Identifying Gene Knockout Strategy Using Bees Hill Flux Balance Analysis (BHFBA) for Improving the Production of Succinic Acid and Glycerol in Saccharomyces cerevisiae

2013 ◽  
pp. 223-233
Author(s):  
Yee Wen Choon ◽  
Mohd Saberi Mohamad ◽  
Safaai Deris ◽  
Rosli Md. Illias ◽  
Lian En Chai ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Succinic Acid ◽  
Flux Balance Analysis ◽  
Gene Knockout ◽  
Flux Balance ◽  
Balance Analysis

A simple metabolic flux balance analysis of biomass and bioethanol production in Saccharomyces cerevisiae fed-batch cultures

2011 ◽  
Vol 16 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Iliana Barrera-Martínez ◽  
R. Axayácatl González-García ◽  
Edgar Salgado-Manjarrez ◽  
Juan S. Aranda-Barradas
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Flux Balance Analysis ◽  
Metabolic Flux ◽  
Bioethanol Production ◽  
Fed Batch ◽  
Batch Cultures ◽  
Flux Balance ◽  
Balance Analysis

scholarly journals Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yee Wen Choon ◽  
Mohd Saberi Mohamad ◽  
Safaai Deris ◽  
Chuii Khim Chong ◽  
Sigeru Omatu ◽  
...  
Keyword(s):  
Growth Rate ◽  
Flux Balance Analysis ◽  
Gene Knockout ◽  
Combinatorial Problem ◽  
Production Yield ◽  
Model Organisms ◽  
Computational Time ◽  
Vast Number ◽  
Flux Balance ◽  
Balance Analysis

Microbial strain optimisation for the overproduction of a desired phenotype has been a popular topic in recent years. Gene knockout is a genetic engineering technique that can modify the metabolism of microbial cells to obtain desirable phenotypes. Optimisation algorithms have been developed to identify the effects of gene knockout. However, the complexities of metabolic networks have made the process of identifying the effects of genetic modification on desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to a combinatorial problem in obtaining optimal gene knockout. The computational time increases exponentially as the size of the problem increases. This work reports an extension of Bees Hill Flux Balance Analysis (BHFBA) to identify optimal gene knockouts to maximise the production yield of desired phenotypes while sustaining the growth rate. This proposed method functions by integrating OptKnock into BHFBA for validating the results automatically. The results show that the extension of BHFBA is suitable, reliable, and applicable in predicting gene knockout. Through several experiments conducted onEscherichia coli, Bacillus subtilis, andClostridium thermocellumas model organisms, extension of BHFBA has shown better performance in terms of computational time, stability, growth rate, and production yield of desired phenotypes.

scholarly journals Producing Succinic Acid in Yeast using A Hybrid of Differential Evolution and Flux Balance Analysis

2013 ◽  
Vol 5 (6) ◽  
pp. 91-100 ◽  
Author(s):  
Ana Haziqah Rashid ◽  
Yee Wen Choon ◽  
Mohd Saberi Mohamad ◽  
Lian En Chai ◽  
Chuii Khim Chong ◽  
...  
Keyword(s):  
Differential Evolution ◽  
Succinic Acid ◽  
Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis

Gene knockout identification for metabolite production improvement using a hybrid of genetic ant colony optimization and flux balance analysis

2015 ◽  
Vol 20 (4) ◽  
pp. 685-693 ◽  
Author(s):  
Abdul Hakim Mohamed Salleh ◽  
Mohd Saberi Mohamad ◽  
Safaai Deris ◽  
Sigeru Omatu ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
Ant Colony Optimization ◽  
Flux Balance Analysis ◽  
Gene Knockout ◽  
Ant Colony ◽  
Metabolite Production ◽  
Flux Balance ◽  
Production Improvement ◽  
Balance Analysis

Identifying a gene knockout strategy using a hybrid of the bat algorithm and flux balance analysis to enhance the production of succinate and lactate in Escherichia coli

2015 ◽  
Vol 20 (2) ◽  
pp. 349-357 ◽  
Author(s):  
Pooi San Chua ◽  
Abdul Hakim Mohamed Salleh ◽  
Mohd Saberi Mohamad ◽  
Safaai Deris ◽  
Sigeru Omatu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Flux Balance Analysis ◽  
Gene Knockout ◽  
Bat Algorithm ◽  
Flux Balance ◽  
Balance Analysis

scholarly journals Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e43006 ◽  
Author(s):  
Carlos Eduardo García Sánchez ◽  
César Augusto Vargas García ◽  
Rodrigo Gonzalo Torres Sáez
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Flux Balance Analysis ◽  
Flux Balance ◽  
Optimization Function ◽  
Balance Analysis
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