Biophysics
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“Biophysics” is a peer-reviewed journal for publication of original experimental and theoretical data not being published elsewhere. Reviews at the request of the Editorial Board or Reviews on the initiative of researches subjected to evaluation by the editors are also encouraged. The scope of the journal covers following research areas: 1) Molecular Biophysics; 2) Cell Biophysics; 3) System Biophysics.
Periodicity – 6 issues per year. Russian ISSN: 0006-3029. English ISSN: 0006-3509 (printed version) and 1555-6654 (online version).
Media registration certificate: № 0110172 от 04.02.1993
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Тек жазылушылар үшін
Том 70, № 6 (2025)
Molecular biophysics
Pro- and Antioxidant Properties of Compositions Based on Endogenous Choline Derivatives
Аннотация
The effect of endogenous quaternary ammonium compounds, derivatives of choline, acetylcholine and L-carnitine, on the decomposition of hydroperoxides has been studied. It has been established that choline and acetylcholine in organic media form joint nanoaggregates (QAC—ROOH), in which the radical decomposition of hydroperoxides is accelerated; immobilized on a solid carrier (microcrystalline cellulose), choline and acetylcholine retain the ability to generate radicals in the presence of hydroperoxides and initiate chain processes of oxidation and radical polymerization. L-carnitine, unlike acetylcholine and choline, is an internal salt, and the R4N+ cation is neutralized by the carboxyl group —COO−, i.e. L-carnitine does not have an external counterion and, probably for this reason, differs in the mechanisms of adsorption and interaction with hydroperoxides from acetylcholine and choline. Individual L-carnitine does not affect lipid oxidation processes, but in combination with 2-ethyl-6-methyl-3-hydroxypyridine forms 2-ethyl-6-methyl-3-hydroxypyridinium carnitinate, which has antioxidant and biological activity. In this paper, choline, L-carnitine, and 2-ethyl-6-methyl-3-hydroxypyridinium carnitinate are compared in terms of growth-stimulating activity using the example of wheat seed germination.
Biophysics. 2025;70(6):1045-1051
1045-1051
Comparative Study of Antioxidant Activity of 4-H Pyran Acids Using Optical Methods and Quantum-Chemical Calculations
Аннотация
The main representatives of 4-H-pyran series acids are meconic, comenic, chelidonic and kojic acids. A wide range of physiological activity has been established with respect to these substances, including neuroprotective, anti-inflammatory, immunomodulatory and regenerating activity. A comparative analysis of the antioxidant activity of these acids in various model systems has been carried out using chemiluminescent, spectrophotometric and fluorescent analysis methods, as well as computational methods of quantum chemistry. It was found that, in relation to lipid, luminol, and pyroxyl radicals, all the acids studied in the work showed a dose-dependent decrease in the intensity of the chemiluminescent reaction, expressed by varying degrees of inhibition for each compound. With respect to the stable radical ABTS+•, all the studied acids also had an inhibitory effect. With varying efficiencies, the studied compounds showed a chelating effect on Fe2+ cations and inhibited the development of the Fenton reaction in the model system. The experimental data obtained on the antiradical activity of the studied compounds correlated with the theoretical calculations of their antioxidant potential. The established antioxidant and chelating properties of the basic acids of the 4-H-pyran series allow them to be considered as potential ligands and components in the synthesis of new complex and hybrid compounds.
Biophysics. 2025;70(6):1052-1067
1052-1067
Production of Polyclonal Antibodies Specific to Obscurin of the Long-Tailed Ground Squirrel Urocitellus undulatus: Problems and Prospects
Аннотация
The obtained polyclonal antibodies specific to the N-sequence (76–289 aa) of obscurin of the long-tailed ground squirrel (Urocitellus undulatus) were used to study the isoform composition of this protein in two striated muscles: the myocardium of the left ventricle and M. gastrocnemius medialis. One low molecular weight isoform of obscurin with a molecular weight of 115 kDa has been identified. No other isoforms of obscurin, including giant A- and B-isoforms, have been detected. Seasonal changes in the levels of the low molecular weight obscurin isoform visualized in the cardiac and skeletal muscles of long-tailed ground squirrels were not observed. Further research could focus on sequencing the obscu gene of long-tailed ground squirrels and analyzing obscurin transcripts to obtain antibodies specific to the giant isoforms of this protein.
Biophysics. 2025;70(6):1068-1074
1068-1074
A Deep Learning Approach to Predict Histone Variant Effects on Nucleosome Stability
Аннотация
Histones play a key role in chromatin organization and gene regulation by modulating nucleosome stability and DNA accessibility. Different histone variants can alter the packing density of DNA and affect cell function. This study demonstrates the successful application of the developed ProBAN neural network to predict the affinity of protein-protein interactions, which can be used to assess the effect of various histone variants on the stability of nucleosomes. It has been shown that the incorporation of histone variants into the nucleosome can stabilize or destabilize the structure of the histone octamer through altered patterns of intermolecular interactions. In particular, replacement histone variants H2A.Z, TSH2A.1-TSH2B.1 (in the form of a dimer) and H3.3 form more stable structures inside the nucleosome than canonical histones, while other variants such as TSH2A.1, TSH2B.1 (separately) and H3.6, demonstrated less stable interactions. The observed differences may explain how cells regulate genes in specialized tissues or during development. These results demonstrate the effect of histone sequence variations on the stability of nucleosomes, which is important for the regulation of transcription and epigenetic mechanisms. The ProBAN algorithm has demonstrated high prediction accuracy, representing a valuable tool for further studying the effect of histone variants on chromatin functioning and disease development.
Biophysics. 2025;70(6):1075-1085
1075-1085
Cell biophysics
Restoration and Interaction of Cytochrome c with Short-Term UV-Irradiated Preparations of Manganese-Stabilizing Protein PsbO and PS II Membranes
Аннотация
The interaction of cytochrome c with UV-irradiated manganese-stabilizing protein PsbO and PS II membranes has been studied. It has been established that UV-irradiated PsbO protein is capable of restoring cytochrome c, and this process is inhibited by superoxide dismutase and stimulated by catalase, which indicates the involvement of reactive oxygen species. A similar reduction of cytochrome c was observed upon the addition of UV-irradiated tyrosine or cystine solutions, which confirms the role of amino acid radicals in this process. It has been demonstrated that UV irradiation causes the dimerization of the PsbO protein. After incubation with cytochrome c for 24 hours, the dimer level decreases, restoring the concentration of monomers. UV-irradiated PS II membranes also restore cytochrome c, and the reduction activity depends on the presence of PsbO in PS II. Oxidized cytochrome c binds more strongly to the PsbO protein and photosystem II than restored cytochrome c. These data suggest that UV irradiation generates reactive groups in the PsbO protein, both in isolated form and as part of photosystem II, that restore cytochrome c. Additionally, irradiation of PsbO protein in solution leads to the formation of intermediate products involving reactive oxygen species, which oxidize restored cytochrome c.
Biophysics. 2025;70(6):1086-1096
1086-1096
Interaction of Ascorbic Acid with Spin-Labeled Derivatives of Stearic Acid Embedded in Liposome Membranes
Аннотация
The interaction of ascorbic acid with nitroxyl radicals from spin labels of 5-doxyl stearic and 16-doxyl stearic acids embedded in phosphatidylcholine liposomal membranes was studied using electron paramagnetic resonance (EPR) spectroscopy. Ascorbic acid was shown to effectively restore the 5-doxyl stearic acid tag in liposomes. After 90 minutes of incubation with 10 mM ascorbic acid, the EPR signal from this label decreased by 70%. After 20 minutes, the signal decreased by only 50%. At the same time, there was a decrease in the EPR amplitude of 16-doxyl stearic acid by no more than 35% after incubation of the liposomes for 120 minutes at a concentration of 100 mM ascorbic acid. It is also significant that the signal of 16-doxyl stearic acid remained stable for more than 3 hours. During the reduction of 5-doxyl stearic acid, an ascorbate radical was formed, but this was not observed for 16-doxyl stearic acid. This is likely due to the limited diffusion of ascorbic acid into the bilayer. In the absence of active transport, ascorbic acid is able to penetrate the membrane and interact with radicals near the polar region, reaching the level of 5-doxyl stearic acid tags. These findings are important for our understanding of the antioxidant role of vitamin C in lipid membranes.
Biophysics. 2025;70(6):1097-1104
1097-1104
Normalization of Ca2+ Homeostasis Does not Lead to Correction of Intracellular pH in Hippocampal Culture Neurons under the Influence of Ammonium Ions
Аннотация
In pathologies associated with excitotoxicity and impaired calcium homeostasis, hyperexcitation of neurons is often observed, including during ischemic stroke, hyperammonemia, and neurodegenerative diseases. In the case of long-term sustained depolarization, this hyperactivity disrupts many processes, including the energy balance of ATP, and can lead to cell death. These reactions are often accompanied by prolonged acidification of the cytosol. It affects the activity of a large number of ion channels dependent on intracellular pH, other molecular objects that regulate the concentration of [Ca2+], and other ions in the cell, as well as the membrane potential. Such processes may additionally lead to hyperexcitation and disruption of ion homeostasis. Understanding the relationship between [Ca2+] and pH, is important for the development of methods to eliminate these dysfunctions. In particular, it remains unclear whether correction of Ca2+ homeostasis entails normalization of pH. In this work, it was shown that the elimination of hyperexcitation manifestations, namely, the ultra-high frequency of [Ca2+] pulses and the elevated level of basal [Ca2+], by using the dopamine D2-like receptor (D2-like) agonist PD-168077 (10 μM) or the α2-adrenergic receptor agonist guanfacine (10 μM) does not lead to a noticeable correction of pH, in hippocampal neurons and astrocytes. Thus, to eliminate the effects of hyperexcitation, pH regulation is a separate task, independent of approaches to normalize calcium homeostasis.
Biophysics. 2025;70(6):1105-1114
1105-1114
The Effect of Combined Static and Alternating Low-Frequency Magnetic Fields on the Respiratory Burst Intensity in Mouse Neutrophils Depending on the Magnitude of the Variable Field Component
Аннотация
The effect of weak combined magnetic fields (CMF): a static magnetic field (60 µT) and a collinear alternating magnetic field at a frequency of 12.6 Hz with amplitudes in the range of 10–2500 nT on the intensity of the respiratory burst in a suspension of mouse neutrophils in response to an activator – the N-formyl–Met–Leu–Phe peptide, recorded by luminol-dependent chemiluminescence was studied. It was shown that a 40-minute exposure to combined magnetic fields preceding the introduction of the activator enhances the respiratory burst in the range of alternating field amplitudes of 40–265 nT.
Biophysics. 2025;70(6):1115-1122
1115-1122
The Effect of Inflammatory Activation on Mitochondrial Function and Expression of Apoptosis Inhibitor Genes in THP-1 Acute Myeloid Leukemia Cells
Аннотация
The key functions of mitochondrial respiration and the expression of genes from the BCL2 and IAP families were studied in THP-1 cells from acute myeloid leukemia, both with lipopolysaccharide (LPS) and zymosan A-induced inflammation, as well as in conditions of aseptic inflammation simulating the inflammatory microenvironment. Three-dimensional cell culture was used to investigate these processes. It was found that both LPS and zymosan-A-induced inflammation and aseptic activation led to a decrease in mitochondrial membrane potential and oxygen consumption. At the same time, there was an increase in proinflammatory cytokines such as IL-1β, TNF-α, and IL-6, as well as reactive oxygen species (ROS) and lactate production. It was also found that in THP-1 cells under conditions of inflammation, there was an upregulation of the expression of genes encoding anti-apoptotic proteins, including BIRC3, BIRC7, BCL2, BCL2L1, BCL2L2 and BCL2A1.
Biophysics. 2025;70(6):1123-1131
1123-1131
Complex systems biophysics
Biogeochemical Engineering Technologies for Creating Artificial Soils
Аннотация
Technologies of biogeochemical engineering for the creation of artificial soils are considered. The need for native biophysical models simulating both natural soil functions and newly created ones for various types of land use is substantiated. It is shown that artificial soils can be created from various materials, including, primarily, various industrial, construction, and household waste. The use of biogeochemical technologies makes it possible to regulate the biogeochemical cycle at the microbial level; relevant examples of such technologies are provided.
Biophysics. 2025;70(6):1132-1142
1132-1142
A Compact Terahertz Radiation Source/Detector Based on a Periodically Corrugated Waveguide
Аннотация
Terahertz biophotonics opens up significant prospects for various biomedical applications. In this paper, we propose a scheme of a compact terahertz device, in which the effect of generation and amplification of terahertz radiation is achieved through the interaction of an electron beam, moving in a vacuum, with an electromagnetic wave of a corrugated waveguide. It is shown that both the generation and amplification mode and the detection mode of terahertz waves are possible in the considered device circuit.
Biophysics. 2025;70(6):1143-1155
1143-1155
The Effect of Ultrasound in the 0.88–8.00 MHz Range on the Cracking Processes of Frozen Cryoprotective Solutions when Cooled to –196oC
Аннотация
During cryopreservation of biological material, the stage of formation of a solid phase (ice) during cooling of living cells and a cryoprotective mixture is of great importance. The formation of ice, along with other factors, significantly affects the survival of cells during the freezing–thawing process. Most researchers limit their studies to a temperature range of 0 to –80oC. This range is considered the most critical due to damage to biological material caused by intracellular and extracellular ice crystal formation. However, the processes that occur during further cooling of the frozen material to storage temperatures (–196oC) are poorly understood. When cooled below –100oC, thermomechanical stress in the frozen medium increases due to its compression, thus causing cracking. Exposure to ultrasound at the initial stage of freezing eliminated supercooling in all studied solutions and significantly altered the temperature curve. This study demonstrates the effect of ultrasonal in the 0.88–8.00 MHz frequency range on the cracking of frozen cryoprotective solutions and the formation of ice microparticles. Freezing was performed in a thin 0.2 mm layer at cooling to –196oC. The shape and size of the ice microparticles were determined by cryomicroscopy. With increasing frequency, the degree of homogeneity (size and area) of the microparticles and the shape factor (degree of roundness) increased. It has been shown that ultrasound can effectively influence the formation of cracks in frozen cryo- protective media, especially in the high-frequency range. The greatest effect of increasing the degree of roundness of microparticles was observed in a medium containing saline solution, 10% dimethyl sulfoxide, and 10% egg yolk.
Biophysics. 2025;70(6):1156-1160
1156-1160
Accumulation of Nitric Oxide Stabilized Forms in Rat Organs As a Result of Dinitrosyl Iron Complexes with N-Acetyl-L-Cysteine Ligand Administration
Аннотация
The EPR method revealed that, as a result of sublingual administration of dinitrosyl iron complexes with the ligand N-acetyl-L-cysteine in rats, the transfer and accumulation of stable forms of nitric oxide (NO) occurs in brain tissue. The magnitude of this effect was found to be similar to that observed in the heart, lungs, and liver of the animals.
Biophysics. 2025;70(6):1161-1166
1161-1166
Radioprotective Effect of Extremely High Frequency Electromagnetic Radiation in vitro: Dependence on Parameters and Exposure Conditions
Аннотация
In modern conditions, open and self-organizing biological systems are exposed to a complex spectrum of multi-frequency and modulated electromagnetic radiation of various frequency ranges. The work is devoted to the study of the effect of X-ray irradiation at a dose of 4 Gy on the level of DNA damage in peripheral blood leukocytes of mice pre-exposed to extremely high frequency electromagnetic radiation (EHF EMR) in vitro depending on the carrier and modulating frequencies, exposure duration, intensity and duty cycle of the modulating signal. Using the DNA comet method, it was found that pre-irradiation of cells with electromagnetic radiation of extremely high frequencies leads to a statistically significant decrease in radiation damage to DNA during pulse modulation of radiation with frequencies of 0.1, 1, 16, 32 and 50 Hz. At the same time, irradiation both in the continuous generation mode and in the case of amplitude modulation by a harmonic signal was ineffective. The greatest radioprotective effect was observed at carrier frequencies of 42.2, 51.8 and 61.22 GHz, exposure duration of 20–30 min, incident power density of 100–250 μW/cm2, and duty cycle of the modulation pulse signal of 2–4. The mechanisms of implementation of the obtained biological effects of extremely high frequency electromagnetic radiation associated with the induction of free radicals are discussed.
Biophysics. 2025;70(6):1167-1176
1167-1176
Medical biophysics
Study of the Role of Resonance Phenomena in Brain Responses to Rhythmic Photos stimulation with Linearly Increasing Frequency
Аннотация
The issue of the mechanisms underlying brain responses to rhythmic photos stimulation is characterized by contradictory opinions. To identify the mechanisms of rhythmic photos stimulation, it is necessary to analyze individual spectra using the most detailed set of stimulation frequencies. In this paper, in order to assess the role of resonance phenomena in the effects of rhythmic photos stimulation, an analysis of the fine structure of individual EEG spectra was performed during rhythmic photos stimulation, the frequency of which smoothly increases linearly from 1 to 20 Hz. It was found that within each of the main EEG frequency ranges (delta, theta, alpha and beta), discrete sections of the individual EEG spectrum are detected that are resonantly activated in the subject when the stimulation frequency or its harmonics coincide with their natural frequency. The basic role of resonance mechanisms is demonstrated when considering the advantages of resonance scanning - a promising version of rhythmic photos stimulation, in which the stimulation parameters are set programmatically with a step-by-step increase in frequency.
Biophysics. 2025;70(6):1177-1181
1177-1181
Characteristics of Gold and Silver Nanoparticles in Antitumor Drugs Aurumacryl and Argacryl
Аннотация
A number of physicochemical characteristics of gold and silver present in the active anticancer drugs Aurumacryl and Argacryl have been investigated. Gold and silver nanoparticles in these preparations were visualized under a microscope, and several physicochemical parameters of the nanoparticles, such as the average diameter and zeta potential, were characterized. The concentration of nanoparticles in a liquid medium was also determined. The mechanism for the formation of metallic silver nanoparticles in Argacryl was studied using spectrophotometric and electron paramagnetic resonance techniques on Argacryl samples in the form of films and powder.
Biophysics. 2025;70(6):1182-1192
1182-1192
Peroxiredoxins as Key Markers of Radioresistance and Potential Targets in Cancer Radiotherapy
Аннотация
Radiation therapy is the cornerstone of the treatment of malignant tumors, but its efficacy is often limited by tumor radioresistance and treatment-related toxicity. Peroxiredoxins, multifunctional proteins with antioxidant and chaperone activity, play a key role in maintaining redox homeostasis, regulating signaling pathways, and mediating radioresistance. Due to these properties, they are considered as prognostic biomarkers and potential therapeutic targets for improving the effectiveness of antitumor radiation therapy. The review presents experimental strategies for overcoming radioresistance through peroxiredoxin modulation, including direct targeting, the use of exogenous proteins, engineered mutants, synthetic peptides, nanoplafforms, and combined effects on the peroxiredoxin–thioredoxin system.
Biophysics. 2025;70(6):1193-1210
1193-1210
Morphological and Dimensional Diversity of Gastric Juice Extracellular Vesicles in the Norm and at Gastric Cancer
Аннотация
Complex morphological and dimensional profiling of extracellular vesicles of human gastric juice by cryo-electron microscopy has been performed. It has been shown that in gastric cancer, the proportion of classical individual vesicles surrounded by a single layer of the plasma membrane increases statistically significantly (up to 74% versus 40% in healthy controls), while the representation of multilayer forms decreases. A comparative analysis of data from cryo-electron microscopy and analysis of nanoparticle trajectories has been carried out, demonstrating that cryo-electron microscopy reveals a significantly higher proportion of particles in the range of 40–70 nm. Thus, the paper describes for the first time the composition of extracellular vesicles of gastric juice and reveals significant differences in the morphological distribution between the norm and pathology, as well as systematic discrepancies between the methods of cryo-electron microscopy and analysis of nanoparticle trajectories in the direction of greater sensitivity of cryo-electron microscopy to small vesicles.
Biophysics. 2025;70(6):1211-1220
1211-1220
The Impact of Normacor and Gelofusin Combination on the Preservation of an Isolated Rat Heart during Pressurized Gaseous Hypothermic Storage with Carbon Monoxide and Oxygen Mixture
Аннотация
One of the key challenges in transplantology is the limited period of safe, hypothermic storage for a donor heart. A promising solution to extend this time is gas hypothermic preservation using mixtures of oxygen and carbon monoxide, or other gas agents. However, standardizing this approach requires selecting the conditions for cardiac arrest and blood removal before gas exposure. The goal of this study was to investigate the feasibility of using hypobaric gas-hypothermic preservation for rat hearts, in combination with the cardioplegic solution Normacor mixed with the plasma substitute Gelofusin. An experimental study was conducted on isolated rat hearts (n = 30). Functional (contractility, heart rate) and morphological parameters were evaluated after 12 and 24 hours of storage at 4°C and 6.5 atm pressure of a CO : O2 (1 : 1) gas mixture. Three preparation protocols were compared: perfusion with "Normacor + Gelofusin" solution at 37°C, perfusion with Custodiol solution at 4°C, and storage without perfusion. It was shown that the "Normacor + Gelofusin" combination ensures stable recovery of cardiac contractile function (~50% of native control) and morphological integrity after 12 and 24 hours. After 12 hours, the Normacor group demonstrated a statistically significant improvement in functional recovery compared to the Custodiol group. Histological analysis revealed moderate, potentially reversible ischemia-reperfusion injuries in all groups after 24 hours of exposure to a gaseous medium. The combination of Normacor and Gelofusin solutions, both allowed for clinical use in Russia, was found to be an effective means for pre-conservative preparation of organs for subsequent gas-hypothermic preservation. This finding suggests that this approach could be introduced into clinical practice to extend the preservation time of donor hearts.
Biophysics. 2025;70(6):1221-1229
1221-1229
Study of the Effect of Photobiomodulation on the Human Intestinal Microbiota in vitro During Normal and Post-Cryopreservation
Аннотация
Dysbiosis of the human intestinal microbiota is a key factor in the pathogenesis of numerous diseases. Current corrective approaches, such as probiotics and fecal microbiota transplantation, are often invasive or exhibit limited efficacy. Photobiomodulation, a promising non-invasive approach, has not yet been thoroughly studied for its direct impact on the microbiome in vitro. The purpose of this study was to investigate the effects of photobiomodulation using red (660 nm) and near-infrared (940 nm) light on restoring the viability of human gut microbiota after cryogenic injury, which was used as a model of stress. The intact microbiota from donor stool samples and a pure culture of Bifidobacterium breve were frozen in liquid nitrogen, leading to the death of approximately 50% of cells. After thawing, the samples were irradiated with low fluences ranging from 10 to 600 J/m2. Microbial viability was assessed using the LIVE/DEAD BacLight bacterial viability kit. For B. breve, growth dynamics were also evaluated under anaerobic conditions during culturing on a microplate. Photobiomodulation did not significantly affect the viability of intact (non-cryopreserved) microorganisms. On the contrary, near-infrared irradiation significantly increased the viability of microorganisms after cryopreservation. Both intestinal microbiota showed a maximum increase of +43% with a dose of 40 J/m2 and B. breve showed a maximum of +10% at doses of 40 and 80 J/m2. Growth stimulation of 8% was observed for B. breve during cultivation after irradiation with 660 nm red light. It has been shown for the first time that photobiomodulation with near-infrared light can effectively restore viability in experiments on human microbiota and the culture of B. breve microorganisms after cryogenic damage. On the contrary, near-infrared light irradiation (940 nm) significantly (p ≤ 0.05) enhanced the viability of cryodamaged samples, with a maximum increase of +43% at 40 J/m2 for the human gut microbiota and +10% at 40 and 80 J/m2 for B. breve. In case of B. breve, stimulation of growth by 8% (p ≤ 0.05) during cultivation was also noted. Irradiation with 660 nm red light did not produce pronounced effects. It has been shown for the first time that near-infrared light photobiomodulation can effectively restore the viability and growth of cryodamaged human gut microbiota and Bifidobacterium breve
in vitro. Cryopreservation can be used as a model to study the damage to the intestinal microbiota and screen for physical and chemical factors that can help to recover microorganisms. The findings from this research could lead to the development of non-invasive methods for rehabilitation and treatment of diseases related to human dysbiosis, such as transabdominal photobiomodulation.
Biophysics. 2025;70(6):1230-1239
1230-1239
Discussions
III-Posed Inverse Tasks in Biophysics. A Biophysical Explanation of This Phenomenon and Its Practical Significance
Аннотация
Since all (or almost all) methods of studying biosystems are invasive, ill-posed inverse problems arise when studying biosystems. Using the example of the study of stereological problems, it is shown what is the incorrectness (ill-posedness) of biophysical problems and what challenges researchers face in solving them.
Biophysics. 2025;70(6):1240-1248
1240-1248