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Sattari S, S. Basak U, Mohiuddin M, Toda M, Komatsuzaki T. Inferring the roles of individuals in collective systems using information-theoretic measures of influence. Biophys Physicobiol 2024; 21:e211014. [PMID: 39175852 PMCID: PMC11338685 DOI: 10.2142/biophysico.bppb-v21.s014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/18/2024] [Indexed: 08/24/2024] Open
Abstract
In collective systems, influence of individuals can permeate an entire group through indirect interactionscom-plicating any scheme to understand individual roles from observations. A typical approach to understand an individuals influence on another involves consideration of confounding factors, for example, by conditioning on other individuals outside of the pair. This becomes unfeasible in many cases as the number of individuals increases. In this article, we review some of the unforeseen problems that arise in understanding individual influence in a collective such as single cells, as well as some of the recent works which address these issues using tools from information theory.
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Affiliation(s)
- Sulimon Sattari
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001‑0020, Japan
| | - Udoy S. Basak
- Pabna University of Science and Technology, Pabna 6600, Bangladesh
| | - M. Mohiuddin
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060‑0812, Japan
- Comilla University, Cumilla 3506, Bangladesh
| | - Mikito Toda
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001‑0020, Japan
- Faculty Division of Natural Sciences, Nara Women’s University, Nara 630‑8506, Japan
- Graduate School of Information Science, University of Hyogo, Kobe, Hyogo 650‑0047, Japan
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001‑0020, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060‑0812, Japan
- Institute for Chemical Reaction Design and Discovery (WPI‑ICReDD), Hokkaido University, Sapporo, Hokkaido 001‑0021, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565‑0871, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki 567‑0047, Japan
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Phillips TA, Marcotti S, Cox S, Parsons M. Imaging actin organisation and dynamics in 3D. J Cell Sci 2024; 137:jcs261389. [PMID: 38236161 PMCID: PMC10906668 DOI: 10.1242/jcs.261389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
The actin cytoskeleton plays a critical role in cell architecture and the control of fundamental processes including cell division, migration and survival. The dynamics and organisation of F-actin have been widely studied in a breadth of cell types on classical two-dimensional (2D) surfaces. Recent advances in optical microscopy have enabled interrogation of these cytoskeletal networks in cells within three-dimensional (3D) scaffolds, tissues and in vivo. Emerging studies indicate that the dimensionality experienced by cells has a profound impact on the structure and function of the cytoskeleton, with cells in 3D environments exhibiting cytoskeletal arrangements that differ to cells in 2D environments. However, the addition of a third (and fourth, with time) dimension leads to challenges in sample preparation, imaging and analysis, necessitating additional considerations to achieve the required signal-to-noise ratio and spatial and temporal resolution. Here, we summarise the current tools for imaging actin in a 3D context and highlight examples of the importance of this in understanding cytoskeletal biology and the challenges and opportunities in this domain.
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Affiliation(s)
- Thomas A. Phillips
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
- Microscopy Innovation Centre, King's College London, Guys Campus, London SE1 1UL, UK
| | - Susan Cox
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
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