This paper has been prepared to commemorate the 70th anniversary of the Institute of Biophysics of the Czech Academy of Sciences (IBP CAS), which has a long-standing tradition in researching the biological effects of ionizing radiation (IR). Radiobiology has recently gained renewed importance due to several compelling factors. The demand for a better understanding of the biological effects of both low and high doses of various types of ionizing radiation, along with improved radiation protection, is increasing-particularly in the context of critical ongoing human activities such as medical diagnostics, radiotherapy, and the operation of nuclear power plants. This demand also extends to newly emerging scenarios, including the development of hadron and FLASH radiotherapy, as well as mixed radiation field exposures related to planned manned missions to Mars. Unfortunately, there is also an urgent need to address the heightened risk of nuclear materials and weapons misuse by terrorists or even rogue states. Additionally, nuclear energy is currently the only viable alternative that can provide efficient, sustainable, and ecological coverage for the dramatically increasing current and future energy demands. Understanding the risks of IR exposure necessitates exploring how different types of IR interact with living organisms at the most fundamental level of complexity, specifically at the level of molecules and their complexes. The rising interest in radiobiology is, therefore, also driven by new experimental opportunities that enable research at previously unimaginable levels of detail and complexity. In this manuscript, we will address the important questions in radiobiology, focusing specifically on the mechanisms of radiation-induced DNA damage and repair within the context of chromatin architecture. We will emphasize the differing effects of photon and high-LET particle radiation on chromatin and DNA. Both forms of IR are encountered on Earth but are particularly significant in space.

• Keywords
• Biological effects of ionizing radiation, Chromatin architecture at micro- and nano-scale, DNA damage and repair, Densely ionizing (high-LET) particle radiation, Institute of biophysics of the Czech academy of sciences, Microscopy, Photon radiation, Radiobiological research, Single molecule localization microscopy (SMLM),
• Publication type
• Journal Article MeSH
• Review MeSH

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

• Publication type
• Journal Article MeSH
• Review MeSH

The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the relationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, persistent 'imaging', principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein trafficking in the cytosol, offers broad flexibility of use.

• Keywords
• Application of mathematical analysis tools to chromatin organization and DNA repair processes, DSB, DNA double-strand break, HR, homologous recombination, IRIF, ionizing radiation induced foci, LET, linear energy transfer, NHEJ, non-homologous end joining, NN, nearest neighbor, PCA, principal component analysis, Persistent homology, Persistent image, Principal component analysis, Ripley distance frequency histograms, SMLM, single molecule localization microscopy, Single molecule localization microscopy (SMLM),
• Publication type
• Journal Article MeSH

Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.

• Keywords
• database pattern analysis, dynamic genome organization, epigenetic interactions, fluorescence microscopy, gene activity oscillations, heterochromatin and self-organization, nucleotide k-mers, organizational and functional networks, topological genome analysis, transposon-effected regulation,
• MeSH
• Cell Differentiation genetics   MeSH
• Cell Nucleus * metabolism   MeSH
• Genome * MeSH
• Publication type
• Congress MeSH
• Review MeSH

(1) Background: In oncology research, a long-standing discussion exists about pros and cons of metal nanoparticle-enhanced radiotherapy and real mechanisms behind the tumor cell response to irradiation (IR) in presence of gold nanoparticles (GNPs). A better understanding of this response is, however, necessary to develop more efficient and safety nanoparticle (NP) types designed to disturb specific processes in tumor cells. (2) Aims and Methods: We combined 3D confocal microscopy and super-resolution single molecule localization microscopy (SMLM) to analyze, at the multiscale, the early and late effects of 10 nm-GNPs on DNA double strand break (DSB) induction and repair in tumor cells exposed to different doses of photonic low-LET (linear energy transfer) radiation. The results were correlated to different aspects of short and long-term cell viability. SkBr3 breast cancer cells (selected for the highest incidence of this cancer type among all cancers in women, and because most breast tumors are treated with IR) were incubated with low concentrations of GNPs and irradiated with 60Co γ-rays or 6 MV X-rays. In numerous post-irradiation (PI) times, ranging from 0.5 to 24 h PI, the cells were spatially (3D) fixed and labeled with specific antibodies against γH2AX, 53BP1 and H3K9me3. The extent of DSB induction, multi-parametric micro- and nano-morphology of γH2AX and 53BP1 repair foci, DSB repair kinetics, persistence of unrepaired DSBs, nanoscale clustering of γH2AX and nanoscale (hetero)chromatin re-organization were measured by means of the mentioned microscopy techniques in dependence of radiation dose and GNP concentration. (3) Results: The number of γH2AX/53BP1 signals increased after IR and an additional increase was observed in GNP-treated (GNP(+)) cells compared to untreated controls. However, this phenomenon reflected slight expansion of the G2-phase cell subpopulation in irradiated GNP(+) specimens instead of enhanced DNA damage induction by GNPs. This statement is further supported by some micro- and nano-morphological parameters of γH2AX/53BP1 foci, which slightly differed for cells irradiated in absence or presence of GNPs. At the nanoscale, Ripley's distance frequency analysis of SMLM signal coordinate matrices also revealed relaxation of heterochromatin (H3K9me3) clusters upon IR. These changes were more prominent in presence of GNPs. The slight expansion of radiosensitive G2 cells correlated with mostly insignificant but systematic decrease in post-irradiation survival of GNP(+) cells. Interestingly, low GNP concentrations accelerated DSB repair kinetics; however, the numbers of persistent γH2AX/53BP1 repair foci were slightly increased in GNP(+) cells. (4) Conclusions: Low concentrations of 10-nm GNPs enhanced the G2/M cell cycle arrest and the proportion of radiosensitive G2 cells, but not the extent of DNA damage induction. GNPs also accelerated DSB repair kinetics and slightly increased presence of unrepaired γH2AX/53BP1 foci at 24 h PI. GNP-mediated cell effects correlated with slight radiosensitization of GNP(+) specimens, significant only for the highest radiation dose tested (4 Gy).

• Keywords
• DNA double strand breaks (DSBs), DNA repair, DNA repair nano-clusters, chromatin nano-architecture rearrangements, gold nanoparticles (GNP), ionizing radiation-induced (repair) foci (IRIF), nanoparticle-enhanced cancer radiotherapy, single-molecule localization microscopy (SMLM),
• Publication type
• Journal Article MeSH