AGECalibratoR, a computational tool for quantitative analysis of weights of amyloid aggregates
Year: 2020
Type: article
Abstract: The semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) was proposed as a method to compare quantitatively sizes of amyloid aggregates. Currently, this approach is widely used for amyloid investigation, but only as a qualitative approach. We developed a pipeline of computer programs AGECalibratoR for amyloid aggregate size evaluation based on the SDD-AGE results. This piptline analyses western blot signal, transformed to optical density profiles with the ImageJ/Fiji software, and estimates the molecular weight of amyloid aggregates. A DNA ladder or any other high molecular weight ladder is required as a reference. The performance of the tool was tested on Sup35 amyloid aggregates present in different [PSI + ] strains of Saccharomyces cerevisiae. Reproducible results were obtained in several replicated experiments. A detailed investigation of factors that can affect the results of SDD-AGE also revealed several limitations of the approach. Summing up, the proposed tool opens new possibilities in the interpretation of SDD-AGE, allowing the quantification and statistical analysis of the results.
Source: HAL
Authors: Drozdova, Polina, B, Barbitoff, Yury, A, Belousov, Mikhail, V, Rogoza, Tatyana, M, Kajava, Andrey, V, Bondarev, Stanislav, A, Zhouravleva, Galina, A
Language: English
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7026554672