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N - CBS
N - CBS

... Molecular INTeraction database. (2002) FEBS Letters, 513(1);135-140. ...
Pantesin HF55
Pantesin HF55

... Pantesin HF55 Pantesin is a high-quality pharmaceutical grade branded form of Pantethine that is a biological active form of Vitamin B5. Pantethine forms the reactive component of Coenzyme A (CoA) and the acyl-carrier protein (ACP). CoA and ACP are extensively involved in carbohydrate, lipid and ami ...
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Phase 1 - Systems Biology Research Group

... –OptKnock: Optknock is a bi-level algorithm that suggests gene deletion strategies leading to the forced overproduction of a specified growth-coupled target metabolite. Briefly, it searches the defined constraint space while simultaneously optimizing for both growth rate and target metabolite secret ...
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Elucidating the essentiality of essential genes in E. coli K-12
Elucidating the essentiality of essential genes in E. coli K-12

... We recently established single-gene deletion library for all of the predicted genes of E. coli K-12 by Wanner’s method [1] and simultaneously 303 genes have been predicted as essential genes in LB medium [2]. Elucidating the essentiality of these essential genes is a key to understand the system lev ...
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Course Specifications General Information

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... • On the other hand, introducing heterologous enzymes subject to different regulatory mechanisms can also result in the release of a bottleneck. • For example, overexpressing a mutated (insensitive to L-phenylalanine) E. coli gene that encoded the bifunctional enzyme chorismate mutase–prephenate deh ...
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Food Biotechnology Dr. Tarek Elbashiti

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Identification of all gene functions within reach

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... To begin breaking down fat, the body breaks triglycerides into glycerol and fatty acids  Most of the energy is stored in the fatty acids (glycerol can be converted to glucose or pyruvate)  Fatty acids usually produce substantially more ATP than glucose (16 carbon fatty acid = 129 ATP) ...
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Mapping the DNA Damage Response

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Inherited Metabolic Diseases Program (IMDP)

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Chapter 4 - Cellular Metabolism

... The enzymes controlling either an anabolic or catabolic sequence of reactions must act in a specific order. B. A sequence of enzyme-controlled reactions is called a metabolic pathway. C. Regulation of Metabolic Pathways ...
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... system, which involves a series of proteins that can carry out the energy transfer reactions. Note the role of atmospheric oxygen in this! ...
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ppt - Chair of Computational Biology

... (a) With advanced biochemical techniques, years of research have led to the precise characterization of individual reactions. As a result, the complete stoichiometries of many metabolic reactions have been characterized. (b) Most of these reactions have been grouped into `traditional pathways' (e.g. ...
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lecture notes-molecular biology-web

... When the cell has an energetically favorable carbon-energy source available, ...
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Metabolic network modelling



Metabolic network reconstruction and simulation allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the Citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.In general, the process to build a reconstruction is as follows: Draft a reconstruction Refine the model Convert model into a mathematical/computational representation Evaluate and debug model through experimentation↑
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