1
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Tian YF, Zhang YP, Wu QM, Pang DW, Liu SL, Wang ZG. Real-Time Imaging of Single Viral mRNA Translation in Live Cells Using CRISPR/dCas13. Anal Chem 2023; 95:16298-16304. [PMID: 37874254 DOI: 10.1021/acs.analchem.3c03365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Translation is one of the many critical cellular activities regulated by viruses following host-cell invasion, and studies of viral mRNA translation kinetics and subcellular localization require techniques for the dynamic, real-time visualization of translation. However, conventional tools for imaging mRNA translation often require coding region modifications that may affect native translation. Here, we achieve dynamic imaging of translation with a tool that labels target mRNAs with unmodified coding regions using a CRISPR/dCas13 system with specific complementary paired guide RNAs. This system enables a real-time dynamic visualization of the translation process and is a promising tool for further investigations of the mechanisms of translation.
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Affiliation(s)
- Yi-Fan Tian
- 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
| | - Yu-Peng Zhang
- 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
| | - Qiu-Mei Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, 1 Xue Fu North Road, Fuzhou 350122, P. R. China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, 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
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2
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Babu AK, Raja MKMM, Zehravi M, Mohammad BD, Anees MI, Prasad C, Yahya BA, Sultana R, Sharma R, Singh J, Khan KA, Siddiqui FA, Khan SL, Emran TB. An overview of polymer surface coated synthetic quantum dots as therapeutics and sensors applications. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 184:1-12. [PMID: 37652186 DOI: 10.1016/j.pbiomolbio.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Quantum dots (QDs) are a class of remarkable materials that have garnered significant attention since their initial discovery. It is noteworthy to mention that it took approximately a decade for these materials to be successfully implemented in practical applications. While QDs have demonstrated notable optical properties, it is important to note that these attributes alone have not rendered them a feasible substitute for traditional organic dyes. Furthermore, it is worth noting that the substance under investigation exhibited inherent toxicity and instability in its initial state, primarily due to the presence of a heavy metal core. In the initial stages of research, it was observed that the integration of nanocomposites had a positive impact on the properties of QDs. The discovery of these nanocomposites was motivated by the remarkable properties exhibited by biocomposites found in nature. Recent discoveries have shed light on the potential utilization of QDs as a viable strategy for drug delivery, offering a promising avenue to enhance the efficacy of current pharmaceuticals and pave the way for the creation of innovative therapeutic approaches. The primary objective of this review was to elucidate the distinctive characteristics that render QDs highly suitable for utilization as nanocarriers. In this study, we will delve into the multifaceted applications of QDs as sensing nanoprobes and their utilization in diverse drug delivery systems. The focus of our investigation was directed toward the utilization of QD/polymer composites in sensing applications, with particular emphasis on their potential as chemical sensors, biosensors, and physical sensors.
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Affiliation(s)
- Ancha Kishore Babu
- Centre of Excellence for Pharmaceutical Sciences, School of Pharmacy, KPJ Healthcare University College, 71800, Nilai, Malaysia
| | - M K Mohan Maruga Raja
- Parul Institute of Pharmacy & Research, Parul University, Vadodara, Gujarat, 391110, India
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Al-Kharj, 11942, Saudi Arabia
| | - Badrud Duza Mohammad
- Department of Pharmaceutical Chemistry, G R T Institute of Pharmaceutical Education and Research, GRT Mahalakshmi Nagar, Tiruttani 631209, Tamil Nadu, India
| | - Mohammed Imran Anees
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, Maharashtra, 431003, India
| | | | - Barrawaz Aateka Yahya
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, Maharashtra, 431003, India
| | - Rokeya Sultana
- Yenepoya Pharmacy College and Research Centre, Yenepoya (Deemed to Be University), Deralakatte, 575022, Mangalore, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia; Applied College, King Khalid University, P. O. Box 9004, Abha, 61413, Saudi Arabia
| | - Falak A Siddiqui
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa, 413520, Maharashtra, India; Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India
| | - Sharuk L Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa, 413520, Maharashtra, India; Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India.
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh.
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3
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Le T, Chiang Y, Hui Y, Le T, Tzeng Y, Sharma N, Chiang W, Hsiao W. In vitroBioimaging of Fluorescent Nanodiamonds. NANODIAMONDS IN ANALYTICAL AND BIOLOGICAL SCIENCES 2023:95-127. [DOI: 10.1002/9781394202164.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
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4
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Li K, Ni J, Tan X, Zhou Q, Chen D, Cao B, Lin J, Lin T, Zhao P, Yuan X, Ni Y. Motion screening of fiducial marker for improved localization precision and resolution in SMLM. OPTICS EXPRESS 2023; 31:26764-26776. [PMID: 37710528 DOI: 10.1364/oe.496761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 09/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) provides unmatched high resolution but relies on accurate drift correction due to the long acquisition time for each field of view. A popular drift correction is implemented via referencing to fiducial markers that are assumed to be firmly immobilized and remain stationary relative to the imaged sample. However, there is so far lack of efficient approaches for evaluating other motions except sample drifting of immobilized markers and for addressing their potential impacts on images. Here, we developed a new approach for quantitatively assessing the motions of fiducial markers relative to the sample via mean squared displacement (MSD) analysis. Our findings revealed that over 90% of immobilized fluorescent beads in the SMLM imaging buffer exhibited higher MSDs compared to stationary beads in dry samples and displayed varying degrees of wobbling relative to the imaged field. By excluding extremely high-MSD beads in each field from drift correction, we optimized drift correction and experimentally measured localization precision. In SMLM experiments of cellular microtubules, we also found that including only relatively low-MSD beads for drift correction significantly improved the image resolution and quality. Our study presents a simple and effective approach to assess the potential relative motions of fiducial markers and emphasizes the importance of pre-screening fiducial markers for improved image quality and resolution in SMLM imaging.
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5
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Santos-Luna D, Sixto-López Y, Bravo-Alfaro D, Cano-Sarmiento C, García H, Correa-Basurto J. Design and simulation of a caprylic acid enzymatically modified phosphatidylcholine micelle using a coarse-grained molecular dynamics simulations approach. J Biomol Struct Dyn 2023; 41:13902-13913. [PMID: 36826442 DOI: 10.1080/07391102.2023.2180434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
Computationally simulated micelle models provide useful structural information on the molecular and biological sciences. One strategy to study the self-aggregation process of surfactant molecules that make up a micelle is through molecular dynamics (MD) simulations. In this study, a theoretical approach with a coarse-grained MD simulation (CG-MD) was employed to evaluate the critical micellar concentration (CMC), the micellization process, building a tridimensional (3D) model system of a micelle using data from the experimentally enzymatically modified phospholipids (PL) by phospholipase A1 (PA1). This required enzymatic interesterification of soybean phosphatidylcholine (PC) with caprylic acid, along with purification and characterization by chromatographic techniques to measure the esterified fatty acids and the corresponding PL composition. The number of molecules used in the CG-MD simulation system was determined from the experimental CMC data which was 0.025%. The molecular composition of the system is: 1 C 18:2, 2 C 8:0/8:0, 3 C 8:0/18:3n-9, 4 C 8:0/18:0, 5 C8:0/18:2n-6, 6 C8:0/18:1n-9, and 7 C 8:0/16:0. According to our theoretical results, the micelle model is structurally stable with an average Rg of 3.64 ± 0.10 Å, and might have an elliptical form with a radius of 24.6 Å. Regarding CMC value there was a relationship between the experimental data of the modified PLs and the theoretical analysis by GC-MD, which suggest that the enzymatic modification of PLs does not affect their self-aggregation properties. Finally, the micellar system obtained in the current research can be used as a simple and useful model to design optimal biocompatible nanoemulsions as possible vehicles for bioactive small molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dalia Santos-Luna
- Unidad de Investigación y Desarrollo de Alimentos, Tecnológico Nacional de México/IT de Veracruz, Veracruz, México
| | - Yudibeth Sixto-López
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja, Granada, Spain
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation) SEPI-ESM, Instituto Politécnico Nacional, México, Mexico City, Mexico
| | - Diego Bravo-Alfaro
- Unidad de Investigación y Desarrollo de Alimentos, Tecnológico Nacional de México/IT de Veracruz, Veracruz, México
| | - Cynthia Cano-Sarmiento
- CONACyT-Unidad de Investigación y Desarrollo de Alimentos, Tecnologico Nacional de México/IT de Veracruz, Veracruz, México
| | - Hugo García
- Unidad de Investigación y Desarrollo de Alimentos, Tecnológico Nacional de México/IT de Veracruz, Veracruz, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation) SEPI-ESM, Instituto Politécnico Nacional, México, Mexico City, Mexico
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6
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Vickers NA, Andersson SB. Synthetic Stochastic Motion Platform for Testing Single Particle Tracking Microscopes. IEEE TRANSACTIONS ON CONTROL SYSTEMS TECHNOLOGY : A PUBLICATION OF THE IEEE CONTROL SYSTEMS SOCIETY 2022; 30:2726-2733. [PMID: 36300161 PMCID: PMC9590407 DOI: 10.1109/tcst.2022.3149597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We describe the design and implementation of a control system for testing the performance of single particle tracking microscopes with the method of synthetic motion. Single particle tracking (SPT) has become a common and powerful tool in the study of biomolecular transport in cellular biology, providing the ability to track individual biological macromolecules in their native environment. Existing methods for testing SPT techniques rely on physical simulations and there is a clear need for experimental-based schemes for both comparing different approaches and for characterizing the accuracy and precision of techniques on particular experimental setups. Synthetic motion, that is, using an actuator such as a nanopositioning stage to drive a particle along a known ground-truth trajectory, is a means for achieving these ends. However, the resolution, accuracy, and flexibility of this method is limited by the actuator static and dynamic characteristics. In this work we apply system identification and model inverse feedforward control to increase actuator bandwidth and address some common actuator nonlinearities, develop a set of dimensionless numbers that describe system limitations, and provide a set of guidelines for the practical use of synthetic motion in SPT.
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Affiliation(s)
- Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215 USA
| | - Sean B Andersson
- Department of Mechanical Engineering and the Division of Systems Engineering, Boston University, Boston, MA, 02215 USA
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7
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Hsiao WW, Le T, Chang H. Applications of Fluorescent Nanodiamond in Biology. ENCYCLOPEDIA OF ANALYTICAL CHEMISTRY 2022:1-43. [DOI: 10.1002/9780470027318.a9776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Abstract
Fluorescent nanodiamond (FND) has emerged as a promising material in several multidisciplinary areas, including biology, chemistry, physics, and materials science. Composed of sp
3
‐carbon atoms, FND offers superior biocompatibility, chemical inertness, a large surface area, tunable surface structure, and excellent mechanical characteristics. The nanoparticle is unique in that it comprises a high‐density ensemble of negatively charged nitrogen‐vacancy (NV
−
) centers that act as built‐in fluorophores and exhibit a number of remarkable optical and magnetic properties. These properties make FND particularly well suited for a wide range of applications, including cell labeling, long‐term cell tracking, super‐resolution imaging, nanoscale sensing, and drug delivery. This article discusses recent applications of FND‐enabled developments in biology.
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8
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Moud AA. Fluorescence Recovery after Photobleaching in Colloidal Science: Introduction and Application. ACS Biomater Sci Eng 2022; 8:1028-1048. [PMID: 35201752 DOI: 10.1021/acsbiomaterials.1c01422] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
FRAP (fluorescence recovery after photo bleaching) is a method for determining diffusion in material science. In industrial applications such as medications, foods, Medtech, hygiene, and textiles, the diffusion process has a substantial influence on the overall qualities of goods. All these complex and heterogeneous systems have diffusion-based processes at the local level. FRAP is a fluorescence-based approach for detecting diffusion; in this method, a high-intensity laser is made for a brief period and then applied to the samples, bleaching the fluorescent chemical inside the region, which is subsequently filled up by natural diffusion. This brief Review will focus on the existing research on employing FRAP to measure colloidal system heterogeneity and explore diffusion into complicated structures. This description of FRAP will be followed by a discussion of how FRAP is intended to be used in colloidal science. When constructing the current Review, the most recent publications were reviewed for this assessment. Because of the large number of FRAP articles in colloidal research, there is currently a dearth of knowledge regarding the growth of FRAP's significance to colloidal science. Colloids make up only 2% of FRAP papers, according to ISI Web of Knowledge.
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Affiliation(s)
- Aref Abbasi Moud
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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9
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Li R, Vedelaar T, Mzyk A, Morita A, Padamati SK, Schirhagl R. Following Polymer Degradation with Nanodiamond Magnetometry. ACS Sens 2022; 7:123-130. [PMID: 34982542 PMCID: PMC8809337 DOI: 10.1021/acssensors.1c01782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023]
Abstract
Degradable polymers are widely used in the biomedical fields due to non-toxicity and great biocompatibility and biodegradability, and it is crucial to understand how they degrade. These polymers are exposed to various biochemical media in medical practice. Hence, it is important to precisely follow the degradation of the polymer in real time. In this study, we made use of diamond magnetometry for the first time to track polymer degradation with nanoscale precision. The method is based on a fluorescent defect in nanodiamonds, which changes its optical properties based on its magnetic surrounding. Since optical signals can be read out more sensitively than magnetic signals, this method allows unprecedented sensitivity. We used a specific mode of diamond magnetometry called relaxometry or T1 measurements. These are sensitive to magnetic noise and thus can detect paramagnetic species (gadolinium in this case). Nanodiamonds were incorporated into polylactic acid (PLA) films and PLA nanoparticles in order to follow polymer degradation. However, in principle, they can be incorporated into other polymers too. We found that T1 constants decreased gradually with the erosion of the film exposed to an alkaline condition. In addition, the mobility of nanodiamonds increased, which allows us to estimate polymer viscosity. The degradation rates obtained using this approach were in good agreement with data obtained by quartz crystal microbalance, Fourier-transform infrared spectroscopy, and atomic force microscopy.
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Affiliation(s)
- Runrun Li
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
| | - Thea Vedelaar
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
| | - Aldona Mzyk
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
- Institute
of Metallurgy and Materials Science, Polish Academy of Sciences, Reymonta 25, Krakow 30-059, Poland
| | - Aryan Morita
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
- Dept.
Dental Biomedical Sciences, Faculty of Dentistry, Universitas Gadjah Mada, Jalan Denta 1, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Sandeep Kumar Padamati
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
| | - Romana Schirhagl
- Groningen
University, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AW, The Netherlands
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10
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Mancini L, Crozat E, Javer A, Lagomarsino MC, Cicuta P. Dynamics of Bacterial Chromosomes by Locus Tracking in Fluorescence Microscopy. Methods Mol Biol 2022; 2476:155-170. [PMID: 35635703 DOI: 10.1007/978-1-0716-2221-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the last two decades, it has been shown that bacterial chromosomes have remarkable spatial organization at various scales, and they display well-defined movements during the cell cycle, for example to reliably segregate daughter chromosomes. More recently, various labs have begun investigating also the short time dynamics (displacements during time intervals of 0.1 s-100 s), which should be related to the molecular structure. Probing these dynamics is analogous to "microrheology" approaches that have been applied successfully to study mechanical response of complex fluids. These studies of chromosome fluctuation dynamics have revealed differences of fluctuation amplitude across the chromosome, and different characters of motion depending on the time window of interest. Different fluctuation amplitudes have also been observed for the same chromosomal loci under antibiotic treatments, with magnitudes that are correlated to changes in intracellular density and thus crowding. We describe how to carry out tracking experiments of single loci and how to analyze locus motility. We point out the importance of considering in the analysis the number of GFP molecules per fluorescent locus, as well as the nature of the protein they are fused to, and also how to measure intracellular density.
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Affiliation(s)
- Leonardo Mancini
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Estelle Crozat
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et de Génétique Moléculaires, Université de Toulouse, CNRS, UPS, Toulouse, France
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Avelino Javer
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
- Physics Department, University of Milan, and INFN, Milan, Italy
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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11
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Vickers NA, Andersson SB. Information Optimal Control for Single Particle Tracking Microscopy. IFAC-PAPERSONLINE 2021; 54:649-654. [PMID: 35265950 PMCID: PMC8903092 DOI: 10.1016/j.ifacol.2021.08.434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We consider the problem of designing a control policy for a laser scanning microscope (LSM) which will minimize the estimation uncertainty when identifying the state and motion model of a fluorescent biological particle. Using the information optimal design framework we pose an optimization problem which seeks to maximize the Fisher information of the particle's state. We then apply optimal control methods to determine the laser trajectory that maximizes a criterion based on the Fisher information. The resulting optimal control policy is a Bang-Singular control which moves the laser to the set of measurement locations that maximize the rate of information accumulation. Simulations demonstrate the ability of the resulting control system to position the laser to measure the particles location with a minimum uncertainty.
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Affiliation(s)
- Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
- Division of Systems Engineering, Boston University, Boston, MA 02155 USA
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12
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Garcia Romeu H, Deville S, Salvati A. Time- and Space-Resolved Flow-Cytometry of Cell Organelles to Quantify Nanoparticle Uptake and Intracellular Trafficking by Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100887. [PMID: 34272923 DOI: 10.1002/smll.202100887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/15/2021] [Indexed: 05/20/2023]
Abstract
The design of targeted nanomedicines requires intracellular space- and time-resolved data of nanoparticle distribution following uptake. Current methods to study intracellular trafficking, such as dynamic colocalization by fluorescence microscopy in live cells, are usually low throughput and require extensive analysis of large datasets to quantify colocalization in several individual cells. Here a method based on flow cytometry to easily detect and characterize the organelles in which nanoparticles are internalized and trafficked over time is proposed. Conventional cell fractionation methods are combined with immunostaining and high-sensitivity organelle flow cytometry to get space-resolved data of nanoparticle intracellular distribution. By extracting the organelles at different times, time-resolved data of nanoparticle intracellular trafficking are obtained. The method is validated by determining how nanoparticle size affects the kinetics of arrival to the lysosomes. The results demonstrate that this method allows high-throughput analysis of nanoparticle uptake and intracellular trafficking by cells, therefore it can be used to determine how nanoparticle design affects their intracellular behavior.
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Affiliation(s)
- Hector Garcia Romeu
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Sarah Deville
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713AV, The Netherlands
- Health Unit, Flemish Institute for Technological Research, Boeretang 200, Mol, 2400, Belgium
| | - Anna Salvati
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713AV, The Netherlands
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13
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Bullerjahn JT, Hummer G. Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. J Chem Phys 2021; 154:234105. [PMID: 34241279 DOI: 10.1063/5.0038174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit on mean-squared-displacement curves. However, this strategy is suboptimal and prone to errors. Recently, it was shown that the increments between the observed positions provide a good estimate for the diffusion coefficient, and their statistics are well-suited for likelihood-based analysis methods. Here, we revisit the problem of extracting diffusion coefficients from single-particle tracking experiments subject to static noise and dynamic motion blur using the principle of maximum likelihood. Taking advantage of an efficient real-space formulation, we extend the model to mixtures of subpopulations differing in their diffusion coefficients, which we estimate with the help of the expectation-maximization algorithm. This formulation naturally leads to a probabilistic assignment of trajectories to subpopulations. We employ the theory to analyze experimental tracking data that cannot be explained with a single diffusion coefficient. We test how well a dataset conforms to the assumptions of a diffusion model and determine the optimal number of subpopulations with the help of a quality factor of known analytical distribution. To facilitate use by practitioners, we provide a fast open-source implementation of the theory for the efficient analysis of multiple trajectories in arbitrary dimensions simultaneously.
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Affiliation(s)
- Jakob Tómas Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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14
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Vickers NA, Andersson SB. Feedforward Control for Single Particle Tracking Synthetic Motion. IFAC-PAPERSONLINE 2021; 53:8878-8883. [PMID: 34027521 PMCID: PMC8135106 DOI: 10.1016/j.ifacol.2020.12.1407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single particle tracking (SPT) is a method to study the transport of biomolecules with nanometer resolution. Unfortunately, recent reports show that systematic errors in position localization and uncertainty in model parameter estimates limits the utility of these techniques in studying biological processes. There is a need for an experimental method with a known ground-truth that tests the total SPT system (sample, microscope, algorithm) on both localization and estimation of model parameters. Synthetic motion is a known ground-truth method that moves a particle along a trajectory. This trajectory is a realization of a Markovian stochastic process that represents models of biomolecular transport. Here we describe a platform for creating synthetic motion using common equipment and well-known, simple methods that can be easily adopted by the biophysics community. In this paper we describe the synthetic motion system and calibration to achieve nanometer accuracy and precision. Steady state input-output characteristics are analyzed with both line scans and grid scans. The resulting relationship is described by an affine transformation, which is inverted and used as a prefilter. Model inverse feed forward control is used to increase the system bandwidth. The system model was identified from frequency response function measurements using an integrated stepped-sine with coherent demodulation built into the FPGA controller. Zero magnitude error tracking controller method was used to invert non-minimum phase zeros to achieve a stable discrete time feed forward filter.
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Affiliation(s)
- Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
- Division of Systems Engineering, Boston University, Boston, MA 02155 USA
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15
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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16
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Escamilla-Ayala AA, Sannerud R, Mondin M, Poersch K, Vermeire W, Paparelli L, Berlage C, Koenig M, Chavez-Gutierrez L, Ulbrich MH, Munck S, Mizuno H, Annaert W. Super-resolution microscopy reveals majorly mono- and dimeric presenilin1/γ-secretase at the cell surface. eLife 2020; 9:56679. [PMID: 32631487 PMCID: PMC7340497 DOI: 10.7554/elife.56679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
γ-Secretase is a multi-subunit enzyme whose aberrant activity is associated with Alzheimer’s disease and cancer. While its structure is atomically resolved, γ-secretase localization in the membrane in situ relies mostly on biochemical data. Here, we combined fluorescent tagging of γ-secretase subunits with super-resolution microscopy in fibroblasts. Structured illumination microscopy revealed single γ-secretase complexes with a monodisperse distribution and in a 1:1 stoichiometry of PSEN1 and nicastrin subunits. In living cells, sptPALM revealed PSEN1/γ-secretase mainly with directed motility and frequenting ‘hotspots’ or high track-density areas that are sensitive to γ-secretase inhibitors. We visualized γ-secretase association with substrates like amyloid precursor protein and N-cadherin, but not with its sheddases ADAM10 or BACE1 at the cell surface, arguing against pre-formed megadalton complexes. Nonetheless, in living cells PSEN1/γ-secretase transiently visits ADAM10 hotspots. Our results highlight the power of super-resolution microscopy for the study of γ-secretase distribution and dynamics in the membrane.
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Affiliation(s)
- Abril Angélica Escamilla-Ayala
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Magali Mondin
- Bordeaux Imaging Center, UMS 3420, CNRS-University of Bordeaux, US4 INSERM, Bordeaux, France
| | - Karin Poersch
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wendy Vermeire
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Laura Paparelli
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB Bio Imaging Core, Leuven, Belgium
| | - Caroline Berlage
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Lucia Chavez-Gutierrez
- Department of Neurosciences, KU Leuven, Leuven, Belgium.,Laboratory of Proteolytic Mechanisms in Neurodegeneration, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Maximilian H Ulbrich
- Institute of Internal Medicine IV, Medical Center of the University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Sebastian Munck
- Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB Bio Imaging Core, Leuven, Belgium
| | - Hideaki Mizuno
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, KU Leuven, Heverlee, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
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17
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Abstract
Quantum dots (QDs) possess optical properties of superbright fluorescence, excellent photostability, narrow emission spectra, and optional colors. Labeled with QDs, single molecules/viruses can be rapidly and continuously imaged for a long time, providing more detailed information than when labeled with other fluorophores. While they are widely used to label proteins in single-molecule-tracking studies, QDs have rarely been used to study virus infection, mainly due to a lack of accepted labeling strategies. Here, we report a general method to mildly and readily label enveloped viruses with QDs. Lipid-biotin conjugates were used to recognize and mark viral lipid membranes, and streptavidin-QD conjugates were used to light them up. Such a method allowed enveloped viruses to be labeled in 2 h with specificity and efficiency up to 99% and 98%, respectively. The intact morphology and the native infectivity of viruses were preserved. With the aid of this QD labeling method, we lit wild-type and mutant Japanese encephalitis viruses up, tracked their infection in living Vero cells, and found that H144A and Q258A substitutions in the envelope protein did not affect the virus intracellular trafficking. The lipid-specific QD labeling method described in this study provides a handy and practical tool to readily "see" the viruses and follow their infection, facilitating the widespread use of single-virus tracking and the uncovering of complex infection mechanisms.IMPORTANCE Virus infection in host cells is a complex process comprising a large number of dynamic molecular events. Single-virus tracking is a versatile technique to study these events. To perform this technique, viruses must be fluorescently labeled to be visible to fluorescence microscopes. The quantum dot is a kind of fluorescent tag that has many unique optical properties. It has been widely used to label proteins in single-molecule-tracking studies but rarely used to study virus infection, mainly due to the lack of an accepted labeling method. In this study, we developed a lipid-specific method to readily, mildly, specifically, and efficiently label enveloped viruses with quantum dots by recognizing viral envelope lipids with lipid-biotin conjugates and recognizing these lipid-biotin conjugates with streptavidin-quantum dot conjugates. It is not only applicable to normal viruses, but also competent to label the key protein-mutated viruses and the inactivated highly virulent viruses, providing a powerful tool for single-virus tracking.
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18
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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: 100] [Impact Index Per Article: 25.0] [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.
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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
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19
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Weiss M. Resampling single-particle tracking data eliminates localization errors and reveals proper diffusion anomalies. Phys Rev E 2019; 100:042125. [PMID: 31770925 DOI: 10.1103/physreve.100.042125] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Single-particle tracking (SPT) is a versatile tool for quantifying diffusional motion in complex soft-matter systems, e.g., in biological specimen. Evaluating SPT data often invokes the fitting of a trajectory's time-averaged mean-square displacement (TA-MSD) with a simple power law, 〈r^{2}(τ)〉_{t}∼τ^{α}, where the scaling exponent α can yield important insights into the nature of the transport process. Biological specimen, for example, frequently feature a diffusion anomaly, i.e., an exponent α<1 ("subdiffusion"). However, due to SPT-inherent static and dynamic localization errors, in combination with typically short trajectories, it is often a real challenge to determine the value of α reliably by simply fitting TA-MSDs. Here a straightforward resampling approach is presented and tested that eliminates both localization errors in the TA-MSD of trajectories originating from subdiffusive fractional Brownian motion processes. As a result, the mean anomaly exponent 〈α〉_{E} of an ensemble of trajectories is revealed in a robust fashion.
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Affiliation(s)
- Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
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20
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Study on intracellular delivery of liposome encapsulated quantum dots using advanced fluorescence microscopy. Sci Rep 2019; 9:10504. [PMID: 31324829 PMCID: PMC6642191 DOI: 10.1038/s41598-019-46732-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Quantum dots increasingly gain popularity for in vivo applications. However, their delivery and accumulation into cells can be challenging and there is still lack of detailed information. Thereby, the application of advanced fluorescence techniques can expand the portfolio of useful parameters for a more comprehensive evaluation. Here, we encapsulated hydrophilic quantum dots into liposomes for studying cellular uptake of these so-called lipodots into living cells. First, we investigated photophysical properties of free quantum dots and lipodots observing changes in the fluorescence decay time and translational diffusion behaviour. In comparison to empty liposomes, lipodots exhibited an altered zeta potential, whereas their hydrodynamic size did not change. Fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), both combined with two-photon excitation (2P), were used to investigate the interaction behaviour of lipodots with an insect epithelial tissue. In contrast to the application of free quantum dots, their successful delivery into the cytosol of salivary gland duct cells could be observed when applying lipodots. Lipodots with different lipid compositions and surface charges did not result in considerable differences in the intracellular labelling pattern, luminescence decay time and diffusion behaviour. However, quantum dot degradation after intracellular accumulation could be assumed from reduced luminescence decay times and blue-shifted luminescence signals. In addition to single diffusing quantum dots, possible intracellular clustering of quantum dots could be assumed from increased diffusion times. Thus, by using a simple and manageable liposome carrier system, 2P-FLIM and 2P-FCS recording protocols could be tested, which are promising for investigating the fate of quantum dots during cellular interaction.
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21
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Recent advances in optical microscopic methods for single-particle tracking in biological samples. Anal Bioanal Chem 2019; 411:4445-4463. [PMID: 30790020 DOI: 10.1007/s00216-019-01638-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022]
Abstract
With the rapid development of optical microscopic techniques, explorations on the chemical and biological properties of target objects in biological samples at single-molecule/particle level have received great attention recently. In the past decades, various powerful techniques have been developed for single-particle tracking (SPT) in biological samples. In this review, we summarize the commonly used optical microscopic methods for SPT, such as total internal reflection fluorescence microscopy (TIRFM), super-resolution fluorescence microscopy (SRM), dark-field optical microscopy (DFM), total internal reflection scattering microscopy (TIRSM), and differential interference contrast microscopy (DICM). We then discuss the image processing and data analysis methods, including particle localization, trajectory reconstruction, and diffusion behavior analysis. The application of SPT on the cell membrane, within the cell, and the cellular invading process of viruses are introduced. Finally, the challenges and prospects of optical microscopic technologies for SPT are delineated.
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22
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Imaging transcription factors dynamics with advanced fluorescence microscopy methods. Mech Dev 2018; 154:60-63. [DOI: 10.1016/j.mod.2018.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 01/18/2023]
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23
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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24
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Microrheology, advances in methods and insights. Adv Colloid Interface Sci 2018; 257:71-85. [PMID: 29859615 DOI: 10.1016/j.cis.2018.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/23/2018] [Accepted: 04/14/2018] [Indexed: 01/19/2023]
Abstract
Microrheology is an emerging technique that probes mechanical response of soft material at micro-scale. Generally, microrheology technique can be divided into active and passive versions. During last two decades, extensive efforts have been paid to improve both the experiment techniques and data analysis methods, especially about how to link consequential particle positions into trajectories. We review the recent advances in microrheology, including improvements in labeling, imaging, data acquiring, data processing and data interpretation. Some of the recent insights in soft matter and living systems gained by using this technique are given. Before these, we also give a very brief description of the basic principles of both active and passive microrheology techniques, and some details about optical particle tracking and DWS.
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25
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Stortz M, Angiolini J, Mocskos E, Wolosiuk A, Pecci A, Levi V. Mapping the dynamical organization of the cell nucleus through fluorescence correlation spectroscopy. Methods 2018; 140-141:10-22. [DOI: 10.1016/j.ymeth.2017.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/01/2017] [Accepted: 12/13/2017] [Indexed: 11/28/2022] Open
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26
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Zhou Y, Zammit P, Carles G, Harvey AR. Computational localization microscopy with extended axial range. OPTICS EXPRESS 2018; 26:7563-7577. [PMID: 29609310 DOI: 10.1364/oe.26.007563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
A new single-aperture 3D particle-localization and tracking technique is presented that demonstrates an increase in depth range by more than an order of magnitude without compromising optical resolution and throughput. We exploit the extended depth range and depth-dependent translation of an Airy-beam PSF for 3D localization over an extended volume in a single snapshot. The technique is applicable to all bright-field and fluorescence modalities for particle localization and tracking, ranging from super-resolution microscopy through to the tracking of fluorescent beads and endogenous particles within cells. We demonstrate and validate its application to real-time 3D velocity imaging of fluid flow in capillaries using fluorescent tracer beads. An axial localization precision of 50 nm was obtained over a depth range of 120μm using a 0.4NA, 20× microscope objective. We believe this to be the highest ratio of axial range-to-precision reported to date.
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27
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Transient Acceleration of Epidermal Growth Factor Receptor Dynamics Produces Higher-Order Signaling Clusters. J Mol Biol 2018; 430:1386-1401. [PMID: 29505756 DOI: 10.1016/j.jmb.2018.02.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 01/25/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Cell signaling depends on spatiotemporally regulated molecular interactions. Although the movements of signaling proteins have been analyzed with various technologies, how spatial dynamics influence the molecular interactions that transduce signals is unclear. Here, we developed a single-molecule method to analyze the spatiotemporal coupling between motility, clustering, and signaling. The analysis was performed with the epidermal growth factor receptor (EGFR), which triggers signaling through its dimerization and phosphorylation after association with EGF. Our results show that the few EGFRs isolated in membrane subdomains were released by an EGF-dependent increase in their diffusion area, facilitating molecular associations and producing immobile clusters. Using a two-color single-molecule analysis, we found that the EGF-induced state transition alters the properties of the immobile clusters, allowing them to interact for extended periods with the cytoplasmic protein, GRB2. Our study reveals a novel correlation between this molecular interaction and its mesoscale dynamics, providing the initial signaling node.
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28
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Abstract
The question of how noncoding RNAs are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding RNA into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.
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Affiliation(s)
- Leonie Ringrose
- Integrated Research Institute for Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
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29
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Vyšniauskas A, Ding D, Qurashi M, Boczarow I, Balaz M, Anderson HL, Kuimova MK. Tuning the Sensitivity of Fluorescent Porphyrin Dimers to Viscosity and Temperature. Chemistry 2017; 23:11001-11010. [PMID: 28480989 PMCID: PMC5575558 DOI: 10.1002/chem.201700740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 01/04/2023]
Abstract
Conjugated porphyrin dimers have emerged as versatile viscosity-sensitive fluorophores that are suitable for quantitative measurements of microscopic viscosity by ratiometric and fluorescence lifetime-based methods, in a concentration-independent manner. Here, we investigate the effect of extended conjugation in a porphyrin-dimer structure on their ability to sense viscosity and temperature. We show that the sensitivity of the fluorescence lifetime to temperature is a unique property of only a few porphyrin dimers.
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Affiliation(s)
| | - Dong Ding
- Chemistry DepartmentImperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Maryam Qurashi
- Chemistry DepartmentImperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Igor Boczarow
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Milan Balaz
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Present address: Underwood International College, Integrated Science and Engineering DivisionYonsei UniversitySeoul03722Republic of Korea
| | - Harry L. Anderson
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Marina K. Kuimova
- Chemistry DepartmentImperial College LondonExhibition RoadLondonSW7 2AZUK
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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31
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Dissecting chromatin-mediated gene regulation and epigenetic memory through mathematical modelling. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Samadikhah HR, Nikkhah M, Hosseinkhani S. Enhancement of cell internalization and photostability of red and green emitter quantum dots upon entrapment in novel cationic nanoliposomes. LUMINESCENCE 2016; 32:517-528. [DOI: 10.1002/bio.3207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/11/2016] [Accepted: 08/02/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Hamid Reza Samadikhah
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
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An Intermittent Model for Intracellular Motions of Gold Nanostars by k-Space Scattering Image Correlation. Biophys J 2016; 109:2246-58. [PMID: 26636936 DOI: 10.1016/j.bpj.2015.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022] Open
Abstract
Anisotropic metallic nanoparticles have been devised as powerful potential tools for in vivo imaging, photothermal therapy, and drug delivery thanks to plasmon-enhanced absorption and scattering cross sections, ease in synthesis and functionalization, and controlled cytotoxicity. The rational design of all these applications requires the characterization of the nanoparticles intracellular trafficking pathways. In this work, we exploit live-cell time-lapse confocal reflectance microscopy and image correlation in both direct and reciprocal space to investigate the intracellular transport of branched gold nanostars (GNSs). Different transport mechanisms, spanning from pure Brownian diffusion to (sub-)ballistic superdiffusion, are revealed by temporal and spatio-temporal image correlation spectroscopy on the tens-of-seconds timescale. According to these findings, combined with numerical simulations and with a Bayesian (hidden Markov model-based) analysis of single particle tracking data, we ascribe the superdiffusive, subballistic behavior characterizing the GNSs dynamics to a two-state switching between Brownian diffusion in the cytoplasm and molecular motor-mediated active transport. For the investigation of intermittent-type transport phenomena, we derive an analytical theoretical framework for Fourier-space image correlation spectroscopy (kICS). At first, we evaluate the influence of all the dynamic and kinetic parameters (the diffusion coefficient, the drift velocity, and the transition rates between the diffusive and the active transport regimes) on simulated kICS correlation functions. Then we outline a protocol for data analysis and employ it to derive whole-cell maps for each parameter underlying the GNSs intracellular dynamics. Capable of identifying even simpler transport phenomena, whether purely diffusive or ballistic, our intermittent kICS approach allows an exhaustive investigation of the dynamics of GNSs and biological macromolecules.
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Seebach J, Cao J, Schnittler HJ. Quantitative dynamics of VE-cadherin at endothelial cell junctions at a glance: basic requirements and current concepts. Discoveries (Craiova) 2016; 4:e63. [PMID: 32309583 PMCID: PMC7159836 DOI: 10.15190/d.2016.10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intercellular junctions of the vascular endothelium are dynamic structures that display a high degree of plasticity, which is required to contribute to their regulation of many physiological and pathological processes including monolayer integrity, barrier function, wound healing and angiogenesis. Vascular endothelial cadherin (VE-cadherin) is connected via catenins to the actin cytoskeleton, both of which are key structures in endothelial junction regulation, and thus are the focus of much investigation. Fluorescence-based live cell imaging is the method of choice to study dynamic remodeling in living cells. Although these methods have been successfully applied to many cell types, investigations of endothelial junction dynamics were for a long time limited as they are largely resistant to transfection using many classical protocols. Application of virus-based gene transduction techniques, together with advanced microscopy, now allows both sufficient expression of fluorescence tagged junction-localized proteins in the endothelium and time-lapse recording over long periods. Using highly spatiotemporally resolved fluorescence microscopy it turned out that endothelial junctions display extensive junction heterogeneity at the subcellular level; a fact that largely limits automated quantification by available software. Recent work describes open software tools to quantitatively analyze large amounts of fluorescence-based image data in either single or confluent epithelial and endothelial cells. Based on quantitative VE-cadherin and actin dynamics novel key players, mechanisms and concepts have been suggested that control endothelial junction dynamics. Here we aim to summarize the recent developments in the field.
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Affiliation(s)
- Jochen Seebach
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster Germany
| | - Jiahui Cao
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster Germany
| | - Hans Joachim Schnittler
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster Germany
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Vorontsova MA, Vekilov PG, Maes D. Characterization of the diffusive dynamics of particles with time-dependent asymmetric microscopy intensity profiles. SOFT MATTER 2016; 12:6926-6936. [PMID: 27489111 DOI: 10.1039/c6sm00946h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We put forth an algorithm to track isolated micron-size solid and liquid particles that produce time-dependent asymmetric intensity patterns. This method quantifies the displacement of a particle in the image plane from the peak of a spatial cross-correlation function with a reference image. The peak sharpness results in subpixel resolution. We demonstrate the utility of the method for tracking liquid droplets with changing shapes and micron-size particles producing images with exaggerated asymmetry. We compare the accuracy of diffusivity determination with particles of known size by this method to that by common tracking techniques and demonstrate that our algorithm is superior. We address several open questions on the characterization of diffusive behaviors. We show that for particles, diffusing with a root-mean-square displacement of 0.6 pixel widths in the time between two successive recorded frames, more accurate diffusivity determinations result from mean squared displacement (MSD) for lag times up to 5 time intervals and that MSDs determined from non-overlapping displacements do not yield more accurate diffusivities. We discuss the optimal length of image sequences and demonstrate that lower frame rates do not affect the accuracy of the estimated diffusivity.
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Affiliation(s)
- Maria A Vorontsova
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA. and Department of Chemistry, University of Houston, Houston, Texas 77204, USA
| | - Dominique Maes
- Structural Biology Brussels, SBB, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
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36
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Emmert M, Witzel P, Heinrich D. Challenges in tissue engineering - towards cell control inside artificial scaffolds. SOFT MATTER 2016; 12:4287-4294. [PMID: 27139622 DOI: 10.1039/c5sm02844b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Control of living cells is vital for the survival of organisms. Each cell inside an organism is exposed to diverse external mechano-chemical cues, all coordinated in a spatio-temporal pattern triggering individual cell functions. This complex interplay between external chemical cues and mechanical 3D environments is translated into intracellular signaling loops. Here, we describe how external mechano-chemical cues control cell functions, especially cell migration, and influence intracellular information transport. In particular, this work focuses on the quantitative analysis of (1) intracellular vesicle transport to understand intracellular state changes in response to external cues, (2) cellular sensing of external chemotactic cues, and (3) the cells' ability to migrate in 3D structured environments, artificially fabricated to mimic the 3D environment of tissue in the human body.
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Affiliation(s)
- M Emmert
- Fraunhofer Institute for Silicate Research ISC, Neunerplatz 2, 97082 Würzburg, Germany. and Julius-Maximilians University Würzburg, Chemical Technology of Material Synthesis, Röntgenring 11, 97070 Würzburg, Germany
| | - P Witzel
- Fraunhofer Institute for Silicate Research ISC, Neunerplatz 2, 97082 Würzburg, Germany. and Julius-Maximilians University Würzburg, Chemical Technology of Material Synthesis, Röntgenring 11, 97070 Würzburg, Germany
| | - D Heinrich
- Fraunhofer Institute for Silicate Research ISC, Neunerplatz 2, 97082 Würzburg, Germany. and Leiden Institute of Physics LION, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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Javer A, Lagomarsino MC, Cicuta P. Bacterial Chromosome Dynamics by Locus Tracking in Fluorescence Microscopy. Methods Mol Biol 2016; 1431:161-173. [PMID: 27283309 DOI: 10.1007/978-1-4939-3631-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial chromosomes have been shown in the last two decades to have remarkable spatial organization at various scales, and also well-defined movements during the cell cycle, for example, to reliably segregate daughter chromosomes. More recently, various labs have begun investigating the short-time dynamics (displacements during time intervals of 0.1-100 s), which one hopes to link to structure, in analogy to "microrheology" approaches applied successfully to study mechanical response of complex fluids. These studies of chromosome fluctuation dynamics have revealed differences of fluctuation amplitude across the chromosome, and different characters of motion depending on the time window of interest. The highly nontrivial motion at the shortest experimentally accessible times is still not fully understood in terms of physical models of DNA and cytosol. We describe how to carry out tracking experiments of single locus and how to analyze locus motility. We point out the importance of considering in the analysis the number of GFP molecules per fluorescent locus.
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Affiliation(s)
- Avelino Javer
- Cavendish Laboratory, University of Cambridge, Room 237, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | | | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Room 237, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK.
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39
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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40
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Pärnaste L, Arukuusk P, Zagato E, Braeckmans K, Langel Ü. Methods to follow intracellular trafficking of cell-penetrating peptides. J Drug Target 2015; 24:508-19. [DOI: 10.3109/1061186x.2015.1095194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ly Pärnaste
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Tartu, Estonia,
| | - Piret Arukuusk
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Tartu, Estonia,
| | - Elisa Zagato
- Laboratory for General Biochemistry and Physical Pharmacy, Ghent, University, Gent, Belgium, and
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Ghent, University, Gent, Belgium, and
| | - Ülo Langel
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Tartu, Estonia,
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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41
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Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice. Q Rev Biophys 2015; 48:323-87. [PMID: 26314367 DOI: 10.1017/s0033583515000013] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AbstractFluorescence recovery after photobleaching (FRAP) is a versatile tool for determining diffusion and interaction/binding properties in biological and material sciences. An understanding of the mechanisms controlling the diffusion requires a deep understanding of structure–interaction–diffusion relationships. In cell biology, for instance, this applies to the movement of proteins and lipids in the plasma membrane, cytoplasm and nucleus. In industrial applications related to pharmaceutics, foods, textiles, hygiene products and cosmetics, the diffusion of solutes and solvent molecules contributes strongly to the properties and functionality of the final product. All these systems are heterogeneous, and accurate quantification of the mass transport processes at the local level is therefore essential to the understanding of the properties of soft (bio)materials. FRAP is a commonly used fluorescence microscopy-based technique to determine local molecular transport at the micrometer scale. A brief high-intensity laser pulse is locally applied to the sample, causing substantial photobleaching of the fluorescent molecules within the illuminated area. This causes a local concentration gradient of fluorescent molecules, leading to diffusional influx of intact fluorophores from the local surroundings into the bleached area. Quantitative information on the molecular transport can be extracted from the time evolution of the fluorescence recovery in the bleached area using a suitable model. A multitude of FRAP models has been developed over the years, each based on specific assumptions. This makes it challenging for the non-specialist to decide which model is best suited for a particular application. Furthermore, there are many subtleties in performing accurate FRAP experiments. For these reasons, this review aims to provide an extensive tutorial covering the essential theoretical and practical aspects so as to enable accurate quantitative FRAP experiments for molecular transport measurements in soft (bio)materials.
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42
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Sanchez L, Patton P, Anthony SM, Yi Y, Yu Y. Tracking single-particle rotation during macrophage uptake. SOFT MATTER 2015; 11:5346-52. [PMID: 26059797 PMCID: PMC4657870 DOI: 10.1039/c5sm00893j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We investigated the rotational dynamics of single microparticles during their internalization by macrophage cells. The microparticles used were triblock patchy particles that display two fluorescent patches on their two poles. The optical anisotropy made it possible to directly visualize and quantify the orientation and rotation of the particles. We show that particles exhibit a mixture of fast and slow rotation as they are uptaken by macrophages and transiently undergo directional rotation during their entry into the cell. The size of the particles and the surface presentation of ligands exerted a negligible influence on this heterogeneity of particle rotation.
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Affiliation(s)
- Lucero Sanchez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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43
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Oxygen depletion speeds and simplifies diffusion in HeLa cells. Biophys J 2015; 107:1873-1884. [PMID: 25418168 DOI: 10.1016/j.bpj.2014.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 12/28/2022] Open
Abstract
Many cell types undergo a hypoxic response in the presence of low oxygen, which can lead to transcriptional, metabolic, and structural changes within the cell. Many biophysical studies to probe the localization and dynamics of single fluorescently labeled molecules in live cells either require or benefit from low-oxygen conditions. In this study, we examine how low-oxygen conditions alter the mobility of a series of plasma membrane proteins with a range of anchoring motifs in HeLa cells at 37°C. Under high-oxygen conditions, diffusion of all proteins is heterogeneous and confined. When oxygen is reduced with an enzymatic oxygen-scavenging system for ≥ 15 min, diffusion rates increase by > 2-fold, motion becomes unconfined on the timescales and distance scales investigated, and distributions of diffusion coefficients are remarkably consistent with those expected from Brownian motion. More subtle changes in protein mobility are observed in several other laboratory cell lines examined under both high- and low-oxygen conditions. Morphological changes and actin remodeling are observed in HeLa cells placed in a low-oxygen environment for 30 min, but changes are less apparent in the other cell types investigated. This suggests that changes in actin structure are responsible for increased diffusion in hypoxic HeLa cells, although superresolution localization measurements in chemically fixed cells indicate that membrane proteins do not colocalize with F-actin under either experimental condition. These studies emphasize the importance of controls in single-molecule imaging measurements, and indicate that acute response to low oxygen in HeLa cells leads to dramatic changes in plasma membrane structure. It is possible that these changes are either a cause or consequence of phenotypic changes in solid tumor cells associated with increased drug resistance and malignancy.
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Anzalone A, Gabriel M, Estrada LC, Gratton E. Spectral properties of single gold nanoparticles in close proximity to biological fluorophores excited by 2-photon excitation. PLoS One 2015; 10:e0124975. [PMID: 25909648 PMCID: PMC4409109 DOI: 10.1371/journal.pone.0124975] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/19/2015] [Indexed: 11/29/2022] Open
Abstract
Metallic nanoparticles (NPs) are able to modify the excitation and emission rates (plasmonic enhancement) of fluorescent molecules in their close proximity. In this work, we measured the emission spectra of 20 nm Gold Nanoparticles (AuNPs) fixed on a glass surface submerged in a solution of different fluorophores using a spectral camera and 2-photon excitation. While on the glass surface, we observed the presence in the emission at least 3 components: i) second harmonic signal (SHG), ii) a broad emission from AuNPS and iii) fluorescence arising from fluorophores nearby. When on the glass surface, we found that the 3 spectral components have different relative intensities when the incident direction of linear polarization was changed indicating different physical origins for these components. Then we measured by fluctuation correlation spectroscopy (FCS) the scattering and fluorescence signal of the particles alone and in a solution of 100 nM EGFP using the spectral camera or measuring the scattering and fluorescence from the particles. We observed occasional fluorescence bursts when in the suspension we added fluorescent proteins. The spectrum of these burst was devoid of the SHG and of the broad emission in contrast to the signal collected from the gold nanoparticles on the glass surface. Instead we found that the spectrum during the burst corresponded closely to the spectrum of the fluorescent protein. An additional control was obtained by measuring the cross-correlation between the reflection from the particles and the fluorescence arising from EGFP both excited at 488 nm. We found a very weak cross-correlation between the AuNPs and the fluorescence confirming that the burst originate from a few particles with a fluorescence signal.
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Affiliation(s)
- Andrea Anzalone
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Manuela Gabriel
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Laura C. Estrada
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
- Centre for Bioactive Discovery in Health and Ageing, School of Science & Technology, University of New England, Armidale, Australia
- * E-mail:
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Lateral motion and bending of microtubules studied with a new single-filament tracking routine in living cells. Biophys J 2015; 106:2625-35. [PMID: 24940780 DOI: 10.1016/j.bpj.2014.04.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 04/07/2014] [Accepted: 04/18/2014] [Indexed: 12/24/2022] Open
Abstract
The cytoskeleton is involved in numerous cellular processes such as migration, division, and contraction and provides the tracks for transport driven by molecular motors. Therefore, it is very important to quantify the mechanical behavior of the cytoskeletal filaments to get a better insight into cell mechanics and organization. It has been demonstrated that relevant mechanical properties of microtubules can be extracted from the analysis of their motion and shape fluctuations. However, tracking individual filaments in living cells is extremely complex due, for example, to the high and heterogeneous background. We introduce a believed new tracking algorithm that allows recovering the coordinates of fluorescent microtubules with ∼9 nm precision in in vitro conditions. To illustrate potential applications of this algorithm, we studied the curvature distributions of fluorescent microtubules in living cells. By performing a Fourier analysis of the microtubule shapes, we found that the curvatures followed a thermal-like distribution as previously reported with an effective persistence length of ∼20 μm, a value significantly smaller than that measured in vitro. We also verified that the microtubule-associated protein XTP or the depolymerization of the actin network do not affect this value; however, the disruption of intermediate filaments decreased the persistence length. Also, we recovered trajectories of microtubule segments in actin or intermediate filament-depleted cells, and observed a significant increase of their motion with respect to untreated cells showing that these filaments contribute to the overall organization of the microtubule network. Moreover, the analysis of trajectories of microtubule segments in untreated cells showed that these filaments presented a slower but more directional motion in the cortex with respect to the perinuclear region, and suggests that the tracking routine would allow mapping the microtubule dynamical organization in cells.
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Marchetti L, Luin S, Bonsignore F, de Nadai T, Beltram F, Cattaneo A. Ligand-induced dynamics of neurotrophin receptors investigated by single-molecule imaging approaches. Int J Mol Sci 2015; 16:1949-79. [PMID: 25603178 PMCID: PMC4307343 DOI: 10.3390/ijms16011949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.
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Affiliation(s)
- Laura Marchetti
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Stefano Luin
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Fulvio Bonsignore
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Teresa de Nadai
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
| | - Fabio Beltram
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Antonino Cattaneo
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
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Vyšniauskas A, Balaz M, Anderson HL, Kuimova MK. Dual mode quantitative imaging of microscopic viscosity using a conjugated porphyrin dimer. Phys Chem Chem Phys 2015; 17:7548-54. [DOI: 10.1039/c5cp00439j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We report a deep red emitting dual viscosity sensor, which allows both the ratiometric and the lifetime imaging of viscosity.
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Affiliation(s)
| | - Milan Balaz
- Chemistry Research Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | - Harry L. Anderson
- Chemistry Research Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
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Griesemer M, Young C, Robinson AS, Petzold L. BiP clustering facilitates protein folding in the endoplasmic reticulum. PLoS Comput Biol 2014; 10:e1003675. [PMID: 24991821 PMCID: PMC4081015 DOI: 10.1371/journal.pcbi.1003675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 05/03/2014] [Indexed: 12/26/2022] Open
Abstract
The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.
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Affiliation(s)
- Marc Griesemer
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States of America
- * E-mail:
| | - Carissa Young
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Anne S. Robinson
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Linda Petzold
- Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America
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Huefner A, Septiadi D, Wilts BD, Patel II, Kuan WL, Fragniere A, Barker RA, Mahajan S. Gold nanoparticles explore cells: Cellular uptake and their use as intracellular probes. Methods 2014; 68:354-63. [DOI: 10.1016/j.ymeth.2014.02.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/24/2014] [Accepted: 02/06/2014] [Indexed: 12/22/2022] Open
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Precisely and accurately localizing single emitters in fluorescence microscopy. Nat Methods 2014; 11:253-66. [PMID: 24577276 DOI: 10.1038/nmeth.2843] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/21/2014] [Indexed: 12/19/2022]
Abstract
Methods based on single-molecule localization and photophysics have brought nanoscale imaging with visible light into reach. This has enabled single-particle tracking applications for studying the dynamics of molecules and nanoparticles and contributed to the recent revolution in super-resolution localization microscopy techniques. Crucial to the optimization of such methods are the precision and accuracy with which single fluorophores and nanoparticles can be localized. We present a lucid synthesis of the developments on this localization precision and accuracy and their practical implications in order to guide the increasing number of researchers using single-particle tracking and super-resolution localization microscopy.
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