1
|
Serbus LR. A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging. Methods Mol Biol 2024; 2739:349-373. [PMID: 38006562 DOI: 10.1007/978-1-0716-3553-7_21] [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: 11/27/2023]
Abstract
The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.
Collapse
Affiliation(s)
- Laura Renee Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
| |
Collapse
|
2
|
Raut P, Obeng B, Waters H, Zimmerberg J, Gosse JA, Hess ST. Phosphatidylinositol 4,5-Bisphosphate Mediates the Co-Distribution of Influenza A Hemagglutinin and Matrix Protein M1 at the Plasma Membrane. Viruses 2022; 14:v14112509. [PMID: 36423118 PMCID: PMC9698905 DOI: 10.3390/v14112509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The fully assembled influenza A virus (IAV) has on its surface the highest density of a single membrane protein found in nature-the glycoprotein hemagglutinin (HA) that mediates viral binding, entry, and assembly. HA clusters at the plasma membrane of infected cells, and the HA density (number of molecules per unit area) of these clusters correlates with the infectivity of the virus. Dense HA clusters are considered to mark the assembly site and ultimately lead to the budding of infectious IAV. The mechanism of spontaneous HA clustering, which occurs with or without other viral components, has not been elucidated. Using super-resolution fluorescence photoactivation localization microscopy (FPALM), we have previously shown that these HA clusters are interdependent on phosphatidylinositol 4,5-biphosphate (PIP2). Here, we show that the IAV matrix protein M1 co-clusters with PIP2, visualized using the pleckstrin homology domain. We find that cetylpyridinium chloride (CPC), which is a positively charged quaternary ammonium compound known for its antibacterial and antiviral properties at millimolar concentrations, disrupts M1 clustering and M1-PIP2 co-clustering at micromolar concentrations well below the critical micelle concentration (CMC). CPC also disrupts the co-clustering of M1 with HA at the plasma membrane, suggesting the role of host cell PIP2 clusters as scaffolds for gathering and concentrating M1 and HA to achieve their unusually high cluster densities in the IAV envelope.
Collapse
Affiliation(s)
- Prakash Raut
- Department of Physics and Astronomy, University of Maine, Orono, ME 04469-5709, USA
| | - Bright Obeng
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469-5735, USA
| | - Hang Waters
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1855, USA
| | - Joshua Zimmerberg
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1855, USA
| | - Julie A. Gosse
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469-5735, USA
| | - Samuel T. Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME 04469-5709, USA
- Correspondence:
| |
Collapse
|
3
|
Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA. Nat Methods 2022; 19:759-769. [PMID: 35654951 DOI: 10.1038/s41592-022-01498-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/15/2022] [Indexed: 12/21/2022]
Abstract
Advances in multiplexed in situ imaging are revealing important insights in spatial biology. However, cell type identification remains a major challenge in imaging analysis, with most existing methods involving substantial manual assessment and subjective decisions for thousands of cells. We developed an unsupervised machine learning algorithm, CELESTA, which identifies the cell type of each cell, individually, using the cell's marker expression profile and, when needed, its spatial information. We demonstrate the performance of CELESTA on multiplexed immunofluorescence images of colorectal cancer and head and neck squamous cell carcinoma (HNSCC). Using the cell types identified by CELESTA, we identify tissue architecture associated with lymph node metastasis in HNSCC, and validate our findings in an independent cohort. By coupling our spatial analysis with single-cell RNA-sequencing data on proximal sections of the same specimens, we identify cell-cell crosstalk associated with lymph node metastasis, demonstrating the power of CELESTA to facilitate identification of clinically relevant interactions.
Collapse
|
4
|
Raut P, Weller SR, Obeng B, Soos BL, West BE, Potts CM, Sangroula S, Kinney MS, Burnell JE, King BL, Gosse JA, Hess ST. Cetylpyridinium chloride (CPC) reduces zebrafish mortality from influenza infection: Super-resolution microscopy reveals CPC interference with multiple protein interactions with phosphatidylinositol 4,5-bisphosphate in immune function. Toxicol Appl Pharmacol 2022; 440:115913. [PMID: 35149080 PMCID: PMC8824711 DOI: 10.1016/j.taap.2022.115913] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 01/12/2023]
Abstract
The COVID-19 pandemic raises significance for a potential influenza therapeutic compound, cetylpyridinium chloride (CPC), which has been extensively used in personal care products as a positively-charged quaternary ammonium antibacterial agent. CPC is currently in clinical trials to assess its effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) morbidity. Two published studies have provided mouse and human data indicating that CPC may alleviate influenza infection, and here we show that CPC (0.1 μM, 1 h) reduces zebrafish mortality and viral load following influenza infection. However, CPC mechanisms of action upon viral-host cell interaction are currently unknown. We have utilized super-resolution fluorescence photoactivation localization microscopy to probe the mode of CPC action. Reduction in density of influenza viral protein hemagglutinin (HA) clusters is known to reduce influenza infectivity: here, we show that CPC (at non-cytotoxic doses, 5-10 μM) reduces HA density and number of HA molecules per cluster within the plasma membrane of NIH-3T3 mouse fibroblasts. HA is known to colocalize with the negatively-charged mammalian lipid phosphatidylinositol 4,5-bisphosphate (PIP2); here, we show that nanoscale co-localization of HA with the PIP2-binding Pleckstrin homology (PH) reporter in the plasma membrane is diminished by CPC. CPC also dramatically displaces the PIP2-binding protein myristoylated alanine-rich C-kinase substrate (MARCKS) from the plasma membrane of rat RBL-2H3 mast cells; this disruption of PIP2 is correlated with inhibition of mast cell degranulation. Together, these findings offer a PIP2-focused mechanism underlying CPC disruption of influenza and suggest potential pharmacological use of this drug as an influenza therapeutic to reduce global deaths from viral disease.
Collapse
Affiliation(s)
- Prakash Raut
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Sasha R Weller
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Bright Obeng
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Brandy L Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Bailey E West
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Christian M Potts
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Suraj Sangroula
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Marissa S Kinney
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - John E Burnell
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Julie A Gosse
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA.
| | - Samuel T Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA.
| |
Collapse
|
5
|
Raut P, Waters H, Zimmberberg J, Obeng B, Gosse J, Hess ST. Localization-Based Super-Resolution Microscopy Reveals Relationship between SARS-CoV2 Spike and Phosphatidylinositol (4,5)-bisphosphate. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2022; 11965:1196503. [PMID: 36051945 PMCID: PMC9432428 DOI: 10.1117/12.2613460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Localization microscopy circumvents the diffraction limit by identifying and measuring the positions of numerous subsets of individual fluorescent molecules, ultimately producing an image whose resolution depends on the uncertainty and density of localization, and whose capabilities are compatible with imaging living specimens. Spectral resolution can be improved by incorporating a dichroic or dispersive element in the detection path of a localization microscope, which can be useful for separation of multiple probes imaged simultaneously and for detection of changes in emission spectra of fluorophores resulting from changes in their environment. These methodological advances enable new biological applications, which in turn motivate new questions and technical innovations. As examples, we present fixed-cell imaging of the spike protein SARS-CoV2 (S) and its interactions with host cell components. Results show a relationship between S and the lipid phosphatidylinositol (4,5)-bisphosphate (PIP2). These findings have ramifications for several existing models of plasma membrane organization.
Collapse
Affiliation(s)
- Prakash Raut
- Department of Physics and Astronomy, University of Maine, Orono, ME 04469-5709
| | - Hang Waters
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1855
| | - Joshua Zimmberberg
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1855
| | - Bright Obeng
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Julie Gosse
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Samuel T. Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME 04469-5709
- corresponding author: ; phone 207 581-1036; fax 207 581-3410
| |
Collapse
|
6
|
Dankovich TM, Rizzoli SO. Challenges facing quantitative large-scale optical super-resolution, and some simple solutions. iScience 2021; 24:102134. [PMID: 33665555 PMCID: PMC7898072 DOI: 10.1016/j.isci.2021.102134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Optical super-resolution microscopy (SRM) has enabled biologists to visualize cellular structures with near-molecular resolution, giving unprecedented access to details about the amounts, sizes, and spatial distributions of macromolecules in the cell. Precisely quantifying these molecular details requires large datasets of high-quality, reproducible SRM images. In this review, we discuss the unique set of challenges facing quantitative SRM, giving particular attention to the shortcomings of conventional specimen preparation techniques and the necessity for optimal labeling of molecular targets. We further discuss the obstacles to scaling SRM methods, such as lengthy image acquisition and complex SRM data analysis. For each of these challenges, we review the recent advances in the field that circumvent these pitfalls and provide practical advice to biologists for optimizing SRM experiments.
Collapse
Affiliation(s)
- Tal M. Dankovich
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- International Max Planck Research School for Neuroscience, Göttingen, Germany
| | - Silvio O. Rizzoli
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- Biostructural Imaging of Neurodegeneration (BIN) Center & Multiscale Bioimaging Excellence Center, Göttingen 37075, Germany
| |
Collapse
|
7
|
Yang JE, Larson MR, Sibert BS, Shrum S, Wright ER. CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy. J Struct Biol 2021; 213:107709. [PMID: 33610654 PMCID: PMC8601405 DOI: 10.1016/j.jsb.2021.107709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.
Collapse
Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Samantha Shrum
- Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States; Morgridge Institute for Research, Madison, WI, 53715, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States.
| |
Collapse
|
8
|
Bernasek SM, Peláez N, Carthew RW, Bagheri N, Amaral LAN. Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Comput Biol 2020; 16:e1007406. [PMID: 32126077 PMCID: PMC7100978 DOI: 10.1371/journal.pcbi.1007406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 03/27/2020] [Accepted: 01/27/2020] [Indexed: 12/01/2022] Open
Abstract
Mosaic analysis provides a means to probe developmental processes in situ by generating loss-of-function mutants within otherwise wildtype tissues. Combining these techniques with quantitative microscopy enables researchers to rigorously compare RNA or protein expression across the resultant clones. However, visual inspection of mosaic tissues remains common in the literature because quantification demands considerable labor and computational expertise. Practitioners must segment cell membranes or cell nuclei from a tissue and annotate the clones before their data are suitable for analysis. Here, we introduce Fly-QMA, a computational framework that automates each of these tasks for confocal microscopy images of Drosophila imaginal discs. The framework includes an unsupervised annotation algorithm that incorporates spatial context to inform the genetic identity of each cell. We use a combination of real and synthetic validation data to survey the performance of the annotation algorithm across a broad range of conditions. By contributing our framework to the open-source software ecosystem, we aim to contribute to the current move toward automated quantitative analysis among developmental biologists.
Collapse
Affiliation(s)
- Sebastian M. Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolás Peláez
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Richard W. Carthew
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, United States of America
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
| |
Collapse
|
9
|
Lambert TJ, Waters JC. Navigating challenges in the application of superresolution microscopy. J Cell Biol 2017; 216:53-63. [PMID: 27920217 PMCID: PMC5223610 DOI: 10.1083/jcb.201610011] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.
Collapse
Affiliation(s)
- Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
10
|
Levental I, Veatch S. The Continuing Mystery of Lipid Rafts. J Mol Biol 2016; 428:4749-4764. [PMID: 27575334 DOI: 10.1016/j.jmb.2016.08.022] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/12/2022]
Abstract
Since its initial formalization nearly 20 years ago, the concept of lipid rafts has generated a tremendous amount of attention and interest and nearly as much controversy. The controversy is perhaps surprising because the notion itself is intuitive: compartmentalization in time and space is a ubiquitous theme at all scales of biology, and therefore, the partitioning of cellular membranes into lateral subdivision should be expected. Nevertheless, the physicochemical principles responsible for compartmentalization and the molecular mechanisms by which they are functionalized remain nearly as mysterious today as they were two decades ago. Herein, we review recent literature on this topic with a specific focus on the major open questions in the field including: (1) what are the best tools to assay raft behavior in living membranes? (2) what is the function of the complex lipidome of mammalian cells with respect to membrane organization? (3) what are the mechanisms that drive raft formation and determine their properties? (4) how can rafts be modulated? (5) how is membrane compartmentalization integrated into cellular signaling? Despite decades of intensive research, this compelling field remains full of fundamental questions.
Collapse
Affiliation(s)
- Ilya Levental
- McGovern Medical School at the University of Texas Houston, Department of Integrative Biology and Pharmacology
| | | |
Collapse
|
11
|
Mlodzianoski MJ, Curthoys NM, Gunewardene MS, Carter S, Hess ST. Super-Resolution Imaging of Molecular Emission Spectra and Single Molecule Spectral Fluctuations. PLoS One 2016; 11:e0147506. [PMID: 27002724 PMCID: PMC4803349 DOI: 10.1371/journal.pone.0147506] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/04/2016] [Indexed: 11/19/2022] Open
Abstract
Localization microscopy can image nanoscale cellular details. To address biological questions, the ability to distinguish multiple molecular species simultaneously is invaluable. Here, we present a new version of fluorescence photoactivation localization microscopy (FPALM) which detects the emission spectrum of each localized molecule, and can quantify changes in emission spectrum of individual molecules over time. This information can allow for a dramatic increase in the number of different species simultaneously imaged in a sample, and can create super-resolution maps showing how single molecule emission spectra vary with position and time in a sample.
Collapse
Affiliation(s)
- Michael J. Mlodzianoski
- Department of Physics and Astronomy, University of Maine, Orono, Maine, United States of America
| | - Nikki M. Curthoys
- Department of Physics and Astronomy, University of Maine, Orono, Maine, United States of America
| | - Mudalige S. Gunewardene
- Department of Physics and Astronomy, University of Maine, Orono, Maine, United States of America
| | - Sean Carter
- Department of Physics and Astronomy, University of Maine, Orono, Maine, United States of America
| | - Samuel T. Hess
- Department of Physics and Astronomy, University of Maine, Orono, Maine, United States of America
- * E-mail:
| |
Collapse
|
12
|
Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
13
|
Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
|
14
|
Stone MB, Veatch SL. Far-red organic fluorophores contain a fluorescent impurity. Chemphyschem 2014; 15:2240-6. [PMID: 24782148 PMCID: PMC4180537 DOI: 10.1002/cphc.201402002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/06/2014] [Indexed: 11/06/2022]
Abstract
Far-red organic fluorophores commonly used in traditional and super-resolution localization microscopy are found to contain a fluorescent impurity with green excitation and near-red emission. This near-red fluorescent impurity can interfere with some multicolor stochastic optical reconstruction microscopy/photoactivated localization microscopy measurements in live cells and produce subtle artifacts in chemically fixed cells. We additionally describe alternatives to avoid artifacts in super-resolution localization microscopy.
Collapse
Affiliation(s)
- Matthew B. Stone
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
| |
Collapse
|
15
|
Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A. Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 2014; 142:5-17. [PMID: 24748502 PMCID: PMC4072926 DOI: 10.1007/s00418-014-1217-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/10/2023]
Abstract
With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM).
Collapse
Affiliation(s)
- H. Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A. Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - P. Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Biomedical Engineering Department, University of California, Irvine, CA USA
| | - M. Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A. Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| |
Collapse
|
16
|
Curthoys NM, Mlodzianoski MJ, Kim D, Hess ST. Simultaneous multicolor imaging of biological structures with fluorescence photoactivation localization microscopy. J Vis Exp 2013:e50680. [PMID: 24378721 DOI: 10.3791/50680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Localization-based super resolution microscopy can be applied to obtain a spatial map (image) of the distribution of individual fluorescently labeled single molecules within a sample with a spatial resolution of tens of nanometers. Using either photoactivatable (PAFP) or photoswitchable (PSFP) fluorescent proteins fused to proteins of interest, or organic dyes conjugated to antibodies or other molecules of interest, fluorescence photoactivation localization microscopy (FPALM) can simultaneously image multiple species of molecules within single cells. By using the following approach, populations of large numbers (thousands to hundreds of thousands) of individual molecules are imaged in single cells and localized with a precision of ~10-30 nm. Data obtained can be applied to understanding the nanoscale spatial distributions of multiple protein types within a cell. One primary advantage of this technique is the dramatic increase in spatial resolution: while diffraction limits resolution to ~200-250 nm in conventional light microscopy, FPALM can image length scales more than an order of magnitude smaller. As many biological hypotheses concern the spatial relationships among different biomolecules, the improved resolution of FPALM can provide insight into questions of cellular organization which have previously been inaccessible to conventional fluorescence microscopy. In addition to detailing the methods for sample preparation and data acquisition, we here describe the optical setup for FPALM. One additional consideration for researchers wishing to do super-resolution microscopy is cost: in-house setups are significantly cheaper than most commercially available imaging machines. Limitations of this technique include the need for optimizing the labeling of molecules of interest within cell samples, and the need for post-processing software to visualize results. We here describe the use of PAFP and PSFP expression to image two protein species in fixed cells. Extension of the technique to living cells is also described.
Collapse
|