RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser. Database URL https://genome.ucsc.edu/.

[RNA-Chromatin Interactome: What? Where? When?]

It was noticed in the early 1960s that a large amount of RNAs is associated with chromatin. What kind of RNAs are they? Where are they located on chromatin? When and in what processes do these RNAs perform their physiologically normal or pathogenic functions? The review describes the modern approaches that help, to some extent, to answer these questions. Consideration is given to the experimental methods that make it possible to obtain the complete RNA-chromatin interactome of a cell or the genome-wide interaction maps of individual RNAs with chromatin, as well as the methods to process the experimental data. Focus is placed on the noncoding RNAs that function in close contact with chromatin and chromatin-associated protein complexes. A variety of biological examples described using the methods makes it clear that RNAs interacting with chromatin play an important role in the functions of cell systems by finely tuning the chromatin architecture and thus changing the level of gene expression.

Analysis of Dynamic Geometric Configuration of the Aortic Channel from the Perspective of Tornado-Like Flow Organization of Blood Flow.

Analysis of the data of morphometry of aortic casts, aortography at different pressures, and multispiral computer tomography of the aorta with contrast and normal pulse pressure showed that geometric configuration of the flow channel of the aorta during the whole cardiac cycle corresponded to the conditions of self-organization of tornado-like quasipotential flow described by exact solutions of the Navier-Stokes equation and continuity of viscous fluid typical for this type of fluid flows. Increasing pressure in the aorta leads to a decrease in the degree of approximation of the channel geometry to the ratio of exact solution and increases the risk of distortions in the structure of the flow. A mechanism of evolution of tornado-like flow in the aorta was proposed.

[Chromatin and Polycomb: Biology and bioinformatics].

All cells of a multicellular eukaryotic organism carry almost the same genome, still they obviously demonstrate phenotypes of very divergent kinds. The most probable explanation of the divergence is that different groups of genes are expressed in cells of different types. Expression is regulated at all steps between DNA and a protein, but transcription regulation is the most common regulatory mechanism. Transcription factors, which bind to specific areas of chromatin, can mediate the regulation. Their binding depends on the chromatin structure, which drastically differs among cell types. The key role in the structural organization is played by covalent histone modifications in chromatin. A combination of particular modifications in a chromatin region determines its structure and, consequently, its accessibility for enzymes. The best studied histone modifications are described in the review. Each modification has its specific mechanism that the cell uses to establish or to eliminate it. Activity of various Polycomb complexes is a key mechanism that represses chromatin and plays a central role, for example, in cell differentiation. The compositions and functionality of Polycomb complexes in various species are considered. Owing to modern experimental techniques, ample data are currently available for histone modifications and other epigenomic features of chromatin in various tissues and organisms, allowing bioinformatic investigation of the epigenome. Many computational and visualization methods have been developed for such studies, and the main of them are covered in the review.

[Intraperitoneal and retromuscular abdominal wall repair using ultra-light and titanium-containing polypropylene mesh (experimental research)]. / Intraperitoneal'naya i retromuskulyarnaya plastika bryushnoi stenki ul'tralegkimi polipropilenovymi i titansoderzhashchimi endoprotezami (eksperimental'noe issledovanie).

AIM: To study experimental possibility of light, ultra-light and titanium-containing endoprostheses implantation for postoperative hernias correction. MATERIAL AND METHODS: Abdominal wall repair was simulated in 72 rabbits. In the first group polypropylene mesh with fibers diameter of 90 microns and surface density of 36 g/m2 was used. In the second group we applied polypropylene mesh with fibers diameter of 65 microns and thin layer of titanium. Their surface density was 16 g/m2. Intraperitoneal onlay mesh (IPOM) and sublay retromuscular (SRM) techniques were used in group 1 and 2 respectively. Animals were taken out from the experiment in 30 and 60 days. Adhesive process in implantation area was evaluated using the method of Egiev V.N. and Lyadov V.K. RESULTS: The most pronounced adhesive process was observed in IPOM series. Type of endoprosthesis and terms of postoperative period did not significant effect adhesive process. SRM method was associated with significantly less pronounced adhesions. Analysis of all data showed that severity of adhesive process was significantly higher in IPOM series compared with SRM technique. CONCLUSION: Our study showed that severity of abdominal adhesive process associated with repair using ultra-light mesh is completely determined by surgical technique and did not depend on type of endoprosthesis and terms of postoperative period. Described implants should be used for retromuscular implantation rather intraperitoneal position.

[Quantitative Evaluation of Intracardiac Blood Flow by Left Ventricle Dynamic Anatovy Based On Exact Solutions of Non-Stationary Navier-Stocks Equations for Selforganized tornado-Like Flows of Viscous Incompresssible Fluid].

New approach to intracardiac blood flow condition analysis based on geometric parameters of left ventricle flow channel has been suggested. Parameters, that used in this method, follow from exact solutions of nonstationary Navier-Stocks equations for selforganized tornado-like flows of viscous incompressible fluid. The main advantage of this method is considering dynamic anatomy of intracardiac cavity and trabeculae relief of left ventricle streamlined surface, both registered in a common mri-process, as flow condition indicator. Calculated quantity options that characterizes blood flow condition can be use as diagnostic criterias for estimation of violation in blood circulation function which entails heart ejection reduction. Developed approach allows to clarify heart jet organization mechanism and estimate the share of the tornado-like flow self-organization in heart ejection structure.

[piRNAs: Biology and Bioinformatics].

The discovery of small noncoding RNAs and their roles in a variety of regulatory mechanisms have led many scientists to look at the principles of functioning of the cells on a completely different side. Small RNA molecules play key roles in important processes such as the co- and posttranscriptional regulation of gene expression, epigenetic modification of DNA and histones and antiviral protection. piRNA is one of the most numerous, although the least-studied class of small noncoding RNAs. piRNA is highly expressed in the germ line of most eukaryotes and its main function is to regulate the activity of mobile elements during embryonic development. Moreover, recent studies reveal moderate activity of piRNA in somatic cells. However, the mechanisms of piRNA biogenesis and function are still poorly understood and are the object of intensive researches. This review presents actual information about the biogenesis and various functions of piRNA, as well as bioinformatical aspects of this field of molecular biology.

[Evolution of non-Coding RNAs in Drosophila melanogaster Genome].

Non-coding RNAs are important regulatory molecules that function due to their specific RNA secondary structure. The secondary RNA structure depends on RNA sequence. It can be represented as a combination of loops, stems and pseudoknot regions. By the structure formation, each separate local part of a RNA structure as well as the whole molecule tend to achieve the minimum of free energy. New mutations may change the free energy of the current RNA structure and thus change the optimal one and change the function of the molecule. The chance to change the structure for a mutation depends on where it is located in the secondary RNA structure. In this research we studied natural selection acting on loop and stem regions of ncRNA of five classes. We tried to associate their selection characteristics to the changes of free energy value. We considered Drosophila melanogaster genome.

[The effect of pH, aeration, and temperature on arachidonic acid synthesis by Mortierella alpina].

The effects of pH, aeration, and temperature on the growth of fungal strain Mortierella alpina LPM-301 and the synthesis of lipids and arachidonic acid in glycerol-containing medium were studied. Arachidonic acid production in the stationary growth phase was found to depend considerably on the pH value; it reached the optimum at pH 6.0 and was irreversibly inhibited at a pH of 3.0. The PO2 values in a range from 10 to 50% showed no marked effect on mycelium growth or the synthesis of lipids and arachidonic acid. The temperature optimum for arachidonic acid production was 20-22 degrees C. Under continuous cultivation, the amount of arachidonic acid reached 29.8% of lipids and 7.4% of biomass. The arachidonic acid yield from the glycerol consumed was 4.1% by mass and 8.8% by energy. It is suggested that arachidonic acid synthesis at an unfavorable pH and elevated temperatures was limited by the activity of A-12-desaturase and by the conversion of linoleic to arachidonic acid, respectively.

[Statistical methods of comparative genomic analysis based on diffusion processes].

Comparative genomics is a powerful tool of genome functional specificity predictions and investigation of evolution specificity. Background of a large field of bioinformatics investigations is a computation of different scores of sequences and comparing them with a threshold. Comparative genomic analysis involves scores comparing for orthological groups of genetic objects. In this paper we represent a statistical approach to comparative genomic analysis, that based on investigation of diffusion in sequence space determined by neutral evolution of sequences. Using this approach we represent several statistics for selection pressure estimation and analyze statistics for several biological problems. We formulate technology of statistics applying to obtain new biological information. This approach is represented as Java-class library.

[Genome-wide identification of functional noncoding RNAs,].

Non-coding RNAs (ncRNAs) are functional transcripts that do not encode proteins. They are involved in many regulation pathways. The only general characteristic shared by many (but not all) known RNAs is folding into complex shapes that are crucial to function and thus should be conserved. This fact can be used for genome-wide prediction of ncRNAs. Our approach is based on computing of local base pairing probabilities and further maximizing of probability for a segment with the use of Nussinoff algorithm. We showed that it allows to efficiently predict known ncRNA and possibly some new ncRNAs.

[Correlations between clusters of protein-DNA binding sites and the binding experimental data allow to predict a structure of regulatory modules].

Here we analyzed an option to predict the structure of cis-regulatory modules that consist of binding sites of different proteins (heterogeneous cis-regulatory modules) using mutual positional correlations between protein-DNA binding experimental data and computationally identified clusters of binding sites for each of the proteins.

[Resistance to cellobiose lipids and specific features of lipid composition in yeast].

The significance of the fatty acid composition and ergosterol content in cells for resistance to cellobiose lipids has been investigated in the cells of mutant Saccharomyces cerevisiae strains that are unable to produce ergosterol or sphingomyelin and in the cells of microorganisms that produce cellobiose lipids. S. cerevisiae mutants were shown to be less sensitive to cellobiose lipids from Cryptococcus humicola than the wild-type strain, and the strains that produced cellobiose lipids were virtually insensitive to this compound as well. The sensitivity of Pseudozyma fusiformata yeast to its own cellobiose lipids was reduced under conditions that favored the production of these compounds. No correlation between the content of ergosterol and sensitivity to cellobiose lipids was observed in S. cerevisiae or in the strains that produced cellobiose lipids. The ratio between the levels of saturated and unsaturated fatty acids in the cells of the mutant strains was correlated to the sensitivity of the cells to cellobiose lipids.

[Chronic purulent otitis media].

This lecture reviews up-to-date information on the classification, etiology, pathogenesis, clinical features, diagnostics, surgical and conservative treatment of chronic purulent otitis media. It is maintained that surgical intervention including sanative and reconstructive procedures as well as hearing improvement measures is currently the preferred approach to the treatment of the disease in question. Special attention is given to different variants of sanative surgery in combination with tympanoplasty. The author emphasizes that the conservative therapy of chronic otitis media has the objective to eliminate exacerbation of the chronic process and does not substitute the surgical treatment.

Correlative microscopy: a potent tool for the study of rare or unique cellular and tissue events.

Biological studies have relied on two complementary microscope technologies - light (fluorescence) microscopy and electron microscopy. Light microscopy is used to study phenomena at a global scale to look for unique or rare events, and it also provides an opportunity for live imaging, whereas the forte of electron microscopy is the high resolution. Traditionally light and electron microscopy observations are carried out in different populations of cells/tissues and a 'correlative' inference is drawn. The advent of true correlative light-electron microscopy has allowed high-resolution imaging by electron microscopy of the same structure observed by light microscopy, and in advanced cases by video microscopy. Thus a rare event captured by low-resolution imaging of a population or transient events captured by live imaging can now also be studied at high resolution by electron microscopy. Here, the potential and difficulties of this approach, along with the most impressive breakthroughs obtained by these methods, are discussed.

[Gas chromatographic determination of N,N-asymmetric dimethylhydrazine in different environmental objects].

The paper describes different guidelines used to develop a procedure for gas chromatographic determination of N,N-asymmetric dimethylhydrazine (NDMH) in various environmental objects in the area of a missile-dismantling base. The authors showed that the use of a capillary column with a 5-microm liquid phase layer on a Kristall-5000 chromatograph with a nitrogenous phosphoric detector (Russia) allowed development of a unified gas chromatographic procedure for determining NDMH in air, water, soil, biological material (urine), and plant cover (moss, couch-grass). The procedures differ in the way how to prepare samples and the analysis itself is based on conversion of NDMH to N,N-dimethylhydrazone-4-nitrobenzaldehyde, its liquid extraction from water, concentration of the extract via evaporation and assay by the internal standard test.

[Orphan genes: function, evolution, composition].

The origin of orphan genes and the function they perform remain an enigmatic problem that modern molecular biology has to solve. The recently developed PHOG database helped to shed light on some aspects of the evolution of these genes. Fast evolution is probably the main factor that shapes this evolutionary process. The speed of molecular evolution reflects the degree of gene conservation, though exceptions from this rule also contribute to the dynamic process of genome evolution during speciation events. The existence of the great number of orphan genes is an artifact of insufficient sequencing. If the DNA of all organisms living on Earth were sequences, then the number of orphan genes will be greatly reduced, giving the way to the genes specific for particular taxonomic groups.