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Related Concept Videos

Yeast Signaling01:28

Yeast Signaling

Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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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.
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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.
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Related Experiment Video

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Inferring the effective TOR-dependent network: a computational study in yeast.

Shahin Mohammadi1, Shankar Subramaniam, Ananth Grama

  • 1Department of Computer Science, Purdue University, West Lafayette, Indiana, USA. mohammadi@purdue.edu.

BMC Systems Biology
|September 6, 2013
PubMed
Summary
This summary is machine-generated.

Calorie restriction extends healthspan by inhibiting the target of rapamycin (TOR) pathway. This study computationally maps TOR effectors to identify key lifespan mediators and their network organization for anti-aging strategies.

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Area of Science:

  • Aging research
  • Systems biology
  • Computational biology

Background:

  • Calorie restriction (CR) is a conserved intervention extending healthspan across species.
  • The target of rapamycin (TOR) pathway mediates CR's effects by sensing nutrients and regulating cellular processes.
  • Inhibiting the TOR pathway genetically or pharmacologically mimics CR's healthspan benefits.

Purpose of the Study:

  • To create a computational map of TOR downstream effectors.
  • To identify key mediators of lifespan extension, their interactions, and network organization.
  • To discover novel targets for anti-aging interventions.

Main Methods:

  • Systematic tracing of information flow from the TOR complex.
  • Developing a statistical framework integrating information flow scores, gene expression data, and regulatory networks.
  • Analyzing differential gene expression in response to rapamycin treatment.

Main Results:

  • A comprehensive map of TOR downstream effectors was computationally derived.
  • The approach successfully identified known pathways and suggested novel targets.
  • A novel framework identified key transcription factors and constructed the TOR pathway's effective response network.

Conclusions:

  • The computational approach predicts cellular responses, including transcriptional and post-translational changes.
  • The effective response network enhances understanding of aging mechanisms and identifies new anti-aging targets.
  • This network can aid in identifying biomarkers for age-related diseases.