bluuebunny/crossref_metadata_2025 huggingface dataset:
Reverberation of the Vela PULSAR WIND NEBULA
Authors: Petrov A. E. , Levenfish K. P. , Ponomaryov G. A.
Published: April 2024

Transonic (withMach numberMs 1) motion of a pulsar relative to the external medium canhelp its compact pulsar wind nebula develop a double-torus X-ray morphology. The double-torus structurecan reverberate as a whole under the dynamic pressure of the external flow. For a flow aligned with thesymmetry axis of the nebula, the response of the double-torus is uniform in azimuth. For a misalignedflow, the leeward sides of the tori respond with some delay relative to their windward sides. The delay cancause a curious swaying in the short midsection of the leeward jet of the compact X-ray nebula. Within theframework of the relativisticmagnetohydrodynamical model of a pulsar wind nebula we study the dynamicsof the nebular outflows contributing to the swaying of the jet. When applied to the Vela X-ray nebula, themodel allows us to naturally relate two distinct phenomena, the swaying of the bright midsection of the Velalee jet and the reverberation of its double-torus.
Investigation of the Ultraluminous X-ray Source VII Zw 403 ULX
in the X-ray and Optical Ranges
Authors: Vinokurov A. S. , Atapin K. E. , Kostenkov A. E. , Solovyeva Yu. N.
Published: April 2024

We present the results of our analysis of the series of X-ray observations, photometric andspectroscopic monitoring for the ultraluminous X-ray source VII Zw 403 ULX (UGC 6456 ULX). Basedon a number of indirect signs, we hypothesize that the accretor in this binary system is a neutron star. Wehave estimated the mass outflow rate in the object’s active state within the supercritical disk wind model tobe ≈4.0 × 10−5 M yr−1.
Modelling of the Decidualization of Mouse Endometrial Stromal Cells with Subsequent Embryo Implantation in vitro
Authors: Gaidamaka A. O. , Muromtsev A. V. , Izmailova L. S. , Marchenko G. A. , Vorotelyak E. A.
Published: April 2024

The decidualization of stromal cells is a key step in acquiring endometrial receptivity to the embryo. This process is regulated by sex steroid hormones, and in the mouse is additionally induced by embryo attachment. There are many protocols for the induction decidualization of stroma in vitro, but most of them require verification of the compliance of the processes occurring in cell culture with those in a living organism. This work focuses on the morphology of stromal cells and the expression activity of genes responsible for the progression of decidualization in 2D culture with subsequent embryo attachment. The feasibility of using several variants of protocols for the induction of decidualization and the possibility of using stromal cells after cryopreservation were also investigated.
Generation of an Induced Pluripotent Stem Cell Line, ICGi042-A, by Reprogramming Peripheral Blood Mononuclear Cells from Parkinson’s Disease Patient with c.1000G>A Mutation in LRRK2 Gene
Authors: Grigor’eva E. V. , Pavlova S. V. , Malakhova A. A. , Medvedev S. P. , Minina J. M. , Vyatkin Y. V. , Khabarova E. A. , Rzaev J. A. , Kovalenko L. V. , Zakian S. M.
Published: April 2024

The search for new polymorphisms associated with hereditary diseases is important for diagnostics and the study of the disease development pathology. We have analyzed clinical exome of a Parkinson’s disease patient and identified single-nucleotide variations in the LRRK2 (c.1000GA, c.2167AG) and PINK1 (c.1562AC) genes. The LRRK2:c.1000GA mutation has uncertain clinical significance, and is interesting for further investigation. We generated induced pluripotent stem cells (IPSCs) from PBMCs of the patient by a non-integrating episomal vectors. IPSCs demonstrate typical morphology and normal karyotype (46,XY), express pluripotency markers (OCT4, SOX2, NANOG, SSEA4, TRA-1-60), and are able to produce derivatives of three germ layers.
High-Quality RNA Extraction and Evaluation of Reference Genes for qPCR Assay of Pinus sylvestris L. Trunk Tissues
Authors: Moshchenskaya Yu. L. , Galibina N. A. , Korzhenevskiy M. A. , Tarelkina T. V. , Nikerova K. M. , Chirva O. V.
Published: April 2024

Scots pine (Pinus sylvestris L.) is a species of tree with heartwood (HW), which is forming during aging of sapwood (SW). Due to clear-cut border between SW and HW P. sylvestris should be used as a model woody plant for studying patterns of HW formation. Currently, molecular genetic methods are used to study the processes of trunk tissues formation in woody plants often. A feature of trunk tissues of coniferous trees is a high content of secondary metabolites, a low content of nucleic acids, and potential partial degradation of RNA. In this work we discuss the choice of most successful method for extraction a high-quality RNA for real-time PCR (RT-PCR) in P. sylvestris trunk tissues along the radial vector “conductive phloem/cambial zone – differentiating xylem – exterior part of SW (1–2 annual rings) – interior part of SW (1–2 annual rings afore transition zone (TZ)) – TZ (2 annual rings afore HW)” for reproducible RT-PCR data. The expression stability of six potential reference genes (Actin1, α-Tubulin, β-Tubulin, Ef1a, GAPDH, UBQ) was assessed in all describe tissues. Differences in expression levels of target genes are shown by data normalization using reference genes with different stability of expression.
Pregastrular Development of Amphibians: Ontogenetic Diversity and Eco-Devo
Authors: Desnitskiy A. G.
Published: April 2024

Comparative and ecological aspects of the reorganizations of early development in the class Amphibia are analyzed. We used data on the developmental diversity in a number of families belonging to the orders Anura and Caudata, in which many species had lost their connection with the aquatic environment. Model representatives of the class Amphibia (Ambystoma mexicanum, Rana temporaria, and Xenopus laevis) have small eggs (no more than 2.5 mm in diameter). In these species, the slowdown in the rate of cell divisions and the loss of synchrony occur at the midblastula stage. However, phylogenetically basal amphibian species (Ascaphus truei, Cryptobranchus alleganiensis) are characterized by the large (4–6 mm in diameter) yolky eggs and a short series of synchronous blastomere divisions (the synchrony is already lost at the 8-cell stage of cleavage). They do not have a “midblastula transition”, which is characteristic of the above model species. On the other hand, many evolutionarily advanced non-model species of caudate and anuran amphibians (for example, Desmognathus fuscus, Gastrotheca riobambae, Philoria sphagnicolus), as well as the basal species, are characterized by the large, yolk-rich eggs and the early loss of cell division synchrony. Phylogenetic analysis suggests that the cleavage pattern of the most extensively studied amphibians, the Mexican axolotl (Caudata) and the African clawed frog (Anura), represents a homoplasy. The midblastula transition, which is characteristic of these two species, might have evolved convergently in these two orders of amphibians as an embryonic adaptation to development in lentic water.
Chemokine CCL2 Activates Hypoxia Response Factors Regulating Pluripotency and Directed Endothelial Differentiation of Human Pluripotent Stem Cells
Authors: Shevchenko A. I. , Arssan A. M. , Zakian S. M. , Zakharova I. S.
Published: April 2024

Human pluripotent stem cell (PSC) research is currently focused on selecting conditions and growth factors that better mimic preimplantation development and germ cell differentiation, which is important for disease modeling using PSC. Previously, it was shown that in the presence of the chemokine CCL2, human PSCs acquire properties attributable for preimplantation blastomeres, namely, they activate the JAK-STAT3 signalling pathway and increase the mRNA level of the hypoxic response genes. However, CCL2 is practically not used in the human PSCs cultivation, and its effect is described in a single study. We continued to study the CCL2 effect on human PSC and showed that human embryonic and induced pluripotent stem cells cultured with CCL2 have an increased protein level of the oxygen-dependent subunits HIF1A and HIF2A, which are necessary to trigger the hypoxic response, as well as elevated protein levels of the key pluripotency transcription factors OCT4, NANOG, KLF4, SOX2, and TFCP2L1. In addition, the presence of CCL2 had a positive effect on directed endothelial differentiation, accelerating the maturation of progenitors and enhancing the angiogenic potential of differentiated derivatives.
Development of N.K. Koltsov Idea about Genetic Organization of Interbands in Drosophila melanogaster Polytene Chromosomes
Authors: Zhimulev I. F. , Vatolina T. Yu. , Levitsky V. G. , Kolesnikova T. D. , Tsukanov A. V.
Published: April 2024

Here for the first time, the organization of promoters of developmental gene promoters and promoter of genes necessary for general cellular functions—the “houskeeping” of the cell in the complete genome of Drosophila melanogaster were studied. Using bioinformatic methods, it has been shown that the genes whose promoters are located in the interbands of polytene chromosomes are enriched in functions associated with general cellular processes, while the rest of the genes (about half of the Drosophila genome) are associated with highly specialized processes occurring during development. In the promoter zone of the housekeeping genes, four specific motifs were found that can be present in different genes individually or in various combinations. A significant part of interband promoters do not contain identified motifs. The analysis carried out using Gene Ontology showed that certain groups of interband genes containing one motif in promoters or their combinations are characterized by the performance of certain functions.
Conservative Protein RCC1 Is a New Component of Black Bands of Drosophila melanogaster Polytene Chromosomes
Authors: Zykova T. Yu. , Maltseva M. V. , Demakov S. A. , Pokholkova G. V. , Veryaskina Yu. A. , Lavrik O. I. , Kolesnikova T. D. , Zhimulev I. F.
Published: April 2024

Previously, the RCC1 gene (Regulator of Chromosome Сondensation 1) was characterized, which is considered a regulator of chromosome condensation in the cell cycle. This gene encodes a nuclear protein whose amino acid sequence is highly conserved among all eukaryotes and consists of seven repeating units. We have shown that all the most prominent black bands of polytene chromosomes (about 250) and the chromocenter bind antibodies to this protein. We found that antibodies to the xenopus RCC1 protein specifically bind to the Drosophila and human RCC1 protein, while in Drosophila lines with under replication suppression, the relative amount of the RCC1 protein increases compared to the wild type.
Expression of the engrailed Homologue in Larvae and Juveniles of the Annelid Alitta virens Characterizes the Formation of Segments from the Growth Zone
Authors: Kairov A. I. , Kozin V. V.
Published: April 2024

The evolutionary origin of segmentation remains to be a mystery. In arthropods, the engrailed gene is recognized as one of the most important and conservative members of the segmentation developmental program. Orthologues of this gene have been identified in annelids, but their role is interpreted ambiguously, because in some species their expression precedes subdivision of the body into segments, but in others it does not. Here we studied the expression of engrailed in the nereid polychaete Alitta virens during metamorphosis and development of the first postlarval segments. Our data support the possible involvement of this gene in the process of segment formation from the growth zone in A. virens. At the larval stages, engrailed is expressed in neuroectodermal cells, in the growth zone, as well as in metameric epidermal cell rows at the anterior boundary of each segment. Upon transition from the metatrochophore to the nectochaete stage, the circular expression domain in the growth zone expands and then resolves into two serial domains. Over time, the distance between these circular domains increases indicating the growth of the first postlarval segment anlage. Formation of subsequent postlarval segments occurs in a similar way. Analyzing our results and literature data, we compared engrailed expression patterns in annelids and arthropods. Our work indicates an absence of conservation in patterning of sequentially developing segments from the growth zone in protostomes. We suggest that in A. virens the anteroposterior axis elongation occurs simultaneously with the specification of a new segment. These features differ from the known models of the growth zone and indicate the possibility that nereids have a specific mechanism of segmentation.
Generation of a Null Mutation of the toothrin Gene by Targeted Homologous Recombination in Drosophila melanogaster
Authors: Kuvaeva E. E. , Kulikova D. A. , Simonova O. B. , Mertsalov I. B.
Published: April 2024

Drosophila toothrin gene is related to the conserved d4 family of genes that encode specific transcription factors. In early works, we investigated the effect of tth gene overexpression and characterized the specific pattern of its expression in the nervous system, but mutations in the tth gene have not yet been found. Null mutants are essential for analyzing gene function and screening of partner genes. Here we report the generation of the first tth gene knockout in Drosophila using a homologous recombination technique.
The Birth of Morphomechanics
Authors: Ermakov A. S.
Published: April 2024

At the early 1970s, in the USSR, L.V. Beloussov and his colleagues from Moscow State University put forward a hypothesis about the possible role of mechanical forces and stresses in the organization of developing living systems. The authors discovered stage-specific patterns of mechanical stresses during amphibian embryonic development and showed that mechanical stresses are necessary for the organization of morphogenesis and cellular differentiation. As a result of the long-term work of Moscow embryologists, morphomechanics, new interdisciplinary science at the intersection of developmental biology and mechanics, was born. In the XXI century, mechanisms of mechano-dependent gene expression, cellular and nuclear mechanotransduction are intensively studied. The idea of the organizing role of mechanical forces and stresses in living systems remains very relevant.
Temperature Compensation of Energy Metabolism in Tadpoles of the Marsh Frog from Different Populations of the Kamchatka Peninsula (Pelophylax ridibundus Pallas 1771, Anura: Amphibia)
Authors: Kleymenov S. Yu. , Lyapkov S. M. , Ozernyuk N. D.
Published: April 2024

The study of the peculiarities of energy metabolism in populations of the marsh frog Pelophylax ridibundus from several reservoirs of the Kamchatka peninsula with different temperature regimes revealed the temperature compensation of this parameter in tadpoles. The linear dependence of the tadpoles metabolic rate on the average annual temperature of habitat was shown. It was found that stable inherited differences in the intensity of tadpoles metabolism were formed in 30–20 years from the moment of the first introduction of the species into the reservoirs of Kamchatka. An assumption is made about the limit of adaptive diapason of the species for the development stage of 39–40 tadpoles of the marsh frog.
Instability of the Mother’s Environment Leads to Reduced Developmental Robustness in Lymnaea stagnalis (Mollusca: Gastropoda)
Authors: Bogomolov A. I. , Kraus Y. A. , Voronezhskaya E. E.
Published: April 2024

Adaptive maternal effects that increase the adaptability of offspring are often caused by stressful conditions that persist in the environment for an extended period of time. The question arises, what is the threshold at which maternal effects cease to be adaptive for offspring and lead to developmental disorders? One of the stressors is considered to be unpredictable changes in environmental conditions. We aimed to test whether a mother’s inhabitation of unstable environment could lead to a decrease of developmental robustness in the embryos of the gastropod mollusk Lymnaea stagnalis. The laboratory population of snails was split into two groups. For the first group, conditions were maintained as stable as possible, with constant water exchange and excessive feeding. The second group was kept under unstable (stressful) conditions, with episodic feeding and water exchange. It turned out that unstable conditions alone did not affect the frequency of developmental anomalies in the offspring. Since serotonin is presumably plays the role of the signaling molecule mediating the maternal effect in L. stagnalis, we subjected embryos of both groups to the biochemical precursor of serotonin (5-HTP). After incubation in 5-HTP, the proportion of embryos with developmental anomalies was significantly higher among the offspring of mothers living in unstable conditions. We confirmed the important role of serotonin as a factor mediating communication between the organisms of mother and offspring by revealing serotoninergic innervation of the hermaphroditic gland (ovotestis) and accumulation of serotonin in the cytoplasm of forming oocytes. Our experiments suggest that under the stressful environmental conditions, serotonin accumulation by the oocyte/zygote may increase to a maladaptive level and lead to a decrease in the robustness of embryonic development.
The Role of Physical Processes in Pollen Wall Morphogenesis: Hypothesis and Experimental Confirmation
Authors: Gabarayeva N. I.
Published: April 2024

The review is devoted to the analysis and generalization of modern knowledge about the mechanisms underlying the ontogeny of the male gametophyte envelope. New and earlier data on exine development аre discussed, and recurrent phases in the development of exine of phylogenetically distant plant species are emphasized. Though exine formation has been shown to be dependent on plenty of genes, the reiteration of exine patterns in different plant species (e. g. columellate, granular, “white-lined” lamellae) suggests that these patterns are based on some non-biological principles of space-filling operations. However, mechanisms involved remained obscure until it became clear that the sequence of structures observed during exine development coincided with the sequence of self-assembling micellar mesophases. It was discovered later that another physical-chemical process – phase separation – participated in exine formation. To confirm that exine-like patterns are capable of generating in vitro by simple physical processes, and their formation does not require regulation at the genome level, some our and other authors’ in vitro experiments were undertaken; the data obtained are discussed. Several series of our new experiments on modeling exine development with mixtures of urface-active substances resulted in some patterns simulating the main types of natural exine. Transmission electron microscopy analysis of the samples has shown that patterns simulating the full range of exine types were obtained by joint action of phase separation and micellar self-assembly. The reconsideration and analysis of our and other authors’ morphogenetic and modeling data revealed that molecular-genetic mechanisms and physical forces work in tandem, with considerable input of physical processes.
Preliminary Exposure to Histone Deacetylase Inhibitors Changes the Direction of Human IPSCs Differentiation with the Formation of Cardiospheres Instead of Skin Organoids
Authors: Abdyev V. K. , Riabinin A. A. , Erofeeva E. D. , Pankratova M. D. , Vorotelak E. A. , Vasiliev A. V.
Published: April 2024

Pluripotent stem cells (PSCs) are a unique cell type that can differentiate into all cell types in the body. In PSC culture, subpopulations with different levels of pluripotency may exist, which leads to different results during their differentiation. One of the key factors that determine the state of pluripotency and influence the differentiation potential of PSCs is the epigenetic state of cells, including the level of histone deacetylation. Activation of histone deacetylase (HDAC) in human and mouse PSCs increases the percentage of heterochromatin. In this work, we used a protocol for the differentiation of embryoid bodies from induced human pluripotent hIPSC cells, designed for the formation of ectoderm and neuroectoderm with their subsequent development into skin organoids. However, after hIPSCs were exposed to HDAC inhibitors (sodium butyrate and valproic acid), the direction of their differentiation changed: mesoderm was formed, which subsequently developed into contracting cardiospheres.
The Distribution of the Germ Plasm Gene germes among Anurans
Authors: Konduktorova V. V. , Fofanova E. G. , Nikishin D. A.
Published: April 2024

The germes gene is a marker of germ plasm and primordial germ cells (PGC) described in the African clawed frog Xenopus laevis. It is known that overexpression of its mutant form negatively affects the formation and migration of PGC. However, until now it was not known how widely this gene is represented in animals of different phylogenetic groups. In this work, we performed bioinformatic analysis of genomic and transcriptome sequences of animals with germ plasm. It turned out that germes homologs are present only in representatives of the genera Xenopus and Hymenochirus of the family Pipidae (order Anura). The obtained results were confirmed by RT-PCR analysis of the expression of germes orthologs in the ovaries of six representatives of different Anura families. Phylogenetic analysis of cloned sequences of germes homologs suggests the appearance of this gene in the ancestors of Pipidae and its secondary loss in the genus Pseudohymenochirus. It is also identified that the amino acid sequences of the functional domains of the Germes protein are rather conservative.
Generation of Induced Pluripotent Stem Cell Line iTAF15Xsk4 from Fibroblasts of a Patient with Microdeletion at Xq24
Authors: Pristyazhnyuk I. E. , Meshcheryakov N. I. , Nikitina T. V. , Kashevarova A. A. , Fedotov D. A. , Tolmacheva E. N. , Minaycheva L. I. , Nazarenko L. P. , Lebedev I. N. , Menzorov A. G.
Published: April 2024

Differentiation of induced pluripotent stem (iPS) cells from patients and healthy donors allows in vitro study of genetic disorders. We have previously reported a clinical case of recurrent pregnancy loss in a patient with skewed X-chromosome inactivation in peripheral blood lymphocytes, endometrium, and buccal epithelium. We have found a 239 kb microdeletion at Xq24 that affected eight genes including UBE2A. In this work, we produced iPS cell line iTAF15Xsk4 from the patient’s skin fibroblasts using non-integrating episomal vectors. iPS cell line had a normal karyotype, expressed pluripotency markers, and upon differentiation in embryoid bodies expressed markers of all three germ layers. This cell line could be used for the UBE2A deficiency syndrome study.
SURFACTIN: BIOLOGICAL ACTIVITY AND THE POSSIBILITY OF AGRICULTURE APPLICATION (REVIEW)
Authors: Kisil O. V. , Trefilov V. S. , Sadykova V. S. , Zvereva M. E. , Kubareva Е. А.
Published: April 2024

Relevant information about surfactin, a cyclic lipopeptide which is one of the strongest bacterial biosurfactants, is summarized in the review. Mechanisms of surfactin biosynthesis and spectrum of surfactin’s native and synthetic isoforms are demonstrated. Surfactin biological activity and its role in regulation of the all processes of strain-producers are analyzed. The application potential of surfactin and its biological derivatives, which were obtained with the usage of surfactin producing strains of the genus Bacillus, for plants protection and stimulation of plant immunity is pointed out.
Antifungal and Reactivation Activity of a Novel Glycine/histidine-rich Linear Peptide from Dog-grass (Elytrigiarepens (L.) Desv. ex Nevski) EARS
Authors: Ryazantsev D. Yu. , Khodzhaev E. Yu. , Kuvarina A. E. , Barashkova A. S. , Rogozhin E. A.
Published: April 2024

Using a combination of solid-phase extraction, affinity chromatography, and analytical reverse-phase HPLC, a new linear peptide was isolated from dog-grass (Elytrigia repens) ears, which does not contain cysteine residues. Identification of its primary structure by Edman automated degradation made it possible to reveal the presence of several polyglycine regions, each consisting of 6–8 residues, between which short fragments consisting of polar amino acid residues are localized. The C-terminal fragment of the molecule is a positively charged site enriched in arginine and histidine residues. The structural features of this peptide determine its functionality. Thus, checking the presence of antimicrobial properties in its recombinant analogue, obtained by heterologous expression in a prokaryotic system, made it possible to determine the MIC for the tested fungal cultures only at sufficiently high active concentrations (52–104 μM). However, this compound had regulatory properties: at a concentration of 25 μM, a reactivating effect was noted, which increased the level of survival of Saccharomyces cerevisiae to UV-irradiation. The data obtained expand the understanding of the functional features of plant defense peptides of an unusual structural type.
Application of Sulfate-reducing Bacteria in Bioremediation from Heavy Metals and Metalloids (Review)
Authors: Bryukhanov A. L. , Khijniak T. V.
Published: April 2024

Pollution of the environment with heavy metals, metalloids and radionuclides is a global problem that seriously affects the state of the biosphere. In particular, chromium compounds have a toxic, mutagenic and carcinogenic effect. The main principle of purification of anthropogenic and natural ecosystems from chromates is the reduction of Cr(VI) to Cr(III), the salts of which are significantly less toxic and insoluble. However, currently used electrochemical and ion-exchange cleaning methods are quite expensive and require the use of special reagents. At the same time, sulfate-reducing bacteria (SRB) are of particular interest for bioremediation of this kind, since many of them are very resistant to high concentrations of heavy metals and are able to effectively reduce them in the presence of hydrogen as an electron donor. The review summarizes known data on the interaction of heavy metals, metalloids and radionuclides with SRB. The features of the metabolism of these microorganisms, leading to intracellular accumulation of heavy metals and metalloids, are considered. Complex and finely regulated enzymatic mechanisms for the reduction of toxic metals (using various cytochromes, hydrogenases, oxidoreductases, highly specific metal reductases, and thioredoxin/thioredoxin-reductase systems), as well as the possibility of using immobilized cells and biofilms of SRB in the effective bioremediation of natural waters, soils, and industrial effluents, are described.
Effect of the Glyoxylate Shunt Inactivation on Biosynthesis of Adipic Acid Through the Inverted Fatty Acid β-oxidation by Escherichia coli Strains
Authors: Gulevich A. Yu. , Skorokhodova A. Yu. , Debabov V. G.
Published: April 2024

Using Escherichia coli MG1655 lacIQ, ∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆fadE, PL-SDφ10-atoB, Ptrc-ideal-4-SDφ10-fadB, PL-SDφ10-tesB, ∆yciA as a core strain, the derivatives capable of synthesizing adipic acid from glucose through the inverted fatty acid β-oxidation pathway were obtained. Biosynthesis of the target compound by recombinants was ensured upon the primary condensation of acetyl-CoA and succinyl-CoA by 3-oxoacyl-CoA thiolase PaaJ and the catalysis of the final reaction of the cycle by acyl-CoA dehydrogenases FadE and FabI. Deletion in the strains of sucCD genes encoding components of succinyl-CoA synthase did not increase the relative intracellular availability of succinyl-CoA for target biosynthetic reactions and did not lead to an increase in adipic acid accumulation by the recombinants. The secretion of succinic and malic acids by the strains with an impaired tricarboxylic acid cycle remained almost unchanged, indicating the activity in the cells of glyoxylate shunt reactions that compete with the cycle reactions for isocitrate, required for succinyl-CoA formation. When isocitrate lyase, malate synthases A and G, and bifunctional kinase/phosphatase isocitrate dehydrogenase were inactivated in strains due to deletion of the aceBAK operon genes and glcB, adipic acid synthesis by recombinants increased threefold and reached 0.33 mM.
Cane Pretreatment by Deep Eutetic Solvents to Increase its Reactivity During Enzymatic Hydrolysis with Cellulases
Authors: Semenova M. V. , Vasil’eva I. S. , Yaropolov A. I. , Sinitsyn A. P.
Published: April 2024

Cane was pretreated with a number of deep eutectic solvents (DES) based on choline chloride (ChCl) as a hydrogen bond acceptor; among hydrogen bond donors, lactic and oxalic acids (LacA and OxA, respectively) were the most effective. Substrate pretreatment conditions (ratio of DES-components, temperature and exposure time) were optimized, leading to the highest yield of reducing sugars (RS) and glucose during subsequent enzymatic hydrolysis with cellulase preparation based on Penicillium verruculosum. It was been established that in the case of a mixture of ChCl with LacA (the molar ratio of components is 1 : 5) pretreatment should be carried out at 80°С for 24 h, and in the case of a mixture of ChCl with OxA (1 : 1) – at 80°С for 6 hours. The degree of conversion of the pretreated substrate after 48 hours of hydrolysis in the presence of the enzyme preparation (EP) B537 was 80 and 86% by absolutely dry substances for selected mixtures of ChCl/LacA and ChCl/OxA, respectively.
Heat Shock Proteins in Сancer Diagnostics
Authors: Guliy O. I. , Staroverov S. A. , Dykman L. A.
Published: April 2024

With the growing number of cancers, new assistive tools are required to obtain extensive molecular profiles of patients to help identify the disease. Early diagnosis of cancer is based on the analysis of relevant biomarkers, which can be used to monitor the population in order to identify the disease until it can be determined using standard methods and is not clinically manifest. One of the potential markers of cancer is heat shock proteins that act as molecular chaperones. Changes in heat shock proteins expression can serve as an important diagnostic marker of the cell’s response to damage. The paper presents a brief overview of the prevalence of oncological diseases in the world, the need of early oncological diagnostics development, as well as the prospects for the use of heat shock proteins in making an oncological diagnosis.
The Perspective Properties and the Directions of Bacillus thuringiensis Use for Plant Protection
Authors: Khairullin R. M. , Sorokan A. V. , Gabdrakhmanova V. F. , Maksimov I. V.
Published: April 2024

One of the urgent problems of plant protection from pests and diseases is the creation of environmentally safe biocontrol agents, the use of which would not be accompanied by an increase of the resistance of insect pests. Microorganisms have great potential in this regard. The most promising group are endophytes, which inhabit the internal tissues of plants and participate in formation of the phenotype of plant organisms. Bacteria of the genus Bacillus are of particular interest due to their wide distribution in the nature, the safety of many species for humans, and the relative ease with which biocontrol means based on Bacillus sp. could be obtained. The review considers the properties and activity of B. thuringiensis as follows: endophytic, insecticidal, antibiotic activity, production of growth regulators and mobilization of plant nutrients, resistance induction, as well as the possibility of constructing new strains using genetic engineering methods.
Corrosive Activity of Microorganisms Isolated from Fouling of Structural Materials in the Coastal Zone of the Barents Sea
Authors: Vlasov D. Yu. , Bryukhanov A. L. , Nyanikova G. G. , Zelenskaya M. S. , Tsarovtseva I. M. , Izatulina A. R.
Published: April 2024

Potentially corrosive active microorganisms isolated from structural materials with signs of biofouling on the coast of Kislaya Bay (Barents Sea, Russia) were studied: sulfate-reducing, iron-oxidizing and sulfur-oxidizing bacteria. Cultures of sulfate-reducing bacteria (Desulfovibrio sp., Halodesulfovibrio sp.), sulfur-oxidizing bacteria (Dietzia sp.), and iron-oxidizing bacteria (Pseudomonas fluorescens, Bacillus sp.) were identified on the basic of the determining the nucleotide sequences of the 16S rRNA gene. The methods of scanning electron microscopy, energy dispersive microanalysis of the chemical composition and X-ray phase analysis revealed significant changes in the structure and chemical composition of the surface layer of steel reinforcement samples exposed for 28 days in the presence of isolated microorganisms that demonstrated their active participation in corrosion processes. It has been shown that the formation of mineral analogues in corrosion products depends on the strains of studied bacteria and peculiarities of their metabolism. Sulfate-reducing bacteria isolated from the littoral zone of the Barents Sea showed the highest activity in the development of corrosion processes.
Prospects to Improving Biological Activity of Agricultural Formulations Based on Bacteria of the Genus Bacillus and Chitosan Nanocomposites
Authors: Yarullina L. G. , Kalatskaja J. N. , Cherepanova E. A. , Yalouskaya N. A. , Tsvetkov V. O. , Ovchinnikov I. A. , Burkhanova G. F. , Rybinskaya K. I. , Sorokan A. V. , Herasimovich K. M. , Zaikina E. A. , Nikolaichuk V. V. , Hileuskaya K. S. , Mardanshin I. S.
Published: April 2024

The review examines the properties of endophytic bacteria of the genus Bacillus as objects of biocontrol, prospects to expand the spectrum of their protective action based on complexes with chitosan derivatives. The mechanisms of direct and indirect effects of bacteria on the protective potential of plants are described, the role of the pro-/antioxidant system in the formation of systemic protective reactions is analyzed. The immunostimulating properties of chitosan derivatives and its modifications with organic molecules and metal nanoparticles are analyzed. The prospects of using Bacillus spp. bacterial complexes with nano- and submicron particles of chitosan derivatives to expand the spectrum of protective action of new biofungicides and immunostimulants based on them are shown.
Methacrylate Redox Systems of Anaerobic Bacteria
Authors: Arkhipova O. V.
Published: April 2024

The review analyzes current information about the anaerobic type of respiration using a non-natural methacrylate compound as an electron acceptor. Both the methacrylate redox systems themselves and the anaerobic bacteria in whose cells they are found are considered. These complexes consist of flavin-containing reductase and multiheme cytochrome(s) c3. The genes of the components of the methacrylate redox systems of different microorganisms are homologous and are organized into one operon. Methacrylate-reducing activity is determined in the periplasm. The only known bacterial acrylate reductase that reduces the natural compound differs from methacrylate redox systems. The physiological role, origin, and research perspectives for this unique enzyme system are discussed.
Mechanisms of Formation and Persistence of Ige Products and Potential Innovative Means of Therapy for Allergic Pathologies
Authors: Chudakov D. B. , Konovalova M. V. , Streltsova M. A. , Shustova O. A. , Generalov A. A. , Fattakhova G. V.
Published: April 2024

The proposed review is devoted to the analysis of the main mechanisms of the formation of IgE-producing cells in the body and a brief review of the main, most striking candidate agents for use in innovative methods of therapy for IgE-dependent pathologies. Data are presented according to which the role of IgE+ plasma cells and various subpopulations of memory B-lymphocytes in the formation and persistence of the state of sensitization to a harmless allergen differs depending on the model system used or the clinical case under study. Therefore, drugs that target signaling pathways involved in the regulation of both plasma cells and memory B-lymphocytes are especially promising in the treatment of allergic diseases. The authors conclude that the components of the cellular response to oxidative stress and related genotoxic stress and ER stress are the most promising as such targets, since (a) all of them directly or indirectly affect the processes that regulate both of these subpopulations; b) are involved in the process of formation and maintenance of local allergic inflammation. The review presents data pointing to the particular promise of using nanoparticles of noble metals and complexes of rare earth metals of lanthanides in this regard, due to their ability to induce long-term effects in small doses due to changes in the properties of innate immunity cells and long-term accumulation in the body.
Characteristics of Bacillus cereus complex Group Strains Isolated from Permafrost in Yakutia for Assessment of Microbiological Risks During Climate Change
Authors: Goncharova Y. O. , Evseeva V. V. , Mironova R. I. , Khlopova K. V. , Bogun A. G. , Sizova A. A. , Solomentsev V. I. , Titareva G. M. , Bahtejeva I. V. , Kravchenko T. B. , Brushkov A. V. , Timofeev V. S. , Ignatov S. G.
Published: April 2024

Strains of Bacillus genus were isolated from soil samples in the permafrost region (Yakutia, Russia). The phenotypic characteristics of the strains are given. The analysis of the obtained data made it possible to assign them to the group Bacillus cereus complex. PCR analysis made it possible to determine the profile of B. cereus toxin synthesis genes in the genomes of the studied strains. Genetic characterization was obtained by RAPD genotyping and using MLVA loci used for genotyping of the anthrax pathogen. The results of genotyping at different levels of resolution made it possible to differentiate the studied strains from the B. anthracis species, to show their intraspecific genetic differences and the degree of relationship. Whole genome sequencing was carried out, based on the data of which MLST genotyping was carried out, which revealed 2 known sequence types and one new one, described for the first time in this work. The results obtained are of practical importance and are extremely interesting from the point of view of the evolution and phylogeography of the B. cereus complex group, since the fact that strains were isolated from permafrost suggests that their age may be much older than expected.
Use of Metabolic Inert Mycobacterium abscessus Cells to Study the Efficiency Of Drugs
Authors: Martini B. A. , Salina E. G.
Published: April 2024

We investigated the effectiveness of antibiotics (amikacin, bedaquiline, linezolid, moxifloxacin, rifampicin) on metabolically inert M. abscessus obtained under conditions of potassium deficiency in vitro. It was found that bedaquiline led to a significant decrease in the ability of bacteria to form colonies on solid media, but did not lead to their death, since it was shown that during cultivation in a liquid medium, they reverted to a state of active division and growth. Moxifloxacin had a bactericidal effect against metabolically inert bacteria, irreversibly and significantly reducing the number of viable cells in culture, which emphasizes the effectiveness of its use for the treatment of infections caused by M. abscessus.
The Obtaining of Recombinant Producer of Trametes hirsuta Versatile Peroxidase VP2 in Penicillium canescens
Authors: Moiseenko K. V. , Fedorova T. V. , Savinova O. S. , Chulkin A. M.
Published: April 2024

The interest in peroxidases of the basidiomycetes secreted enzyme complex is due to their wide substrate specificity and the ability of these enzymes to participate in the biodegradation of such difficultly degradable biopolymers as lignin. However, due to the difficulty of isolating these enzymes from native sources, their study is difficult. In this work, expression vectors were created that carried the sequence encoding the T. hirsuta LE-BIN072 versatile peroxidase VP2, which was transformed into the genome of the P. canescens strain. Screening of transformants showed the presence of peroxidase activity up to 1 U/mL. Fragments of the target protein in the culture liquid of the selected transformants were identified by mass spectrometric analysis. A new strain of P. canescens pVP2D-6, a producer of the recombinant universal peroxidase VP2 T. hirsuta LE-BIN072, was obtained for the first time, and the ability of the enzyme complex secreted by it to modify alkaline lignin was shown.
Microbial 1,2-dehydrogenation of 6 Alpha-Methylhydrocortisone 11-trifluoroacetate
Authors: Savinova T. S. , Arinbasarova A. Yu. , Kazantsev A. V. , Savinova O. S. , Lukashev N. V.
Published: April 2024

Transformation of 11-trifluoroacetate 6α-methylhydrocortisone (11-TFA MHC) by cells of actinobacteria Arthrobacter (Nocardioides) was carried out in the presence of α-cyclodextrin (α-CD). The composition and dynamics of the transformation products accumulation in the culture medium at various pH values and the ratio of α-CD/substrate were studied. It was shown that the addition of α-CD to the transformation medium at pH less than 7 promotes an increase in the rate of 1,2-dehydrogenation with the formation of 6 α-methylprednisolone 11-trifluoroacetate (11-TFA MPL). At pH over 7, the primary process is the hydrolysis of the 11β-trifluoroacetyloxy group. In this case, the participation of α-CD in these processes as an acceptor of the trifluoroacetyl ion is not excluded.
Optimization of Aerobic Synthesis of Succinic Acid from Glucose by Recombinant Escherichia coli Strains Through the Variant Tricaboxylic Acid Cycle Mediated by the Action of 2-ketoglutarate-decarboxylase
Authors: Skorokhodova A. Yu. , Gulevich A. Yu. , Debabov V. G.
Published: April 2024

The biosynthesis of succinic acid from glucose by the previously engineered E. coli strain SUC1.0 (pMW119-kgd) (MG1655 ∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PLglk, PtacgalP, ∆aceBAK, ∆glcB, ∆sdhAB, pMW119-kgd) was optimized. The yield of the target substance was increased, upon the activation in the strain of the variant tricarboxylic acid cycle, mediated by the action of heterologous 2-ketoglutarate decarboxylase, due to the intensification of the anaplerotic formation of oxaloacetic acid. Inactivation of the nonspecific thioesterase YciA in the strain did not considerably change the biosynthetic characteristics of the producer. The enhancement of the expression of native phosphoenolpyruvate carboxylase led to an increase in the yield of the target compound by the recombinant synthesizing succinic acid via the reactions of the native tricarboxylic acid cycle from 25 to 42%, and from 67 to 75% upon the induced expression of Mycobacterium tuberculosis 2-ketoglutarate decarboxylase. Expression in the strain of pyruvate carboxylase gene from Bacillus subtilis resulted in an increase in the yield of succinic acid up to 84%. Functioning in whole-cell biocatalyst mode, the engineered strain SUC1.0 PL-pycA (pMW119-kgd) demonstrated a substrate to target product conversion ratio reaching 93%, approaching the corresponding theoretical maximum.
New eGFP Mutant with Intact C- and N-Termini and Affinity for Ni2+
Authors: Tarabarova A. G. , Yurkova M. S. , Fedorov A. N.
Published: April 2024

The green fluorescent protein GFP has long been used in research practice as a molecular tool. It is often used as a fusion partner. To create fusion constructs, target molecules are attached to the N- or C-terminus of GFP. On the other hand, the N- or C-termini of GFP required to create fusion constructs are also used to attach affinity tags that is greatly facilitating purification. Simultaneous introduction of affinity tag and GFP to both or the same end of GFP can create steric hindrances both in the process of biosynthetic folding of the construct and in its affinity purification. This work is devoted to the production of GFP with a His-tag introduced into the polypeptide chain. This work resulted in eGFP157_7H protein with an embedded His-tag and free N- and C-termini to create fusion proteins. The added His-tag will allow purification of the construct with GFP by metal-chelated affinity chromatography under native conditions. The resulting eGFP157_7H variant retained the original fluorescent properties completely similar to those of wild-type eGFP.
Series of formulas for bhattacharyya parameters in the theory of polar codes
Authors: Kolesnikov S. G , Leontiev V. M
Published: April 2024

Bhattacharyya parameters are used in the theory of polar codes to determine positions of frozen and information bits. These parameters characterize rate of polarization of channels WN(i), 1 ≤ i ≤ N, which are constructed in a special way from the original channel W, where N = 2n is the channel length, n = 1, 2, .... In the case where W is a binary symmetric memoryless channel, we present two series of formulas for the parameters Z(WN(i)): for i = N - 2k + 1, 0 ≤ k ≤ n, and for i = N/2 - 2k + 1, 1 ≤ k ≤ n - 2. The formulas require of the order of $\binom{2^{n-k}+2^k-1}{2^k} 2^{2^k}$ addition operations for the first series and of the order of $\binom{2^{n-k-1}+2^k-1}{2^k} 2^{2^k}$ for the second. In the cases i = 1, N/4 + 1, N/2 + 1, N, the obtained expressions for the parameters have been simplified by computing the sums in them. We show potential generalizations for the values of i in the interval (N/4, N). We also study combinatorial properties of the polarizing matrix GN of a polar code with Arıkan’s kernel. In particular, we establish simple recurrence relations between rows of the matrices GN and GN/2.
Postmodernism: philosophical paradigm or sociological explanatory scheme?
Authors: Diskin Iosif E.
Published: April 2024

The question of the scientific status of the postmodernism concept is relevant because of the fact that scientists appeal to it without reflecting on the boundaries and possibilities of its use. At the same time, the relevant use of the provisions of this concept requires an analysis of the problems that have become an incentive for its appearance, as well as of the structure of social environments whose consciousness corresponds to the conceptual foundations of postmodernism. For these environments, postmodernism is a relevant philosophical paradigm. It is shown that the total problematization of the moral foundations of social life, carried out by postmodernists, significantly limits the amount of social environments for which postmodernism is able to act as a relevant sociological explanatory scheme. These boundaries of relevance are significant for social environments that are not ready to problematize the moral foundations of their individual and social lives.
The policy of Germany in military sphere: drift from the concept of “strategic restraint”?
Authors: Trunov Philipp O.
Published: April 2024

As the key aggressor in World War II, Germany has to indefinitely comply with a set of stern restrictions considering the development and use of the national military potential. FRG’s attitude towards the principle until the early 2020s is studied. Key attention is paid to the cases where Germany abandoned the restrictions which had been limiting the realization of its ambitions as a world power. “Russian (Soviet) threat” has become the main pretext (but not the reason) for FRG’s remilitarization. However, in such cases Germany has ignored its own historic responsibility to the USSR and the Russian Federation. The framework conditions of the Bundeswehr development, outlined by Konrad Adenauer, are considered. The direction of the remilitarization (since the end of 2010s), as well as the features of Bundeswehr usage inside and outside the NATO zone of responsibility, are studied. It is concluded that the majority of these measures show the drift away from the “strategic restraint” concept.