Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Autophagy

Autophagy

Autophagy is a self-digesting process by which a cell protects itself from threats both within and outside the cell, ranging from abnormal proteins to invading bacteria. In this process, obsolete components of the cell and invading microbes are degraded by hydrolytic enzymes active in an acidic environment of the lysosomal lumen.
An autophagic pathway consists of a series of signaling events activated in response to diverse stress and physiological conditions such as food deprivation,...

Delivery Pathways to the Lysosome

Delivery Pathways to the Lysosome

Eukaryotic cells use different mechanisms to eliminate toxic waste obsolete and worn-out substances. Lysosomes play a pivotal role in this, and hence, these substances are carried to the lysosome from other parts of the cell and extracellular space through different pathways. The most elaborately studied pathways to the lysosome are the endocytic pathways.
Endocytosis
In endocytosis, the cell membrane takes up macromolecules and particles from the surrounding medium. Clathrin-mediated...

Autophagic Cell Death

Autophagic Cell Death

Christian de Duve discovered “autophagy,” a process in which cellular components are engulfed by membrane-bound organelles called autophagosomes. The autophagosomes then fuse with lysosomes to digest the enclosed contents. Autophagy is generally activated in cells to prevent cell death. However, cell death is triggered when the damage is beyond repair.
Autophagy and Apoptosis
Autophagy can activate apoptosis. In normal conditions, the autophagy activating protein Beclin-1 and...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....

You might also read

Related Articles

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

Sort by

Same author

A single-cell atlas identifies oncogenic transcriptional programs and immune escape mechanisms in CTCL.

Blood·2026

Same author

Deciphering the interaction of tetrabenazine with lactoferrin: Insights from molecular dynamics and multi-spectroscopic approaches.

International journal of biological macromolecules·2026

Same author

Antimicrobial efficacy of cyanobacterium Synechococcus pevalekii extracts against MDR bacteria and fungi; an integrated GC-MS, molecular docking and MD simulation study.

Antonie van Leeuwenhoek·2026

Same author

Systems Biology of the Microsatellite Signature in 156 Genomes of the Viral Family Rhabdoviridae.

Current microbiology·2026

Same author

Integrated bioactivity assessment of the cyanobacterium plectonema terebrans extract: an in vitro and in silico study.

Antonie van Leeuwenhoek·2026

Same author

Prospects and challenges in intracellular delivery of therapeutic proteins.

Pharmacological reports : PR·2026

Search research articles

Related Experiment Video

Updated: Aug 23, 2025

Evaluation of LC3-II Release via Extracellular Vesicles in Relation to the Accumulation of Intracellular LC3-positive Vesicles

Evaluation of LC3-II Release via Extracellular Vesicles in Relation to the Accumulation of Intracellular LC3-positive Vesicles

Published on: October 18, 2024

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.

Zarnain Jamil¹, Arif Uddin², Syed Sahajada Mahafujul Alam¹

¹Applied BioChemistry (ABC) Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India.

|October 27, 2022

Summary

This study analyzes codon usage bias in human autophagy genes, revealing low bias and identifying key evolutionary forces. Understanding these patterns is vital for comprehending autophagy

Keywords:

autophagy-related (ATG) genes codon usage bias minimum free energy (mFE)mutation pressure natural selection

More Related Videos

Assessing Autophagic Flux by Measuring LC3, p62, and LAMP1 Co-localization Using Multispectral Imaging Flow Cytometry

Assessing Autophagic Flux by Measuring LC3, p62, and LAMP1 Co-localization Using Multispectral Imaging Flow Cytometry

Published on: July 21, 2017

Study of Protein-protein Interactions in Autophagy Research

Study of Protein-protein Interactions in Autophagy Research

Published on: September 9, 2017

Related Experiment Videos

Last Updated: Aug 23, 2025

Evaluation of LC3-II Release via Extracellular Vesicles in Relation to the Accumulation of Intracellular LC3-positive Vesicles

Evaluation of LC3-II Release via Extracellular Vesicles in Relation to the Accumulation of Intracellular LC3-positive Vesicles

Published on: October 18, 2024

Assessing Autophagic Flux by Measuring LC3, p62, and LAMP1 Co-localization Using Multispectral Imaging Flow Cytometry

Assessing Autophagic Flux by Measuring LC3, p62, and LAMP1 Co-localization Using Multispectral Imaging Flow Cytometry

Published on: July 21, 2017

Study of Protein-protein Interactions in Autophagy Research

Study of Protein-protein Interactions in Autophagy Research

Published on: September 9, 2017

Area of Science:

Molecular Biology
Genomics
Evolutionary Biology

Background:

Autophagy is crucial in human diseases like cancer and neurodegenerative disorders.
Autophagy is regulated by autophagy-related (ATG) genes.
Codon usage bias (CUB) analysis offers insights into gene evolution and regulation.

Purpose of the Study:

To investigate the nucleotide composition and synonymous codon usage patterns of human autophagy genes.
To determine the influence of evolutionary forces on the CUB of these genes.

Main Methods:

Retrieved coding sequences (CDS) of human autophagy genes from NCBI.
Analyzed nucleotide composition and codon usage patterns using bioinformatics tools.
Calculated Effective Number of Codons (ENC) and Relative Synonymous Codon Usage (RSCU).

Main Results:

Human autophagy genes exhibit an overall low codon usage bias (mean ENC = 45.05).
Genes are marginally rich in GC content, influencing codon usage.
Identified 3 over-represented and 10 under-represented codons.

Conclusions:

Natural selection and mutational pressure are the primary drivers of CUB in human autophagy genes.
Findings contribute to understanding the genome biology and molecular evolution of autophagy.