Genome Features of Probiotic Bifidobacteria Determining Their Strain-Specific Properties.

The aim of the study was to analyze the genome features of the probiotic strains Bifidobacterium longum 379, Bifidobacterium bifidum 1, and Bifidobacterium bifidum 791 and study their antiviral activity. Materials and Methods: Whole genome sequencing of three strains of bifidobacteria was performed on the MiSeq platform (Illumina Inc., USA). The genomes were annotated using the Prokka v. 1.11 utility and RAST genomic server. The individual genetic determinants were searched using the ResFinder 3.2, PathogenFinder, PlasmidFinder, RAST, and Bagel 4 software. The antiviral activity of the strains against influenza A viruses was studied using MDCK cells (Madin-Darby canine kidney cells), the epidemic strain of influenza A/Lipetsk/1V/2018 (H1N1 pdm09) (EPI_ISL_332798), the highly pathogenic avian influenza virus A/common gull/Saratov/1676/2018 (H5N6) strain (EPI_ISL_336925), and neutral red vital dye. Results: The genomes of all studied strains contained determinants responsible for utilization of carbohydrates of plant origin; the genes of key enzymes for the synthesis of tryptophan and folic acid are present in the genomes of B. longum 379 and B. bifidum 791. A feature of the B. bifidum 791 genome is the presence of determinants responsible for the synthesis of thermostable type I bacteriocins - flavucin and lasso peptide. The B. bifidum 791 strain was found to show pronounced antiviral activity against both the strains of influenza A, the supernatant of which suppressed viral replication in vitro up to a dilution of 1:8, and the cells inhibited viral reproduction up to a concentration of 6·106 CFU/ml. Conclusion: The analysis of complete genomes of B. longum 379, B. bifidum 1, and B. bifidum 791 showed features that determine their strain-specific properties, the findings on which were previously made empirically based on indirect signs. In the genomes of B. longum 379 and B. bifidum 791 strains, in contrast to B. bifidum 1 strain, key enzymes for the synthesis of tryptophan and folic acid were found. These substances have an impact on the human body in many ways, including having a thymoleptic effect (reducing emotional stress, irritability, anxiety, eliminating lethargy, apathy, melancholy, anxiety) and regulating cognitive activity. The presence of determinants responsible for the synthesis of thermostable type I bacteriocins in the genome of B. bifidum 791 strain determines its pronounced antiviral activity.

Colon Microbiocenosis and Its Correction in Patients Receiving Programmed Hemodialysis.

The aim of the investigation was to study the species composition of colon microbiocenosis in patients with chronic kidney disease receiving programmed hemodialysis treatment and to evaluate the efficacy of its correction using a new immobilized synbiotic. MATERIALS AND METHODS: Samples of colon microbiota from 62 patients undergoing programmed hemodialysis were studied before and after a course of diet therapy that included probiotic components, in particular, the immobilized synbiotic LB-complex L. Isolation of microorganisms was carried out according to our original method; for bacteria identification, a MALDI-TOF Autoflex speed mass spectrometer (Bruker Daltonik, Germany) was used in the Biotyper program mode. The results were assessed using the criteria proposed by the authors and based on the OST 91500.11.0004-2003. The efficacy of the immobilized synbiotic was determined based on the clinical data, questionnaires, and bacteriological tests. RESULTS: In patients receiving programmed hemodialysis (before the start of the diet therapy), chronic moderate inflammation and azotemia were found. Dysbiotic changes in microbiocenosis were revealed in all the examined patients; in the absence or suppression of lacto- and bifidoflora, the number and diversity of Bacteroides spp., Clostridium spp., Collinsella spp., Eggerthella spp. and other bacteria increased, which was consistent with the theory of functional redundancy of gut microbiota. From the answers to the questionnaires, a decrease in the quality of life was found (up to 70 points out of 100) according to six of the eight scales used. After the combined therapy using the synbiotic LB-complex L in the study group, 56% of the examined patients showed their microbiocenosis restored to normal; no grade III dysbiosis was detected in any patient. There was a significant decrease in CRP and ESR in these patients and an improvement in the quality of life by criteria reflecting physical health. CONCLUSION: In patients receiving programmed hemodialysis, the addition of a probiotic component in the diet therapy restores the evolutionarily determined structure of the microbiocenosis, normalizes its functions, and leads to an overall improvement in health and quality of life.

[Evaluation of anti-candida activity of metabolites of enterococcal clinical isolates.]

When studying the effect of the metabolic products of clinical isolates of enterococci on the viability of Candida albicans, it was found that metabolites of all tested strains of Enterococcus faecium, E. faecalis had a fungistatic effect. At the same time a reliable fungicidal effect is a strain-specific feature. It is better to use the method of delayed antagonism on double-layer agar to assess the antifungal effect of enterococcal metabolism products.

[CHARACTERISTICS OF BIOLOGICAL AND MOLECULAR-GENETIC PROPERTIES OF LACTOBACILLUS FERMENTUM 90 TC-4 PROBIOTIC STRAIN].

AIM: Confirmation of taxonomic position of Lactobacillus fermentum 90 TC-4 strain using phenotypic (classic microbiological, MALDI TOF mass-spectrometry) and genetic (16S rRNA gene segment sequencing and full genome sequencing) methods. MATERIALS AND METHODS: Object of the study--Lactobacillus fermentum 90 TC-4 strains from various collections. Mass-spectrometric analysis was carried out using Autoflex MALDI TOF mass-spectrometer (Bruker Daltonics, Germany), study of biochemical properties of the strain was carried out using API 50 CHL strips (Biomerueux, France), "DNA-sorb B" kitwas used for isolation ofgenome DNA (CRIE, Moscow). Sequencing of the accumulated fragments of 16S rRNA gene was carried out using GenomeLab GeXP sequencing (Beckman Coulter, USA), full genome sequencing was carried out in MiSeq platform (Illumina). Assembly of genome and bioinformation analysis was carried out using BLAST program (www.blast.ncbi.nlm.nih.gov/blast.cgi), "CLC Bio Assembly" and genome server RAST (rast.nmpdr.org). RESULTS: L. fermentum 90 TC-4 strain was established to be contaminated by L. plantarum culture in a series of cases. As a result of identification of a pure culture of L. fermentum 90 TC-4 strain using a specter of high-technology methods, membership of the strain in L. fer- mentum species has been proven. CONCLUSION: Taxonomic status of L. fermentum 90 TC-4 strain was confirmed.

[Lactobacillus fermentum 90 TC-4 taxonomic status confirmation using whole genome sequencing and MALDI TOF mass spectrum].

With the use of whole genome sequencing, the taxonomic status of Lactobacillus fermentum 90 TC-4 strain from Russian collections were studied. Complex analysis of phenotypical and genetic properties was conducted using phenotypic and molecular genetic methods. The main characteristics of the genome and biochemical activity profile of the strain were determined. A comparative analysis of the mass spectrum of ribosomal proteins of the strain, its biochemical properties, a fragment of 16S rRNA gene sequencing, and the entire genome revealed that the present strain belongs to the species L. fermentum, confirming its taxonomic status in accordance with modern taxonomy.

Oxygen diffusion in marine-derived tissue engineering scaffolds.

This paper addresses the computation of the effective diffusivity in new bioactive glass (BG) based tissue engineering scaffolds. High diffusivities facilitate the supply of oxygen and nutrients to grown tissue as well as the rapid disposal of toxic waste products. The present study addresses required novel types of bone tissue engineering BG scaffolds that are derived from natural marine sponges. Using the foam replication method, the scaffold geometry is defined by the porous structure of Spongia Agaricina and Spongia Lamella. These sponges present the advantage of attaining scaffolds with higher mechanical properties (2-4 MPa) due to a decrease in porosity (68-76%). The effective diffusivities of these structures are compared with that of conventional scaffolds based on polyurethane (PU) foam templates, characterised by high porosity (>90%) and lower mechanical properties (>0.05 MPa). Both the spatial and directional variations of diffusivity are investigated. Furthermore, the effect of scaffold decomposition due to immersion in simulated body fluid (SBF) on the diffusivity is addressed. Scaffolds based on natural marine sponges are characterised by lower oxygen diffusivity due to their lower porosity compared with the PU replica foams, which should enable the best oxygen supply to newly formed bone according the numerical results. The oxygen diffusivity of these new BG scaffolds increases over time as a consequence of the degradation in SBF.

A comparative study of oxygen diffusion in tissue engineering scaffolds.

Tissue engineering scaffolds are designed to support tissue self-healing within physiological environments by promoting the attachment, growth and differentiation of relevant cells. Newly formed tissue must be supplied with sufficient levels of oxygen to prevent necrosis. Oxygen diffusion is the major transport mechanism before vascularization is completed and oxygen is predominantly supplied via blood vessels. The present study compares different designs for scaffolds in the context of their oxygen diffusion ability. In all cases, oxygen diffusion is confined to the scaffold pores that are assumed to be completely occupied by newly formed tissue. The solid phase of the scaffolds acts as diffusion barrier that locally inhibits oxygen diffusion, i.e. no oxygen passes through the scaffold material. As a result, the oxygen diffusivity is determined by the scaffold porosity and pore architecture. Lattice Monte Carlo simulations are performed to compare the normalized oxygen diffusivities in scaffolds obtained by the foam replication (FR) method, robocasting and sol-gel foaming. Scaffolds made by the FR method were found to have the highest oxygen diffusivity due to their high porosity and interconnected pores. These structures enable the best oxygen supply for newly formed tissue among the scaffold types considered according to the present numerical predictions.

Structural stability and energy of a Pd2Ni nanofilm: ab initio calculations.

Recently, using molecular dynamics simulation in conjunction with an embedded-atom method potential, we have predicted Pd2Ni surface-sandwich ordering at the nanoscale. These findings open up a range of opportunities for the synthesis of new kinds of Pd-Ni nanostructures such as a five-layer Pd2Ni nanofilm from which a Pd2Ni nanotube might be fabricated. In this paper, we report on an ab initio spatial optimization and structural energy calculation of a five-layer Pd2Ni nanofilm, which are performed using plane-wave pseudopotential total energy calculations in the generalized gradient approximation of density functional theory. The results of the ab-initio calculations show that the five-layer Pd2Ni nanofilm is structurally stable and its energy is approximately 0.4 eV higher than the energy of a bulk crystal alloy having the same composition.

[Chromosome control of apomixis in maize-gamagrass hybrids].

The results of long-term studies on the transmission of the mode of asexual reproduction through seeds to maize from gamagrass, a closely related wild plant, performed in the Laboratory of Plant Cytology and Apomixis are summarized. The first apomictic hybrids between Zea mays and Tripsacum dactyloides were obtained in this laboratory more than 40 years ago and have been maintained until the present time. Cytogenetic studies on the hybrids have shown that at least nine chromosomes of the wild parent are necessary for the expression of asexual reproduction through seeds. In addition, the genes controlling two elements of apomixis (apomeiosis and parthenogenesis) have been found to be inherited independently from each other.

[Indication and identification of Lactobacillus spp. with the use of polymerase chain reaction].

AIM: The aim of the work is the development of laboratory test for indication and identification of Lactobacillus spp. by the polymerase chain reaction. MATERIALS AND METHODS: The work is developed on the base of the GenBank/EMBL data about genetic sequences of the Lactobacillus spp. The sequences of DNA were studied with the help of the ClustalW program. The strains of the Lactobacillus spp., which are the object of the research, have been registered in Russian collection of industrial microorganisms. RESULTS: The laboratory test of nested-PCR for indication and identification L. plantarum, L. fermentum, L. acidophilus, L. delbrueckii, L. casei, L. rhamnosus was performed. The specificity of the nested-PCR was correlated with the control analyses of monoculture Lactobacillus spp. and commercial products. CONCLUSION: The new developed laboratory nested-PCR test may be use in control system of milk foods enriched by probiotic microorganisms.

[Reflected wave and isolated systolic hypertension: problems of pathogenesis and therapy]. / Otrazhennaia volna i izolirovannaia sistolicheskaia arterial'naia gipertoniia: voprosy patogeneza i terapii.

The value of reflected (tidal) wave amplitude in the pathogenesis of isolated systolic hypertension (ISH) is discussed and main characteristics of elastic properties of arteries (compliance, distensibility, rigidity, pulse wave velocity, and amplitude of reflected wave) are considered. In ISH systolic and pulse blood pressures are associated with augmentation of the reflected wave amplitude. Increased pulse wave velocity characteristic of ISH leads to displacement of reflected wave from diastole to systole. Summation of two waves (primary and reflected) causes elevation of systolic blood pressure. Choice of antihypertensive drugs for the treatment of ISH is determined by their action on pulse wave velocity, delay of reflected wave and arterial compliance. Preferable agents are angiotensin converting enzyme inhibitors, calcium antagonists, diuretics and beta-blockers with vasodilating properties. In bradycardia with high stroke volume normalization of heart rate can be achieved by M-anticholinergic drugs and theophylline.

[PHO2 and GCN4 transcription activators in the regulation of Saccharomyces cerevisiae acid phosphatase synthesis]. / Aktivatory transkriptsii PHO2 i GCN4 v reguliatsii sinteza kislykh fosfataz drozhzhei Saccharomyces cerevisiae.

The possibility of substitution of the PHO2 activator protein by GCN4 protein in transcriptional regulation of acid phosphatase genes PHO5 and PHO11 was demonstrated in the yeast Saccharomyces cerevisiae. We observed the increase in acid phosphatase synthesis in the case of gcn4-delta 1 pho2-delta 1 mutant transformed with YCp88 (GCN4-wt) plasmid in comparison with that in nontransformed cells. The mode of repression of acid phosphatase synthesis in two types of transformants gcn4-delta 1 pho2-delta 1 (GCN4-wt) and gcn4-delta 1 pho2-delta 1 (PHO2-wt) was studied. It wat demonstrated that repression of acid phosphatase synthesis in the first type of transformants took place at lower concentration of Pi than was necessary for the second type of transformants. The model of interactions between the GCN4 activator protein and PHO regulatory factors is proposed.