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Accumulation of ubiquitinated protein aggregates is a hallmark of most aging-related neurodegenerative disorders. Autophagy has been found to be involved in the selective clearance of these protein aggregates, and this process is called aggrephagy. Here we provide two protocols for the investigation of protein aggregation and their removal by autophagy using western blotting and immunofluorescence techniques in Drosophila brain. Investigating the role of aggrephagy at the cellular and organismal level is important for the development of therapeutic interventions against aging-related diseases.

Assays to Monitor Aggrephagy in Drosophila Brain