Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque.

The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones' open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A-T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A-T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A-T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13-15 pN·nm).

Changes in Number and Antibacterial Activity of Silver Nanoparticles on the Surface of Suture Materials during Cyclic Freezing.

This article presents the results of the 10-fold cyclic freezing (-37.0 °C) and thawing (0.0 °C) effect on the number and size range of silver nanoparticles (AgNPs). AgNPs were obtained by the cavitation-diffusion photochemical reduction method and their sorption on the fiber surface of various suture materials, perlon, silk, and catgut, was studied. The distribution of nanoparticles of different diameters before and after the application of the cyclic freezing/thawing processes for each type of fibers studied was determined using electron microscopy. In general, the present study demonstrates the effectiveness of using the technique of 10-fold cyclic freezing. It is applicable to increase the absolute amount of AgNPs on the surface of the suture material with a simultaneous decrease in the size dispersion. It was also found that the application of the developed technique leads to the overwhelming predominance of nanoparticles with 1 to 15 nm diameter on all the investigated fibers. In addition, it was shown that after the application of the freeze/thaw method, the antibacterial activity of silk and catgut suture materials with AgNPs was significantly higher than before their treatment by cyclic freezing.

Influence of Environmental Parameters on the Stability of the DNA Molecule.

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

DNA Dynamics under Periodic Force Effects.

The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on various factors. The aim of this study was to examine the molecular dynamics of DNA under the influence of external periodic influences with different frequencies. In the present paper, within the framework of a mechanical model without simplifications, we investigated the effect of various frequencies of external periodic action in the range from 1011 s-1 to 108 s-1 on the dynamics of a DNA molecule. It was shown that under the influence of an external periodic force, a DNA molecule can perform oscillatory movements with a specific frequency characteristic of this molecule, which differs from the frequency of the external influence ω. It was found that the frequency of such specific vibrations of a DNA molecule depends on the sequence of nucleotides. Using the developed mathematical model describing the rotational motion of the nitrogenous bases around the sugar-phosphate chain, it is possible to calculate the frequency and amplitude of the oscillations of an individual DNA area. Such calculations can find application in the field of molecular nanotechnology.

Evaluation of effectiveness of a new treatment method for healing infected wounds: an animal model.

OBJECTIVE: To evaluate the effectiveness of a new treatment method in healing superficial infected wounds compared with surgical debridement with chlorhexidine solution. METHOD: In this animal model, two wounds were created on the back of 10 male adult rabbits. Wounds treated by Method 1 were debrided using 0.02% chlorhexidine aqueous solution and an antibiotic topical ointment. Wounds treated by Method 2 wounds were treated using a newly developed device which enabled visual monitoring of the wound as it was treated with various pharmacological solutions (including antiseptic, antiseptic oxidant and an osmotically active agent) specifically formulated for each wound healing stage. Wound area size (using digital planimetry) and time taken to clean the wound were recorded, and biopsies were taken, at the beginning of the study and at various timepoints throughout. RESULT: It was observed that both wound cleaning and wound healing were accelerated by treatment with method 2 compared with method 1 (by 43.8% and 36.7%, respectively). There were also a significantly smaller number of complications in these wounds [p=0.0044] due to the positive ratios of neutrophils and fibroblasts in the wound cavities (from the third to the fourteenth day after wound modelling). CONCLUSION: Wounds treated with the new device in method 2 had a shorter wound healing time than wounds treated with a traditional method. The automated influx-outflow of solutions removed any fragments of necrotic tissue from the wound surface. Wounds were able to be monitored without the need to remove dressings. The transparent, airtight film, which allowed for wound monitoring without the need to remove dressings, meant that suturing was not required. This resulted in no complications in the wounds treated by this new method.

Electrophysiological Activity and Survival Rate of Rats Nervous Tissue Cells Depends on D/H Isotopic Composition of Medium.

The deuterium content modification in an organism has a neuroprotective effect during the hypoxia model, affecting anxiety, memory and stress resistance. The aim of this work was to elucidate the possible mechanisms of the medium D/H composition modification on nerve cells. We studied the effect of an incubation medium with a 50 ppm deuterium content compared to a medium with 150 ppm on: (1) the activity of Wistar rats' hippocampus CA1 field neurons, (2) the level of cultured cerebellar neuron death during glucose deprivation and temperature stress, (3) mitochondrial membrane potential (MMP) and the generation of reactive oxygen species in cultures of cerebellar neurons. The results of the analysis showed that the incubation of hippocampal sections in a medium with a 50 ppm deuterium reduced the amplitude of the pop-spike. The restoration of neuron activity was observed when sections were returned to the incubation medium with a 150 ppm deuterium content. An environment with a 50 ppm deuterium did not significantly affect the level of reactive oxygen species in neuron cultures, while MMP decreased by 16-20%. In experiments with glucose deprivation and temperature stress, the medium with 50 ppm increased the death of neurons. Thus, a short exposure of nerve cells in the medium with 50 ppm deuterium acts as an additional stressful factor, which is possibly associated with the violation of the cell energy balance. The decrease in the mitochondrial membrane potential, which is known to be associated with ATP synthesis, indicates that this effect may be associated with the cell energy imbalance. The decrease in the activity of the CA1 field hippocampal neurons may reflect reversible adaptive changes in the operation of fast-reacting ion channels.

Reduction of Deuterium Level Supports Resistance of Neurons to Glucose Deprivation and Hypoxia: Study in Cultures of Neurons and on Animals.

The effect of a reduced deuterium (D) content in the incubation medium on the survival of cultured neurons in vitro and under glucose deprivation was studied. In addition, we studied the effect of a decrease in the deuterium content in the rat brain on oxidative processes in the nervous tissue, its antioxidant protection, and training of rats in the T-shaped maze test under hypoxic conditions. For experiments with cultures of neurons, 7-8-day cultures of cerebellar neurons were used. Determination of the rate of neuronal death in cultures was carried out using propidium iodide. Acute hypoxia with hypercapnia was simulated in rats by placing them in sealed vessels with a capacity of 1 L. The effect on oxidative processes in brain tissues was assessed by changes in the level of free radical oxidation and malondialdehyde. The effect on the antioxidant system of the brain was assessed by the activity of catalase. The study in the T-maze was carried out in accordance with the generally accepted methodology, the skill of alternating right-sided and left-sided loops on positive reinforcement was developed. This work has shown that a decrease in the deuterium content in the incubation medium to a level of -357‱ has a neuroprotective effect, increasing the survival rate of cultured neurons under glucose deprivation. When exposed to hypoxia, a preliminary decrease in the deuterium content in the rat brain to -261‱ prevents the development of oxidative stress in their nervous tissue and preserves the learning ability of animals in the T-shaped maze test at the level of the control group. A similar protective effect during the modification of the 2H/1H internal environment of the body by the consumption of DDW can potentially be used for the prevention of pathological conditions associated with the development of oxidative stress with damage to the central nervous system.

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA.

In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.