Olga S. Sokolova

This paper presents and critically reviews the results of original and some literature based experimental studies conducted by the authors last years on the structural organization of DNA in dormant (starvation stress), anabiotic dormant (4 HR treatment) E. coli cells, as well as the K12 &[Delta]dps strain, which lacks the Dps protein (Dps null E. coli). The experimental data includes small-angle synchrotron radiation diffraction (SAXS) and transmission electron microscopy (TEM) data. Synchrotron radiation diffraction experiments on K12&[Delta]dps cells allowed us to conclude that peaks at 44.3, 22.1, and 14.8 angstrom resolutions are associated exclusively with ordered DNA organization. Peaks at 44.3, 22.1, and 14.8 angstrom resolutions are also observed for samples of dormant (starvation stress) cells and anabiotically dormant cells. Therefore, this ordered DNA organization also applies to samples of dormant and anabiotically dormant cells. A model is proposed that considers the ordered DNA organization in the cell as a cholesteric liquid crystal. The powder diffraction pattern calculated based on this model is compared with experimental small angle X ray scattering (SAXS) data obtained on Dps-null cell samples. The model completely reproduces the key features of the experimental diffraction pattern from Dps-null cell samples. Accordingly, the cholesteric liquid crystal model corresponds to DNA packaging in dormant and anabiotically dormant cells. Cholesteric liquid crystal ordering should be further considered in all models of cellular DNA packaging. To address the question of which structural organization of DNA predominates in the cell: the cholesteric liquid crystal or nanocrystalline or whether they coexist and fully manifest themselves under different external conditions, it is necessary to utilize the latest methodological advances in structural analysis.

Pseudomonas aeruginosa poses major public health threats, due to its robust, treatment-resistant biofilms, which contribute to multi-drug resistance. Bacteriophages offer a promising alternative. This study evaluates giant Phikzvirus and conventional Pbunavirus phages against pre-formed biofilms from four multi-drug-resistant P. aeruginosa clinical isolates. We tested six phages (three Phikzvirus, three Pbunavirus) against four clinical strains, isolated from chronic urological and pulmonary infections (Ur1, Ur14, Lu3, Lu9) at MOIs 0.001–0.1, quantifying biofilm biomass by crystal violet and visualizing architecture by SEM. Phage treatment leads to significant disrupted biofilms in three isolates achieving more than 50% reduction—comparable with typical antibiotic efficacy against mature biofilms. All biofilms retained their EPS architecture after the treatment, as revealed by SEM, suggesting that residual eDNA-polysaccharide complexes could maintain structural cohesion even after bacterial lysis. The phage’s ability to reduce biofilm biomass demonstrated a significant dependence on the multiplicity of infection (MOI). The best results of anti-biofilm activity of phages (reduction in biofilm biomass by more than 75%) were observed for the phage phiKZ for two strains—Ur1 at MOI = 0.001 and Lu9 at MOI = 0.01—and for the phage phi14/1 for the Ur1 strain at MOI = 0.001. The biofilm formed by the antibiotic-resistant clinical isolate Ur14 demonstrated exceptional resistance to both types of bacteriophages despite the sensitivity of bacteria of this strain to the studied phages. This highlights the need for personalized phage therapy, where tailored phage cocktails are selected for each specific bacterial strain to achieve optimal destruction of the biofilm.

Wound infections due to antibiotic resistance pose a global public health problem. Phage therapy is a promising approach to address this issue. To improve localization, phage stability, delivery, and antibacterial performance, we propose polymer mix gel microbeads encapsulated with phages as a model for the delivery of phiKZ bacteriophage to combat Pseudomonas aeruginosa. Phages were loaded into the alginate pre-gel under magnetic stirring, with further cross-linking by chitosan and/or Ca²⁺ ions. The obtained gel microbeads were characterized using FTIR and Raman spectroscopy, and their cytotoxicity and antimicrobial properties were evaluated. This study demonstrated the efficient loading of high-titer phage lysate, achieving up to 99% encapsulation efficiency for alginate–chitosan microbeads. The key characteristics of the microbeads include stable physicochemical properties, slow but continuous phage release over 48 h in physiological saline, and low cytotoxicity. The phage-loaded microbeads demonstrated strong in vitro antimicrobial activity against P. aeruginosa PAO1, resulting in mean reductions of 6.9 log₁₀ and 4.8 log₁₀ CFU/mL for alginate and alginate–chitosan formulations, respectively. This corresponded to a decrease in bacterial concentration from approximately 1.1 × 10¹¹ CFU/mL in untreated controls to 1.1 × 10⁵ CFU/mL and 7.7 × 10⁶ CFU/mL for alginate and alginate–chitosan formulations after 3 h of incubation.

Biochemistry has a strong interest in ion channels, a diverse group of membrane proteins. This group has long remained difficult to study at the structural level, but much progress has been made in recent decades with improvements in biochemical methods and computational procedures. Voltage-gated ion channels undergo conformational changes upon functioning, and multiple models of activation mechanisms were proposed based on experimental data. This review focuses on the structural studies of the functioning of voltage-gated ion channels, which are accompanied by conformational changes in proteins, and the methodological advances that allow their observation. Particular attention is paid to the lipid modulation of ion channels, as well as to the use of various lipids and membrane mimetics to stabilize specific conformations of ion channels. Modern experimental methods that allow obtaining ion channel proteins in specific functional states are discussed, including cryoelectron microscopy and cryoelectron tomography. NMR (Nuclear Magnetic Resonance) spectroscopy approaches and molecular modeling studies of conformational dynamics of ion channels and their isolated domains are also discussed. Finally, new algorithms for studying the conformational mobility of proteins have been recently developed, which help to better understand the mechanisms of ion channel domain movements.

Shiga toxin-converting bacteriophages play a critical role in the emergence and virulence of pathogenic Escherichia coli strains. Despite their significance, detailed structural information on these phages remains scarce. Here we present a high-resolution cryo-electron microscopy and proteomic analysis of the phi24B bacteriophage, revealing an icosahedral capsid with T=9 symmetry, decorated by a processed esterase protein (gp84) and stabilized by cementing proteins. The tail assembly comprises a dodecameric portal, two rings of adapter proteins sharing a common fold, a hexameric nozzle, six lateral tail fibers, and a flexible central needle fiber. The binding sites of the fibers are described. Comparative analysis indicates conservation of the tail structure with related podoviruses but very different peripheral features.

Systèmes hybrides pour application automobile: Dans cette thèse, les sandwichs acier/polymère/acier renforcés ou non et leurs composants, ainsi que leurs propriétés mécaniques et de mise en forme (ou formage) ont été étudiés pour la fabrication des pièces d'automobiles. Les caractéristiques physico-chimiques responsables de la cohésion métal-polymère tout comme de l’usinabilité des sandwichs par emboutissage profond et étirage Erichsen n’ont pas été assez étudiés. Elles sont analysées dans ce travail. Nous avons observé que l'influence des traitements de surface tels que le « traitement corona » peut changer la morphologie de la surface du polymère de base et introduire des groupes fonctionnels polaires sur les surfaces. Le traitement plasma a été utilisé pour activer les surfaces de l’acier avant le "roll-bonding". L'étude a révélé que les sandwichs sans inserts ont une grande aptitude au formage par emboutissage profond, proche de celle de l'acier.

Studying the mechanisms by which Gram-negative heterotrophic bacteria transition from active metabolism to dormancy is an important task, as it is directly related to the problem of bacterial antibiotic resistance and the spread of nosocomial infections. Using electron microscopy, microbiology, and molecular modeling, we investigated the dose-dependent mechanisms of action of 4-hexylresorcinol (4HR), a chemical analog of the anabiosis autoinducer, on the cell membranes of Gram-negative bacteria (using Escherichia coli as an example), leading to the formation of stressed, dormant, and mummified cells. It was shown that 4HR penetrates membranes equally easily both as single molecules and as micelles, distributing itself across the membrane so that the hydrocarbon radicals are aligned parallel to the lipid tails. When micelles penetrate the membrane, uneven distribution of 4HR within and between leaflets occurs, as well as lipid redistribution within the membrane, leading to the appearance of a third peak on the phospholipid electron density profile and a third black band in the membrane region in TEM images of such cells. At 4HR concentrations in solution of 200 µM, its micelles cover the cell membranes in a thick layer, penetrate into the membrane, and completely saturate it. Even higher concentrations create agglomerates or actually micellar arrays within the cell membranes, leading to cell death through mummification.

Jumbo bacteriophages possess exceptionally large capsids accommodating genomes that encode additional proteins, which support their infection and replication. A distinctive structural element, known as the inner body, has been observed in a number of phiKZ-like phage particles and its proteins are believed to play an essential role in phage genome organization and ejection. However, the precise localization and three-dimensional structure of the inner body have remained elusive. Here, we applied the high-dose cryo-electron microscopy (“bubblegram”) approach to localize the inner body within the capsid of phiKZ-like jumbo phage phiK601. The inner body was resolved as a cylindrical structure approximately 22 nm in diameter, tilted by ~ 20° relative to the tail axis and positioned asymmetrically, likely contacting the portal vertex and the opposing capsid edge. It is surrounded by 17 concentric layers of packaged DNA and exhibits positional flexibility within the capsid.

DNA compaction in Escherichia coli cells was studied by synchrotron radiation diffraction and transmission electron microscopy. The aim was to identify DNA

The 5th Russian International Conference Cryo-Electron Microscopy 2025: Achievements and Prospects (RICCEM-2025) was held at the Biology Faculty of Lomonos