Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0640
A. Mitina, N. Orlova, A. Dergilev, Yuriy Orlov
One of the fundamental tasks in bioinformatics involves searching for repeats, which are statistically heterogeneous segments within DNA sequences and complete genomes of microorganisms. Theoretical approaches to analyzing the complexity of macromolecule sequences (DNA, RNA, and proteins) were established prior to the availability of complete genomic sequences. These approaches have experienced a resurgence due to the proliferation of mass parallel sequencing technologies and the exponential growth of accessible data. This article explores contemporary computer methods and existing programs designed to assess DNA text complexity as well as construct profiles of properties for analysing the genomic structures of microorganisms. The article offers a comprehensive overview of available online programs designed for detecting and visualising repeats within genetic text. Furthermore, the paper introduces a novel computer-based implementation of a method to evaluate the linguistic complexity of text and its compression using Lempel-Ziv. This approach aims to identify structural features and anomalies within the genomes of microorganisms. The article also provides examples of profiles generated through the analysis of text complexity. Application of these complexity estimates in the analysis of genome sequences, such as those of the SARS-CoV-2 coronavirus and the Mumps Orthorubulavirus, is discussed. Specific areas of low complexity within the genetic text have been successfully identified in this research.
生物信息学的基本任务之一是搜索重复序列，即 DNA 序列和微生物完整基因组中的统计异质性片段。在获得完整基因组序列之前，分析大分子序列（DNA、RNA 和蛋白质）复杂性的理论方法已经确立。随着大规模并行测序技术的普及和可访问数据的指数级增长，这些方法又重新兴起。本文探讨了当代计算机方法和现有程序，这些方法和程序旨在评估 DNA 文本的复杂性，以及构建用于分析微生物基因组结构的特性曲线。文章全面概述了用于检测和可视化基因文本中重复序列的现有在线程序。此外，文章还介绍了一种基于计算机的新方法，该方法利用 Lempel-Ziv 评估文本的语言复杂性并进行压缩。这种方法旨在识别微生物基因组中的结构特征和异常。文章还举例说明了通过分析文本复杂性生成的剖面图。文章讨论了这些复杂性估计值在基因组序列分析中的应用，如 SARS-CoV-2 冠状病毒和腮腺炎正粘病毒的基因组序列。这项研究成功确定了基因文本中复杂度较低的特定区域。
{"title":"COMPUTATIONAL TOOLS FOR THE DNA TEXT COMPLEXITY ESTIMATES FOR MICROBIAL GENOMES STRUCTURE ANALYSIS","authors":"A. Mitina, N. Orlova, A. Dergilev, Yuriy Orlov","doi":"10.29039/rusjbpc.2023.0640","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0640","url":null,"abstract":"One of the fundamental tasks in bioinformatics involves searching for repeats, which are statistically heterogeneous segments within DNA sequences and complete genomes of microorganisms. Theoretical approaches to analyzing the complexity of macromolecule sequences (DNA, RNA, and proteins) were established prior to the availability of complete genomic sequences. These approaches have experienced a resurgence due to the proliferation of mass parallel sequencing technologies and the exponential growth of accessible data. This article explores contemporary computer methods and existing programs designed to assess DNA text complexity as well as construct profiles of properties for analysing the genomic structures of microorganisms. The article offers a comprehensive overview of available online programs designed for detecting and visualising repeats within genetic text. Furthermore, the paper introduces a novel computer-based implementation of a method to evaluate the linguistic complexity of text and its compression using Lempel-Ziv. This approach aims to identify structural features and anomalies within the genomes of microorganisms. The article also provides examples of profiles generated through the analysis of text complexity. Application of these complexity estimates in the analysis of genome sequences, such as those of the SARS-CoV-2 coronavirus and the Mumps Orthorubulavirus, is discussed. Specific areas of low complexity within the genetic text have been successfully identified in this research.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"80 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0643
S. Leontieva
The MN12SX/6-31++G(d,p)/SMD theory level exactly reproduced both positions of the main maximum and short-wavelength shoulder of OX750 absorption in an aqueous solution. The optimal functional for calculating the vibronic absorption spectra of different oxazine dyes in an aqueous solution was discussed based on the author’s present and previous studies. The absorption spectrum shoulder is caused by the vibronic transition. The vibrations involved in vibronic transitions correspond to large-scale molecular movements, are low-frequency, and very weak compared to the others. However, excitation significantly influences the vibrations including the most intensive ones. Photoinduced charge redistribution is local and there is no charge transfer over the dye molecule as a whole. Aliphatic hydrogen atoms prevent water molecules from accessing the N24 nitrogen atom. Considering H-bonded "solute-solvent" interactions by three water molecules led to a redshift of the entire spectrum by ≈15 nm. A strengthening of H-bonds with water molecules upon OX750 excitation was found, which explains this bathochromic effect. The intensity of low-frequency vibrations (including those involved in vibronic transitions) increases with the addition of bound water molecules, especially in an excited state. The vibration of the N-H bond of the imino group is strengthened (especially in an excited state) due to water molecule binding. Noticeable polarization of one water molecule bounded was revealed upon dye excitation. The vibronic model was also applied to calculate the emission spectrum of OX750 in the aqueous media.
MN12SX/6-31++G(d,p)/SMD 理论水平精确再现了水溶液中 OX750 吸收的主最大值和短波长肩的位置。根据作者目前和以往的研究，讨论了计算水溶液中不同噁嗪染料振子吸收光谱的最佳函数。吸收光谱肩是由振子跃迁引起的。参与振子跃迁的振动与大尺度分子运动相对应，频率较低，与其他振动相比非常微弱。然而，激发会对振动（包括最强烈的振动）产生重大影响。光诱导的电荷再分布是局部的，染料分子整体上没有电荷转移。脂肪族氢原子阻止水分子进入 N24 氮原子。考虑到三个水分子的 H 键 "溶质-溶剂 "相互作用，整个光谱的红移≈15 nm。研究发现，OX750 激发后，与水分子的 H 键作用得到加强，这也是这种浴色效应的原因。随着结合水分子的加入，特别是在激发态，低频振动的强度（包括参与振动跃迁的振动）会增加。由于水分子的结合，亚氨基的 N-H 键振动增强（尤其是在激发态）。染料激发时，一个水分子结合的极化现象明显。振子模型还被用于计算 OX750 在水介质中的发射光谱。
{"title":"VIBRONIC SPECTRA OF OXAZINE 750 DYE IN AQUEOUS MEDIA: A COMPUTATIONAL STUDY","authors":"S. Leontieva","doi":"10.29039/rusjbpc.2023.0643","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0643","url":null,"abstract":"The MN12SX/6-31++G(d,p)/SMD theory level exactly reproduced both positions of the main maximum and short-wavelength shoulder of OX750 absorption in an aqueous solution. The optimal functional for calculating the vibronic absorption spectra of different oxazine dyes in an aqueous solution was discussed based on the author’s present and previous studies. The absorption spectrum shoulder is caused by the vibronic transition. The vibrations involved in vibronic transitions correspond to large-scale molecular movements, are low-frequency, and very weak compared to the others. However, excitation significantly influences the vibrations including the most intensive ones. Photoinduced charge redistribution is local and there is no charge transfer over the dye molecule as a whole. Aliphatic hydrogen atoms prevent water molecules from accessing the N24 nitrogen atom. Considering H-bonded \"solute-solvent\" interactions by three water molecules led to a redshift of the entire spectrum by ≈15 nm. \u0000A strengthening of H-bonds with water molecules upon OX750 excitation was found, which explains this bathochromic effect. The intensity of low-frequency vibrations (including those involved in vibronic transitions) increases with the addition of bound water molecules, especially in an excited state. The vibration of the N-H bond of the imino group is strengthened (especially in an excited state) due to water molecule binding. Noticeable polarization of one water molecule bounded was revealed upon dye excitation. The vibronic model was also applied to calculate the emission spectrum of OX750 in the aqueous media.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"12 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141380243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0652
D. Lavrichenko, A. Tkachuk, E. Kladchenko, A. Andreeva
In this work, using the methods of flow cytometry and laser diffraction, the analysis of the functional state of hemocytes (osmotic fragility, the ratio of cell types in the hemolymph, the ability to produce ROS) was carried out of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1819), acclimatized to low (6 ‰, 10 ‰, 14 ‰) and high salinity (24%, 30 %). Acclimation to different salinity led to a multidirectional change in the cellular composition of the hemolymph of mussels, the most pronounced effect was observed at low salinity. At the same time, both in conditions of low and high salinity, an increase in the intracellular concentration of ROS in hemocytes was noted, which may indicate the development of oxidative stress. In addition, with all changes in salinity, a shift in the osmotic fragility curve was recorded. The results of this work showed that the Mediterranean mussel has a pronounced tolerance to short-term (48 h) fluctuations in salinity, while the decrease in salinity was accompanied by more pronounced functional changes. In turn, the shift in the osmotic resistance curve indicates the involvement of cellular mechanisms of osmoregulation in Mediterranean mussels in adapting to short-term changes in salinity.
{"title":"THE EFFECT OF SHORT-TERM SALINITY CHANGES ON THE FUNCTIONAL FEATURES OF MEDITERRANEAN MUSSEL HEMOCYTES","authors":"D. Lavrichenko, A. Tkachuk, E. Kladchenko, A. Andreeva","doi":"10.29039/rusjbpc.2023.0652","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0652","url":null,"abstract":"In this work, using the methods of flow cytometry and laser diffraction, the analysis of the functional state of hemocytes (osmotic fragility, the ratio of cell types in the hemolymph, the ability to produce ROS) was carried out of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1819), acclimatized to low (6 ‰, 10 ‰, 14 ‰) and high salinity (24%, 30 %). Acclimation to different salinity led to a multidirectional change in the cellular composition of the hemolymph of mussels, the most pronounced effect was observed at low salinity. At the same time, both in conditions of low and high salinity, an increase in the intracellular concentration of ROS in hemocytes was noted, which may indicate the development of oxidative stress. In addition, with all changes in salinity, a shift in the osmotic fragility curve was recorded. The results of this work showed that the Mediterranean mussel has a pronounced tolerance to short-term (48 h) fluctuations in salinity, while the decrease in salinity was accompanied by more pronounced functional changes. In turn, the shift in the osmotic resistance curve indicates the involvement of cellular mechanisms of osmoregulation in Mediterranean mussels in adapting to short-term changes in salinity.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"150 6‐8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0639
E. Lesovaya, O. Sadykova, P. Lobachevsky
Interpretation of the growth of a malignant tumor and its response to therapeutic treatment requires consideration of its heterogeneity, taking into account the presence in it of a small subpopulation of tumor stem cells along with ordinary tumor cells. In present work, a mathematical model is proposed that combines two basic concepts of the theory of tumor growth - stochastic growth and the presence of a subpopulation of tumor stem cells. The model is a system of ordinary differential equations that describes the dynamics of subpopulations of tumor cells, taking into account different types of division and transitions between them. An important feature of the system is the maintenance of the equilibrium proportion of tumor stem cells in an unirradiated tumor using feedback. The model was used to interpret experimental data on inhibition of tumor growth after protons irradiation at a dose of 10 Gy only and the combined treatment of irradiation and the inhibitor of DNA synthesis AraC in laboratory mice with grafted melanoma B16. The effect of irradiation only and irradiation in combination with AraC is included in the system using a parameter describing the probability of loss of the cell's ability to successfully divide. As a result, the dependence of tumor volume on time calculated for cases without irradiation, after irradiation and after irradiation with AraC serves as a good approximation of experimental data, which makes it possible to evaluate the parameters of the system.
{"title":"MODELING OF HETEROGENEOUS TUMOR DYNAMICS. THE INFLUENCE OF PROTON IRRADIATION ONLY AND IN COMBINATION WITH DNA SYNTHESIS INHIBITOR – ARAC","authors":"E. Lesovaya, O. Sadykova, P. Lobachevsky","doi":"10.29039/rusjbpc.2023.0639","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0639","url":null,"abstract":"Interpretation of the growth of a malignant tumor and its response to therapeutic treatment requires consideration of its heterogeneity, taking into account the presence in it of a small subpopulation of tumor stem cells along with ordinary tumor cells. In present work, a mathematical model is proposed that combines two basic concepts of the theory of tumor growth - stochastic growth and the presence of a subpopulation of tumor stem cells. The model is a system of ordinary differential equations that describes the dynamics of subpopulations of tumor cells, taking into account different types of division and transitions between them. An important feature of the system is the maintenance of the equilibrium proportion of tumor stem cells in an unirradiated tumor using feedback. The model was used to interpret experimental data on inhibition of tumor growth after protons irradiation at a dose of 10 Gy only and the combined treatment of irradiation and the inhibitor of DNA synthesis AraC in laboratory mice with grafted melanoma B16. The effect of irradiation only and irradiation in combination with AraC is included in the system using a parameter describing the probability of loss of the cell's ability to successfully divide. As a result, the dependence of tumor volume on time calculated for cases without irradiation, after irradiation and after irradiation with AraC serves as a good approximation of experimental data, which makes it possible to evaluate the parameters of the system.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"3 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141378739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0637
G. Morozova, M. Muny'os, A. Ivanov, T. Kulinich, S. Romanov
Biophysical control of radiation exposure to humans in the areas of nuclear reactors, in space flight conditions, as well as during radiation therapy, is relevant today. In this regard, the following tasks were solved in this work: 1) study of the leukocytes reactions in the blood after a single exposure to 60Co γ-radiation on the blood in vitro; 2) mathematical modeling of the fast immune responses using energy indicators of cells. By use of the luminescent microscope, lymphocytes and neutrophils were recognized and examined in donor venous blood smears, vitally stained with a cationic probe 4-(n-dimethylaminostyril)-1-methylpyridinium (DSM). Cell energy activity (EA) in each population was characterized by the sum of transmembrane potentials (TMP) on the outer and mitochondrial membranes, which was assessed by DSM fluorescence intensity and color in cell mitochondria and nuclei. Dose-dependent γ-irradiation effects were evaluated on the basis of digital fluorescent images computer analysis. It was found in the experiments that the change in the TMP of after blood γ - irradiation in doses of 1Gy-5Gy depends on their initial EA. An S-shaped dose dependence was revealed for the irradiated lymphocytes energy activity. The greatest effect of cells energy decrease occurs after irradiation with 4 Gy dose. A model of T-dependent immune responses is proposed in the form a system of nonlinear differential equations before and after blood irradiation, where the concentrations for five cell populations are replaced by their fluorescent variables, which reflect the number of active mitochondria in each population. Such a model is also adequate for describing the rapid phase of the immune response after single-hit radiation exposure of the body.
{"title":"INVESTIGAISTION AND MODELING OF LEUKOCYTE RESPONSES IN THE BLOOD TO γ- IRRADIATION USING ENERGY PARAMETERS OF IMMUNE NETWORK CELLS","authors":"G. Morozova, M. Muny'os, A. Ivanov, T. Kulinich, S. Romanov","doi":"10.29039/rusjbpc.2023.0637","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0637","url":null,"abstract":"Biophysical control of radiation exposure to humans in the areas of nuclear reactors, in space flight conditions, as well as during radiation therapy, is relevant today. In this regard, the following tasks were solved in this work: 1) study of the leukocytes reactions in the blood after a single exposure to 60Co γ-radiation on the blood in vitro; 2) mathematical modeling of the fast immune responses using energy indicators of cells. By use of the luminescent microscope, lymphocytes and neutrophils were recognized and examined in donor venous blood smears, vitally stained with a cationic probe 4-(n-dimethylaminostyril)-1-methylpyridinium (DSM). Cell energy activity (EA) in each population was characterized by the sum of transmembrane potentials (TMP) on the outer and mitochondrial membranes, which was assessed by DSM fluorescence intensity and color in cell mitochondria and nuclei. Dose-dependent γ-irradiation effects were evaluated on the basis of digital fluorescent images computer analysis. It was found in the experiments that the change in the TMP of after blood γ - irradiation in doses of 1Gy-5Gy depends on their initial EA. An S-shaped dose dependence was revealed for the irradiated lymphocytes energy activity. The greatest effect of cells energy decrease occurs after irradiation with 4 Gy dose. A model of T-dependent immune responses is proposed in the form a system of nonlinear differential equations before and after blood irradiation, where the concentrations for five cell populations are replaced by their fluorescent variables, which reflect the number of active mitochondria in each population. Such a model is also adequate for describing the rapid phase of the immune response after single-hit radiation exposure of the body.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0646
A. Montiel del Cueto, Adrian Ernandes Sant'yago, M. Gonzalez Flores, C. Palomino Jimenez, E. Mendez Albores, M. Gonzalez Fuentes
A microbial fuel cell is a bioelectrochemical device that uses microorganisms, such as electrogenic bacteria, capable of generating electricity. However, the electrical energy generated depends mainly on the ability of the microorganisms present in the anode to decompose the organic matter contained in an effluent. In this work, an electrochemical setting formed as an anode and a cathode of graphite felt were connected in an electrical circuit to electro-stimulate microorganisms to enhance the biofilm on the anode. In this sense, different potential values were imposed in several electrochemical cells to evaluate chemical oxygen demand, volatile solids, and bacteria increase. Dunnett method was used to find significant differences between treatments, taking a sample without treatment as the control sample.
{"title":"STATISTICAL EVALUATION FOR BACTERIA ELECTRO-STIMULATION USING THE DUNNETT METHOD FOR A MICROBIAL FUEL CELL","authors":"A. Montiel del Cueto, Adrian Ernandes Sant'yago, M. Gonzalez Flores, C. Palomino Jimenez, E. Mendez Albores, M. Gonzalez Fuentes","doi":"10.29039/rusjbpc.2023.0646","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0646","url":null,"abstract":"A microbial fuel cell is a bioelectrochemical device that uses microorganisms, such as electrogenic bacteria, capable of generating electricity. However, the electrical energy generated depends mainly on the ability of the microorganisms present in the anode to decompose the organic matter contained in an effluent. In this work, an electrochemical setting formed as an anode and a cathode of graphite felt were connected in an electrical circuit to electro-stimulate microorganisms to enhance the biofilm on the anode. In this sense, different potential values were imposed in several electrochemical cells to evaluate chemical oxygen demand, volatile solids, and bacteria increase. Dunnett method was used to find significant differences between treatments, taking a sample without treatment as the control sample.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"166 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141375906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0634
A. Lelekov, V. Klochkova, A. Poplavskaya
The study of light-dependent growth of butch culture Phaeodactylum tricornutum has been carried out. Based on the developed mathematical model of the true absorption spectrum, an express method for determining the concentration of photosynthetic pigments without interfering with the growth process of the culture was proposed. In the exponential phase at an irradiance of 120 μE·m-2·s-1, the maximum specific synthesis rates of chlorophylls a and c were determined, which were 1,4 times higher than the specific growth rate of the culture and amounted to 0,3 day-1. On the eighth day of the experiment, a kink in the growth curve was observed, which was expressed as a decrease in both growth rate and chlorophyll production. At the transition to the linear growth phase, the maximum productivity of Pheodactylum was 0,15 g·l-1·day-1, and chlorophyll production was 3,44 and 2,85 mg·l-1·day-1 a and c, respectively. The dependence of the integral light absorption coefficient on chlorophyll a concentration was obtained, which is described by the Bouguer-Lambert-Bera law with a sufficient degree of accuracy; the specific light absorption coefficient was 0,10 m2·g-1 dry matter and 0,008 m2·mg-1 chlorophyll a. Comparison of the results obtained with literature data showed that at irradiances of 120 μE·m-2·s-1 and 602 μE·m-2·s-1 the specific rates of chlorophyll a synthesis are the same, and the maximum specific growth rate of Ph. tricornutum culture increases proportionally with increasing light intensity from 0,23 to 0,91 day-1. The results obtained indicate that chlorophyll a synthesis is determined not by the effective light intensity, but by the amount of reserve biomass accumulated during the previous light period.
对丁孔培养物 Phaeodactylum tricornutum 的光依赖性生长进行了研究。根据所建立的真实吸收光谱数学模型，提出了一种在不干扰培养物生长过程的情况下测定光合色素浓度的快速方法。在辐照度为 120 μE-m-2-s-1 的指数期，测定了叶绿素 a 和 c 的最大特定合成率，比培养物的特定生长率高 1.4 倍，达到 0.3 天-1。在实验的第八天，观察到生长曲线出现扭结，表现为生长速度和叶绿素产量的下降。在过渡到线性生长阶段时，Pheodactylum 的最大生产力为 0.15 克-升-1-天-1，叶绿素产量分别为 3.44 和 2.85 毫克-升-1-天-1 a 和 c。根据布盖尔-兰伯特-贝拉（Bouguer-Lambert-Bera）定律，得出了整体光吸收系数与叶绿素 a 浓度的关系，并对其进行了足够精确的描述；比光吸收系数为 0.10 m2-g-1（干物质）和 0.008 m2-mg-1 （叶绿素 a）。将所得结果与文献数据进行比较后发现，在 120 μE-m-2-s-1 和 602 μE-m-2-s-1 的辐照度下，叶绿素 a 的特定合成率是相同的。研究结果表明，叶绿素 a 的合成不是由有效光照强度决定的，而是由前一个光照周期积累的储备生物量决定的。
{"title":"PRODUCTION CHARACTERISTICS OF BATCH CULTURE PHAEODACTYLUM TRICORNUTUM BOHLIN DURING PHOTOADAPTATION","authors":"A. Lelekov, V. Klochkova, A. Poplavskaya","doi":"10.29039/rusjbpc.2023.0634","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0634","url":null,"abstract":"The study of light-dependent growth of butch culture Phaeodactylum tricornutum has been carried out. Based on the developed mathematical model of the true absorption spectrum, an express method for determining the concentration of photosynthetic pigments without interfering with the growth process of the culture was proposed. In the exponential phase at an irradiance of 120 μE·m-2·s-1, the maximum specific synthesis rates of chlorophylls a and c were determined, which were 1,4 times higher than \u0000the specific growth rate of the culture and amounted to 0,3 day-1. On the eighth day of the experiment, a kink in the growth curve was observed, which was expressed as a decrease in both growth rate and chlorophyll production. At the transition to the linear growth phase, the maximum productivity of Pheodactylum was 0,15 g·l-1·day-1, and chlorophyll production was 3,44 and 2,85 mg·l-1·day-1 a and c, respectively. The dependence of the integral light absorption coefficient on chlorophyll a concentration was obtained, which is described by the Bouguer-Lambert-Bera law with a sufficient degree of accuracy; \u0000the specific light absorption coefficient was 0,10 m2·g-1 dry matter and 0,008 m2·mg-1 chlorophyll a. Comparison of the results obtained with literature data showed that at irradiances of 120 μE·m-2·s-1 and 602 μE·m-2·s-1 the specific rates of chlorophyll a synthesis are the same, and the maximum specific growth rate of Ph. tricornutum culture increases proportionally with increasing light intensity from 0,23 to \u00000,91 day-1. The results obtained indicate that chlorophyll a synthesis is determined not by the effective light intensity, but by the amount of reserve biomass accumulated during the previous light period.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"110 s425","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141377057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0651
A. Botin, A. Pulin, A. Gavrilov, T. Popova, A. Cordova
The relevance of the problem. The widespread and uncontrolled use of antibacterial drugs not only in medicine, but also in agriculture, animal husbandry, and the food industry has led to the spread of multi-resistant strains resistant to the most common antibacterial drugs. In search of alternative strategies for the prevention and control of bacterial infection, attention is increasingly being paid to bacteriophage (phage) therapy. With a wide range of genetic engineering capabilities, these bacterial viruses can be modified to achieve precise control and detection of bacteria and thus serve as a new source of antimicrobial agents. In addition to being used in antimicrobial therapy, phages can also be used as transport systems for drug delivery, as vaccines, or can be used for nanosembly of new materials, since phages themselves, their fragments and components are nanoobjects and functioning nanomachines, the assembly process of which is extremely relevant. The purpose of this article is: to analyze and summarize the most important information on the topic of bacteriophages, methods of their determination and effective transformation in modern science, to evaluate the achievements of modern research in the process of assembling heads (capsids) and laying intracapsid DNA in caudate bacteriophages (phage lambda and phage T4), the production of genetically modified phages and a review of the main prospects for the development of this direction.
问题的相关性。抗菌药物不仅在医学领域，而且在农业、畜牧业和食品工业中的广泛和无节制使用，导致了对最常见的抗菌药物具有抗药性的多重耐药菌株的传播。为了寻找预防和控制细菌感染的替代策略，噬菌体疗法日益受到关注。这些细菌病毒具有广泛的基因工程能力，可以通过改造实现对细菌的精确控制和检测，从而成为抗菌剂的新来源。除了用于抗菌治疗外，噬菌体还可用作给药运输系统、疫苗，或用于新材料的纳米组装，因为噬菌体本身、其片段和成分都是纳米物体和功能纳米机器，其组装过程具有极大的相关性。本文的目的是：分析和总结有关噬菌体这一主题的最重要信息、现代科学中确定和有效转化噬菌体的方法、评价现代研究在组装头（噬菌盖）和铺设尾状噬菌体（λ噬菌体和 T4 噬菌体）噬菌盖内 DNA 过程中取得的成就、转基因噬菌体的生产以及对这一方向主要发展前景的回顾。
{"title":"SELF-ORGANIZATION IN VIRUSES FORMATION: THE NANO-PROCESS OF ASSEMBLING HEADS (CAPSIDS) AND LAYING DNA ON THE EXAMPLE OF TAILED BACTERIOPHAGES (LAMBDA, T4)","authors":"A. Botin, A. Pulin, A. Gavrilov, T. Popova, A. Cordova","doi":"10.29039/rusjbpc.2023.0651","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0651","url":null,"abstract":"The relevance of the problem. The widespread and uncontrolled use of antibacterial drugs not only in medicine, but also in agriculture, animal husbandry, and the food industry has led to the spread of multi-resistant strains resistant to the most common antibacterial drugs. In search of alternative strategies for the prevention and control of bacterial infection, attention is increasingly being paid to bacteriophage (phage) therapy. With a wide range of genetic engineering capabilities, these bacterial viruses can be modified to achieve precise control and detection of bacteria and thus serve as a new source of antimicrobial agents. In addition to being used in antimicrobial therapy, phages can also be used as transport systems for drug delivery, as vaccines, or can be used for nanosembly of new materials, since phages themselves, their fragments and components are nanoobjects and functioning nanomachines, the assembly process of which is extremely relevant. The purpose of this article is: to analyze and summarize the most important information on the topic of bacteriophages, methods of their determination and effective transformation in modern science, to evaluate the achievements of modern research in the process of assembling heads (capsids) and laying intracapsid DNA in caudate bacteriophages (phage lambda and phage T4), the production of genetically modified phages and a review of the main prospects for the development of this direction.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"160 10‐12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0641
M. Aristarkhov, A. Dergilev, A. Potapova, P. Ivanov-Rostovtsev, Yuriy Orlov
The pursuit of microRNA target genes necessitates the creation of novel software and web services. MicroRNAs, abbreviated as short non-coding RNA molecules, hold a pivotal role in metabolic regulation, plant responses to environmental stress, and gene expression. Gaining insights into microRNA functions and investigating their target genes can advance drug development and address biotechnological challenges. However, the study and identification of microRNA targets within the genome present technical obstacles. MicroRNA molecules may not exhibit complete complementarity with their mRNA targets. These molecules either contribute to mRNA degradation or inhibit translation, and this process can transpire without full target complementarity. Consequently, the delineation of targets solely based on the principle of complementarity lacks unequivocal clarity. Moreover, a single microRNA molecule can correspond to multiple target genes simultaneously. The solution entails harnessing substantial datasets, employing machine learning techniques, and leveraging neural networks. In bioinformatics, neural networks serve a variety of functions, encompassing the analysis of biomedical data, diagnostics, prediction, classification, and nucleotide sequence segmentation. The pursuit and anticipation of microRNA targets through machine learning methods are currently undergoing vigorous development. A comparative assessment of contemporary neural networks for this task has been executed. A neural network-driven web service for microRNA prediction has been created. The server aspect of the service was developed using the Python programming language and the Flask library. The Mitar neural network, founded on deep learning, was employed. This network demonstrates heightened precision in predicting microRNA targets. We deliberate on the applications of miRNA prediction in gene expression analysis. Sustained research efforts are imperative to enhance the efficiency and broaden the capabilities of the developed computer system.
{"title":"WEB-SERVICES FOR MICRORNA TARGET PREDICTION USING NEURAL NETWORKS","authors":"M. Aristarkhov, A. Dergilev, A. Potapova, P. Ivanov-Rostovtsev, Yuriy Orlov","doi":"10.29039/rusjbpc.2023.0641","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0641","url":null,"abstract":"The pursuit of microRNA target genes necessitates the creation of novel software and web services. MicroRNAs, abbreviated as short non-coding RNA molecules, hold a pivotal role in metabolic regulation, plant responses to environmental stress, and gene expression. Gaining insights into microRNA functions and investigating their target genes can advance drug development and address biotechnological challenges. However, the study and identification of microRNA targets within the genome present technical obstacles. MicroRNA molecules may not exhibit complete complementarity with their mRNA targets. These molecules either contribute to mRNA degradation or inhibit translation, and this process can transpire without full target complementarity. Consequently, the delineation of targets solely based on the principle of complementarity lacks unequivocal clarity. Moreover, a single microRNA molecule can correspond to multiple target genes simultaneously. The solution entails harnessing substantial datasets, employing machine learning techniques, and leveraging neural networks. In bioinformatics, neural networks serve a variety of functions, encompassing the analysis of biomedical data, diagnostics, prediction, classification, and nucleotide sequence segmentation. The pursuit and anticipation of microRNA targets through machine learning methods are currently undergoing vigorous development. A comparative assessment of contemporary neural networks for this task has been executed. A neural network-driven web service for microRNA prediction has been created. The server aspect of the service was developed using the Python programming language and the Flask library. The Mitar neural network, founded on deep learning, was employed. This network demonstrates heightened precision in predicting microRNA targets. We deliberate on the applications of miRNA prediction in gene expression analysis. Sustained research efforts are imperative to enhance the efficiency and broaden the capabilities of the developed computer system.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"106 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.29039/rusjbpc.2023.0647
V. Turkina, P. Iarema, A. Mayorova, N. Orlova, E. Savina, Yuriy Orlov
Computer reconstruction of gene networks—sets of interacting macromolecules with common functions – is a complex task in bioinformatics. Gene networks, presented as graphical structures, offer a convenient means of visualization and provide qualitatively new insights into the set of studied genes and their biological functions. Expanding further, we explore associative gene networks related to diseases. These networks encompass not only genes and their products (proteins, metabolites, non-coding RNA and drug compounds) but also common disease indicators (symptoms, phenotypic manifestations). Software tools aimed at reconstructing gene network graphs are undergoing active development worldwide and find significant utility in biomedicine. We evaluate available online bioinformatics tools for gene network reconstruction based on gene lists and corresponding computer analysis pipelines. We delve into examples showcasing the utilization of online programs for analyzing the glioma gene network. The proposed approach can be extended to other functional gene sets linked to diseases. Scrutinizing the structure of disease-associated gene networks enables the identification of pivotal genes, which can serve as therapeutic targets. Employing similar bioinformatics strategies, gene networks of intricate disorders such as Parkinson's disease, dementia, schizophrenia, breast cancer, and other cancers have been explored. We delve into the applications of computer programs for gene network analysis and address pedagogical aspects of the field.
{"title":"RECONSTRUCTION OF GENE AND ASSOCIATIVE NETWORKS OF DISEASES TO SEARCH FOR TARGET GENES","authors":"V. Turkina, P. Iarema, A. Mayorova, N. Orlova, E. Savina, Yuriy Orlov","doi":"10.29039/rusjbpc.2023.0647","DOIUrl":"https://doi.org/10.29039/rusjbpc.2023.0647","url":null,"abstract":"Computer reconstruction of gene networks—sets of interacting macromolecules with common functions – is a complex task in bioinformatics. Gene networks, presented as graphical structures, offer a convenient means of visualization and provide qualitatively new insights into the set of studied genes and their biological functions. Expanding further, we explore associative gene networks related to diseases. These networks encompass not only genes and their products (proteins, metabolites, non-coding RNA and drug compounds) but also common disease indicators (symptoms, phenotypic manifestations). Software tools aimed at reconstructing gene network graphs are undergoing active development worldwide and find significant utility in biomedicine. We evaluate available online bioinformatics tools for gene network reconstruction based on gene lists and corresponding computer analysis pipelines. We delve into examples showcasing the utilization of online programs for analyzing the glioma gene network. The proposed approach can be extended to other functional gene sets linked to diseases. Scrutinizing the structure of disease-associated gene networks enables the identification of pivotal genes, which can serve as therapeutic targets. Employing similar bioinformatics strategies, gene networks of intricate disorders such as Parkinson's disease, dementia, schizophrenia, breast cancer, and other cancers have been explored. We delve into the applications of computer programs for gene network analysis and address pedagogical aspects of the field.","PeriodicalId":169374,"journal":{"name":"Russian Journal of Biological Physics and Chemisrty","volume":"65 s253","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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