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

Gene Regulation During Sporulation01:17

Gene Regulation During Sporulation

456
Sporulation is a complex developmental process that allows certain Gram-positive bacteria, such as Bacillus subtilis and Clostridium species, to survive extreme environmental conditions. This process is tightly regulated by a series of signaling cascades and transcriptional controls, ensuring the formation of a highly resistant endospore.Sporulation is triggered by unfavorable conditions, such as nutrient depletion, and is governed by a phosphorelay system. One of the sensor kinases, such as...
456
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

962
Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
962
Lysogenic Cycle of Bacteriophages00:43

Lysogenic Cycle of Bacteriophages

67.4K
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
67.4K
Lytic Cycle of Bacteriophages01:30

Lytic Cycle of Bacteriophages

77.5K
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
77.5K
Testosterone: Functions and Regulation01:26

Testosterone: Functions and Regulation

2.1K
The intricate hormonal interplay essential for male reproductive health begins with the release of gonadotropin-releasing hormone (GnRH) by the hypothalamus. This hormone prompts the pituitary gland to secrete follicle-stimulating hormone (FSH) and luteinizing hormone (LH). LH targets the Leydig cells in the testes, stimulating them to produce and release testosterone. In concert with testosterone, FSH acts on the Sertoli cells within the seminiferous tubules to facilitate the release of...
2.1K
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

4.5K
The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent...
4.5K

You might also read

Related Articles

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

Sort by
Same author

Nucleosome spacing across cell types, diseases, and ages.

Nucleic acids research·2026
Same author

CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.

Nucleic acids research·2025
Same author

Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor.

Genome medicine·2025
Same author

Predicting p53-dependent cell transitions from thermodynamic models.

The Journal of chemical physics·2024
Same author

Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor.

bioRxiv : the preprint server for biology·2024
Same author

Nucleosome reorganisation in breast cancer tissues.

Clinical epigenetics·2024

Related Experiment Video

Updated: Jan 22, 2026

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics
09:23

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics

Published on: January 5, 2024

2.5K

Predicting gene-regulation functions: lessons from temperate bacteriophages.

Vladimir B Teif1

  • 1Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Vladimir.Teif@bioquant.uni-heidelberg.de

Biophysical Journal
|April 8, 2010
PubMed
Summary

Predicting gene-regulation functions (GRFs) from DNA sequences is challenging. This study reveals complex GRFs in bacteriophage regulatory elements, suggesting non-Boolean logic and conserved topologies for functionally similar systems.

More Related Videos

Characterization and Functional Prediction of Bacteria in Ovarian Tissues
10:12

Characterization and Functional Prediction of Bacteria in Ovarian Tissues

Published on: October 23, 2021

3.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.7K

Related Experiment Videos

Last Updated: Jan 22, 2026

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics
09:23

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics

Published on: January 5, 2024

2.5K
Characterization and Functional Prediction of Bacteria in Ovarian Tissues
10:12

Characterization and Functional Prediction of Bacteria in Ovarian Tissues

Published on: October 23, 2021

3.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.7K

Area of Science:

  • * Molecular Biology
  • * Systems Biology
  • * Bioinformatics

Background:

  • * Gene-regulation functions (GRFs) characterize cis-regulatory modules (CRMs) by linking transcription factor concentrations to promoter activity.
  • * Predicting GRFs directly from DNA sequences remains a significant challenge in molecular biology.

Purpose of the Study:

  • * To systematically analyze and predict GRFs from the sequences of lysogeny-lysis CRMs in various temperate bacteriophages.
  • * To explain experimental observations, such as the role of Cro protein in the lambda phage switch.
  • * To develop a framework for understanding and modeling complex gene regulation.

Main Methods:

  • * Comparative analysis of CRMs from Lactobacillus casei phage A2, Escherichia coli phages lambda and 186, and Lactococcal phage TP901-1.
  • * Investigating the impact of DNA looping and long-range interactions on GRFs.
  • * Applying non-Boolean logic models to describe GRF behavior.

Main Results:

  • * Complex GRFs arise from factors like DNA looping and multilayer assembly, defying simple linear models.
  • * A three-state non-Boolean logic adequately describes the studied CRMs, unlike Boolean logic.
  • * Conserved GRF topologies were observed across different phage CRMs, suggesting potential universality.
  • * Identified transformations enable GRF shaping for system-level analysis.

Conclusions:

  • * GRFs are complex and cannot always be reduced to linear functions of binding site occupancy or simple Boolean logic.
  • * Functional equivalence of CRMs may correlate with topological equivalence of their GRFs.
  • * The findings provide a foundation for predicting and modeling gene regulation in diverse genetic systems.