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

Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

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 years,...
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

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 years,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Biological Clocks and Seasonal Responses02:45

Biological Clocks and Seasonal Responses

The circadian—or biological—clock is an intrinsic, timekeeping, molecular mechanism that allows plants to coordinate physiological activities over 24-hour cycles called circadian rhythms. Photoperiodism is a collective term for the biological responses of plants to variations in the relative lengths of dark and light periods. The period of light-exposure is called the photoperiod.

You might also read

Related Articles

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

Sort by
Same author

Independent, ongoing clade-specific expansions of IS<i>5</i> elements in <i>Pseudomonas syringae</i>.

Microbial genomics·2026
Same author

The EPS-I exopolysaccharide transforms <i>Ralstonia</i> wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Psychedelic fungi.

Current biology : CB·2025
Same author

CLOCI: unveiling cryptic fungal gene clusters with generalized detection.

Nucleic acids research·2024
Same author

Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction.

mSystems·2024
Same author

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma.

PloS one·2023
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jul 3, 2026

Monitoring Cell-autonomous Circadian Clock Rhythms of Gene Expression Using Luciferase Bioluminescence Reporters
10:38

Monitoring Cell-autonomous Circadian Clock Rhythms of Gene Expression Using Luciferase Bioluminescence Reporters

Published on: September 27, 2012

Generalized Gene Cluster Detection Using CLOCI.

Zachary Konkel1, Jason Slot2

  • 1Department of Plant Pathology, The Ohio State University, Columbus, OH, USA. konkel.8@osu.edu.

Methods in Molecular Biology (Clifton, N.J.)
|July 2, 2026
PubMed
Summary
This summary is machine-generated.

We developed CLOCI, a new algorithm for unbiased detection of metabolic gene clusters (MGCs). CLOCI identifies novel MGC classes by analyzing gene evolution signatures, aiding small molecule discovery and understanding genome organization.

Keywords:
BiosyntheticDetectionFungiHomologous locusMetabolic gene clustersSynteny

More Related Videos

A User-friendly and Powerful R Analysis of Large-scale Datasets
10:56

A User-friendly and Powerful R Analysis of Large-scale Datasets

Published on: November 4, 2025

The Use of Mouse Splenocytes to Assess Pathogen-associated Molecular Pattern Influence on Clock Gene Expression
06:50

The Use of Mouse Splenocytes to Assess Pathogen-associated Molecular Pattern Influence on Clock Gene Expression

Published on: July 24, 2018

Related Experiment Videos

Last Updated: Jul 3, 2026

Monitoring Cell-autonomous Circadian Clock Rhythms of Gene Expression Using Luciferase Bioluminescence Reporters
10:38

Monitoring Cell-autonomous Circadian Clock Rhythms of Gene Expression Using Luciferase Bioluminescence Reporters

Published on: September 27, 2012

A User-friendly and Powerful R Analysis of Large-scale Datasets
10:56

A User-friendly and Powerful R Analysis of Large-scale Datasets

Published on: November 4, 2025

The Use of Mouse Splenocytes to Assess Pathogen-associated Molecular Pattern Influence on Clock Gene Expression
06:50

The Use of Mouse Splenocytes to Assess Pathogen-associated Molecular Pattern Influence on Clock Gene Expression

Published on: July 24, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Metabolic Engineering

Background:

  • Metabolic gene clusters (MGCs) are crucial genomic regions encoding diverse metabolic functions.
  • Current detection methods often overlook novel or uncommon MGC classes, limiting natural product discovery and ecological insights.
  • Unbiased algorithms are needed to comprehensively identify MGCs and understand genome organization.

Purpose of the Study:

  • To develop a generalized, unbiased algorithm for detecting all classes of MGCs.
  • To enable the discovery of novel natural products and uncharacterized MGCs.
  • To provide a more precise definition of genome organization through comprehensive MGC identification.

Main Methods:

  • CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier) was developed as a function-agnostic gene cluster detection algorithm.
  • CLOCI identifies signatures of coordinated gene evolution underlying MGCs.
  • The algorithm detects selection on gene colocalization by identifying homologous locus groups and uses proxies like gene loss and horizontal transfer to identify MGCs.

Main Results:

  • CLOCI provides a generalized framework for MGC detection, moving beyond canonical biosynthetic gene clusters.
  • The algorithm is capable of identifying previously overlooked MGC classes.
  • CLOCI facilitates a more comprehensive understanding of MGC repertoires and their evolutionary dynamics.

Conclusions:

  • CLOCI offers a powerful, unbiased approach to MGC identification, expanding the scope of natural product discovery.
  • This method enhances our ability to study the ecology and evolution of organisms by revealing a broader spectrum of MGCs.
  • CLOCI contributes to a more accurate and complete understanding of genome organization and metabolic potential.