1
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Diloknawarit B, Lee K, Choo P, Odom TW. Nanoparticle Anisotropy Increases Targeting Interactions on Live-Cell Membranes. ACS Nano 2024. [PMID: 38684051 DOI: 10.1021/acsnano.4c02700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
This paper describes how branch lengths of anisotropic nanoparticles can affect interactions between grafted ligands and cell-membrane receptors. Using live-cell, single-particle tracking, we found that DNA aptamer-gold nanostar nanoconstructs with longer branches showed improved binding efficacy to human epidermal growth factor receptor 2 (HER2) on cancer cell membranes. Inhibiting nanoconstruct-HER2 binding promoted nonspecific interactions, which increased the rotational speed of long-branched nanoconstructs but did not affect that of short-branched constructs. Bivariate analysis of the rotational and translational dynamics showed that longer branch lengths increased the ratio of targeting to nontargeting interactions. We also found that longer branches increased the nanoconstruct-cell interaction times before internalization and decreased intracellular trafficking velocities. Differences in binding efficacy revealed by single-particle dynamics can be attributed to the distinct protein corona distributions on short- and long-branched nanoconstructs, as validated by transmission electron microscopy. Minimal protein adsorption at the high positive curvature tips of long-branched nanoconstructs facilitated binding of DNA aptamer ligands to HER2. Our study reveals the significance of nanoparticle branch length in regulating local chemical environment and interactions with live cells at the single-particle level.
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Affiliation(s)
- Bundit Diloknawarit
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Kwahun Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Priscilla Choo
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Teri W Odom
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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2
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Lee A, Simon AA, Boyreau A, Allain-Courtois N, Lambert B, Pradère JP, Saltel F, Cognet L. Identification of Early Stage Liver Fibrosis by Modifications in the Interstitial Space Diffusive Microenvironment Using Fluorescent Single-Walled Carbon Nanotubes. Nano Lett 2024. [PMID: 38669477 DOI: 10.1021/acs.nanolett.4c00955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
During liver fibrosis, recurrent hepatic injuries lead to the accumulation of collagen and other extracellular matrix components in the interstitial space, ultimately disrupting liver functions. Early stages of liver fibrosis may be reversible, but opportunities for diagnosis at these stages are currently limited. Here, we show that the alterations of the interstitial space associated with fibrosis can be probed by tracking individual fluorescent single-walled carbon nanotubes (SWCNTs) diffusing in that space. In a mouse model of early liver fibrosis, we find that nanotubes generally explore elongated areas, whose lengths decrease as the disease progresses, even in regions where histopathological examination does not reveal fibrosis yet. Furthermore, this decrease in nanotube mobility is a purely geometrical effect as the instantaneous nanotube diffusivity stays unmodified. This work establishes the promise of SWCNTs both for diagnosing liver fibrosis at an early stage and for more in-depth studies of the biophysical effects of the disease.
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Affiliation(s)
- Antony Lee
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, 33400 Talence, France
- CNRS - UMR 5298, LP2N, Institut d'Optique Graduate School, 33400 Talence, France
- CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Institut Curie, Université PSL, Sorbonne Université, 75005 Paris, France
| | - Apolline A Simon
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, 33400 Talence, France
- CNRS - UMR 5298, LP2N, Institut d'Optique Graduate School, 33400 Talence, France
- CNRS, Bordeaux INP, ICMCB, UMR 5026, Univ. Bordeaux, 33600 Pessac, France
| | - Adeline Boyreau
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, 33400 Talence, France
- CNRS - UMR 5298, LP2N, Institut d'Optique Graduate School, 33400 Talence, France
| | - Nathalie Allain-Courtois
- Inserm, UMR1312, BRIC, Bordeaux Institute of Oncology, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Benjamin Lambert
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, 33400 Talence, France
- CNRS - UMR 5298, LP2N, Institut d'Optique Graduate School, 33400 Talence, France
| | - Jean-Philippe Pradère
- Institut RESTORE - UMR 1301 - Inserm/5070-CNRS/EFS, Univ. P. Sabatier, 31037 Toulouse, France
| | - Frédéric Saltel
- Inserm, UMR1312, BRIC, Bordeaux Institute of Oncology, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Laurent Cognet
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, 33400 Talence, France
- CNRS - UMR 5298, LP2N, Institut d'Optique Graduate School, 33400 Talence, France
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3
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Le T, Ferling I, Qiu L, Nabaile C, Assunção L, Roskelley CD, Grinstein S, Freeman SA. Redistribution of the glycocalyx exposes phagocytic determinants on apoptotic cells. Dev Cell 2024; 59:853-868.e7. [PMID: 38359833 DOI: 10.1016/j.devcel.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Phagocytes remove dead and dying cells by engaging "eat-me" ligands such as phosphatidylserine (PtdSer) on the surface of apoptotic targets. However, PtdSer is obscured by the bulky exofacial glycocalyx, which also exposes ligands that activate "don't-eat-me" receptors such as Siglecs. Clearly, unshielding the juxtamembrane "eat-me" ligands is required for the successful engulfment of apoptotic cells, but the mechanisms underlying this process have not been described. Using human and murine cells, we find that apoptosis-induced retraction and weakening of the cytoskeleton that anchors transmembrane proteins cause an inhomogeneous redistribution of the glycocalyx: actin-depleted blebs emerge, lacking the glycocalyx, while the rest of the apoptotic cell body retains sufficient actin to tether the glycocalyx in place. Thus, apoptotic blebs can be engaged by phagocytes and are targeted for engulfment. Therefore, in cells with an elaborate glycocalyx, such as mucinous cancer cells, this "don't-come-close-to-me" barrier must be removed to enable clearance by phagocytosis.
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Affiliation(s)
- Trieu Le
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Iuliia Ferling
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lanhui Qiu
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clement Nabaile
- Department of Learning and Research in Biology, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Leonardo Assunção
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Calvin D Roskelley
- Department of Cellular and Physiological Sciences, the Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sergio Grinstein
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Spencer A Freeman
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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4
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Broadbent D, Barnaba C, Schmidt JC. Tracking the transition from an ATG9A vesicle to an autophagosome. Autophagy 2024; 20:976-977. [PMID: 37405380 PMCID: PMC11062357 DOI: 10.1080/15548627.2023.2232641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
ABBREVIATIONS ATG: autophagy-related proteins; ULK1/2: Unc-51-Like activating Kinases; PI3Ks: Phosphoinositide 3-Kinases; ATG2A: autophagy-related protein 2A; ATG5: autophagy-related protein 5; ATG16: autophagy-related protein 16; ATG8: autophagy-related protein 8; U2OS: human bone osteosarcoma epithelial cell; LC3B: microtubule-associated protein 1A/1B Light Chain 3B; GABARAPL1: GABA type A Receptor-Associated Protein Like 1; ATG9A: autophagy-related protein 9A; ATG13: autophagy-related protein 13; SQSTM1: Sequestosome-1/p62; WIPI2: WD repeat domain, Phosphoinositide Interacting 2; PI3P: Phosphoinositide-3-phosphate.
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Affiliation(s)
- David Broadbent
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Carlo Barnaba
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI, USA
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5
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Ohayon S, Taib L, Verma NC, Iarossi M, Bhattacharya I, Marom B, Huttner D, Meller A. Full-Length Single Protein Molecules Tracking and Counting in Thin Silicon Channels. Adv Mater 2024:e2314319. [PMID: 38461367 DOI: 10.1002/adma.202314319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/25/2024] [Indexed: 03/11/2024]
Abstract
Emerging single-molecule protein sensing techniques are ushering in a transformative era in biomedical research. Nevertheless, challenges persist in realizing ultra-fast full-length protein sensing, including loss of molecular integrity due to protein fragmentation, biases introduced by antibodies affinity, identification of proteoforms, and low throughputs. Here, a single-molecule method for parallel protein separation and tracking is introduced, yielding multi-dimensional molecular properties used for their identification. Proteins are tagged by chemo-selective dual amino-acid specific labels and are electrophoretically separated by their mass/charge in custom-designed thin silicon channel with subwavelength height. This approach allows analysis of thousands of individual proteins within a few minutes by tracking their motion during the migration. The power of the method is demonstrated by quantifying a cytokine panel for host-response discrimination between viral and bacterial infections. Moreover, it is shown that two clinically-relevant splice isoforms of Vascular endothelial growth factor (VEGF) can be accurately quantified from human serum samples. Being non-destructive and compatible with full-length intact proteins, this method opens up ways for antibody-free single-protein molecule quantification.
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Affiliation(s)
- Shilo Ohayon
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Liran Taib
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | | | - Marzia Iarossi
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Ivy Bhattacharya
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Barak Marom
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Diana Huttner
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
- Russell Berrie Nanotechnology Institute, Technion-IIT, Haifa, 3200003, Israel
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6
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Ao J, Ma AX, Li J, Wang CY, Fu DD, Du L, Yu C, Liu SL, Wang ZG, Pang DW. Real-Time Dissection of the Exosome Pathway for Influenza Virus Infection. ACS Nano 2024; 18:4507-4519. [PMID: 38270127 DOI: 10.1021/acsnano.3c11309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Exosomes play an important role in the spread of viral infections and immune escape. However, the exact ability and mechanisms by which exosomes produced during viral infections (vExos) infect host cells are still not fully understood. In this study, we developed a dual-color exosome labeling strategy that simultaneously labels the external and internal structures of exosomes with quantum dots to enable in situ monitoring of the transport process of vExos in live cells using the single-particle tracking technique. Our finding revealed that vExos contains the complete influenza A virus (IAV) genome and viral ribonucleoprotein complexes (vRNPs) proteins but lacks viral envelope proteins. Notably, these vExos have the ability to infect cells and produce progeny viruses. We also found that vExos are transported in three stages, slow-fast-slow, and move to the perinuclear region via microfilaments and microtubules. About 30% of internalized vExos shed the external membrane and release the internal vRNPs into the cytoplasm by fusion with endolysosomes. This study suggested that vExos plays a supporting role in IAV infection by assisting with IAV propagation in a virus-independent manner. It emphasizes the need to consider the infectious potential of vExos and draws attention to the potential risk of exosomes produced by viral infections.
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Affiliation(s)
- Jian Ao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Ai-Xin Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Jing Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Chun-Yu Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Dan-Dan Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Lei Du
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Cong Yu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
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7
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Wu YL, Lee K, Diloknawarit B, Odom TW. Ligand Separation on Nanoconstructs Affects Targeting Selectivity to Protein Dimers on Cell Membranes. Nano Lett 2024; 24:519-524. [PMID: 38126338 DOI: 10.1021/acs.nanolett.3c04641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This work demonstrates that targeting ligand density on nanoparticles can affect interactions between the nanoconstructs and cell membrane receptors. We discovered that when the separation between covalently grafted DNA aptamers on gold nanostars was comparable to the distance between binding sites on a receptor dimer (matched density; MD), nanoconstructs exhibited a higher selectivity for binding to the dimeric form of the protein. Single-particle dynamics of MD nanoconstructs showed slower rotational rates and larger translational footprints on cancer cells expressing more dimeric forms of receptors (dimer+) compared with cells having more monomeric forms (dimer-). In contrast, nanoconstructs with either increased (nonmatched density; NDlow) or decreased ligand spacing (NDhigh) had minimal changes in dynamics on either dimer+ or dimer- cells. Real-time, single-particle analyses can reveal the importance of nanoconstruct ligand density for the selective targeting of membrane receptors in live cells.
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Affiliation(s)
- Yuhao Leo Wu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kwahun Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Bundit Diloknawarit
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Teri W Odom
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
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8
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Cayuela López A, García-Cuesta EM, Gardeta SR, Rodríguez-Frade JM, Mellado M, Gómez-Pedrero JA, S. Sorzano CO. TrackAnalyzer: A Fiji/ImageJ toolbox for a holistic analysis of tracks. Biol Imaging 2023; 3:e18. [PMID: 38510172 PMCID: PMC10951927 DOI: 10.1017/s2633903x23000181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/16/2023] [Accepted: 09/08/2023] [Indexed: 03/22/2024]
Abstract
Current live-cell imaging techniques make possible the observation of live events and the acquisition of large datasets to characterize the different parameters of the visualized events. They provide new insights into the dynamics of biological processes with unprecedented spatial and temporal resolutions. Here we describe the implementation and application of a new tool called TrackAnalyzer, accessible from Fiji and ImageJ. Our tool allows running semi-automated single-particle tracking (SPT) and subsequent motion classification, as well as quantitative analysis of diffusion and intensity for selected tracks relying on the graphical user interface (GUI) for large sets of temporal images (X-Y-T or X-Y-C-T dimensions). TrackAnalyzer also allows 3D visualization of the results as overlays of either spots, cells or end-tracks over time, along with corresponding feature extraction and further classification according to user criteria. Our analysis workflow automates the following steps: (1) spot or cell detection and filtering, (2) construction of tracks, (3) track classification and analysis (diffusion and chemotaxis), and (4) detailed analysis and visualization of all the outputs along the pipeline. All these analyses are automated and can be run in batch mode for a set of similar acquisitions.
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Affiliation(s)
- Ana Cayuela López
- Biocomputing Unit, National Centre for Biotechnology, Cantoblanco, Madrid, Spain
| | - Eva M. García-Cuesta
- Department of Immunology and Oncology, National Centre for Biotechnology, Cantoblanco, Madrid, Spain
| | - Sofía R. Gardeta
- Department of Immunology and Oncology, National Centre for Biotechnology, Cantoblanco, Madrid, Spain
| | | | - Mario Mellado
- Department of Immunology and Oncology, National Centre for Biotechnology, Cantoblanco, Madrid, Spain
| | - José Antonio Gómez-Pedrero
- Applied Optics Complutense Group, Faculty of Optics and Optometry, University Complutense of Madrid, Madrid, Spain
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9
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Pol E, Côme E, Merlaud Z, Gouhier J, Russeau M, Scotto-Lomassese S, Moutkine I, Marques X, Lévi S. NKCC1 and KCC2 Chloride Transporters Have Different Membrane Dynamics on the Surface of Hippocampal Neurons. Cells 2023; 12:2363. [PMID: 37830575 PMCID: PMC10571912 DOI: 10.3390/cells12192363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Na-K-2Cl cotransporter 1 (NKCC1) regulates chloride influx in neurons and thereby GABAA receptor activity in normal and pathological conditions. Here, we characterized in hippocampal neurons the membrane expression, distribution and dynamics of exogenous NKCC1a and NKCC1b isoforms and compared them to those of the chloride extruder K-Cl cotransporter 2 (KCC2). We found that NKCC1a and NKCC1b behave quite similarly. NKCC1a/1b but not KCC2 are present along the axon initial segment where they are confined. Moreover, NKCC1a/1b are detected in the somato-dendritic compartment at a lower level than KCC2, where they form fewer, smaller and less compact clusters at perisynaptic and extrasynaptic sites. Interestingly, ~60% of dendritic clusters of NKCC1a/1b are colocalized with KCC2. They are larger and brighter than those devoid of KCC2, suggesting a particular NKCC1a/1b-KCC2 relationship. In agreement with the reduced dendritic clustering of NKCC1a/1b compared with that of KCC2, NKCC1a/1b are more mobile on the dendrite than KCC2, suggesting weaker cytoskeletal interaction. NKCC1a/b are confined to endocytic zones, where they spend more time than KCC2. However, they spend less time in these compartments than at the synapses, suggesting that they can rapidly leave endocytic zones to increase the membrane pool, which can happen in pathological conditions. Thus, NKCC1a/b have different membrane dynamics and clustering from KCC2, which helps to explain their low level in the neuronal membrane, while allowing a rapid increase in the membrane pool under pathological conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sabine Lévi
- Institut du Fer à Moulin, Institut National de la Santé Et de la Recherche Médicale (INSERM) UMR-S 1270, Sorbonne Université, 75005 Paris, France; (E.P.); (E.C.); (Z.M.); (J.G.); (M.R.); (S.S.-L.); (I.M.); (X.M.)
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10
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Meszaros J, Geggier P, Manning JJ, Asher WB, Javitch JA. Methods for automating the analysis of live-cell single-molecule FRET data. Front Cell Dev Biol 2023; 11:1184077. [PMID: 37655158 PMCID: PMC10466402 DOI: 10.3389/fcell.2023.1184077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/21/2023] [Indexed: 09/02/2023] Open
Abstract
Single-molecule FRET (smFRET) is a powerful imaging platform capable of revealing dynamic changes in the conformation and proximity of biological molecules. The expansion of smFRET imaging into living cells creates both numerous new research opportunities and new challenges. Automating dataset curation processes is critical to providing consistent, repeatable analysis in an efficient manner, freeing experimentalists to advance the technical boundaries and throughput of what is possible in imaging living cells. Here, we devise an automated solution to the problem of multiple particles entering a region of interest, an otherwise labor-intensive and subjective process that had been performed manually in our previous work. The resolution of these two issues increases the quantity of FRET data and improves the accuracy with which FRET distributions are generated, increasing knowledge about the biological functions of the molecules under study. Our automated approach is straightforward, interpretable, and requires only localization and intensity values for donor and acceptor channel signals, which we compute through our previously published smCellFRET pipeline. The development of our automated approach is informed by the insights of expert experimentalists with extensive experience inspecting smFRET trajectories (displacement and intensity traces) from live cells. We test our automated approach against our recently published research on the metabotropic glutamate receptor 2 (mGluR2) and reveal substantial similarities, as well as potential shortcomings in the manual curation process that are addressable using the algorithms we developed here.
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Affiliation(s)
- Jozsef Meszaros
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Peter Geggier
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Jamie J. Manning
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Wesley B. Asher
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Jonathan A. Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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11
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Wen X, Sang Y, Zhang Y, Ge F, Jing G, He Y. Direct Observation of Nanotracer Transport in Swarming Bacteria during Antibiotic Adaptation. ACS Nano 2023. [PMID: 37256562 DOI: 10.1021/acsnano.2c12785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microorganisms inevitably encounter environmental variations and thus need to develop necessary strategies to adjust the colonies for survival. Here, we use cooperating Serratia marcescens bacteria to reveal how the whole population responds to a gradually deteriorating habitat. When subjected to antibiotics with increasing doses, the swarming bacteria transform weak homogeneous turbulent flows to nematic jet flows with defects and vortices on a large scale, by which bacteria exploit these coherent flows to transfer material and/or information. We elucidate a complete view of detailed spatiotemporal transport behavior in such microscale active turbulence with single-nanoparticle tracking. The nanoparticles in these active flows are brought into the state with the up limit of superdiffusion by the bacterial collective response to the stronger antibiotic stimulation. Strikingly, we found that, under the strengthening stimulation from antibiotics, bacteria with only a small fraction of their community get elongated and facilitate the drastic turbulence transition and an enhanced superdiffusion. These findings imply a possible collective response mechanism against environmental variations.
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Affiliation(s)
- Xiaodong Wen
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yuqian Sang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yongyu Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Feng Ge
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Guangyin Jing
- School of Physics, Northwest University, Xi'An, 710127, China
| | - Yan He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
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12
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Kim J, Martin OJF. Trap-and-Track for Characterizing Surfactants at Interfaces. Molecules 2023; 28:molecules28062859. [PMID: 36985832 PMCID: PMC10058797 DOI: 10.3390/molecules28062859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Understanding the behavior of surfactants at interfaces is crucial for many applications in materials science and chemistry. Optical tweezers combined with trajectory analysis can become a powerful tool for investigating surfactant characteristics. In this study, we perform trap-and-track analysis to compare the behavior of cetyltrimethylammonium bromide (CTAB) and cetyltrimethylammonium chloride (CTAC) at water-glass interfaces. We use optical tweezers to trap a gold nanoparticle and statistically analyze the particle's movement in response to various surfactant concentrations, evidencing the rearrangement of surfactants adsorbed on glass surfaces. Our results show that counterions have a significant effect on surfactant behavior at the interface. The greater binding affinity of bromide ions to CTA+ micelle surfaces reduces the repulsion among surfactant head groups and enhances the mobility of micelles adsorbed on the interface. Our study provides valuable insights into the behavior of surfactants at interfaces and highlights the potential of optical tweezers for surfactant research. The development of this trap-and-track approach can have important implications for various applications, including drug delivery and nanomaterials.
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Affiliation(s)
- Jeonghyeon Kim
- Nanophotonics and Metrology Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Olivier J F Martin
- Nanophotonics and Metrology Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
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13
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Kim J, Lee S, Lee YK, Seong B, Kim HM, Kyeong S, Kim W, Ham K, Pham XH, Hahm E, Mun JY, Safaa MA, Lee YS, Jun BH, Park HS. In Vitro Tracking of Human Umbilical Vein Endothelial Cells Using Ultra-Sensitive Quantum Dot-Embedded Silica Nanoparticles. Int J Mol Sci 2023; 24:ijms24065794. [PMID: 36982869 PMCID: PMC10052325 DOI: 10.3390/ijms24065794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The nanoscale spatiotemporal resolution of single-particle tracking (SPT) renders it a powerful method for exploring single-molecule dynamics in living cells or tissues, despite the disadvantages of using traditional organic fluorescence probes, such as the weak fluorescent signal against the strong cellular autofluorescence background coupled with a fast-photobleaching rate. Quantum dots (QDs), which enable tracking targets in multiple colors, have been proposed as an alternative to traditional organic fluorescence dyes; however, they are not ideally suitable for applying SPT due to their hydrophobicity, cytotoxicity, and blinking problems. This study reports an improved SPT method using silica-coated QD-embedded silica nanoparticles (QD2), which represent brighter fluorescence and are less toxic than single QDs. After treatment of QD2 in 10 μg/mL, the label was retained for 96 h with 83.76% of labeling efficiency, without impaired cell function such as angiogenesis. The improved stability of QD2 facilitates the visualization of in situ endothelial vessel formation without real-time staining. Cells retain QD2 fluorescence signal for 15 days at 4 °C without significant photobleaching, indicating that QD2 has overcome the limitations of SPT enabling long-term intracellular tracking. These results proved that QD2 could be used for SPT as a substitute for traditional organic fluorophores or single quantum dots, with its photostability, biocompatibility, and superior brightness.
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Affiliation(s)
- Jaehi Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Sunray Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Yeon Kyung Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Bomi Seong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyung-Mo Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - San Kyeong
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Wooyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Kyeongmin Ham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Xuan-Hung Pham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Eunil Hahm
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Ji Yeon Mun
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | | | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyun-Sook Park
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
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14
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Gu S, Tzingounis AV, Lykotrafitis G. Differential Control of Small-conductance Calcium-activated Potassium Channel Diffusion by Actin in Different Neuronal Subcompartments. Function (Oxf) 2023; 4:zqad018. [PMID: 37168495 PMCID: PMC10165553 DOI: 10.1093/function/zqad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Small-conductance calcium-activated potassium (SK) channels show a ubiquitous distribution on neurons, in both somatodendritic and axonal regions. SK channels are associated with neuronal activity regulating action potential frequency, dendritic excitability, and synaptic plasticity. Although the physiology of SK channels and the mechanisms that control their surface expression levels have been investigated extensively, little is known about what controls SK channel diffusion in the neuronal plasma membrane. This aspect is important, as the diffusion of SK channels at the surface may control their localization and proximity to calcium channels, hence increasing the likelihood of SK channel activation by calcium. In this study, we successfully investigated the diffusion of SK channels labeled with quantum dots on human embryonic kidney cells and dissociated hippocampal neurons by combining a single-particle tracking method with total internal reflection fluorescence microscopy. We observed that actin filaments interfere with SK mobility, decreasing their diffusion coefficient. We also found that during neuronal maturation, SK channel diffusion was gradually inhibited in somatodendritic compartments. Importantly, we observed that axon barriers formed at approximately days in vitro 6 and restricted the diffusion of SK channels on the axon initial segment (AIS). However, after neuron maturation, SK channels on the AIS were strongly immobilized, even after disruption of the actin network, suggesting that crowding may cause this effect. Altogether, our work provides insight into how SK channels diffuse on the neuronal plasma membrane and how actin and membrane crowding impacts SK channel diffusion.
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Affiliation(s)
- Shiju Gu
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Anastasios V Tzingounis
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269, USA
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15
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Sheung JY, Garamella J, Kahl SK, Lee BY, McGorty RJ, Robertson-Anderson RM. Motor-driven advection competes with crowding to drive spatiotemporally heterogeneous transport in cytoskeleton composites. Front Phys 2022; 10:1055441. [PMID: 37547053 PMCID: PMC10403238 DOI: 10.3389/fphy.2022.1055441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cytoskeleton-a composite network of biopolymers, molecular motors, and associated binding proteins-is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous subdiffusion to superdiffusion and advection. Yet, recapitulating and understanding these properties-ubiquitous to the cytoskeleton and other out-of-equilibrium soft matter systems-remains challenging. Here, we combine light sheet microscopy with differential dynamic microscopy and single-particle tracking to elucidate anomalous and advective transport in actomyosin-microtubule composites. We show that particles exhibit multi-mode transport that transitions from pronounced subdiffusion to superdiffusion at tunable crossover timescales. Surprisingly, while higher actomyosin content increases the range of timescales over which transport is superdiffusive, it also markedly increases the degree of subdiffusion at short timescales and generally slows transport. Corresponding displacement distributions display unique combinations of non-Gaussianity, asymmetry, and non-zero modes, indicative of directed advection coupled with caged diffusion and hopping. At larger spatiotemporal scales, particles in active composites exhibit superdiffusive dynamics with scaling exponents that are robust to changing actomyosin fractions, in contrast to normal, yet faster, diffusion in networks without actomyosin. Our specific results shed important new light on the interplay between non-equilibrium processes, crowding and heterogeneity in active cytoskeletal systems. More generally, our approach is broadly applicable to active matter systems to elucidate transport and dynamics across scales.
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Affiliation(s)
- Janet Y. Sheung
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Jonathan Garamella
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
| | - Stella K. Kahl
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
| | - Brian Y. Lee
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Ryan J. McGorty
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
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16
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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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17
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Heckert A, Dahal L, Tjian R, Darzacq X. Recovering mixtures of fast-diffusing states from short single-particle trajectories. eLife 2022; 11:e70169. [PMID: 36066004 PMCID: PMC9451534 DOI: 10.7554/elife.70169] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.
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Affiliation(s)
- Alec Heckert
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Liza Dahal
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
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18
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Nissen M, Förster R, Wieduwilt T, Lorenz A, Jiang S, Hauswald W, Schmidt MA. Nanoparticle Tracking in Single-Antiresonant-Element Fiber for High-Precision Size Distribution Analysis of Mono- and Polydisperse Samples. Small 2022; 18:e2202024. [PMID: 35988130 DOI: 10.1002/smll.202202024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Accurate determination of the size distribution of nanoparticle ensembles remains a challenge in nanotechnology-related applications due to the limitations of established methods. Here, a microstructured fiber-assisted nanoparticle tracking analysis (FaNTA) realization is introduced that breaks existing limitations through the recording of exceptionally long trajectories of rapidly diffusing polydisperse nanoparticles, resulting in excellent sizing precision and unprecedented separation capabilities of bimodal nanoparticle mixtures. An effective-single-mode antiresonant-element fiber allows to efficiently confine nanoparticles in a light-guiding microchannel and individually track them over more than 1000 frames, while aberration-free imaging is experimentally confirmed by cross-correlation analysis. Unique features of the approach are (i) the highly precise determination of the size distribution of monodisperse nanoparticle ensembles (only 7% coefficient of variation) and (ii) the accurate characterization of individual components in a bimodal mixture with very close mean diameters, both experimentally demonstrated for polymer nanospheres. The outstanding performance of the FaNTA realization can be quantified by introducing a new model for the bimodal separation index. Since FaNTA is applicable to all types of nano-objects down to sub-20 nm diameters, the method will improve the precision standard of mono- and polydisperse nanoparticle samples such as nano-plastics or extracellular vesicles.
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Affiliation(s)
- Mona Nissen
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
- Abbe Center of Photonics and Faculty of Physics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743, Jena, Germany
| | - Ronny Förster
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Torsten Wieduwilt
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Adrian Lorenz
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Shiqi Jiang
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
- Abbe Center of Photonics and Faculty of Physics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743, Jena, Germany
| | - Walter Hauswald
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Markus A Schmidt
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
- Abbe Center of Photonics and Faculty of Physics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743, Jena, Germany
- Otto Schott Institute of Material Research, Friedrich Schiller University Jena, Fraunhoferstr. 6, 07743, Jena, Germany
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19
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Sigaeva A, Hochstetter A, Bouyim S, Chipaux M, Stejfova M, Cigler P, Schirhagl R. Single-Particle Tracking and Trajectory Analysis of Fluorescent Nanodiamonds in Cell-Free Environment and Live Cells. Small 2022; 18:e2201395. [PMID: 36038355 DOI: 10.1002/smll.202201395] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Diamond magnetometry can provide new insights on the production of free radicals inside live cells due to its high sensitivity and spatial resolution. However, the measurements often lack intracellular context for the recorded signal. In this paper, the possible use of single-particle tracking and trajectory analysis of fluorescent nanodiamonds (FNDs) to bridge that gap is explored. It starts with simulating a set of different possible scenarios of a particle's movement, reflecting different modes of motion, degrees of confinement, as well as shapes and sizes of that confinement. Then, the insights from the analysis of the simulated trajectories are applied to describe the movement of FNDs in glycerol solutions. It is shown that the measurements are in good agreement with the previously reported findings and that trajectory analysis yields meaningful results, when FNDs are tracked in a simple environment. Then the much more complex situation of FNDs moving inside a live cell is focused. The behavior of the particles after different incubation times is analyzed, and the possible intracellular localization of FNDs is deducted from their trajectories. Finally, this approach is combined with long-term magnetometry methods to obtain maps of the spin relaxation dynamics (or T1) in live cells, as FNDs move through the cytosol.
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Affiliation(s)
- Alina Sigaeva
- University Medical Center Groningen, Groningen University, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Axel Hochstetter
- Research & Development, Life on a Chip e.K., Brunnenaecker 5, 73571, Goeggingen, Germany
| | - Sighom Bouyim
- University Medical Center Groningen, Groningen University, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Mayeul Chipaux
- Institute of Physics, Life on Chip e.K., École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Miroslava Stejfova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, Prague, 166 10, Czech Republic
| | - Petr Cigler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, Prague, 166 10, Czech Republic
| | - Romana Schirhagl
- University Medical Center Groningen, Groningen University, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
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20
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van Heerden B, Vickers NA, Krüger TPJ, Andersson SB. Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective. Small 2022; 18:e2107024. [PMID: 35758534 PMCID: PMC9308725 DOI: 10.1002/smll.202107024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 04/07/2022] [Indexed: 05/14/2023]
Abstract
Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.
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Affiliation(s)
- Bertus van Heerden
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215, USA
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21
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Liu Y, Lu Y, Tang Z, Cao Y, Huang D, Wu F, Zhang Y, Li C, Chen G, Wang Q. Single-particle fluorescence tracking combined with TrackMate assay reveals highly heterogeneous and discontinuous lysosomal transport in freely orientated axons. Biotechnol J 2022; 17:e2200006. [PMID: 35765726 DOI: 10.1002/biot.202200006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/12/2022]
Abstract
Axonal transport plays a significant role in the establishment of neuronal polarity, axon growth, and synapse formation during neuronal development. The axon of a naturally growing neuron is a highly complex and multifurcated structure with a large number of bends and branches. Nowadays, the study of dynamic axonal transport in morphologically complex neurons is greatly limited by the technological barrier. Here, a sparse gene transfection strategy was developed to locate fluorescent mCherry in the lysosome of primary neurons, thus enabling us to track the lysosome-based axonal transport with a single-particle resolution. Thereby, several axonal transport models were observed, including the forward or backward transport model, stop-and-go model, repeated back-and-forth transport model, and cross-branch transport model. Then, the accurate single-particle velocity quantification by TrackMate revealed a highly heterogeneous and discontinuous transportation process of lysosome-based axonal transport in freely orientated axons. And, multiple physical factors, such as the axonal structure and the size of particles, were disclosed to affect the velocity of particle transporting in freely orientated axons. The combined single-particle fluorescence tracking and TrackMate assay can be served as a facile tool for evaluating axonal transport in neuronal development and axonal transport-related diseases.
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Affiliation(s)
- Yongyang Liu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yaxin Lu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Zhiyong Tang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Yuheng Cao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Dehua Huang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Feng Wu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Yejun Zhang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Chunyan Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Guangcun Chen
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Qiangbin Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, China
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22
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Yuan JW, Zhang YN, Liu YR, Li W, Dou SX, Wei Y, Wang PY, Li H. Diffusion Behaviors of Integrins in Single Cells Altered by Epithelial to Mesenchymal Transition. Small 2022; 18:e2106498. [PMID: 34921576 DOI: 10.1002/smll.202106498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cell morphology and migration depend critically on the adhesions on the extracellular matrix (ECM), determined by the transmembrane protein integrins. The epithelial to mesenchymal transition (EMT) is a prominent transformation process in which adherent cells acquire a mesenchymal phenotype and a promoted migration. EMT plays important roles in embryonic development and cancer metastasis, and its hallmarks include the acquisition of front-back cell polarity and loss of cell-cell contact. However, how integrins dynamically regulate cell-ECM adhesions and cellular behaviors during EMT is still unclear. Using single-particle tracking of β1-integrins labeled with quantum dots, the temporal-spatial on-membrane dynamics of integrins in the EMT of MCF10A cells is revealed. β1-integrins exhibit significantly enhanced dynamics, which temporally behave more diffusive and less immobilized, and spatially become distributed asymmetrically with front regions being more dynamic. These dynamic alterations are shown to arise from microtubule remodeling in EMT. The results shed new light on the EMT mechanism from the cell-ECM adhesion perspective, and suggest that the enhanced integrin diffusion may represent as a new hallmark of EMT.
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Affiliation(s)
- Jing-Wen Yuan
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Ning Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Yu-Ru Liu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wei
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
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23
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Martens KJA, Turkowyd B, Endesfelder U. Raw Data to Results: A Hands-On Introduction and Overview of Computational Analysis for Single-Molecule Localization Microscopy. Front Bioinform 2022; 1:817254. [PMID: 36303761 PMCID: PMC9580916 DOI: 10.3389/fbinf.2021.817254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/28/2021] [Indexed: 09/28/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) is an advanced microscopy method that uses the blinking of fluorescent molecules to determine the position of these molecules with a resolution below the diffraction limit (∼5-40 nm). While SMLM imaging itself is becoming more popular, the computational analysis surrounding the technique is still a specialized area and often remains a "black box" for experimental researchers. Here, we provide an introduction to the required computational analysis of SMLM imaging, post-processing and typical data analysis. Importantly, user-friendly, ready-to-use and well-documented code in Python and MATLAB with exemplary data is provided as an interactive experience for the reader, as well as a starting point for further analysis. Our code is supplemented by descriptions of the computational problems and their implementation. We discuss the state of the art in computational methods and software suites used in SMLM imaging and data analysis. Finally, we give an outlook into further computational challenges in the field.
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Affiliation(s)
- Koen J. A. Martens
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Bartosz Turkowyd
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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24
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Matsushita K, Nakahara C, Kimura S, Sakamoto N, Ii S, Miyoshi H. Intranuclear mesoscale viscoelastic changes during osteoblastic differentiation of human mesenchymal stem cells. FASEB J 2021; 35:e22071. [PMID: 34820910 DOI: 10.1096/fj.202100536rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/07/2021] [Accepted: 11/12/2021] [Indexed: 11/11/2022]
Abstract
Cell nuclei behave as viscoelastic materials. Dynamic regulation of the viscoelastic properties of nuclei in living cells is crucial for diverse biological and biophysical processes, specifically for intranuclear mesoscale viscoelasticity, through modulation of the efficiency of force propagation to the nucleoplasm and gene expression patterns. However, how the intranuclear mesoscale viscoelasticity of stem cells changes with differentiation is unclear and so is its biological significance. Here, we quantified the changes in intranuclear mesoscale viscoelasticity during osteoblastic differentiation of human mesenchymal stem cells. This analysis revealed that the intranuclear region is a viscoelastic solid, probably with a higher efficiency of force transmission that results in high sensitivity to mechanical signals in the early stages of osteoblastic differentiation. The intranuclear region was noted to alter to a viscoelastic liquid with a lower efficiency, which is responsible for the robustness of gene expression toward terminal differentiation. Additionally, evaluation of changes in the mesoscale viscoelasticity due to chromatin decondensation and correlation between the mesoscale viscoelasticity and local DNA density suggested that size of gap and flexibility of chromatin meshwork structures, which are modulated depending on chromatin condensation state, determine mesoscale viscoelasticity, with various rates of contribution in different differentiation stages. Given that chromatin within the nucleus condenses into heterochromatin as stem cells adopt a specific lineage by restricting transcription, viscoelasticity is perhaps a key factor in cooperative regulation of the nuclear mechanosensitivity and gene expression pattern for stem cell differentiation.
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Affiliation(s)
- Kojiro Matsushita
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
| | - Chiharu Nakahara
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
| | - Shun Kimura
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoya Sakamoto
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
| | - Satoshi Ii
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
| | - Hiromi Miyoshi
- Department of Mechanical Systems Engineering, Graduate School of Systems Design, Tokyo Metropolitan University, Hachioji, Japan
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25
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Maizón HB, Barrantes FJ. A deep learning-based approach to model anomalous diffusion of membrane proteins: the case of the nicotinic acetylcholine receptor. Brief Bioinform 2021; 23:6409696. [PMID: 34695840 DOI: 10.1093/bib/bbab435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
We present a concatenated deep-learning multiple neural network system for the analysis of single-molecule trajectories. We apply this machine learning-based analysis to characterize the translational diffusion of the nicotinic acetylcholine receptor at the plasma membrane, experimentally interrogated using superresolution optical microscopy. The receptor protein displays a heterogeneous diffusion behavior that goes beyond the ensemble level, with individual trajectories exhibiting more than one diffusive state, requiring the optimization of the neural networks through a hyperparameter analysis for different numbers of steps and durations, especially for short trajectories (<50 steps) where the accuracy of the models is most sensitive to localization errors. We next use the statistical models to test for Brownian, continuous-time random walk and fractional Brownian motion, and introduce and implement an additional, two-state model combining Brownian walks and obstructed diffusion mechanisms, enabling us to partition the two-state trajectories into segments, each of which is independently subjected to multiple analysis. The concatenated multi-network system evaluates and selects those physical models that most accurately describe the receptor's translational diffusion. We show that the two-state Brownian-obstructed diffusion model can account for the experimentally observed anomalous diffusion (mostly subdiffusive) of the population and the heterogeneous single-molecule behavior, accurately describing the majority (72.5 to 88.7% for α-bungarotoxin-labeled receptor and between 73.5 and 90.3% for antibody-labeled molecules) of the experimentally observed trajectories, with only ~15% of the trajectories fitting to the fractional Brownian motion model.
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Affiliation(s)
- Héctor Buena Maizón
- Laboratory of Molecular Neurobiology, Biomedical Research institute (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
| | - Francisco J Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research institute (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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26
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Olsén E, Jõemetsa S, González A, Joyce P, Zhdanov VP, Midtvedt D, Höök F. Diffusion of Lipid Nanovesicles Bound to a Lipid Membrane Is Associated with the Partial-Slip Boundary Condition. Nano Lett 2021; 21:8503-8509. [PMID: 34403260 PMCID: PMC8517973 DOI: 10.1021/acs.nanolett.1c02092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During diffusion of nanoparticles bound to a cellular membrane by ligand-receptor pairs, the distance to the laterally mobile interface is sufficiently short for their motion to depend not only on the membrane-mediated diffusivity of the tethers but also in a not yet fully understood manner on nanoparticle size and interfacial hydrodynamics. By quantifying diffusivity, velocity, and size of individual membrane-bound liposomes subjected to a hydrodynamic shear flow, we have successfully separated the diffusivity contributions from particle size and number of tethers. The obtained diffusion-size relations for synthetic and extracellular lipid vesicles are not well-described by the conventional no-slip boundary condition, suggesting partial slip as well as a significant diffusivity dependence on the distance to the lipid bilayer. These insights, extending the understanding of diffusion of biological nanoparticles at lipid bilayers, are of relevance for processes such as cellular uptake of viruses and lipid nanoparticles or labeling of cell-membrane-residing molecules.
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Affiliation(s)
- Erik Olsén
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - Silver Jõemetsa
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - Adrián González
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - Paul Joyce
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
- UniSA:
Clinical and Health Sciences, University
of South Australia, 5000 Adelaide, Australia
| | - Vladimir P. Zhdanov
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
- Boreskov
Institute of Catalysis, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Daniel Midtvedt
- Department
of Physics, University of Gothenburg, SE-41296 Göteborg, Sweden
| | - Fredrik Höök
- Department
of Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
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27
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Tan X, Welsher K. Particle-by-Particle In Situ Characterization of the Protein Corona via Real-Time 3D Single-Particle-Tracking Spectroscopy*. Angew Chem Int Ed Engl 2021; 60:22359-22367. [PMID: 34015174 PMCID: PMC8763617 DOI: 10.1002/anie.202105741] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/05/2022]
Abstract
Nanoparticles (NPs) adsorb proteins when exposed to biological fluids, forming a dynamic protein corona that affects their fate in biological environments. A comprehensive understanding of the protein corona is lacking due to the inability of current techniques to precisely measure the full corona in situ at the single-particle level. Herein, we introduce a 3D real-time single-particle tracking spectroscopy to "lock-on" to single freely diffusing polystyrene NPs and probe their individual protein coronas, primarily using bovine serum albumin (BSA) as a model system. The fluorescence signals and diffusive motions of the tracked NPs enable quantification of the "hard corona" using mean-squared displacement analysis. Critically, this method's particle-by-particle nature enabled a lock-in-type frequency filtering approach to extract the full protein corona, despite the typically confounding effect of high background signal from unbound proteins. From these results, the dynamic in situ full protein corona is observed to contain twice the number of proteins compared to the ex situ-measured "hard" protein corona.
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Affiliation(s)
- Xiaochen Tan
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, USA
| | - Kevin Welsher
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, USA
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28
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Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. Nano Lett 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
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Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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29
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Ferreira JS, Kellermayer B, Carvalho AL, Groc L. Interplay between NMDA receptor dynamics and the synaptic proteasome. Eur J Neurosci 2021; 54:6000-6011. [PMID: 34405467 DOI: 10.1111/ejn.15427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/16/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Proteasome activity at the excitatory synapse plays an important role in neuronal communication. The proteasome translocation to synapses is mediated by neuronal activity, in particular the activation of N-methyl-d-aspartate receptors (NMDARs). These receptors are composed of different subunits with distinct trafficking properties that provide various signalling and plasticity features to the synapse. Yet whether the interplay between the proteasome and NMDAR relies on specific subunit properties remain unclear. Using a combination of single molecule and immunocytochemistry imaging approaches in rat hippocampal neurons, we unveil a specific interplay between GluN2B-containing NMDARs (GluN2B-NMDARs) and the synaptic proteasome. Sustained proteasome activation specifically increases GluN2B-NMDAR (not GluN2A-NMDAR) lateral diffusion. In addition, when GluN2B-NMDAR expression is downregulated, the proteasome localization decreases at glutamatergic synapses. Collectively, our data fuel a model in which the cellular dynamics and location of GluN2B-NMDARs and proteasome are intermingled, shedding new lights on the NMDAR-dependent regulation of synaptic adaptation.
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Affiliation(s)
- Joana S Ferreira
- IINS-Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, University of Bordeaux, Bordeaux, France
| | - Blanka Kellermayer
- IINS-Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, University of Bordeaux, Bordeaux, France.,CNC-Center for Neuroscience and Cell Biology of Coimbra, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ana Luísa Carvalho
- CNC-Center for Neuroscience and Cell Biology of Coimbra, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Laurent Groc
- IINS-Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, University of Bordeaux, Bordeaux, France
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30
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Pinholt HD, Bohr SS, Iversen JF, Boomsma W, Hatzakis NS. Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion. Proc Natl Acad Sci U S A 2021; 118:e2104624118. [PMID: 34321355 DOI: 10.1073/pnas.2104624118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Single-particle tracking (SPT) analysis of individual biomolecules is an indispensable tool for extracting quantitative information from dynamic biological processes, but often requires some a priori knowledge of the system. Here we present “single-particle diffusional fingerprinting,” a more general approach for extraction of diffusional patterns in SPT independently of the biological system. This method extracts a set of descriptive features for each SPT trajectory, which are ranked upon classification to yield mechanistic insights for the species under comparison. We demonstrate its capacity to yield a dictionary of diffusional traits across multiple systems (e.g., lipases hydrolyzing fat, transcription factors diffusing in cells, and nanoparticles in mucus), supporting its use on multiple biological phenomena (e.g., drug delivery, receptor dynamics, and virology). Single-particle tracking (SPT) is a key tool for quantitative analysis of dynamic biological processes and has provided unprecedented insights into a wide range of systems such as receptor localization, enzyme propulsion, bacteria motility, and drug nanocarrier delivery. The inherently complex diffusion in such biological systems can vary drastically both in time and across systems, consequently imposing considerable analytical challenges, and currently requires an a priori knowledge of the system. Here we introduce a method for SPT data analysis, processing, and classification, which we term “diffusional fingerprinting.” This method allows for dissecting the features that underlie diffusional behavior and establishing molecular identity, regardless of the underlying diffusion type. The method operates by isolating 17 descriptive features for each observed motion trajectory and generating a diffusional map of all features for each type of particle. Precise classification of the diffusing particle identity is then obtained by training a simple logistic regression model. A linear discriminant analysis generates a feature ranking that outputs the main differences among diffusional features, providing key mechanistic insights. Fingerprinting operates by both training on and predicting experimental data, without the need for pretraining on simulated data. We found this approach to work across a wide range of simulated and experimentally diverse systems, such as tracked lipases on fat substrates, transcription factors diffusing in cells, and nanoparticles diffusing in mucus. This flexibility ultimately supports diffusional fingerprinting’s utility as a universal paradigm for SPT diffusional analysis and prediction.
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31
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Moses ME, Lund PM, Bohr SSR, Iversen JF, Kæstel-Hansen J, Kallenbach AS, Iversen L, Christensen SM, Hatzakis NS. Single-Molecule Study of Thermomyces lanuginosus Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium. ACS Appl Mater Interfaces 2021; 13:33704-33712. [PMID: 34235926 DOI: 10.1021/acsami.1c08809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lipases comprise one of the major enzyme classes in biotechnology with applications within, e.g., baking, brewing, biocatalysis, and the detergent industry. Understanding the mechanisms of lipase function and regulation is therefore important to facilitate the optimization of their function by protein engineering. Advances in single-molecule studies in model systems have provided deep mechanistic insights on lipase function, such as the existence of functional states, their dependence on regulatory cues, and their correlation to activity. However, it is unclear how these observations translate to enzyme behavior in applied settings. Here, single-molecule tracking of individual Thermomyces lanuginosus lipase (TLL) enzymes in a detergency application system allowed real-time direct observation of spatiotemporal localization, and thus diffusional behavior, of TLL enzymes on a lard substrate. Parallelized imaging of thousands of individual enzymes allowed us to observe directly the existence and quantify the abundance and interconversion kinetics between three diffusional states that we recently provided evidence to correlate with function. We observe redistribution of the enzyme's diffusional pattern at the lipid-water interface as well as variations in binding efficiency in response to surfactants and calcium, demonstrating that detergency effectors can drive the sampling of lipase functional states. Our single-molecule results combined with ensemble activity assays and enzyme surface binding efficiency readouts allowed us to deconvolute how application conditions can significantly alter protein functional dynamics and/or surface binding, both of which underpin enzyme performance. We anticipate that our results will inspire further efforts to decipher and integrate the dynamic nature of lipases, and other enzymes, in the design of new biotechnological solutions.
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Affiliation(s)
- Matias E Moses
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Philip M Lund
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Josephine F Iversen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Lars Iversen
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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32
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Opatovski N, Shalev Ezra Y, Weiss LE, Ferdman B, Orange-Kedem R, Shechtman Y. Multiplexed PSF Engineering for Three-Dimensional Multicolor Particle Tracking. Nano Lett 2021; 21:5888-5895. [PMID: 34213332 DOI: 10.1021/acs.nanolett.1c02068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Three-dimensional spatiotemporal tracking of microscopic particles in multiple colors is a challenging optical imaging task. Existing approaches require a trade-off between photon efficiency, field of view, mechanical complexity, spectral specificity, and speed. Here, we introduce multiplexed point-spread-function engineering that achieves photon-efficient, 3D multicolor particle tracking over a large field of view. This is accomplished by first chromatically splitting the emission path of a microscope to different channels, engineering the point-spread function of each, and then recombining them onto the same region of the camera. We demonstrate our technique for simultaneously tracking five types of emitters in vitro as well as colocalization of DNA loci in live yeast cells.
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33
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Speckner K, Weiss M. Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts. Entropy (Basel) 2021; 23:892. [PMID: 34356433 PMCID: PMC8303845 DOI: 10.3390/e23070892] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023]
Abstract
Single-particle tracking (SPT) has become a powerful tool to quantify transport phenomena in complex media with unprecedented detail. Based on the reconstruction of individual trajectories, a wealth of informative measures become available for each particle, allowing for a detailed comparison with theoretical predictions. While SPT has been used frequently to explore diffusive transport in artificial fluids and inside living cells, intermediate systems, i.e., biochemically active cell extracts, have been studied only sparsely. Extracts derived from the eggs of the clawfrog Xenopus laevis, for example, are known for their ability to support and mimic vital processes of cells, emphasizing the need to explore also the transport phenomena of nano-sized particles in such extracts. Here, we have performed extensive SPT on beads with 20 nm radius in native and chemically treated Xenopus extracts. By analyzing a variety of distinct measures, we show that these beads feature an anti-persistent subdiffusion that is consistent with fractional Brownian motion. Chemical treatments did not grossly alter this finding, suggesting that the high degree of macromolecular crowding in Xenopus extracts equips the fluid with a viscoelastic modulus, hence enforcing particles to perform random walks with a significant anti-persistent memory kernel.
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Affiliation(s)
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany;
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Klatt O, Repetto D, Brockhaus J, Reissner C, El Khallouqi A, Rohlmann A, Heine M, Missler M. Endogenous β-neurexins on axons and within synapses show regulated dynamic behavior. Cell Rep 2021; 35:109266. [PMID: 34133920 DOI: 10.1016/j.celrep.2021.109266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/21/2020] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Neurexins are key organizer molecules that regulate synaptic function and are implicated in autism and schizophrenia. β-neurexins interact with numerous cell adhesion and receptor molecules, but their neuronal localization remains elusive. Using single-molecule tracking and high-resolution microscopy to detect neurexin1β and neurexin3β in primary hippocampal neurons from knockin mice, we demonstrate that endogenous β-neurexins are present in fewer than half of excitatory and inhibitory synapses. Moreover, we observe a large extrasynaptic pool of β-neurexins on axons and show that axonal β-neurexins diffuse with higher surface mobility than those transiently confined within synapses. Stimulation of neuronal activity further increases the mobility of synaptic and axonal β-neurexins, whereas inhibition causes the opposite. Blocking ectodomain cleavage by metalloproteases also reduces β-neurexin mobility and enhances glutamate release. These findings suggest that the surface mobility of endogenous β-neurexins inside and outside of synapses is dynamically regulated and linked to neuronal activity.
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Affiliation(s)
- Oliver Klatt
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany; Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Daniele Repetto
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Johannes Brockhaus
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Carsten Reissner
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Abderazzaq El Khallouqi
- Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Astrid Rohlmann
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Martin Heine
- Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany.
| | - Markus Missler
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany.
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Rosendale M, Flores J, Paviolo C, Pagano P, Daniel J, Ferreira J, Verlhac JB, Groc L, Cognet L, Blanchard-Desce M. A Bottom-Up Approach to Red-Emitting Molecular-Based Nanoparticles with Natural Stealth Properties and their Use for Single-Particle Tracking Deep in Brain Tissue. Adv Mater 2021; 33:e2006644. [PMID: 33890332 DOI: 10.1002/adma.202006644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Fluorescent nanoparticles dedicated to bioimaging applications should possess specific properties that have to be maintained in the aqueous, reactive, and crowded biological environment. These include chemical and photostability, small size (on the scale of subcellular structures), biocompatibility, high brightness, and good solubility. The latter is a major challenge for inorganic nanoparticles, which require surface coating to be made water soluble. Molecular-based fluorescent organic nanoparticles (FONs) may prove a promising, spontaneously water-soluble alternative, whose bottom-up design allows for the fine-tuning of individual properties. Here, the critical challenge of controlling the interaction of nanoparticles with cellular membranes is addressed. This is a report on bright, size-tunable, red-emitting, naturally stealthy FONs that do not require the use of antifouling agents to impede interactions with cellular membranes. As a proof of concept, single FONs diffusing up to 150 µm deep in brain tissue are imaged and tracked.
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Affiliation(s)
- Morgane Rosendale
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
| | - Jessica Flores
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
| | - Chiara Paviolo
- LP2N, Institut d'Optique & CNRS, Univ. Bordeaux, UMR 5298, Rue François Mitterrand, Talence, 33400, France
| | - Paolo Pagano
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
| | - Jonathan Daniel
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
| | - Joana Ferreira
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, UMR 5297, 146 Rue Léo Saignat, Bordeaux, 33076, France
| | - Jean-Baptiste Verlhac
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
| | - Laurent Groc
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, UMR 5297, 146 Rue Léo Saignat, Bordeaux, 33076, France
| | - Laurent Cognet
- LP2N, Institut d'Optique & CNRS, Univ. Bordeaux, UMR 5298, Rue François Mitterrand, Talence, 33400, France
| | - Mireille Blanchard-Desce
- Institut des Sciences Moléculaires, CNRS, Univ. Bordeaux, Bordeaux INP, UMR 5255, 351 Cours de la Libération, Talence, 33405, France
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Polenghi A, Nieus T, Guazzi S, Gorostiza P, Petrini EM, Barberis A. Kainate Receptor Activation Shapes Short-Term Synaptic Plasticity by Controlling Receptor Lateral Mobility at Glutamatergic Synapses. Cell Rep 2021; 31:107735. [PMID: 32521260 PMCID: PMC7296349 DOI: 10.1016/j.celrep.2020.107735] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/26/2020] [Accepted: 05/14/2020] [Indexed: 01/24/2023] Open
Abstract
Kainate receptors (KARs) mediate postsynaptic currents with a key impact on neuronal excitability. However, the molecular determinants controlling KAR postsynaptic localization and stabilization are poorly understood. Here, we exploit optogenetic and single-particle tracking approaches to study the role of KAR conformational states induced by glutamate binding on KAR lateral mobility at synapses. We report that following glutamate binding, KARs are readily and reversibly trapped at glutamatergic synapses through increased interaction with the β-catenin/N-cadherin complex. We demonstrate that such activation-dependent synaptic immobilization of KARs is crucial for the modulation of short-term plasticity of glutamatergic synapses. Thus, the present study unveils the crosstalk between conformational states and lateral mobility of KARs, a mechanism regulating glutamatergic signaling, particularly in conditions of sustained synaptic activity. Anchoring of KARs at glutamatergic synapses depends on receptor-glutamate binding KARs activation/desensitization promotes receptors trapping at glutamatergic synapses N-cadherins mediate the KAR activation/desensitization-dependent anchoring at synapses Synaptic trapping of desensitized KARs affects short-term synaptic plasticity
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Affiliation(s)
- Alice Polenghi
- Synaptic Plasticity of Inhibitory Networks, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Thierry Nieus
- Department of Biomedical and Clinical Sciences "L. Sacco," University of Milan, Milan, Italy
| | - Stefania Guazzi
- Synaptic Plasticity of Inhibitory Networks, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Pau Gorostiza
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Network Biomedical Research Center in Bioengineering, Biomaterials and Nanotechnology (CIBER-BBN), 50018 Zaragoza, Spain
| | - Enrica Maria Petrini
- Synaptic Plasticity of Inhibitory Networks, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Andrea Barberis
- Synaptic Plasticity of Inhibitory Networks, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy.
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Mylvaganam S, Riedl M, Vega A, Collins RF, Jaqaman K, Grinstein S, Freeman SA. Stabilization of Endothelial Receptor Arrays by a Polarized Spectrin Cytoskeleton Facilitates Rolling and Adhesion of Leukocytes. Cell Rep 2021; 31:107798. [PMID: 32579925 PMCID: PMC7548125 DOI: 10.1016/j.celrep.2020.107798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022] Open
Abstract
Multivalent complexes of endothelial adhesion receptors (e.g., selectins) engage leukocytes to orchestrate their migration to inflamed tissues. Proper anchorage and sufficient density (clustering) of endothelial receptors are required for efficient leukocyte capture and rolling. We demonstrate that a polarized spectrin network dictates the stability of the endothelial cytoskeleton, which is attached to the apical membrane, at least in part, by the abundant transmembrane protein CD44. Single-particle tracking revealed that CD44 undergoes prolonged periods of immobilization as it tethers to the cytoskeleton. The CD44-spectrin "picket fence" alters the behavior of bystander molecules-notably, selectins-curtailing their mobility, inducing their apical accumulation, and favoring their clustering within caveolae. Accordingly, depletion of either spectrin or CD44 virtually eliminated leukocyte rolling and adhesion to the endothelium. Our results indicate that a unique spectrin-based apical cytoskeleton tethered to transmembrane pickets-notably, CD44-is essential for proper extravasation of leukocytes in response to inflammation.
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Affiliation(s)
- Sivakami Mylvaganam
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, 19-9800, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Magdalena Riedl
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, 19-9800, Toronto, ON M5G 0A4, Canada
| | - Anthony Vega
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Richard F Collins
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, 19-9800, Toronto, ON M5G 0A4, Canada
| | - Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sergio Grinstein
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, 19-9800, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON M5B 1W8, Canada.
| | - Spencer A Freeman
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, 19-9800, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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Abstract
Asymmetric cell division yields two distinct daughter cells by mechanisms that underlie stem cell behavior and cellular diversity in all organisms. The bacterium Caulobacter crescentus is able to orchestrate this complex process with less than 4,000 genes. This article describes a strategy deployed by Caulobacter where a regulatory protein, PopA, is programed to perform distinct roles based on its subcellular address. We demonstrate that, depending on the availability of a second messenger molecule, PopA adopts either a monomer or dimer form. The two oligomeric forms interact with different partners at the two cell poles, playing a critical role in the degradation of a master transcription factor at one pole and flagellar assembly at the other pole. Asymmetric cell division generates two daughter cells with distinct characteristics and fates. Positioning different regulatory and signaling proteins at the opposing ends of the predivisional cell produces molecularly distinct daughter cells. Here, we report a strategy deployed by the asymmetrically dividing bacterium Caulobacter crescentus where a regulatory protein is programmed to perform distinct functions at the opposing cell poles. We find that the CtrA proteolysis adaptor protein PopA assumes distinct oligomeric states at the two cell poles through asymmetrically distributed c-di-GMP: dimeric at the stalked pole and monomeric at the swarmer pole. Different polar organizing proteins at each cell pole recruit PopA where it interacts with and mediates the function of two molecular machines: the ClpXP degradation machinery at the stalked pole and the flagellar basal body at the swarmer pole. We discovered a binding partner of PopA at the swarmer cell pole that together with PopA regulates the length of the flagella filament. Our work demonstrates how a second messenger provides spatiotemporal cues to change the physical behavior of an effector protein, thereby facilitating asymmetry.
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Jamali V, Hargus C, Ben-Moshe A, Aghazadeh A, Ha HD, Mandadapu KK, Alivisatos AP. Anomalous nanoparticle surface diffusion in LCTEM is revealed by deep learning-assisted analysis. Proc Natl Acad Sci U S A 2021; 118:e2017616118. [PMID: 33658362 PMCID: PMC7958372 DOI: 10.1073/pnas.2017616118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The motion of nanoparticles near surfaces is of fundamental importance in physics, biology, and chemistry. Liquid cell transmission electron microscopy (LCTEM) is a promising technique for studying motion of nanoparticles with high spatial resolution. Yet, the lack of understanding of how the electron beam of the microscope affects the particle motion has held back advancement in using LCTEM for in situ single nanoparticle and macromolecule tracking at interfaces. Here, we experimentally studied the motion of a model system of gold nanoparticles dispersed in water and moving adjacent to the silicon nitride membrane of a commercial LC in a broad range of electron beam dose rates. We find that the nanoparticles exhibit anomalous diffusive behavior modulated by the electron beam dose rate. We characterized the anomalous diffusion of nanoparticles in LCTEM using a convolutional deep neural-network model and canonical statistical tests. The results demonstrate that the nanoparticle motion is governed by fractional Brownian motion at low dose rates, resembling diffusion in a viscoelastic medium, and continuous-time random walk at high dose rates, resembling diffusion on an energy landscape with pinning sites. Both behaviors can be explained by the presence of silanol molecular species on the surface of the silicon nitride membrane and the ionic species in solution formed by radiolysis of water in presence of the electron beam.
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Affiliation(s)
- Vida Jamali
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Cory Hargus
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Assaf Ben-Moshe
- Department of Chemistry, University of California, Berkeley, CA 94720
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Amirali Aghazadeh
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720
| | - Hyun Dong Ha
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kranthi K Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - A Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
- Kavli Energy NanoScience Institute, Berkeley, CA 94720
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Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. eLife 2021; 10:64207. [PMID: 33616037 PMCID: PMC7987339 DOI: 10.7554/elife.64207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face. Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes. The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs. Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.
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Affiliation(s)
- Seongjin Park
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Emily M Heideman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Muhammad S Azam
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Matthew A Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
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Egloff S, Runser A, Klymchenko A, Reisch A. Size-Dependent Electroporation of Dye-Loaded Polymer Nanoparticles for Efficient and Safe Intracellular Delivery. Small Methods 2021; 5:e2000947. [PMID: 34927896 DOI: 10.1002/smtd.202000947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/13/2020] [Indexed: 06/14/2023]
Abstract
Efficient and safe delivery of nanoparticles (NPs) into the cytosol of living cells constitutes a major methodological challenge in bio-nanotechnology. Electroporation allows direct transfer of NPs into the cytosol by forming transient pores in the cell membrane, but it is criticized for invasiveness, and the applicable particle sizes are not well defined. Here, in order to establish principles for efficient delivery of NPs into the cytosol with minimal cytotoxicity, the influence of the size of NPs on their electroporation and intracellular behavior is investigated. For this study, fluorescent dye-loaded polymer NPs with core sizes between 10 and 40 nm are prepared. Optimizing the electroporation protocol allows minimizing contributions of endocytosis and to study directly the effect of NP size on electroporation. NPs of <20 nm hydrodynamic size are efficiently delivered into the cytosol, whereas this is not the case for NPs of >30 nm. Moreover, only particles of core size <15 nm diffuse freely throughout the cytosol. While electroporation at excessive electric fields induces cytotoxicity, the use of small NPs <20 nm allows efficient delivery at mild electroporation conditions. These results give clear methodological and design guidelines for the safe delivery of NPs for intracellular applications.
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Affiliation(s)
- Sylvie Egloff
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Anne Runser
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Andrey Klymchenko
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Andreas Reisch
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
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42
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Tavakoli S, Kari OK, Turunen T, Lajunen T, Schmitt M, Lehtinen J, Tasaka F, Parkkila P, Ndika J, Viitala T, Alenius H, Urtti A, Subrizi A. Diffusion and Protein Corona Formation of Lipid-Based Nanoparticles in the Vitreous Humor: Profiling and Pharmacokinetic Considerations. Mol Pharm 2021; 18:699-713. [PMID: 32584047 PMCID: PMC7856631 DOI: 10.1021/acs.molpharmaceut.0c00411] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 06/25/2020] [Indexed: 12/30/2022]
Abstract
The vitreous humor is the first barrier encountered by intravitreally injected nanoparticles. Lipid-based nanoparticles in the vitreous are studied by evaluating their diffusion with single-particle tracking technology and by characterizing their protein coronae with surface plasmon resonance and high-resolution proteomics. Single-particle tracking results indicate that the vitreal mobility of the formulations is dependent on their charge. Anionic and neutral formulations are mobile, whereas larger (>200 nm) neutral particles have restricted diffusion, and cationic particles are immobilized in the vitreous. PEGylation increases the mobility of cationic and larger neutral formulations but does not affect anionic and smaller neutral particles. Convection has a significant role in the pharmacokinetics of nanoparticles, whereas diffusion drives the transport of antibodies. Surface plasmon resonance studies determine that the vitreal corona of anionic formulations is sparse. Proteomics data reveals 76 differentially abundant proteins, whose enrichment is specific to either the hard or the soft corona. PEGylation does not affect protein enrichment. This suggests that protein-specific rather than formulation-specific factors are drivers of protein adsorption on nanoparticles in the vitreous. In summary, our findings contribute to understanding the pharmacokinetics of nanoparticles in the vitreous and help advance the development of nanoparticle-based treatments for eye diseases.
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Affiliation(s)
- Shirin Tavakoli
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Otto Kalevi Kari
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Tiina Turunen
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Tatu Lajunen
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Mechthild Schmitt
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Julia Lehtinen
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Fumitaka Tasaka
- Pharmaceutics
& Pharmacology Department, Global R&D, Santen Pharmaceutical
Co., Ltd., 8916-16 Takayama-cho, Ikoma, Nara 630-0101, Japan
| | - Petteri Parkkila
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Joseph Ndika
- Human
Microbiome Research, Faculty of Medicine, University of Helsinki, P.O. Box 21, 00290 Helsinki, Finland
| | - Tapani Viitala
- Division
of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
| | - Harri Alenius
- Human
Microbiome Research, Faculty of Medicine, University of Helsinki, P.O. Box 21, 00290 Helsinki, Finland
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Arto Urtti
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014, Helsinki, Finland
- Institute
of Chemistry, St. Petersburg State University, Petergof, Universitetskii pr. 26, 198504 St. Petersburg, Russia
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Astrid Subrizi
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
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43
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Pan Q, Sun D, Xue J, Hao J, Zhao H, Lin X, Yu L, He Y. Real-Time Study of Protein Phase Separation with Spatiotemporal Analysis of Single-Nanoparticle Trajectories. ACS Nano 2021; 15:539-549. [PMID: 33348982 DOI: 10.1021/acsnano.0c05486] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Liquid-liquid phase separation (LLPS) underlies the formation mechanism of membraneless biomolecular condensates locally to perform important physiological functions such as selective autophagy, but little is known about the relationship between their dynamic structural organization and biophysical properties. Here, a dark-field microscopy based single plasmonic nanoparticle tracking (DFSPT) technique was introduced to simultaneously monitor the diffusion dynamics of multiple gold nanorod (AuNR) probes in a protein LLPS system and to quantitatively characterize the spatiotemporal heterogeneity of the LLPS condensates during their phase transformation. Based on spatially and temporally resolved analysis of the diffusional behavior of the AuNRs, structure and material properties of p62 condensates, such as the viscoelasticity, the compartmentalization, and the recruitment of protein-covered nanoparticles into the large droplet, have been observed. Moreover, the nonsmooth droplet interface, its solidification after further phase transition or maturation, and the size effect of the inner vacuoles have also been revealed. Our method can be potentially applied to in vitro investigation of different reconstituted membrane-free biomolecular condensates and in vivo study of their dynamic evolution.
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Affiliation(s)
- Qi Pan
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Daxiao Sun
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianfeng Xue
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jie Hao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Hansen Zhao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xijian Lin
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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44
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Abstract
Brain diseases are becoming a more and more serious threat to human health. Many critical properties of the transport mechanisms of drugs in live brains remain poorly understood. In this work, single-particle tracking was used to dissect the transport dynamics of wheat germ agglutinin (WGA) in live brain and characterize the geometry and rheology of the extracellular space (ECS). The results revealed that the movements of WGA were influenced by the specific-binding molecules and the nature of the ECS. We further analyzed the mobility behaviors of WGA globally and quantitatively and found that movement of WGA in brain cells of acute slices was an active transport process associated with actin filaments and microtubules. This work paves the way for studies aiming at characterizing the biophysics of drug transport in the context of live brains, which may contribute to developing potential new therapeutic applications for brain diseases.
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Affiliation(s)
- Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Lei Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, and Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Hua-Jie Chen
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yusi Hu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Hong-Peng Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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45
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Stanislavsky A, Weron A. Look at Tempered Subdiffusion in a Conjugate Map: Desire for the Confinement. Entropy (Basel) 2020; 22:E1317. [PMID: 33287082 PMCID: PMC7712244 DOI: 10.3390/e22111317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
The Laplace distribution of random processes was observed in numerous situations that include glasses, colloidal suspensions, live cells, and firm growth. Its origin is not so trivial as in the case of Gaussian distribution, supported by the central limit theorem. Sums of Laplace distributed random variables are not Laplace distributed. We discovered a new mechanism leading to the Laplace distribution of observable values. This mechanism changes the contribution ratio between a jump and a continuous parts of random processes. Our concept uses properties of Bernstein functions and subordinators connected with them.
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Affiliation(s)
- Aleksander Stanislavsky
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland;
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46
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Ward AE, Kiessling V, Pornillos O, White JM, Ganser-Pornillos BK, Tamm LK. HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo-electron and TIRF microscopy. J Biol Chem 2020; 295:15183-15195. [PMID: 32788212 PMCID: PMC7650252 DOI: 10.1074/jbc.ra120.014466] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/19/2020] [Indexed: 12/13/2022] Open
Abstract
To enter a cell and establish infection, HIV must first fuse its lipid envelope with the host cell plasma membrane. Whereas the process of HIV membrane fusion can be tracked by fluorescence microscopy, the 3D configuration of proteins and lipids at intermediate steps can only be resolved with cryo-electron tomography (cryoET). However, cryoET of whole cells is technically difficult. To overcome this problem, we have adapted giant plasma membrane vesicles (or blebs) from native cell membranes expressing appropriate receptors as targets for fusion with HIV envelope glycoprotein-expressing pseudovirus particles with and without Serinc host restriction factors. The fusion behavior of these particles was probed by TIRF microscopy on bleb-derived supported membranes. Timed snapshots of fusion of the same particles with blebs were examined by cryo-ET. The combination of these methods allowed us to characterize the structures of various intermediates on the fusion pathway and showed that when Serinc3 or Serinc5 (but not Serinc2) were present, later fusion products were more prevalent, suggesting that Serinc3/5 act at multiple steps to prevent progression to full fusion. In addition, the antifungal amphotericin B reversed Serinc restriction, presumably by intercalation into the fusing membranes. Our results provide a highly detailed view of Serinc restriction of HIV-cell membrane fusion and thus extend current structural and functional information on Serinc as a lipid-binding protein.
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Affiliation(s)
- Amanda E Ward
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Judith M White
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
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47
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Kure JL, Andersen CB, Mortensen KI, Wiseman PW, Arnspang EC. Revealing Plasma Membrane Nano-Domains with Diffusion Analysis Methods. Membranes (Basel) 2020; 10:E314. [PMID: 33138102 DOI: 10.3390/membranes10110314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Nano-domains are sub-light-diffraction-sized heterogeneous areas in the plasma membrane of cells, which are involved in cell signalling and membrane trafficking. Throughout the last thirty years, these nano-domains have been researched extensively and have been the subject of multiple theories and models: the lipid raft theory, the fence model, and the protein oligomerization theory. Strong evidence exists for all of these, and consequently they were combined into a hierarchal model. Measurements of protein and lipid diffusion coefficients and patterns have been instrumental in plasma membrane research and by extension in nano-domain research. This has led to the development of multiple methodologies that can measure diffusion and confinement parameters including single particle tracking, fluorescence correlation spectroscopy, image correlation spectroscopy and fluorescence recovery after photobleaching. Here we review the performance and strengths of these methods in the context of their use in identification and characterization of plasma membrane nano-domains.
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48
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Zhang RL, Pratiwi FW, Chen BC, Chen P, Wu SH, Mou CY. Simultaneous Single-Particle Tracking and Dynamic pH Sensing Reveal Lysosome-Targetable Mesoporous Silica Nanoparticle Pathways. ACS Appl Mater Interfaces 2020; 12:42472-42484. [PMID: 32657564 DOI: 10.1021/acsami.0c07917] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanoparticle (NP)-based targeted drug delivery is intended to transport therapeutically active molecules to specific cells and particular intracellular compartments. However, there is limited knowledge regarding the complete route of NPs in this targeting scenario. In this study, simultaneously performing motion and dynamic pH sensing using single-particle tracking (SPT) leads to an alternative method of gaining insights into the mesoporous silica nanoparticle's (MSN) journey in targeting lysosome. Two different pH-sensitive dyes and a reference dye are incorporated into mesoporous silica nanoparticles (MSNs) via co-condensation to broaden the measurable pH range (pH 4-7.5) of the nanoprobe. The phosphonate, amine, and lysosomal sorting peptides (YQRLGC) are conjugated onto the MSN's surface to study intracellular nano-biointeractions of two oppositely charged and lysosome-targetable MSNs. The brightness and stability of these MSNs allow their movement and dynamic pH evolution during their journey to be simultaneously monitored in real time. Importantly, a multidimensional analysis of MSN's movement and local pH has revealed new model intracellular dynamic states and distributions of MSNs, previously inaccessible when using single parameters alone. A key result is that YQRLGC-conjugated MSNs took an alternative route to target lysosomes apart from the traditional one, which sped up to 4 h and enhanced their targeting efficiency (up to 32%). The findings enrich our understanding of the intracellular journey of MSNs. This study offers complementary information on correlating the surface design with the full pathway of nanoparticles to achieve targeted delivery of therapeutic payload.
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Affiliation(s)
- Rong-Lin Zhang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Feby Wijaya Pratiwi
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Research Center for Applied Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Si-Han Wu
- Graduate Institute of Nanomedicine and Medical Engineering, Taipei Medical University, 250 Wu Xinyi Street, Taipei 11031, Taiwan
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Nanomedicine and Medical Engineering, Taipei Medical University, 250 Wu Xinyi Street, Taipei 11031, Taiwan
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49
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Khalin I, Heimburger D, Melnychuk N, Collot M, Groschup B, Hellal F, Reisch A, Plesnila N, Klymchenko AS. Ultrabright Fluorescent Polymeric Nanoparticles with a Stealth Pluronic Shell for Live Tracking in the Mouse Brain. ACS Nano 2020; 14:9755-9770. [PMID: 32680421 DOI: 10.1021/acsnano.0c01505] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Visualizing single organic nanoparticles (NPs) in vivo remains a challenge, which could greatly improve our understanding of the bottlenecks in the field of nanomedicine. To achieve high single-particle fluorescence brightness, we loaded polymer poly(methyl methacrylate)-sulfonate (PMMA-SO3H) NPs with octadecyl rhodamine B together with a bulky hydrophobic counterion (perfluorinated tetraphenylborate) as a fluorophore insulator to prevent aggregation-caused quenching. To create NPs with stealth properties, we used the amphiphilic block copolymers pluronic F-127 and F-68. Fluorescence correlation spectroscopy and Förster resonance energy transfer (FRET) revealed that pluronics remained at the NP surface after dialysis (at one amphiphile per 5.5 nm2) and prevented NPs from nonspecific interactions with serum proteins and surfactants. In primary cultured neurons, pluronics stabilized the NPs, preventing their prompt aggregation and binding to neurons. By increasing dye loading to 20 wt % and optimizing particle size, we obtained 74 nm NPs showing 150-fold higher single-particle brightness with two-photon excitation than commercial Nile Red-loaded FluoSpheres of 39 nm hydrodynamic diameter. The obtained ultrabright pluronic-coated NPs enabled direct single-particle tracking in vessels of mice brains by two-photon intravital microscopy for at least 1 h, whereas noncoated NPs were rapidly eliminated from the circulation. Following brain injury or neuroinflammation, which can open the blood-brain barrier, extravasation of NPs was successfully monitored. Moreover, we demonstrated tracking of individual NPs from meningeal vessels until their uptake by meningeal macrophages. Thus, single NPs can be tracked in animals in real time in vivo in different brain compartments and their dynamics visualized with subcellular resolution.
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Affiliation(s)
- Igor Khalin
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, D-81377 Munich, Germany
| | - Doriane Heimburger
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Nina Melnychuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Bernhard Groschup
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, D-81377 Munich, Germany
| | - Farida Hellal
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, D-81377 Munich, Germany
- Cluster for Systems Neurology (SyNergy), Munich 81377, Germany
| | - Andreas Reisch
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, D-81377 Munich, Germany
- Cluster for Systems Neurology (SyNergy), Munich 81377, Germany
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
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50
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Chen Z, Shaw A, Wilson H, Woringer M, Darzacq X, Marqusee S, Wang Q, Bustamante C. Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments. Proc Natl Acad Sci U S A 2020; 117:21328-35. [PMID: 32817484 DOI: 10.1073/pnas.2006900117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale. Theoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis, and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. To date, experimental observations of catalysis-enhanced enzyme diffusion have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an anti-Brownian electrokinetic (ABEL) trap and in-solution single-particle tracking, we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ∼20% enhancement seen in parallel FCS experiments using p-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte Carlo simulations, we establish that pNPP-induced dye blinking at the ∼10-ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution single-particle tracking and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.
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