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Bradley JJ, Martinez VA, Arlt J, Royer JR, Poon WCK. Sizing multimodal suspensions with differential dynamic microscopy. SOFT MATTER 2023; 19:8179-8192. [PMID: 37850499 PMCID: PMC10619199 DOI: 10.1039/d3sm00593c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Differential dynamic microscopy (DDM) can be used to extract the mean particle size from videos of suspensions. However, many suspensions have multimodal particle size distributions, for which a single 'mean' is not a sufficient description. After clarifying how different particle sizes contribute to the signal in DDM, we show that standard DDM analysis can extract the mean sizes of two populations in a bimodal suspension given prior knowledge of the sample's bimodality. Further, the use of the CONTIN algorithm obviates the need for such prior knowledge. Finally, we show that by selectively analysing portions of the DDM images, we can size a trimodal suspension where the large particles would otherwise dominate the signal, again without prior knowledge of the trimodality.
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Affiliation(s)
- Joe J Bradley
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Vincent A Martinez
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Jochen Arlt
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - John R Royer
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Wilson C K Poon
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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2
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Ma W, Balta VA, Pan W, Rimer JD, Sullivan DJ, Vekilov PG. Nonclassical mechanisms to irreversibly suppress β-hematin crystal growth. Commun Biol 2023; 6:783. [PMID: 37500754 PMCID: PMC10374632 DOI: 10.1038/s42003-023-05046-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
Hematin crystallization is an essential element of heme detoxification of malaria parasites and its inhibition by antimalarial drugs is a common treatment avenue. We demonstrate at biomimetic conditions in vitro irreversible inhibition of hematin crystal growth due to distinct cooperative mechanisms that activate at high crystallization driving forces. The evolution of crystal shape after limited-time exposure to both artemisinin metabolites and quinoline-class antimalarials indicates that crystal growth remains suppressed after the artemisinin metabolites and the drugs are purged from the solution. Treating malaria parasites with the same agents reveals that three- and six-hour inhibitor pulses inhibit parasite growth with efficacy comparable to that of inhibitor exposure during the entire parasite lifetime. Time-resolved in situ atomic force microscopy (AFM), complemented by light scattering, reveals two molecular-level mechanisms of inhibitor action that prevent β-hematin growth recovery. Hematin adducts of artemisinins incite copious nucleation of nonextendable nanocrystals, which incorporate into larger growing crystals, whereas pyronaridine, a quinoline-class drug, promotes step bunches, which evolve to engender abundant dislocations. Both incorporated crystals and dislocations are known to induce lattice strain, which persists and permanently impedes crystal growth. Nucleation, step bunching, and other cooperative behaviors can be amplified or curtailed as means to control crystal sizes, size distributions, aspect ratios, and other properties essential for numerous fields that rely on crystalline materials.
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Affiliation(s)
- Wenchuan Ma
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Victoria A Balta
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Weichun Pan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
- Department of Applied Chemistry, Zhejiang Gongshang University, Hangzhou, Zhejiang, 314423, China
| | - Jeffrey D Rimer
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA.
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA.
| | - David J Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Peter G Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA.
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA.
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Verwei HN, Lee G, Leech G, Petitjean II, Koenderink GH, Robertson-Anderson RM, McGorty RJ. Quantifying Cytoskeleton Dynamics Using Differential Dynamic Microscopy. J Vis Exp 2022:10.3791/63931. [PMID: 35781524 PMCID: PMC10398790 DOI: 10.3791/63931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Cells can crawl, self-heal, and tune their stiffness due to their remarkably dynamic cytoskeleton. As such, reconstituting networks of cytoskeletal biopolymers may lead to a host of active and adaptable materials. However, engineering such materials with precisely tuned properties requires measuring how the dynamics depend on the network composition and synthesis methods. Quantifying such dynamics is challenged by variations across the time, space, and formulation space of composite networks. The protocol here describes how the Fourier analysis technique, differential dynamic microscopy (DDM), can quantify the dynamics of biopolymer networks and is particularly well suited for studies of cytoskeleton networks. DDM works on time sequences of images acquired using a range of microscopy modalities, including laser-scanning confocal, widefield fluorescence, and brightfield imaging. From such image sequences, one can extract characteristic decorrelation times of density fluctuations across a span of wave vectors. A user-friendly, open-source Python package to perform DDM analysis is also developed. With this package, one can measure the dynamics of labeled cytoskeleton components or of embedded tracer particles, as demonstrated here with data of intermediate filament (vimentin) networks and active actin-microtubule networks. Users with no prior programming or image processing experience will be able to perform DDM using this software package and associated documentation.
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Affiliation(s)
- Hannah N Verwei
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University
| | - Gloria Lee
- Department of Physics and Biophysics, University of San Diego
| | - Gregor Leech
- Department of Physics and Biophysics, University of San Diego
| | - Irene Istúriz Petitjean
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology
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Yang DS, Saeedi A, Davtyan A, Fathi M, Sherman MB, Safari MS, Klindziuk A, Barton MC, Varadarajan N, Kolomeisky AB, Vekilov PG. Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils. Proc Natl Acad Sci U S A 2021; 118:e2015618118. [PMID: 33653952 PMCID: PMC7958401 DOI: 10.1073/pnas.2015618118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The protein p53 is a crucial tumor suppressor, often called "the guardian of the genome"; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.
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Affiliation(s)
- David S Yang
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Aram Davtyan
- Department of Chemistry, Rice University, Houston, TX 77251
| | - Mohsen Fathi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Mohammad S Safari
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, TX 77251
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77251
| | - Peter G Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204;
- Department of Chemistry, University of Houston, Houston, TX 77204
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Higler R, Frijns RAM, Sprakel J. Diffusion Decoupling in Binary Colloidal Systems Observed with Contrast Variation Multispeckle Diffusing Wave Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5793-5801. [PMID: 30955341 PMCID: PMC6495389 DOI: 10.1021/acs.langmuir.8b03745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/07/2019] [Indexed: 06/09/2023]
Abstract
In the study of colloidal glasses, crystallization is often suppressed by leveraging size polydispersity, ranging from systems where particle sizes exhibit a continuous distribution to systems composed of particles of two or more distinct sizes. The effects of the disparities in size of the particles on the colloidal glass transition are not yet completely understood. Especially, the question of the existence of a decoupled glass transition between the large and small population remains. In order to measure colloidal dynamics on very long time scales and to disentangle the dynamics of the two populations, we employ contrast variation multispeckle diffusing wave spectroscopy. With this method, we aim to analyze the effect of size ratio, a = rPS/ rpNIPAM, on particle dynamics near the glass transition of a binary colloidal system. We find that both for long-time (α-) and short-time (β-) relaxation, the dynamics of the small particles either completely decouple from the large ones ( a = 0.2), moving freely through a glassy matrix, or are identical to the dynamics of the larger-sized population ( a = 0.37 and 1.44). For a size ratio of 0.37, we find a single-glass transition for both particle populations. The postulated double-glass transition in simulations and theory is not observed.
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Affiliation(s)
- Ruben Higler
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Raoul A. M. Frijns
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE Wageningen, The Netherlands
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7
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Cerbino R. Quantitative optical microscopy of colloids: The legacy of Jean Perrin. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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