The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses.

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.

Two novel transcriptional reporter systems for monitoring Helicobacter pylori stress responses.

Helicobacter pylori, a human pathogen linked to many stomach diseases, is well adapted to colonize aggressive gastric environments, and its virulence factors contribute this adaptation. Here, we report the construction of two novel H. pylori vectors, pSv2 and pSv4, carrying a reporter gene fused to the promoters of virulence factor genes for monitoring the response of single H. pylori cells to various stresses. H. pylori cryptic plasmids were modified by the introduction of the Escherichia coli origin of replication, chloramphenicol resistance cassette, and promoterless gfp gene to produce E. coli/H. pylori shuttle vectors. The promoter regions of vacA and ureA genes encoding well-characterized H. pylori virulence factors were fused to the promoterless gfp gene. Recording the GFP fluorescence signal from the genetically modified H. pylori cells immobilized in specifically designed microfluidic devices revealed the response of transcriptional reporter systems to osmotic stress, acidic stress, elevated Ni2+ concentration or iron chelation. Our observations validate the utility of the pSv2 and pSv4 vectors to monitor the regulation of virulence factor genes in diverse strains and clinical isolates of H. pylori.

Medicinal leech antimicrobial peptides lacking toxicity represent a promising alternative strategy to combat antibiotic-resistant pathogens.

The rise of antibiotic resistance has necessitated the development of alternative strategies for the treatment of infectious diseases. Antimicrobial peptides (AMPs), components of the innate immune response in various organisms, are promising next-generation drugs against bacterial infections. The ability of the medicinal leech Hirudo medicinalis to store blood for months with little change has attracted interest regarding the identification of novel AMPs in this organism. In this study, we employed computational algorithms to the medicinal leech genome assembly to identify amino acid sequences encoding potential AMPs. Then, we synthesized twelve candidate AMPs identified by the algorithms, determined their secondary structures, measured minimal inhibitory concentrations against three bacterial species (Escherichia coli, Bacillus subtilis, and Chlamydia thrachomatis), and assayed cytotoxic and haemolytic activities. Eight of twelve candidate AMPs possessed antimicrobial activity, and only two of them, 3967 (FRIMRILRVLKL) and 536-1 (RWRLVCFLCRRKKV), exhibited inhibition of growth of all tested bacterial species at a minimal inhibitory concentration of 10 µmol. Thus, we evidence the utility of the developed computational algorithms for the identification of AMPs with low toxicity and haemolytic activity in the medicinal leech genome assembly.

O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104.

Glycerophosphate-containing O-specific polysaccharides (OPSs) were obtained by mild acidic degradation of lipopolysaccharides isolated from Escherichia coli type strain O81 and E. coli strain HS3-104 from horse feces. The structures of both OPSs and of the oligosaccharide derived from the strain O81 OPS by treatment with 48% HF were studied by monosaccharide analysis and one- and two-dimensional 1H- and 13C-NMR spectroscopy. Both OPSs had similar structures and differed only in the presence of a side-chain glucose residue in the strain HS3-104 OPS. The genes and the organization of the O-antigen biosynthesis gene cluster in both strains are almost identical with the exception of the gtr gene cluster responsible for glucosylations in the strain HS3-104, which is located elsewhere in the genome.

Analysis of Gut Microbiota in Patients with Parkinson's Disease.

Gut microbiota of patients with Parkinson's disease and healthy volunteers was analyzed by the method of high throughput 16S rRNA sequencing of bacterial genomes. In patients with Parkinson's diseases, changes in the content of 9 genera and 15 species of microorganisms were revealed: reduced content of Dorea, Bacteroides, Prevotella, Faecalibacterium, Bacteroides massiliensis, Stoquefichus massiliensis, Bacteroides coprocola, Blautia glucerasea, Dorea longicatena, Bacteroides dorei, Bacteroides plebeus, Prevotella copri, Coprococcus eutactus, and Ruminococcus callidus, and increased content of Christensenella, Catabacter, Lactobacillus, Oscillospira, Bifidobacterium, Christensenella minuta, Catabacter hongkongensis, Lactobacillus mucosae, Ruminococcus bromii, and Papillibacter cinnamivorans. This microbiological pattern of gut microflora can trigger local inflammation followed by aggregation of α-synuclein and generation of Lewy bodies.

[Primary candidate rna biomarker screening by RNA-seq for prostate cancer diagnostics].

The RNA-seq approach for prostate cancer candidate RNA biomarkers screening in plasma and urine obtained by minimally invasive or noninvasive methods is proved to be feasible. Significant amount of RNA biomarkers associated with prostate cancer according to the literature were found in plasma and urine samples obtained from patients with benign prostatic hyperplasia (BPH). The number of detected markers was shown to vary in accordance with method of library preparation used for transcriptome profiling. The detection of known RNA biomarkers for prostate cancer in urine and plasma samples shows the feasibility of such method for minimally invasive diagnostics. The fact of presence of the same RNA biomarkers in samples from patients with BPH suggests their possible lack of specificity and confirms the need for further research in this area.

[Spatial Frequencies Priority in Attentional Capture].

It was investigated whether the spatial frequencies are equal in their competition for attention. Two images of the same object were simultaneously presented (eccentricity 7 a.d.). They differed in spatial frequency. Attention capture was determined by the shift of gaze. Stimuli with spatial frequency 0.5, 1, 2, 4 and 8 cpd were used. The specific order of the spatial frequencies to attract attention was found. It was revealed that this sequence does not change when the category of objects changes.

[Using Kirlian photography method for risk assessment of the thyroid gland pathology development in adults].

The article considers possibilities of the use of the express method based on the Kirlian-effect to detect prenosological signs of pathology of the thyroid gland. Type of Kirlian emission form fingers was compared with the form of disease, its pathogenesis, clinical peculiarities and ultrasonic data. Obtained data were used to form criteria for different group of the risk development of thyroid gland pathology.

[Dipole sources localization of late components of event-related potentials during effective and ineffective visual search].

The question concerning the mechanisms for choice of relevant information is disputable. One point of view is that competition of entrance information for selective attention may be parallel if a target has a distinguishing character. The other one suggests that a search for relevant information is always successive but takes different rates. We examined the relevancy of these approaches by means of comparison of cortical areas involved in a decision-making process in the visual search tasks realized with the different effectiveness. The method of the ERP dipole sources localization was used. The ERPs to images in visual search tasks with different "difficulty" were recorded. Distribution of cortical sources of the ERP late components was analyzed. A task complication resulted in an activity focus displacement from the occipital to frontal cortical areas. The results suggest different mechanisms for effective and ineffective search and testify that the processes of the relevant information selection may be simultaneous and successive.

Reflection of the effectiveness of heterosensory integration in measures of event-linked potentials.

The phenomenon of bimodal event-linked potential mismatch and summation of unimodal responses were used to study the relationship between mismatch amplitude and the effectiveness of visual-auditory integration. The effectiveness of integration was assessed in terms of the extent to which experimental measures approached the parameters of the "ideal observer." The greater the effectiveness of integration, the greater the focus of mismatch shifted from the occipital to the frontal areas of the cortex. The greatest correlation between mismatch amplitude and the effectiveness of visual-auditory integration was seen in the left frontal cortex.

[Representation of heterosensory integration effectiveness in parameters of event-related potentials].

A phenomenon of a mismatch of the bimodal ERP and the sum of unimodal ERPs was used in our research. It was investigated how the mismatch amplitude depends on audio-visual integration effectiveness. The effectiveness was calculated on basis of approximation degree of an experimental performance to parameters of "ideal observer". It was determined, the higher the subject's integration effectiveness is, the rostraler the mismatch focus localization is. The highest correlation of the mismatch amplitude and the audio-visual integration effectiveness was revealed in the left frontal cortex.

[Using of kirlean-graphic express-method for appropriate prescription of medications].

56 patients with head vascular disturbances have been observed. Kirlean-graphic and REG data have been compared and their correlation has been found. Kirlian radiation reflects types of compensatory reactions of the adaptation. The use of the method is useful for early detection of disturbances in energy circulation of brain vessels during selection of health-improving drugs.

[Problem of visual segmentation and spatial-frequency filtration]. / Problema zritel'noi segmentatsii i prostranstvenno-chastotnaia fil'tratsiia.

The analysis of the visual segmentation problem involved questions concerned with a signal description as a result of linear filtering, nature following nonlinear transformations, and possible role of a spatial attention in pooling. Different approaches to the visual segmentation problem are compared. Our data suggest a model of visual segmentation. It uses the universal principle of linear filters pooling at second-order mechanisms. The pooling mechanism is characterized by position, spatial frequency and orientation tuning an is selective in respect to pattern size. The most activated pooling mechanisms are "targets" for selective attention. It is shown that the information selected this way is necessary and sufficient for recognition. Multiple representation of a visual scene with different resolution and hierarchical principle of description organise the recognition as successive specification.

[Size as a parameter for tuning visual attention]. / Razmer kak parametr nastroiki zritel'nogo vnimaniia.

The ability of visual attention to tune to the stimulus size (when this size could not be described by spatial frequencies) was studies. Sinusoidal gratings with frequencies of 1.5, 3, and 6 cycle/degree were used as test stimuli. All these stimuli consisted of 3 periods, consequently, they had different sizes: 2 x 2, 1 x 1, and 0.5 x 0.5 degrees. Three reference stimuli had the same sizes but were constructed as a superposition of all the test frequencies. The reference stimulus of suprathreshold contrast was displayed for 400 ms to the left or to the right of a fixation point at a distance of 3 degrees. After that, the test stimulus of threshold contrast was for 100 ms displayed symmetrically to the fixation point on the other side. Subjects were instructed that the sizes of the reference and test stimuli were the same. It was found that the probability of test detection decreased with increase in the difference between the sizes of the reference and test stimuli. Since in our experiments the spatial frequency could not be used for tuning visual attention, the obtained results suggest that there are specialized mechanisms in the visual system for estimation of the general image size.

Integrated databases and computer systems for studying eukaryotic gene expression.

MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

[Evoked potentials to sound in the visual cortex in the cat]. / Vyzvannye potentsialy na zvuk v zritel'noi kore mozge u koshek.

The obtained data on the appearance in the cat visual cortex (VC) of evoked potentials (EPs) with short (4-5 ms) and long (80-90 ms) latencies in response to sounds, lead to the conclusion about a complex, phasic character of VC activity change under the action of inadequate stimuli. The dependence of short-latency EPs on the sound intensity has been found, which is expressed in the initial increase of amplitude and a reduction of temporal parameters, followed by stabilization of their values at further increase of stimulation intensity. Cortical nature of the observed EPs has been proved.