At the same time, their core regions are highly resistant to proteases and denaturing agents, and are also protected against the replacement of hydrogen by deuterium (H/D exchange) . Individual protein molecules of such complexes form numerous β-sheets, which causes their specific properties. It has been validated by artificially created images of rod-shape objects with predefined parameters and micrographs of Sup35NM protein fibrils.Īmyloids are large protein aggregates in a form of unbranched fibrils.
#IMAGEJ SOFTWARE NATURE PAPER FREE#
Plugin FibrilJ which is presentedin this paper is free of DiameterJ or BoneJ weaknesses. FibrilJ usage may unify the process of diameter and persistence length calculation and it may also contribute to comparison of results obtained by different research groups. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils on average diameters, lengths and persistence lengths. Solution method: For this purpose we developed a FibrilJ plugin for ImageJ/FiJi program with an open source code. They have unspecified accuracy of these objects measurements and do not calculate the objects distribution on average diameters and persistence lengths. They do not provide the necessary functionality for the automatic recognition of amyloids on the substrate and filtering objects by a number of parameters. These above mentioned plugins are not designed for the study of amyloids and have never been used or validated for them.
Also, approaches that involve calculations of the end-to-end distances and contour lengths of biopolymers were used to determine their persistence lengths using ImageJ/FiJi. The ImageJ/FiJi community provides BoneJ plugin for bones analysis and DiameterJ plugin for nanofibers analysis, which have the function of determining the diameter of the respective objects. ImageJ/FiJi is open-source software and one of the most commonly used program for image processing.
#IMAGEJ SOFTWARE NATURE PAPER MANUAL#
The manual measurements of these parameters take a lot of time and, due to the human factor, are insufficiently representative. The lattermost parameter was introduced for the characteristic of bending stiffness of amyloids similarly to that in a model of wormlike chain for polymers. Usually it is required to process images containing hundreds of amyloids to obtain statistically reliable data on the distribution of the thickness, length and persistence length (a basic mechanical property quantifying the stiffness of a polymer). At the moment new methods of amyloids analysis based on electronic and probe microscopy are particularly popular. The structural organization of the amyloid aggregates at the molecular level is a key problem in this area. Therefore, various amyloids, in particular their topology, are widely studied in an enormous number of papers. Formation of amyloids by different proteins leads to the emergence of a number of serious human diseases, including Alzheimer’s, Parkinson’s and Huntington’s diseases. Nature of problem: Amyloids are large protein aggregates that form unbranched fibrils. Programming language: ImageJ Macro Language Novel data obtained by SEM for Sup35NM protein fibrils immobilized on silicon and gold substrates are also presented and analyzed. The plugin has been validated by the processing of TEM images of fibrils formed by Sup35NM yeast protein and artificially created images of rod-shape objects with predefined parameters. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils by diameters, lengths and persistence lengths. For this purpose we developed an open-source FibrilJ plugin for the ImageJ/FiJi program. The estimation of mean values of fibrils diameter, length and bending stiffness on micrographs is a major challenge. Application of microscopy to evaluate the morphology and size of filamentous proteins and amyloids requires new and creative approaches to simplify and automate the image processing.
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