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Smith AW. Recent applications of fluorescence correlation spectroscopy in live cells. Curr Opin Chem Biol 2024; 81:102480. [PMID: 38905722 DOI: 10.1016/j.cbpa.2024.102480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
As a time-domain analogue of fluorescence imaging, FCS offers valuable insights into molecular dynamics, interactions, and concentrations within living cells. The primary insight generated by FCS is molecular mobility and concentration, which makes it useful for investigating molecular-scale details without the need for enrichment or separation. A specific strength of FCS is the ability to probe protein-protein interactions in live cells and several recent applications in this area are summarized. FCS is also used to investigate plasma membrane protein organization, with many applications to cell surface receptors and the mechanisms of drug binding. Finally, FCS is undergoing continual methodological innovations, such as imaging FCS, SPIM-FCS PIE-FCCS, STED-FCS, three-color FCS, and massively parallel FCS, which extend the capabilities to investigate molecular dynamics at different spatial and temporal scales. These innovations enable detailed examinations of cellular processes, including cellular transport and the spatial organization of membrane proteins.
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Affiliation(s)
- Adam W Smith
- Texas Tech University, Department of Chemistry & Biochemistry, Lubbock, TX, USA.
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2
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Longo E, Scalisi S, Lanzanò L. Segmented fluorescence correlation spectroscopy (FCS) on a commercial laser scanning microscope. Sci Rep 2024; 14:17555. [PMID: 39080338 PMCID: PMC11289089 DOI: 10.1038/s41598-024-68317-7] [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: 05/15/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Performing accurate Fluorescence Correlation Spectroscopy (FCS) measurements in cells can be challenging due to cellular motion or other intracellular processes. In this respect, it has recently been shown that analysis of FCS data in short temporal segments (segmented FCS) can be very useful to increase the accuracy of FCS measurements inside cells. Here, we demonstrate that segmented FCS can be performed on a commercial laser scanning microscope (LSM), even in the absence of the dedicated FCS module. We show how data can be acquired on a Leica SP8 confocal microscope and then exported and processed with a custom software in MATLAB. The software performs segmentation of the data to extract an average ACF and measure the diffusion coefficient in specific subcellular regions. First of all, we measure the diffusion of fluorophores of different size in solution, to show that good-quality ACFs can be obtained in a commercial LSM. Next, we validate the method by measuring the diffusion coefficient of GFP in the nucleus of HeLa cells, exploiting variations of the intensity to distinguish between nucleoplasm and nucleolus. As expected, the measured diffusion coefficient of GFP is slower in the nucleolus relative to nucleoplasm. Finally, we apply the method to HeLa cells expressing a PARP1 chromobody to measure the diffusion coefficient of PARP1 in different subcellular regions. We find that PARP1 diffusion is slower in the nucleolus compared to the nucleoplasm.
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Affiliation(s)
- Elisa Longo
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia, 64, 95123, Catania, Italy
| | - Silvia Scalisi
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia, 64, 95123, Catania, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia, 64, 95123, Catania, Italy.
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.
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3
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Li L, Qu J, Liu W, Peng B, Cong S, Yu H, Zhang B, Li Y. Advancements in Characterization Techniques for Microemulsions: From Molecular Insights to Macroscopic Phenomena. Molecules 2024; 29:2901. [PMID: 38930964 PMCID: PMC11206267 DOI: 10.3390/molecules29122901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/09/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Microemulsions are thermodynamically stable, optically isotropic, transparent, or semi-transparent mixed solutions composed of two immiscible solvents stabilized by amphiphilic solutes. This comprehensive review explores state-of-the-art techniques for characterizing microemulsions, which are versatile solutions essential across various industries, such as pharmaceuticals, food, and petroleum. This article delves into spectroscopic methods, nuclear magnetic resonance, small-angle scattering, dynamic light scattering, conductometry, zeta potential analysis, cryo-electron microscopy, refractive index measurement, and differential scanning calorimetry, examining each technique's strengths, limitations, and potential applications. Emphasizing the necessity of a multi-technique approach for a thorough understanding, it underscores the importance of integrating diverse analytical methods to unravel microemulsion structures from molecular to macroscopic scales. This synthesis provides a roadmap for researchers and practitioners, fostering advancements in microemulsion science and its wide-ranging industrial applications.
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Affiliation(s)
- Longfei Li
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
- College of New Energy and Materials, China University of Petroleum-Beijing, Beijing 102249, China;
- National Elite Institute of Engineering, China National Petroleum Corporation (CNPC), Beijing 102200, China
| | - Jiepeng Qu
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
- National Elite Institute of Engineering, China National Petroleum Corporation (CNPC), Beijing 102200, China
- School of Rare Earth, University of Science and Technology of China, Hefei 230026, China
| | - Weidong Liu
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
| | - Baoliang Peng
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
| | - Sunan Cong
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
| | - Haobo Yu
- College of New Energy and Materials, China University of Petroleum-Beijing, Beijing 102249, China;
| | - Biao Zhang
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
| | - Yingying Li
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; (L.L.); (J.Q.); (B.P.); (S.C.); (B.Z.); (Y.L.)
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Singh PK, Rybak JA, Schuck RJ, Barrera FN, Smith AW. Phosphatidylinositol (4,5)-bisphosphate drives the formation of EGFR and EphA2 complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592400. [PMID: 38746348 PMCID: PMC11092790 DOI: 10.1101/2024.05.03.592400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Receptor tyrosine kinases (RTKs) regulate many cellular functions and are important targets in pharmaceutical development, particularly in cancer treatment. EGFR and EphA2 are two key RTKs that are associated with oncogenic phenotypes. Several studies have reported functional interplay between these receptors, but the mechanism of interaction is still unresolved. Here we utilize a time-resolved fluorescence spectroscopy called PIE-FCCS to resolve EGFR and EphA2 interactions in live cells. We tested the role of ligands and found that EGF, but not ephrin A1 (EA1), stimulated hetero-multimerization between the receptors. To determine the effect of anionic lipids, we targeted phospholipase C (PLC) activity to alter the abundance of phosphatidylinositol (4,5)-bisphosphate (PIP 2 ). We found that higher PIP 2 levels increased homo-multimerization of both EGFR and EphA2, as well as hetero-multimerization. This study provides a direct characterization of EGFR and EphA2 interactions in live cells and shows that PIP 2 can have a substantial effect on the spatial organization of RTKs.
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Luu P, Fraser SE, Schneider F. More than double the fun with two-photon excitation microscopy. Commun Biol 2024; 7:364. [PMID: 38531976 DOI: 10.1038/s42003-024-06057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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Affiliation(s)
- Peter Luu
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Scott E Fraser
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
- Alfred Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Falk Schneider
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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Tang WH, Sim SR, Aik DYK, Nelanuthala AVS, Athilingam T, Röllin A, Wohland T. Deep learning reduces data requirements and allows real-time measurements in imaging FCS. Biophys J 2024; 123:655-666. [PMID: 38050354 PMCID: PMC10995408 DOI: 10.1016/j.bpj.2023.11.3403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/06/2023] Open
Abstract
Imaging fluorescence correlation spectroscopy (FCS) is a powerful tool to extract information on molecular mobilities, actions, and interactions in live cells, tissues, and organisms. Nevertheless, several limitations restrict its applicability. First, FCS is data hungry, requiring 50,000 frames at 1-ms time resolution to obtain accurate parameter estimates. Second, the data size makes evaluation slow. Third, as FCS evaluation is model dependent, data evaluation is significantly slowed unless analytic models are available. Here, we introduce two convolutional neural networks-FCSNet and ImFCSNet-for correlation and intensity trace analysis, respectively. FCSNet robustly predicts parameters in 2D and 3D live samples. ImFCSNet reduces the amount of data required for accurate parameter retrieval by at least one order of magnitude and makes correct estimates even in moderately defocused samples. Both convolutional neural networks are trained on simulated data, are model agnostic, and allow autonomous, real-time evaluation of imaging FCS measurements.
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Affiliation(s)
- Wai Hoh Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore
| | - Shao Ren Sim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Daniel Ying Kia Aik
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Ashwin Venkata Subba Nelanuthala
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | | | - Adrian Röllin
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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Sudderick ZR, Glover JD. Periodic pattern formation during embryonic development. Biochem Soc Trans 2024; 52:75-88. [PMID: 38288903 PMCID: PMC10903485 DOI: 10.1042/bst20230197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
During embryonic development many organs and structures require the formation of series of repeating elements known as periodic patterns. Ranging from the digits of the limb to the feathers of the avian skin, the correct formation of these embryonic patterns is essential for the future form and function of these tissues. However, the mechanisms that produce these patterns are not fully understood due to the existence of several modes of pattern generation which often differ between organs and species. Here, we review the current state of the field and provide a perspective on future approaches to studying this fundamental process of embryonic development.
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Affiliation(s)
- Zoe R. Sudderick
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
| | - James D. Glover
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
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