Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis

Autoimmunity is intrinsically driven by memory T and B cell clones inappropriately targeted at self-antigens. Selective depletion or suppression of self-reactive T cells remains a holy grail of autoimmune therapy, but disease-associated T cell receptors (TCRs) and cognate antigenic epitopes remained elusive. A TRBV9-containing CD8+ TCR motif was recently associated with the pathogenesis of ankylosing spondylitis, psoriatic arthritis and acute anterior uveitis, and cognate HLA-B*27-presented epitopes were identified. Following successful testing in nonhuman primate models, here we report human TRBV9+ T cell elimination in ankylosing spondylitis. The patient achieved remission within 3 months and ceased anti-TNF therapy after 5 years of continuous use. Complete remission has now persisted for 4 years, with three doses of anti-TRBV9 administered per year. We also observed a profound improvement in spinal mobility metrics and the Bath Ankylosing Spondylitis Metrology Index (BASMI). This represents a possibly curative therapy of an autoimmune disease via selective depletion of a TRBV-defined group of T cells. The anti-TRBV9 therapy could potentially be applicable to other HLA-B*27-associated spondyloarthropathies. Such targeted elimination of the underlying cause of the disease without systemic immunosuppression could offer a new generation of safe and efficient therapies for autoimmunity.

Magnetic Nanocomposite Materials Based on Fe3O4 Nanoparticles with Iron and Silica Glycerolates Shell: Synthesis and Characterization

Novel magnetic nanocomposite materials based on Fe3O4 nanoparticles coated with iron and silica glycerolates (MNP@Fe(III)Glyc and MNP@Fe(III)/SiGlyc) were obtained. The synthesized nanocomposites were characterized using TEM, XRD, TGA, VMS, Mössbauer and IR spectroscopy. The amount of iron and silica glycerolates in the nanocomposites was calculated from the Mössbauer spectroscopy, ICP AES and C,H-elemental analysis. Thus, it has been shown that the distribution of Fe in the shell and core for MNP@Fe(III)Glyc and MNP@Fe(III)/SiGlyc is 27:73 and 32:68, respectively. The synthesized nanocomposites had high specific magnetization values and a high magnetic response to the alternating magnetic field. The hydrolysis of shells based on Fe(III)Glyc and Fe(III)/SiGlyc in aqueous media has been studied. It has been demonstrated that, while the iron glycerolates shell of MNP@Fe(III)Glyc is resistant to hydrolysis, the silica glycerolates shell of MNP@Fe(III)/SiGlyc is rather labile and hydrolyzed by 76.4% in 24 h at 25 °C. The synthesized materials did not show cytotoxicity in in vitro experiments (MTT-assay). The data obtained can be used in the design of materials for controlled-release drug delivery.

TCR repertoire profiling revealed antigen-driven CD8+ T cell clonal groups shared in synovial fluid of patients with spondyloarthritis

Spondyloarthritis (SpA) comprises a number of inflammatory rheumatic diseases with overlapping clinical manifestations. Strong association with several HLA-I alleles and T cell infiltration into an inflamed joint suggest involvement of T cells in SpA pathogenesis. In this study, we performed high-throughput T cell repertoire profiling of synovial fluid (SF) and peripheral blood (PB) samples collected from a large cohort of SpA patients. We showed that synovial fluid is enriched with expanded T cell clones that are shared between patients with similar HLA genotypes and persist during recurrent synovitis. Using an algorithm for identification of TCRs involved in immune response we discovered several antigen-driven CD8+ clonal groups associated with risk HLA-B*27 or HLA-B*38 alleles. We further show that these clonal groups were enriched in SF and had higher frequency in PB of SpA patients vs healthy donors, implying their relevance to SpA pathogenesis. Several of the groups were shared among patients with different SpAs that suggests a common immunopathological mechanism of the diseases. In summary, our results provide evidence for the role of specific CD8+ T cell clones in pathogenesis of SpA.

Individual iron(iii) glycerolate: synthesis and characterisation

Iron(ii) and iron(iii) salts of strong acids form iron glycerolates on heating at 180 °C with glycerol in the presence of an equivalent amount of alkali. Individual iron(iii) glycerolate was obtained for the first time. When Fe₃O₄ magnetic nanoparticles were heated with glycerol, an iron(iii) glycerolate shell was formed on their surface.

Individual iron(iii) glycerolate was obtained and characterized; a method for the preparation of an iron(iii) glycerolate shell on the surface of Fe₃O₄ MNPs was proposed.

Imaging of Intracellular Hydrogen Peroxide Production with HyPer upon Stimulation of HeLa Cells with EGF

Reactive oxygen species (ROS) regulate both normal cell functions by activating a number of enzymatic cascades and pathological processes in many diseases by inducing oxidative stress. For many years since the discovery of ROS in biological systems there were no adequate methods of detection and quantification of these molecules inside the living cells. We developed the first genetically encoded fluorescent indicator for intracellular detection of hydrogen peroxide, HyPer, that can be used for imaging of H₂O₂ production by cells under various physiological and pathological conditions. Unlike most known ROS indicators, HyPer allows for the generation of real-time image series that give precise information about the time course and intensity of H₂O₂ changes in any compartment of interest. In this chapter we describe the method of confocal imaging of hydrogen peroxide production in HeLa cells upon stimulation with epidermal growth factor. The technique described may be accepted with minimal variations for the use in other cell lines upon various conditions leading to H₂O₂ production.

Testing of monoclonal antibodies against the T-cell receptor associated with ankylosing spondylitis

In the last decade there has been a tendency to move away from the symptomatic treatment and embrace targeted therapies. This process is underpinned by the accumulated knowledge of the mechanisms underlying the pathogenesis of diseases and driven by the advances in biotechnologies. T-cell receptors with variable TRBV9 β-chain regions have been recently associated with spondyloarthritis including its subtype, ankylosing spondylitis. The aim of this work was to engineer a chimeric monoclonal antibody targeting the variable region of the T-cell receptor β-chain encoded by the TRBV9 gene segment and assess its specificity and cytotoxicity. Using flow cytometry and next generation sequencing, we demonstrate that the engineered chimeric antibody is highly specific and exhibits cytotoxic activity against its target. Approaches based on the use of therapeutic chimeric antibodies against pathogenic T-clones may hold great promise for the therapy of autoimmune disorders in general and AS in particular.

Live-Cell STED Microscopy with Genetically Encoded Biosensor

Of the various super-resolution techniques, stimulated emission depletion (STED) microscopy achieves the best temporal resolution at high spatial resolution, enabling live-cell imaging beyond the diffraction limit. However, STED and most other super-resolution imaging methods utilize a particular type of information extractable from the raw data, namely the positions of fluorophores. To expand on the use of super-resolution techniques, we report here the live-cell STED microscopy of a dynamic biosensor. Using the fluorescent H2O2 sensor HyPer2 for subdiffraction imaging, we were able not only to image filaments with superior resolution by localizing emission but also to trace H2O2 produced within living cell by monitoring brightness of the probe. STED microscopy of HyPer2 demonstrates potential utility of FP-based biosensors for super-resolution experiments in situ and in vivo.

Phototoxic effects of lysosome-associated genetically encoded photosensitizer KillerRed

KillerRed is a unique phototoxic red fluorescent protein that can be used to induce local oxidative stress by green-orange light illumination. Here we studied phototoxicity of KillerRed targeted to cytoplasmic surface of lysosomes via fusion with Rab7, a small GTPase that is known to be attached to membranes of late endosomes and lysosomes. It was found that lysosome-associated KillerRed ensures efficient light-induced cell death similar to previously reported mitochondria- and plasma membrane-localized KillerRed. Inhibitory analysis demonstrated that lysosomal cathepsins play an important role in the manifestation of KillerRed-Rab7 phototoxicity. Time-lapse monitoring of cell morphology, membrane integrity, and nuclei shape allowed us to conclude that KillerRed-Rab7-mediated cell death occurs via necrosis at high light intensity or via apoptosis at lower light intensity. Potentially, KillerRed-Rab7 can be used as an optogenetic tool to direct target cell populations to either apoptosis or necrosis.

Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling

The decrease of TCR diversity with aging has never been studied by direct methods. In this study, we combined high-throughput Illumina sequencing with unique cDNA molecular identifier technology to achieve deep and precisely normalized profiling of TCR β repertoires in 39 healthy donors aged 6-90 y. We demonstrate that TCR β diversity per 10(6) T cells decreases roughly linearly with age, with significant reduction already apparent by age 40. The percentage of naive T cells showed a strong correlation with measured TCR diversity and decreased linearly up to age 70. Remarkably, the oldest group (average age 82 y) was characterized by a higher percentage of naive CD4(+) T cells, lower abundance of expanded clones, and increased TCR diversity compared with the previous age group (average age 62 y), suggesting the influence of age selection and association of these three related parameters with longevity. Interestingly, cross-analysis of individual TCR β repertoires revealed a set >10,000 of the most representative public TCR β clonotypes, whose abundance among the top 100,000 clones correlated with TCR diversity and decreased with aging.

[Preparation of prokaryotic cDNA for high-throughput transcriptome analysis]

High contents of non-coding RNA in total bacteria RNA complicates considerably transcriptome analysis using standard approaches like high-throughput sequencing, gene expression profiles, subtractive hybridization. We suggest a procedure of preparation of bacterial cDNA for transcriptomics that includes rRNA and tRNA depletion with preservation of relative abundance of coding sequences. The method is based on the second order hybridization kinetics and unique properties of Kanchatka crab duplex-specific nuclease. The method efficacy was demonstrated on a model experiments.

[Application of the duplex-specific nuclease for fast analysis of single nucleotide polymorphisms and detection of target DNA in complex PCR products]

We have developed a simple method for fast analysis of single nucleotide polymorphisms and identification of target clones from cloned complex PCR products. The method utilizes Kamchatka crab duplex-specific nuclease and universal fluorescent probe and is alternative to laborious screening procedures using radioactive probes, restriction analysis followed by gel electrophoresis or expensive sequencing. The method efficacy was demonstrated in several model experiments.

[Architectonics of gastrointestinal microbial community]

Architectonics of gastrointestinal microbial community in colonic mucosa and feces was studied in patients with different gastrointestinal pathologies and without them. The study model was comprised of Bifidobacteria, Lactobacteria, E.coli, Enterococci, Staphylococci, and Candida. Communities of mucosal and fecal microbes appear to be organized in a definite manner, with most microorganisms forming either indigenous or indigenous-transient associations. Multicomponent indigenous-transient associations prevail in fecal communities, few-component indigenous one or individual microbes in parietal colonic mucin. The structure of community from colonic mucosa overlying a tumour proved identical with that from the apparently normal tissue whereas the community from an inflammed site was structurally closer to the fecal one.

[Candida and Saccharomyces spp. fungal associations in fecal microbiocenosis of diabetes patients and healthy subjects]

The article is devoted to analysis of pathogenic and diagnostic significance of Candida and Saccharomyces co-existence in diabetic patients. These transient fungi are known to be present in fecal microbiocenosis of both healthy subjects and patients with diabetes mellitus. However, their overall occurrence is significantly increased in the disease and the structure of the biocenosis undergoes alteration. These data confirm the role of yeast-like fungi in pathogenesis of diabetes. The diagnostic value of detection of monospecific and mixed populations of Candida and Saccharomyces spp. is not very high, but their presence in feces, especially in women, may be regarded as a sign of disturbed carbohydrate metabolism.

[Clinico-laboratory associations of candidial infection persistence in diabetes mellitus]

Population heterogeneity of Candida spp. in feces of patients with diabetes mellitus (DM) demonstrated in our earlier studies prompted to focus on the persistence of candidial infection depending on demographic characteristics of the patients and clinical features of DM. We examined 64 patients with DM and 40 practically healthy subjects aged 20-60 yr. The seeding rate (%) of short-lived (emerged on day 0 or 1) and long-lived (emerged on both days 0 and 1) of Candida spp. cultures was determined. The short-lived fraction of microorganisms most frequently occurred in patients below 50 yr without clinico-laboratory signs of DM and the history of candidiasis (coincidence rate 75.0%, p < 0.001). The long-lived fraction was characteristic of patients with the history of candidiasis having DM of less than 5 yr in duration and glycated hemoglobin over 7.8 mmol/l without complications taking oral hypoglycemic agents (80%, p < 0.001). Candida spp. were totally absent in patients with late diabetic complications, duration of disease over 5 yr, glycated hemoglobin level below 7.8%, and candidiasis-free history. It is concluded that clinico-laboratory characteristics and demographic factors determine persistence of Candida spp. in feces of DM patients.

[Experimental simulation of the structure of gastrointestinal microbial biocenosis]

Structural analysis of human and rat gastrointestinal microbial communities revealed their general similarity. The structure of microbial biocenosis in ileum parietal mucin appears to be highly sensitive to nutritional factors. Inadequate nutrition leads to destruction of microbial microassociations in parietal mucin, a calcium-deficient diet has similar effect in feces. Fiber-rich diets stimulates build-up of indigenous communities while artificial nutrients and calcium-enriched diets promote formation of mixed indigenous-transient microbial associations. Bacteria themselves prove to be weak modifiers of the observed effects.

[Colonization of the rat gastrointestinal tract by Staphylococcus aureus biotopes]

Six groups of Wistar rats were fed different diets. Intestinal mural and fecal microflora was analysed. Four types of colonization of trointestinal tract were distinguished after intragastric administration of Staphylococcus aureus depending on a variety of factors affecting composition of microbial communities. Mechanisms of colonization ensuring circulation of S. aureus in the gastrointestinal tract are discussed.

Thermolabile duplex-specific nuclease

Using random mutagenesis of the gene encoding duplex-specific nuclease from the king crab we found a new mutant that retained all properties of the wild-type protein, but exhibited a much lower thermal stability. This enzyme, denoted thermolabile duplex-specific nuclease (DSN-TL), exhibits high processivity and selective cleavage of dsDNA. The inactivation temperature for DSN-TL is 15-20 degrees C lower than that of the widely used DNase I and shrimp nuclease, and its catalytic activity is more than 10 times higher. Moreover, DSN-TL is resistant to proteinase K treatment. These properties make DSN-TL very useful for removing genomic DNA from RNA samples intended for quantitative RT-PCR.

Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?

Kamchatka crab duplex-specific nuclease (Par_DSN) has been classified as a member of the family of DNA/RNA non-specific beta-beta-alpha metal finger (bba-Me-finger) nucleases, the archetype of which is the nuclease from Serratia marcescens. Although the enzyme under investigation seems to belong to the family of S. marcescens nucleases, Par_DSN exhibits a marked preference for double-stranded DNA as a substrate and this property is unusual for other members of this family. We have searched other Arthropod species and identified a number of novel Par_DSN homologs. A phylogenetic analysis demonstrates that the Par_DSN-like enzymes constitute a separate branch in the evolutionary tree of bba-Me-finger nucleases. Combining sequence analysis and site-directed mutagenesis, we found that Par_DSN and its homologs possess the nuclease domain that is slightly longer than that of classic Serratia relatives. The active site composition of Par_DSN is similar but not identical to that of classic Serratia nucleases. Based on these findings, we proposed a new classification of Par_DSN-like nucleases.

Normalization of full-length enriched cDNA

Analysis of rare messages in cDNA libraries is extremely difficult due to the substantial variations in the abundance of different transcripts in cells and tissues. Therefore, for rare transcript searches and analyses, the generation of equalized (normalized) cDNA is essential. Several cDNA normalization methods have been developed since 1990. A number of these methods have been optimized for the normalization of full-length enriched cDNA, and used in various applications, including transcriptome analysis and functional screening of cDNA libraries. One such procedure (named DSN-normalization) is based on the unique properties of duplex-specific nuclease (DSN) from kamchatka crab and allows the generation of normalized cDNA libraries with a high gene discovery rate.

[Influence of various dietary intakes on the rat's parietal microflora composition]

It was established that specific and quantitative characteristics of microecosystem of parietal mucin of rat's gastrointestinal tract, significantly varied depending on diet. Microbiocenosis of the colon was the most liable to alimental factor, but in the small intestine it was more depending on the endogenic factors of macroorganism. The principle of forming of microecosystem of parietal mucin of rat's gastrointestinal tract subject to composition of the diet was considered in the article.

Imaging of intracellular hydrogen peroxide production with HyPer upon stimulation of HeLa cells with epidermal growth factor

Reactive oxygen species (ROS) regulate both normal cell functions by activating a number of enzymatic cascades and pathological processes in many diseases by inducing oxidative stress. For many years since the discovery of ROS in biological systems, there were no adequate methods of detection and quantification of these molecules inside the living cells. We developed the first genetically encoded fluorescent indicator for the intracellular detection of hydrogen peroxide, HyPer, that can be used for imaging of H2O2 production by cells under various physiological and pathological conditions. Unlike most known ROS indicators, HyPer allows the generation of a real-time image series that give precise information about the time course and intensity of H2O2 changes in any compartment of interest. In this chapter, we describe the method of confocal imaging of hydrogen peroxide production in HeLa cells upon stimulation with epidermal growth factor. The technique described may be accepted with minimal variations for the use in other cell lines upon various conditions leading to H2O2, production.

[The role of food factor in the forming of the variety of the characteristics of fecal microbiocenosis in rats]

The researchers studied mechanisms of the forming of fecal microbiocenosis in rats on different diets. The composition of nutritional elements had a significant effect on the qualitative and quantitative composition of both indigenous and transitory fecal microflora. Under scant diet, the leading role in the forming of intestinal microbiocenosis belonged to macroorganism characteristics, while under excessive nutrition intestinal microbiocenosis depended mostly on the composition of the dietary intake. The study found that excessive nutrition lowered competition for the nutrition substrate, and indigenous microflora no more prevented the growth of transitory one.

[Influence of various levels of vitamin D and calcium in the diet on variability of microbes association of rats]

It is established, that the microecological system of intestines microbes association structurally reacts to the maintenance of vitamin D and calcium in food. Thus change of frequency of occurrence, the specific maintenance and a dispersion of separate components of system is observed. Besides character and force of correlation communications between concentration of microbes varies. The revealed principles of formation and change of microbic community of intestines enable to define mechanisms of selective management of microbic components microbes association.

[Substrate phase state and time factor in variability of human fecal microbiota]

Effects of substrate phase state and time factor on variability of human fecal microbiota were studied. It was shown that microecological system of native feces was characterized by marked time-dependent variability. It is unstable and begins to destruct after 24 hours of cultivation. The most sensitive elements of the system were bifidobacteria and Escherichia coli. Change of phase state of biotope eliminated the effect of factor limiting the microecosystem development, which allowed species of obligate and transitory microflora to freely colonize the growth substrate and interact with each other. The mentioned facts demonstrate that fecal microbiota exists in the environment of excess of growth substrate, which colonization is limited by cluster structure of biotope of native feces. It was concluded that phase state of growth substrate and duration of cultivation are important factors determining the population variability of fecal microbiota.

Bright far-red fluorescent protein for whole-body imaging

For deep imaging of animal tissues, the optical window favorable for light penetration is in near-infrared wavelengths, which requires proteins with emission spectra in the far-red wavelengths. Here we report a far-red fluorescent protein, named Katushka, which is seven- to tenfold brighter compared to the spectrally close HcRed or mPlum, and is characterized by fast maturation as well as a high pH-stability and photostability. These unique characteristics make Katushka the protein of choice for visualization in living tissues. We demonstrate superiority of Katushka for whole-body imaging by direct comparison with other red and far-red fluorescent proteins. We also describe a monomeric version of Katushka, named mKate, which is characterized by high brightness and photostability, and should be an excellent fluorescent label for protein tagging in the far-red part of the spectrum.

[Influence of Bacillus cereus on microbiocenosis of gastrointestinal tract in rats]

The modifying effect of Bacillus cereus on intestinal microbiocenosis was investigated in eubiotic and disbiotic female rats. Qualitative and quantitative characteristics of gut and mucosal microflora from different parts of rats' intestine were studied before and after intragastral application of B. cereus suspension. The single application of B. cereus suspension resulted in appearance of this bacterium in feces and in parietal mucin from all parts of the intestine. In eubiotic rats compared with disbiotic, B. cereus adhere to parietal mucin much more efficiently and supplanted indigenous microflora. During disbiosis B. cereus sometimes had stimulating effect on the intestinal microbiocenosis. Gut microbiocenosis appeared to be more resistant to B. cereus invasion than mucosal. This fact was considered to be the evidence of higher sensitivity of mucosal microbiocenosis to short-term influence of exogenous microbial factor.

[Microbiocenosis of parietal mucin in gastrointestinal tract of rats with induced disbiosis]

Comparative study of qualitative and quantitative characteristics of parietal mucin microbiocenosis in rats with alimentary induced disbiosis was performed. It has been shown that disbiosis was associated with changes in parietal microflora which were observed mainly in colon mucosa. Disbiosis in parietal area, in contrast to central area manifested by changes in quantitative characteristics of microbiocenosis. Results of the study allowed to suppose that parietal mucosal microbiocenosis was more stable than gut one and that this stability was determined by endogenous homeostatic factors of the host.

[Influence of different diets on special formation of fecal microbes association]

Aim of the present study was research special formation fecal microbes association depending on different diets. The three groups rats were fed diets to be different on quality and quantity composition. Was established, that diet composition exert influence to frequency situated and contents of all types of fecal microbes. In situation of nutrients deficiency there were not microbes synergism. In situation of increase diet components had been formatting synergetic microbes association, include all of bacteria's types. As result of the present study is the demonstrated possibility nonprobiotic correction dysbiotic condition with different diet's components.

[Comparative evaluation of the safety of poly- and and oligoguanidines]

The antimicrobial activity and microenvironmental safety of poly- and oligoguanidine antiseptics were compared. E. coli and St. aureus test strains were found to be more sensitive to chlorohexidine bigluconate (CHB) upon a long (24 hour) exposure and to polyhexamethylene guanidine derivatives on short (30-second) contact. It is concluded that unlike polyguanidine antiseptics, CHB is more ecologically dangerous; when used for rapid disinfection, it can provoke impairment in the microenvironmental balance outside the area of application. The findings show it expedient to assess the microenvironmental safety of antimicrobial agents in order to prevent ecological catastrophes.

[Study of the influence of Staphylococcus aureus on gastrointestinal tract microbiocenosis in rats]

The authors studied the modifying effect of Staphylococcus aureus on the microbial composition of gastrointestinal tract microbiocenosis. The subjects were female rats in the condition of eubiosis or dysbiosis. The species and quantitative composition of the fecal microflora and the parietal mucin in different parts of the intestine were studied after an intragastral administration of St. aureus suspension. A single introduction of St. aureus into the gastrointestinal tract of rats led to the appearance of this microbe in the feces and parietal mucin in all the parts of the intestine regardless the initial condition of the intestinal microbiocenosis. The indigenous microflora, both in eubiotic and dysbiotic conditions, practically did not respond to an intragastral administration of staphylococcus, except a little decrease in the proportion of bifidobacteria. Meanwhile, there was a significant increase in the incidence of candid detection. The indigenous parietal microflora changed more substantially, which demonstrates a higher sensitivity of the parietal microbiocenosis to a short-time exposure to an exogenous microbial factor.

[The adhesive properties of lactobacteria and escherichiae in different divisions of human gastrointestinal tract under normal and pathologic conditions]

A comparison of the adhesive properties of lactobacteria and escherichiae in different divisions of human gastrointestinal tract under normal and pathologic conditions was conducted. The study shows that the population changeability of the adhesive properties of lactobacteria and escherichiae is determined by localization of the strain in the gastrointestinal tract, and morphofunctional condition of the intestinal wall. Bacteria's adhesiveness to glycocalix of intestinal epithelial cells is higher in the left half of the colon than in the right one, and is still higher in feces. Their co-adhesiveness changes in the reverse order. Bacteria localized in the parietal mucin of inflamed segments, possess low capability of forming microcolonies, and high adhesiveness to glycocalix. The results of the study demonstrate that the choice of therapeutic probiotic bacterial strains should depend on the anatomic localization of the lesion and the character of gastrointestinal pathology.

[Comparison of the methods of evaluation of the microbiological danger of antimicrobial agents by the example of oligo- and polyguanidines]

The article contains the results of comparison of the methods of evaluation of the microbiological danger of antimicrobial agents by the example of oligo- and polyguanidines. The study demonstrates that choice of an adequate study model (a bacterial or protozoa species) and exposure time depends on the characteristics of the preparation to be tested. It shows that the microbocide activity of polyguanidines should be studied on a bacterial model using long (24 hours) exposure. The most sensitive to XG6 was a protozoa culture in short-time exposure. To evaluate the biological danger ofantimicrobial agents, it is also possible to apply techniques that allow revealing reversable physiological changes in a culture of test objects.

[A study of human fecal microbiocenosis by experimental in vitro modeling of constipation]

A study of human fecal microbiocenosis using experimental in vitro modeling of constipation was carried out. The study revealed certain dynamics of the incidence, proportion and ratio of microorganisms isolated from the feces at various stages of cultivation. The character of the changes of these parameters depended on the type of the microorganism. According to the results of the experiment, transitory flora (staphylococci; candidas) begins to disappear within the first day of cultivation. If intestinal evacuation is retarded for more than 2 or 3 days, distortion of the microbiological characteristics of the residential microflora, bifidobacteria and escherichiae, is possible. These processes may lead to a false positive result of dysbiosis analysis. The authors conclude that dysbiotic changes in constipation are caused by fecal retention. That is why correct diagnostics of dysbiosis is possible only after regular everyday stool is reestablished.

[A study of parietal gastrointeatinal microflora of rats after oral administration of probiotics]

The article is dedicated to one of the topical problems of medical microecology, possibility of modification of parietal gastrointestinal microflora by oral administration of various probiotics, and evaluation of the effects of such modification. The results of the study show that parietal gastrointestinal microflora can be modified by oral administration of probiotics.

[Application of the duplex-specific nuclease preference method to the analysis of point mutations in human genes]

A new modification of the single nucleotide polymorphism (SNP) analysis (DSNP, duplex-specific nuclease preference) method using the duplex-specific nuclease from the king crab was proposed. The method was used to study SNPs in the following human genes: kRAS, nRAS, hRAS, and p53, the genes of blood coagulation factor V, methyltetrahydrofolate reductase, prothrombin, and apolipoprotein E and a deletion in the BRCA1 gene. DSNP was shown to be useful for the estimation of the mutant allele content in DNA samples. A system for the simultaneous identification of several adjacent single-nucleotide polymorphisms in the kRAS gene was proposed. The approaches could be used to develop test systems for the detection of SNPs in human genes. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2005, vol. 31, no. 6; see also http://www.maik.ru.

[Microbiocenosis of parietal mucin in the gastrointestinal tract of rats]

The qualitative and quantitative composition of the microbial community in parietal mucin at different areas of the gastrointestinal tract (GIT) of rats was revealed. The pronounced variability in the quantitative and qualitative characteristics of microbiocenosis in parietal mucin of rats at different sections was revealed. The differences were most pronounced in the passage from upper to lower GIT sections, the large intestine found to be the richest biocenosis. The microbial composition of rat feces was faintly associated with the GIT parietal microbiocenosis. The individual areas of GIT mucosa were unique of their microbial characteristics and organization. This makes it possible to regard them as relatively independent biotopes and indicates that it is impossible to evaluate the microbial community by one of the colonic mucosal sifes.

[Study of the parietal microflora in the rat intestine]

The article deals with the adaptation of the existing method of the isolation of microorganisms from parietal mucin of the intestine of experimental animals (rats) with a view to ensure the methodological uniformity of investigations. The effectiveness of the method of sparing disintegration of parietal mucin taken from the mucous membrane of the gastrointestinal tract, specially developed for human biomaterial, and its adequacy for microbiological investigations of the digestive organs of rats have been confirmed. A certain similarity between the microbiocenosis of the parietal mucin in the intestine of humans and rats has been established.

A method for the preparation of normalized cDNA libraries enriched with full-length sequences

We developed a new method for the preparation of normalized cDNA libraries enriched with full-length sequences. It is based on the properties of the recently characterized duplex-specific nuclease from the hepatopancreas of the Kamchatka crab. The duplex-specific nuclease is thermostable, it effectively cleaves double-stranded DNA and is inactive toward single-stranded DNA (Shagin et al., Genome Res., 2002, vol. 12, pp. 1935-1942). Our method enables the normalization of cDNA samples enriched with full-length sequences without use of laborious and ineffective stages of physical separation. The efficiency of the method was demonstrated in model experiments using cDNA samples from several human tissues.

[A family of genes of multidomain free lectins from a planarian: structure, expression, and use as markers for regeneration monitoring ]

A family of genes of the agamic race of planarian Girardia tigrina were described that encode proteins that belong to the superfamily of C-type lectins and were demonstrated to have a unique domain organization. The genes are differentially expressed in the planarian body. The protein products of at least two genes (scarf2 and gtlec1) are expressed in specifically differentiated gland cells of the planarian and secreted into the environment through long cell necks. A comparison of the results obtained by electron microscopy and immunohistochemistry with literature data allows the assignment of these cells to the group of adhesion glands. The observation of the regeneration of the cell necks in normal and artificial two-headed planaria indicated that the dorsoventral contact at the edge of the head part of the planarian body directs and maintains the growth of the gtLec1-producing cell necks during regeneration. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 6; see also http://www.maik.ru.

Molecular cloning and characterization of an endo-1,3-beta-D-glucanase from the mollusk Spisula sachalinensis

cDNA encoding the endo-1,3-beta-d-glucanase from Spisula sachalinensis (LIV) was amplified by PCR using oligonucleotides deduced from the N-terminal end peptide sequence. Predicted enzyme structure consists of 444 amino acids with a signal sequence. The mature enzyme has 316 amino acids and its deduced amino acid sequence coincides completely with the N-terminal end (38 amino acids) of the beta-1,3-glucanase (LIV) isolated from the mollusk. The enzyme sequence from Val 121 to Met 441 reveals closest homology with Pacifastacus leniusculus lipopolysaccharide- and beta-1,3-glucan-binding protein and with coelomic cytolytic factors from Lumbricus terrestris. The mollusk glucanase also shows 36% identity and 56% similarity with beta-1,3-glucanase of the sea urchin Strongylocentrotus purpuratus. It is generally considered that invertebrate glucanase-like proteins containing the bacterial glucanase motif have evolved from an ancient beta-1,3-glucanase gene, but most of them lost their glucanase activity in the course of evolution and retained only the glucan-binding activity. A more detailed evaluation of the protein folding elicited very interesting relationships between the active site of LIV and other enzymes, which hydrolyze native glucans.

Simple cDNA normalization using kamchatka crab duplex-specific nuclease

We developed a novel simple cDNA normalization method [termed duplex-specific nuclease (DSN) normalization] that may be effectively used for samples enriched with full-length cDNA sequences. DSN normalization involves the denaturation-reassociation of cDNA, degradation of the double-stranded (ds) fraction formed by abundant transcripts and PCR amplification of the equalized single-stranded (ss) DNA fraction. The key element of this method is the degradation of the ds fraction formed during reassociation of cDNA using the kamchatka crab DSN, as described recently. This thermostable enzyme displays a strong preference for cleaving ds DNA and DNA in DNA-RNA hybrid duplexes compared with ss DNA and RNA, irrespective of sequence length. We developed normalization protocols for both first-strand cDNA [when poly(A)+ RNA is available] and amplified cDNA (when only total RNA can be obtained). Both protocols were evaluated in model experiments using human skeletal muscle cDNA. We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique.

[The parietal mucin microbial population in different sections of the human gastrointestinal tract]

Microbiological examinations of the human-colon parietal mucin were made in different sections of the human gastrointestinal tract (GIT). Biopsy samples of the human colon mucus tunic were used as the research material. Convincing data were found by research on the importance of the anatomic-and-morphological factor in shaping-up of microbiocenosis of the colon-wall parietal mucin. It was established that, depending on a GIT section, not only the quantitative and qualitative composition of normal microflora but also the nature of inter-microbe interactions are subject to changes. In particular, biopsy materials of the small-intestine parietal mucin are much different from that of the colon. The colon section from the ascending colon to the sigmoid colon has, with some exceptions, an identical microbial composition. At the same time, the rectum is significantly different from other colon sections. The results are suggestive of the below cluster-type pattern of parietal biological material: microorganisms are clustered as small domains with certain specific and quantitative compositions. It was established that, although feces and parietal mucin have a similar species composition of microorganisms, still, there is a number of essential differences between them in as far as the frequency ratio and the microorganism concentration are concerned, which signifies a certain degree of isolation of the above biopsy materials. Finally, a certain isolation degree of the feces biopsy materials and of the parietal ones was established.

[A study of the human parietal gastrointestinal tract microflora in health and disease]

An original technique was used to investigate the human colon mucin in different pathologies of gastrointestinal tract. The microbial pattern of the biotope in question was found to be dependable on a morphological-and-functional condition of the intestinal wall. It is noteworthy, that not only its quantitative and qualitative composition but also the nature of the inter-microbe relations and the "specific content" of microbes are subject to changes. A correlation was established between the studied characteristics of the human parietal gastrointestinal biotope and the biochemical blood parameters. The results revealed a new chain in the pathogenesis of disbiotic processes occurring in the colon mucous tunic. The diagnostic value of microbiological parameters of the human colon mucous tunic is under discussion.

[An analysis of the strain homogeneity of parietal biotopes of the gastrointestinal tract]

The lumen and parietal biotopes of the human gastrointestinal tract were investigated, i.e. the antibiotic sensitivity of strains E. coli and Enterococcus faecalis residing in them were comparatively analyzed. Certain isolation degrees not only of the parietal and fecal biotopes but also of certain micro-regions in the intestine wall were detected. The obtained data confirm a previously made assumption on the cluster distribution of microorganisms in the parietal mucin. The distinct strain differences between the parietal and fecal biotopes are not enough to completely extrapolate the available characteristics of the lumen microflora on the parietal microbiocenose. The above stated underlines the necessity in purpose-oriented research of parietal microbe populations of "internal" biotopes.

[Correction of rate and structure of ventricular rhythm in permanent atrial fibrillation: a novel pathogenetic approach]

AIM

To analyze action of digoxin and some non-digitalis drugs (beta-blockers, verapamil, amiodarone, d,l-sotalol) and their combinations on electrical activity of atria, frequency and structure of ventricular rhythm in patients with permanent atrial fibrillation.

MATERIAL AND METHODS

One hundred patients with permanent atrial fibrillation and heart rate at rest above 80 bpm were divided into 9 treatment groups. High-resolution orthogonal Frank lead ECG was recorded before and after allocated treatment. Analysis included construction of ff-waves periodograms, histograms of RR interval, cardiointervalograms and application of autocorrelation function.

RESULTS

It was demonstrated that frequency and form (structure) of ventricular rhythm was determined not only by the state of AV conduction but also by value of basic period of ff-waves. The mechanisms of ventricular rate deceleration by investigated drugs were not identical. beta-blockers and verapamil directly slowed AV conduction without changing parameters of ff-waves and differed from each other only in action on parameters of concealed conduction in AV node. Action of digoxin in patients with ff-waves period equal to or exceeding 0,15 s was biphasic. During phase I shortening of ff-wave period (by 0.025+/-0.012 s) occurred. This was associated with increase of their concealed conduction through AV node. The latter phenomenon represented independent mechanism of ventricular rhythm deceleration. During phase II of digoxin action direct inhibition of AV conduction took place. Amiodarone and d,l-sotalol increased basic ff-waves period. This facilitated their conduction through AV node. Greater heart rate slowing effect of d,l-sotalol was attributed to its ability to augment concealed conduction. Due to their antiarrhythmic qualities amiodarone and d,l-sotalol slowed heart rate in patients with peak RR duration in the region of 0.28-0.46 s. These patients often had bi- and tri-modal structure of interval RR histogram. Changes of ventricular rhythm structure during use of various drugs were different. Action of digoxin was most whilst that of beta-blockers least favorable.

CONCLUSION

Choice of a drug for treatment of permanent atrial fibrillation should be conducted with consideration of ff-waves periodicity, parameters of RR interval histogram, and characteristics of ventricular rhythm structure.