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 Stress Responses in Bacteria01:30

Other Stress Responses in Bacteria

110
Bacteria have global regulatory systems that control several types of stress mechanisms. These include Pho regulon and the heat shock response, which are essential systems for environmental adaptation, such as nutrient limitation and proteotoxic stress. The Pho regulon and the heat shock response exemplify bacterial resilience, enabling rapid adaptation to fluctuating environmental conditions.Pho RegulonBacteria require phosphorus for essential cellular processes, including nucleic acid...
110
Applications of Stress01:04

Applications of Stress

432
Consider a structure made of a boom and a rod designed to support a load. These two components are connected by a pin and stabilized by brackets and pins. The boom and the rod are detached from their supports to assess the different stresses imposed on this structure, and a free-body diagram is drawn. Then, all the forces applied, including the load acting on the structure, are identified. The reaction forces exerted on both the boom and the rod are computed using the equilibrium equations.
The...
432
Ribosome Profiling02:24

Ribosome Profiling

3.7K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.7K
Stress Response System01:21

Stress Response System

337
The stress response system, also known as the fight-or-flight response, is the body's automatic physiological reaction to perceived threats. Hans Selye introduced the concept of General Adaptation Syndrome (GAS) to describe the predictable pattern of changes that occur in response to stress. GAS consists of three sequential stages: alarm, resistance, and exhaustion. This model helps explain how chronic stress can contribute to health problems.
Alarm stage
In the alarm stage, the body's...
337
Protein Networks02:26

Protein Networks

4.1K
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,...
4.1K
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

225
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
225

You might also read

Related Articles

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

Sort by
Same author

Nutritional and Biochemical Diversity in Beans Accessions from Three <i>Phaseolus</i> Species Using Multiomics Characterization.

ACS nutrition science·2026
Same author

Unraveling Plant Recombination Patterns: Insights From Genome k-mers.

Plant direct·2025
Same author

Evolving Treatment of Opioid Use Disorder in American Family Physician.

American family physician·2025
Same author

Methylomes as key features for predicting recombination in some plant species.

Plant molecular biology·2024
Same author

Prediction of crossover recombination using parental genomes.

PloS one·2023
Same author

Corrigendum: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization.

Frontiers in plant science·2023

Related Experiment Video

Updated: Oct 14, 2025

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.5K

Identifying stress responsive genes using overlapping communities in co-expression networks.

Camila Riccio-Rengifo1, Jorge Finke2, Camilo Rocha2

  • 1Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana, Cali, Colombia. camila.riccio@javerianacali.edu.co.

BMC Bioinformatics
|November 8, 2021
PubMed
Summary

This study introduces a new workflow to pinpoint plant genes responding to treatments, like salt stress in rice. It identifies 19 key rice genes for improving salinity tolerance.

Keywords:
Co-expression networkLASSOOryza sativaOverlapping communitiesPhenotypic traitsRiceSalinityStress-responsive genes

More Related Videos

Measurements of Physiological Stress Responses in C. Elegans
10:36

Measurements of Physiological Stress Responses in C. Elegans

Published on: May 21, 2020

14.3K
Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

3.7K

Related Experiment Videos

Last Updated: Oct 14, 2025

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.5K
Measurements of Physiological Stress Responses in C. Elegans
10:36

Measurements of Physiological Stress Responses in C. Elegans

Published on: May 21, 2020

14.3K
Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

3.7K

Area of Science:

  • Plant genetics
  • Molecular biology
  • Bioinformatics

Background:

  • Identifying genes responsive to specific treatments is crucial for crop improvement.
  • Existing methods may not fully capture complex gene-regulatory networks.

Purpose of the Study:

  • To develop and validate a novel workflow for identifying treatment-responsive genes in plants.
  • To extend and generalize Weighted Gene Co-expression Network Analysis (WGCNA) for enhanced gene discovery.

Main Methods:

  • RNA sequencing read counts and phenotypic data analyzed.
  • Hierarchical Link Clustering used for module detection in gene co-expression networks.
  • LASSO regression applied to link gene modules with phenotypic responses.

Main Results:

  • Workflow applied to rice (Oryza sativa) under salt stress.
  • Identified 19 candidate genes involved in salt stress response.
  • Genes associated with shoot potassium content, shoot biomass, and root biomass.

Conclusions:

  • Introduced a framework to effectively reduce the search space for treatment-responsive genes.
  • Facilitates experimental validation by focusing on a smaller subset of high-relevance genes.
  • Provides potential target genes for enhancing rice salinity tolerance.