Analysis of Ionizing Radiation Induced DNA Damage by Superresolution dSTORM Microscopy

The quantitative detection of radiation caused DNA double-strand breaks (DSB) by immunostained γ-H2AX foci using direct stochastic optical reconstruction microscopy (dSTORM) provides a deeper insight into the DNA repair process at nanoscale in a time-dependent manner.

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FOM2021 presentation

WE-PAR2-B Fluorescence V: Probes, labelling, Bio Applications II 
(Room B, 2021.03.31.)

  • 15:10-15:25: Anti-Stokes Fluorescence Microscopy with Alexa Fluor 568.
    T. Gajdos, M. Erdélyi (University of Szeged, Department of Optics and Quantumelectronics, Hungary)

Full Program >>

[HU] Introduction video for students

Lab intriduction video for students (2021):

…and how we moved in in 2014:

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PhD graduation

Our college, Tamás Gajdos has successfully completed the Physics PhD program at the University of Szeged. His dissertation was written under the title „Superresolution localization microscopy using multiple modalities” and was defended with a result of 96% on November 20th. The dissertation and the thesis synopsis can be accessed from SZTE Repository of Dissertations.

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Syndecan-4 Modulates Cell Polarity and Migration by Influencing Centrosome Positioning and Intracellular Calcium Distribution

In collaboration with the Muscle Adaptation Group, we have published a new paper in Frontiers in Cell and Developmental Biology. Our join research venture studied the regeneration process in the tissue on a molecular level.

Becsky, Daniel, et al. “Syndecan-4 Modulates Cell Polarity and Migration by Influencing Centrosome Positioning and Intracellular Calcium Distribution.” Frontiers in Cell and Developmental Biology (2020).

https://doi.org/10.3389/fcell.2020.575227

Here are some Large Images captured with our system:

Hot-Band Anti-Stokes Fluorescence Properties of Alexa Fluor 568

Hot-band absorption and anti-Stokes emission properties of an organic fluorescent dye, Alexa Fluor 568, were characterized and compared with those of Rhodamine 101. The comparison of the properties (e.g., quantum efficiency, spectral distribution, thermal properties, and fluorescence lifetime) between the two dyes confirms that both dyes undergo the same process when excited in the red spectral region. Possible undesirable crosstalk effects and applications in dSTORM microscopy were demonstrated and discussed.

Gajdos, T., Hopp, B. & Erdélyi, M. Hot-Band Anti-Stokes Fluorescence Properties of Alexa Fluor 568. J Fluoresc (2020). doi: 10.1007/s10895-020-02496-0

https://rdcu.be/b2vGh

Nanoscale reconstruction of sarcomeres

Sarcomeres are extremely highly ordered macromolecular assemblies where structural organization is intimately linked to their functionality as contractile units. Although the structural basis of actin and Myosin interaction is revealed at a quasiatomic resolution, much less is known about the molecular organization of the I-band and H-zone. We report the development of a powerful nanoscopic approach, combined with a structure-averaging algorithm, that allowed us to determine the position of 27 sarcomeric proteins in Drosophila melanogaster flight muscles with a quasimolecular, ∼5- to 10-nm localization precision. With this protein localization atlas and template-based protein structure modeling, we have assembled refined I-band and H-zone models with unparalleled scope and resolution. In addition, we found that actin regulatory proteins of the H-zone are organized into two distinct layers, suggesting that the major place of thin filament assembly is an M-line–centered narrow domain where short actin oligomers can form and subsequently anneal to the pointed end.

Nanoscopy reveals the layered organization of the sarcomeric H-zone and I-band complexes – Szilárd Szikora, Tamás Gajdos, Tibor Novák, Dávid Farkas, István Földi, Peter Lenart, Miklós Erdélyi, József Mihály

https://rupress.org/jcb/article/219/1/e201907026/132617/Nanoscopy-reveals-the-layered-organization-of-the

https://doi.org/10.1083/jcb.201907026

Bio-Protocol: e3654

(in-press: 2020/06/20)
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Quantification of DNA damage induced repair focus formation via super-resolution dSTORM localization microscopy

… based on our new analysis method, we were able to show the number of nucleosomes in each nanofocus that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is one of the first demonstration of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize spatial organization of nanofoci by parametric determination of topological similarity.

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TestSTORM & rainSTORM 2019 May updates

We have released the latest version (v2.1.3) of TestSTORM. Here are the changes:

  • Significant memory reduction for the simulations (should be between 2 and 4 times).
  • Performance improvement when running the simulation with large number of labels.
  • Axial position for the “Array” pattern now can be set in the GUI. It is useful for generating calibration files for the astigmatic 3D simulations.
  • Some minor fixes for v2.1.1

Also we backported a minor feature from the development branch and released rainSTORM v3.1.7. Here are the changes:

  • Backport ExportBoxTracker tool to export localization data from selected ROIs on the Super-Resolution Image.
  • Updated Auto Drift Algorithm with comments.
  • Removed the BaSDI Drift Correction button from the GUI, as the implementation wasn’t as good as expected.

Visit us at FOM 2019

Poster Session 2 (Tuesday, April 16, 17.50–19.05):

  • P2-A/10 Multimodal Localization Microscopy with Efficient Photon Collection – T. Gajdos, Zs. Cserteg, Sz. Szikora, J. Mihály, B. B. H. Kovács, T. Novák, M. Erdélyi (University of Szeged, Hungary)
  • P2-C/12 Quantification of DNA Double-Strand Breaks via STORM Localization Microscopy – D. Varga, H. Majoros, Zs. Újfaludi, T. Pankotai, M. Erdélyi (University of Szeged, Hungary)

Full program>>