51
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Waigh TA. Advances in the microrheology of complex fluids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:074601. [PMID: 27245584 DOI: 10.1088/0034-4885/79/7/074601] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
New developments in the microrheology of complex fluids are considered. Firstly the requirements for a simple modern particle tracking microrheology experiment are introduced, the error analysis methods associated with it and the mathematical techniques required to calculate the linear viscoelasticity. Progress in microrheology instrumentation is then described with respect to detectors, light sources, colloidal probes, magnetic tweezers, optical tweezers, diffusing wave spectroscopy, optical coherence tomography, fluorescence correlation spectroscopy, elastic- and quasi-elastic scattering techniques, 3D tracking, single molecule methods, modern microscopy methods and microfluidics. New theoretical techniques are also reviewed such as Bayesian analysis, oversampling, inversion techniques, alternative statistical tools for tracks (angular correlations, first passage probabilities, the kurtosis, motor protein step segmentation etc), issues in micro/macro rheological agreement and two particle methodologies. Applications where microrheology has begun to make some impact are also considered including semi-flexible polymers, gels, microorganism biofilms, intracellular methods, high frequency viscoelasticity, comb polymers, active motile fluids, blood clots, colloids, granular materials, polymers, liquid crystals and foods. Two large emergent areas of microrheology, non-linear microrheology and surface microrheology are also discussed.
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Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Rd., Manchester, M13 9PL, UK. Photon Science Institute, University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
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52
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DeVore MS, Stich DG, Keller AM, Cleyrat C, Phipps ME, Hollingsworth JA, Lidke DS, Wilson BS, Goodwin PM, Werner JH. Note: Time-gated 3D single quantum dot tracking with simultaneous spinning disk imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:126102. [PMID: 26724083 PMCID: PMC4676784 DOI: 10.1063/1.4937477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We describe recent upgrades to a 3D tracking microscope to include simultaneous Nipkow spinning disk imaging and time-gated single-particle tracking (SPT). Simultaneous 3D molecular tracking and spinning disk imaging enable the visualization of cellular structures and proteins around a given fluorescently labeled target molecule. The addition of photon time-gating to the SPT hardware improves signal to noise by discriminating against Raman scattering and short-lived fluorescence. In contrast to camera-based SPT, single-photon arrival times are recorded, enabling time-resolved spectroscopy (e.g., measurement of fluorescence lifetimes and photon correlations) to be performed during single molecule/particle tracking experiments.
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Affiliation(s)
- M S DeVore
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - D G Stich
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - A M Keller
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - C Cleyrat
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - M E Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - J A Hollingsworth
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - D S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - B S Wilson
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - P M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
| | - J H Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop G755, Los Alamos, New Mexico 87545, USA
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54
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Anthony S, Carroll-Portillo A, Timlin J. Dynamics and Interactions of Individual Proteins in the Membrane of Single, Living Cells. Methods Mol Biol 2015; 1346:185-207. [PMID: 26542723 DOI: 10.1007/978-1-4939-2987-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Total internal reflection fluorescence (TIRF) microscopy is a powerful technique for interrogating protein dynamics in the membranes of living single cells. Receptor-ligand interactions are of particular interest for improving our understanding of cell signaling networks in a variety of applications. Here, we describe methods for fluorescently labeling individual receptors and their ligands, conducting single-molecule TIRF microscopy of receptors and ligands in single, living cells, and importantly, performing image analysis on the resulting time sequence of images to extract quantitative dynamics. While we use Toll-like receptor 4 and its ligand lipopolysaccharide as a specific example, the methods are general and readily extendable to other receptor-ligand systems of importance in cellular biology.
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Affiliation(s)
- Stephen Anthony
- Sandia National Laboratories, Bioenergy and Defense Technologies, 5800, Albuquerque, NM, 87185, USA
| | - Amanda Carroll-Portillo
- Sandia National Laboratories, Bioenergy and Defense Technologies, 5800, Albuquerque, NM, 87185, USA
| | - Jerilyn Timlin
- Sandia National Laboratories, Bioenergy and Defense Technologies, 5800, Albuquerque, NM, 87185, USA.
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55
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Ashley TT, Andersson SB. Method for simultaneous localization and parameter estimation in particle tracking experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052707. [PMID: 26651723 DOI: 10.1103/physreve.92.052707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 06/05/2023]
Abstract
We present a numerical method for the simultaneous localization and parameter estimation of a fluorescent particle undergoing a discrete-time continuous-state Markov process. In particular, implementation of the method proposed in this work yields an approximation to the posterior density of the particle positions over time in addition to maximum likelihood estimates of fixed, unknown parameters. The method employs sequential Monte Carlo methods and can take into account complex, potentially nonlinear noise models, including shot noise and camera-specific readout noise, as well as a wide variety of motion models and observation models, including those representing recent engineered point spread functions. We demonstrate the technique by applying it to four scenarios, including a particle undergoing free, confined, and tethered diffusions.
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Affiliation(s)
- Trevor T Ashley
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Division of Systems Engineering, Boston University, Boston, Massachusetts 02215, USA
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57
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Reisch A, Runser A, Arntz Y, Mély Y, Klymchenko AS. Charge-controlled nanoprecipitation as a modular approach to ultrasmall polymer nanocarriers: making bright and stable nanoparticles. ACS NANO 2015; 9:5104-5116. [PMID: 25894117 DOI: 10.1021/acsnano.5b00214] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ultrasmall polymer nanoparticles are rapidly gaining importance as nanocarriers for drugs and contrast agents. Here, a straightforward modular approach to efficiently loaded and stable sub-20-nm polymer particles is developed. In order to obtain ultrasmall polymer nanoparticles, we investigated the influence of one to two charged groups per polymer chain on the size of particles obtained by nanoprecipitation. Negatively charged carboxylate and sulfonate or positively charged trimethylammonium groups were introduced into the polymers poly(d,l-lactide-co-glycolide) (PLGA), polycaprolactone (PCL), and poly(methyl methacrylate) (PMMA). According to dynamic light scattering, atomic force and electron microscopy, the presence of one to two charged groups per polymer chain can strongly reduce the size of polymer nanoparticles made by nanoprecipitation. The particle size can be further decreased to less than 15 nm by decreasing the concentration of polymer in the solvent used for nanoprecipitation. We then show that even very small nanocarriers of 15 nm size preserve the capacity to encapsulate large amounts of ionic dyes with bulky counterions at efficiencies >90%, which generates polymer nanoparticles 10-fold brighter than quantum dots of the same size. Postmodification of their surface with the PEG containing amphiphiles Tween 80 and pluronic F-127 led to particles that were stable under physiological conditions and in the presence of 10% fetal bovine serum. This modular route could become a general method for the preparation of ultrasmall polymer nanoparticles as nanocarriers of contrast agents and drugs.
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Affiliation(s)
- Andreas Reisch
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Anne Runser
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Youri Arntz
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401 Illkirch, France
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60
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Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont JC, Mc Guire C, Nowack MK, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, VAN Brempt R, Visser Y, Guérin CJ. Developing 3D SEM in a broad biological context. J Microsc 2015; 259:80-96. [PMID: 25623622 PMCID: PMC4670703 DOI: 10.1111/jmi.12211] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/28/2014] [Indexed: 12/25/2022]
Abstract
When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.
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Affiliation(s)
- A Kremer
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - S Lippens
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - S Bartunkova
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - B Asselbergh
- VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - C Blanpain
- IRIBHM, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - M Fendrych
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.,Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - A Goossens
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - M Holt
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - S Janssens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Respiratory Medicine, Ghent University, Ghent, Belgium.,GROUP-ID Consortium, Ghent University and University Hospital, Ghent, Belgium
| | - M Krols
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - J-C Larsimont
- IRIBHM, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - C Mc Guire
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - M K Nowack
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - X Saelens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - A Schertel
- Carl Zeiss Microscopy, GmbH, Oberkochen, Germany
| | - B Schepens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - M Slezak
- Center for the Biology of Disease, VIB, Leuven, Belgium
| | - V Timmerman
- VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - C Theunis
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - R VAN Brempt
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - Y Visser
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - C J Guérin
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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