Biophysics is an interdisciplinary science that applies the theories and methods of physics to understand biological systems. It encompasses a wide range of topics, from the molecular mechanisms within cells to the physical properties of organisms and ecosystems. The goal of biophysics is to uncover the physical principles underlying the structure and function of biological molecules, cells, and cellular systems, providing a deeper understanding of life itself. The Institute of Biophysics, Czech Academy of Sciences (IBP) stands as a beacon of excellence in the field of biophysical research in the Czech Republic. This article delves into its history, structure, research areas, and major scientific achievements, highlighting the role of IBP in the global scientific community.

• Keywords
• Biophysical methods, Biophysics, DNA damage repair, Ionizing radiation, Radiotherapy,
• Publication type
• Journal Article MeSH
• Review 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

DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes-DSB formation, repair and misrepair-are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging "correlated multiscale structuromics" can revolutionarily enhance our knowledge in this field.

• Keywords
• DNA damage and repair, DNA double-strand breaks (DSBs), DSB repair pathway choice and hierarchy, chromatin architecture, ionizing radiation, ionizing radiation-induced foci (IRIFs), linear energy transfer (LET), single-molecule localization microscopy (SMLM), superresolution microscopy,
• Publication type
• Journal Article MeSH
• Review MeSH

The spatial arrangement of some genetic elements relative to chromosome territories and in parallel with the cell nucleus was investigated in human lymphocytes. The structure of the chromosome territories was studied in chromosomes containing regions (clusters) of highly expressed genes (HSA 9, 17) and those without such clusters (HSA 8, 13). In chromosomes containing highly expressed regions, the elements pertaining to these regions were found close to the centre of the nucleus on the inner sides of chromosome territories; those pertaining to regions with low expression were localized close to the nuclear membrane on the opposite sides of the territories. In chromosomes with generally low expression (HSA 8, 13), the elements investigated were found symmetrically distributed over the territories. Based on the investigations of the chromosome structure, the following conclusions are suggested: (1) Chromosome territories have a non-random internal 3D structure with defined average mutual positions between elements. For example, RARalpha, TP53 and Iso-q of HSA 17 are nearer to each other than they are to the HSA 17 centromere. (2) The structure of a chromosome territory reflects the number and chromosome location of clusters of highly expressed genes. (3) Chromosome territories behave to some extent as solid bodies: if the territory is found closer to the nuclear centre, the individual genetic elements of this chromosome are also found, on average, closer the centre of the nucleus. (4) The positions of centromeres are, on average, nearer to the fluorescence weight centre of the territory (FWCT) than to genes. (5) Active genes are not found near the centromeres of their own territory. A simple model of the structure of chromosome territory is proposed.

• MeSH
• Cell Nucleus genetics   MeSH
• Centromere genetics   MeSH
• Euchromatin genetics   MeSH
• Genes MeSH
• Heterochromatin genetics   MeSH
• In Situ Hybridization, Fluorescence MeSH
• Nuclear Envelope genetics   MeSH
• Cell Compartmentation MeSH
• Humans MeSH
• Chromosomes, Human, Pair 17 ultrastructure   MeSH
• Chromosomes, Human ultrastructure   MeSH
• Lymphocytes diagnostic imaging   MeSH
• Monte Carlo Method MeSH
• Models, Genetic MeSH
• Computer Simulation MeSH
• Image Processing, Computer-Assisted MeSH
• Ultrasonography MeSH
• Imaging, Three-Dimensional * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• Euchromatin MeSH
• Heterochromatin MeSH

Higher-order compartments of nuclear chromatin have been defined according to the replication timing, transcriptional activity, and information content (Ferreira et al. 1997, Sadoni et al. 1999). The results presented in this work contribute to this model of nuclear organization. Using different human blood cells, nuclear positioning of genes, centromeres, and whole chromosomes was investigated. Genes are located mostly in the interior of cell nuclei; centromeres are located near the nuclear periphery in agreement with the definition of the higher-order compartments. Genetic loci are found in specific subregions of cell nuclei which form distinct layers at defined centre-of-nucleus to locus distances. Inside these layers, the genetic loci are distributed randomly. Some chromosomes are polarized with genes located in the inner parts of the nucleus and centromere located on the nuclear periphery; polar organization was not found for some other chromosomes. The internal structure of the higher-order compartments as well as the polar and non-polar organization of chromosomes are basically conserved in different cell types and at various stages of the cell cycle. Some features of the nuclear structure are conserved even in differentiated cells and during cellular repair after irradiation, although shifted positioning of genetic loci was systematically observed during these processes.

• MeSH
• Cell Nucleus genetics   radiation effects   ultrastructure   MeSH
• Cell Cycle MeSH
• Bone Marrow Cells radiation effects   ultrastructure   MeSH
• Centromere radiation effects   MeSH
• Genes radiation effects   MeSH
• HL-60 Cells MeSH
• In Situ Hybridization, Fluorescence MeSH
• Interphase MeSH
• Cell Compartmentation MeSH
• Leukopoiesis MeSH
• Humans MeSH
• Chromosomes, Human radiation effects   MeSH
• Lymphocytes cytology   radiation effects   ultrastructure   MeSH
• U937 Cells MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH