European Biophysics Journal最新文献

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.

There has been a great interest in developing the phage-containing remedy against plague caused by antimicrobial resistant strains of Yersinia pestis, which have been increasingly isolated in recent years from sick humans and animals. Studies thus are under way to develop a “phage cocktail”, which is expected to be effective against a wide range of pathogenic strains. Our paper sheds light on the role of Y. pestis antigen PsaA in reception of the phage L-413C, which might be a possible component of such a “cocktail”. Using optical trapping (OT) and atomic force microscopy (AFM), we showed that PsaA-positive cells and PsaA-coated beads or cantilevers bound more effectively to a substrate coated with L-413C rather than Pokrovskaya phage. Comparing two isogenic strains of Y. pestis (EV and EV∆psaA), we found that when bacteria and phages are co-incubated under slightly acidic pH, as if in a eukaryotic cell, PsaA-positive cells bound the phage L-413C more effectively. There is good evidence to say that L-413C may become a component of a new anti-plague therapy due to its high ability to interact with the pili-forming protein PsaA from the outer membrane of Y. pestis.

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.

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.

Knowledge of the hydrophobicity of amino acids is essential to understanding the structure and function of proteins. One of the most useful tools for this purpose has been the use of hydrophobicity scales. In these scales, each amino acid is attributed with a numerical value that characterizes its hydrophobic or hydrophilic behavior in a protein. These values depend on the particular methodologies used to obtain them. In the present work, we present a way to infer a hydrophobicity scale for all the amino acids from their partial atomic charge from the uniCHARMM force field. All amino acids are more or less soluble in water as they need to be easily bioavailable in the cell medium. It is during the folding process of a polypeptide chain, that an amino acid goes from a soluble state to be part of a folded protein within a cohesive hydrophobic core. In the present work, we have implemented a model and a formula that considers hydrophilicity as the ability of the atoms of amino acids to interact with water, being proportional to the accessibility to the solvent and its partial charge, depending on its sign. On the other hand, hydrophobicity is considered to be more intense the lower the charge on the atom and also proportional to the accessibility of the atom. This procedure improves the accuracy of protein hydrophobicity calculations down to the atomic level.

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.