Search results for: Nikolai V. Tomilin

Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: Irena Markovska, Nikolai Zaicev, Bogdan Bogdanov, Dimitar Georgiev, Yancho Hristov

Abstract:

The present paper deals with problems related to the possibilities to use fractal systems to solve some important scientific and practical problems connected with filtering and separation of aqueous phases from organic ones. For this purpose a special separator have been designed. The reactor was filled with a porous material with fractal dimension, which is an integral part of the set for filtration and separation of emulsions. As a model emulsion hexadecan mixture with water in equal quantities (1:1) was used. We examined the hydrodynamics of the separation of the emulsion at different rates of submission of the entrance of the reactor.

Keywords: pilot reactor, fractal systems, separation, emulsions

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Authors: Irena Markovska, Dimitar Rusev, Nikolai Zaicev, Bogdan Bogdanov, Dimitar Georgiev, Yancho Hristov

Abstract:

A prototype model of an emulsion separator was designed and manufactured. Generally, it is a cylinder filled with different fractal modules. The emulsion was fed into the reactor by a peristaltic pump through an inlet placed at the boundary between the two phases. For hydrodynamic design and sizing of the reactor the assumptions of the theory of filtration were used and methods to describe the separation process were developed. Based on this methodology and using numerical methods and software of Autodesk the process is simulated in different operating modes. The basic hydrodynamic characteristics - speed and performance for different types of fractal systems and decisions to optimize the design of the reactor were also defined.

Keywords: fractal systems, reactor, separation, emulsions

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Authors: Nikolai Krainiukov, Boris Melnikov

Abstract:

We study the properties of maximal prefix codes. The codes have many applications in computer science, theory of formal languages, data processing and data classification. Our approaches to study use finite state automata (so-called flower automata) for the representation of prefix codes. An important task is the decomposition of prefix codes into prime prefix codes (factors). We discuss properties of such prefix code decompositions. A linear time algorithm is designed to find the prime decomposition. We used the GAP computer algebra system, which allows us to perform algebraic operations for free semigroups, monoids and automata.

Keywords: Maximal prefix code, regular languages, flower automata, prefix code decomposing.

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Authors: Nikolai V. Barulin, Vitaly Yu. Plavskii

Abstract:

This work contains information about the influence low-level optical irradiation on sperm motility of sturgeon fish. On the basis of given and earlier received data the following conclusion has been made. Among the photophysical processes of a resonant and not resonant nature (oriented action of light; action of gradient forces; dipole-dipole interaction; termooptical processes), which are capable to cause the photobiological effects depended on such laserspecific characteristics as polarization and coherency, determining influence belongs to oriented action of light and dipole-dipole interactions among the processes studied in the present work.

Keywords: sturgeon, aquaculture, fish sperm, laser, optical irradiation, sperm motility

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Authors: Robert I. Nigmatulin, Raisa Kh. Bolotnova, Nailya K. Vakhitova, Andrey S. Topolnikov, Svetlana I. Konovalova, Nikolai A. Makhota

Abstract:

The theoretical investigation is carried out to describe the effect of increase of pressure waves amplitude in clean and bubbly liquid. The goal of the work is to capture the regime of multiple magnification of acoustic and shock waves in the liquid, which enables to get appropriate conditions to enlarge collapses of micro-bubbles. The influence of boundary conditions and frequency of the governing acoustic field is studied for the case of the cylindrical acoustic resonator. It has been observed the formation of standing waves with large amplitude at resonant frequencies. The interaction of the compression wave with gas and vapor bubbles is investigated for the convergent channel. It is shown theoretically that the chemical reactions, which occur inside gas bubbles, provide additional impulse to the wave, that affect strongly on the collapses of the vapor bubbles

Keywords: acoustics, cavitation, detonation, shock waves

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