Advertisement

Topics

A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models.

08:00 EDT 22nd September 2018 | BioPortfolio

Summary of "A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models."

Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silico gene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites production. Global optimization algorithms have been widely used for identifying gene knockout strategies. However, their productions were less than theoretical maximum and the algorithms are easily trapped into local optima. These algorithms also require a very large computation time to obtain acceptable results. This is due to the complexity of the metabolic models which are high dimensional and contain thousands of reactions. In this paper, a hybrid algorithm of Cuckoo Search and Minimization of Metabolic Adjustment is proposed to overcome the aforementioned problems. The hybrid algorithm searches for the near-optimal set of gene knockouts that leads to the overproduction of metabolites. Computational experiments on two sets of genome-scale metabolic models demonstrate that the proposed algorithm is better than the previous works in terms of growth rate, Biomass Product Couple Yield, and computation time.

Affiliation

Journal Details

This article was published in the following journal.

Name: Computers in biology and medicine
ISSN: 1879-0534
Pages: 112-119

Links

DeepDyve research library

PubMed Articles [10662 Associated PubMed Articles listed on BioPortfolio]

A hybrid Q-learning sine-cosine-based strategy for addressing the combinatorial test suite minimization problem.

The sine-cosine algorithm (SCA) is a new population-based meta-heuristic algorithm. In addition to exploiting sine and cosine functions to perform local and global searches (hence the name sine-cosine...

Maintaining maximal metabolic flux by gene expression control.

One of the marvels of biology is the phenotypic plasticity of microorganisms. It allows them to maintain high growth rates across conditions. Studies suggest that cells can express metabolic enzymes a...

Metabolic Signaling to the Nucleus in Cancer.

Nutrient-sensing mechanisms ensure that cellular activities are coordinated with nutrient availability. Recent work has established links between metabolite pools and protein post-translational modifi...

Metabolic Adjustment of Arabidopsis Root Suspension Cells during Adaptation to Salt Stress and Mitotic Stress Memory.

Sessile plants reprogram their metabolic and developmental processes during adaptation to prolonged environmental stresses. To understand the molecular mechanisms underlying adaptation of plant cells ...

Study of the metabolomic relationship between lung cancer and chronic obstructive pulmonary disease based on direct infusion mass spectrometry.

The high prevalence of lung cancer (LC) has triggered the search of biomarkers for early diagnosis of this disease. For this purpose the study of metabolic changes related to the development of lung c...

Clinical Trials [4240 Associated Clinical Trials listed on BioPortfolio]

Hybrid SA RGP Center/S-H Skirt Daily Wear 90 Day Multicenter Study

The purpose of the study is to demonstrate that the SynergEyes SA Hybrid Contact Lens clinical performance is substantially equivalent to that of the SynergEyes A Hybrid Lens when studied:...

Hybrid APC Assisted EMR for Large Colon Polyps

The purpose of this study to evaluate and examine, weather use of Hybrid Argon Plasma Coagulation (APC) as adjunct to endoscopic mucosal resection (EMR) will reduce the risk of residual or...

Genomewide Search for Loci Underlying Metabolic Syndrome

To identify the genes involved in the metabolic syndrome.

The Role of Platelet Surface α2β1 Integrin Expression as a Risk Factor in Thrombotic and/or Bleeding Complications

This study will begin to define these critical determinants for patients undergoing procedures in the hybrid interventional cardiology/cardiac surgery suite. In future studies, the data o...

Alcohol Consumption and Circulating Metabolites

Alcohol consumption is a risk factor for numerous health conditions and an important cause of death. Identifying metabolites associated with alcohol consumption may provide insights into t...

Medical and Biotech [MESH] Definitions

Volume of biological fluid completely cleared of drug metabolites as measured in unit time. Elimination occurs as a result of metabolic processes in the kidney, liver, saliva, sweat, intestine, heart, brain, or other site.

Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.

Brain disorders resulting from inborn metabolic errors, primarily from enzymatic defects which lead to substrate accumulation, product reduction, or increase in toxic metabolites through alternate pathways. The majority of these conditions are familial, however spontaneous mutation may also occur in utero.

The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.

Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Relevant Topic

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...


Searches Linking to this Article