1
|
Johnson A, Welsher KD. Single-nanoparticle electrophoretic mobility determination and trapping using active-feedback 3D tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602591. [PMID: 39131346 PMCID: PMC11312477 DOI: 10.1101/2024.07.08.602591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EM on a per-particle basis. Single-nanoparticle EM is determined by using active feedback to "lock on" to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EM in various ionic strengths (0.25-5 mM) and found decreased EM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.
Collapse
Affiliation(s)
- Alexis Johnson
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Kevin D Welsher
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| |
Collapse
|
2
|
Müller JA, Schäffler N, Kellerer T, Schwake G, Ligon TS, Rädler JO. Kinetics of RNA-LNP delivery and protein expression. Eur J Pharm Biopharm 2024; 197:114222. [PMID: 38387850 DOI: 10.1016/j.ejpb.2024.114222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lipid nanoparticles (LNPs) employing ionizable lipids are the most advanced technology for delivery of RNA, most notably mRNA, to cells. LNPs represent well-defined core-shell particles with efficient nucleic acid encapsulation, low immunogenicity and enhanced efficacy. While much is known about the structure and activity of LNPs, less attention is given to the timing of LNP uptake, cytosolic transfer and protein expression. However, LNP kinetics is a key factor determining delivery efficiency. Hence quantitative insight into the multi-cascaded pathway of LNPs is of interest to elucidate the mechanism of delivery. Here, we review experiments as well as theoretical modeling of the timing of LNP uptake, mRNA-release and protein expression. We describe LNP delivery as a sequence of stochastic transfer processes and review a mathematical model of subsequent protein translation from mRNA. We compile probabilities and numbers obtained from time resolved microscopy. Specifically, live-cell imaging on single cell arrays (LISCA) allows for high-throughput acquisition of thousands of individual GFP reporter expression time courses. The traces yield the distribution of mRNA life-times, expression rates and expression onset. Correlation analysis reveals an inverse dependence of gene expression efficiency and transfection onset-times. Finally, we discuss why timing of mRNA release is critical in the context of codelivery of multiple nucleic acid species as in the case of mRNA co-expression or CRISPR/Cas gene editing.
Collapse
Affiliation(s)
- Judith A Müller
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | - Nathalie Schäffler
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | - Thomas Kellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, Munich, Germany
| | - Gerlinde Schwake
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | | | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany.
| |
Collapse
|
3
|
Zalejski J, Sun J, Sharma A. Unravelling the Mystery inside Cells by Using Single-Molecule Fluorescence Imaging. J Imaging 2023; 9:192. [PMID: 37754956 PMCID: PMC10532472 DOI: 10.3390/jimaging9090192] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Live-cell imaging is a powerful technique to study the dynamics and mechanics of various biological molecules like proteins, organelles, DNA, and RNA. With the rapid evolution of optical microscopy, our understanding of how these molecules are implicated in the cells' most critical physiological roles deepens. In this review, we focus on how spatiotemporal nanoscale live-cell imaging at the single molecule level allows for profound contributions towards new discoveries in life science. This review will start by summarizing how single-molecule tracking has been used to analyze membrane dynamics, receptor-ligand interactions, protein-protein interactions, inner- and extra-cellular transport, gene expression/transcription, and whole organelle tracking. We then move on to how current authors are trying to improve single-molecule tracking and overcome current limitations by offering new ways of labeling proteins of interest, multi-channel/color detection, improvements in time-lapse imaging, and new methods and programs to analyze the colocalization and movement of targets. We later discuss how single-molecule tracking can be a beneficial tool used for medical diagnosis. Finally, we wrap up with the limitations and future perspectives of single-molecule tracking and total internal reflection microscopy.
Collapse
Affiliation(s)
| | | | - Ashutosh Sharma
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA; (J.Z.); (J.S.)
| |
Collapse
|
4
|
Tan X, Hou S, Niver A, Zhang C, Johnson A, Welsher KD. Active-Feedback 3D Single-Molecule Tracking Using a Fast-Responding Galvo Scanning Mirror. J Phys Chem A 2023; 127:6320-6328. [PMID: 37477600 PMCID: PMC11025461 DOI: 10.1021/acs.jpca.3c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Real-time three-dimensional single-particle tracking (RT-3D-SPT) allows continuous detection of individual freely diffusing objects with high spatiotemporal precision by applying closed-loop active feedback in an optical microscope. However, the current tracking speed in RT-3D-SPT is primarily limited by the response time of the control actuators, impeding long-term observation of fast diffusive objects such as single molecules. Here, we present an RT-3D-SPT system with improved tracking performance by replacing the XY piezoelectric stage with a galvo scanning mirror with an approximately 5 times faster response rate (∼5 kHz). Based on the previously developed 3D single-molecule active real-time tracking (3D-SMART), this new implementation with a fast-responding galvo mirror eliminates the mechanical movement of the sample and allows a more rapid response to particle motion. The improved tracking performance of the galvo mirror-based implementation is verified through simulation and proof-of-principle experiments. Fluorescent nanoparticles and ∼1 kB double-stranded DNA molecules were tracked via both the original piezoelectric stage and new galvo mirror implementations. With the new galvo-based implementation, notable increases in tracking duration, localization precision, and the degree to which the objects are locked to the center of the detection volume were observed. These results suggest that faster control response elements can expand RT-3D-SPT to a broader range of chemical and biological systems.
Collapse
Affiliation(s)
- Xiaochen Tan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Shangguo Hou
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Anastasia Niver
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Chen Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Alexis Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Kevin D Welsher
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
5
|
Vickers NA, Sharifi F, Andersson SB. Information optimization of laser scanning microscopes for real-time feedback-driven single particle tracking. OPTICS EXPRESS 2023; 31:21434-21451. [PMID: 37381243 PMCID: PMC10316749 DOI: 10.1364/oe.485357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/02/2023] [Accepted: 05/28/2023] [Indexed: 06/30/2023]
Abstract
Real-time feedback-driven single particle tracking (RT-FD-SPT) is a class of microscopy techniques that uses measurements of finite excitation/detection volume in a feedback control loop to actuate that volume and track with high spatio-temporal resolution a single particle moving in three dimensions. A variety of methods have been developed, each defined by a set of user-defined choices. Selection of those values is typically done through ad hoc, off-line tuning for the best perceived performance. Here we present a mathematical framework, based on optimization of the Fisher information, to select those parameters such that the best information is acquired for estimating parameters of interest, such as the location of the particle, specifics of the excitation beam such as its dimensions or peak intensity, or the background noise. For concreteness, we focus on tracking of a fluorescently-labeled particle and apply this framework to determine the optimal parameters for three existing fluorescence-based RT-FD-SPT techniques with respect to particle localization.
Collapse
Affiliation(s)
- Nicholas A. Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - Fatemeh Sharifi
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Sean B. Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA 02215, USA
| |
Collapse
|
6
|
Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
Collapse
Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
7
|
Zhang X, Li H, Ma Y, Zhong D, Hou S. Study liquid-liquid phase separation with optical microscopy: A methodology review. APL Bioeng 2023; 7:021502. [PMID: 37180732 PMCID: PMC10171890 DOI: 10.1063/5.0137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Intracellular liquid-liquid phase separation (LLPS) is a critical process involving the dynamic association of biomolecules and the formation of non-membrane compartments, playing a vital role in regulating biomolecular interactions and organelle functions. A comprehensive understanding of cellular LLPS mechanisms at the molecular level is crucial, as many diseases are linked to LLPS, and insights gained can inform drug/gene delivery processes and aid in the diagnosis and treatment of associated diseases. Over the past few decades, numerous techniques have been employed to investigate the LLPS process. In this review, we concentrate on optical imaging methods applied to LLPS studies. We begin by introducing LLPS and its molecular mechanism, followed by a review of the optical imaging methods and fluorescent probes employed in LLPS research. Furthermore, we discuss potential future imaging tools applicable to the LLPS studies. This review aims to provide a reference for selecting appropriate optical imaging methods for LLPS investigations.
Collapse
Affiliation(s)
| | | | - Yue Ma
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | | | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
8
|
Chen P, Kang Q, Niu J, Jing Y, Zhang X, Yu B, Qu J, Lin D. Fluorescence lifetime tracking and imaging of single moving particles assisted by a low-photon-count analysis algorithm. BIOMEDICAL OPTICS EXPRESS 2023; 14:1718-1731. [PMID: 37078048 PMCID: PMC10110318 DOI: 10.1364/boe.485729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) has been widely used in the field of biological research because of its high specificity, sensitivity, and quantitative ability in the sensing cellular microenvironment. The most commonly used FLIM technology is based on time-correlated single photon counting (TCSPC). Although the TCSPC method has the highest temporal resolution, the data acquisition time is usually long, and the imaging speed is slow. In this work, we proposed a fast FLIM technology for fluorescence lifetime tracking and imaging of single moving particles, named single particle tracking FLIM (SPT-FLIM). We used feedback-controlled addressing scanning and Mosaic FLIM mode imaging to reduce the number of scanned pixels and the data readout time, respectively. Moreover, we developed a compressed sensing analysis algorithm based on alternating descent conditional gradient (ADCG) for low-photon-count data. We applied the ADCG-FLIM algorithm on both simulated and experimental datasets to evaluate its performance. The results showed that ADCG-FLIM could achieve reliable lifetime estimation with high accuracy and precision in the case of a photon count less than 100. By reducing the photon count requirement for each pixel from, typically, 1000 to 100, the acquisition time for a single frame lifetime image could be significantly shortened, and the imaging speed could be improved to a great extent. On this basis, we obtained lifetime trajectories of moving fluorescent beads using the SPT-FLIM technique. Overall, our work offers a powerful tool for fluorescence lifetime tracking and imaging of single moving particles, which will promote the application of TCSPC-FLIM in biological research.
Collapse
|
9
|
Weiss LE, Love JF, Yoon J, Comerci CJ, Milenkovic L, Kanie T, Jackson PK, Stearns T, Gustavsson AK. Single-molecule imaging in the primary cilium. Methods Cell Biol 2023; 176:59-83. [PMID: 37164543 PMCID: PMC10509820 DOI: 10.1016/bs.mcb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The primary cilium is an important signaling organelle critical for normal development and tissue homeostasis. Its small dimensions and complexity necessitate advanced imaging approaches to uncover the molecular mechanisms behind its function. Here, we outline how single-molecule fluorescence microscopy can be used for tracking molecular dynamics and interactions and for super-resolution imaging of nanoscale structures in the primary cilium. Specifically, we describe in detail how to capture and quantify the 2D dynamics of individual transmembrane proteins PTCH1 and SMO and how to map the 3D nanoscale distributions of the inversin compartment proteins INVS, ANKS6, and NPHP3. This protocol can, with minor modifications, be adapted for studies of other proteins and cell lines to further elucidate the structure and function of the primary cilium at the molecular level.
Collapse
Affiliation(s)
- Lucien E Weiss
- Department of Engineering Physics, Polytechnique Montréal, Montreal, QC, Canada.
| | - Julia F Love
- Department of Chemistry, Rice University, Houston, TX, United States
| | | | - Colin J Comerci
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | | | - Tomoharu Kanie
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States; Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, United States; Rockefeller University, New York City, NY, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States; Department of BioSciences, Rice University, Houston, TX, United States; Institute of Biosciences and Bioengineering, Rice University, Houston, TX, United States; Smalley-Curl Institute, Rice University, Houston, TX, United States.
| |
Collapse
|
10
|
Ball DA, Jalloh B, Karpova TS. Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics. Int J Mol Sci 2022; 23:ijms232415895. [PMID: 36555532 PMCID: PMC9781480 DOI: 10.3390/ijms232415895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Cellular functions depend on the dynamic assembly of protein regulator complexes at specific cellular locations. Single Molecule Tracking (SMT) is a method of choice for the biochemical characterization of protein dynamics in vitro and in vivo. SMT follows individual molecules in live cells and provides direct information about their behavior. SMT was successfully applied to mammalian models. However, mammalian cells provide a complex environment where protein mobility depends on numerous factors that are difficult to control experimentally. Therefore, yeast cells, which are unicellular and well-studied with a small and completely sequenced genome, provide an attractive alternative for SMT. The simplicity of organization, ease of genetic manipulation, and tolerance to gene fusions all make yeast a great model for quantifying the kinetics of major enzymes, membrane proteins, and nuclear and cellular bodies. However, very few researchers apply SMT techniques to yeast. Our goal is to promote SMT in yeast to a wider research community. Our review serves a dual purpose. We explain how SMT is conducted in yeast cells, and we discuss the latest insights from yeast SMT while putting them in perspective with SMT of higher eukaryotes.
Collapse
|
11
|
Podh NK, Das A, Dey P, Paliwal S, Mehta G. Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae. STAR Protoc 2022; 3:101900. [PMID: 36595957 PMCID: PMC9732415 DOI: 10.1016/j.xpro.2022.101900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/22/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. 1 and Ball et al..2.
Collapse
Affiliation(s)
- Nitesh Kumar Podh
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Ayan Das
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Partha Dey
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Sheetal Paliwal
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Gunjan Mehta
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India,Corresponding author
| |
Collapse
|
12
|
Johnson C, Exell J, Lin Y, Aguilar J, Welsher KD. Capturing the start point of the virus-cell interaction with high-speed 3D single-virus tracking. Nat Methods 2022; 19:1642-1652. [PMID: 36357694 PMCID: PMC10154077 DOI: 10.1038/s41592-022-01672-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 09/30/2022] [Indexed: 11/12/2022]
Abstract
The early stages of the virus-cell interaction have long evaded observation by existing microscopy methods due to the rapid diffusion of virions in the extracellular space and the large three-dimensional cellular structures involved. Here we present an active-feedback single-particle tracking method with simultaneous volumetric imaging of the live cell environment called 3D-TrIm to address this knowledge gap. 3D-TrIm captures the extracellular phase of the infectious cycle in what we believe is unprecedented detail. We report what are, to our knowledge, previously unobserved phenomena in the early stages of the virus-cell interaction, including skimming contact events at the millisecond timescale, orders of magnitude change in diffusion coefficient upon binding and cylindrical and linear diffusion modes along cellular protrusions. Finally, we demonstrate how this method can move single-particle tracking from simple monolayer culture toward more tissue-like conditions by tracking single virions in tightly packed epithelial cells. This multiresolution method presents opportunities for capturing fast, three-dimensional processes in biological systems.
Collapse
Affiliation(s)
| | - Jack Exell
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Yuxin Lin
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | | |
Collapse
|
13
|
Nguyen MC, Berto P, Valentino F, Kanoufi F, Tessier G. Spectroscopy of individual Brownian nanoparticles in real-time using holographic localization. OPTICS EXPRESS 2022; 30:43182-43194. [PMID: 36523022 DOI: 10.1364/oe.463115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/18/2022] [Indexed: 06/17/2023]
Abstract
Individual nanoparticle spectroscopic characterization is fundamental, but challenging in liquids. While confocal selectivity is necessary to isolate a particle in a crowd, Brownian motion constantly offsets the particle from the light collection volume. Here, we present a system able to acquire holograms and reconstruct them to precisely determine the 3D position of a particle in real time. These coordinates drive an adaptive system comprising two galvanometric mirrors (x,y, transverse directions) and a tunable lens (z, longitudinal) which redirect light scattered from the corresponding region of space towards the confocal entrance of a spectrometer, thus allowing long spectral investigations on individual, freely-moving particles. A study of the movements and spectra of individual 100 nm Au nanoparticles undergoing two types of aggregations illustrates the possibilities of the method.
Collapse
|
14
|
Niver AJ, Welsher KD. Combined online Bayesian and windowed estimation of background and signal localization facilitates active-feedback particle tracking in complex environments. J Chem Phys 2022; 157:184108. [PMID: 36379789 PMCID: PMC9652022 DOI: 10.1063/5.0118317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/21/2022] [Indexed: 11/14/2022] Open
Abstract
Despite successes in tracking single molecules in vitro, the extension of active-feedback single-particle methods to tracking rapidly diffusing and unconfined proteins in live cells has not been realized. Since the existing active-feedback localization methods localize particles in real time assuming zero background, they are ill-suited to track in the inhomogeneous background environment of a live cell. Here, we develop a windowed estimation of signal and background levels using recent data to estimate the current particle brightness and background intensity. These estimates facilitate recursive Bayesian position estimation, improving upon current Kalman-based localization methods. Combined, online Bayesian and windowed estimation of background and signal (COBWEBS) surpasses existing 2D localization methods. Simulations demonstrate improved localization accuracy and responsivity in a homogeneous background for selected particle and background intensity combinations. Improved or similar performance of COBWEBS tracking extends to the majority of signal and background combinations explored. Furthermore, improved tracking durations are demonstrated in the presence of heterogeneous backgrounds for multiple particle intensities, diffusive speeds, and background patterns. COBWEBS can accurately track particles in the presence of high and nonuniform backgrounds, including intensity changes of up to three times the particle's intensity, making it a prime candidate for advancing active-feedback single fluorophore tracking to the cellular interior.
Collapse
Affiliation(s)
- Anastasia J. Niver
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Kevin D. Welsher
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
15
|
van Heerden B, Kruger T. Theoretical comparison of real-time feedback-driven single-particle tracking techniques. J Chem Phys 2022; 157:084111. [DOI: 10.1063/5.0096729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Real-time feedback-driven single-particle tracking is a technique that uses feedbackcontrol to enable single-molecule spectroscopy of freely diffusing particles in nativeor near-native environments. A number of different RT-FD-SPT approaches exist,and comparisons between methods based on experimental results are of limited usedue to differences in samples and setups. In this study, we used statistical calcu-lations and dynamical simulations to directly compare the performance of differentmethods. The methods considered were the orbital method, the Knight's Tour (gridscan) method and MINFLUX, and we considered both fluorescence-based and inter-ferometric scattering (iSCAT) approaches. There is a fundamental trade-off betweenprecision and speed, with the Knight's Tour method being able to track the fastestdiffusion but with low precision, and MINFLUX being the most precise but onlytracking slow diffusion. To compare iSCAT and fluorescence, different biologicalsamples were considered, including labeled and intrinsically fluorescent samples. Thesuccess of iSCAT as compared to fluorescence is strongly dependent on the particlesize and the density and photophysical properties of the fluorescent particles. Usinga wavelength for iSCAT that is negligibly absorbed by the tracked particle allowsan increased illumination intensity, which results in iSCAT providing better trackingfor most samples. This work highlights the fundamental aspects of performance inRT-FD-SPT and should assist with the selection of an appropriate method for a par-ticular application. The approach used can easily be extended to other RT-FD-SPTmethods.
Collapse
|
16
|
van Heerden B, Vickers NA, Krüger TPJ, Andersson SB. Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107024. [PMID: 35758534 PMCID: PMC9308725 DOI: 10.1002/smll.202107024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 04/07/2022] [Indexed: 05/14/2023]
Abstract
Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.
Collapse
Affiliation(s)
- Bertus van Heerden
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215, USA
| |
Collapse
|
17
|
Spatiotemporal three-dimensional transport dynamics of endocytic cargos and their physical regulations in cells. iScience 2022; 25:104210. [PMID: 35479412 PMCID: PMC9035719 DOI: 10.1016/j.isci.2022.104210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
Intracellular transport, regulated by complex cytoarchitectures and active driving forces, is crucial for biomolecule translocations and relates to many cellular functions. Despite extensive knowledge obtained from two-dimensional (2D) experiments, the real three-dimensional (3D) spatiotemporal characteristics of intracellular transport is still unclear. With 3D single-particle tracking, we comprehensively studied the transport dynamics of endocytic cargos. With varying timescale, the intracellular transport changes from thermal-dominated 3D-constrained motion to active-dominated quasi-2D motion. Spatially, the lateral motion is heterogeneous with peripheral regions being faster than perinuclear regions, while the axial motion is homogeneous across the cells. We further confirmed that such anisotropy and heterogeneity of vesicle transport result from actively directed motion on microtubules. Strikingly, inside the vesicles, we observed endocytic nanoparticles make diffusive motions on their inner membranes when microtubules are absent, suggesting endocytic cargos are normally localized at the inner vesicle membranes through a physical connection to the microtubules outside during transport. Endocytic transport changes from 3D-constrained to quasi-2D motions with timescales Lateral motion is heterogeneous while axial motion is homogeneous across the cells Microtubules cause the anisotropy and heterogeneity of vesicle transport Endocytic particles make diffusive motion on the inner membrane of vesicles
Collapse
|
18
|
Flores-Valle A, Seelig JD. Axial motion estimation and correction for simultaneous multi-plane two-photon calcium imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:2035-2049. [PMID: 35519241 PMCID: PMC9045928 DOI: 10.1364/boe.445775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Two-photon imaging in behaving animals is typically accompanied by brain motion. For functional imaging experiments, for example with genetically encoded calcium indicators, such brain motion induces changes in fluorescence intensity. These motion-related intensity changes or motion artifacts can typically not be separated from neural activity-induced signals. While lateral motion, within the focal plane, can be corrected by computationally aligning images, axial motion, out of the focal plane, cannot easily be corrected. Here, we developed an algorithm for axial motion correction for non-ratiometric calcium indicators taking advantage of simultaneous multi-plane imaging. Using temporally multiplexed beams, recording simultaneously from at least two focal planes at different z positions, and recording a z-stack for each beam as a calibration step, the algorithm separates motion-related and neural activity-induced changes in fluorescence intensity. The algorithm is based on a maximum likelihood optimisation approach; it assumes (as a first order approximation) that no distortions of the sample occurs during axial motion and that neural activity increases uniformly along the optical axis in each region of interest. The developed motion correction approach allows axial motion estimation and correction at high frame rates for isolated structures in the imaging volume in vivo, such as sparse expression patterns in the fruit fly brain.
Collapse
Affiliation(s)
- Andres Flores-Valle
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
- International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Johannes D Seelig
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
| |
Collapse
|
19
|
de Jonge WJ, Patel HP, Meeussen JVW, Lenstra TL. Following the tracks: how transcription factor binding dynamics control transcription. Biophys J 2022; 121:1583-1592. [PMID: 35337845 PMCID: PMC9117886 DOI: 10.1016/j.bpj.2022.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Transcription, the process of copying genetic information from DNA to messenger RNA, is regulated by sequence-specific DNA binding proteins known as transcription factors (TFs). Recent advances in single-molecule tracking (SMT) technologies have enabled visualization of individual TF molecules as they diffuse and interact with the DNA in the context of living cells. These SMT studies have uncovered multiple populations of DNA binding events characterized by their distinctive DNA residence times. In this perspective, we review recent insights into how these residence times relate to specific and non-specific DNA binding, as well as the contribution of TF domains on the DNA binding dynamics. We discuss different models that aim to link transient DNA binding by TFs to bursts of transcription and present an outlook for how future advances in microscopy development may broaden our understanding of the dynamics of the molecular steps that underlie transcription activation.
Collapse
Affiliation(s)
- Wim J de Jonge
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
| |
Collapse
|
20
|
Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
Collapse
Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
| |
Collapse
|
21
|
Jiang S, Förster R, Lorenz A, Schmidt MA. Three-dimensional tracking of nanoparticles by dual-color position retrieval in a double-core microstructured optical fiber. LAB ON A CHIP 2021; 21:4437-4444. [PMID: 34617084 DOI: 10.1039/d1lc00709b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Elastic light scattering-based three-dimensional (3D) tracking of objects at the nanoscale level is essential for unlocking the dynamics of individual species or interactions in fields such as biology or surface chemistry. In this work, we introduce the concept of dual-color 3D tracking in a double-core microstructured optical fiber that for the first time allows for full 3D reconstruction of the trajectory of a diffusing nanoparticle in a water-filled fiber-integrated microchannel. The use of two single-mode cores provides two opposite decaying evanescent fields of different wavelengths within the microchannel, bypassing spatial domains of ambiguous correlation between the scattered intensity and position. The novelty of the fiber design is the use of two slightly different single-mode cores, preventing modal crosstalk and thus allowing for longitudinally invariant dual-color illumination across the entire field of view. To demonstrate the capabilities of the scheme, a single gold nanosphere (80 nm) diffusing in the water-filled microchannel was tracked for a large number of images (about 32 000) at a high frame rate (1.389 kHz) over a long time (23 s), with the determined hydrodynamic diameters matching expectations. The presented 3D tracking approach yields unique opportunities to unlock processes at the nanoscale level and is highly relevant for a multitude of fields, particularly within the context of understanding sophisticated interaction of diffusing species with functionalized surfaces within the context of bioanalytics, nanoscale materials science, surface chemistry or life science.
Collapse
Affiliation(s)
- Shiqi Jiang
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany.
- Abbe Center of Photonics and Faculty of Physics, FSU Jena, 07745 Jena, Germany
| | - Ronny Förster
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany.
| | - Adrian Lorenz
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany.
| | - Markus A Schmidt
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany.
- Abbe Center of Photonics and Faculty of Physics, FSU Jena, 07745 Jena, Germany
- Otto Schott Institute of Material Research, FSU Jena, 07745 Jena, Germany
| |
Collapse
|
22
|
Tan X, Welsher K. Particle‐by‐Particle In Situ Characterization of the Protein Corona via Real‐Time 3D Single‐Particle‐Tracking Spectroscopy**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaochen Tan
- Department of Chemistry Duke University Durham NC 27708 USA
| | - Kevin Welsher
- Department of Chemistry Duke University Durham NC 27708 USA
| |
Collapse
|
23
|
Tan X, Welsher K. Particle-by-Particle In Situ Characterization of the Protein Corona via Real-Time 3D Single-Particle-Tracking Spectroscopy*. Angew Chem Int Ed Engl 2021; 60:22359-22367. [PMID: 34015174 PMCID: PMC8763617 DOI: 10.1002/anie.202105741] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/05/2022]
Abstract
Nanoparticles (NPs) adsorb proteins when exposed to biological fluids, forming a dynamic protein corona that affects their fate in biological environments. A comprehensive understanding of the protein corona is lacking due to the inability of current techniques to precisely measure the full corona in situ at the single-particle level. Herein, we introduce a 3D real-time single-particle tracking spectroscopy to "lock-on" to single freely diffusing polystyrene NPs and probe their individual protein coronas, primarily using bovine serum albumin (BSA) as a model system. The fluorescence signals and diffusive motions of the tracked NPs enable quantification of the "hard corona" using mean-squared displacement analysis. Critically, this method's particle-by-particle nature enabled a lock-in-type frequency filtering approach to extract the full protein corona, despite the typically confounding effect of high background signal from unbound proteins. From these results, the dynamic in situ full protein corona is observed to contain twice the number of proteins compared to the ex situ-measured "hard" protein corona.
Collapse
Affiliation(s)
- Xiaochen Tan
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, USA
| | - Kevin Welsher
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, USA
| |
Collapse
|
24
|
Zhang C, Welsher K. Information-Efficient, Off-Center Sampling Results in Improved Precision in 3D Single-Particle Tracking Microscopy. ENTROPY (BASEL, SWITZERLAND) 2021; 23:498. [PMID: 33921987 PMCID: PMC8143542 DOI: 10.3390/e23050498] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022]
Abstract
In this work, we present a 3D single-particle tracking system that can apply tailored sampling patterns to selectively extract photons that yield the most information for particle localization. We demonstrate that off-center sampling at locations predicted by Fisher information utilizes photons most efficiently. When performing localization in a single dimension, optimized off-center sampling patterns gave doubled precision compared to uniform sampling. A ~20% increase in precision compared to uniform sampling can be achieved when a similar off-center pattern is used in 3D localization. Here, we systematically investigated the photon efficiency of different emission patterns in a diffraction-limited system and achieved higher precision than uniform sampling. The ability to maximize information from the limited number of photons demonstrated here is critical for particle tracking applications in biological samples, where photons may be limited.
Collapse
Affiliation(s)
| | - Kevin Welsher
- Department of Chemistry, Duke University, Durham, NC 27708, USA;
| |
Collapse
|
25
|
Melnyk O, Jones R, Macêdo R, Garbovskiy Y, Hagen G, Glushchenko AV, Spendier K, Camley RE. Fast Switching Dual-Frequency Nematic Liquid Crystal Tunable Filters. ACS PHOTONICS 2021; 8:1222-1231. [PMID: 34095347 PMCID: PMC8174839 DOI: 10.1021/acsphotonics.1c00151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We develop tunable optical filters with dual-frequency nematic liquid crystal optical retarders to enable fast switching between the passed wavelengths. The filters are composed of a series of two liquid crystal optical retarders. We select the specific thicknesses of the liquid crystal retarders and use individual biasing schemes to continuously tune the wavelength and bandwidth of the filter. This enables fine-tuned filter switching speeds of filter operation in the ms regime. We present theoretical predictions and experimental results for the electro-optical filter characterization as well as an example application for our filter in total internal reflection fluorescence microscopy. We find that our filter switching speeds can be as short as a few ms, an order of magnitude improvement over typical mechanical filter wheel switching speeds. The quality of our fluorescence images is similar to those obtained by conventional filters.
Collapse
Affiliation(s)
- Olha Melnyk
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| | - Reed Jones
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| | - Rair Macêdo
- James Watt School of Engineering, Electronics & Nanoscale Engineering Division, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Yuriy Garbovskiy
- Department of Physics and Engineering Physics, Central Connecticut State University, New Britain, Connecticut 06050, United States
| | - Guy Hagen
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| | - Anatoliy V Glushchenko
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| | - Kathrin Spendier
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| | - Robert E Camley
- UCCS Biofrontiers Center and Department of Physics and Energy Science, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918, United States
| |
Collapse
|
26
|
Levin M, Bel G, Roichman Y. Measurements and characterization of the dynamics of tracer particles in an actin network. J Chem Phys 2021; 154:144901. [PMID: 33858166 DOI: 10.1063/5.0045278] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks. Surprisingly, the diffusion of a tracer particle in a network of a purified protein, actin, was found to conform to the continuous time random walk type (CTRW). We set out to resolve this discrepancy by studying the tracer particle diffusion using two different tracer particle sizes, in actin networks of different mesh sizes. We find that the ratio of tracer particle size to the characteristic length scale of a bio-polymer network plays a crucial role in determining the type of diffusion it performs. We find that the diffusion of the tracer particles has features of fBm when the particle is large compared to the mesh size, of normal diffusion when the particle is much smaller than the mesh size, and of the CTRW in between these two limits. Based on our findings, we propose and verify numerically a new model for the motion of the tracer in all regimes. Our model suggests that diffusion in actin networks consists of fBm of the tracer particle coupled with caging events with power-law distributed escape times.
Collapse
Affiliation(s)
- Maayan Levin
- Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Golan Bel
- Department of Solar Energy and Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Yael Roichman
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
27
|
Goldman YE. No hype in hyperspace. Biophys J 2021; 120:1306-1308. [PMID: 33711256 DOI: 10.1016/j.bpj.2021.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 10/22/2022] Open
Affiliation(s)
- Yale E Goldman
- Department of Physiology and Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
28
|
Klymchenko AS, Liu F, Collot M, Anton N. Dye-Loaded Nanoemulsions: Biomimetic Fluorescent Nanocarriers for Bioimaging and Nanomedicine. Adv Healthc Mater 2021; 10:e2001289. [PMID: 33052037 DOI: 10.1002/adhm.202001289] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Lipid nanoemulsions (NEs), owing to their controllable size (20 to 500 nm), stability and biocompatibility, are now frequently used in various fields, such as food, cosmetics, pharmaceuticals, drug delivery, and even as nanoreactors for chemical synthesis. Moreover, being composed of components generally recognized as safe (GRAS), they can be considered as "green" nanoparticles that mimic closely lipoproteins and intracellular lipid droplets. Therefore, they attracted attention as carriers of drugs and fluorescent dyes for both bioimaging and studying the fate of nanoemulsions in cells and small animals. In this review, the composition of dye-loaded NEs, methods for their preparation, and emerging biological applications are described. The design of bright fluorescent NEs with high dye loading and minimal aggregation-caused quenching (ACQ) is focused on. Common issues including dye leakage and NEs stability are discussed, highlighting advanced techniques for their characterization, such as Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS). Attempts to functionalize NEs surface are also discussed. Thereafter, biological applications for bioimaging and single-particle tracking in cells and small animals as well as biomedical applications for photodynamic therapy are described. Finally, challenges and future perspectives of fluorescent NEs are discussed.
Collapse
Affiliation(s)
- Andrey S. Klymchenko
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Fei Liu
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
| | - Mayeul Collot
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Nicolas Anton
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
| |
Collapse
|
29
|
Abstract
To date, single molecule studies have been reliant on tethering or confinement to achieve long duration and high temporal resolution measurements. Here, we present a 3D single-molecule active real-time tracking method (3D-SMART) which is capable of locking on to single fluorophores in solution for minutes at a time with photon limited temporal resolution. As a demonstration, 3D-SMART is applied to actively track single Atto 647 N fluorophores in 90% glycerol solution with an average duration of ~16 s at count rates of ~10 kHz. Active feedback tracking is further applied to single proteins and nucleic acids, directly measuring the diffusion of various lengths (99 to 1385 bp) of single DNA molecules at rates up to 10 µm2/s. In addition, 3D-SMART is able to quantify the occupancy of single Spinach2 RNA aptamers and capture active transcription on single freely diffusing DNA. 3D-SMART represents a critical step towards the untethering of single molecule spectroscopy. Single molecule observation has been limited to tethered molecules to ensure that the target remains in the field of view (FOV). Here, the authors develop a real-time tracking method that locks onto rapidly diffusing targets and tracks them in a 3D volume, enabling single molecules to remain in the FOV for minutes at a time.
Collapse
|
30
|
Liu SL, Wang ZG, Xie HY, Liu AA, Lamb DC, Pang DW. Single-Virus Tracking: From Imaging Methodologies to Virological Applications. Chem Rev 2020; 120:1936-1979. [PMID: 31951121 PMCID: PMC7075663 DOI: 10.1021/acs.chemrev.9b00692] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Uncovering
the mechanisms of virus infection and assembly is crucial
for preventing the spread of viruses and treating viral disease. The
technique of single-virus tracking (SVT), also known as single-virus
tracing, allows one to follow individual viruses at different parts
of their life cycle and thereby provides dynamic insights into fundamental
processes of viruses occurring in live cells. SVT is typically based
on fluorescence imaging and reveals insights into previously unreported
infection mechanisms. In this review article, we provide the readers
a broad overview of the SVT technique. We first summarize recent advances
in SVT, from the choice of fluorescent labels and labeling strategies
to imaging implementation and analytical methodologies. We then describe
representative applications in detail to elucidate how SVT serves
as a valuable tool in virological research. Finally, we present our
perspectives regarding the future possibilities and challenges of
SVT.
Collapse
Affiliation(s)
- Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Hai-Yan Xie
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , P. R. China
| | - An-An Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), and Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM) , Ludwig-Maximilians-Universität , München , 81377 , Germany
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology , Wuhan University , Wuhan 430072 , P. R. China
| |
Collapse
|