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Biophysics
Journal Prestige (SJR): 0.216  Number of Followers: 9  Hybrid journal (It can contain Open Access articles)ISSN (Print) 1555-6654 - ISSN (Online) 0006-3509 Published by Springer-Verlag  [2468 journals]
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- Single SARS Virus Mutation as a Possible Cause of the Predominance of
Asymptomatic COVID-19 Infection Forms-
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Abstract: To explain the predominance of asymptomatic SARS-CoV-2 infection forms, a single virus mutation was hypothesized to change the virus population by affecting its two important parameters, virus infectiousness and pathogenicity. According to the hypothesis, susceptible and asymptomatic forms affect the rate of change in infectiousness and pathogenicity, thereby influencing the infection and incidence rates and eventually altering the proportion of asymptomatic and symptomatic cases. A mathematical model was constructed on the basis of this hypothesis and identified using data from the first wave of COVID-19 in St. Petersburg to check whether changes in microbiological parameters of the model correlate with changes in the proportion of asymptomatic and symptomatic cases. It was concluded that a single virus mutation can affect the proportion.
PubDate: 2023-04-01
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- A Toolbox for Visualization of Sequencing Coverage Signal
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Abstract: Whole genome sequencing data allow access not only to information about genetic variation, but also provide an opportunity to evaluate the overall genome stability. Sequencing coverage signal considered as the number of fragments aligned to a given region within the genome can be used as a trustworthy source of data both on discovery of genomic rearrangements and the current state of whole genome sequencing as well as on accuracy of structural variant predictions by computational algorithms. The latter is of utmost importance, since various tools for finding gene rearrangements often produce conflicting results concerning gene rearrangement events. However, until recently, validation of predicted variants presented a significant challenge, mainly due to the lack of information sources allowing researchers to work directly with coverage signals and to visualize the signals with high precision. The present study proposes Sequence COverage ProfilEs (SCOPE), a prototype toolset that includes databases, web interface, and a series of programs for the processing of sequencing data, as well as for visualization and storage of signal coverage profiles. The computing platform and the interface are equipped with open-source software, support local host deployment, and allow users to process and analyze their own sequencing data.
PubDate: 2023-04-01
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- The Stability of a Collagen Gel after UV Irradiation
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Abstract: Type I collagen is the most common extracellular matrix protein in the human body that provides the basis of tissue structure and regulates cellular functions. In the process of vital activity, the components of the extracellular matrix, in particular collagen, are exposed to ultraviolet radiation. The purpose of this work was to study the effect of ultraviolet irradiation on the stability and structure of collagen fibrils. It has been shown that ultraviolet irradiation had a stabilizing effect on a collagen gel at a concentration of 0.5 mg/mL. The analysis of the diameters of collagen fibrils after ultraviolet irradiation by scanning electron microscopy revealed no change in their size. The area of spreading of cells cultured on collagen fibrils after ultraviolet irradiation was higher compared to the area of cells cultured on collagen fibrils without treatment. It was shown by IR-Fourier spectroscopy that ultraviolet irradiation caused a shift of the amide A band of collagen to a lower frequency region, which indicated a change in the structural order of collagen.
PubDate: 2023-04-01
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- The Amazing DNA Macromolecule: Computer Modeling of its 3D Structure and
the Diversity of Watson–Crick Conformations in the Duplex-
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Abstract: The development of ideas about the 3D structure of DNA and the mechanisms of its formation, from the discovery of the double helix to the present day, is considered. Methods of modeling the 3D structure at different steps of the study of the central molecule of life are reviewed. The results of calculations of intra- and intermolecular interactions among macromolecule subunits provide grounds for the discussion of the marvelous expediency in DNA molecular structure and its adaptability to important biological functions. New data about the substantial contribution of the chemically monotonous and conformationally flexible sugar-phosphate backbone to the formation of the sequence-dependent 3D structure of DNA are presented. The conformational diversity of DNA manifests itself in both the formation of duplexes (and even triplexes or quadruplexes) with different base pair geometries and the formation of duplexes with Watson–Crick nucleoside pairs containing local conformations falling into different regions of the torsion angles of the sugar-phosphate backbone, i.e., different conformational classes. According to our calculations, these classes can be divided into two groups. One of them includes local conformations in which torsion angles are close to one of the energy minimums of the isolated elementary repeating fragment, while the second group consists of conformations where one or more of these angles deviate from that of the nearest energy minimum by more than 30°. The patterns of the formation of local 3D structures in these two groups differ significantly.
PubDate: 2023-04-01
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- Alteration of Enzyme-substrate Interactions by Ultra-high Dilutions of the
Substrate-
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Abstract: Enzymatic reactions are the chemical foundation of life, and are widely used in industry as well. In this regard, finding new ways to optimize enzyme-substrate interactions is a matter of great importance that requires further methodological scrutiny. In this work, we examined the effect of a panel of ultra-high dilutions (UHDs) of luciferin ranging from 1010 to 10102 on luciferin-luciferase reaction of fireflies. Luciferin substrate concentration varied from 0.0025 to 2.5 nM and concentration of ATP was constant. Comparison of the bioluminescence intensity after the addition of various UHDs of luciferin or UHDs of water to the bioluminescent system showed some multidirectional and significant differences. The number of individual UHDs from the studied panel for which significant differences were detected increased sharply with the reduction in the substrate concentration to 0.0025 nM. Similar comparison of the effects of UHDs of a non-specific control imidazole and UHDs of water on the signal intensity did not uncover any differences. Thus, it may be concluded that the presence of UHDs of luciferin specifically inhibits the luciferin-luciferase reaction.
PubDate: 2023-04-01
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- Study of the Mechanism of Interaction of Ficin with a Graft Copolymer of
Carboxymethyl Cellulose Sodium Salt and N-vinylimidazole Using Molecular
Docking, as Well as Infrared and Raman Spectroscopy-
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Abstract: The mechanism of interaction of ficin with a graft copolymer of the sodium salt of carboxymethylcellulose and N-vinylimidazole has been investigated by methods of flexible molecular docking, infrared and Raman spectroscopy. Functional groups and fragments of graft copolymer molecules, as well as amino-acid residues forming the primary structure of the enzyme that interacts between the ficin and the graft copolymer, have been identified. It was shown that Raman spectroscopy gives more complete representation of fragments of graft copolymer macromolecules interacting with protein compared to infrared spectroscopy. It has been found that the amino-acid residues forming the active site of ficin were involved in the formation of hydrogen bonds and hydrophobic interactions with the graft copolymer, which led to an increase in the proteolytic activity of the conjugated enzyme.
PubDate: 2023-04-01
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- Prediction of Metabolic Activity of Rowing Athletes Based on Blood Serum
Biochemical Analysis-
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Abstract: Determination of the state of metabolism is an urgent problem in sports medicine. Biochemical and hematological blood parameters reflect the predominance of either anabolic or catabolic processes in metabolism, which depend on the intensity and duration of training. This study was conducted to determine the predominance of metabolic processes in 21 male rowing athletes (age, 22.55 ± 3.68 years; height, 189.62 ± 6.34 cm; and weight, 88.65 ± 8.55 kg). Monitoring of blood parameters and the level of intensity of training made it possible to establish a linear discriminant function, with which eight main blood parameters were determined for prediction of the metabolic state: creatinine (p < 0.001), uric acid (p < 0.001), urea (p < 0.001), testosterone (p < 0.001), alkaline phosphatase (p < 0.001), albumin (p < 0.05), total calcium (p < 0.05), and total protein (p < 0.05). The reliability of the developed prediction of metabolic activity of athletes using linear discriminant functions was confirmed by a strong positive correlation (r = 0.88; p < 0.001) with the results of assessing the activity of the neuroendocrine system. The accuracy of determining the metabolic state was 91.8%.
PubDate: 2023-04-01
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- Simulation Modeling of Glutamate Cysteine Ligase Activity
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Abstract: Glutathione (γ-glutamyl-cysteinyl-glycine) is one of the main intracellular antioxidants that play an important role in cellular metabolism. In mammalian cells, glutathione is synthesized in two stages, the first of which is catalyzed by glutamate–cysteine ligase and is limiting. In this study, a stochastic algorithm based on Markov chains with continuous time was used to simulate glutamate-cysteine ligase functioning. Several catalytic mechanisms were considered, taking the reverse inhibition of glutathione into account, as well as ATP binding order. Based on the physiological concentrations of the metabolites involved in the reaction, the rate of work of glutamate–cysteine ligase of human erythrocytes was calculated. Among the possible options for the substrate binding to the active site of the enzyme under study, only the mechanism involving primary ATP binding allows obtaining a value for the reaction rate corresponding to the experimentally measured glutamate-cysteine ligase activity at physiological substrate levels. In the case of other substrate binding schemes, the difference in rates was more than an order of magnitude. The analysis performed allows to conclude that when modeling glutathione biosynthesis under in vivo conditions, it is necessary to take into account both the ATP concentration and the reverse inhibition by glutathione.
PubDate: 2023-04-01
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- Alanine: The Usual and the Unexpected
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Abstract: Based on experimental data, one can note the abnormally large contribution of alanine to the stabilization of the alpha helix and other protein conformations. Independent (including experimental) data indicate a particularly large contribution of alanine to the stabilization of the alpha helix. At the same time, positive contributions were revealed, both to the entropy and to the enthalpy of the system. The high contribution of alanine to the enthalpy of alpha helix formation contradicts the generally accepted view that entropy should decrease during the formation of regular structures in proteins. Alanine stabilizes two types of secondary structure out of three, the alpha helix and the left helix of the “polyproline II” type; alanine also stabilizes the beta structure in fibrillar proteins. The stabilizing effect of alanine on the structure of the alpha helix extends to both natively unfolded proteins and alpha helix–substrate conjugates. In short, it would not be an exaggeration to say that the problem of the formation of the secondary structure of protein is reduced to the problem of alanine. The revealed contradictions are paradoxical and their interpretation (first of all, the substantiation of the contribution of alanine to the enthalpy of melting in terms of fundamental physics) is currently absent. However, the data and comments presented in this paper inspire hope for progress in resolving thes contradictions.
PubDate: 2023-04-01
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- Shift of Prooxidant–Antioxidant Balance in Laboratory Animals at Five
Times Higher Deuterium Content in Drinking Water-
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Abstract: Water containing 750 ppm deuterium was used to simulate the isotopic composition of water in ice caps at the poles of Mars and tested for effect on oxidative processes in the liver and blood of laboratory animals. Prolonged consumption of deuterium-rich water was found to increase the deuterium content in the blood plasma to 487 ppm. Higher antioxidant activity was consequently observed the liver and blood plasma. The effect of a medium containing 487 ppm deuterium on the secondary structure of bovine serum albumin (BSA) was additionally studied in a model experiment. Lower intensities were observed in circular dichroism (CD) and intrinsic tryptophan fluorescence spectra, indicating that conformational changes arose in albumin structure when the deuterium content increased in the incubation medium. The study provides a basis for further research of how drinking water with a higher deuterium content (700–1000 ppm) affects living systems, to understand the possibility of life on Mars.
PubDate: 2023-04-01
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- Melting Calorimetry of Rat Liver Nuclei in the Presence of Magnesium Ions
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Abstract: Differential scanning calorimetry (DSC) was used to determine the thermodynamic parameters of intranuclear chromatin decondensation induced in rat liver nuclei by decreasing the concentration of magnesium ions from 5 to 0 mM. Core histones, relaxed DNA, and topologically constrained DNA were shown to be involved consecutively in chromatin melting in a temperature range of 70–100°C. Both Tm and ΔH of individual peaks proved also to depend on the Mg2+ concentration in the buffer. In nuclei with condensed chromatin, Mg2+ ions used at 5 mM significantly increased Tm of core histones (by ~7°C) as compared with their Tm in unfolded chromatin, but decreased Tm of both relaxed and constrained nuclear DNA (by ~2.5 and ~7.5°С, respectively). The melting enthalpy of the peaks significantly increased in the presence of Mg2+. A decrease in the molecular weight of intranuclear DNA abolished the stabilizing effect of Mg2+ on core histones. A new peak with Tm above 100°С became detectable when the Mg2+ concentration exceeded 5 mM, possibly reflecting the thermal behavior of some Mg-induced aggregates. Possible mechanisms underlying the thermal behavior of chromatin within the nucleus are discussed.
PubDate: 2023-04-01
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- Genome-Wide Association Study of Copy Number Variation in Flax Through the
Lens of Genome Integrity-
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Abstract: Classical methods for identification of genetic variants associated with certain macroscopic phenotypic traits are, as a rule, limited to analysis of single nucleotide polymorphisms. Copy number variations and more general structural variants may provide a plethora of useful information due to the magnitude of the changes they induce. However, their use in genome-wide association studies is seriously limited mostly due to the uncertainties in their discovery by computational algorithms from genomic data (i.e., failure to resolve an event with nucleotide resolution). Nevertheless, in certain cases, such analysis is possible and may yield valuable results. Our recent work revealed genetic variants (single nucleotide polymorphisms) possibly related to phenotypic traits determining fiber quality in flax. Here, we decided to extend the analyses to structural variants, namely copy number variations. Importantly, we use a novel high-coverage dataset allowing accurate prediction of copy number variations. Altogether, a list of 41 candidate genes associated with five quantitative phenotypic traits was compiled. Furthermore, the genome stability metric developed earlier facilitated stratification of copy number variant loci with regard to their stability. On the whole, our analysis suggests that the genomic regions less resilient to external and internal stresses are more susceptible to changes associated with the studied phenotypic traits.
PubDate: 2023-04-01
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- Agar Freezing Solution for Long-Term Cryopreservation of Brain Slices from
Nonhibernating Animals-
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Abstract: Malfunction of ionotropic glutamate receptors, such as the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors, has previously been observed after long-term cryopreservation of rat brain slices at –10°C for 30–50 days. To elucidate the factors in cryodamage to AMPA- and NMDA-dependent mechanisms, artificial cerebrospinal fluid (aCSF) solutions containing agar at various concentrations (33, 44, and 50%) were used for cryopreservation of rat olfactory cortex slices. After cryopreservation, the slices were warmed to 37°C and the amplitudes of AMPA and NMDA potentials, which reflected the activities of the AMPA and NMDA mechanisms, were evaluated and compared with those obtained before cryopreservation. AMPA and NMDA potentials changed differently depending on the agar concentration in aCSF. In solutions with 33% agar, the amplitude of AMPA potentials increased by 60%, whereas the amplitude of NMDA potentials remained the same as before cryopreservation. At a 44% agar concentration, the AMPA and NMDA potential amplitudes increased by 70 and 80%, respectively. A complete recovery of the activities of the AMPA and NMDA mechanisms was achieved after cryopreservation in a freezing solution with 50% agar. Under these conditions, the amplitudes of AMPA and NMDA potentials were the same as before cryopreservation. Agar added to an aCSF solution was thus identified as a cryoprotectant that protects the AMPA- and NMDA-dependent mechanisms from cryoinjury. Thus, the results obtained indicate that agar added to the artificial cerebrospinal fluid solution is a cryoprotectant that protects AMPA- and NMDA-dependent mechanisms from cryoinjury. The freezing solution (artificial cerebrospinal fluid and agar) developed for cryopreservation of brain explants of nonhibernating animals will be used to create a nervous tissue cryobank.
PubDate: 2023-04-01
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- On the Use of Kolmogorov Equations to Determine the Characteristics of Ion
Channels-
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Abstract: This article discusses a method for identifying the electrical conduction dynamic properties of voltage-gated ion channels. These channels are characterized by their multiple energy barriers, referred to as gate particles. The innovative method is developed using the Markov random processes theory, an approach that utilizes continuous time and and defined states. The number of states was taken to be equal to the number of energy barriers in the channel plus one. If random flows that switch the gate particles between an open and a closed state are Poisson processes, then a system of Kolmogorov linear differential equations for state probabilities is possible to use to mathematically describe the similar system channels. It is possible to find out the intensities of poisson event flows dependences on membrane potential for it fixed values, based on the model and voltage-clamp test results published in open access journals. Function parameters that describe the intensity of ion transitions through the channel in the Kolmogorov equation can be restored using the generalized least squares method. Examples of determining the transition intensities are described for two types of voltage-gated potassium channels, delayed rectifier potassium channels (IKdr, two identical activation gate particles) and channels with fast activation and inactivation processes (IKa, three identical activation and one inactivation gate particles). It is shown that channel activation and deactivation are described by solving the general Kolmogorov equation.
PubDate: 2023-04-01
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- Part of Anti-COVID Therapy Based on a Theoretical Model Describing
Mechanics of Contact Interaction between Coronavirus and Cell Membrane-
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Abstract: This article proposes a theoretical model of mechanical feedback in pattern formation on deforming a membrane when coronavirus enters a cell. Coronavirus stiff and flexible spike proteins attach to ACE2 receptors on the cell membrane of the target cell. TMPRSS2 triggers the fusion of the viral and cell membranes with the formation of a fusion pore leading to opening of a capsid surrounded by the coronavirus envelope and viral RNA release into the cell. Based on mechanical feedback analysis of contact interaction and elastic shell theory, a critical value of cell radius, at which a fusion pore is formed and membrane damage occurs locally, is determined. The results revealed that the smaller the cell size, the less likely that the cell will be damaged mechanically when exposed to the virus. One of the ways to reduce the cell size is to decrease intracellular fluid volume through the use of medicines – diuretics. The critical value of cell radius is inversely proportional to the value of binding energy at the time of attachment of the coronavirus to the cell membrane. Further research is required to improve our knowledge of the dependency of binding energy on the shape and sizes of spikelike bumps for various types of coronavirus strains. It may be predicted that when a new coronavirus strain will emerge, it may produce lower binding energy to cell surface and the severity of the disease may decrease. It is necessary to verify the conclusions of the theoretical study by experimental methods.
PubDate: 2023-04-01
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- Influence of pH on the Conformation of a Modified Aptamer to Nucleolin
Protein-
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Abstract: The search for agents for targeted delivery of anticancer drugs remains a crucial challenge for medicine. In this context, DNA aptamers targeting cancer cell-specific proteins have medical use. At the same time, additional fine-tuning of aptamer properties to diminish their affinity for potential target cells outside tumor tissues makes the aptamers promising tools in clinical applications due to reduced immunogenicity and fewer side effects. One of the approaches is to employ the deregulation of acidity in cancer cells and tissues. In this work, the AS1411 aptamer to nucleolin was modified by adding a nucleotide sequence to its binding site to create a pH-sensitive linker. UV melting and fluorescence methods were employed to demonstrate that the conformation of the new aptamer depends on pH of the medium.
PubDate: 2023-04-01
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- The Possibilities of Studying Biological Objects on a Pulsed Reactor
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Abstract: Small-angle scattering makes it possible to solve structural biology problems without special sample preparation, which is typical for such methods as X-ray diffraction on protein crystals or cryoelectronic microscopy of proteins. This review provides examples of using small-angle scattering to solve biological problems. It is proposed to introduce into practice the use of small-angle scattering as a method of quality control of the assembly of proteins and protein complexes, as well as testing the identity of the structural organization of biological objects in the native state in prepared samples before measurements by X-ray diffraction or cryo-electron microscopy. The possibilities of the YUMO small-angle neutron scattering spectrometer on the IBR-2 pulse reactor (Laboratory of Neutron Physics of the Joint Institute for Nuclear Research, Dubna, Russia) for solving a wide range of problems, including in biophysics, structural biology, and biotechnology are shown. The main results of studies of various biological systems using small-angle neutron scattering at the YUMO installation are considered. The possibilities of developing methods of structural biology using small-angle scattering, including protein crystallization, are shown.
PubDate: 2023-04-01
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- Theranostics for Oncological Therapy: The Results of World Research and
Development Methods-
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Abstract: Theranostics is a field of medicine where drugs are developed that are both therapeutic agents and tools for the early diagnosis of diseases. Their application is primarily associated with the targeted delivery of the agent to target cells. The development of a clinically effective theranostic drug will be the biggest breakthrough in medicine. This analytical mini-review describes modern approaches to solving problems of theranostics of oncological diseases. Recent studies on the use of radiopharmaceuticals and systems for the MRI imaging of cancerous tumors that are, at the same time, a therapeutic agent are described; information is given on the use of various systems based on fluorescent molecules, in particular, anti-Stokes fluorophores, whose signal is clearly distinguishable under the background fluorescence of tissues surrounding cancer cells, compared with other fluorescent substances. Information is also provided on the comparative use of classical chemotherapeutic agents and promising drugs based on natural substances with less toxicity, such as sulforaphane and cytochrome c.
PubDate: 2023-04-01
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- Influence of Neurotrophic Factors on Protein Composition during Somatic
Nerve Injury and Regeneration-
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Abstract: The levels of neurotrophic factors and the protein composition of somatic nerve membranes were studied during injury and survival of nerves in rats exposed to the action of clobetasol. It was shown that the drug administered intramuscularly induced a more pronounced increase in the level of neurotrophic growth factors and structural proteins responsible for recovery processes than the drug released from a hydrogel derived from microbial polysaccharides; it also stabilized the content of the total protein fraction in the damaged somatic nerves. Proteins of the injured neural conductor degraded less in animals receiving intramuscular injections of clobetasol, probably because the drug administered by injection had better availability than the drug administered from hydrogel composite (slow drug release). In addition, an increase in the amounts of DNA and some protein fractions indicated that clobetasol contributed the activation of genes associated with remyelination. We suppose that clobetasol can stimulate synthesis of neurotrophic growth factors, thereby triggering the phosphatidylinositol-3-kinase and mitogen-activated protein kinase signaling pathways that regulate the processes of cytoskeletal reorganization and axonal growth, as well as enhance the synthesis of structural and axonal proteins necessary to restore the functional activity of the injured nerve fibers.
PubDate: 2023-04-01
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- Effect of Alginate Fabric Dressing with Silver Nanoparticles on the Course
of Wound Process in Laboratory Animals-
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Abstract: Alginates varying in modifying additives (primarily, chitosan) and physical treatment methods are used to design prototypes of innovative wound dressings. The aims of the study were to create a prototype sodium alginate fabric wound dressing with silver nanoparticles (AgNPs) subjected to ten freeze–thaw cycles, to assess its properties, and to evaluate its efficacy in treating the purulent wound process in rats. The original technology of ten freeze–thaw cycles was shown to significantly increase the AgNP amount in the sodium alginate wound dressing, primarily by increasing the amount of AgNPs no larger than 15 nm in diameter, which exert the highest antibacterial activity. The wound dressing with AgNPs reduced the metabolic disturbances in the local function of the nonspecific defense system. On days 3 and 5 after wounding, free radical oxidation indices were more favorable and the levels of antioxidant enzymes (catalase and superoxide dismutase (SOD)) in wound tissue were lower than observed upon application of a wound dressing with AgNPs, but without alginate, or after daily wound debridement without using alginate or AgNPs.
PubDate: 2023-04-01
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