Method for developing culture medium using genome information and in silico analysis
AssigneeKorea Advanced Institute of Science and Technology
InventorsSang Yup Lee, Ho Nam Chang, Hyohak Song, Tae Yong Kim, Bo-Kyung Choi
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Abstract
A method for developing a culture medium using genome information and in silico analysis. In one implementation, the method involves developing a minimal synthetic medium, including the steps of constructing a metabolic network using genome information of prokaryotic cell or eukaryotic cell, selecting components of the minimal synthetic medium removing any one among external metabolites from the constructed metabolic network and conducting metabolic flux analysis using in silico simulation, and determining a final culture medium by actual culture.
Claims17
A method for developing a culture medium using in silico analysis and genome information, comprising the steps of:
- (a) constructing a metabolic network using genome information of target eukaryotic cell or prokaryotic cell;
- (b) removing any one among external metabolites from the constructed metabolic network and conducting metabolic flux analysis using in silico simulation;
- (c) determining the removed external metabolite as a component of a minimal synthetic medium when a objective function value is 0 after the in silico simulation, wherein the objective function value is 0 if any one of the components required by eukaryotic or prokaryotic cell cannot be produced, or returning to step (b) when the objective function value is not 0;
- (d) confirming whether a relevant metabolite can be produced internally and used without providing it externally when relevant metabolic reaction formula exists after examining the relevant reaction formula and deficient enzymes through comparison with other organism species synthesizing the metabolite by itself;
- (e) determining components of a minimal synthetic medium determined by repeating steps (b) to (d) as a minimal synthetic medium for in silico;
- and
- (f) determining a final culture medium after culturing target eukaryotic or prokaryotic cells in the determined minimal synthetic medium for in silico.
A method for developing a culture medium for producing succinic acid using in silico analysis and genome information, comprising the steps of:
- (a) constructing a metabolic network using genome information of eukaryotic cell or prokaryotic cell having succinic acid-producing ability;
- (b) removing any one among external metabolites from the constructed metabolic network and conducting metabolic flux analysis using in silico simulation;
- (c) determining the removed external metabolite as a component of a minimal synthetic medium when a objective function value is 0 after the in silico simulation, wherein the objective function value is 0 if any one of the components required by eukaryotic or prokaryotic cell cannot be produced, or returning to step (b) when the objective function value is not 0;
- (d) confirming whether a relevant metabolite can be produced internally and used without providing it externally when relevant metabolic reaction formula exists after examining the relevant reaction formula and deficient enzymes through the comparison with other organism species synthesizing the metabolite by itself;
- (e) determining components of a minimal synthetic medium determined by repeating steps (b) to (d) as a minimal synthetic medium for in silico;
- and
- (f) determining a final culture medium after culturing target eukaryotic or prokaryotic cells having the ability to produce succinic acid in the determined the minimal synthetic medium for in silico.
Dependencies are inferred from the claim text.