Metabolic Reconstruction
Metabolic Reconstruction - Related Videos
00:52
What is Metabolism?
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2019
Overview Metabolism represents all of the chemical activity in a cell, including reactions that build molecules (anabolism) and those that break molecules down (catabolism). Anabolic reactions require energy, whereas catabolic reactions provide it. Thus, metabolism describes how cells transform energy through a variety of chemical reactions, which are often made more efficient with the help of enzymes. Metabolism Is the Sum of All of the Chemical Reactions That Take Place in an Organism
05:41
Metabolic Profile Analysis of Zebrafish Embryos
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Cited by 42 •
2013
Zebrafish represent a powerful vertebrate model that has been under-utilised for metabolic studies. Here we describe a rapid way to measure the in vivo metabolic profile of developing zebrafish that allows the comparison of different mitochondrial function parameters between genetically or pharmacologically manipulated embryos, thereby increasing the applicability of this organism.
10:19
An Introduction to Cell Metabolism
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2023
In cells, critical molecules are either built by joining together individual units like amino acids or nucleotides, or broken down into smaller components. Respectively, the reactions responsible for this are referred to as anabolic and catabolic. These reactions require or produce energy typically in the form of a “high-energy” molecule called ATP. Together, these processes make up “Cell Metabolism,” and are hallmarks of healthy, living cells.JoVE’s introduction to cell metabolism briefly...
08:28
Metabolic Labeling
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2023
Metabolic labeling is used to probe the biochemical transformations and modifications that occur in a cell. This is accomplished by using chemical analogs that mimic the structure of natural biomolecules. Cells utilize analogs in their endogenous biochemical processes, producing compounds that are labeled. The label allows for the incorporation of detection and affinity tags, which can then be used to elucidate metabolic pathways using other biochemical analytical techniques, such as SDS-PAGE...
06:59
Characterization of Metabolic Status in Nonhuman Primates with the Intravenous Glucose Tolerance Test
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Cited by 7 •
2016
The goal of this protocol is to present a standard method to perform intravenous glucose tolerance tests (IVGTTs) to assess glycemic control in nonhuman primates and assess their metabolic status from healthy to dysmetabolic.
FAQs
Genome annotation provides the starting link between sequence information and candidate metabolic functions. During reconstruction, researchers associate annotated genes with enzyme-catalyzed reactions and connect those reactions through shared metabolites. This converts gene-level evidence into a network that can be examined for possible cellular material and energy flows. The quality of these associations directly affects model predictions.
Stoichiometric constraints describe how reaction quantities must relate within the network, allowing researchers to evaluate feasible material and energy flows rather than arbitrary combinations. When paired with flux balance analysis, these constraints support predictions under defined environmental conditions. Changing those conditions can therefore reveal altered nutrient requirements, growth possibilities, or metabolic limitations.
A reconstructed network can be analyzed after representing the loss of a gene-associated reaction, allowing researchers to examine possible changes in cellular metabolism. The resulting predictions may indicate altered growth, nutrient requirements, or metabolic bottlenecks. Comparing these outcomes with the undeleted model helps generate hypotheses about gene function and guides experiments in microbial physiology.
The workflow begins with a genome sequence and its annotation, followed by identification of associated enzyme-catalyzed reactions and metabolites. Researchers then assemble these elements into a network and apply stoichiometric constraints. Under defined environmental conditions, flux balance analysis can evaluate possible flows and produce predictions about growth, nutrient use, or metabolic limitations.
Researchers use this approach when they need to connect genome information with broader cellular behavior. In microbial physiology and systems biology, models can examine growth, nutrient requirements, and metabolic bottlenecks. The same framework supports biotechnology studies and investigations of disease-associated metabolic alterations, where predicted network behavior can help focus experimental questions.
Predicted growth patterns, nutrient requirements, bottlenecks, and responses to environmental changes provide testable expectations about cellular metabolism. Researchers can use these results to formulate hypotheses and design experiments, including studies of gene deletions. Agreement or disagreement between predictions and observations helps identify which metabolic relationships merit further investigation within the biological system.