1
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Paupiah AL, Marques X, Merlaud Z, Russeau M, Levi S, Renner M. Introducing Diinamic, a flexible and robust method for clustering analysis in single-molecule localization microscopy. BIOLOGICAL IMAGING 2023; 3:e14. [PMID: 38487695 PMCID: PMC10936397 DOI: 10.1017/s2633903x23000156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/26/2023] [Accepted: 06/22/2023] [Indexed: 03/17/2024]
Abstract
Super-resolution microscopy allowed major improvements in our capacity to describe and explain biological organization at the nanoscale. Single-molecule localization microscopy (SMLM) uses the positions of molecules to create super-resolved images, but it can also provide new insights into the organization of molecules through appropriate pointillistic analyses that fully exploit the sparse nature of SMLM data. However, the main drawback of SMLM is the lack of analytical tools easily applicable to the diverse types of data that can arise from biological samples. Typically, a cloud of detections may be a cluster of molecules or not depending on the local density of detections, but also on the size of molecules themselves, the labeling technique, the photo-physics of the fluorophore, and the imaging conditions. We aimed to set an easy-to-use clustering analysis protocol adaptable to different types of data. Here, we introduce Diinamic, which combines different density-based analyses and optional thresholding to facilitate the detection of clusters. On simulated or real SMLM data, Diinamic correctly identified clusters of different sizes and densities, being performant even in noisy datasets with multiple detections per fluorophore. It also detected subdomains ("nanodomains") in clusters with non-homogeneous distribution of detections.
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Affiliation(s)
- Anne-Lise Paupiah
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Xavier Marques
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
- Museum National d’Histoire Naturelle, CNRS UMR 7196-INSERM U1154, Paris, France
| | - Zaha Merlaud
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Marion Russeau
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Sabine Levi
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Marianne Renner
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
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2
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Abstract
Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.
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Affiliation(s)
- Siewert Hugelier
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
| | - P L Colosi
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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He Y, Yao Y, Qi D, Wang Z, Jia T, Liang J, Sun Z, Zhang S. High-speed super-resolution imaging with compressive imaging-based structured illumination microscopy. OPTICS EXPRESS 2022; 30:14287-14299. [PMID: 35473175 DOI: 10.1364/oe.453554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Structured illumination microscopy (SIM) has been widely applied to investigating fine structures of biological samples by breaking the optical diffraction limitation. So far, video-rate imaging has been obtained in SIM, but the imaging speed was still limited due to the reconstruction of a super-solution image through multi-sampling, which hindered the applications in high-speed biomedical imaging. To overcome this limitation, here we develop compressive imaging-based structured illumination microscopy (CISIM) by synergizing SIM and compressive sensing (CS). Compared with conventional SIM, CISIM can greatly improve the super-resolution imaging speed by extracting multiple super-resolution images from one compressed image. Based on CISIM, we successfully reconstruct the super-resolution images in biological dynamics, and analyze the effect factors of image reconstruction quality, which verify the feasibility of CISIM. CISIM paves a way for high-speed super-resolution imaging, which may bring technological breakthroughs and significant applications in biomedical imaging.
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4
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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5
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Cebecauer M. A Tribute to Professor Katharina Gaus. FRONTIERS IN BIOINFORMATICS 2021; 1:801115. [PMID: 36303790 PMCID: PMC9580897 DOI: 10.3389/fbinf.2021.801115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
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6
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Kutz S, Zehrer AC, Svetlitckii R, Gülcüler Balta GS, Galli L, Kleber S, Rentsch J, Martin-Villalba A, Ewers H. An Efficient GUI-Based Clustering Software for Simulation and Bayesian Cluster Analysis of Single-Molecule Localization Microscopy Data. FRONTIERS IN BIOINFORMATICS 2021; 1:723915. [PMID: 36303736 PMCID: PMC9581037 DOI: 10.3389/fbinf.2021.723915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Ligand binding of membrane proteins triggers many important cellular signaling events by the lateral aggregation of ligand-bound and other membrane proteins in the plane of the plasma membrane. This local clustering can lead to the co-enrichment of molecules that create an intracellular signal or bring sufficient amounts of activity together to shift an existing equilibrium towards the execution of a signaling event. In this way, clustering can serve as a cellular switch. The underlying uneven distribution and local enrichment of the signaling cluster’s constituting membrane proteins can be used as a functional readout. This information is obtained by combining single-molecule fluorescence microscopy with cluster algorithms that can reliably and reproducibly distinguish clusters from fluctuations in the background noise to generate quantitative data on this complex process. Cluster analysis of single-molecule fluorescence microscopy data has emerged as a proliferative field, and several algorithms and software solutions have been put forward. However, in most cases, such cluster algorithms require multiple analysis parameters to be defined by the user, which may lead to biased results. Furthermore, most cluster algorithms neglect the individual localization precision connected to every localized molecule, leading to imprecise results. Bayesian cluster analysis has been put forward to overcome these problems, but so far, it has entailed high computational cost, increasing runtime drastically. Finally, most software is challenging to use as they require advanced technical knowledge to operate. Here we combined three advanced cluster algorithms with the Bayesian approach and parallelization in a user-friendly GUI and achieved up to an order of magnitude faster processing than for previous approaches. Our work will simplify access to a well-controlled analysis of clustering data generated by SMLM and significantly accelerate data processing. The inclusion of a simulation mode aids in the design of well-controlled experimental assays.
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Affiliation(s)
- Saskia Kutz
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Ando C. Zehrer
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | | | - Gülce S. Gülcüler Balta
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucrezia Galli
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne Kleber
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Rentsch
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helge Ewers
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Helge Ewers,
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7
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Multi-color Molecular Visualization of Signaling Proteins Reveals How C-Terminal Src Kinase Nanoclusters Regulate T Cell Receptor Activation. Cell Rep 2020; 33:108523. [PMID: 33357425 DOI: 10.1016/j.celrep.2020.108523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/07/2020] [Accepted: 11/24/2020] [Indexed: 11/22/2022] Open
Abstract
Elucidating the mechanisms that controlled T cell activation requires visualization of the spatial organization of multiple proteins on the submicron scale. Here, we use stoichiometrically accurate, multiplexed, single-molecule super-resolution microscopy (DNA-PAINT) to image the nanoscale spatial architecture of the primary inhibitor of the T cell signaling pathway, Csk, and two binding partners implicated in its membrane association, PAG and TRAF3. Combined with a newly developed co-clustering analysis framework, we find that Csk forms nanoscale clusters proximal to the plasma membrane that are lost post-stimulation and are re-recruited at later time points. Unexpectedly, these clusters do not co-localize with PAG at the membrane but instead provide a ready pool of monomers to downregulate signaling. By generating CRISPR-Cas9 knockout T cells, our data also identify that a major risk factor for autoimmune diseases, the protein tyrosine phosphatase non-receptor type 22 (PTPN22) locus, is essential for Csk nanocluster re-recruitment and for maintenance of the synaptic PAG population.
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8
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Nino DF, Djayakarsana D, Milstein JN. FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy. PLoS Comput Biol 2020; 16:e1008479. [PMID: 33290385 PMCID: PMC7748281 DOI: 10.1371/journal.pcbi.1008479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/18/2020] [Accepted: 10/30/2020] [Indexed: 12/03/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python. We have developed an accurate, highly-efficient and flexible algorithm for quantifying spatial clustering in large, 3-dimensional single-molecule localization microscopy (SMLM) datasets. Our method, FOCAL3D, is provided as an open-source software package written in Python. FOCAL3D scales linearly with the number of localizations and the algorithmic parameters may be systematically optimized so that the resulting analysis is insensitive to variation over a range of parameter choices. We initially validate the performance and parametric insensitivity of FOCAL3D on simulated datasets, then apply the algorithm to 3-dimensional, astigmatic dSTORM images of the nuclear pore complex in human osteosarcoma cells.
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Affiliation(s)
- Daniel F. Nino
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Daniel Djayakarsana
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joshua N. Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- * E-mail:
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9
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Spark A, Kitching A, Esteban-Ferrer D, Handa A, Carr AR, Needham LM, Ponjavic A, Santos AM, McColl J, Leterrier C, Davis SJ, Henriques R, Lee SF. vLUME: 3D virtual reality for single-molecule localization microscopy. Nat Methods 2020; 17:1097-1099. [PMID: 33046895 PMCID: PMC7612967 DOI: 10.1038/s41592-020-0962-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022]
Abstract
vLUME is a virtual reality software package designed to render large three-dimensional single-molecule localization microscopy datasets. vLUME features include visualization, segmentation, bespoke analysis of complex local geometries and exporting features. vLUME can perform complex analysis on real three-dimensional biological samples that would otherwise be impossible by using regular flat-screen visualization programs.
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Affiliation(s)
| | | | | | - Anoushka Handa
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | | | - Aleks Ponjavic
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Ana Mafalda Santos
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Simon J Davis
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, UK.
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10
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Pike JA, Khan AO, Pallini C, Thomas SG, Mund M, Ries J, Poulter NS, Styles IB. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics 2020; 36:1614-1621. [PMID: 31626286 PMCID: PMC7162425 DOI: 10.1093/bioinformatics/btz788] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 09/03/2019] [Accepted: 10/17/2019] [Indexed: 01/23/2023] Open
Abstract
Motivation Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure. Results We present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data. Availability and implementation RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Abdullah O Khan
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chiara Pallini
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Steven G Thomas
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.,Department of Biochemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Natalie S Poulter
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK
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11
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Khater IM, Nabi IR, Hamarneh G. A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods. PATTERNS (NEW YORK, N.Y.) 2020; 1:100038. [PMID: 33205106 PMCID: PMC7660399 DOI: 10.1016/j.patter.2020.100038] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule localization microscopy (SMLM) is a relatively new imaging modality, winning the 2014 Nobel Prize in Chemistry, and considered as one of the key super-resolution techniques. SMLM resolution goes beyond the diffraction limit of light microscopy and achieves resolution on the order of 10-20 nm. SMLM thus enables imaging single molecules and study of the low-level molecular interactions at the subcellular level. In contrast to standard microscopy imaging that produces 2D pixel or 3D voxel grid data, SMLM generates big data of 2D or 3D point clouds with millions of localizations and associated uncertainties. This unprecedented breakthrough in imaging helps researchers employ SMLM in many fields within biology and medicine, such as studying cancerous cells and cell-mediated immunity and accelerating drug discovery. However, SMLM data quantification and interpretation methods have yet to keep pace with the rapid advancement of SMLM imaging. Researchers have been actively exploring new computational methods for SMLM data analysis to extract biosignatures of various biological structures and functions. In this survey, we describe the state-of-the-art clustering methods adopted to analyze and quantify SMLM data and examine the capabilities and shortcomings of the surveyed methods. We classify the methods according to (1) the biological application (i.e., the imaged molecules/structures), (2) the data acquisition (such as imaging modality, dimension, resolution, and number of localizations), and (3) the analysis details (2D versus 3D, field of view versus region of interest, use of machine-learning and multi-scale analysis, biosignature extraction, etc.). We observe that the majority of methods that are based on second-order statistics are sensitive to noise and imaging artifacts, have not been applied to 3D data, do not leverage machine-learning formulations, and are not scalable for big-data analysis. Finally, we summarize state-of-the-art methodology, discuss some key open challenges, and identify future opportunities for better modeling and design of an integrated computational pipeline to address the key challenges.
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Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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12
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Griffié J, Peters R, Owen DM. An agent-based model of molecular aggregation at the cell membrane. PLoS One 2020; 15:e0226825. [PMID: 32032349 PMCID: PMC7006917 DOI: 10.1371/journal.pone.0226825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the plasma membrane. However, modelling approaches capable of recapitulating these observations are in their infancy, partly because of the extremely complex array of biophysical factors which influence molecular distributions and dynamics in the plasma membrane. We propose here a highly abstracted approach: an agent-based model dedicated to the study of molecular aggregation at the plasma membrane. We show that when molecules are modelled as though they can act (diffuse) in a manner which is influenced by their molecular neighbourhood, many of the distributions observed in cells can be recapitulated, even though such sensing and response is not possible for real membrane molecules. As such, agent-based offers a unique platform which may lead to a new understanding of how molecular clustering in extremely complex molecular environments can be abstracted, simulated and interpreted using simple rules.
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Affiliation(s)
- Juliette Griffié
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
- * E-mail: (JG); (DO)
| | - Ruby Peters
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
| | - Dylan M. Owen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
- * E-mail: (JG); (DO)
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13
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Shannon MJ, Pineau J, Griffié J, Aaron J, Peel T, Williamson DJ, Zamoyska R, Cope AP, Cornish GH, Owen DM. Differential nanoscale organisation of LFA-1 modulates T-cell migration. J Cell Sci 2019; 133:jcs.232991. [PMID: 31471459 PMCID: PMC7614863 DOI: 10.1242/jcs.232991] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
Effector T-cells rely on integrins to drive adhesion and migration to facilitate their immune function. The heterodimeric transmembrane integrin LFA-1 (αLβ2 integrin) regulates adhesion and migration of effector T-cells through linkage of the extracellular matrix with the intracellular actin treadmill machinery. Here, we quantified the velocity and direction of F-actin flow in migrating T-cells alongside single-molecule localisation of transmembrane and intracellular LFA-1. Results showed that actin retrograde flow positively correlated and immobile actin negatively correlated with T-cell velocity. Plasma membrane-localised LFA-1 forms unique nano-clustering patterns in the leading edge, compared to the mid-focal zone, of migrating T-cells. Deleting the cytosolic phosphatase PTPN22, loss-of-function mutations of which have been linked to autoimmune disease, increased T-cell velocity, and leading-edge co-clustering of pY397 FAK, pY416 Src family kinases and LFA-1. These data suggest that differential nanoclustering patterns of LFA-1 in migrating T-cells may instruct intracellular signalling. Our data presents a paradigm where T-cells modulate the nanoscale organisation of adhesion and signalling molecules to fine tune their migration speed, with implications for the regulation of immune and inflammatory responses.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Michael J Shannon
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Judith Pineau
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Juliette Griffié
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Jesse Aaron
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Tamlyn Peel
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - David J Williamson
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Rose Zamoyska
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Andrew P Cope
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - Georgina H Cornish
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - Dylan M Owen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK .,Institute of Immunology and Immunotherapy and Department of Mathematics and Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TQ, UK
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14
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Post RAJ, van der Zwaag D, Bet G, Wijnands SPW, Albertazzi L, Meijer EW, van der Hofstad RW. A stochastic view on surface inhomogeneity of nanoparticles. Nat Commun 2019; 10:1663. [PMID: 30971686 PMCID: PMC6458121 DOI: 10.1038/s41467-019-09595-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/19/2019] [Indexed: 01/16/2023] Open
Abstract
The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage. Determining the spatial arrangement of molecules on a nanoparticle’s surface is key to understanding its interactions. Here, the authors use dSTORM imaging and probabilistic modelling to map the distribution of fluorophores on a nanoparticle, finding that ligand coverage is heterogeneous and highly variable between individual particles.
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Affiliation(s)
- R A J Post
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - D van der Zwaag
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,DSM Coating Resins, P.O. Box 123, 5145 PE, Waalwijk, The Netherlands
| | - G Bet
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science 'Ulisse Dini', University of Florence, 50134, Florence, Italy
| | - S P W Wijnands
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - L Albertazzi
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - E W Meijer
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - R W van der Hofstad
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
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15
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Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. PLoS Comput Biol 2019; 15:e1006199. [PMID: 30689627 PMCID: PMC6366722 DOI: 10.1371/journal.pcbi.1006199] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 02/07/2019] [Accepted: 11/20/2018] [Indexed: 11/19/2022] Open
Abstract
Within influenza virus infected cells, viral genomic RNA are selectively packed into progeny virions, which predominantly contain a single copy of 8 viral RNA segments. Intersegmental RNA-RNA interactions are thought to mediate selective packaging of each viral ribonucleoprotein complex (vRNP). Clear evidence of a specific interaction network culminating in the full genomic set has yet to be identified. Using multi-color fluorescence in situ hybridization to visualize four vRNP segments within a single cell, we developed image-based models of vRNP-vRNP spatial dependence. These models were used to construct likely sequences of vRNP associations resulting in the full genomic set. Our results support the notion that selective packaging occurs during cytoplasmic transport and identifies the formation of multiple distinct vRNP sub-complexes that likely form as intermediate steps toward full genomic inclusion into a progeny virion. The methods employed demonstrate a statistically driven, model based approach applicable to other interaction and assembly problems.
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16
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Peters R, Griffié J, Burn GL, Williamson DJ, Owen DM. Quantitative fibre analysis of single-molecule localization microscopy data. Sci Rep 2018; 8:10418. [PMID: 29991683 PMCID: PMC6039472 DOI: 10.1038/s41598-018-28691-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/21/2018] [Indexed: 11/18/2022] Open
Abstract
Single molecule localization microscopy (SMLM) methods produce data in the form of a spatial point pattern (SPP) of all localized emitters. Whilst numerous tools exist to quantify molecular clustering in SPP data, the analysis of fibrous structures has remained understudied. Taking the SMLM localization coordinates as input, we present an algorithm capable of tracing fibrous structures in data generated by SMLM. Based upon a density parameter tracing routine, the algorithm outputs several fibre descriptors, such as number of fibres, length of fibres, area of enclosed regions and locations and angles of fibre branch points. The method is validated in a variety of simulated conditions and experimental data acquired using the image reconstruction by integrating exchangeable single-molecule localization (IRIS) technique. For this, the nanoscale architecture of F-actin at the T cell immunological synapse in both untreated and pharmacologically treated cells, designed to perturb actin structure, was analysed.
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Affiliation(s)
- Ruby Peters
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
| | - Juliette Griffié
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Garth L Burn
- Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - David J Williamson
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
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17
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Khater IM, Meng F, Wong TH, Nabi IR, Hamarneh G. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Sci Rep 2018; 8:9009. [PMID: 29899348 PMCID: PMC5998020 DOI: 10.1038/s41598-018-27216-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/24/2018] [Indexed: 12/04/2022] Open
Abstract
Quantitative approaches to analyze the large data sets generated by single molecule localization super-resolution microscopy (SMLM) are limited. We developed a computational pipeline and applied it to analyzing 3D point clouds of SMLM localizations (event lists) of the caveolar coat protein, caveolin-1 (Cav1), in prostate cancer cells differentially expressing CAVIN1 (also known as PTRF), that is also required for caveolae formation. High degree (strongly-interacting) points were removed by an iterative blink merging algorithm and Cav1 network properties were compared with randomly generated networks to retain a sub-network of geometric structures (or blobs). Machine-learning based classification extracted 28 quantitative features describing the size, shape, topology and network characteristics of ∼80,000 blobs. Unsupervised clustering identified small S1A scaffolds corresponding to SDS-resistant Cav1 oligomers, as yet undescribed larger hemi-spherical S2 scaffolds and, only in CAVIN1-expressing cells, spherical, hollow caveolae. Multi-threshold modularity analysis suggests that S1A scaffolds interact to form larger scaffolds and that S1A dimers group together, in the presence of CAVIN1, to form the caveolae coat.
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Affiliation(s)
- Ismail M Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fanrui Meng
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Timothy H Wong
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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18
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Raghunathan K, Kenworthy AK. Dynamic pattern generation in cell membranes: Current insights into membrane organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2018-2031. [PMID: 29752898 DOI: 10.1016/j.bbamem.2018.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
It has been two decades since the lipid raft hypothesis was first presented. Even today, whether these nanoscale cholesterol-rich domains are present in cell membranes is not completely resolved. However, especially in the last few years, a rich body of literature has demonstrated both the presence and the importance of non-random distribution of biomolecules on the membrane, which is the focus of this review. These new developments have pushed the experimental limits of detection and have brought us closer to observing lipid domains in the plasma membrane of live cells. Characterization of biomolecules associated with lipid rafts has revealed a deep connection between biological regulation and function and membrane compositional heterogeneities. Finally, tantalizing new developments in the field have demonstrated that lipid domains might not just be associated with the plasma membrane of eukaryotes but could potentially be a ubiquitous membrane-organizing principle in several other biological systems. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Krishnan Raghunathan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, PA 15224, USA.
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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Calvo V, Izquierdo M. Imaging Polarized Secretory Traffic at the Immune Synapse in Living T Lymphocytes. Front Immunol 2018; 9:684. [PMID: 29681902 PMCID: PMC5897431 DOI: 10.3389/fimmu.2018.00684] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/20/2018] [Indexed: 12/20/2022] Open
Abstract
Immune synapse (IS) formation by T lymphocytes constitutes a crucial event involved in antigen-specific, cellular and humoral immune responses. After IS formation by T lymphocytes and antigen-presenting cells, the convergence of secretory vesicles toward the microtubule-organizing center (MTOC) and MTOC polarization to the IS are involved in polarized secretion at the synaptic cleft. This specialized mechanism appears to specifically provide the immune system with a fine strategy to increase the efficiency of crucial secretory effector functions of T lymphocytes, while minimizing non-specific, cytokine-mediated stimulation of bystander cells, target cell killing and activation-induced cell death. The molecular bases involved in the polarized secretory traffic toward the IS in T lymphocytes have been the focus of interest, thus different models and several imaging strategies have been developed to gain insights into the mechanisms governing directional secretory traffic. In this review, we deal with the most widely used, state-of-the-art approaches to address the molecular mechanisms underlying this crucial, immune secretory response.
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Affiliation(s)
- Víctor Calvo
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid, Spain
| | - Manuel Izquierdo
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid, Spain
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