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Mashanov GI, Molloy JE. Single molecule dynamics in a virtual cell combining a 3-dimensional matrix model with random walks. Sci Rep 2024; 14:20032. [PMID: 39198682 PMCID: PMC11358523 DOI: 10.1038/s41598-024-70925-2] [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] [Received: 04/17/2024] [Accepted: 08/22/2024] [Indexed: 09/01/2024] Open
Abstract
Recent advances in light microscopy have enabled single molecules to be imaged and tracked within living cells and this approach is impacting our understanding of cell biology. Computer modeling and simulation are important adjuncts to the experimental cycle since they aid interpretation of experimental results and help refine, test and generate hypotheses. Object-oriented computer modeling is particularly well-suited for simulating random, thermal, movements of individual molecules as they interact with other molecules and subcellular structures, but current models are often limited to idealized systems consisting of unit volumes or planar surfaces. Here, a simulation tool is described that combines a 3-dimensional, voxelated, representation of the cell consisting of subcellular structures (e.g. nucleus, endoplasmic reticulum, cytoskeleton, vesicles, and filopodia) combined with numerical floating-point precision simulation of thousands of individual molecules moving and interacting within the 3-dimensional space. Simulations produce realistic time-series video sequences comprising single fluorophore intensities and realistic background noise which can be directly compared to experimental fluorescence video microscopy data sets.
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Affiliation(s)
| | - Justin E Molloy
- The Francis Crick Institute, London, NW1 1AT, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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Yu P, Duan Z, Liu S, Pachon I, Ma J, Hemstreet GP, Zhang Y. Drug-Induced Nephrotoxicity Assessment in 3D Cellular Models. MICROMACHINES 2021; 13:mi13010003. [PMID: 35056167 PMCID: PMC8780064 DOI: 10.3390/mi13010003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022]
Abstract
The kidneys are often involved in adverse effects and toxicity caused by exposure to foreign compounds, chemicals, and drugs. Early predictions of these influences are essential to facilitate new, safe drugs to enter the market. However, in current drug treatments, drug-induced nephrotoxicity accounts for 1/4 of reported serious adverse reactions, and 1/3 of them are attributable to antibiotics. Drug-induced nephrotoxicity is driven by multiple mechanisms, including altered glomerular hemodynamics, renal tubular cytotoxicity, inflammation, crystal nephropathy, and thrombotic microangiopathy. Although the functional proteins expressed by renal tubules that mediate drug sensitivity are well known, current in vitro 2D cell models do not faithfully replicate the morphology and intact renal tubule function, and therefore, they do not replicate in vivo nephrotoxicity. The kidney is delicate and complex, consisting of a filter unit and a tubular part, which together contain more than 20 different cell types. The tubular epithelium is highly polarized, and maintaining cellular polarity is essential for the optimal function and response to environmental signals. Cell polarity depends on the communication between cells, including paracrine and autocrine signals, as well as biomechanical and chemotaxis processes. These processes affect kidney cell proliferation, migration, and differentiation. For drug disposal research, the microenvironment is essential for predicting toxic reactions. This article reviews the mechanism of drug-induced kidney injury, the types of nephrotoxicity models (in vivo and in vitro models), and the research progress related to drug-induced nephrotoxicity in three-dimensional (3D) cellular culture models.
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Affiliation(s)
- Pengfei Yu
- Difficult & Complicated Liver Diseases and Artificial Liver Center, Fourth Department of Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China; (P.Y.); (Z.D.); (S.L.)
- Beijing Municipal Key Laboratory of Liver Failure and Artificial Liver Treatment Research, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Zhongping Duan
- Difficult & Complicated Liver Diseases and Artificial Liver Center, Fourth Department of Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China; (P.Y.); (Z.D.); (S.L.)
- Beijing Municipal Key Laboratory of Liver Failure and Artificial Liver Treatment Research, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Shuang Liu
- Difficult & Complicated Liver Diseases and Artificial Liver Center, Fourth Department of Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China; (P.Y.); (Z.D.); (S.L.)
- Beijing Municipal Key Laboratory of Liver Failure and Artificial Liver Treatment Research, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Ivan Pachon
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA;
| | - Jianxing Ma
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA;
| | | | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA;
- Correspondence: ; Tel.: +1-336-713-1189
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Bošnjak B, Do KTH, Förster R, Hammerschmidt SI. Imaging dendritic cell functions. Immunol Rev 2021; 306:137-163. [PMID: 34859450 DOI: 10.1111/imr.13050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/14/2022]
Abstract
Dendritic cells (DCs) are crucial for the appropriate initiation of adaptive immune responses. During inflammation, DCs capture antigens, mature, and migrate to lymphoid tissues to present foreign material to naïve T cells. These cells get activated and differentiate either into pathogen-specific cytotoxic CD8+ T cells that destroy infected cells or into CD4+ T helper cells that, among other effector functions, orchestrate antibody production by B cells. DC-mediated antigen presentation is equally important in non-inflammatory conditions. Here, DCs mediate induction of tolerance by presenting self-antigens or harmless environmental antigens and induce differentiation of regulatory T cells or inactivation of self-reactive immune cells. Detailed insights into the biology of DCs are, therefore, crucial for the development of novel vaccines as well as the prevention of autoimmune diseases. As in many other life science areas, our understanding of DC biology would be extremely restricted without bioimaging, a compilation of methods that visualize biological processes. Spatiotemporal tracking of DCs relies on various imaging tools, which not only enable insights into their positioning and migration within tissues or entire organs but also allow visualization of subcellular and molecular processes. This review aims to provide an overview of the imaging toolbox and to provide examples of diverse imaging techniques used to obtain fundamental insights into DC biology.
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Affiliation(s)
- Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Kim Thi Hoang Do
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155) Hannover Medical School, Hannover, Germany.,German Centre for Infection Research (DZIF), Hannover, Germany
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Mashanov GI, Nenasheva TA, Mashanova A, Lape R, Birdsall NJM, Sivilotti L, Molloy JE. Heterogeneity of cell membrane structure studied by single molecule tracking. Faraday Discuss 2021; 232:358-374. [PMID: 34647559 PMCID: PMC8704140 DOI: 10.1039/d1fd00035g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterogeneity in cell membrane structure, typified by microdomains with different biophysical and biochemical properties, is thought to impact on a variety of cell functions. Integral membrane proteins act as nanometre-sized probes of the lipid environment and their thermally-driven movements can be used to report local variations in membrane properties. In the current study, we have used total internal reflection fluorescence microscopy (TIRFM) combined with super-resolution tracking of multiple individual molecules, in order to create high-resolution maps of local membrane viscosity. We used a quadrat sampling method and show how statistical tests for membrane heterogeneity can be conducted by analysing the paths of many molecules that pass through the same unit area of membrane. We describe experiments performed on cultured primary cells, stable cell lines and ex vivo tissue slices using a variety of membrane proteins, under different imaging conditions. In some cell types, we find no evidence for heterogeneity in mobility across the plasma membrane, but in others we find statistically significant differences with some regions of membrane showing significantly higher viscosity than others. We use total internal reflection fluorescence microscopy combined with super-resolution tracking of multiple individual molecules, in order to create high-resolution maps of local membrane viscosity.![]()
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Affiliation(s)
| | - Tatiana A Nenasheva
- Koltzov Institute of Developmental Biology, 26 Vavilova Str., Moscow, 119334, Russia
| | - Alla Mashanova
- School of Life and Medical Sciences, University of Hertfordshire, College Lane, Hatfield, Hertfordshire, AL10 9AB, UK
| | - Remigijus Lape
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, Gower St., London, UK
| | | | - Lucia Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, Gower St., London, UK
| | - Justin E Molloy
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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von Diezmann L, Rog O. Single-Molecule Tracking of Chromatin-Associated Proteins in the C. elegans Gonad. J Phys Chem B 2021; 125:6162-6170. [PMID: 34097417 DOI: 10.1021/acs.jpcb.1c03040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biomolecules are distributed within cells by molecular-scale diffusion and binding events that are invisible in standard fluorescence microscopy. These molecular search kinetics are key to understanding nuclear signaling and chromosome organization and can be directly observed by single-molecule tracking microscopy. Here, we report a method to track individual proteins within intact C. elegans gonads and apply it to study the molecular dynamics of the axis, a proteinaceous backbone that organizes meiotic chromosomes. Using either fluorescent proteins or enzymatically ligated dyes, we obtain multisecond trajectories with a localization precision of 15-25 nm in nuclei actively undergoing meiosis. Correlation with a reference channel allows for accurate measurement of protein dynamics, compensating for movements of the nuclei and chromosomes within the gonad. We find that axis proteins exhibit either static binding to chromatin or free diffusion in the nucleoplasm, and we separately quantify the motion parameters of these distinct populations. Freely diffusing axis proteins selectively explore chromatin-rich regions, suggesting they are circumventing the central phase-separated region of the nucleus. This work demonstrates that single-molecule microscopy can infer nanoscale-resolution dynamics within living tissue, expanding the possible applications of this approach.
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Feil R, Lehners M, Stehle D, Feil S. Visualising and understanding cGMP signals in the cardiovascular system. Br J Pharmacol 2021; 179:2394-2412. [PMID: 33880767 DOI: 10.1111/bph.15500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/14/2021] [Accepted: 04/01/2021] [Indexed: 12/21/2022] Open
Abstract
cGMP is an important signalling molecule in humans. Fluorescent cGMP biosensors have emerged as powerful tools for the sensitive analysis of cGMP pathways at the single-cell level. Here, we briefly outline cGMP's multifaceted role in (patho)physiology and pharmacotherapy. Then we summarise what new insights cGMP imaging has provided into endogenous cGMP signalling and drug action, with a focus on the cardiovascular system. Indeed, the use of cGMP biosensors has led to several conceptual advances, such as the discovery of local, intercellular and mechanosensitive cGMP signals. Importantly, single-cell imaging can provide valuable information about the heterogeneity of cGMP signals within and between individual cells of an isolated cell population or tissue. We also discuss current challenges and future directions of cGMP imaging, such as the direct visualisation of cGMP microdomains, simultaneous monitoring of cGMP and other signalling molecules and, ultimately, cGMP imaging in tissues and animals under close-to-native conditions.
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Affiliation(s)
- Robert Feil
- Interfakultäres Institut für Biochemie, University of Tübingen, Tübingen, Germany
| | - Moritz Lehners
- Interfakultäres Institut für Biochemie, University of Tübingen, Tübingen, Germany
| | - Daniel Stehle
- Interfakultäres Institut für Biochemie, University of Tübingen, Tübingen, Germany
| | - Susanne Feil
- Interfakultäres Institut für Biochemie, University of Tübingen, Tübingen, Germany
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Short B. Single molecule imaging reveals a slice of life. J Gen Physiol 2021; 153:211602. [PMID: 33332557 PMCID: PMC7754681 DOI: 10.1085/jgp.202012840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
JGP study describes method to trace the real-time movements of individual membrane proteins in live tissue slices.
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