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

Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

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...
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Gene Regulation in Microbial Communities: Quorum Sensing01:28

Gene Regulation in Microbial Communities: Quorum Sensing

Quorum sensing is a mechanism of bacterial communication that enables coordinated gene expression in response to changes in population density. This facilitates collective behaviors that enhance survival, resource acquisition, and ecological adaptation. This process relies on small signaling molecules called autoinducers that accumulate as bacterial populations grow. When a critical threshold concentration of autoinducers is reached, bacterial cells collectively modify gene expression,...
Mutations in Microorganisms01:18

Mutations in Microorganisms

Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...

You might also read

Related Articles

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

Sort by
Same author

We wait for disease to shout-What if we listened when biology whispered?

Cell systems·2026
Same author

A lifespan clock tells the biology of time.

Nature medicine·2025
Same author

Bile acids segregate metabolic syndrome in a cohort of 100 deeply phenotyped horses.

Communications biology·2025
Same author

Early Detection of Wellness-to-Disease Transitions in the AI Era: Implications for Pharmacology and Toxicology.

Annual review of pharmacology and toxicology·2025
Same author

Placental network differences among obstetric syndromes identified with an integrated multiomics approach.

Communications biology·2025
Same author

<i>APOE</i> genotype and biological age impact inter-omic associations related to bioenergetics.

Aging·2025
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: May 26, 2026

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

Genetic co-occurrence network across sequenced microbes.

Pan-Jun Kim1, Nathan D Price

  • 1Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America.

Plos Computational Biology
|January 6, 2012
PubMed
Summary
This summary is machine-generated.

We mapped gene co-occurrence (correlogs) and anti-occurrence (anti-correlogs) in bacteria. This reveals functional gene relationships, aiding synthetic biology and understanding microbial communities.

More Related Videos

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

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Related Experiment Videos

Last Updated: May 26, 2026

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

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

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Organismal phenotype arises from gene product interactions, shaping genome evolution.
  • Genomes serve as historical records of gene associations within natural lifestyles.

Purpose of the Study:

  • To construct a comprehensive map of gene-gene co-occurrence (correlogs) and anti-occurrence (anti-correlogs) across bacterial species.
  • To identify and quantify direct gene associations, distinguishing functional interactions from indirect correlations.

Main Methods:

  • Analyzed thousands of orthologs across approximately 600 bacterial species.
  • Adapted methods from reverse engineering transcriptional regulatory networks to quantify gene associations.
  • Utilized phylogenetic profiling to infer functional gene coupling.

Main Results:

  • Developed a gene association map revealing correlogous (co-occurring) and anti-correlogous (non-co-occurring) gene pairs.
  • Correlogous associations strongly correlate with physically interacting proteins and co-expressed transcripts, identifying functionally obligatory interactions.
  • Discovered a global organization of gene association modules interconnected by anti-correlogous crosstalk.

Conclusions:

  • Gene association maps provide insights into functional gene relationships and genome evolution.
  • Phylogenetic profiling effectively infers gene functional coupling, applicable to diverse microbial communities.
  • This approach can guide gene import strategies in synthetic biology.