Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Other Glycolytic Pathways01:24

Other Glycolytic Pathways

The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
Introduction to Metabolism01:30

Introduction to Metabolism

Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...
Operon Model01:23

Operon Model

The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Glycolysis01:23

Glycolysis

Glycolysis, the Embden-Meyerhof pathway, is a central metabolic pathway involved in glucose catabolism. It is highly conserved across most organisms, reflecting its fundamental role in cellular energy production. This process occurs in the cytoplasm and can function both in the presence and absence of oxygen, making it versatile for various organisms and environmental conditions.Stages of GlycolysisGlycolysis is a ten-step pathway that converts glucose into pyruvate, generating a net gain of...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Mental health, biological aging, and lifestyle mediate the associations between social determinants of health and dementia.

Journal of advanced research·2026
Same author

Integrated physiological, transcriptomic, and metabolomic analysis of exogenous trehalose regulating cold tolerance in grape callus.

BMC plant biology·2026
Same author

CXCL10/SLC11A1 Axis Exacerbates Septic Liver Injury by Regulating Neutrophil Extracellular Traps Formation to Drive Macrophage Pro‑Inflammatory Polarization.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Admission body temperature and in-hospital mortality in critically ill children with pneumonia: a retrospective cohort study.

BMC pediatrics·2026
Same author

Bone marrow plasma cytokine composition indicates acute myeloid leukemia progression and treatment response.

Frontiers in cell and developmental biology·2026
Same author

Effects of Deheading and Intestinal Removal on Protein Degradation and Quality Changes in Chilled <i>Litopenaeus vannamei</i>.

Foods (Basel, Switzerland)·2026

Related Experiment Video

Updated: Jun 6, 2026

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Pathway knockout and redundancy in metabolic networks.

Yong Min1, Xiaogang Jin, Ming Chen

  • 1College of Computer Sciences, Zhejiang University, Hangzhou 310027, China. myong@zju.edu.cn

Journal of Theoretical Biology
|November 16, 2010
PubMed
Summary

This study introduces a new pathway knockout algorithm to better measure redundancy in cellular networks. The method improves upon existing tools by analyzing elementary flux modes (EFMs) under various perturbation scenarios.

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Related Experiment Videos

Last Updated: Jun 6, 2026

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Area of Science:

  • Systems Biology
  • Metabolic Networks
  • Network Robustness

Background:

  • Cellular network stability relies on component redundancy (genes, enzymes, pathways).
  • Quantifying this redundancy in metabolic networks remains a challenge.
  • Existing methods lack effectiveness in diverse perturbation scenarios.

Purpose of the Study:

  • To develop an improved quantitative measure for redundancy in metabolic networks.
  • To address limitations of current redundancy estimation tools.
  • To analyze redundancy under targeted attacks and different knockout strategies.

Main Methods:

  • Development of a pathway knockout algorithm based on elementary flux mode (EFM) analysis.
  • Calculation of redundancy as the average ratio of remaining EFMs post-knockout.
  • Comparison with enzyme knockout methods using mean-field analysis.
  • Validation in metabolic networks of Escherichia coli, human hepatocytes, and erythrocytes.

Main Results:

  • The pathway knockout algorithm provides a more comprehensive redundancy measure, especially under targeted attacks.
  • Mean-field analysis shows pathway knockout offers insights beyond single or multiple enzyme knockouts.
  • Redundancy in essential and non-essential amino acid sub-networks of E. coli is found to be similar, with essential pathways potentially being more redundant.

Conclusions:

  • The proposed pathway knockout algorithm enhances the quantitative assessment of metabolic network redundancy.
  • Pathway knockout captures structural asymmetries missed by enzyme knockout.
  • The findings challenge previous assumptions about redundancy in essential amino acid synthesis pathways.