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Development and Application of Super-Resolution Imaging Methods for Biological Research
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Development and Application of Super-Resolution Imaging Methods for Biological Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 May 2021) | Viewed by 21079

Special Issue Editor

Dr. Kiryl Piatkevich

E-Mail Website
Guest Editor
1. McGovern Institute for Brain Research, Cambridge, MA, USA
2. Molecular BioEngineering Group, School of Life Sciences, Westlake University, Hangzhou, China
Interests: fluorescent biosensors; optogenetics; expension microscop; neuroengineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Biological research and biomedicine are increasingly reliant on optical methods for imaging the structure and function of biological systems. Addressing the most pressing needs in biological research requires visualization and mapping biomolecules with nanoscale precision. Recent advances in optical techniques in combination with the development of novel molecular probes made it possible to break the diffraction limit of conventional optical microscopy, establishing super-resolution microscopy, for which the 2014 Nobel Prize in Chemistry was awarded. The field of super-resolution microscopy remains extremely dynamic and fast-growing and new methods and techniques are emerging all the time.

We would like to kindly invite you to contribute to the Special Issue "Development and Application of Super-Resolution Imaging Methods for Biological Research" of the International Journal of Molecular Sciences (Impact Factor 4.556). The Special Issue will elucidate the development and application of new imaging methods and techniques that enable sub-diffraction imaging of biological systems. Novel molecular probes and sample preparation techniques that enhance existing super-resolution methods or provide new modalities in super-resolution imaging are also within the scope of the Special Issue. Papers may also focus on addressing important biological questions using super-resolution imaging techniques. The Special Issue will provide a forum for sharing and discussing perspectives on the development of the field within biological research. Review articles can cover recent advances in the field of super-resolution microscopy or molecular probes for super-resolution microscopy, or novel or emerging techniques for sub-diffraction imaging.

Dr. Kiryl Piatkevich
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • 4Pi microscopy
  • STED and two-photon STED
  • RESOLFT
  • localization microscopy
  • structured illumination microscopy
  • super-resolution optical fluctuation imaging
  • light-sheet microscopy
  • expansion microscopy
  • light-induced photoconversion
  • application of photostable emitters
  • tissue clearing
  • sample magnification via isotropic expansion
  • multiplexed staining
  • fluorescent proteins
  • advanced antibodies and nanobodies
  • novel or special dyes
  • new instrumentation and new techniques
  • enhanced resolution
  • in vivo application
  • large sample imaging
  • high throughput, working distance

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Published Papers (5 papers)

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Research

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21 pages, 4123 KiB  
Article
Optimization of Advanced Live-Cell Imaging through Red/Near-Infrared Dye Labeling and Fluorescence Lifetime-Based Strategies
by Magalie Bénard, Damien Schapman, Christophe Chamot, Fatéméh Dubois, Guénaëlle Levallet, Hitoshi Komuro and Ludovic Galas
Int. J. Mol. Sci. 2021, 22(20), 11092; https://doi.org/10.3390/ijms222011092 - 14 Oct 2021
Cited by 4 | Viewed by 3363
Abstract
Fluorescence microscopy is essential for a detailed understanding of cellular processes; however, live-cell preservation during imaging is a matter of debate. In this study, we proposed a guide to optimize advanced light microscopy approaches by reducing light exposure through fluorescence lifetime (τ) exploitation [...] Read more.
Fluorescence microscopy is essential for a detailed understanding of cellular processes; however, live-cell preservation during imaging is a matter of debate. In this study, we proposed a guide to optimize advanced light microscopy approaches by reducing light exposure through fluorescence lifetime (τ) exploitation of red/near-infrared dyes. Firstly, we characterized key instrumental elements which revealed that red/near-infrared laser lines with an 86x (Numerical Aperture (NA) = 1.2, water immersion) objective allowed high transmission of fluorescence signals, low irradiance and super-resolution. As a combination of two technologies, i.e., vacuum tubes (e.g., photomultiplier) and semiconductor microelectronics (e.g., avalanche photodiode), type S, X and R of hybrid detectors (HyD-S, HyD-X and HyD-R) were particularly adapted for red/near-infrared photon counting and τ separation. Secondly, we tested and compared lifetime-based imaging including coarse τ separation for confocal microscopy, fitting and phasor plot analysis for fluorescence lifetime microscopy (FLIM), and lifetimes weighting for enhanced stimulated emission depletion (STED) nanoscopy, in light of red/near-infrared multiplexing. Mainly, we showed that the choice of appropriate imaging approach may depend on fluorochrome number, together with their spectral/lifetime characteristics and STED compatibility. Photon-counting mode and sensitivity of HyDs together with phasor plot analysis of fluorescence lifetimes enabled the flexible and fast imaging of multi-labeled living H28 cells. Therefore, a combination of red/near-infrared dyes labeling with lifetime-based strategies offers new perspectives for live-cell imaging by enhancing sample preservation through acquisition time and light exposure reduction. Full article
(This article belongs to the Special Issue Development and Application of Super-Resolution Imaging Methods for Biological Research)
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Review

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17 pages, 5623 KiB  
Review
Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm
by Tanveer Teranikar, Jessica Lim, Toluwani Ijaseun and Juhyun Lee
Int. J. Mol. Sci. 2022, 23(3), 1643; https://doi.org/10.3390/ijms23031643 - 31 Jan 2022
Cited by 4 | Viewed by 3112
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright [...] Read more.
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system’s point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration. Full article
(This article belongs to the Special Issue Development and Application of Super-Resolution Imaging Methods for Biological Research)
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25 pages, 4125 KiB  
Review
Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging?
by Paweł Matryba, Kacper Łukasiewicz, Monika Pawłowska, Jacek Tomczuk and Jakub Gołąb
Int. J. Mol. Sci. 2021, 22(13), 6730; https://doi.org/10.3390/ijms22136730 - 23 Jun 2021
Cited by 2 | Viewed by 3923
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a [...] Read more.
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems. Full article
(This article belongs to the Special Issue Development and Application of Super-Resolution Imaging Methods for Biological Research)
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19 pages, 3557 KiB  
Review
How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription
by Peter Hoboth, Ondřej Šebesta and Pavel Hozák
Int. J. Mol. Sci. 2021, 22(13), 6694; https://doi.org/10.3390/ijms22136694 - 22 Jun 2021
Cited by 11 | Viewed by 3156
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery [...] Read more.
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression. Full article
(This article belongs to the Special Issue Development and Application of Super-Resolution Imaging Methods for Biological Research)
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Graphical abstract

19 pages, 6359 KiB  
Review
Studying SARS-CoV-2 with Fluorescence Microscopy
by Lidia V. Putlyaeva and Konstantin A. Lukyanov
Int. J. Mol. Sci. 2021, 22(12), 6558; https://doi.org/10.3390/ijms22126558 - 18 Jun 2021
Cited by 18 | Viewed by 6348
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a [...] Read more.
The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a powerful technology enabling detailed investigation of virus–cell interactions in fixed and live samples with high specificity. While spatial resolution of conventional fluorescence microscopy is not sufficient to resolve all virus-related structures, super-resolution fluorescence microscopy can solve this problem. In this paper, we review the use of fluorescence microscopy to study SARS-CoV-2 and related viruses. The prospects for the application of the recently developed advanced methods of fluorescence labeling and microscopy—which in our opinion can provide important information about the molecular biology of SARS-CoV-2—are discussed. Full article
(This article belongs to the Special Issue Development and Application of Super-Resolution Imaging Methods for Biological Research)
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