European Biophysics Journal最新文献

{"title":"Professor Emil Paleček: seven decades with electrodes and biomolecules at the Institute of Biophysics of the CAS.","authors":"Miroslav Fojta, Jan Paleček","doi":"10.1007/s00249-025-01771-x","DOIUrl":"https://doi.org/10.1007/s00249-025-01771-x","url":null,"abstract":"<p><p>This year we celebrate seventy years since the establishment of the Institute of Biophysics of the Czechoslovak Academy of Sciences (IBP) (founded on January 1, 1955). If we look into the biography of Professor Emil Paleček (born on October 3, 1930), one of the most world-recognized personalities associated with the Institute and one of the most cited Czech scientists, known as the founder of nucleic acids electrochemistry, we are drawn to the same year, i.e. 1955, as the year in which Emil Paleček finished his studies in biochemistry and joined the IBP, where he worked with admirable vitality, enthusiasm and dedication until his death (October 30, 2018). In the context of celebration of founding of the Institute, we would like to commemorate in this article a personality who significantly influenced the history of the Institute alongside the important discoveries and research directions that defined his extremely successful career. We prefer this form, which is a sort of a mini-review of the most important results of the laboratory obtained under EP's leadership over 63 years, presented in mutual context and natural relations. For his life's work, Professor Paleček received many prestigious awards, with the Czech Head Award in 2014 and the Neuron Foundation Award in 2017 being the most distinguished.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Image analysis tools for improved characterization of nuclear chromatin patterns by confocal fluorescence microscopy.","authors":"Mohammadmehdi Roushenas, Marco Salerno, Virginia Bazzurro, Elena Gatta, Alberto Diaspro","doi":"10.1007/s00249-025-01770-y","DOIUrl":"https://doi.org/10.1007/s00249-025-01770-y","url":null,"abstract":"<p><p>We have collected fluorescence images of fixed cell nuclei of two different types-HeLa and HepG2-with DNA labeled by a standard fluorophore, and have devised three different quantitative parameters aimed to describe the distribution of the nuclear chromatin. The parameters are the fractal dimension, associated with the intricacy and hierarchical structure of chromatin; the total perimeter of local maxima, associated with the amount of chromatin domains; and the radial distance of angularly averaged intensity profile maximum, associated with the possible occurrence of a peak density at a characteristic distance from the nucleus center. Our results suggested that it was possible to differentiate the two types of cells in the 3D space of the defined parameters. Therefore, these parameters appear promising in identifying specific functional patterns in chromatin. At the same time, the negative control of different runs of measurements on the same cell type also showed at least partial differentiation. Thus, the tool proposed here for nuclear chromatin pattern characterization is probably sensitive to the cell life cycle moment almost as much as to the cell type and should be tested further on cells synchronized at the same phase during their cycle.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fragmentation of nucleoli in senescent cancer cells is associated with increased levels of polyadenylated transcripts derived from noncoding regions of rDNA units.","authors":"Jana Sochorová, Emilie Lukášová, Eva Volfová Polanská, Kateřina Řehůřková, Aleš Kovařík","doi":"10.1007/s00249-025-01773-9","DOIUrl":"https://doi.org/10.1007/s00249-025-01773-9","url":null,"abstract":"<p><p>In this study, we investigated the behavior of rDNA loci in senescent MCF-7 mammary cancer cells induced by gamma irradiation. To analyze changes in nucleolar structure we used rDNA-FISH and immunohistochemical staining with fibrillarin and UBF transcription factor. The expression levels of rDNAs and nucleolar proteins were determined by RNA-seq of total and poly-A libraries. The cytological and molecular parameters of nucleoli were monitored throughout the 7-day interval following irradiation. Senescent cells exhibited a higher proportion of smaller nucleoli as compared to cycling cells, indicating nucleolar fragmentation. The rDNA copy number and expression of rDNA variants remained stable in cycling and senescent cells. However, the levels of polyadenylated rRNA species derived from external (5'ETS) and internal (ITS1) rDNA spacers tend to increase (c.2 fold) following irradiation. At the protein level, senescent cells showed decreased levels of fibrillarin and UBF transcription factor while localization of both proteins in the nucleolus was not impaired. We conclude that withdrawal from cell cycle does not change expression patterns of rDNA variants. However, defects in rRNA processing may lead to fragmentation of nucleoli in senescent cells.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uptake of gold nanoparticles in HeLa cells observed by confocal microscopy shows dependency on particle size and shape.","authors":"Kimiya Pakravanan, Virginia Bazzurro, Marco Salerno, Alberto Diaspro","doi":"10.1007/s00249-025-01769-5","DOIUrl":"10.1007/s00249-025-01769-5","url":null,"abstract":"<p><p>Uptake of gold nanoparticles by HeLa cells fixed at different incubation times of up to eight hours was investigated using 3D confocal laser scanning microscopy followed by image analysis. The cell bodies were characterized by fluorescence labeling, whereas the gold nanoparticles were identified by light scattering. The amount of nanoparticles uptaken at different times was evaluated with Fiji according to a dedicated protocol. We assessed the effect of particle size (80 and 150 nm diameter spheres) and shape (spheres vs \"urchins\") on their uptake. The large spherical nanoparticles presented approximately fourfold higher levels of uptake than the nanourchins. Also, the spheres presented a clearly increasing uptake in the time profile, reaching a maximum around seven hours and then showing a slight decrease. We ascribe this behavior to a lower aptitude of the cells for taking up nanoparticles with either urchin shape or smaller size and to the possible presence of competing kinetics for exocytosis at the longest times. Live experiments confirmed for the time profile a relatively flat cell response to the urchins and an increasing response to the spheres, yet with a final plateau. However, in the live case, the internalization levels were as low for the spheres as for the urchins.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural adaptability of SARS-CoV-2 Nsp1 with the host network.","authors":"Monikaben Padariya, Ted Hupp, Umesh Kalathiya","doi":"10.1007/s00249-025-01762-y","DOIUrl":"https://doi.org/10.1007/s00249-025-01762-y","url":null,"abstract":"<p><p>The SARS-CoV-2 non-structural protein 1 (Nsp1) acts at multiple points toward the host cell to trigger its mRNA cleavage and decay. Nsp1 is found binding with the 40S ribosomal subunit and inhibiting the translation process, as well as docking with different cyclophilins. Herein, we evaluated the structural physicochemical properties of SARS-CoV-2 Nsp1 protein implementing different computational techniques. The Nsp1 was found to form a structured α-helical C-terminal region, following a conformational switch at residue S166 that is necessary for binding the 40S ribosome subunit. Similarly, the presence of cyclophilins stabilizes the Nsp1 C-terminus making a tilt movement at position 166. In the 40S ribosome-Nsp1 machinery, both the ribosomal uS3 and eS30 components were found equally interacting with Nsp1, which guided construction of their pharmacophores. Among a set of studied cyclophilins, FKBP1B showed the highest affinity with Nsp1 and PPIH made least interactions. The majority of cyclophilins dock to the conserved Nsp1 loop or linker region, which connects the C-terminus to the central domain. Our findings revealed that Nsp1 has a versatile C-terminus region which changes its conformations with respect to its host binding partner. Identified novel binding sites within the Nsp1 can assist in understanding its networking (in current or future such infections), as well as support drug discovery programs aimed at targeting the coronavirus family.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From survival of irradiated mice to modern molecular insights: a seventy-year journey in radiobiology at the institute of biophysics, Czech academy of sciences.","authors":"Jiří Toufar, Lucie Toufarová, Iva Falková, Alena Bačíková, Martin Falk","doi":"10.1007/s00249-025-01765-9","DOIUrl":"https://doi.org/10.1007/s00249-025-01765-9","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive model for evolving density and viscosity gradients in band-forming ultracentrifugation.","authors":"Lukas Dobler, Emre Brookes, Piotr Grodzki, Maciej Lisicki, Borries Demeler, Helmut Cölfen, Piotr Szymczak","doi":"10.1007/s00249-025-01759-7","DOIUrl":"https://doi.org/10.1007/s00249-025-01759-7","url":null,"abstract":"<p><p>Band-forming experiments allow the study of a wide variety of systems by overlaying two solutions with different densities in an analytical ultracentrifuge. Despite their potential benefits over other methods, these experiments are rarely used because all available fitting software encounters systematic errors, failing to account for the evolving gradient in density and viscosity due to diffusive mixing between the two layers. We develop and experimentally validate a predictive model for the purely diffusive mixing of two solutions in a cylindrical system. Capturing the space- and time-dependent evolution of density and viscosity in band-forming experiments, the model enhances their interpretation and underscores the need for analysis software to account for these dynamic changes.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Studying SARS-CoV-2 ssRNA key sequence combining Fourier transform infrared spectroscopy and theoretical folding model.","authors":"Tiziana Mancini, Federica Bertelà, Marta Di Fabrizio, Salvatore Macis, Rosanna Mosetti, Stefano Lupi, Annalisa D'Arco","doi":"10.1007/s00249-025-01766-8","DOIUrl":"https://doi.org/10.1007/s00249-025-01766-8","url":null,"abstract":"<p><p>Fourier transform infrared (FTIR) vibrational spectroscopy is widely used for the analysis of both protein and deoxyribonucleic acid (DNA) secondary structures, being one of the most sensitive vibrational methods to changes in molecular structure. Despite this, only few FTIR studies on ribonucleic acids (RNAs) are available. Here, we investigated a stabilized in vitro transcribed synthetic single-stranded RNA (ssRNA) from wild-type SARS-CoV-2 virus through FTIR spectroscopy and computational methods. We carried out RNA FTIR spectroscopic analysis identifying four main spectral regions of interest associated with the vibrations of sugar and phosphate backbone, base-sugar and bases. Starting from the nucleotides' sequence, we applied two folding predictions to the ssRNA fragment, obtaining the most likely secondary and tertiary structures of the RNA fragment. These predictions have finally been compared to experimental data leading to a comprehensive structural investigation. Our results represent a step forward in understanding the structure of the SARS-CoV-2 ssRNA fragment and a promising potential starting point for sensing applications.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spectroscopic studies of sequence-dependent conformational transitions in asymmetric G/C rich double-stranded DNA.","authors":"Petra Školáková, Iva Kejnovská, Daniel Renčiuk","doi":"10.1007/s00249-025-01767-7","DOIUrl":"https://doi.org/10.1007/s00249-025-01767-7","url":null,"abstract":"<p><p>Nucleic acids, molecules essential for all life, can adopt many alternative structures besides the well-known right-handed double helix, some of which have been reported to exist and function in vivo. One of the most appropriate methods for structural studies of nucleic acids is circular dichroism spectroscopy, utilizing structure-induced chirality due to the asymmetric winding of absorbing nucleobases. Using electronic CD and absorption spectroscopies in combination with melting experiments, we analyzed a conformational equilibrium between DNA double helix and two alternative conformations of nucleic acids, cytosine i-motifs and guanine quadruplexes, as a function of the primary structure of model G/C-rich sequences, containing blocks of G and C runs in particular DNA strands. This paper is a part of special issue dedicated to 70th anniversary of the Biophysical Institute of the Czech Academy of Sciences, where circular dichroism spectroscopy of nucleic acids has been used successfully and impactfully for many years.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microfluidics for protein interaction studies: current methods, challenges, and future perspectives.","authors":"Matthias M Schneider, Tuomas P J Knowles, Sandro Keller, Georg Krainer","doi":"10.1007/s00249-025-01763-x","DOIUrl":"https://doi.org/10.1007/s00249-025-01763-x","url":null,"abstract":"<p><p>Proteins are the key molecular players of life, carrying out their functions through interactions. Microfluidic technologies have emerged as powerful tools for studying protein interactions with exquisite sensitivity, resolution, and throughput. In this review, we highlight recent advances in microfluidic approaches for protein interaction studies. We first explore continuous-flow microfluidics, which utilize diffusion-based techniques and electrophoretic methods, before examining the role of droplet microfluidics in probing protein interactions. We provide an overview of the diverse applications of these technologies in biophysical research, drug discovery, and clinical diagnostics. We conclude with a discussion of the potential of microfluidics for driving future innovations and emerging opportunities.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}