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

Dietary Connections01:23

Dietary Connections

61.6K
In biological systems, most metabolic pathways are interconnected. The cellular respiration processes that convert glucose to ATP—such as glycolysis, pyruvate oxidation, and the citric acid cycle—tie into those that break down other organic compounds. As a result, various foods—from apples to cheese to guacamole—end up as ATP. In addition to carbohydrates, food also contains proteins and lipids—such as cholesterol and fats. All of these organic compounds are used...
61.6K
C4 Pathway and CAM01:27

C4 Pathway and CAM

48.9K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
48.9K
Functions of Connective Tissues01:17

Functions of Connective Tissues

14.9K
Connective tissues perform a broad range of functions in the body. Their primary function is to connect and link different tissues in the body and act as packaging material between tissues. The areolar tissue, a connective tissue prototype, commonly cements various tissue types in diverse body organs. In contrast, adipose tissue cushions internal organs while insulating the body from heat loss.
Hard connective tissues, such as bones and cartilage, provide structure and support to the body.
14.9K
Loose Connective Tissue01:26

Loose Connective Tissue

9.4K
Loose connective tissue is found between many organs. Its main function is to absorb shock and bind tissues together. It also allows water, salts, and various nutrients to diffuse into cells that are embedded in it or present in adjacent tissues.
Adipose Tissue
Adipose tissue consists primarily of fat storage cells called adipocytes and little extracellular matrix. A large number of capillaries present within adipose tissue allow rapid mobilization of lipid molecules. White adipose tissue is...
9.4K
Introduction to Connective Tissues01:11

Introduction to Connective Tissues

13.5K
Connective tissues are one of the four main tissue types in humans that are extensively present in the body. They are characterized by cells embedded in an extracellular matrix (ECM) composed of a ground substance and three main types of protein fibers— collagen, elastic, and reticular fibers. The ground substance of connective tissues can range from a watery and jelly-like consistency to mineralized and hard. The wide variety of cells in the connective tissues include fibroblasts,...
13.5K
Classification of Connective Tissues01:30

Classification of Connective Tissues

14.7K
The connective tissues have different properties and functions in the human body. They are broadly categorized into proper, supporting, or fluid connective tissues.
Connective Tissue Proper
Connective tissue proper is the most abundant class of connective tissues. As its name implies, it predominantly connects different tissues in the body. Depending on the cell types, ground substance, viscosity, and fiber types in the ECM, connective tissue proper is further categorized into loose and dense....
14.7K

You might also read

Related Articles

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

Sort by
Same author

<i>Escherichia coli</i> and <i>Salmonella</i>: their past, present, and future in scientific research and publications.

Microbiology and molecular biology reviews : MMBR·2026
Same author

The EcoCyc database (2025).

EcoSal Plus·2025
Same author

Revisiting the y-ome of Escherichia coli.

Nucleic acids research·2024
Same author

An evaluation of ChatGPT and Bard (Gemini) in the context of biological knowledge retrieval.

Access microbiology·2024
Same author

Improved BioCyc Operon Prediction: Revisiting the Operon Prediction Problem.

bioRxiv : the preprint server for biology·2024
Same author

The Genome Explorer genome browser.

mSystems·2024

Related Experiment Video

Updated: Jan 25, 2026

Measuring Nitrite and Nitrate, Metabolites in the Nitric Oxide Pathway, in Biological Materials using the Chemiluminescence Method
08:25

Measuring Nitrite and Nitrate, Metabolites in the Nitric Oxide Pathway, in Biological Materials using the Chemiluminescence Method

Published on: December 25, 2016

23.1K

Using Pathway Covering to Explore Connections among Metabolites.

Peter E Midford1, Mario Latendresse2, Paul E O'Maille3

  • 1Bioinformatics Research Group, SRI, International, Menlo Park, CA 94025, USA. midford@ai.sri.com.

Metabolites
|May 5, 2019
PubMed
Summary
This summary is machine-generated.

Interpreting metabolite changes is challenging. Pathway Covering is a new algorithm that identifies essential metabolic pathways, simplifying analysis of experimental metabolomics data.

Keywords:
BioCycmetabolite setsoptimizationpathwaysset theory

More Related Videos

Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography
13:26

Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography

Published on: August 11, 2016

12.7K
Identification and Quantification of Deranged Metabolites in Critically Ill Patients Using NMR-Based Metabolomics
11:02

Identification and Quantification of Deranged Metabolites in Critically Ill Patients Using NMR-Based Metabolomics

Published on: November 29, 2024

1.2K

Related Experiment Videos

Last Updated: Jan 25, 2026

Measuring Nitrite and Nitrate, Metabolites in the Nitric Oxide Pathway, in Biological Materials using the Chemiluminescence Method
08:25

Measuring Nitrite and Nitrate, Metabolites in the Nitric Oxide Pathway, in Biological Materials using the Chemiluminescence Method

Published on: December 25, 2016

23.1K
Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography
13:26

Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography

Published on: August 11, 2016

12.7K
Identification and Quantification of Deranged Metabolites in Critically Ill Patients Using NMR-Based Metabolomics
11:02

Identification and Quantification of Deranged Metabolites in Critically Ill Patients Using NMR-Based Metabolomics

Published on: November 29, 2024

1.2K

Area of Science:

  • Metabolomics
  • Systems Biology
  • Bioinformatics

Background:

  • Interpreting changes in metabolite abundance due to experimental treatments or disease states is a significant challenge in metabolomics.
  • Existing methods may not efficiently integrate pathway information with metabolite data.

Purpose of the Study:

  • To introduce and evaluate a novel algorithm, Pathway Covering, for identifying a minimal set of metabolic pathways that encompass a given list of metabolites.
  • To provide a computational tool that aids in the interpretation of metabolomics data by visualizing key metabolic pathways.

Main Methods:

  • The Pathway Covering algorithm takes a list of metabolites and determines a minimum-cost set of metabolic pathways covering all input metabolites.
  • Five cost functions were employed: constant cost, two large-pathway penalizing methods, a function-based preference, and a metabolic flux-based approach.
  • The algorithm's performance was assessed using datasets from the Metabolomics Workbench.

Main Results:

  • The Pathway Covering algorithm successfully identifies a minimum-cost set of metabolic pathways for a given list of metabolites.
  • The algorithm's output can be visualized as a 'pathway collage', highlighting the covered metabolites.
  • The algorithm is most effective when applied to statistically significant metabolites with defined fold-changes and directionality.

Conclusions:

  • Pathway Covering offers a robust method for interpreting complex metabolomics data by focusing on essential metabolic pathways.
  • The algorithm provides a valuable tool for researchers to understand biological responses to perturbations.
  • The Pathway Covering algorithm is integrated into Pathway Tools software and the BioCyc website for broader accessibility.