Characterization of CoCas9 nuclease from Capnocytophaga ochracea.

Cas9 nucleases are widely used for genome editing and engineering. Cas9 enzymes encoded by CRISPR-Cas defence systems of various prokaryotic organisms possess different properties such as target site preferences, size, and DNA cleavage efficiency. Here, we biochemically characterized CoCas9 from Capnocytophaga ochracea, a bacterium that inhabits the oral cavity of humans and contributes to plaque formation on teeth. CoCas9 recognizes a novel 5'-NRRWC-3' PAM and efficiently cleaves DNA in vitro. Functional characterization of CoCas9 opens ways for genetic engineering of C. ochracea using its endogenous CRISPR-Cas system. The novel PAM requirement makes CoCas9 potentially useful in genome editing applications.

[Development and preservation of specific T-cell immunity after COVID-19 or vaccination against this infection].

Aim evaluation of specific T-cell immunity against SARS-CoV-2 in primary and secondary response to virus antigens by screening method. MATERIALS AND METHODS: Patients were tested 11.5 months after COVID-19 and 610 months before and after vaccination. Healthy volunteers were screened before, 26 times during the vaccination course, and 68 months after revaccination with the Sputnik V vaccine. IgG and IgM antibodies to SARS-CoV-2 were detected by ELISA using commercially available kits (Vector-Best, Russia). Antigenic (AG) activation of T cells in the fraction of bloods mononuclear cells was assessed by IFN- production after AG stimulation in the wells of plates from ELISA kits intended for detection of antibodies against SARS-CoV-2. Data were processed by MS Excel and Statistica 10.0 software. RESULTS: AG-specific T cells were detected in 88.5% of vaccinated healthy volunteers, half of whom were found to have T cells appearing earlier than antibodies to AG. After 6-8 months, the level of AG activation decreases. Following the revaccination, the level of AG activation of memory T cells in vitro increases within six months in 76.9100.0% of vaccinated subjects. On the contrary, after COVID-19, 86.7% of individuals had in their blood the AG-specific T cells with high activity at the time of vaccination. The activity of T cells recognizing the RBD domain of the SARS-CoV-2 S protein and the proportion of individuals who had these cells in their blood increased after the vaccination of reconvalescents. CONCLUSION: T-cell immunity against SARS-CoV-2 antigens has been shown to persist for 6 months after illness. In vaccinated individuals without history of COVID-19, such duration of the preservation of AG-specific T cells in blood was only achieved after the revaccination.

[Assesment of specific T-cell immunity to SARS-CoV-2 virus antigens in COVID-19 reconvalescents].

INTRODUCTION: The development of the COVID-19 pandemic has stimulated the scientific research aimed at studying of the mechanisms of formation the immunity against SARS-CoV-2. Currently, there is a need to develop a domestic simple and cost-effective specific method suitable for monitoring of T-cell response against SARS-CoV-2 in reconvalescents and vaccinated individuals. AIM: Development of a screening method for evaluation specific T-cell immunity against SARS-CoV-2. MATERIALS AND METHODS: Total 40 individuals who had mild to moderate COVID-19 and 20 healthy volunteers who did not have a history of this disease were examined. The presence and levels of IgG and IgM antibodies to SARS-CoV-2 were identified in participants sera by ELISA using the diagnostic kits from JSC Vector-Best (Novosibirsk, Russian Federation). Antigenic stimulation of mononuclear cells was carried out on commercial plates with adsorbed whole-virion inactivated SARS-CoV-2 antigen (State Research Center of Virology and Biotechnology VECTOR Novosibirsk, Russian Federation). The concentration of IFN- was measured in ELISA using the test systems from JSC Vector-Best (Novosibirsk, Russian Federation). The immunophenotyping of lymphocytes was performed on a flow cytometer Cytomics FC500 (Beckman Coulter, USA). Statistical data processing was carried out using the Microsoft Excel and STATISTICA 10 software package. RESULTS: Stimulation of mononuclear cells isolated from the peripheral blood with whole-virion inactivated SARS-CoV-2 antigen fixed at the bottom of the wells of a polystyrene plate showed a significantly higher median response in terms of IFN- production in 40 people who had history of COVID-19 compared to 20 healthy blood donors (172.1 [34.3575.1] pg/ml versus 15.4 [6.925.8] pg/ml, p 0.0001). There was no difference in median IFN- levels in supernatants collected from unstimulated mononuclear cells from COVID-19 reconvalescents and healthy donors (2.7 [0.411.4] pg/ml versus 0.8 [0.023.3] pg/ml, p 0.05). The overall sensitivity and specificity of this method were 73% (95% CI 5888%) and 100% (95% CI 100100%), respectively, at a cut-off of 50 pg/ml. CONCLUSION: The developed method for assessment of the cellular immune response to SARS-CoV-2 can be used as a screening method for monitoring the T-cell response in a population against a new coronavirus infection in recovered people.

Evaluation of antiviral activity of terpenophenols and some of their N- and O-derivatives.

A comparative evaluation of the antiviral activity of a number of new and previously synthesized terpenophenols and their N- or O-containing derivatives against the A/Puerto Rico/8/34 (H1N1) virus strain was carried out. 2-Isobornylphenol, 1,2-dihydroxy-6-isobornyl-4-methylbenzene, 2-isobornyl-1,4-benzoquinone, and N-butyl-4-hydroxy-3,5-diisobornylbenzamide showed the highest activity.

Early-onset oral cancer as a clinical entity: aetiology and pathogenesis.

Oral squamous cell carcinoma (OSCC) is one of the most important medical and socio-economic problems in many of the developed countries worldwide, due to the high mortality. The incidence of OSCC among individuals under 45 years of age is growing every year; however, the aetiological factors and pathogenetic mechanisms are poorly understood. This review summarizes the available information regarding clinicopathological features, extrinsic and intrinsic aetiological factors, and the molecular and immune landscape of early-onset OSCC. This cancer shows high recurrence rates and is not associated with the aetiological factors specific to adult-onset OSCC. Young adults with OSCC are not infected with human papillomavirus and rarely consume alcohol or tobacco, but more frequently use smokeless tobacco. Data from single studies indicate the hereditary nature of early-onset OSCC: the KIR2DL1+-HLA-C2+ genotype and MMP-1 2 G allele are frequently detected in young patients. Early-onset OSCC shows specific genetic, epigenetic, transcriptomic, and proteomic changes. The tumour microenvironment in early-onset OSCC is tolerogenic rather than immunogenic. All of the data suggest that OSCC in young patients is a separate clinical entity with a specific aetiology and pathogenesis. Further studies are needed to reveal the causes and molecular targets of early-onset OSCC for the development of preventive and therapeutic strategies.

Triethylamine-Based Salts: Protic Ionic Liquids or Molecular Complexes?

Amines can interact with protic acids with different degrees of proton transfer, which can lead to the formation of both hydrogen-bonded complexes and protic ionic liquids (PILs) in which the hydrogen bond between the cation and anion contributes to the formation of ion pairs. This work is devoted to studying the degree of proton transfer from different acids (hydrochloric, nitric, phosphoric, acetic, propionic, benzoic, and salicylic) to triethylamine (TEA). The results of quantum-chemical calculations based on the density functional theory (DFT) and thermal (phase transition and destruction temperatures) and physicochemical (conductivity, viscosity) characteristics of the compounds show that TEA interaction with acetic and propionic acids leads to the formation of hydrogen-bonded complexes. The B3LYP-GD3 method also shows that the interaction between TEA and benzoic acid is more energetically favorable for the formation of a molecular complex, whereas the obtained experimental data are more characteristic of a protic ionic liquid. For the other acids studied, the calculation and experimental data confirm salt formation. The geometric and energy parameters of the H-bond have been calculated both in the molecular complexes and in the ion pairs. The QTAIM theory was used to localize critical points of the hydrogen bonds and to calculate their properties.

[Approaches to the estimation of some parameters of humoral and cellular immune response to bacteriophages.]

The aim of the study was to develop some approaches to evaluate the basic parameters of the humoral and cellular immune response to a bacteriophage, taking into account the multifactorial aspects of its interaction with both the pathogen and the macroorganism. The necessary reagents were obtained and a line of diagnostic ELISA test systems was designed to allow semi-quantitative assessment of the anti-bacteriophage IgG-antibody level in serum or other biological human fluids, as well as in preparations obtained from human blood. The need for neutralization reaction to determine the effect of detected antibodies on phage activity against a target bacterium has been proven. Testing the approaches used in the investigation of patients' blood sera showed that antibodies to bacteriophages synthesized during phage therapy are not always neutralizing. Also approaches have been developed to evaluate cell immunity reactions to bacteriophage namely to identify T-lymphocytes (T-helpers and cytotoxic lymphocytes) that can be activated in the presence of the phage under study (by expressing the early activation marker (CD69) and by the ability to produce IFNγ). Approbation of the technique in the study of lymphcytes in patients during phage therapy showed the presence of activated cells by both the CD69 expression and IFNγ production, the dynamics of which depended on the timing and frequency of therapy. The appearance of neutralizing anti-phage antibodies and corresponding activated T-lymphocytes should be taken into account in phage therapy, the effectiveness of which can directly depend not only on the activity of the phage against the target bacterium, but also on the response of the patient's immune system to the bacteriophage.

Conditions for Collection of Placental Tissue Samples for Culturing of Multipotent Mesenchymal Stromal Cells.

Placentas from women aged 25-32 years with normal course of gestation were studied. It is essential to stick to certain methodological approaches for preparing viable multipotent mesenchymal stromal cell culture and to carry out morphological (macro and micro) evaluation of the chorionic villi, umbilical cords, and placentas. At stage I of the study, patients' histories, labor course, and examinations of the newborns should be analyzed to exclude women with genital and extragenital diseases. At stage II, it is essential to stick to special regulations and methods for collection of specimens of the cord, amnion, and placental tissue proper. Histological control of the placental structures collected for multipotent mesenchymal stromal cell culturing is obligatory.

[Ecological-hygienic evaluation of the environment of territories being adjacent to decultivated uranium mines].

On the territory of Kazakhstan there are uranium deposits, many ofwhich are in mothballed since times of perestroika. Often, the mines are flooded and represent a "time-delay bomb". Inside of mines various there are accumulated gases of both organic and inorganic nature, periodically thrown out and adversely affecting on the health of local populations. The aim of the study was the investigation of the state of the environment of Esilsky district of the Akmola region by common pollutants and chemicals. As the basic variable for the investigation of ambient air there was accepted the maximum one-time concentration of suspended substances, phenol, nitrogen dioxide, sulfur dioxide. The results were evaluated in relation to the MPC for the analyzed substance in the air according to maximal single MPC (MPCms) and daily average MPC (MPCda). The content of metals in the water was determined with the use of spectrophotometer PD-303S. Evaluation of the results was executed in relation of the MPC of substances in water, by means of the comparison with the requirements of Federal standards for drinking water, samples from drinking water sources. There were executed calculations of the overall index of water pollution (IWVgen), the index of water pollution by heavy metals (IWVhm). Chemical analysis of soil was carried out with the use of spectrophotometer PD- 303S (Japan), the photometer expert-003 "Ekoniks". Evaluation of the results was carried out with the respect to the MPC in the soil, the toxicity of all components. Summarizing soil pollution index was evaluated for metals contained in the soil at the level of more than or equal to 1 MAC. The settlement Krasnogorskiy and the village of Kalachi were found to be characterized by a low level of air pollution, increased rigidity of drinking water exceeded the maximum permissible concentrations of copper by 3.45 times and chloride by 1.17 times in the soil cover.

Ectopic pregnancy following in vitro fertilization: meta-analysis and single-center experience during 6 years.

BACKGROUND: Ectopic pregnancy (EP) has been reported to occur in 1.4-5.4% of all clinical pregnancies resulting from in vitro fertilization (IVF) and embryo transfer (ET). Data on factors associated with abnormal embryo implantation following assisted conception are limited. MATERIALS AND METHODS: A systematic review and meta-analysis was performed to determine whether there is an association between the day (cleavage-stage, D3, versus blastocyst, D5) or the type (fresh versus frozen/thawed) of ET and EP rate. Risk factors for EP were evaluated in a retrospective study of 1194 women, who achieved pregnancy at our IVF unit between 2010 and 2016. RESULTS: Sixteen papers were considered for the meta-analysis. EP rate did not differ between D3 and D5 fresh ET groups (RR = 0.99, 95%CI: 0.76-1.30) and was higher after fresh versus frozen ET (RR = 1.56, 95%CI: 1.25-1.95). At our clinic, 21 (1.76%) pregnancies were documented as ectopic. The risk of EP was associated with tubal pathology (OR = 3.37, 95%CI: 1.39-8.2), previous appendectomy and past chlamydial infection. CONCLUSIONS: Present meta-analysis suggests that EP rate is similar following fresh blastocyst and cleavage ETs, but is significantly reduced after frozen compared with fresh ET. Our own findings demonstrate that tubal pathology has the major impact on EP occurrence following assisted conception.

Comparative Analysis of the Proliferative Potential of Human Mesenchymal Stromal Cells from Extraembryonic Organs, Endometrium, and Adipose Tissue.

Proliferative activity of mesenchymal stromal cells isolated from five sources (chorionic villi, Wharton's jelly, amnion, endometrium, and adipose tissue) was compared by flow cytometry and real-time PCR (by the content of mRNA of genes encoding of cell cycle regulators). Mesenchymal stromal cells derived from the endometrium demonstrated maximum stability and high proliferative potential.

[Control levels of Sin3 histone deacetylase for spontaneous and UV-induced mutagenesis in yeasts Saccharomyces cerevisiae].

SIN3 gene product operates as a repressor for a huge amount of genes in Saccharomyces cerevisiae. Sin3 protein with a mass of about 175 kDa is a member of the RPD3 protein complex with an assessed mass of greater than 2 million Da. It was previously shownthat RPD3 gene mutations influence recombination and repair processes in S. cerevisiae yeasts. We studied the impacts of the sin3 mutation on UV-light sensitivity and UV-induced mutagenesis in budding yeast cells. The deletion ofthe SIN3 gene causes weak UV-sensitivity of mutant budding cells as compared to the wild-type strain. These results show that the sin3 mutation decreases both spontaneous and UV-induced levels of levels. This fact is hypothetically related to themalfunction of ribonucleotide reductase activity regulation, which leads to a decrease in the dNTP pool and the inaccurate error-prone damage bypass postreplication repair pathway, which in turn provokes a reduction in the incidence of mutations.

[The virulence factors of Mycobacterium tuberculosis: genetic control, new conceptions].

The problem of Mycobacterium tuberculosis virulence, together with drug resistance, is becoming key for the design of drugs with a new mechanism of action and the production of modern concepts and tuberculosis treatment schemes. The review describes gene complexes and their products, including mycolic acids and global regulatory systems at the level of transcriptional, translational, and post-translational modification, etc. The criteria for selection of virulence/pathogenicity factors that might be used for comparative genomic analysis of strains differing in the degree of virulence were recommended. The experimental approaches and test systems for an adequate estimation of the virulence degree of different strains of M. tuberculosis were analyzed.

[Interaction of the HSM3 gene with genes initiating homologous recombination repair in yeast Saccharomyces cerevisiae].

It was assumed previously that the mutator phenotype of the hms3 mutant was determined by processes taking place in the D-loop. As a next step, genetic analysis was performed to study the interactions between the hsm3 mutation and mutations of the genes that control the initial steps of the D-loop formation. The mutations of the MMS4 and XRS2 genes, which initiate the double-strand break formation and subsequent repair, were shown to completely block HSM3-dependent UV-induced mutagenesis. Mutations of the RAD51, RAD52, and RAD54 genes, which are also involved in the D-loop formation, only slightly decreased the level of UV-induced mutagenesis in the hsm3 mutant. Similar results were observed for the interaction of hsm3 with the mph1 mutation, which stabilizes the D-loop. In contrast, the shu1 mutation, which destabilizes the D-loop structure, led to an extremely high level of UV-induced mutagenesis and displayed epistatic interactions with the hsm3 mutation. The results made it possible to assume that the hsm3 mutation destabilizes the D-loop, which is a key substrate of both Rad5- and Rad52-dependent postreplicative repair pathways.

[Interaction of gene HSM3 with genes of the epistatic RAD6 group in yeast Saccharomyces cerevisiae].

In eukaryotes, damage tolerance of matrix DNA is mainly determined by the repair pathway under the control of the RAD6 epistatic group of genes. T this pathway is also a main source of mutations generated by mutagenic factors. The results of our recent studies show that gene HSM3 participating in the control of adaptive mutagenesis increases the frequency of mutations induced by different mutagens. Mutations rad18, rev3, and mms2 controlling various stages of the RAD6 pathway are epistatic with mutation hsm3 that decreases UV-induced mutagenesis to the level typical for single radiation-sensitive mutants. The level of mutagenesis in the double mutant srs2 hsm3 was lower than in both single mutants. Note that a decrease in the level of mutagenesis relative to the single mutant srs2 depends on the mismatch repair, since this level in the triple mutant srs2 hsm3 pms 1 corresponds to that in the single mutant srs2. These data show that the mutator phenotype hsm3 is probably determined by processes occurring in a D loop. In a number of current works, the protein Hsm3 was shown to participate in the assembly of the proteasome complex S26. The assembly of proteasomes is governed by the N-terminal domain. Our results demonstrated that the Hsm3 protein contains at least two domains; the N-terminal part of the domain is responsible for the proteasome assembly, whereas the C-terminal portion of the protein is responsible for mutagenesis.

[Surface active properties of isobornylphenols in systems with different degrees of complexity].

Interrelations between the structure of the semi-synthetic phenolic antioxidants -- isobornylphenols and their surface active properties were studied in the chemical (the lecithin aggregation in hexane) and biological (the incubation with the blood erythrocytes) model systems. It has been shown that all studied compounds are able to affect the lecithin aggregation in hexane: the share of the main fraction of the L micelles decreases with increasing the share of particles of greater size. The effect substantially depends on hindered OH group and the presence of the intramolecular hydrogen bond in molecule. The cytotoxic properties of isobornylphenols (the concentration is 100 M) are predominantly due to the molecule structure. The interrelation between the aggregate size of the main fraction of L in the presence of the studied compounds and the discocyte share during mice blood erythrocyte incubation in their presence for 4 h is revealed. Thus, this provides the possibility to assume that the ability of the different biological active substances to affect the lecithin aggregation in non-polar solvent could be used as a model system for the initial assessment of their surface active properties.

Specific mechanism of use-dependent channel block of calcium-permeable AMPA receptors provides activity-dependent inhibition of glutamatergic neurotransmission.

This study examined the blocking action of the selective channel blocker of calcium-permeable (CP) AMPA receptors, N1-(1-phenylcyclohexyl)pentane-1,5-diaminium bromide (IEM-1925), on excitatory postsynaptic currents in rat neostriatal and cortical neurons and in fly neuromuscular junctions. In both preparations, the blocking of CP-AMPA receptor currents increased along with the stimulation frequency. The continuous presence of kainate, which activates AMPA receptors, in the external solution also caused an enhanced blocking effect. Likewise, decrease of the synaptic release by lowering calcium concentration resulted in significant reduction of the blocking action. The activity dependence of the block is explained using the guarded receptor model. The drug molecule can only bind if the channel is open. After the channel has closed, the drug molecule remains trapped inside. However, the trapped molecule slowly egresses from closed channels to the cytoplasm. The total block effect is determined by the equilibrium between accumulation of the drug in the open channels and relief from the closed channels. Therefore, the conditions that favour the open state result in enhanced inhibition. This significant finding reveals a new way to modulate CP-AMPAR-mediated transmission using a physiologically relevant approach. Moreover, it allows the involvement of CP-AMPARs in the physiological and pathological processes ­ such as high-frequency synaptic activity or increase of the steady-state glutamate concentration ­ to be examined.

DNA methylation patterns of metaphase chromosomes in human preimplantation embryos.

We performed a stage-by-stage study of DNA methylation patterns in metaphase chromosomes from blastomeres of triploid and abnormal diploid human embryos. QFH-banded homologous parental chromosomes differ in their DNA methylation patterns at the metaphase of the 1st cleavage division. Chromosomes of both parental genomes are gradually demethylated at subsequent cleavages, undergoing hemimethylation in 2-cell embryos. At the 4-cell stage hypomethylated chromosomes initially appear and are further registered until the blastocyst stage. The proportion of hemimethylated and hypomethylated chromosomes varies between the blastomeres since the 4-cell stage with no preference for certain chromosomes to be hemi- or hypomethylated demonstrates random segregation of hypomethylated, undermethylated and methylated chromatids during cell cleavage. By the blastocyst stage the chromosomes acquire band- and, thus, chromosome-specific methylation patterns, with 5-methylcytosine-rich DNA preferentially accumulated in R- and T-bands and in the short arms of acrocentric chromosomes. Thus, demethylaton and remethylation of parental genomes of human embryos proceeds in the same manner from the 1st metaphase stage up to the blastocyst. These processes involve all chromosomes and all bands from each chromosome and lead to establishment of chromosome-specific DNA methylation patterns by the blastocyst stage with no differences between homologous chromosomes.

[Genetic analysis of the Hsm3 protein domain structure in yeast Saccharomyces cerevisiae].

Gene HSM3 encodes the Hsm3 protein involved in the minor branch in the system responsible for the correction of mismatched bases in DNA structure and controls replicative and reparative spontaneous mutagenesis in yeast Saccharomyces cerevisiae. Spontaneous and UV-induced mutagenesis was studied in three mutant alleles of gene HSM3, and repair effectivity of artificial heteroduplexes was assessed in DNA molecule. The resuts of these studies allowed establishment of the protein domain structure of protein Hsm3 and functions of each domain: the N-terminal domain is responsible for binding to mispaired bases, and the C-terminal domain ensures the interaction with other proteins involved in the system of mismatched base correction.

[Cytogenetic effects of cholinotropic preparations mixture on Chironomus plumosus (Diptera) larvae in vivo].

Morphometric analysis of changes in nucleolar organizer (NO), Balbiani rings (BR)--BR(B), BR(1G), BR(2G) and chromosome I arm B puff activities, and in chromosome compactness of Chironomus plumosus (Diptera) polytene chromosomes was carried out in acute period under separate and combined influence of atropine and pilocarpine. Supression effect of cholinotropic preparations mixture was revealed. Suppression of NO activity with atropine concentration increase in the mixture served as criterion of toxicity.