Number of the records: 1
Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)
- 1.
SYSNO ASEP 0571534 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM) Author(s) Weidner, J. (DE)
Neitzel, Ch. (DE)
Gote, M. (DE)
Deck, J. (DE)
Kuentzelmann, K. (DE)
Pilarczyk, G. (DE)
Falk, Martin (BFU-R) RID, ORCID
Hausmann, M. (DE)Number of authors 8 Source Title Computational and Structural Biotechnology Journal. - : Elsevier - ISSN 2001-0370
Roč. 21, MAR 2023 (2023), s. 2018-2034Number of pages 17 s. Publication form Print - P Language eng - English Country NL - Netherlands Keywords Single molecule localization microscopy ; (smlm) ; Ripley distance frequency histograms ; Persistent homology ; Persistent image ; Principal component analysis ; Application of mathematical analysis tools to ; chromatin organization and DNA repair ; processes Subject RIV CE - Biochemistry OECD category Biochemistry and molecular biology R&D Projects GC20-04109J GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support BFU-R - RVO:68081707 UT WOS 000957506000001 EID SCOPUS 85150022783 DOI 10.1016/j.csbj.2023.03.009 Annotation The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the re-lationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, per-sistent 'imaging', principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein traf-ficking in the cytosol, offers broad flexibility of use. (c) 2023 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative-commons.org/licenses/by-nc-nd/4.0/). Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2024 Electronic address https://www.sciencedirect.com/science/article/pii/S2001037023001083?via%3Dihub
Number of the records: 1