scholarly journals Efficient Reaction Deletion Algorithms for Redesign of Constraint-based Metabolic Networks for Metabolite Production with Weak Coupling

2021 ◽  
Vol 14 (0) ◽  
pp. 12-21
Author(s):  
Takeyuki Tamura
Keyword(s):  
Weak Coupling ◽  
Metabolic Networks ◽  
Metabolite Production

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

2021 ◽  
Vol 1 ◽  
Author(s):  
Yier Ma ◽  
Takeyuki Tamura
Keyword(s):  
Large Scale ◽  
Metabolic Networks ◽  
Solution Space ◽  
Design Strategies ◽  
Metabolite Production ◽  
Dynamic Solution ◽  
Space Division ◽  
A Genome ◽  
Balance Analysis ◽  
Genome Scale

Flux balance analysis (FBA) is a crucial method to analyze large-scale constraint-based metabolic networks and computing design strategies for strain production in metabolic engineering. However, as it is often non-straightforward to obtain such design strategies to produce valuable metabolites, many tools have been proposed based on FBA. Among them, GridProd, which divides the solution space into small squares by focusing on the cell growth rate and the target metabolite production rate to efficiently find the reaction deletion strategies, was extended to CubeProd, which divides the solution space into small cubes. However, as GridProd and CubeProd naively divide the solution space into equal sizes, even places where solutions are unlikely to exist are examined. To address this issue, we introduce dynamic solution space division methods based on CubeProd for faster computing by avoiding searching in places where the solutions do not exist. We applied the proposed method DynCubeProd to iJO1366, which is a genome-scale constraint-based model of Escherichia coli. Compared with CubeProd, DynCubeProd significantly accelerated the calculation of the reaction deletion strategy for each target metabolite production. 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 is one of the most effective methods in existence, could not. The developed software is available on https://github.com/Ma-Yier/DynCubeProd.

Hypoxic metabolism in wild rice (Zizania palustris): enzyme induction and metabolite production

1993 ◽  
Vol 89 (1) ◽  
pp. 165-171 ◽  
Author(s):  
Douglas G. Muench ◽  
O. William Archibold ◽  
Allen G. Good
Keyword(s):  
Enzyme Induction ◽  
Wild Rice ◽  
Metabolite Production ◽  
Zizania Palustris

Absorption and fluorescence study of an antiferromagnet with alternating strong and weak coupling : RbMnCl3

1984 ◽  
Vol 45 (7) ◽  
pp. 1143-1148 ◽  
Author(s):  
R. Moncorgé ◽  
B. Briat ◽  
J.C. Canit
Keyword(s):  
Weak Coupling ◽  
Fluorescence Study

De novo metabolite production through co-cultivation of different fungal species on solid media

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
A Azzollini ◽  
JL Wolfender ◽  
K Gindro
Keyword(s):  
De Novo ◽  
Fungal Species ◽  
Metabolite Production ◽  
Solid Media

Concrete mechanical behaviour and calcium leaching weak coupling

2006 ◽  
Vol 10 (9) ◽  
pp. 1147-1175 ◽  
Author(s):  
Laurie Lacarrièrre ◽  
Alain Sellier ◽  
Xavier Bourbon
Keyword(s):  
Mechanical Behaviour ◽  
Weak Coupling ◽  
Calcium Leaching

Analysis on Electricigen Genomes and Metabolic Networks

2012 ◽  
Vol 18 (6) ◽  
pp. 1075
Author(s):  
Jing GUO ◽  
Zixiang XU ◽  
Yaxing FU ◽  
Biyun LIU ◽  
Jing MENG ◽  
...  
Keyword(s):  
Metabolic Networks

MetaGen: a Promising Tool for Modeling Metabolic Networks From KEGG*

2010 ◽  
Vol 37 (1) ◽  
pp. 63-68 ◽  
Author(s):  
Ting-Ting ZHOU ◽  
Kin-Fung YUNG ◽  
Chung Keith CHAN Chun ◽  
Zheng-Hua WANG ◽  
Yun-Ping ZHU ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Promising Tool
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