2m

CmpX Affects Virulence in Pseudomonas aeruginosa Through the Gac/Rsm Signaling Pathway and by Modulating c-di-GMP Levels

Anjali Y. Bhagirath, Deepti Somayajula, Yanqi Li, Kangmin Duan
2017 Journal of Membrane Biology  
Pseudomonas aeruginosa is the leading cause of morbidity and mortality in patients with chronic diseases, neutropenia and those with immunocompromise.  ...  Pulmonary infection with P. aeruginosa in patients with cystic fibrosis can result in respiratory failure and death.  ...  M9 minimal media was used as a control. B. Siderophore production assay for PA1611. PAO, PA(ΔPA1611), and PA(pAK1611) strains were grown overnight in the presence of 100 mM iron at 37°C.  ... 
doi:10.1007/s00232-017-9994-6 pmid:29063141 fatcat:rj5kcgygrbadlbp7y6cnkgmazu

Recent developments in parameter estimation and structure identification of biochemical and genomic systems

I-Chun Chou, Eberhard O. Voit
2009 Mathematical Biosciences  
BST was chosen for these tasks because of its unique structural flexibility and the fact that the structure and regulation of a biological system are mapped essentially one-to-one onto the parameters of  ...  The article concludes with a discussion of the present state of the art and with a description of open questions.  ...  Siren Veflingstad and two anonymous reviewers for critically reading the manuscript and providing constructive suggestions.  ... 
doi:10.1016/j.mbs.2009.03.002 pmid:19327372 pmcid:PMC2693292 fatcat:rqnk3f34w5g2xl4qcwicbnwtnm

Recent advances in wearable sensors for animal health management

Suresh Neethirajan
2017 Sensing and Bio-Sensing Research  
Globally, a number of sensors being produced for animal health management are at various stages of commercialization.  ...  This review paper discusses the scope of different wearable technologies for animals, nano biosensors and advanced molecular biology diagnostic techniques for the detection of various infectious diseases  ...  of Agriculture, Food and Rural Affairs (030143) for funding this study.  ... 
doi:10.1016/j.sbsr.2016.11.004 fatcat:dxwkpzjcrnbkjikznkychpljtm

A Special issue on Multidisciplinary research to promote the applications in Biological sciences

Guest Editor Dr. M. Manikandan
2022 International Journal of Life Science and Pharma Research  
The purpose of this special issue is to build a community of authors and readers to discuss the latest research and develop new ideas and research directions.  ...  This provides a platform for the researchers to publish their innovative research findings.  ...  Acknowledgement The authors express their gratitude towards the host institution and Biozone, Chennai.  ... 
doi:10.22376/ijpbs/ijlpr/sp22/2022.1-154 fatcat:rcydgammlzgodof3kw3fcdgpji

Microbial ureases: significance, regulation, and molecular characterization

H L Mobley, R P Hausinger
1989 Microbiological reviews  
Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha.  ...  Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits.  ...  ACKNOWLEDGMENTS We thank members of our laboratories for review of the manuscript, Martha Lynch for editorial assistance, and Jack Vaith for reprint retrieval.  ... 
pmid:2651866 pmcid:PMC372718 fatcat:i2omygzkzremzmbkmf2qudmsve

Microbial ureases: significance, regulation, and molecular characterization

H L Mobley, R P Hausinger
1989 Microbiological reviews  
ACKNOWLEDGMENTS We thank members of our laboratories for review of the manuscript, Martha Lynch for editorial assistance, and Jack Vaith for reprint retrieval.  ...  This work was supported by Public Health Service grants A122387 and A123328 from the National Institutes of Health and by the Michigan State University Agricultural Experimental Station.  ...  The product ammonia can be taken up and utilized by soil microbes and plants. However, in many environments the level of available nitrogen compounds is inadequate for optimal crop production.  ... 
doi:10.1128/mr.53.1.85-108.1989 fatcat:3ezfq6gjy5gzxeudbvfnowpvxi

Quorum Sensing and Phenazines are Involved in Biofilm Formation by Pseudomonas chlororaphis (aureofaciens) Strain 30-84

V. S. R. K. Maddula, Z. Zhang, E. A. Pierson, L. S. Pierson
2006 Microbial Ecology  
Antibiotics were used at the following concentrations (µg/µl) for Escherichia coli: ampicillin (100), gentamycin (25),Quantification of Pyocyanin (PYO).  ...  The phzI gene of Pseudomonas aureofaciens 30-84 is responsible for the production of a diffusible signal required for phenazine antibiotic production. Gene 168:49-53. 58. Zhang, Z., and L. S.  ...  Of the many, the Tn5 vectors, a series of 'plasposons' for mutagenesis and one-step cloning of the Tn mutation is very useful (Dennis and Zylstra 1998 developed.  ... 
doi:10.1007/s00248-006-9064-6 pmid:16897305 fatcat:3vqj5dpmnfdzdcuf3zqo636okm

DGHM Lecture 2015

2015 International Journal of Medical Microbiology  
Methods: We evaluated optimal hybridization and labeling conditions for the array by comparing experiments with reference strains to computed in silico hybridizations.  ...  Therefore EHEC will be incubated in EcN spent culture minimal medium and examined for the Stx production via a Stx-ELISA.  ...  Therefore, GPC can be used as a carbon source for S. aureus and GlpQ is important to metabolize this compound.  ... 
doi:10.1016/j.ijmm.2015.09.002 fatcat:yuxjcmjr4ffapmmbe54v2jofxy
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