Maksim Patrushev

Immanuel Kant Baltic Federal University | IKSUR · Chemistry and Biology Institute

In accordance with the order of the President of the Russian Federation, the National Research Center “Kurchatov Institute” is creating the National Genomic Information Database (NGID). According to the amendments to Federal Law dated December 29, 2022, it is mandatory for organizations involved in genetic engineering and the production or supply o...

Synthetic biology is an interdisciplinary field of science and technology aimed at developing methods and approaches to design and construct living systems at different levels of their organization based on engineering principles. The work describes the main characteristics of synthetic biology, one of the most promising and interesting directions...

The process of the digitalization of biological information is currently in its early stages of development and is characterized by the accelerated exponential growth of databases, which offers great opportunities for the development of personalized medicine, biodiversity conservation, the development of biotechnology and agriculture, but, at the s...

Cryogenic soils are the most important terrestrial carbon reservoir on the planet. However, the relationship between soil microbial diversity and CO2 emission by cryogenic soils is poorly studied. This is especially important in the context of rising temperatures in the high Arctic which can lead to the activation of microbial processes in soils an...

For the first time, 41 grape varieties of the Don Valley (Rostov oblast) are genotyped, for most of them complete pedigree was restored. Contrary to the widely held belief, most varieties are not related to the Vitis vinifera cultivars of Western Europe and Transcaucasia. Only two varieties (Pukhlyakovskiy Belyi and Moldavskiy) are identical with r...

Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from Ruminococcus bromii sp. entitled RbCas12a, which is able to efficiently cleave target DNA templat...

Probiotic supplements are currently widely used in cattle feeding practices. However, knowledge regarding the genomic landscape of cattle probiotic microorganisms is relatively scarce and is based on analogies with human probiotics. Here, we report on the draft genome sequences of two Enterococcus lactis strains, VKPM B-4989 and VKPM B-4992, which...

Acinetobacter pittii strain B-3780 is a prospective degrader of oil and methanol, isolated from industrial wastewater. Here, we present the draft genome sequence of strain B-3780, obtained using Illumina sequencing of the fragment genomic library.

The draft genome sequence of Rhodococcus erythropolis VKPM Ac-1659, a putative oil-degrading strain, is reported. This genome sequence may provide better insights into the diversity and evolution of the genes responsible for hydrocarbon degradation in soil microorganisms.

Mitochondria are energy producing organelles of the eukaryotic cell, involved in the synthesis of key metabolites, calcium homeostasis and apoptosis. Protein biosynthesis in these organelles is a relic of its endosymbiotic origin. While mitochondrial translational factors have homologues among prokaryotes, they possess a number of unique traits. Re...

The draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia) is presented. The complete genome assembly was of 2 713 207 bp with predicted completeness of 99.38%. Genome structural annotation revealed 2674 protein-coding genes, 127 pseudogenes and 77 RNA g...

Objectives. To study the expression of various neurotransmitter transporters (glutamate, aspartate, lactate, choline) in cultures of astrocytes from different part of the brain (cortex, hippocampus, and brainstem) in rats aged three and 11 days. Materials and methods. An experimental study was performed using 24 Rattus norvegicus rats aged three (n...

The draft genome sequence of Bacillus sp. VKPM B-3276, a mesophilic, gram-positive bacterium, isolated from dead Culex pipiens larvae is presented. This strain was deposited in the Russian National Collection of Industrial Microorganisms as a prospective candidate for development of new entomopathogenic agents. The genome of Bacillus sp. VKPM B-327...

Data on the draft genome sequence of Bifidobacterium longumsubsp. longum strain Ac-1636 is presented in this report. This strain, isolated from the digestive tract of one-year old healthy infant, was deposited in the Russian National Collection of Industrial Microorganisms as a prospective candidate for development of probiotics and probiotic foods...

Two sets of reactants for modelling neurogenesis (SRMN) were developed based on the designed and tested genetic structures of lentiviral vectors. SRMN-1 contains the genetic construct LVV-GFAP-GCaMP3 and is intended for cellspecific transduction in astroglia cells. SRMN-2 contains the genetic construct LVV-PRSx8-TN-XXL and is intended for the pheno...

Two sets of reactants for modelling neurogenesis (SRMN) were developed based on the designed and tested genetic structures of lentiviral vectors. SRMN-1 contains the genetic construct LVV-GFAP-GCaMP3 and is intended for cellspecific transduction in astroglia cells. SRMN-2 contains the genetic construct LVV-PRSx8-TN-XXL and is intended for the pheno...

An experimental study has been carried out aiming at studying the expression of solute carriers (SLC) superfamily of the following neuromediators: glutamate, aspartate, lactate and choline. The study has been conducted on the pure culture of astroglial cells isolated from the brain in 3-day and 11-day rats. Expression of transporter genes in astroc...

Two sets of reactants for modeling neurogenesis (SRMN) have been developed that are based on the designed and tested genetic structures based on lentiviral vector. SRMN-1 contains genetic construct LVV-GFAP-GCaMP3, it is intended for cell-specific transduction of astroglia cells. SRMN-2 contains genetic construct LVV-PRSx8-TN-XXL, it is intended fo...

Central nervous system controls all the processes of the body through carefully honed neural network. This continuous activity is carried out with the help of neurons, glial cells and extracellular matrix. This review presents the main components of the extracellular matrix and characteristics of their participation in normal and pathological proce...

A fragment of the research project devoted to the development of genetic control of exocytosis is presented in the work, which can further ensure the success of targeted therapy of various diseases, including neurodegenerative ones. For the purpose of specific transfection of intracellular cascades in astrocytes in vivo, we have developed an experi...

Aim: To investigate the expression of transporters of different neurotransmitters (glutamate, aspartate, lactate, choline) in the culture of astrocytes isolated from different regions of the brain (cortex, hippocampus and brainstem) in 3- and 11-day rats. Material and methods: An experimental study was performed on 24 3- (n=12) and 11-days (n=12...

It is now well-known that astrocytes, GLAST+ cells, are active participants in the tripartite synapse. However, today there is an opinion that synapse represents tetrapartite structure, which includes pre- and postsynaptic neurons, astrocytes and the extracellular matrix (ECM) which is formed by glycoproteins and proteoglycans released by neighbour...

Dps is a multifunctional homododecameric protein that oxidizes Fe²⁺ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well...

Dps binds genomic DNA in a non-random manner. A: Correlation between the number of reads from immunoprecipitated and control libraries calculated for 100 bp bins (second experiment). All points, corresponding to rRNAs operons are marked in red. Blue dots correspond to the regions containing bins with R>1.4 in the first experiment (Fig 2A). Dashed l...

Typical Dps-binding sites are 100–130 bp in size. Histograms demonstrating the size-dependent distribution of the Dps-binding sites, revealed in two ChIP-seq experiments by CLC GW (A) and the Matcher (B) (blue and green plots, respectively). Solid and dashed lines correspond to the peaks found with default and stringent settings, respectively. The...

Deletion of dps significantly affects fis expression. A: Profiles of the Dps binding sites obtained in the two experiments (indicated) for the genomic region associated with the dusB-fis operon (running window of nine 35 bp bins). Disposition of genes is indicated by blue horizontal arrows. Genes transcribed as a polycistronic unit are underlined b...

Dps-bound and unbound regions found by the Matcher-based approach. (XLSX)

Dps reproducibly binds to the operons of ribosomal proteins, leaving the lacZYA, mhpR-lacI and mhpABCDFE operons unbound. Profiles of the Dps binding sites obtained in the two experiments (indicated) for the genomic region containing two operons of genes encoding ribosomal proteins (A) and operons of metabolic genes (B) (running window of nine 35 b...

Primers used in the study. (DOC)

Deletion of dps significantly affects expression of the rho gene. A: Profiles of the Dps binding sites obtained in two experiments (indicated) for the genomic region associated with the rho gene. Disposition of genes is indicated by blue horizontal arrows. Genes transcribed as a polycistronic unit are underlined by magenta line. Vertical arrows mar...

Peak regions found by CLC GW in both experiment using different settings. (XLSX)

Deletion of dps affected expression of oppD without any impact on oppA and oppB. A: Profiles of the Dps binding sites obtained in the two experiments (indicated) for the genomic region associated with the oppABCDF operon (running window of nine 35 bp bins). Disposition of genes is indicated by blue horizontal arrows. Genes transcribed as a polycist...

The aim of this paper is to create a multi-functional neuro-device and to study the possibilities of long-term monitoring of several physiological parameters of an organism controlled by brain activity with transmitting the data to the exoskeleton. To achieve this goal, analytical review of modern scientific-and-technical, normative, technical, and...

The work aims to produce a scientific and technological potential in the field of telemedicine for the timely detection and abortion of the cardiovascular system (CVS) diseases through the remote monitoring of the major physiological measures in a human. For this purpose, an experimental model of the hardware-software package was designed and devel...

Mitochondria import hundreds of different precursor proteins from the cytosol, and only 13 proteins are encoded by mtDNA itself. Recent investigations demonstrated real size of mitochondrial proteome and complexity of their functions There are many methods using for mitochondrial proteome profiling, that help to understand a molecular mechanisms of...

A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA gene sequence analysis placed the novel isolate in the crenarchaeal genus Thermofilum; Thermofilum pendens was its cl...

Mitochondria possess their own genome that, despite its small size, is critically important for their functioning, as it encodes several dozens of RNAs and proteins. All biochemical processes typical for bacterial and nuclear DNA are described in mitochondrial matrix: replication, repair, recombination, and transcription. Commonly, their mechanisms...

Mitochondria are key cellular organelles responsible for many different functions. The molecular biology of mitochondria is continuously subject to comprehensive studies. However, detailed mechanisms of mitochondrial biogenesis are still unclear. Fusion and fission are among the most enigmatic processes connected with mitochondria. On the other han...

Investigation on the use of capacitive pressure sen-sor chip model to demonstrate the measurement of changes in the length of the signal due to changes in the simulated pressure. Implement wireless trans-mission of power in order to demonstrate the minia-ture pressure measurement implant possibility fur-ther manufacturing.

Apart from the nucleus, the mitochondrion is the only organelle of an animal cell that contains its own genome. Mitochondrial DNA is much less in size than the nuclear one and codes for only several dozens of biological macromolecules. Nevertheless, mutations in mitochondrial genes often result in the occurrence of serious hereditary neuromuscular...

Crenarchaeota – one of two major archaeal phyla - comprises five orders, among which Thermoproteales is the first to be discovered and one of the best studied. The family Thermofilaceae represents a deep lineage within Thermoproteales and consists so far of one validly described genus and species, Thermofilum pendens, initially isolated from a solf...

The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910bT, was determined. The genome comprises a 1,750,259-bp circular chromosome containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding sequences. In silico genome-genome hybridization suggests the proposal of a novel species, “Thermofilum ador...

The complete genome sequence of a novel halophilic archaeon, Salinarchaeum sp. strain HArcht-Bsk1T, was determined using next-generation sequencing. The genome comprises a 3,255,260-bp circular chromosome with a G+C content of 66.7%. Automatic annotation of the genome revealed a single rRNA operon, 45 tRNAs, and 3,013 protein-coding gene sequences.

A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA bas...

Astrocytes might function as brain interoceptors capable of detecting different (chemo)sensory modalities and transmitting sensory information to the relevant neural networks controlling vital functions. For example, astrocytes that reside near the ventral surface of the brainstem (central respiratory chemosensitive area) respond to physiological d...

Many countries consider healthcare a priority area of development. Its future milestones lie in two key dimensions: social - combating common and complex diseases, and economic - establishing S&T basis that will provide leadership, or at least a decent niche in the global markets. The paper provides the results of a study conducted by the HSE in co...

The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910bT, was determined. The genome comprises a 1,750,259-bp circular chromosome containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding sequences. In silico genome-genome hybridization suggests the proposal of a novel species, "Thermofilum ador...

Opisthorchis felineus DNA extraction methods from fecal samples were compared. Comparative analysis of selected methods of DNA extraction from fecal samples containing eggs O. felineus, revealed that the most effective method for the identification of opisthorchiasis by PCR protocol is upgraded through the use of magnetic particles.

Exogenous thyroid hormones are regulators of cellular metabolism that involves, along with other cell structures, mitochondria. Mechanisms of the influence of thyroid hormones on the biogenesis of mtDNA are not fully understood due to their pleiotropic nature. Different ways of regulation of mitochondrial biogenesis by thyroid hormones are discusse...

Changes in the number of mitochondrial DNA (mtDNA) copies and alterations in its transcription were followed in the blood cells of mice after their exposure to X-rays; also, extracellular mtDNA fragments were registered in the blood serum of these mice. By a real time polymerase chain reaction (RT-PCR), a sharp increase in mtDNA copy number one hou...

Recently, we demonstrated that the release of mtDNA fragments from mitochondria occurs as a result of the opening of a non-specific pore in the inner mitochondrial membrane. Here, we show that irradiation of mice stimulates the appearance of mtDNA fragments in the cytosolic fractions of the brain. The fragments of mtDNA were found as early as 1h af...

A nessessary condition for normal functioning of mitochondria is the maintenance of certain numbers of intact mtDNA molecules. In the present study, we investigasted changes in the number of mtDNA copies in brain and spleen cells of mice subjected to irradiation. For the first time, we observed the irradiation-induced output of mtDNA fragments into...

Fragments of mitochondrial DNA are released from mitochondria upon opening of the mitochondrial permeability transition pore. Cyclosporin A, an inhibitor of pore opening, completely prevented the release of mitochondrial fragments. Induction of mitochondrial permeability transition and subsequent release of the fragments of mitochondrial DNA could...