Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates

Introduction

Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.

Methods

To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.

Results

We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters.

Discussion

We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.

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.

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy

The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.

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.

Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy

Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using “shotgun” metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course. Additionally, for two of the subjects, the samples were collected 1 month after the end of the treatment. The samples were subject to “shotgun” (whole-genome) metagenomic sequencing using Illumina HiSeq platform. The reads are deposited in the ENA (project ID: PRJEB18265).

[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]

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]

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+ ++.

Spatial Extent of Masking by Sine-Wave Gratings

The contrast threshold for detection of a target consisting of 1.5 periods of a sine wave was determined as a function of the number of cycles in a sinusoidal mask with the same spatial frequency and orientation. The test frequencies were 2, 4, and 8 cycles deg−1. The masks were spatial-frequency modulated so as to equate their spectral extent. Stimuli were seen monocularly in Maxwellian view at a mean luminance of 10 cd m−2. The contrast threshold in a backward masking paradigm was determined by a 2AFC staircase. Data were obtained from three subjects with normal vision.

It was found that as the number of cycles in the mask was increased, the contrast threshold fell, but only to a certain level. The full range of the threshold decrement was about 2 dB. At all the spatial frequencies tested, the final threshold level was reached with 3 cycles in the mask and then remained unaffected by a further increase in the number of cycles.

The results implicate frequency-tuned mechanisms of very restricted spatial extent. It is suggested that these may underlie processing of spatially distributed information at the post-striate stages.

[Evoked potentials to sound in the visual cortex in the cat]

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.