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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,...

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Related Experiment Video

Updated: Apr 17, 2026

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Published on: May 3, 2013

Structured illumination microscopy and correlative microscopy to study autophagy.

Laure-Anne Ligeon¹, Nicolas Barois², Elisabeth Werkmeister³

¹Cellular Microbiology and Physics of Infection, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, F-59021 Lille, France; CNRS UMR8204, F-59021 Lille, France; University of Lille-Nord de France, F-59021 Lille, France.

Methods (San Diego, Calif.)

|February 11, 2015

Summary

Autophagy recycles cellular components. Correlative light and electron microscopy (CLEM) helps distinguish LC3-associated phagocytosis (LAP) from autophagosomes by analyzing LC3 protein localization and vacuole structure.

Keywords:

Autophagy Correlative light-electron microscopy LC3-associated phagocytosis Structured illumination microscopy

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Last Updated: Apr 17, 2026

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

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Published on: May 3, 2013

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Published on: March 31, 2023

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

Published on: July 21, 2017

Area of Science:

Cell Biology
Molecular Biology
Microscopy Techniques

Background:

Autophagy is a fundamental eukaryotic process for cellular degradation and recycling.
This pathway is vital across the tree of life and is more complex than initially understood.
Recent research has identified novel routes like LC3-associated phagocytosis (LAP) and non-canonical autophagy.

Purpose of the Study:

To highlight the utility of correlative light electron microscopy (CLEM) in addressing complex autophagy questions.
To differentiate between autophagosomes and LAP vacuoles using advanced imaging techniques.
To investigate the recruitment and localization of autophagy-related (Atg) proteins.

Main Methods:

Structured Illumination Microscopy (SIM) for visualizing Atg protein dynamics.
Light microscopy for tracking LC3 protein recruitment.
Electron microscopy for ultrastructural analysis of LC3-vacuoles.
Correlative Light and Electron Microscopy (CLEM) to combine these approaches.

Main Results:

SIM enables detailed observation of Atg protein recruitment during autophagy.
LC3 recruitment is effectively monitored via light microscopy.
Electron microscopy provides crucial ultrastructural details of LC3-vacuoles.
CLEM successfully integrates light and electron microscopy data.

Conclusions:

CLEM is a powerful tool for resolving ambiguities in autophagy research.
The combined approach aids in distinguishing between LAP and canonical autophagosomes.
This methodology enhances the understanding of autophagy pathway complexity and regulation.