1
|
Wills MF, Alejo CB, Hundt N, Hudson AJ, Eperon IC. FluoroTensor: Identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning. Comput Struct Biotechnol J 2024; 23:918-928. [PMID: 38375530 PMCID: PMC10875188 DOI: 10.1016/j.csbj.2024.02.004] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
The identification of photobleaching steps in single molecule fluorescence imaging is a well-established procedure for analysing the stoichiometries of molecular complexes. Nonetheless, the method is challenging with protein fluorophores because of the high levels of noise, rapid bleaching and highly variable signal intensities, all of which complicate methods based on statistical analyses of intensities to identify bleaching steps. It has recently been shown that deep learning by convolutional neural networks can yield an accurate analysis with a relatively short computational time. We describe here an improved use of such an approach that detects bleaching events even in the first time point of observation, and we have included this within an integrated software package incorporating fluorescence spot detection, colocalisation, tracking, FRET and photobleaching step analyses of single molecules or complexes. This package, known as FluoroTensor, is written in Python with a self-explanatory user interface.
Collapse
Affiliation(s)
- Max F.K. Wills
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Carlos Bueno Alejo
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Chemistry, University of Leicester, UK
| | - Nikolas Hundt
- Department of Cellular Physiology, Ludwig-Maximilians-Universität München, Germany
| | - Andrew J. Hudson
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Chemistry, University of Leicester, UK
| | - Ian C. Eperon
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, UK
| |
Collapse
|
2
|
Belapurkar V, Mahadeva Swamy HS, Singh N, Kedia S, Setty SRG, Jose M, Nair D. Real-time heterogeneity of supramolecular assembly of amyloid precursor protein is modulated by an endocytic risk factor PICALM. Cell Mol Life Sci 2023; 80:295. [PMID: 37726569 DOI: 10.1007/s00018-023-04939-w] [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: 04/05/2023] [Revised: 07/10/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023]
Abstract
Recently, the localization of amyloid precursor protein (APP) into reversible nanoscale supramolecular assembly or "nanodomains" has been highlighted as crucial towards understanding the onset of the molecular pathology of Alzheimer's disease (AD). Surface expression of APP is regulated by proteins interacting with it, controlling its retention and lateral trafficking on the synaptic membrane. Here, we evaluated the involvement of a key risk factor for AD, PICALM, as a critical regulator of nanoscale dynamics of APP. Although it was enriched in the postsynaptic density, PICALM was also localized to the presynaptic active zone and the endocytic zone. PICALM colocalized with APP and formed nanodomains with distinct morphological properties in different subsynaptic regions. Next, we evaluated if this localization to subsynaptic compartments was regulated by the C-terminal sequences of APP, namely, the "Y682ENPTY687" domain. Towards this, we found that deletion of C-terminal regions of APP with partial or complete deletion of Y682ENPTY687, namely, APP-Δ9 and APP-Δ14, affected the lateral diffusion and nanoscale segregation of APP. Lateral diffusion of APP mutant APP-Δ14 sequence mimicked that of a detrimental Swedish mutant of APP, namely, APP-SWE, while APP-Δ9 diffused similar to wild-type APP. Interestingly, elevated expression of PICALM differentially altered the lateral diffusion of the APP C-terminal deletion mutants. These observations confirm that the C-terminal sequence of APP regulates its lateral diffusion and the formation of reversible nanoscale domains. Thus, when combined with autosomal dominant mutations, it generates distinct molecular patterns leading to onset of Alzheimer's disease (AD).
Collapse
Affiliation(s)
- Vivek Belapurkar
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
- Interdisciplinary Institute for Neuroscience CNRS UMR5297, University of Bordeaux, Bordeaux, France
| | - H S Mahadeva Swamy
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
- Tata Institute for Genetics and Society, Bengaluru, India
| | - Nivedita Singh
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Shekhar Kedia
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Subba Rao Gangi Setty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Mini Jose
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
3
|
Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. Nano Converg 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [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] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
Collapse
Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
4
|
Bussmann H, Häberlein H, Boonen G, Drewe J, Butterweck V, Franken S. Effect of St. John's wort extract Ze 117 on the lateral mobility of β(1)-adrenergic receptors in C6 cells. Biomed Pharmacother 2023; 157:114006. [PMID: 36395608 DOI: 10.1016/j.biopha.2022.114006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Depression has been associated with altered signal transduction of serotonergic, dopaminergic and adrenergic neurotransmitter systems in the brain. Signaling relies on receptor-ligand interactions and subsequent regulatory processes, but also on lateral receptor mobility. The aim of this study was to investigate the effect of the St. John's wort extract Ze 117 on the lateral mobility of SNAP-tagged β1-adrenergic receptors (β1AR) in the plasma membrane of C6 cells under both, non-stimulating and isoprenaline-stimulating conditions. Single particle tracking (SPT) was used, whereby the registered trajectories were evaluated by variational Bayesian treatment of a hidden Markov model (vbSPT) and packing coefficient (Pc) analysis with respect to diffusion coefficients, receptor state occupancies and confinement. Three different diffusion states were identified, differing in their diffusion coefficients. Treatment with Ze 117 [25 µg/ml] decreased the mobility of the β1AR, which was manifested by a relative increase in the slow-diffusing state S1 (0.21-0.30) compared to control and by an increase in receptor confinement (79.4-68.1 nm). After isoprenaline stimulation of control cells, the slow-diffusing state was more pronounced, whereas confinement was not affected. In summary, SPT has been shown to be a powerful method to analyze lateral receptor mobility. Furthermore, the present study identified a correlation between Ze 117 treatment and β1AR mobility.
Collapse
|
5
|
Dickson BH, Heit B. Analysis of Efferocytic Receptor Dynamics and Synapse Formation in a Frustrated Efferocytosis Model. Methods Mol Biol 2023; 2692:61-77. [PMID: 37365461 DOI: 10.1007/978-1-0716-3338-0_5] [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] [Indexed: 06/28/2023]
Abstract
Efferocytes express multiple receptors that mediate the recognition and engulfment of apoptotic cells through a process known as efferocytosis. Ligation of these receptors induces the formation of a structured efferocytic synapse that mediates the engulfment of the apoptotic cell by the efferocyte. The lateral diffusion of these receptors allows for clustering-mediated receptor activation and is central for the formation of the efferocytic synapse. This chapter describes a single particle tracking protocol to analyze the diffusion of efferocytic receptors within a frustrated efferocytosis model. This enables high-resolution tracking of efferocytic receptors throughout synapse formation, allowing the user to simultaneously quantify synapse formation and the dynamics of receptor diffusion as the efferocytic synapse evolves.
Collapse
Affiliation(s)
- Brandon H Dickson
- Department of Microbiology and Immunology, and The Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, and The Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, Canada.
- Robarts Research Institute, London, ON, Canada.
| |
Collapse
|
6
|
Mortensen JS, Bohr SSR, Harloff-Helleberg S, Hatzakis NS, Saaby L, Nielsen HM. Physical and barrier changes in gastrointestinal mucus induced by the permeation enhancer sodium 8-[(2-hydroxybenzoyl)amino]octanoate (SNAC). J Control Release 2022; 352:163-178. [PMID: 36314534 DOI: 10.1016/j.jconrel.2022.09.034] [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: 05/10/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Drug delivery systems (DDS) for oral delivery of peptide drugs contain excipients that facilitate and enhance absorption. However, little knowledge exists on how DDS excipients such as permeation enhancers interact with the gastrointestinal mucus barrier. This study aimed to investigate interactions of the permeation enhancer sodium 8-[(2-hydroxybenzoyl)amino]octanoate (SNAC) with ex vivo porcine intestinal mucus (PIM), ex vivo porcine gastric mucus (PGM), as well as with in vitro biosimilar mucus (BM) by profiling their physical and barrier properties upon exposure to SNAC. Bulk mucus permeability studies using the peptides cyclosporine A and vancomycin, ovalbumin as a model protein, as well as fluorescein-isothiocyanate dextrans (FDs) of different molecular weights and different surface charges were conducted in parallel to mucus retention force studies using a texture analyzer, rheological studies, cryo-scanning electron microscopy (cryo-SEM), and single particle tracking of fluorescence-labelled nanoparticles to investigate the effects of the SNAC-mucus interaction. The exposure of SNAC to PIM increased the mucus retention force, storage modulus, viscosity, increased nanoparticle confinement within PIM as well as decreased the permeation of cyclosporine A and ovalbumin through PIM. Surprisingly, the viscosity of PGM and the permeation of cyclosporine A and ovalbumin through PGM was unaffected by the presence of SNAC, thus the effect of SNAC depended on the regional site that mucus was collected from. In the absence of SNAC, the permeation of different molecular weight and differently charged FDs through PIM was comparable to that through BM. However, while bulk permeation of neither of the FDs through PIM was affected by SNAC, the presence of SNAC decreased the permeation of FD4 and increased the permeation of FD150 kDa through BM. Additionally, and in contrast to observations in PIM, nanoparticle confinement within BM remained unaffected by the presence of SNAC. In conclusion, the present study showed that SNAC altered the physical and barrier properties of PIM, but not of PGM. The effects of SNAC in PIM were not observed in the BM in vitro model. Altogether, the study highlights the need for further understanding how permeation enhancers influence the mucus barrier and illustrates that the selected mucus model for such studies should be chosen with care.
Collapse
Affiliation(s)
- J S Mortensen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - S S-R Bohr
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; Department of Chemistry, Nano-Science Center, Faculty of Science, University of Copenhagen, Bülowsvej 17, DK-1870 Frederiksberg, Denmark
| | - S Harloff-Helleberg
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - N S Hatzakis
- Department of Chemistry, Nano-Science Center, Faculty of Science, University of Copenhagen, Bülowsvej 17, DK-1870 Frederiksberg, Denmark; Novo Nordisk Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - L Saaby
- CNS Drug Delivery and Barrier Modelling, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; Bioneer A/S, Kogle Alle 2, DK-2970 Hørsholm, Denmark
| | - H M Nielsen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
| |
Collapse
|
7
|
Park C, Jung S, Park H. Single vesicle tracking for studying synaptic vesicle dynamics in small central synapses. Curr Opin Neurobiol 2022; 76:102596. [PMID: 35803103 DOI: 10.1016/j.conb.2022.102596] [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: 02/03/2022] [Revised: 04/20/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022]
Abstract
Sustained neurotransmission is driven by a continuous supply of synaptic vesicles to the release sites and modulated by synaptic vesicle dynamics. However, synaptic vesicle dynamics in synapses remain elusive because of technical limitations. Recent advances in fluorescence imaging techniques have enabled the tracking of single synaptic vesicles in small central synapses in living neurons. Single vesicle tracking has uncovered a wealth of new information about synaptic vesicle dynamics both within and outside presynaptic terminals, showing that single vesicle tracking is an effective tool for studying synaptic vesicle dynamics. Particularly, single vesicle tracking with high spatiotemporal resolution has revealed the dependence of synaptic vesicle dynamics on the location, stages of recycling, and neuronal activity. This review summarizes the recent findings from single synaptic vesicle tracking in small central synapses and their implications in synaptic transmission and pathogenic mechanisms of neurodegenerative diseases.
Collapse
Affiliation(s)
- Chungwon Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 11 Biopolis Way, 138667, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong; Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong.
| |
Collapse
|
8
|
Cheng HJ, Hsu CH, Hung CL, Lin CY. A review for Cell and Particle Tracking on Microscopy Images using Algorithms and Deep Learning Technologies. Biomed J 2021; 45:465-471. [PMID: 34628059 PMCID: PMC9421944 DOI: 10.1016/j.bj.2021.10.001] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/06/2023] Open
Abstract
Time-lapse microscopy images generated by biological experiments have been widely used for observing target activities, such as the motion trajectories and survival states. Based on these observations, biologists can conclude experimental results or present new hypotheses for several biological applications, i.e. virus research or drug design. Many methods or tools have been proposed in the past to observe cell and particle activities, which are defined as single cell tracking and single particle tracking problems, by using algorithms and deep learning technologies. In this article, a review for these works is presented in order to summarize the past methods and research topics at first, then points out the problems raised by these works, and finally proposes future research directions. The contributions of this article will help researchers to understand past development trends and further propose innovative technologies.
Collapse
Affiliation(s)
- Hui-Jun Cheng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China; Department of Computer Science and Information Engineering, Providence University, Taichung 43301, Taiwan
| | - Ching-Hsien Hsu
- Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan; Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology, School of Mathematics and Big Data, Foshan University, Foshan 528000, China; Department of Medical Research, China Medical University Hospital, China Medical University, Taiwan
| | - Che-Lun Hung
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; Department of Computer Science and Communication Engineering, Providence University, Taichung 43301, Taiwan
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan; Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, Taiwan.
| |
Collapse
|
9
|
Bally M, Block S, Höök F, Larson G, Parveen N, Rydell GE. Physicochemical tools for studying virus interactions with targeted cell membranes in a molecular and spatiotemporally resolved context. Anal Bioanal Chem 2021; 413:7157-7178. [PMID: 34490501 PMCID: PMC8421089 DOI: 10.1007/s00216-021-03510-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022]
Abstract
The objective of this critical review is to provide an overview of how emerging bioanalytical techniques are expanding our understanding of the complex physicochemical nature of virus interactions with host cell surfaces. Herein, selected model viruses representing both non-enveloped (simian virus 40 and human norovirus) and enveloped (influenza A virus, human herpes simplex virus, and human immunodeficiency virus type 1) viruses are highlighted. The technologies covered utilize a wide range of cell membrane mimics, from supported lipid bilayers (SLBs) containing a single purified host membrane component to SLBs derived from the plasma membrane of a target cell, which can be compared with live-cell experiments to better understand the role of individual interaction pairs in virus attachment and entry. These platforms are used to quantify binding strengths, residence times, diffusion characteristics, and binding kinetics down to the single virus particle and single receptor, and even to provide assessments of multivalent interactions. The technologies covered herein are surface plasmon resonance (SPR), quartz crystal microbalance with dissipation (QCM-D), dynamic force spectroscopy (DFS), total internal reflection fluorescence (TIRF) microscopy combined with equilibrium fluctuation analysis (EFA) and single particle tracking (SPT), and finally confocal microscopy using multi-labeling techniques to visualize entry of individual virus particles in live cells. Considering the growing scientific and societal needs for untangling, and interfering with, the complex mechanisms of virus binding and entry, we hope that this review will stimulate the community to implement these emerging tools and strategies in conjunction with more traditional methods. The gained knowledge will not only contribute to a better understanding of the virus biology, but may also facilitate the design of effective inhibitors to block virus entry.
Collapse
Affiliation(s)
- Marta Bally
- Department of Clinical Microbiology & Wallenberg Centre for Molecular Medicine, Umeå University, 901 85, Umeå, Sweden
| | - Stephan Block
- Department of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, 413 45, Gothenburg, Sweden.
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Gustaf E Rydell
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, 413 46, Gothenburg, Sweden
| |
Collapse
|
10
|
Rotter DAO, Heger C, Oviedo-Bocanegra LM, Graumann PL. Transcription-dependent confined diffusion of enzymes within subcellular spaces of the bacterial cytoplasm. BMC Biol 2021; 19:183. [PMID: 34474681 PMCID: PMC8414670 DOI: 10.1186/s12915-021-01083-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/13/2020] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Knowledge on the localization and mobility of enzymes inside bacterial cells is scarce, but important for understanding spatial regulation of metabolism. The four central enzymes (Rib enzymes) of the riboflavin (RF) biosynthesis pathway in the Gram positive model bacterium Bacillus subtilis have been studied extensively in vitro, especially the heavy RF synthase, a large protein complex with a capsid structure formed by RibH and an encapsulated RibE homotrimer, which mediates substrate-channeling. However, little is known about the behavior and mobility of these enzymes in vivo. RESULTS We have investigated the localization and diffusion of the Rib enzymes in the cytoplasm of B. subtilis. By characterizing the diffusion of Rib enzymes in live cells using single particle tracking (SPT) we provide evidence for confined diffusion at the cell poles and otherwise Brownian motion. A majority of RibH particles showed clear nucleoid occlusion and a high degree of confined motion, which is largely abolished after treatment with Rifampicin, revealing that confinement is dependent on active transcription. Contrarily, RibE is mostly diffusive within the cell, showing only 14% encapsulation by RibH nanocompartments. By localizing different diffusive populations within single cells, we find that fast diffusion occurs mostly across the nucleoids located in the cell centers, while the slower, confined subdiffusion occurs at the crowded cell poles. CONCLUSIONS Our results provide evidence for locally different motion of active enzymes within the bacterial cytoplasm, setting up metabolic compartmentalization mostly at the poles of cells.
Collapse
Affiliation(s)
- Daniel A O Rotter
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Christoph Heger
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Luis M Oviedo-Bocanegra
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany.
| |
Collapse
|
11
|
Colin C, Suraniti E, Abell E, Sémont A, Sojic N, Diolez P, Arbault S. Single-Particle Tracking Method in Fluorescence Microscopy to Monitor Bioenergetic Responses of Individual Mitochondria. Methods Mol Biol 2021; 2276:153-63. [PMID: 34060039 DOI: 10.1007/978-1-0716-1266-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The spectroscopic methods commonly used to study mitochondria bioenergetics do not show the diversity of responses within a population of mitochondria (isolated or in a cell), and/or cannot measure individual dynamics. New methodological developments are necessary in order to improve quantitative and kinetic resolutions and eventually gain further insights on individual mitochondrial responses, such as studying activities of the mitochondrial permeability transition pore (mPTP ). The work reported herein is devoted to study responses of single mitochondria within a large population after isolation from cardiomyocytes. Mitochondria were preloaded with a commonly used membrane potential sensitive dye (TMRM), they are then deposited on a plasma-treated glass coverslip and subsequently energized or inhibited by additions of usual bioenergetics effectors. Responses were analyzed by fluorescence microscopy over few thousands of mitochondria simultaneously with a single organelle resolution. We report an automatic method to analyze each image of time-lapse stacks based on the TrackMate-ImageJ plug-in and specially made Python scripts. Images are processed to eliminate defects of illumination inhomogeneity, improving by at least two orders of magnitude the signal/noise ratio. This method enables us to follow the track of each mitochondrion within the observed field and monitor its fluorescence changes, with a time resolution of 400 ms, uninterrupted over the course of the experiment. Such methodological improvement is a prerequisite to further study the role of mPTP in single mitochondria during calcium transient loading.
Collapse
|
12
|
Feng X, Leong WH, Xia K, Liu CF, Liu GQ, Rendler T, Wrachtrup J, Liu RB, Li Q. Association of Nanodiamond Rotation Dynamics with Cell Activities by Translation-Rotation Tracking. Nano Lett 2021; 21:3393-3400. [PMID: 33847115 DOI: 10.1021/acs.nanolett.0c04864] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Correlated translation-orientation tracking of single particles can provide important information for understanding the dynamics of live systems and their interaction with the probes. However, full six-dimensional (6D) motion tracking has yet to be achieved. Here, we developed synchronized 3D translation and 3D rotation tracking of single diamond particles based on nitrogen-vacancy center sensing. We first performed 6D tracking of diamond particles attached to a giant plasma membrane vesicle to demonstrate the method. Quantitative analysis of diamond particles' motion allowed elimination of the geometric effect and revealed the net rotation on the vesicle. 6D tracking was then applied to measure live cell dynamics. Motion characteristics of nanodiamonds on cell membranes under various controlled physiological conditions suggest that the nanodiamonds' rotation is associated with cell metabolic activities. Our technique extends the toolbox of single particle tracking and provides a unique solution to problems where correlated analysis of translation and rotation is critical.
Collapse
Affiliation(s)
- Xi Feng
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Weng-Hang Leong
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Kangwei Xia
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Chu-Feng Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Gang-Qin Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Torsten Rendler
- 3rd Institute of Physics and Center for Applied Quantum Technologies, University of Stuttgart, 70569 Stuttgart, Germany
| | - Joerg Wrachtrup
- 3rd Institute of Physics and Center for Applied Quantum Technologies, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ren-Bao Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The Hong Kong Institute of Quantum Information Science and Technology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Centre for Quantum Coherence, The Chinese University of Hong Kong, Hong Kong, China
| | - Quan Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The Hong Kong Institute of Quantum Information Science and Technology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Centre for Quantum Coherence, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
13
|
Paviolo C, Cognet L. Near-infrared nanoscopy with carbon-based nanoparticles for the exploration of the brain extracellular space. Neurobiol Dis 2021; 153:105328. [PMID: 33713842 DOI: 10.1016/j.nbd.2021.105328] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding the physiology and pathology of the brain requires detailed knowledge of its complex structures as well as dynamic internal processes at very different scales from the macro down to the molecular dimensions. A major yet poorly described brain compartment is the brain extracellular space (ECS). Signalling molecules rapidly diffuse through the brain ECS which is complex and dynamic structure at numerous lengths and time scales. In recent years, characterization of the ECS using nanomaterials has made remarkable progress, including local analysis of nanoscopic dimensions and diffusivity as well as local chemical sensing. In particular, carbon nanomaterials combined with advanced optical technologies, biochemical and biophysical analysis, offer novel promises for understanding the ECS morphology as well as neuron connectivity and neurochemistry. In this review, we present the state-of-the-art in this quest, which mainly focuses on a type of carbon nanomaterial, single walled carbon nanotubes, as fluorescent nanoprobes to unveil the ECS features in the nanometre domain.
Collapse
Affiliation(s)
- Chiara Paviolo
- LP2N, Institut d'Optique Graduate School, CNRS, Université de Bordeaux, 33400 Talence, France
| | - Laurent Cognet
- LP2N, Institut d'Optique Graduate School, CNRS, Université de Bordeaux, 33400 Talence, France.
| |
Collapse
|
14
|
Small C, Martínez-Mármol R, Amor R, Meunier FA, Joensuu M. Combining Single Molecule Super-Resolution Imaging Techniques to Unravel the Nanoscale Organization of the Presynapse. Methods Mol Biol 2021; 2233:265-86. [PMID: 33222141 DOI: 10.1007/978-1-0716-1044-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The fusion of synaptic vesicles with the plasma membrane underpins neurotransmission. A number of presynaptic proteins play a critical role in overcoming the energy barrier inherent to the fusion of the negatively charged vesicular and plasma membranes. Emerging concepts suggest that this process is hierarchical and dependent on rapid and transient reorganization of proteins in and out of small nanoclusters located in the active zones of nerve terminals. Examining the nanoscale organization of presynaptic molecules requires super-resolution microscopy to overcome the limits of conventional light microscopy. In this chapter, we describe three super-resolution techniques that allow for the examination of the nanoscale organization of proteins within live hippocampal nerve terminals. We used (1) single-particle tracking photoactivated localization microscopy (sptPALM) to resolve the mobility and clustering of syntaxin1A (STX1A), (2) universal Point Accumulation Imaging in Nanoscale Topography (uPAINT) to study the mobility of a pool of vesicular-associated membrane protein 2 (VAMP2) transiting on the plasma membrane, and (3) subdiffractional Tracking of Internalized Molecules (sdTIM) to track VAMP2-positive recycling synaptic vesicles in conjunction with Cholera Toxin subunit B (CTB), which has recently been shown to be trafficked retrogradely from the presynapse to the cell body via signaling endosomes.
Collapse
|
15
|
Shechtman Y. Recent advances in point spread function engineering and related computational microscopy approaches: from one viewpoint. Biophys Rev 2020; 12:10.1007/s12551-020-00773-7. [PMID: 33210213 PMCID: PMC7755951 DOI: 10.1007/s12551-020-00773-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 01/13/2023] Open
Abstract
This personal hybrid review piece, written in light of my recipience of the UIPAB 2020 young investigator award, contains a mixture of my scientific biography and work so far. This paper is not intended to be a comprehensive review, but only to highlight my contributions to computation-related aspects of super-resolution microscopy, as well as their origins and future directions.
Collapse
Affiliation(s)
- Yoav Shechtman
- Department of Biomedical Engineering and Lorry Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
| |
Collapse
|
16
|
Feng J, He Y. Long-distance Transport in Bacterial Swarms Revealed by Single Nanoparticle Tracking. Bio Protoc 2020; 10:e3812. [PMID: 33659465 DOI: 10.21769/bioprotoc.3812] [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: 05/05/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 11/02/2022] Open
Abstract
During swarming, high density flagella-driven bacteria migrate collectively in a swirling pattern on wet agar surfaces, immersed in a thin viscous fluid layer called "swarm fluid". Though the fluid environment has essential role in the emergence of swarming behavior, the microscopic mechanisms of it in mediating the cooperation of bacteria populations are not fully understood. Here, instead of micro-sized tracers used in previous research, we use gold nanorods as single particle tracers to probe the dynamics of the swarm fluid. This protocol includes five major parts: (1) the culture of swarming bacterial colony; (2) the preparations of gold nanorod tracers and the micro-spraying technique which are used to put the nanotracers into the upper fluid of bacterial swarms; (3) imaging and tracking; (4) other necessary control experiments; (5) data analysis and fitting of physical models. With this method, the nano-sized tracers could move long distances above motile cells without direct collisions with the bacteria bodies. In this way, the microscopic dynamics of the swarm fluid could be tracked with high spatiotemporal resolution. Moreover, the comprehensive analysis of multi-particle trajectories provides systematic visualization of the fluid dynamics. The method is promising to probe the fluid dynamics of other natural or artificial active matter systems.
Collapse
Affiliation(s)
- Jingjing Feng
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yan He
- Department of Chemistry, Tsinghua University, Beijing, China
| |
Collapse
|
17
|
Hernaiz-Llorens M, Roselló-Busquets C, Durisic N, Filip A, Ulloa F, Martínez-Mármol R, Soriano E. Growth cone repulsion to Netrin-1 depends on lipid raft microdomains enriched in UNC5 receptors. Cell Mol Life Sci 2021; 78:2797-820. [PMID: 33095273 DOI: 10.1007/s00018-020-03663-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 05/08/2020] [Revised: 09/08/2020] [Accepted: 09/30/2020] [Indexed: 01/15/2023]
Abstract
During brain development, Uncoordinated locomotion 5 (UNC5) receptors control axonal extension through their sensing of the guidance molecule Netrin-1. The correct positioning of receptors into cholesterol-enriched membrane raft microdomains is crucial for the efficient transduction of the recognized signals. However, whether such microdomains are required for the appropriate axonal guidance mediated by UNC5 receptors remains unknown. Here, we combine the use of confocal microscopy, live-cell FRAP analysis and single-particle tracking PALM to characterize the distribution of UNC5 receptors into raft microdomains, revealing differences in their membrane mobility properties. Using pharmacological and genetic approaches in primary neuronal cultures and brain cerebellar explants we further demonstrate that disrupting raft microdomains inhibits the chemorepulsive response of growth cones and axons against Netrin-1. Together, our findings indicate that the distribution of all UNC5 receptors into cholesterol-enriched raft microdomains is heterogeneous and that the specific localization has functional consequences for the axonal chemorepulsion against Netrin-1.
Collapse
|
18
|
Ilhan B, Schoppink JJ, Mugele F, Duits MHG. Spherical probes for simultaneous measurement of rotational and translational diffusion in 3 dimensions. J Colloid Interface Sci 2020; 576:322-329. [PMID: 32447022 DOI: 10.1016/j.jcis.2020.05.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/17/2020] [Revised: 04/17/2020] [Accepted: 05/08/2020] [Indexed: 01/10/2023]
Abstract
Real time visualization and tracking of colloidal particles with 3D resolution is essential for probing the local structure and dynamics in complex fluids. Although tracking translational motion of spherical particles is well-known, accessing rotational dynamics of such particles remains a great challenge. Here, we report a novel approach of using fluorescently labeled raspberry-like colloids with an optical anisotropy to concurrently track translational and rotational dynamics in 3 dimensions. The raspberry-like particles are coated by a silica layer of adjustable thickness, which allows tuning the surface roughness. The synthesis and applicability of the proposed method is demonstrated by two types of probes: rough and smoothened. The accuracies of measuring Mean Squared (Angular) Displacements are also demonstrated by using these 2 probes dispersed in 2 different solvents. The presented 3D trackable colloids offer a high potential for wide range of applications and studies, such as probing the dynamics of crystallization, phase transitions, biological interactions and the effect of surface roughness on diffusion.
Collapse
Affiliation(s)
- Beybin Ilhan
- Physics of Complex Fluids Group and MESA+ Institute, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, the Netherlands.
| | - Jelle J Schoppink
- Physics of Complex Fluids Group and MESA+ Institute, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, the Netherlands
| | - Frieder Mugele
- Physics of Complex Fluids Group and MESA+ Institute, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, the Netherlands
| | - Michael H G Duits
- Physics of Complex Fluids Group and MESA+ Institute, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, the Netherlands
| |
Collapse
|
19
|
Li Y, Yi J, Liu W, Liu Y, Liu J. Gaining insight into cellular cardiac physiology using single particle tracking. J Mol Cell Cardiol 2020; 148:63-77. [PMID: 32871158 DOI: 10.1016/j.yjmcc.2020.08.011] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022]
Abstract
Single particle tracking (SPT) is a robust technique to monitor single-molecule behaviors in living cells directly. By this approach, we can uncover the potential biological significance of particle dynamics by statistically characterizing individual molecular behaviors. SPT provides valuable information at the single-molecule level, that could be obscured by simple averaging that is inherent to conventional ensemble measurements. Here, we give a brief introduction to SPT including the commonly used optical implementations, fluorescence labeling strategies, and data analysis methods. We then focus on how SPT has been harnessed to decipher myocardial function. In this context, SPT has provided novel insight into the lateral diffusion of signal receptors and ion channels, the dynamic organization of cardiac nanodomains, subunit composition and stoichiometry of cardiac ion channels, myosin movement along actin filaments, the kinetic features of transcription factors involved in cardiac remodeling, and the intercellular communication by nanotubes. Finally, we speculate on the prospects and challenges of applying SPT to future questions regarding cellular cardiac physiology using SPT.
Collapse
Affiliation(s)
- Ying Li
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Jing Yi
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Wenjuan Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Yun Liu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Guangdong Province, China.
| | - Jie Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| |
Collapse
|
20
|
Bussmann H, Schulte-Michels J, Bingel M, Meurer F, Aatz S, Häberlein F, Franken S, Häberlein H. A comparative study on the influence of an ivy preparation and an ivy/thyme combination on the β 2-adrenergic signal transduction. Heliyon 2020; 6:e03960. [PMID: 32514478 DOI: 10.1016/j.heliyon.2020.e03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 02/05/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 11/21/2022] Open
Abstract
The β2-adrenergic receptor (β2AR) is relevant for surfactant formation in alveolar type 2 cells and reduction of intracellular calcium concentration in bronchial muscle cells and thus for secretolytic and bronchospasmolytic effects. Herbal medicinal products that affect the β2AR system are used to treat common cold and bronchitis accompanied with mucus covered and narrowed airways. The present work compares the influence of an ivy preparation and an ivy/thyme combination on the β2-adrenergic signal transduction. For receptor binding studies and characterization of the lateral mobility of β2AR we have used single molecule detection by fluorescence correlation spectroscopy and single particle tracking. For the determination of both the second messenger cAMP and the internalization of β2AR we have generated luciferase based reporter cell lines, which produce a cAMP-dependent luciferase in the cytosol and express β2AR with extracellular luciferase moiety in the plasma membrane. While both preparations increased the β2AR binding, a significant increase of the cAMP level was observed only for the ivy preparation, which can be explained by the inhibited internalization of HiBiT-tagged β2AR under stimulating conditions. In contrast, isoprenaline-mediated internalization of HiBiT-tagged β2AR of ivy/thyme combination pre-treated cells was not inhibited. Cells comparatively pre-treated with a thyme preparation did not show inhibition of ß2AR internalization either. Furthermore, SNAP-tagged β2AR of ivy preparation pre-treated cells, which were not internalized after isoprenaline stimulation, showed a redistribution from fast-to-slowly diffusing β2AR. A corresponding redistribution of these receptors was not observed after pre-treatment with both the ivy/thyme combination and the thyme preparation. Comparable to the ivy/thyme combination, no decrease in the intratrack transitioning probability ratio (p23/p32) for fast and slow diffusing β2AR was found for the thyme preparation, which, however, significantly decreased for control cells and for pre-treatment with the ivy preparation under stimulating conditions. It can therefore be concluded that the thyme fluid extract fraction in the ivy/thyme combination may have in part a negative effect on the β2-adrenergic signal transduction.
Collapse
|
21
|
Kovtun O, Thal LB, Josephs T, Rosenthal SJ. Quantitative Analysis of Single Quantum Dot Trajectories. Methods Mol Biol 2020; 2135:109-23. [PMID: 32246331 DOI: 10.1007/978-1-0716-0463-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single quantum dot tracking (SQDT) is a powerful technique for interrogating biomolecular dynamics in living cells and tissue. SQDT has particularly excelled in driving discovery at the single-molecule level in the fields of neuronal communication, plasma membrane organization, viral infection, and immune system response. Here, we briefly characterize various elements of the SQDT analytical framework and provide the reader with a detailed set of executable commands to implement commonly used algorithms for SQDT data processing.
Collapse
|
22
|
Mieskes F, Wehnekamp F, Plucińska G, Thong R, Misgeld T, Lamb DC. Trajectory data of antero- and retrograde movement of mitochondria in living zebrafish larvae. Data Brief 2020; 29:105280. [PMID: 32190718 PMCID: PMC7068625 DOI: 10.1016/j.dib.2020.105280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 01/21/2023] Open
Abstract
Recently, a large number of single particle tracking (SPT) approaches have been developed. Generally, SPT techniques can be split into two groups: ex post facto approaches where trajectory extraction is carried out after data acquisition and feedback based approaches that perform particle tracking in real time [1]. One feedback approach is 3D Orbital Tracking, where the laser excitation beam is rotated in a circle about the object, generating a so called orbit [2,3]. By calculating the particle position from the detected intensity after every orbit in relation to its center, this method allows the microscope to follow a single object in real time. The high spatiotemporal resolution of this method and the potential to optically manipulate the followed object during the measurement promises to yield new deep insights into biological systems [4-7]. By upgrading this approach in a way that the specimen is recentered by a xy-stage on the center of the microscope, particle tracking with this long-range tracking feature is no longer limited to the covered field-of-view. This allows for the observation of mitochondrial trafficking in living zebrafish embryos over long distances. Here, we provide the raw data for antero- and retrograde movement of mitochondria labelled with photo-activatable green fluorescent protein (mitoPAGFP). It relates to the scientific article "Nanoresolution real-time 3D orbital tracking for studying mitochondrial trafficking in vertebrate axons in vivo" [8]. By applying a correlation analysis on the trajectories, it is possible to distinguish between active transport and pausing events with less biasing compared to the mean squared displacement approach.
Collapse
Affiliation(s)
- Frank Mieskes
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM), Nanosystems Initiative Muünchen (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Fabian Wehnekamp
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM), Nanosystems Initiative Muünchen (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Gabriela Plucińska
- Munich Cluster for Systems Neurology (SNergy), Center for Integrated Protein Science (CIPSM), German Center for Neurodegenerative Diseases (DZNE), Institute of Neuronal Cell Biology, Technische Universitätt München, Munich, Germany
| | - Rachel Thong
- Munich Cluster for Systems Neurology (SNergy), Center for Integrated Protein Science (CIPSM), German Center for Neurodegenerative Diseases (DZNE), Institute of Neuronal Cell Biology, Technische Universitätt München, Munich, Germany
| | - Thomas Misgeld
- Munich Cluster for Systems Neurology (SNergy), Center for Integrated Protein Science (CIPSM), German Center for Neurodegenerative Diseases (DZNE), Institute of Neuronal Cell Biology, Technische Universitätt München, Munich, Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM), Nanosystems Initiative Muünchen (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| |
Collapse
|
23
|
Jin C, Che B, Guo Z, Li C, Liu Y, Wu W, Wang S, Li D, Cui Z, Liang M. Single virus tracking of Ebola virus entry through lipid rafts in living host cells. Biosaf Health 2020; 2:25-31. [PMID: 32835208 PMCID: PMC7347359 DOI: 10.1016/j.bsheal.2019.12.009] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 12/20/2022] Open
Abstract
Ebola virus (EBOV) is one of the most pathogenic viruses in humans which can cause a lethal hemorrhagic fever. Understanding the cellular entry mechanisms of EBOV can promote the development of new therapeutic strategies to control virus replication and spread. It has been known that EBOV virions bind to factors expressed at the host cell surface. Subsequently, the virions are internalized by a macropinocytosis-like process, followed by being trafficked through early and late endosomes. Recent researches indicate that the entry of EBOV into cells requires integrated and functional lipid rafts. Whilst lipid rafts have been hypothesized to play a role in virus entry, there is a current lack of supporting data. One major technical hurdle is the lack of effective approaches for observing viral entry. To provide evidence on the involvement of lipid rafts in the entry process of EBOV, we generated the fluorescently labeled Ebola virus like particles (VLPs), and utilized single-particle tracking (SPT) to visualize the entry of fluorescent Ebola VLPs in live cells and the interaction of Ebola VLPs with lipid rafts. In this study, we demonstrate the compartmentalization of Ebola VLPs in lipid rafts during entry process, and inform the essential function of lipid rafts for the entry of Ebola virus. As such, our study provides evidence to show that the raft integrity is critical for Ebola virus pathogenesis and that lipid rafts can serve as potential targets for the development of novel therapeutic strategies.
Collapse
Affiliation(s)
- Cong Jin
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
- National Center for AIDS/STD Control and Prevention, China CDC, Beijing 102206, China
| | - Bin Che
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Zhengyuan Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuan Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Yang Liu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Wei Wu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Shiwen Wang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Dexin Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mifang Liang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention (IVDC), Chinese Center for Disease control and Prevention (China CDC), Beijing 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
24
|
Abstract
The polymerization-depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.
Collapse
|
25
|
Abstract
The ability to image single molecules in living cells has been impaired by the absence of bright, photostable fluorophores. Quantum dots (QDs) offer an attractive solution to this problem due to their exceptional photostability and brightness. Here, we describe in detail a protocol to chemically deliver functionalized QDs into the cytosol of living cells, based on cell-penetrating poly(disulfide)s (CPDs). This protocol is highly efficient and delivers hundreds of QDs per cell after incubation of cells with functionalized QDs at nanomolar concentrations. We also detail a pipeline for automated detection and tracking of diffusive QDs in living cells, which may provide a useful means to study the biophysical properties of the cytosol and their dynamics. Last, we describe a protocol for conjugating streptavidin fusion proteins to QDs, in order to permit the codelivery of QDs with functional proteins of interest into cells. The protocol has been successfully applied to a broad range of different cell types, thus offering a flexible and generalizable means to image single molecules in living cells.
Collapse
|
26
|
Abstract
Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.
Collapse
Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
27
|
Gardini L, Arbore C, Capitanio M, Pavone FS. A protocol for single molecule imaging and tracking of processive myosin motors. MethodsX 2019; 6:1854-1862. [PMID: 31508322 PMCID: PMC6726715 DOI: 10.1016/j.mex.2019.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/13/2019] [Indexed: 10/31/2022] Open
Abstract
Myosin is a large family of actin-based molecular motors, which includes efficient intracellular transporters that move cargoes and material essential for cell's life. Here, we describe protocols for labelling single myosin motors with quantum dots, tracking them in an in vitro reconstituted single-molecule motility assay, acquiring image stacks and analyzing them. We describe the required steps to obtain trajectories of single myosin motors from which fundamental biophysical parameters such as the motor velocity, run length and step size can be derived. We also describe protocols for an ensemble actin gliding assay, which is valuable to test the motor viability and its ensemble properties. The protocols allow probing the effect of changes in nucleotides, ions, and buffer composition on the motor properties and are easily generalizable to track the movements of different motor proteins.
Collapse
Affiliation(s)
- Lucia Gardini
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy
| | - Claudia Arbore
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
| |
Collapse
|
28
|
Kodippili GC, Putt KS, Low PS. Evidence for three populations of the glucose transporter in the human erythrocyte membrane. Blood Cells Mol Dis 2019; 77:61-6. [PMID: 30974390 DOI: 10.1016/j.bcmd.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/23/2022]
Abstract
Glucose transporter 1 (GLUT1) is one of 13 members of the human equilibrative glucose transport protein family and the only glucose transporter thought to be expressed in human erythrocyte membranes. Although GLUT1 has been shown to be anchored to adducin at the junctional spectrin-actin complex of the membrane through interactions with multiple proteins, whether other populations of GLUT1 also exist in the human erythrocyte membrane has not been examined. Because GLUT1 plays such a critical role in erythrocyte biology and since it comprises 10% of the total membrane protein, we undertook to evaluate the subpopulations of erythrocyte GLUT1 using single particle tracking. By monitoring the diffusion of individual AlexaFluor 488-labeled GLUT1 molecules on the surfaces of intact erythrocytes, we are able to identify three distinct subpopulations of GLUT1. While the mobility of the major subpopulation is similar to that of the anion transporter, band 3, both a more mobile and more anchored subpopulation also exist. From these studies, we conclude that ~65% of GLUT1 resides in similar or perhaps the same protein complex as band 3, while the remaining 1/3rd are either freely diffusing or interacting with other cytoskeletally anchored membrane protein complexes.
Collapse
|
29
|
Abstract
The nuclear envelope (NE) is an essential cellular structure that contributes to nuclear stability, organization, and function. Mutations in NE-associated proteins result in a myriad of pathologies with widely diverse clinical manifestations, ages of onsets, and affected tissues. Notably, several hundred disease-causing mutations have been mapped to the LMNA gene, which encodes the intermediate filament proteins lamin A and C, two of the major architectural components of the nuclear envelope. However, how NE dysfunction leads to the highly variable pathologies observed in patient cells and tissues remains poorly understood. One model suggests alterations in the dynamic properties of the nuclear lamina and its associated proteins contribute to disease phenotype. Here, we describe the application of single molecule tracking (SMT) methodology to characterize the behavior of nuclear envelope transmembrane proteins and nuclear lamins in their native cellular environment at the single molecule level. As proof-of-concept, we demonstrate by SMT that Halo-tagged lamin B1, Samp1, lamin A, and lamin AΔ50 have distinct binding and kinetic properties, and we identify several disease-relevant mutants which exhibit altered binding dynamics. SMT is also able to separately probe the dynamics of the peripheral and the nucleoplasmic populations of lamin A mutants. We suggest that SMT is a robust and sensitive method to investigate the relationship between pathogenic mutations or cellular processes and protein dynamics at the NE.
Collapse
Affiliation(s)
- Leonid A Serebryannyy
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA
| | - David A Ball
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Tatiana S Karpova
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
30
|
Abstract
Export of mRNA transcripts from the cell nucleus is a complex and multistep process, regulated by various proteins and control mechanisms. Recent studies have demonstrated the rapid passage of mRNA-protein complexes (mRNPs) through the nuclear pore complex (NPC) as well as the ability to detect mRNPs stalled at the NPC during inhibition of the mRNA export process. In this chapter, we describe ways to block mRNA export and present an image analysis method to identify mRNPs stuck at the NPC during such blocks. Using the MS2 mRNA-tagging system to track single mRNPs in living cells we are able to examine their intracellular distribution and dynamics both in the nucleoplasm and at the nuclear periphery. We use this method to identify and count the number of static mRNPs anchored to the nuclear envelope under different conditions of mRNA export inhibition.
Collapse
Affiliation(s)
- Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel.
| |
Collapse
|
31
|
Zhu Q, Smith EA. Diaphanous-1 affects the nanoscale clustering and lateral diffusion of receptor for advanced glycation endproducts (RAGE). Biochim Biophys Acta Biomembr 2018; 1861:43-49. [PMID: 30401627 DOI: 10.1016/j.bbamem.2018.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022]
Abstract
The interactions between the cytoplasmic protein diaphanous-1 (Diaph1) and the receptor for advanced glycation endproducts (RAGE) drive the negative consequences of RAGE signaling in several disease processes. Reported in this work is how Diaph1 affects the nanoscale clustering and diffusion of RAGE measured using super-resolution stochastic optical reconstruction microscopy (STORM) and single particle tracking (SPT). Altering the Diaph1 binding site has a different impact on RAGE diffusion compared to when Diaph1 expression is reduced in HEK293 cells. In cells with reduced Diaph1 expression (RAGE-Diaph1-/-), the average RAGE diffusion coefficient is increased by 35%. RAGE diffusion is known to be influenced by the dynamics of the actin cytoskeleton. Actin labeling shows that a reduced Diaph1 expression leads to cells with reduced filopodia density and length. In contrast, when two RAGE amino acids that interact with Diaph1 are mutated (RAGERQ/AA), the average RAGE diffusion coefficient is decreased by 16%. Since RAGE diffusion is slowed when the interaction between Diaph1 and RAGE is disrupted, the interaction of the two proteins results in faster RAGE diffusion. In both RAGERQ/AA and RAGE-Diaph1-/- cells the number and size of RAGE clusters are decreased compared to cells expressing RAGE and native concentrations of Diaph1. This work shows that Diaph1 has a role in affecting RAGE clusters and diffusion.
Collapse
Affiliation(s)
- Qiaochu Zhu
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States
| | - Emily A Smith
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States.
| |
Collapse
|
32
|
Landvogt L, Ruland JA, Montellese C, Siebrasse JP, Kutay U, Kubitscheck U. Observing and tracking single small ribosomal subunits in vivo. Methods 2018; 153:63-70. [PMID: 30194975 DOI: 10.1016/j.ymeth.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 06/05/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomes are formed of a small and a large subunit (SSU/LSU), both consisting of rRNA and a plethora of accessory proteins. While biochemical and genetic studies identified most of the involved proteins and deciphered the ribosomal synthesis steps, our knowledge of the molecular dynamics of the different ribosomal subunits and also of the kinetics of their intracellular trafficking is still limited. Adopting a labelling strategy initially used to study mRNA export we were able to fluorescently stain the SSU in vivo. We chose DIM2/PNO1 (Defective In DNA Methylation 2/Partner of NOb1) as labelling target and created a stable cell line carrying an inducible SNAP-DIM2 fusion protein. After bulk labelling with a green fluorescent dye combined with very sparse labelling with a red fluorescent dye the nucleoli and single SSU could be visualized simultaneously in the green and red channel, respectively. We used single molecule microscopy to track single SSU in the nucleolus and nucleoplasm. Resulting trajectory data were analyzed by jump-distance analysis and the variational Bayes single-particle tracking approach. Both methods allowed identifying the number of diffusive states and the corresponding diffusion coefficients. For both nucleoli and nucleoplasm we could identify mobile (D = 2.3-2.8 µm2/s), retarded (D = 0.18-0.31 µm2/s) and immobilized (D = 0.04-0.05 µm2/s) SSU fractions and, as expected, the size of the fractions differed in the two compartments. While the fast mobility fraction matches perfectly the expected nuclear mobility of the SSU (D = 2.45 µm2/s), we were surprised to find a substantial fraction (33%) of immobile SSU in the nucleoplasm, something not observed for inert control molecules.
Collapse
Affiliation(s)
- Lisa Landvogt
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Jan Andreas Ruland
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Christian Montellese
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Jan Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany.
| |
Collapse
|
33
|
Chang CC, Edwald E, Veatch S, Steel DG, Gafni A. Interactions of amyloid-β peptides on lipid bilayer studied by single molecule imaging and tracking. Biochim Biophys Acta Biomembr 2018; 1860:1616-1624. [PMID: 29580771 DOI: 10.1016/j.bbamem.2018.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 12/17/2022]
Abstract
The amyloid-β peptides (Aβ40 and Aβ42) feature prominently in the synaptic dysfunction and neuronal loss associated with Alzheimer's disease (AD). This has been proposed to be due either to interactions between Aβ and cell surface receptors affecting cell signaling, or to the formation of calcium-permeable channels in the membrane that disrupt calcium homeostasis. In both mechanisms the cell membrane is the primary cellular structure with which Aβ interacts. Aβ concentrations in human bodily fluids are very low (pM-nM) rendering studies of the size, composition, cellular binding sites and mechanism of action of the oligomers formed in vivo very challenging. Most studies, therefore, have utilized Aβ oligomers prepared at micromolar peptide concentrations, where Aβ forms oligomeric species which possess easily observable cell toxicity. Such toxicity has not been observed when nM concentrations of peptide are used in the experiment highlighting the importance of employing physiologically relevant peptide concentrations for the results to be of biological significance. In this paper single-molecule microscopy was used to monitor Aβ oligomer formation and diffusion on a supported lipid bilayer at nanomolar peptide concentrations. Aβ monomers, the dominant species in solution, tightly associate with the membrane and are highly mobile whereas trimers and higher-order oligomers are largely immobile. Aβ dimers exist in a mixture of mobile and immobile states. Oligomer growth on the membrane is more rapid for Aβ40 than for the more amyloidogenic Aβ42 but is largely inhibited for a 1:1 Aβ40:Aβ42 mixture. The mechanism underlying these Aβ40-Aβ42 interactions may feature in Alzheimer's pathology.
Collapse
Affiliation(s)
- Chun-Chieh Chang
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elin Edwald
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duncan G Steel
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ari Gafni
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
34
|
Bailey DM, Kovtun O, Rosenthal SJ. Antibody-Conjugated Single Quantum Dot Tracking of Membrane Neurotransmitter Transporters in Primary Neuronal Cultures. Methods Mol Biol 2018; 1570:165-177. [PMID: 28238136 DOI: 10.1007/978-1-4939-6840-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Indexed: 02/25/2023]
Abstract
Single particle tracking (SPT) experiments have provided the scientific community with invaluable single-molecule information about the dynamic regulation of individual receptors, transporters, kinases, lipids, and molecular motors. SPT is an alternative to ensemble averaging approaches, where heterogeneous modes of motion might be lost. Quantum dots (QDs) are excellent probes for SPT experiments due to their photostability, high brightness, and size-dependent, narrow emission spectra. In a typical QD-based SPT experiment, QDs are bound to the target of interest and imaged for seconds to minutes via fluorescence video microscopy. Single QD spots in individual frames are then linked to form trajectories that are analyzed to determine their mean square displacement, diffusion coefficient, confinement index, and instantaneous velocity. This chapter describes a generalizable protocol for the single particle tracking of membrane neurotransmitter transporters on cell membranes with either unmodified extracellular antibody probes and secondary antibody-conjugated quantum dots or biotinylated extracellular antibody probes and streptavidin-conjugated quantum dots in primary neuronal cultures. The neuronal cell culture, the biotinylation protocol and the quantum dot labeling procedures, as well as basic data analysis are discussed.
Collapse
Affiliation(s)
- Danielle M Bailey
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sandra J Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute for Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| |
Collapse
|
35
|
Sum CH, Shortall SM, Nicastro JA, Slavcev R. Specific Systems for Imaging. Exp Suppl 2018; 110:69-97. [PMID: 30536227 DOI: 10.1007/978-3-319-78259-1_3] [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: 06/09/2023]
Abstract
Microscopy allows for the characterization of small objects invisible to the naked eye, a technique that, since its conception, has played a key role in the development across nearly every field of science and technology. Given the nanometer size of the materials explored in the field of nanotechnology, the contributions of modern microscopes that can visualize these materials are indispensable, and the ever-improving technology is paramount to the future success of the field. This chapter will focus on four fundamental areas of microscopy used in the field of nanotechnology including fluorescence microscopy (Sect. 3.1), particle tracking and photoactivated localization microscopy (Sect. 3.2), quantum dots and fluorescence resonance energy transfer (Sect. 3.3), and cellular MRI and PET labeling (Sect. 3.4). The functionality, as well as the current and recommended usage of each given imaging system, will be discussed.
Collapse
|
36
|
Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X. Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Methods Mol Biol 2018; 1814:541-559. [PMID: 29956254 PMCID: PMC6225527 DOI: 10.1007/978-1-4939-8591-3_32] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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] [Indexed: 12/03/2022]
Abstract
In the past decade, live-cell single molecule imaging studies have provided unique insights on how DNA-binding molecules such as transcription factors explore the nuclear environment to search for and bind to their targets. However, due to technological limitations, single molecule experiments in living specimens have largely been limited to monolayer cell cultures. Lattice light-sheet microscopy overcomes these limitations and has now enabled single molecule imaging within thicker specimens such as embryos. Here we describe a general procedure to perform single molecule imaging in living Drosophila melanogaster embryos using lattice light-sheet microscopy. This protocol allows direct observation of both transcription factor diffusion and binding dynamics. Finally, we illustrate how this Drosophila protocol can be extended to other thick samples using single molecule imaging in live mouse embryos as an example.
Collapse
Affiliation(s)
- Mustafa Mir
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Michael Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Astou Tangara
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Hernan Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
37
|
De Rossi MC, Wetzler DE, Benseñor L, De Rossi ME, Sued M, Rodríguez D, Gelfand V, Bruno L, Levi V. Mechanical coupling of microtubule-dependent motor teams during peroxisome transport in Drosophila S2 cells. Biochim Biophys Acta Gen Subj 2017; 1861:3178-3189. [PMID: 28935608 DOI: 10.1016/j.bbagen.2017.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 04/28/2017] [Revised: 09/04/2017] [Accepted: 09/15/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Intracellular transport requires molecular motors that step along cytoskeletal filaments actively dragging cargoes through the crowded cytoplasm. Here, we explore the interplay of the opposed polarity motors kinesin-1 and cytoplasmic dynein during peroxisome transport along microtubules in Drosophila S2 cells. METHODS We used single particle tracking with nanometer accuracy and millisecond time resolution to extract quantitative information on the bidirectional motion of organelles. The transport performance was studied in cells expressing a slow chimeric plus-end directed motor or the kinesin heavy chain. We also analyzed the influence of peroxisomes membrane fluidity in methyl-β-ciclodextrin treated cells. The experimental data was also confronted with numerical simulations of two well-established tug of war scenarios. RESULTS AND CONCLUSIONS The velocity distributions of retrograde and anterograde peroxisomes showed a multimodal pattern suggesting that multiple motor teams drive transport in either direction. The chimeric motors interfered with the performance of anterograde transport and also reduced the speed of the slowest retrograde team. In addition, increasing the fluidity of peroxisomes membrane decreased the speed of the slowest anterograde and retrograde teams. GENERAL SIGNIFICANCE Our results support the existence of a crosstalk between opposed-polarity motor teams. Moreover, the slowest teams seem to mechanically communicate with each other through the membrane to trigger transport.
Collapse
Affiliation(s)
- María Cecilia De Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Dinámica Intracelular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Diana E Wetzler
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Dinámica Intracelular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Lorena Benseñor
- Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - María Emilia De Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales y Ciclo Básico Común, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Astronomía y Física del Espacio (IAFE), Buenos Aires, Argentina
| | - Mariela Sued
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Buenos Aires, Argentina
| | - Daniela Rodríguez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Buenos Aires, Argentina
| | - Vladimir Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Luciana Bruno
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires, Argentina.
| | - Valeria Levi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Dinámica Intracelular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
| |
Collapse
|
38
|
Longfils M, Röding M, Altskär A, Schuster E, Lorén N, Särkkä A, Rudemo M. Single particle raster image analysis of diffusion for particle mixtures. J Microsc 2017; 269:269-281. [PMID: 28862754 DOI: 10.1111/jmi.12625] [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: 03/31/2017] [Accepted: 08/09/2017] [Indexed: 11/26/2022]
Abstract
Recently we complemented the raster image correlation spectroscopy (RICS) method of analysing raster images via estimation of the image correlation function with the method single particle raster image analysis (SPRIA). In SPRIA, individual particles are identified and the diffusion coefficient of each particle is estimated by a maximum likelihood method. In this paper, we extend the SPRIA method to analyse mixtures of particles with a finite set of diffusion coefficients in a homogeneous medium. In examples with simulated and experimental data with two and three different diffusion coefficients, we show that SPRIA gives accurate estimates of the diffusion coefficients and their proportions. A simple technique for finding the number of different diffusion coefficients is also suggested. Further, we study the use of RICS for mixtures with two different diffusion coefficents and investigate, by plotting level curves of the correlation function, how large the quotient between diffusion coefficients needs to be in order to allow discrimination between models with one and two diffusion coefficients. We also describe a minor correction (compared to published papers) of the RICS autocorrelation function.
Collapse
Affiliation(s)
- M Longfils
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - M Röding
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - A Altskär
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - E Schuster
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - N Lorén
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - A Särkkä
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - M Rudemo
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
39
|
Bannai H. Molecular membrane dynamics: Insights into synaptic function and neuropathological disease. Neurosci Res 2017; 129:47-56. [PMID: 28826905 DOI: 10.1016/j.neures.2017.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 04/12/2017] [Revised: 07/14/2017] [Accepted: 07/26/2017] [Indexed: 11/19/2022]
Abstract
The fluid mosaic model states that molecules in the plasma membrane can freely undergo lateral diffusion; however, in neurons and glia, specific membrane molecules are concentrated in cellular microdomains to overcome the randomizing effects of free diffusion. This specialized distribution of membrane molecules is crucial for various cell functions; one example is the accumulation of neurotransmitter receptors at the postsynaptic neuronal membrane, which enables efficient synaptic transmission. Quantum dot-single particle tracking (QD-SPT) is a super-resolution imaging technique that uses semiconductor nanocrystal quantum dots as fluorescent probes, and is a powerful tool for analyzing protein and lipid behavior in the plasma membrane. In this article, we review studies implementing QD-SPT in neuroscience research and important data gleaned using this technology. Recent QD-SPT experiments have provided critical insights into the mechanism and physiological relevance of membrane self-organization in neurons and astrocytes in the brain. The mobility of some membrane molecules may become abnormal in cellular models of epilepsy and Alzheimer's disease. Based on these findings, we propose that the behavior of membrane molecules reflects the condition of neurons in pathological disease states.
Collapse
Affiliation(s)
- Hiroko Bannai
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute (BSI), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| |
Collapse
|
40
|
Cardarelli F. Time-resolved biophysical approaches to nucleocytoplasmic transport. Comput Struct Biotechnol J 2017; 15:299-306. [PMID: 28435614 PMCID: PMC5388937 DOI: 10.1016/j.csbj.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/25/2017] [Indexed: 12/26/2022] Open
Abstract
Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores). The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed.
Collapse
|
41
|
Carozza S, Culkin J, van Noort J. Accuracy of the detection of binding events using 3D single particle tracking. BMC Biophys 2017; 10:3. [PMID: 28344779 PMCID: PMC5364544 DOI: 10.1186/s13628-017-0035-8] [Citation(s) in RCA: 2] [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: 10/21/2016] [Accepted: 03/03/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion. This issue is of particular importance in an experiment aiming to quantify dynamic processes. RESULTS Here, we present simulations and 3D tracking experiments with Gold Nanorods freely diffusing in glycerol solution to establish the best analysis parameters to extract the diffusion coefficient. We applied this knowledge to the detection of a temporary change in diffusion, as it can occur due to the transient binding of a particle to an immobile structure within the cell, and tested its dependence on the magnitude of the change in diffusion and duration of this event. CONCLUSIONS The simulations show that the spatial accuracy of particle tracking generally does not limit the detection of short binding events. Careful analysis of the magnitude of the change in diffusion and the number of frames per binding event is required for accurate quantification of such events.
Collapse
Affiliation(s)
- Sara Carozza
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Postbus 9504, Leiden, 2300RA Netherlands
| | - Jamie Culkin
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Postbus 9504, Leiden, 2300RA Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Postbus 9504, Leiden, 2300RA Netherlands
| |
Collapse
|
42
|
Lund FW, Wüstner D. Quantitative Co-Localization and Pattern Analysis of Endo-Lysosomal Cargo in Subcellular Image Cytometry and Validation on Synthetic Image Sets. Methods Mol Biol 2017; 1594:93-128. [PMID: 28456978 DOI: 10.1007/978-1-4939-6934-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Late endosomes and lysosomes (LE/LYSs) play a central role in trafficking of endocytic cargo, secretion of exosomes, and hydrolysis of ingested proteins and lipids. Failure in such processes can lead to lysosomal storage disorders in which a particular metabolite accumulates within LE/LYSs. Analysis of endocytic trafficking relies heavily on quantitative fluorescence microscopy, but evaluation of the huge image data sets is challenging and demands computer-assisted statistical tools. Here, we describe how to use SpatTrack ( www.sdu.dk/bmb/spattrack ), an imaging toolbox, which we developed for quantification of the distribution and dynamics of endo-lysosomal cargo from fluorescence images of living cells. First, we explain how to analyze experimental images of endocytic processes in Niemann Pick C2 disease fibroblasts using SpatTrack. We demonstrate how to quantify the location of the sterol-binding protein NPC2 in LE/LYSs relative to cholesterol -rich lysosomal storage organelles (LSOs) stained with filipin. Second, we show how to simulate realistic vesicle patterns in the cell geometry using Markov Chain Monte Carlo and suitable inter-vesicle and cell-vesicle interaction potentials. Finally, we use such synthetic vesicle patterns as "ground truth" for validation of two-channel analysis tools in SpatTrack, revealing their high reliability. An improved version of SpatTrack for microscopy-based quantification of cargo transport through the endo-lysosomal system accompanies this protocol.
Collapse
|
43
|
Plewes MR, Burns PD, Graham PE, Hyslop RM, Barisas BG. Effect of fish oil on lateral mobility of prostaglandin F 2α (FP) receptors and spatial distribution of lipid microdomains in bovine luteal cell plasma membrane in vitro. Domest Anim Endocrinol 2017; 58:39-52. [PMID: 27643975 PMCID: PMC5135567 DOI: 10.1016/j.domaniend.2016.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 11/16/2022]
Abstract
Lipid microdomains are ordered regions on the plasma membrane of cells, rich in cholesterol and sphingolipids, ranging in size from 10 to 200 nm in diameter. These lipid-ordered domains may serve as platforms to facilitate colocalization of intracellular signaling proteins during agonist-induced signal transduction. It is hypothesized that fish oil will disrupt the lipid microdomains, increasing spatial distribution of these lipid-ordered domains and lateral mobility of the prostaglandin (PG) F2α (FP) receptors in bovine luteal cells. The objectives of this study were to examine the effects of fish oil on (1) the spatial distribution of lipid microdomains, (2) lateral mobility of FP receptors, and (3) lateral mobility of FP receptors in the presence of PGF2α on the plasma membrane of bovine luteal cells in vitro. Bovine ovaries were obtained from a local abattoir and corpora lutea were digested using collagenase. In experiment 1, lipid microdomains were labeled using cholera toxin subunit B Alexa Fluor 555. Domains were detected as distinct patches on the plasma membrane of mixed luteal cells. Fish oil treatment decreased fluorescent intensity in a dose-dependent manner (P < 0.01). In experiment 2, single particle tracking was used to examine the effects of fish oil treatment on lateral mobility of FP receptors. Fish oil treatment increased microdiffusion and macrodiffusion coefficients of FP receptors as compared to control cells (P < 0.05). In addition, compartment diameters of domains were larger, and residence times were reduced for receptors in fish oil-treated cells (P < 0.05). In experiment 3, single particle tracking was used to determine the effects of PGF2α on lateral mobility of FP receptors and influence of fish oil treatment. Lateral mobility of receptors was decreased within 5 min following the addition of ligand for control cells (P < 0.05). However, lateral mobility of receptors was unaffected by addition of ligand for fish oil-treated cells (P > 0.10). The data presented provide strong evidence that fish oil causes a disruption in lipid microdomains and affects lateral mobility of FP receptors in the absence and presence of PGF2α.
Collapse
Affiliation(s)
- M R Plewes
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | - P D Burns
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639.
| | - P E Graham
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | - R M Hyslop
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, Colorado, 80639
| | - B G Barisas
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| |
Collapse
|
44
|
Giger K, Habib I, Ritchie K, Low PS. Diffusion of glycophorin A in human erythrocytes. Biochim Biophys Acta 2016; 1858:2839-2845. [PMID: 27580023 DOI: 10.1016/j.bbamem.2016.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 07/06/2016] [Revised: 08/15/2016] [Accepted: 08/25/2016] [Indexed: 11/19/2022]
Abstract
Several lines of evidence suggest that glycophorin A (GPA) interacts with band 3 in human erythrocyte membranes including: i) the existence of an epitope shared between band 3 and GPA in the Wright b blood group antigen, ii) the fact that antibodies to GPA inhibit the diffusion of band 3, iii) the observation that expression of GPA facilitates trafficking of band 3 from the endoplasmic reticulum to the plasma membrane, and iv) the observation that GPA is diminished in band 3 null erythrocytes. Surprisingly, there is also evidence that GPA does not interact with band 3, including data showing that: i) band 3 diffusion increases upon erythrocyte deoxygenation whereas GPA diffusion does not, ii) band 3 diffusion is greatly restricted in erythrocytes containing the Southeast Asian Ovalocytosis mutation whereas GPA diffusion is not, and iii) most anti-GPA or anti-band 3 antibodies do not co-immunoprecipitate both proteins. To try to resolve these apparently conflicting observations, we have selectively labeled band 3 and GPA with fluorescent quantum dots in intact erythrocytes and followed their diffusion by single particle tracking. We report here that band 3 and GPA display somewhat similar macroscopic and microscopic diffusion coefficients in unmodified cells, however perturbations of band 3 diffusion do not cause perturbations of GPA diffusion. Taken together the collective data to date suggest that while weak interactions between GPA and band 3 undoubtedly exist, GPA and band 3 must have separate interactions in the membrane that control their lateral mobility.
Collapse
Affiliation(s)
- Katie Giger
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Ibrahim Habib
- INSERM, UMR_S1134, Laboratory of Excellence GR-Ex, Université Paris-Diderot, Institut National de la Transfusion Sanguine, 75015 Paris, France
| | - Ken Ritchie
- Department of Physics, Purdue University, West Lafayette, IN 47907, United States
| | - Philip S Low
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States.
| |
Collapse
|
45
|
Wüstner D, Modzel M, Lund FW, Lomholt MA. Imaging approaches for analysis of cholesterol distribution and dynamics in the plasma membrane. Chem Phys Lipids 2016; 199:106-35. [PMID: 27016337 DOI: 10.1016/j.chemphyslip.2016.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022]
Abstract
Cholesterol is an important lipid component of the plasma membrane (PM) of mammalian cells, where it is involved in control of many physiological processes, such as endocytosis, cell migration, cell signalling and surface ruffling. In an attempt to explain these functions of cholesterol, several models have been put forward about cholesterol's lateral and transbilayer organization in the PM. In this article, we review imaging techniques developed over the last two decades for assessing the distribution and dynamics of cholesterol in the PM of mammalian cells. Particular focus is on fluorescence techniques to study the lateral and inter-leaflet distribution of suitable cholesterol analogues in the PM of living cells. We describe also several methods for determining lateral cholesterol dynamics in the PM including fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single particle tracking (SPT) and spot variation FCS coupled to stimulated emission depletion (STED) microscopy. For proper interpretation of such measurements, we provide some background in probe photophysics and diffusion phenomena occurring in cell membranes. In particular, we show the equivalence of the reaction-diffusion approach, as used in FRAP and FCS, and continuous time random walk (CTRW) models, as often invoked in SPT studies. We also discuss mass spectrometry (MS) based imaging of cholesterol in the PM of fixed cells and compare this method with fluorescence imaging of sterols. We conclude that evidence from many experimental techniques converges towards a model of a homogeneous distribution of cholesterol with largely free and unhindered diffusion in both leaflets of the PM.
Collapse
|
46
|
Lenn T, Leake MC. Single-molecule studies of the dynamics and interactions of bacterial OXPHOS complexes. Biochim Biophys Acta 2016; 1857:224-31. [PMID: 26498189 DOI: 10.1016/j.bbabio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022]
Abstract
Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in time and space until recently. Several pioneering single-molecule studies have emerged over the last decade in particular, which have illuminated our knowledge of OXPHOS, most especially on model bacterial systems. Here, we discuss these recent findings of bacterial OXPHOS, many of which generate time-resolved information of the OXPHOS machinery with the native physiological context intact. These new investigations are transforming our knowledge not only of the molecular arrangement of OXPHOS components in live bacteria, but also of the way components dynamically interact with each other in a functional state. These new discoveries have important implications towards putative supercomplex formation in bacterial OXPHOS in particular. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
Collapse
|
47
|
Wang YY, Nunn KL, Harit D, McKinley SA, Lai SK. Minimizing biases associated with tracking analysis of submicron particles in heterogeneous biological fluids. J Control Release 2015; 220:37-43. [PMID: 26478013 DOI: 10.1016/j.jconrel.2015.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 06/16/2015] [Revised: 08/31/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Tracking the dynamic motion of individual nanoparticles or viruses offers quantitative insights into their real-time behavior and fate in different biological environments. Indeed, particle tracking is a powerful tool that has facilitated the development of drug carriers with enhanced penetration of mucus, brain tissues and other extracellular matrices. Nevertheless, heterogeneity is a hallmark of nanoparticle diffusion in such complex environments: identical particles can exhibit strongly hindered or unobstructed diffusion within microns of each other. The common practice in 2D particle tracking, namely analyzing all trackable particle traces with equal weighting, naturally biases towards rapidly diffusing sub-populations at shorter time scales. This in turn results in misrepresentation of particle behavior and a systematic underestimate of the time necessary for a population of nanoparticles to diffuse specific distances. We show here via both computational simulation and experimental data that this bias can be rigorously corrected by weighing the contribution by each particle trace on a 'frame-by-frame' basis. We believe this methodology presents an important step towards objective and accurate assessment of the heterogeneous transport behavior of submicron drug carriers and pathogens in biological environments.
Collapse
Affiliation(s)
- Ying-Ying Wang
- Department of Biophysics, Johns Hopkins University, 3400 North Charles St, Baltimore, MD 21218, USA
| | - Kenetta L Nunn
- UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina - Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Dimple Harit
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina - Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Scott A McKinley
- Mathematics Department, University of Florida, 1400 Stadium Road, Gainesville, FL 32611, USA
| | - Samuel K Lai
- UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina - Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA; Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina - Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, 125 Mason Farm Road, Chapel Hill, NC 27599, USA.
| |
Collapse
|
48
|
Angeli E, Volpe A, Fanzio P, Repetto L, Firpo G, Guida P, Savio RL, Wanunu M, Valbusa U. Simultaneous Electro-Optical Tracking for Nanoparticle Recognition and Counting. Nano Lett 2015; 15:5696-5701. [PMID: 26225640 PMCID: PMC5146980 DOI: 10.1021/acs.nanolett.5b01243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 05/21/2023]
Abstract
We present the first detailed experimental observation and analysis of nanoparticle electrophoresis through a nanochannel obtained with synchronous high-bandwidth electrical and camera recordings. Optically determined particle diffusion coefficients agree with values extracted from fitting electrical transport measurements to distributions from 1D Fokker-Planck diffusion-drift theory. This combined tracking strategy enables optical recognition and electrical characterization of nanoparticles in solution, which can have a broad range of applications in biology and materials science.
Collapse
Affiliation(s)
- Elena Angeli
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
- Corresponding Authors. ,
| | - Andrea Volpe
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Paola Fanzio
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Luca Repetto
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Patrizia Guida
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Roberto Lo Savio
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Meni Wanunu
- Department of Physics and Chemistry/Chemical Biology, Northeastern University, Boston 02115, Massachusetts, United States
- Corresponding Authors. ,
| | - Ugo Valbusa
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| |
Collapse
|
49
|
Deville S, Penjweini R, Smisdom N, Notelaers K, Nelissen I, Hooyberghs J, Ameloot M. Intracellular dynamics and fate of polystyrene nanoparticles in A549 Lung epithelial cells monitored by image (cross-) correlation spectroscopy and single particle tracking. Biochim Biophys Acta 2015; 1853:2411-9. [PMID: 26164626 DOI: 10.1016/j.bbamcr.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/19/2015] [Accepted: 07/07/2015] [Indexed: 11/20/2022]
Abstract
Novel insights in nanoparticle (NP) uptake routes of cells, their intracellular trafficking and subcellular targeting can be obtained through the investigation of their temporal and spatial behavior. In this work, we present the application of image (cross-) correlation spectroscopy (IC(C)S) and single particle tracking (SPT) to monitor the intracellular dynamics of polystyrene (PS) NPs in the human lung carcinoma A549 cell line. The ensemble kinetic behavior of NPs inside the cell was characterized by temporal and spatiotemporal image correlation spectroscopy (TICS and STICS). Moreover, a more direct interpretation of the diffusion and flow detected in the NP motion was obtained by SPT by monitoring individual NPs. Both techniques demonstrate that the PS NP transport in A549 cells is mainly dependent on microtubule-assisted transport. By applying spatiotemporal image cross-correlation spectroscopy (STICCS), the correlated motions of NPs with the early endosomes, late endosomes and lysosomes are identified. PS NPs were equally distributed among the endolysosomal compartment during the time interval of the experiments. The cotransport of the NPs with the lysosomes is significantly larger compared to the other cell organelles. In the present study we show that the complementarity of ICS-based techniques and SPT enables a consistent elaborate model of the complex behavior of NPs inside biological systems.
Collapse
|
50
|
DeVore MS, Stich DG, Keller AM, Ghosh Y, Goodwin PM, Phipps ME, Stewart MH, Cleyrat C, Wilson BS, Lidke DS, Hollingsworth JA, Werner JH. Three dimensional time-gated tracking of non-blinking quantum dots in live cells. Proc SPIE Int Soc Opt Eng 2015; 9338. [PMID: 25932286 DOI: 10.1117/12.2082943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Single particle tracking has provided a wealth of information about biophysical processes such as motor protein transport and diffusion in cell membranes. However, motion out of the plane of the microscope or blinking of the fluorescent probe used as a label generally limits observation times to several seconds. Here, we overcome these limitations by using novel non-blinking quantum dots as probes and employing a custom 3D tracking microscope to actively follow motion in three dimensions (3D) in live cells. Signal-to-noise is improved in the cellular milieu through the use of pulsed excitation and time-gated detection.
Collapse
Affiliation(s)
- Matthew S DeVore
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Dominik G Stich
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Aaron M Keller
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Yagnaseni Ghosh
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Mary E Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Michael H Stewart
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington D.C. 20375, USA
| | - Cédric Cleyrat
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Bridget S Wilson
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jennifer A Hollingsworth
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - James H Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| |
Collapse
|