Search

Two hairpin hexa(N-methylpyrrole)carboxamide DNA minor groove binders (MGB) were linked together via their N-termini in head-to-head orientation. Complex formation between these bis-MGB conjugates and target DNA has been studied using DNase I footprinting, circular dichroism, thermal dissociation, and molecular modeling. DNase I footprint revealed binding of these conjugates to all the sites of 492 b.p. DNA fragment containing (A/T)(n)X(m)(A/T)(p) sequences, where n>3, p>3; m=1,2; X = A,T,G, or C. Binding affinity depended on the sequence context of the target. CD experiments and molecular modeling showed that oligo(N-methylpyrrole)carboxamide moieties in the complex form two short antiparallel hairpins rather than a long parallel head-to-head hairpin. Binding of bis-MGB also stabilized a target duplex thermodynamically. Sequence specificity of bis-MGB/DNA binding was validated using bis-conjugates of sequence-specific hairpin (N-methylpyrrole)/(N-methylimidazole) carboxamides. In order to increase the size of recognition sequence, the conjugates of bis-MGB with triplex-forming oligonucleotides (TFO) were synthesized and compared to TFO conjugated with single MGB hairpin unit. Bis-MGB-oligonucleotide conjugates also bind to two blocks of three and more A.T/T.A pairs similarly to bis-MGB alone, independently of the oligonucleotide moiety, but with lower affinity. However, the role of TFO in DNA recognition was demonstrated for mono-MGB-TFO conjugate where the binding was detected mainly in the area of the target sequence consisting of both MGB and TFO recognition sites. Basing on the molecular modeling, three-dimensional models of both target DNA/bis-MGB and target DNA/TFO-bis-MGB complexes were built, where bis-MGB forms two antiparallel hairpins. According to the second model, one MGB hairpin is in the minor groove of 5'-adjacent A/T sequence next to the triplex-forming region, whereas the other one occupies the minor groove of the TFO binding polypurine tract. All these data together give a key information for the construction of MGB-MGB and MGB-oligonucleotide conjugates possessing high specificity and affinity for the target double-stranded DNA.

The article addresses the integrated approach in training bachelor's degree students for creative professional activity on the basis of engineering invention, as exemplified by the Elite Engineering Education Program implemented at National Research Tomsk Polytechnic University.

Engineering education is one of Russia’s priority development areas allowing the country to increase the competitive capacity of its economy in the present world by establishing an effective segment of the national innovative system. Russian national research technical universities are regarded as a powerful force to train highly professional engineering specialists. An essential part of future engineer’s professionalism is foreign language proficiency, particularly proficiency in English as the language of international importance. A range of language skills that students should acquire through mastering a basic educational programme within the chosen direction of training will help them fully realise their potential and become competitive at the international level. In this article, the requirements for bachelor engineers’ foreign language competences determined by the Federal State Educational Standard of Higher Professional Education (FSES HPE) in Russia are analysed for their correspondence to the country’s and global demands that are currently challenging professional engineers. The research procedure and the principles of selecting directions of engineering training for the present analysis are provided, the obtained results are presented and the corresponding conclusions are made. Further, National Research Tomsk Polytechnic University (TPU) best practices of priority engineering training are described. It is believed that the university’s experience can be successfully adopted by other Russian institutions of higher professional education aimed at training professional engineers for the benefit of the country. DOI: 10.5901/mjss.2015.v6n3s1p290

Synthetic minor groove-binding pyrrole–imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications.

New conjugates of triplex-forming pyrimidine oligo(2'-O-methylribonucleotides) with one or two 'head-to-head' hairpin oligo(N-methylpyrrole carboxamide) minor-groove binders (MGBs) attached to the terminal phosphate of the oligonucleotides with a oligo(ethylene glycol) linker were synthesized. It was demonstrated that, under appropriate conditions, the conjugates form stable complexes with double-stranded DNA (dsDNA) similarly to triplex-forming oligo(deoxyribonucleotide) (TFO) conjugates containing 5-methylated cytosines. Kinetic and thermodynamic parameters of the complex formation were evaluated by gel-shift assay and thermal denaturation. Higher melting temperatures (Tm), faster complex formation, and lower dissociation constants (Kd) of the triple helices (6-7 nM) were observed for complexes of MGB-oligo(2'-O-methylribonucleotide) conjugates with the target dsDNA compared to the nonconjugated individual components. Interaction of MGB moieties with the HIV proviral DNA fragment was indicated by UV/VIS absorption changes at 320 nm in the melting curves. The introduction of thymidine via a 3',3'-type 'inverted' phosphodiester linkage at the 3'-end of oligo(2'-O-methylribonucleotide) conjugates (3'-protection) had no strong influence on triplex formation, but slightly affected complex stability. At pH 6.0, when one or two hairpin MGBs were attached to the oligonucleotide, both triplex formation and minor-groove binding played important roles in complex formation. When two 'head-to-head' oligo(N-methylpyrrole) ligands were attached to the same terminal phosphate of the oligonucleotide or the linker, binding was observed at pH >7.5 and at high temperatures (up to 74 degrees). However, under these conditions, binding was retained only by the MGB part of the conjugate.

The international community is facing global challenges in the new millennium, such as securing peace, ensuring security, supporting proper functioning of the international economy, fighting international terrorism, improving health-care, and providing environmental sustainability. The way these challenges may be met will determine the future of mankind. These challenges can be met only by way of the broad co-operation of nations and by joint effort of the whole international community. The situation, as it exists today, requires the establishment of a new world order, which would be able to provide for the survival of humanity. However, to attain this goal, it is necessary to increase the level of global system governance considerably. Increasing the level of international system governance is the key global issue, and the way it is resolved will determine the adjustment of other global problems. The focal nature of this issue has been many times underscored by statesmen and by the resolutions of intergovernmental organizations and NGOs. The UN Secretary General stated in the UN 2000 Progress Report that "more efficient world governance is required, under which I mean joint conduct of international affairs". 1 The concept of the foreign policy of Russia stresses the need "to increase the level of governance of the international system", which provides for "the strengthening of the role of international institutions and mechanisms in the world economy and politics". 2 International law occupies an important place amongst such institutions and mechanisms. The level of international system governance greatly depends upon the efficiency of international law. Increasing the level of international system governance is directly

In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

The article describes the results of structural analysis of the German-English hybrid terms of the information security sphere. The obtained data testify to the serious impact of the English influence on German primarily in the peripheral sphere of the German language stock. The hybridity is stated as a result of aggregation of the literary German lexical system and language mixing owning to an invasive borrowing process.

Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5′ ends of housekeeping genes. As a rule, interbands display preferential “head-to-head” orientation of genes. They are enriched for “broad” class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5′-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called “grey” bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.

The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs.

The time inside the mutant selection window (TMSW) has been shown to be less predictive of selection of fluoroquinolone-resistant bacteria than the ratio of the area under the concentration–time curve to minimum inhibitory concentration (AUC/MIC). To explore the different predictive powers of TMSW and AUC/MIC, enrichment of ciprofloxacin-resistant mutants of four Escherichia coli strains was studied in an in vitro dynamic model at widely ranging TMSW values. Each organism was exposed to twice-daily ciprofloxacin for 3 days. Peak antibiotic concentrations were simulated to be close to the MIC, between the MIC and the mutant prevention concentration (MPC), and above the MPC, with TMSW varying from 0% to 100% of the dosing interval. Amplification of resistant mutants was monitored by plating on medium with 8× MIC of the antibiotic. For each organism, TMSW plots of the area under the bacterial mutant concentration–time curve (AUBCM) exhibited a hysteresis loop: at a given TMSW that corresponds to the points on the ascending portion of the bell-shaped AUBCM–AUC/MIC curve [when the time above the MPC (T>MPC) was zero], the AUBCM was greater than at the same TMSW related to the descending portion (T>MPC > 0). A sigmoid function fits these separate data sets well for combined data with the four organisms (r2 = 0.81 and 0.92, respectively), in contrast to fitting the whole data pool while ignoring the AUC/MIC–resistance relationship (r2 = 0.61). These data allow the appropriate use of TMSW as a predictor of bacterial resistance.

The article provides an overview of personal and professional competence development in students of Elite Engineering Educational Program in Tomsk Polytechnic University, as well as procedures and criteria used to measure it, and provides a comparison of the resulting values with those of the students of traditional programs.

A series of non-covalent hybrids of 5′-pyrene conjugates of homo-oligoribonucleotides and homo-oligodeoxyribonucleotides of different length with oxidized carboxyl-functionalized single-walled carbon nanotubes (SWCNTs) was prepared. The comparative study of adsorption of 5′-pyrene conjugates of oligonucleotides onto SWCNT surface has been performed. The features of the hybrids formation were studied by measuring of ζ-potential and fluorescence titration. Pyrene conjugates of oligoribonucleotides were shown to interact with SWCNTs more efficiently than oligodeoxyribonucleotides, with oligonucleotide length slightly hindering the adsorption. The TEM study proved the adsorption of pyrene conjugates of oligonucleotides onto the surface of functionalized SWCNTs, with the sites of adsorption being visualized after staining by contrasting agent.

3D computer simulation of mechanical behavior of a brittle porous material under uniaxial compression is considered. The movable cellular automaton method, which is a representative of particle methods in solid mechanics, is used for computation. In an initial structure the automata are positioned in FCC packing. The pores are set up explicitly by removing single automata from the initial structure. The computational results show that the curves of dependence of strength and elastic properties of the modeled specimens on porosity have a break at the porosity value about 20 %, i.e. percolation threshold. The obtained results are in close agreement with available experimental data.

Background: The vitamin D metabolite 1,25(OH) 2D3 (VitD3) is a potent immunosuppressive drug and, among others, is used for topical treatment of psoriasis. A proposed mechanism of VitD3-mediated suppression is priming of dendritic cells (DCs) to induce regulatory T (Treg) cells. Objective: Currently, there is confusion about the phenotype of VitD3-induced Treg cells and the DC-derived molecules driving their development. We investigated Treg cell induction after VitD3 priming of 2 distinct skin DC subsets: Langerhans cells (LCs) and dermal dendritic cells (DDCs). Methods: LCs and DDCs primed with VitD3 were cocultured with allogeneic naive T cells. The phenotype and function of the DCs and induced T cells were analyzed. Results: Both VitD3-primed DC subtypes induced T cells with regulatory activity. Unexpectedly, whereas the Treg cell populations generated by VitD3-primed LCs were CD25(hi) CD127(lo) forkhead box protein 3 (Foxp3)-positive cells, which meet the criteria of classical inducible Treg cells, the T cells developing in response to VitD3-primed DDCs were Foxp3(-) T(R)1 cells expressing IL-10. Inhibition experiments revealed that LC-derived TGF-beta is a key factor in the induction of Foxp3 1 Treg cells, whereas DDC-derived IL-10 is important for the induction of IL-10(+) T(R)1 cells. Conclusion: Thus we report the novel finding that distinct but closely related DC subsets are differentially programmed by VitD3 to support development of either TGF-beta-dependent Foxp3(+) Treg cells or IL-10-dependent IL-10(+) Treg cells. (J Allergy Clin Immunol 2011;127:1532-40.)

We designed tandems of oligo(2'-O-methylribonucleotides) conjugates containing two bispyrene (5'-bisPyr and 3'-bisPyr) groups on their junction for detection of C677T polymorphism in the methylenetetrahydrofolate reductase gene (MHTFR). The potential of SNP detection with multipyrene tandems of oligo(2'-O-methylribonucleotides) was demonstrated.

A combination of ESR and31P NMR techniques was used to study the mechanism of the radiosensitizing influence of misonidazole (MISO) on mouse tumors and liver. The MISO injection (1 g/kg) was shown to cause significant metabolic changes in tumors, such as an increase in the content of nitrosyl complexes, increases in adenosine diphosphate and inorganic phosphate levels, and decreases in phosphomonoesters, phosphodiesters, adenosine triphosphate and phosphocreatine in the initial period of observation. These alterations were accompanied by slight cytosol alkalinization (pH shift ca 0.15). A decrease in the ESR signal intensity of Mo5+-containing enzymes, an increase in the cytochrome P-450 signal and a significant increase in the free radical signal were observed in liver after MISO treatment. Local irradiation of tumors (30 Gy) 30 min after MISO injection led to the enhancement and prolongation of nearly all the effects induced by MISO treatment. The combined effect of MISO and irradiation was not simply the sum of their separate effects. It is suggested that radiation enhances cytotoxic effects of nitrocompounds on hypoxic tumor cells, inhibiting glycolysis and inducing greater production of toxic and highly reactive intermediates resulting from incomplete nitro group reduction. The latter appears to be considered as the major factor involved in the radiosensitizing action of nitrocompounds.

Genetically modified mono-nuclear cell fraction from human umbilical cord blood (HUCB) expressing human vascular endothelial growth factor (VEGF) and mouse neural L 1 cell adhesion molecule (L 1 CAM) were used for gene-stem cell therapy of transgenic G 93 A mice adopted as an animal amyotrophic lateral sclerosis (ALS) model. We generated non-viral plasmid constructs, expressing human VEGF 165 (pcDNA-VEGF) and mouse neural L 1 cell adhesion molecule (pcDNA-mL 1 CAM). Mono-nuclear fraction of HUCB cells were transiently transfected by electro-poration with a mixture of expression plasmids (pcDNA-VEGF + pcDNA-mL 1 CAM). Sixteen transgenic female and male mice were randomly assigned to three groups: (1) transplantation of genetically modified HUCB cells expressing L 1 and VEGF ( n = 6), (2) transplantation of un-transfected HUCB cells ( n = 5), and (3) control group ( n = 5). In first two experimental groups 1 × 10 6 cells were injected retro-orbitally in pre-symptomatic 22–25-week-old G 93 A mice. Our results demonstrate that HUCB cells successfully grafted into nervous tissue of ALS mice and survived for over 3 months. Therefore, genetically modified HUCB cells migrate in the spinal cord parenchyma, proliferate, but instead of transforming into nerve cells, they differentiate into endothelial cells forming new blood vessels. We propose that: (A) expression of mouse neural L 1 CAM is responsible for increased homing and subsequent proliferation of transplanted cells at the site of neuro-degeneration, (B) expression of human VEGF directs HUCB cell differentiation into endothelial cells, and (C) neuro-protective effect may stem from the delivery of various neuro-trophic factors from newly formed blood vessels.

We report here the design and synthesis of new mono- and bis-pyrene-labeled oligo(2'-O-methylribonucleotide) tandems as perspective probes for SNP detection. The detection strategy is based on the eximer formation when two or more pyrene groups are brought into close proximity upon hybridization of the tandem components with DNA. The potential of SNP detection with tandems of pyrene-labeled oligo(2'-O-methylribonucleotides) by duplex melting curve analysis based on excimer fluorescence registration was demonstrated.

We have developed a new method for the preparation of oligodeoxyribonucleotides and oligo(2'-O-methylribonucleotides) that contain a 2'-phosphorylated ribonucleoside residue, and optimized it to avoid 2' -3' -isomerization and chain cleavage. Structures of the 2' -phosphorylated oligonucleotides were confirmed by MALDI-TOF MS and enzymatic digestion, and the stability of their duplexes with DNA and RNA was investigated. 2'-Phosphorylated oligonucleotides may be useful intermediates for the introduction of various chemical groups for a wide range of applications.