bluuebunny/crossref_metadata_2025 huggingface dataset:
Local Faunistic Association of the Water Fleas (Crustacea: Cladocera) in the Water Bodies of Left Bank of the Lena River near Town of Yakutsk and Its Vicinities (Yakutia Russia)
Authors: Andreeva L. V. , Seleznev D. G. , Garibian P. G. , Kotov A. A.
Published: April 2024

In this study, we investigated a species composition of the water fleas (Crustacea: Cladocera) in the water bodies of the left bank of the Lena River near Yakutsk and its vicinities. Local faunistic associations characteristics of this region were identified using a statistical approach based on the binomial distribution function. As a result of the study, 68 taxa were identified and eight very distinct groups of taxa constituting the cores of local faunistic associations of the branchiopod crustaceans in various water bodies and/or various biotopes within one water body were drawn out. We have demonstrated that the water bodies of the Lena River valley and the watershed differ both in species composition and in associations of the Cladocera. At least one species association of the Cladocera is confined to the ponds with a visible anthropogenic influence. Thus, it is possible to identify not only species that are typical for urban water bodies, but also local faunistic associations, the presence of which in the city indicates a significant anthropogenic pressure. At the same time, the identified clusters can be interpreted in terms of our knowledge of the individual species preferences to water bodies of different types and different ecological zones of a certain water body.
Approaches to Determining Reference Values of Physiological Parameters of Freshwater Crayfish (Decapoda, Astacidae)
Authors: Kuznetsova T. V. , Ljubimtsev V. A. , Sladkova S. V. , Kholodkevich S. V.
Published: April 2024

Physiological parameters objectively reflect the health state of the organism and can serve as effective auxiliary criteria in determining the quality of the environment. However, significant variability of physiological and biochemical parameters is known in invertebrates, and, in particular, in crustaceans. In order to overcome these limitations and increase certainty in the assessment of the biological effects of toxicants, the authors proposed approaches and methods for the selection of reference groups of crayfish based on monitoring of their heart rate at rest and under the short-term standardized functional tests, allowing to assess the functional state of crayfish and their adaptive capabilities.
Planispiral Valvatids (Mollusca: Gastropoda: Valvatidae) of Subgenus Sibirovalvata in Upper Ob Basin
Authors: Andreeva S. I. , Kuzmenkin D. V. , Krasnogorova A. N.
Published: April 2024

In reservoirs and watercourses of the Upper Ob basin (south of Western Siberia) two representatives of the family Valvatidae (Valvatidae) of the subgenus Sibirovalvata, having a planispiral shell, have been noted. It is shown that two species of planispiral mollusks from this subgenus live in the region: Valvata (Sibirovalvata) frigida and V. (S.) sibirica. On the material from the Upper Ob basin, significant conchological differences between V. (S.) frigida and V. (S.) sibirica by key morphometric indices. According to the results of comparison with the material from the north of Western Siberia, it was found that the shells of the northern (basin of the Taz River) and southern (basin of the Upper Ob) populations of V. (S.) frigida and V. (S.) sibirica differ very slightly in morphometric indices, which indicates a slight variability of these traits within the range. At the same time, the detected significant differences between the northern and southern populations in the absolute size of the shell can presumably be explained by the conditions of specific habitats. At the same time, a more favorable temperature regime in the south may be offset by a lack of oxygen, including during the summer-autumn low water period.
Najas marina (Hydrocharitaceae) in Southern Middle Siberia, Refinds after a Century-Old Recess1
Authors: Efimov D. Yu. , Pimenov A. V. , Bobrov A. A.
Published: April 2024

In the south of the Krasnoyarsk Territory (Middle Siberia, Russia), the presence of N. marina was confirmed by new findings, in addition to historical collections, which were made more than 100 years ago in the South-Minusinsk basin. We have found this species additionally in three lakes in the North-Minusinsk basin, which are the northernmost localities in the Krasnoyarsk Territory. According to our findings, published data, and herbarium collections from Middle Siberia and adjacent regions, all specimens of large Najas belong to N. marina s. str. The species occur in lakes situated in landscapes with marine and lacustrine deposits in intermountain depressions with a continental arid climate. The increase of aridity of climate in southern Siberia will contribute to competitive advantages for populations of N. marina, their emerging and distribution in the studied area in connection with decreasing water level and increasing salinity which happen time to time and has fluctuating character.
Understanding Relationship between Length and Weight with Otolith Dimension of Tenualosa ilisha from Hooghly River (India)1
Authors: Majhi Bhuban Mohan , Lianthumluaia  , Sarkar Uttam Kumar , Nath Ashim Kumar
Published: April 2024

The Indian hilsa shad, Tenualosa ilisha (Hamilton, 1822), is a highly valued fish of the Indo Pacific region. This paper represents the length-weight relationships (LWR), condition factor (K), relative condition factor (Kn), and otolith dimension of hilsa, throughout the Hooghly River (West Bengal) from January to December 2020. The value of exponent “b” in the equation W = cLb was 2.6 for the species. It suggests the growth rate almost follows the cube law. Most of the population under study complied with the ideal b-value. Regression analysis indicated a high positive correlation between length and weight in the species (R2 = 0.76). The Kn shows their general well-being to be good in the river. The relationships between total fish weight and otolith biometry parameters such as long arm (L.A) length, short arm (S.A) length, L.A/S.A, and diameter (D) were examined. Linear regressions have represented fish weight-otolith biometry relationships. Regression analysis indicated a strong positive relationship between body weight and otolith length (R2 = 0.848), otolith diameter (R2 = 0.803), and short arm length of otolith (R2 = 0.678), but no relationship was found between L.A/S.A of otolith and fish weight. This strong relationship between fish weight and otolith length and diameter of T. ilisha, reflects that otolith length and diameter could become the best predictor of fish weight.
The Resistance of Waters to Trophy Increases as a Result of Processes in Their Ecotone Areas (according to Phytoplankton Indicators)
Authors: Sakharova E. G. , Korneva L. G.
Published: April 2024

According to the saprobity index, estimated by the phytoplankton biomass, the degree of organic pollution of ecotone areas (the mouth of the Il’d River and the littoral of the Volga reach of the Rybinsk reservoir) was determined. The saprobity index in protected shallow waters was 1.83 in 2009 and 2.07 in 2010; in the pelagial – 2.14 and 2.13 in 2009 and 2010 respectively. In the “river-reservoir” system, the lowest average values of the saprobity index were noted in the mouth area of the Il’d River: in 2009 – 1.94, in 2010 – 1.87, in 2011 – 1.88. In the river and the reservoir, its values were higher: 2.05 and 2.07 in 2009, 1.96 and 2.08 in 2010, and 1.97 and 1.99 in 2011 respectively. The decrease in saprobity in shallow waters and at the mouth of the river, compared to the bordering water, indicates a higher intensity of self-purification processes, which can ensure the sustainability of the ecosystem of the reservoir as a whole. Abnormal weather phenomena, in particular, high summer water temperatures, can lead to destabilization of the features of ecotone algocenoses, as a result, to a violation of the process of self-purification of the reservoir.
Responses of Unio pictorum to the Presence of Toxic and Non-Toxic Strains of Microcystis aeruginosa
Authors: Sharov A. N. , Zaytseva T. B. , Medvedeva N. G.
Published: April 2024

In order to assess the impact of cyanobacteria on mollusks under experimental conditions, the interaction of toxic and non-toxic strains of cyanobacteria Microcystis aeruginosa (Kützing) Kützing and bivalve mollusks Unio pictorum (L., 1758) was studied. Cyanobacteria have a negative effect on bivalve mollusks: 40% death of mollusks and deterioration of their adaptive capacity were recorded when co-cultivated with M. aeruginosa at a high cell concentration. At the same time, there was no difference in the mortality of mollusks incubated with toxic and non-toxic cyanobacteria. A decrease in the content of microcystin LR in the presence of bivalves was revealed. No statistically significant increase in the number of cyanobacteria in the water was noted after transit passage through the digestive system of bivalves.
Epithelial-mesenchymal transition of breast cancer cells activated by SNAIL1 transcription factor
Authors: Litovka N. I , Zhitnyak I. Y , Gloushankova N. A
Published: April 2024

Cancer cells use the program of epithelial-mesenchymal transition for initiation of the invasion-metastasis cascade. Using confocal and video-microscopy, in breast cancer MCF-7 cells undergoing Snail1-induced epithelial-mesenchymal transition reorganization of cytoskeleton was studied. We used the line of MCF-7 cells stably expressing tetOff SNAI1 construct (MCF-7-SNAI1 cells). After tetracycline washing and Snail1 activation MCF-7-SNAI1 cells underwent EMT and acquired a migratory phenotype retaining expression of E-cadherin. We identified five variants of the mesenchymal phenotype, differing in cell morphology and migration rate. Migrating cells had high degree of plasticity which allowed them to quickly change both the phenotype and the speed of movement. The changes of phenotype of MCF-7-SNAI1 cells are based on Arp2/3-mediated branched actin polymerization in lamellipodia, myosin-based contractility in the zone behind the nucleus, redistribution of adhesive proteins from cell-cell contacts to the leading edge and reorganization of intermediate keratin filaments.
The effect of deletions of genes encoding Pho3p and Bgl2p on the polyphosphate level, stress adaptation and attachment of these proteins in Saccharomyces cerevisiae cell wall
Authors: Kalebina T. S , Kulakovskaya E. V , Rekstina V. V , Trilisenko L. V , Ziganshin R. H , Marmiy N. V , Esipov D. S , Kulakovskaya T. V
Published: April 2024

Inorganic polyphosphates (polyP), according to literature data, are involved in the regulatory processes of molecular complex of the Saccharomyces cerevisiae cell wall (CW). The aim of the work was to reveal relationship between polyP, acid phosphatase Pho3p, and the major CW protein, glucanosyl transglycosylase Bgl2p, which is the main glucan-remodelling enzyme with amyloid properties. It has been shown that the yeast cells with deletion of the PHO3 gene contain more high molecular alkali-soluble polyP and are also more resistant to exposure to alkali and manganese ions compared to the wild type strain. This suggests that Pho3p is responsible for hydrolysis of the high molecular polyP on the surface of yeast cells, and these polyP belong to the stress resistance factors. The S. cerevisiae strain with deletion of the BGL2 gene is similar to the Δpho3 strain both in the level of high molecular alkali-soluble polyP and in the increased resistance to alkali and manganese. Comparative analysis of the CW proteins demonstrated correlation between the extractability of the acid phosphatase and Bgl2p, and also revealed a change in the mode of Bgl2p attachment to the CW of the strain lacking Pho3p. It has been suggested that Bgl2p and Pho3p are able to form a metabolon or its parts that connects biogenesis of the main structural polymer of the CW, glucan, and catabolism of an important regulatory polymer, polyphosphates.
Role of BDNF in neuroplasticity associated with alcohol dependence
Authors: Peregud D. I , Baronets V. Yu , Terebilina N. N , Gulyaeva N. V
Published: April 2024

Chronic alcohol consumption is characterized by disturbances of neuroplasticity. Brain-derived neurotrophic factor (BDNF) may mechanistically participate in this process. Here we aimed to review actual experimental and clinical data related to BDNF involvement in neuroplasticity in the context of alcohol dependence. As shown in experiments on the rodents alcohol consumption is accompanied brain region-specific changes of BDNF expression and by structural and behavioral impairments. BDNF reverses aberrant neuroplasticity during alcohol intoxication. According to clinical data indices characterized BDNF demonstrate close relationship with consequences of alcohol dependence. Polymorphism rs6265 within BDNF gene interacts with macrostructural changes in the brain, while peripheral BDNF concentration may reflect anxiety, depression and cognitive decline. Thus, BDNF is involved in mechanisms of alcohol-related aberrant neuroplasticity, while polymorphisms within BDNF gene and peripheral BDNF concentration may be biomarkers, diagnostic or prognostic factors in clinics of alcoholism.
Acute and chronic lipopolysaccharide-induced stress changes expression of proinflammatory cytokine genes in the rat brain region-specifically and affects learning and memory
Authors: Zaichenko M. I , Philenko P. , Sidorina V. , Grigoryan G. A
Published: April 2024

The purpose of the current work was a comparative analysis of the effects of acute and chronic lipopolysaccharide stress on behavior of rats in the Morris water maze and expression of mRNA proinflammatory cytokines and BDNF in different brain structures. The relevance of this study is related with a weak knowledge of the effects of acute and chronic stress on manifestation of cognitive brain functions, ambiguity of influences of both stresses on the hypothalamic-pituatary axis and expression of the proinflammatory cytokines genes, as well as contradictory data in the literature. In experiments on rats, the acute lipopolysaccharide (LPS) stress improved learning in the Morris water maze. For the period of learning, the rats swam on average less distance to reach a hidden platform and spent less time in the outer zone of the pool (tigmotaxis) and had a low speed compared to the control animals and a group of rats with chronic LPS stress. In a probe trial without a platform in the pool there were no significant differences between groups on time spent in the platform quadrant and distance swum. The acute stress produced a substantial increase of TNF-α and IL-1β concentration in the hippocampus and amygdala, but not in the frontal cortex relative to the control animals. Although the chronic stress increased the levels of TNF-α and IL-1β in the amygdala and hippocampus compared to the control groups, the significance between the groups was only marginal and the concentration of BDNF did not differ from the control animals in none of the structures mentioned. The concentration of IL-6 marginally increased in acute LPS stress in the amygdala and marginally decreased chronic LPS stress in the hippocamus relative to the saline control groups. In total, the most clear molecular-biochemical changes occurred in the amygdala and hippocampus, where the increase of interleukines TNF-α and IL-1β were seen in the acute and chronic LPS stress and no changes in BDNF concentration in the frontal cortex.
Glucocorticoids orchestrate adult hippocampal plasticity: growing points and translational aspects
Authors: Gulyaeva N. V
Published: April 2024

The review analyzes modern concepts regarding the control of various mechanisms of the hippocampal neuroplasticity in adult mammals and humans by glucocorticoids. Glucocorticoid hormones ensure the coordinated functioning of key components and mechanisms of hippocampal plasticity: neurogenesis, glutamatergic neurotransmission, microglia and astrocytes, systems of neurotrophic factors, neuroinflammation, protease activities, metabolic hormones, neurosteroids. Regulatory mechanisms are diverse; along with the direct action of glucocorticoids through their receptors, there are indirect glucocorticoid-dependent effects, as well as numerous interactions between various systems and components. Despite the fact that many connections in this complex regulatory scheme have not yet been established, the study of the factors and mechanisms considered in the review forms growth points in the field of glucocorticoid-regulated processes in the brain and primarily in the hippocampus. These studies are fundamentally important for the translation into the clinic and the potential treatment/prevention of common diseases of the emotional and cognitive spheres and respective comorbid conditions.
Effect of neurodegenerative mutations in NEFL gene on thermal denaturation of the neurofilament light chain protein
Authors: Nefedova V. V , Yampolskaya D. S , Kleymenov S. Y , Chebotareva N. A , Matyushenko A. M , Levitsky D. I
Published: April 2024

The effects of amino acid substitutions E90K, N98S and A149V in the light chain of neurofilaments (NFL) on the structure and thermal denaturation of the NFL molecule was investigated. By using the circular dichroism spectroscopy, it was shown that these substitutions do not lead to a changes in the α-helical structure of NFL, but they caused a noticeable effects on the stability of the molecule. We also identified calorimetric domains in the NFL structure by using the differential scanning calorimetry. It was shown that the E90K replacement lead to the disappearance of the low-temperature thermal transition (domain 1). The mutations lead to changes in the enthalpy of melting of NFL domains, as well as lead to significant changes in the melting temperatures (Tm) of some calorimetric domains. Thus, despite the fact that all these amino acid substitutions are associated with the development of Charcot-Marie-Tooth neuropathy, and two of them are even located very close to each other in the coiled-coil domain 1A, they differently effects on the structure and stability of the NFL molecule.
Resistom Streptomyces rimosus - a reservoir of resistance genes to aminoglycoside antibiotics
Authors: Alekseeva M. G , Rudakova N. N , Ratkin A. V , Mavletova D. A , Danilenko V. N
Published: April 2024

The study of aminoglycoside acetyltransferases in actinobacteria of the genus Streptomyces is an integral part of the study of soil bacteria as the main reservoir and possible source of drug resistance genes. Previously, in the strain Streptomyces rimosus ATCC 10970 (producing oxyteteracycline), which is resistant to most natural aminoglycoside antibiotics, we have identified and biochemically characterized 3 aminoglycoside phosphotransferases, which cause resistance to kanamycin, neomycin, paromomycin, streptomycin, and hygromycin B. In the presented work, it was shown that resistance to other AGs in this strain is associated with the presence of the enzyme aminoglycoside acetyltransferase, belonging to the AAC(2′) subfamily. Induction of the expression of the gene, designated by us as aac(2′)-If, in Escherichia coli cells determines resistance to a wide range of natural aminoglycoside antibiotics (neomycin, gentamicin, tobramycin, sisomycin, and paromomycin) and to an increase in the minimum inhibitory concentrations of these antibiotics.
Hereditary conditions associated with elevated cancer risk in childhood
Authors: Suspitsin E. N , Imyanitov E. N
Published: April 2024

The widespread use of next-generation sequencing (NGS) technologies revealed that a significant percentage of tumors in children develop as a part of monogenic hereditary diseases. Predisposition to the development of pediatric neoplasms is characteristic of a wide range of conditions including hereditary tumor syndromes, primary immunodeficiencies, rasopathies, and phakomatosis. The mechanisms of tumor molecular pathogenesis are diverse and include disturbances in signaling cascades, defects in DNA repair, chromatin remodeling, and microRNA processing. Timely diagnosis of tumor-associated syndromes is important for the proper choice of cancer treatment, genetic counseling of families, and the development of surveillance programs. The review describes the spectrum of neoplasms characteristic of the most common syndromes and the molecular pathogenesis of these diseases.
S-glutathionylation and S-nitrosylation as modulators of redox-dependent processes in cancer cell
Authors: Kalinina E. V , Novichkova M. D
Published: April 2024

The development of oxidative/nitrosative stress associated with the activation of oncogenic pathways is a consequence of an increase in the level of generation of reactive oxygen and nitrogen species (ROS/RNS) in tumor cells. The action of ROS/RNS is dual: high levels cause cell death and limit tumor growth at certain phases of malignant neoplasm development, while low concentrations allow oxidative/nitrosative modifications of key redox-dependent residues in regulatory proteins. The reversibility of such modifications as S-glutathionylation/S-nitrosylation, which occur through the electrophilic attack of ROS/RNS on the nucleophilic residues of Cys, provides redox switching in the activity of signaling proteins and the ability to control the processes of proliferation and programmed death. The level of S-glutathionylated and S-nitrosylated proteins is controlled by the balance between S-glutathionylation/deglutathionylation and S-nitrosylation/denitrosylation, the ratio of which depends on the cellular redox status. The degree of S-glutathionylation and S-nitrosylation of protein targets and their ratio largely determines the state and directions of signaling pathways in cancer cells. The review discusses the features of S-glutathionylation and S-nitrosylation reactions in cancer cells, the balance of systems that control their activity and their relationship with redox-dependent processes and tumor growth.
Histone methyltransferases as a new target for the epigenetic action by vorinostat
Authors: Maksimova V. P , Makus J. V , Popova V. G , Prus A. Yu , Usalka O. G , Trapeznikova E. S , Zhidkova E. M , Belitsky G. A , Yakubovskaya M. G
Published: April 2024

Aberrant methylation and acetylation of histones are characteristic changes in the system of epigenetic regulation of gene expression accompanying the process of malignant transformation of the cell. Vorinostat is the epigenetic modulator that actively used in clinical oncology practice. The antitumor activity of vorinostat is considered to be associated with only with the inhibition of histone deacetylases. The effects of this drug on histone methylation have not been sufficiently studied. Using the HeLa TI test system, which allows evaluating the integral effect of epigenetically active compounds by activating the expression of the reporter gene GFP, and knockdown of genes by small interfering RNAs, we showed that the inhibitory effect of vorinostat is directed not only at HDAC1, but also at EZH2, SUV39H1, SUV39H2, SUV420H1. Using Western blotting, the ability of vorinostat to suppress the expression of enzymes EZH2, SUV39H1/2, SUV420H1 was confirmed and, in addition, its ability to inhibit the expression of enzymes SUV420H2 and DOT1L was revealed. The data obtained expand the understanding of the epigenetic effects of vorinostat and demonstrate the need for a large-scale analysis of its activity in relation to other epigenetic enzymes. A detailed understanding of the mechanism of epigenetic action of vorinostat will contribute to its more adequate use in the treatment of tumors with an aberrant epigenetic profile.
Molecular mechanisms of tumor cell stemness modulation during formation of spheroids: a review
Authors: Ponomarev A. S , Gilazieva Z. E , Solovyova V. V , Rizvanov A. A
Published: April 2024

Cancer stem cells (CSCs), their properties and interaction with the microenvironment are of interest in modern medicine and biology. There are many studies on the emergence of CSCs and their involvement in tumor pathogenesis. The most important property inherent to CSCs is their stemness. Stemness combines the ability of the cell to maintain its pluripotency, give rise to differentiated cells and interact with the environment to maintain a balance between dormancy, proliferation and regeneration. While adult stem cells exhibit these properties by participating in tissue homeostasis, CSCs behave as their malignant equivalents. High tumor resistance to therapy, the ability to differentiate, activate angiogenesis and metastasis arise precisely due to stemness of CSCs. These cells can be used as a target for therapy of different types of cancer. Laboratory models are needed to study cancer biology and find new therapeutic strategies. A promising direction is three-dimensional tumor models or spheroids. Such models form properties resembling stemness in a natural tumor. By modifying spheroids, it becomes possible to investigate the effect of therapy on CSCs, thus contributing to the development of anti-tumor drug test systems. The review examines the niche of CSCs, the possibility of their study using three-dimensional spheroids, and existing markers for assessing stemness of CSCs.
Constitutive androstane receptor agonist initiates metabolic activity required for hepatocite proliferation
Authors: Mazin M. E , Perevalova A. M , Yarushkin A. A , Pustylnyak Y. A , Rogachev A. D , Prokopyeva E. A , Gulyaeva L. F , Pustylnyak V. O
Published: April 2024

Constitutive androstane receptor (CAR, NR1I3) activation by chemical compounds evokes liver hyperplasia in rodent. 1,4-Bis[2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP), a mouse CAR agonist, is most commonly used to study chemically induced liver hyperplasia and hepatocyte proliferation in vivo. TCPOBOP is potent murine liver chemical mitogen, which induces rapid direct liver hyperplasia independent of liver injury. In recent years, a lot of data has been accumulated on the transcription program that characterizes TCPOBOP-induced hepatocyte proliferation. However, there are scarce data about metabolic requirements of hepatocytes dividing upon treatment with xenobiotics. In present study, we employed liquid chromatography - mass spectrometry technology combined with statistical analysis to develop a metabolite profile of small biomolecules, to identify key metabolic changes in male mouse liver tissue after TCPOBOP administration. Analysis of biochemical pathways of the differentially affected metabolites in mouse livers demonstrated significant TCPOBOP-mediated enrichment of several processes including those relevant to nucleotide metabolism, amino acid metabolism, and energy substrate metabolism. Our findings provide evidence to support the conclusion that CAR agonist, TCPOBOP, initiates an intracellular program that promotes the global coordinated metabolic activities required for hepatocyte proliferation. Our metabolic data may provide novel insight into the biological mechanisms that occur during TCPOBOP-induced hepatocyte proliferation in mice.
Hybrid implants based on calcium-magnesium silicate ceramic diopside as a carrier of recombinant BMP-2 and demineralized bone matrix as a scaffold: ectopic osteogenesis in intramuscular implantation in mice
Authors: Karyagina A. S , Orlova P. A , Zhulina A. V , Krivozubov M. S , Grunina T. M , Strukova N. V , Nikitin K. E , Manskikh V. N , Senatov F. S
Published: April 2024

High efficiency of hybrid implants based on calcium-magnesium silicate ceramic diopside as a carrier of recombinant BMP-2 and xenogenic demineralized bone matrix (DBM) as a scaffold for bone tissue regeneration was demonstrated previously on the model of critical size cranial defects in mice. In order to investigate the possibility of using these implants for growing autologous bone tissue using the in vivo bioreactor principle in the patient’s own body, the effectiveness of the ectopic osteogenesis induced by them in intramuscular implantation in mice was studied. At 7 µg dose of BMP-2 per implant, after 1 week we observed a dense agglomeration of cells, probably skeletal muscle satellite precursor cells, with areas of intense chondrogenesis, the initial stage of indirect osteogenesis, around the implants. After 12 weeks, a dense bone capsule of trabecular structure was formed, covered with periosteum, with mature bone marrow located in the spaces between the trabeculae. The capsule volume was about 8-10 times the volume of the original implant. There were practically no signs of inflammation and foreign body reaction. Microcomputer tomography data showed a significant increase of the relative bone volume, number of trabeculae and bone tissue density in the group with BMP-2 in comparison with the group without BMP-2. Considering that DBM can be obtained in practically unlimited quantities, of the required size and shape, and the BMP-2 used, which is obtained by synthesis in E. coli cells, is relatively inexpensive, further development of the in vivo bioreactor model based on hybrid implants from BMP-2, diopside and xenogenic DBM seems promising.
State-of-the-art approaches for heterologous expression of bispecific antibodies targeting solid tumors
Authors: Misorin A. K , Chernyshova D. O , Karbyshev M. S
Published: April 2024

Bispecific antibodies (bsAbs) belong to the group of promising biotherapeutics, as their structural and functional features provide versatility. To put it simply, bsAbs bind two antigens or two epitopes on one antigen simultaneously, moreover, they are capable of directing effector immune cells to cancer cells and delivering payloads (radionuclides, toxic agents, and immunological payloads) to target cells, thus offering a broad spectrum of clinical applications. Current review is focused on bsAbs platform engineering technologies, current progress and prospects in utilization and selection of various heterologous expression systems for protein production. Furthermore we share our view on the future of the bsAbs development for solid tumor therapy.
Non-immunoglobulin synthetic binding proteins for oncology
Authors: David T. I , Pestov N. B , Korneenko T. V , Barlev N. A
Published: April 2024

Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold’s ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
Dimeric ACE2-FC is equivalent to monomeric ACE2 in the surrogate virus neutralization test
Authors: Kolesov D. E , Gaiamova E. A , Orlova N. A , Vorobiev I. I
Published: April 2024

Angiotensin converting enzyme 2 (ACE2) is the main cellular receptor for the dangerous sarbecoviruses SARS-CoV and SARS-CoV-2. Its recombinant extracellular domain is used to monitor the level of the protective humoral immune response to a viral infection or vaccine using a surrogate virus neutralization test (sVNT). Soluble ACE2 is also being considered as an antiviral therapy option potentially insensitive to changes in the SARS-CoV-2 spike protein. For widespread sVHT testing, it is necessary to use ACE2 preparations or ACE2 conjugates with constant properties. Previously, we obtained a cell line that produces soluble monomeric ACE2 and showed that this variant of ACE2 can be used in sBHT, preferably in the form of a conjugate with horseradish peroxidase. To obtain a stable and universally applicable form of soluble ACE2, a cell line was obtained that produced the ACE2-Fc fusion protein with high productivity, more than 150 mg/l of the target protein during cultivation in a stirred flask. Affinity-purified ACE2-Fc is a mixture of dimeric and tetrameric forms, but allows one to obtain linearizable antibody inhibition curves for complexation with the receptor-binding domain of the SARS-CoV-2 spike protein. The ACE2-Fc-HRP based sVHT testing system can be used to practically measure the levels of virus-neutralizing antibodies against various circulating variants of the SARS-CoV-2 virus.
Analysis of some biochemical properties of recombinant siberian roe deer (Capreolus pygargus) chymosin obtained in the mammalian cell culture (CHO-K1)
Authors: Murashkin D. E , Belenkaya S. V , Bondar A. A , Elchaninov V. V , Shcherbakov D. N
Published: April 2024

The structure of the Siberian roe deer (Capreolus pygargus) chymosin gene has been established for the first time and its exon/intron organization has been determined. The coding part of the C. pygargus chymosin gene was reconstructed and obtained as a DNA clone using the Golden Gate method. Comparative analysis of the sequences of prochymosins of roe deer, cow and single-humped camel revealed a number of amino acid substitutions in the sites forming the substrate-binding cavity of the enzyme and affecting the specificity subsites S4 and S1′ + S3′. The recombinant plasmid pIP1-Cap was constructed using the integration vector pIP1 for the expression of the roe deer prochymosin gene in CHO-K1 cells. A polyclone of CHO-K1-CYM-Cap cells was obtained, providing synthesis and secretion of recombinant prochymosin into the culture fluid of the producer. As a result of zymogen activation, a recombinant roe deer chymosin preparation with a total milk-clotting activity of 468.4 ± 11.1 IMCU/ml was obtained. The yield of recombinant roe deer chymosin was 500 mg/liter or ≈ 468,000 IMCU/liter, which exceeds the yield of genetically engineered chymosins in most of the expression systems used. The main biochemical properties of the obtained enzyme were compared with commercial preparations of recombinant chymosins of single-humped camel (Camelus dromedarius) and cow (Bos taurus). The specific milk-clotting activity of recombinant C. pygargus chymosin was 938 ± 22 IMCU/mg of protein and was comparable with the indicators of comparison enzymes. The nonspecific proteolytic activity of recombinant roe deer chymosin was 1.4-4.5 times higher than that of cow and camel enzymes. In terms of coagulation specificity, the recombinant C. pygargus chymosin occupied an intermediate position between the genetically engineered analogues of B. taurus and C. dromedarius chymosins. The threshold of thermal stability of recombinant roe deer chymosin was equal to 55°C. At 60°C, the enzyme retained
Ultra-fast mass spectrometry for plant biochemistry: proteomics response of winter wheat to iron pre-sowing treatment
Authors: Kusainova T. T , Emekeeva D. D , Kazakova E. M , Gorshkov V. A , Kjeldsen F. , Kuskov M. L , Zhigach A. N , Olkhovskaya I. P , Bogoslovskaya O. A
Published: April 2024

In recent years, ultrafast chromatography-mass spectrometry profiling of proteomes has been actively developed for biochemical studies. These methods are intended for fast/rapid monitoring of cell response to a biotic stimulus, correlation of molecular changes with biological processes and phenotype changes. To increase agricultural production, new biotechnologies are being introduced, including the use of nanomaterials. At the same time, thorough testing of new fertilizers and investigation of mechanisms of biotic effects on the germination, growth, and development of plants are required. The aim of this work was to adapt the method of ultrafast chromatography and mass spectrometry for rapid quantitative profiling of molecular changes in 7-day-old wheat seedlings that occur in response to pre-sowing seed treatment with iron compounds. The experimental method is capable of analyzing up to 200 samples per day; its practical value lies in carrying out the proteomic express diagnostics of the biotic action of new treatments, including those for agricultural needs. The regulation of photosynthesis, biosynthesis of chlorophyll, porphyrin- and tetrapyrrole-containing compounds, glycolysis in shoot tissues, and polysaccharide metabolism in root tissues were shown after seed treatments with suspensions containing a polymeric film former (PEG-400, Na-CMC, Na2-EDTA), iron (II, III) nanoparticles or iron (II) sulfate. Observations at the protein level were consistent with the results of morphometry, measurements of superoxide dismutase activity and microelement analysis of 3-day-old germinated seeds and shoots and roots of 7-day-old seedlings. A characteristic molecular signature has been proposed to determine the regulation of photosynthesis and glycolytic process at the protein level. Such a signature is considered as a potential marker of the biotic effect of seed treatment with iron compounds and will be confirmed by further studies.
Changes in activity of H+-ATPase of plasma membrane as a link between forming electrical signals and induction of photosynthetic responses in higher plants
Authors: Sukhova E. M , Yudina L. M , Sukhov V. S
Published: April 2024

Action of numerous adverse environmental factors on higher plants is spatially-heterogenous; it means that induction of a systemic adaptive response requires generation and propagation stress signals. Electrical signals (ESs) induced by local action of stressors include action potential, variation potential, and system potential and participate in forming fast physiological changes at the level of the whole plant, including photosynthetic responses. Generation of these ESs is accompanied by changes in activity of H+-ATPase which is the main system of electrogenic proton transport across the plasma membrane. Literature data show that the changes in H+-ATPase activity and related changes in intra- and extracellular pH play a key role in ESs-induced photosynthetic inactivation in non-irritated parts of plants. This inactivation is caused by both suppression of CO2 flux into mesophyll cells in leaves, which can be induced by the apoplast alkalization and, probably, cytoplasm acidification, and direct influence of acidification of stroma and lumen of chloroplasts on photosynthetic light and, probably, dark reactions. Result of the ESs-induced photosynthetic inactivation is increasing tolerance of photosynthetic machinery to action of adverse factors and probability of survive of plants.
Membrane potential generation by cytochrome bd
Authors: Borisov V. B
Published: April 2024

This treatise gives an overview of current thinking on the mechanism of generation of a transmembrane electric potential difference (Δψ) during the catalytic cycle of a bd-type triheme terminal quinol oxidase. It is assumed that the main contribution to the Δψ formation is made by the movement of H+ across the membrane along the intraprotein hydrophilic proton-conducting pathway from the cytoplasm to the active site for oxygen reduction of this bacterial enzyme.
Similarity and difference in the photochemistry of type I and II rhodopsins
Authors: Ostrovsky M. A , Smitienko O. A , Bochenkova A. V , Feldman T. B
Published: April 2024

The diversity of retinal-containing proteins in nature is extremely large. The fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of rhodopsin types I and II is carried out. The results of experimental studies of direct and reverse photoreactions of rhodopsin types I (bacteriorhodopsin) and II (visual rhodopsin) in the femto- and picosecond time interval, photo-reversible reaction of rhodopsin type II (octopus rhodopsin), photovoltaic reactions of rhodopsin types I and II, as well as quantum chemical calculations of forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The question of the probable convergent evolution of rhodopsin types I and II is discussed.
Markers of end-stage renal disease progression: beyond the GFR
Authors: Yakupova E. I , Abramicheva P. A , Bocharnikov A. D , Andrianova N. V , Plotnikov E. Y
Published: April 2024

Chronic kidney disease may progress to end-stage renal disease (ESRD) with a high risk of morbidity and mortality. ESRD requires immediate initiation of therapy or a decision on dialysis or kidney transplantation. Therefore, timely diagnosis of pathology progression is critical for many patients. ESRD is associated with pathological changes, including inflammation, fibrosis, endocrine disorders and following epigenetic changes in various cells, all these alterations could serve as markers for ESRD identification. This review summarizes conventional and promising biomarkers of ESRD, which can be evaluated in kidney tissue, blood, or urine. Some of them are narrowly specific to a particular pathology, while others are more versatile. We suggested several universal inflammatory, fibrotic, hormonal, and epigenetic markers indicative of severe deterioration of renal function and progression of ESRD for improvement of ESRD diagnostics.
Retrotransposons and telomeres
Authors: Kalmykova A. I , Sokolova O. A
Published: April 2024

Transposable elements (TEs) comprise a significant part of eukaryotic genomes being a major source of genome instability and mutagenesis. Cellular defense systems suppress the TE expansion at all stages of their life cycle. Piwi proteins and Piwi-interacting RNAs (piRNAs) are key elements of the anti-transposon defense system, which control TE activity in metazoan gonads preventing inheritable transpositions and developmental defects. In this review, we discuss various regulatory mechanisms by which small RNAs combat TE activity. However, active transposons persist, suggesting these powerful anti-transposon defense mechanisms have a limited capacity. A growing body of evidence suggests that increased TE activity coincides with genome reprogramming and telomere lengthening in different species. In the Drosophila fruit fly, whose telomeres consist only of retrotransposons, a piRNA-mediated mechanism is required for telomere maintenance and their length control. Therefore, the efficacy of protective mechanisms must be finely balanced in order not only to suppress the activity of transposons, but also to maintain the proper length and stability of telomeres. Structural and functional relationship between the telomere homeostasis and LINE1 retrotransposon in human cells indicates a close link between selfish TEs and the vital structure of the genome, telomeres. This relationship, which permits the retention of active TEs in the genome, is reportedly a legacy of the retrotransposon origin of telomeres. The maintenance of telomeres and the execution of other crucial roles that TEs acquired during the process of their domestication in the genome serve as a type of payment for such a “service.”
Nucleotide excision repair. Methods of determination the efficiency functioning
Authors: Popov A. A , Petruseva I. O , Naumenko N. V , Lavrik O. I
Published: April 2024

The nucleotide excision repair (NER) system is responsible for removing a wide range of bulky damages from DNA, making a significant contribution to maintaining the stability of the genome. The efficiency with which the proteins of the NER system recognize and remove bulky damages depends on many factors and has important clinical and diagnostic significance. The review examines the current understanding of the molecular basis of the functioning of the NER system in eukaryotic cells, as well as analyzes the methods and approaches that are used to study the efficiency functioning of this DNA repair system both in vitro and ex vivo.
Characteristics of PRIMPOL knockout А549 cell response to genоtoxic stress
Authors: Gromova A. S , Boldinova E. O , Kim D. V , Chuprov-netochin R. N , Leonov S. V , Pustovalova M. V , Zharkov D. O , Makarova A. V
Published: April 2024

Human DNA primase/polymerase PrimPol synthesizes DNA primers de novo after replication fork stalling at damaged DNA sites, contributing to DNA damage tolerance. The contribution of PrimPol in response to the various types of DNA damage is not fully understood. We obtained the lung carcinoma cells A549 with PRIMPOL knockout and characterized its response to DNA damage caused by hydrogen peroxide, methylmethanesulfonate (MMS), cisplatin, bleomycin and ionizing radiation. Knockout of PRIMPOL reduced the number of proliferating cells and cells in G2 phase after treatment with MMS, caused a more pronounced delay of cisplatin-treated cells in S phase. A significant increase in the proportion of apoptotic cells was noted in PRIMPOL-/- cells in response to ionizing radiation at a dose of 10 Gy, while the proportion of cells prone to necroptosis increased significantly in both parental and knockout cells at any radiation dose. Under conditions of oxidative stress stimulated by hydrogen peroxide, PRIMPOL knockout increased cell viability, measured by the MTT method. The data obtained indicate the involvement of PRIMPOL in modulating stress-adaptive responses to various types of genotoxic stress.
A new mouse strain with mutation in the NFE2L2 (NRF2 gene
Authors: Egorov E. S , Kondratenko N. D , Averina O. A , Permyakov O. A , Emelyanova M. A , Prikhodko A. S , Zinovkina L. A , Sergiev P. V , Zinovkin R. A
Published: April 2024

The transcription factor NRF2 is involved in inflammatory reactions, maintenance of redox balance, metabolism of xenobiotics, and is of particular interest for aging studies. In the present work, CRISPR/Cas9 genome editing technology was used to generate NRF2ΔNeh2 mice containing a substitution of eight amino acid residues at the N-terminus of the NRF2 protein, upstream of the functional Neh2 domain, which ensures binding of NRF2 to its inhibitor KEAP1. Heterozygote NRF2wt/ΔNeh2 mice gave birth to homozygous mice with lower than expected frequency, accompanied by their increased embryonic lethality and visual signs of anemia. Mouse embryonic fibroblasts (MEFs) from NRF2ΔNeh2/ΔNeh2 homozygotes showed impaired resistance to oxidative stress compared to wild-type MEFs. The tissues of homozygous NRF2ΔNeh2/ΔNeh2 animals had a decreased expression of NRF2 target genes: NAD(P)H: Quinone oxidoreductase-1 (Nqo1); aldehyde oxidase-1 (Aox1); glutathione-S-transferase A4 (Gsta4); while the relative mRNA level of monocyte chemoattractant protein 1 (Ccl2), vascular cell adhesion molecule 1 (Vcam1) and chemokine Cxcl8 was increased. Thus, the resulting mutation in the Nfe2l2 gene partially impaired the function of this transcription factor, expanding the insights into the functional role of the unstructured N-terminus of NRF2. The obtained NRF2ΔNeh2 mouse line can be used as a model object for studying various pathologies associated with oxidative stress and inflammation.