Vol 2, No 3 (2010)


Letter from the Editors

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Acta Naturae. 2010;2(3):1-1
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Russian Federation State Prize in Science and Technology for 2009

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The Russian Federation State Prize in the field of Science and Technology for 2009 for "A Set of Scientific Works on the Development of Laser and Information Technologies in Medicine" (Presidential Decree N° 678, dated June 6th, 2010) was awarded jointly to Doctor of Physical and Mathematical Sciences, Academician of the Russian Academy of Sciences, Director of the Institute of Laser and Information Technologies, Russian Academy of Sciences, V. Ya. Panchenko; to Doctor of Medical Sciences, Academician of the Russian Academy of Medical Sciences, Deputy Director of the Burdenko Neurosurgery Research Institute, Russian Academy of Medical Science, A.A. Potapov; and to Doctor of Medical Sciences, Russian Academy of Medical Sciences, Academician of the Russian Academy of Sciences, Director of Herzen Cancer Research Institute V.I. Chissov.
Acta Naturae. 2010;2(3):6-9
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Alexander Potapov: "Neurosurgery uses advancements in modern biology in all of its aspects

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Alexander Potapov, laureate of the State Prize of the Russian Federation in Science and Technology for 2009, doctor of medical sciences, academician, Russian Academy of Medical Sciences, and deputy director of the N.N. Burdenko Scientific Research Institute of Neurosurgery of RAMS, talks to Acta Naturae about the achievements in modern neurosurgery, the latest developments in the field, and the close convergence between basic biology and clinical practice.
Acta Naturae. 2010;2(3):10-12
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Science in Universities: Ordered to Live

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An unprecedented act of financial support, in the form of 90 billion rubles for leading Russian universities, has rocked the professional community. With stakes in the development of university science and research, the State has started to take action towards strengthening and amplifying science programs. After determining leading universities (including both research and federal centers) which, in addition to enjoying a high status also receive additional funds, the Ministry of Education and Science has unveiled a new competition for higher educational institutions. This competition focuses on cooperation with business, strengthening the infrastructure needed for innovation, and attracting leading scientists. As early as this fall, the winners are expected to begin receiving funding to the tune of millions of rubles, which should allow them to pursue the most daring and ambitious projects.
Acta Naturae. 2010;2(3):13-16
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Universities and Business Cooperation Contest Results

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The results of the second round of the Universities and Business Cooperation Contests have been announced. Deputy Minister of Education and Science Sergey Mazurenko discussed the successes and difficulties related to state support based on Government Resolutions N218 and 21 at a briefing on October 6, 2010.
Acta Naturae. 2010;2(3):17-18
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International Evaluation Procedure for Supergrants

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Sergey Ivanets, director of the department of international integration at the Ministry of Education and Science, talks about the specifics of the evaluation procedures for inviting leading scientists (Decree of the Government of the Russian Federation dated April 9, 2010, N 220: "On Measures for Attracting Leading Scientists into Russian Higher Professional Educational Institutions")
Acta Naturae. 2010;2(3):19-20
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Toll-Like Receptors (TLRs): The Role in Tumor Progression

Shchebliakov D.V., Logunov D.Y., Tukhvatulin A.I., Shmarov M.M., Naroditsky B.S., Ginzburg A.L.


Toll-like receptors (TLRs) are major components of the innate immune system that recognize the conserved molecular structures of pathogens (pathogen-associated molecular patterns; PAMPs). TLRs are found omega seamaster midsize replica in many different cell types, ranging from epithelial to immunocompetent cells. TLR binding triggers the expression of several adapter proteins and downstream kinases, leading to the induction of key pro-inflammatory mediators. This results in the activation of both the innate immune response (elevated expression of antiapoptotic proteins, proinflammatory cytokines, and antibacterial proteins), as well as the adaptive immune response (maturation of the dendritic cells, antigen presentation, etc.). In consequence of their ability to enhance the specific and nonspecific immune reactions of an organism, TLR agonists are widely used in the therapy of infectious diseases and, as adjuvants, in the therapy of malignant neoplasia. However, to date, rolex imitation jewellery TLRs have had the opposite effects on tumor progression. On the one hand, TLR ligands can suppress tumor growth. On the other hand, TLR agonists can promote the survival of malignant cells and increase their resistance to chemotherapy. The purpose of this review is to summarize the available data on the effects of TLRs and their agonists on tumor progression, as well as the mechanisms underlying the differences in the effects of best replica watches sites 2020TLRs on tumor growth.
Acta Naturae. 2010;2(3):21-29
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Molecular Basis of Mammalian Embryonic Stem Cell Pluripotency and Self-Renewal

Medvedev S.P., Shevchenko A.I., Zakian S.M.


Mammalian embryonic stem cells (ESC) have a number of specific properties that make them a unique object of fundamental and applied studies. In culture, ESC can remain in an infinitely undifferentiated state and differentiate into descendants of all three germ layers - ectoderm, endoderm, and mesoderm - that is, they can potentially produce more than 200 cell types comprising the body of an adult mammal. These properties of ESC are refered to as self-renewal and pluripotency. In this review, the basic signal pathways implicated in the maintenance of ESC pluripotency are considered. The major genes comprising a subsystem of “internal regulators of pluripotency,” their protein products and regulators, are characterized, and interaction with other factors is described as well. The role of epigenetic mechanisms and microRNAs in the system of ESC self-renewal and pluripotency, as well as the relationship between pluripotency and X-chromosome inactivation in female mammals, is discussed.
Acta Naturae. 2010;2(3):30-46
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Protein Engineering of Penicillin Acylase

Tishkov V.I., Savin S.S., Yasnaya A.S.


Penicillin acylases (PA) are widely used for the production of semi-synthetic β-lactam antibiotics and chiral compounds. In this review, the latest achievements in the production of recombinant enzymes are discussed, as well as the results of PA type G protein engineering.
Acta Naturae. 2010;2(3):47-61
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PEDF - A Noninhibitory Serpin with Neurotrophic Activity

Minkevich N.I., Lipkin V.M., Kostanyan I.A.


The pigment epithelium-derived factor (PEDF) is a glycoprotein with a molecular weight of 50 kDa belonging to the noninhibitory serpin family. It regulates several physiological processes, such as stimulation of retinoblastoma cell differentiation into neuron cells, and facilitation of the growth and viability of photoreceptor cells and neurons of the central nervous system. Moreover, this factor protects neuronal cells against apoptosis. PEDF is not only a neurotrophic factor, but also a natural angiogenesis inhibitor. This protein, as well as its biologically active fragments, possesses significant neuroprotective, neurotrophic, and antiangiogenic capabilities. The precise molecular mechanisms underpinning the effects of PEDF are still not quite clear. However, this protein generates great interest as a promising drug for the therapy of a wide range of neurodegenerative, ophthalmological, and oncological diseases. This review is a summary of what is known today about the structural features, biochemical properties, and multimodal functions of PEDF.
Acta Naturae. 2010;2(3):62-71
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Association of ERAP1 Allelic Variants with Risk of Ankylosing Spondylitis

Zvyagin I.V., Dorodnykh V.Y., Mamedov I.Z., Staroverov D.B., Bochkova A.G., Rebrikov D.V., Lebedev Y.B.


Ankylosing spondylitis (AS) belongs to a group of autoimmune diseases affecting the axial skeleton. Beside the hla-b*27 allele, several other human genes that control the variety processes of immune homeostasis are considered to be associated with AS manifestation in different human populations. Among strong associated non-MHC genes erap 1 encoding the endoplasmic reticulum aminopeptidase 1 isoform was recently identified by single nucleotide polymorphisms (SNPs) meta analysis. In our study we inspected the genetic association of five non-synonymous coding SNPs from erapl with AS in Caucasians. We implemented the SSP-PCR system for precise genotyping of 87 hla-b*27 positive AS patients and 77 hla-b*27 healthy donors from the Russian population. Considerable differences in allele’s frequencies within patients vs control cohort were shown for 3 of 5 SNPs under investigation. Using the EM-algorhitm we reconstructed 3-marker haplotypes that distinguish with high probability two cohorts due to differences in the haplotypes frequencies. In such a way both the sensitive, CCT, haplotype and the protective, TTC, one were predicted. To verify the calculation we determined genuine frequencies of 5-marker haplotypes in AS cohort by haplotyping of individual cDNA samples using improved SSP-PCR primer set. We demonstrated that the frequencies of in silica reconstucted haplotypes and the frequencies of experimentally detected haplotypes are in a good agreement. Frequency of the risk haplotype CCT (rs17482078/10050860/2287987) detected within AS cohort reaches 88%, as well as the frequency calculated by EM-algorhitm.
Acta Naturae. 2010;2(3):72-77
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Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice

Ignatov D.V., Skvortsov T.A., Majorov K.B., Apt A.S., Azhikina T.L.


We performed a comparative analysis of Mycobacterium avium transcriptomes (strain 724R) in infected mice of two different strains- resistant and susceptible to infection. Sets of mycobacterial genes transcribed in lung tissue were defined, and differentially transcribed genes were revealed. Our results indicate that M. avium genes coding for enzymes of the Krebs cycle, oxidative phosphorylation, NO reduction, fatty acid biosynthesis, replication, translation, and genome modification are expressed at high levels in the lungs of genetically susceptible mice. The expression of genes responsible for cell wall properties, anaerobic nitrate respiration, fatty acid degradation, synthesis of polycyclic fatty acid derivatives, and biosynthesis of mycobactin and other polyketides is increased in the resistant mice. In the resistant host environment, Mycobacterium avium apparently transitions to a latent state caused by the deficiency in divalent cations and characterised by anaerobic respiration, degradation of fatty acids, and modification of cell wall properties.
Acta Naturae. 2010;2(3):78-84
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Fingerprint-like Analysis of "Nanoantibody" Selection by Phage Display Using Two Helper Phage Variants

Tillib S.V., Ivanova T.I., Vasilev L.A.


This paper discusses the selection of mini-antibody (nanoantibody, nanobody® or single domain antibody) sequences of desired specificity by phage display-based method using a generated library of antigen-binding domains of special heavy-chain only antibodies (single-stranded antibodies) of immunized camel. A comprehensive comparison of the efficiency of parallel selection procedures was performed by using the traditional (M13KO7) and modified (with N-terminal deletion in the surface gIII protein) helper phages. These two methods are partly complementary, and by using them in parallel one can significantly improve the selection efficiency. Parallel restriction analysis (finger-printing) of PCR-amplified cloned sequences coding for mini-antibodies (HMR-analysis) is proposed for identifying individual clones, as a replacement to sequencing (to a certain extent). Using this method, unique data were collected on the selection of mini-antibody variants with the required specificity at various stages of a multi-stage selection procedure. It has been shown that different sequences coding for mini-antibodies are selected in different ways, and that, if this feature is not taken into account, some mini-antibody variants may be lost.
Acta Naturae. 2010;2(3):85-93
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Regulation of Store-Operated Channels by Scaffold Proteins in A431 Cells

Shalygin A.V., Ryazantseva M.A., Glushankova L.N., Bezprozvanny I.B., Mozhayeva G.N., Kaznacheyeva E.V.


Store-operated channels are major calcium influx pathways in nonexitable cells. Homer scaffold proteins are well known for their role in regulating calcium signaling. Here we report on a detailed single-channel level characterization of native store-operated channels regulated by Homer scaffold proteins in A431 carcinoma cells. By applying the single-channel patch-clamp technique, we found that different types of store-operated calcium channels have different sensitivities to Homer proteins.
Acta Naturae. 2010;2(3):94-100
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Oligonucleotide Microarray for the Identification of Carbapenemase Genes of Molecular Classes A, B, and D

Ulyashova M.M., Khalilova Y.I., Rubtsova M.Y., Edelstein M.V., Alexandrova I.A., Egorov A.M.


This work is a report on the development of a method of hybridization analysis on DNA microarrays for the simultaneous identification and typing of carbapenemase-encoding genes. These enzymes are produced by the microorganisms that are responsible for causing infectious diseases. The method involves several steps, including DNA extraction from clinical samples and amplification of carbapenemase genes by multiplex PCR with simultaneous labelling by biotin. Following that, hybridization of the labeled PCR products with oligonucleotide probes immobilized on the surface of a nitrocellulose-based DNA microarray occurs. The biotin molecules attached to the DNA duplexes are detected by using conjugates of streptavidin-horseradish peroxidase, which is then quantified by colorimetric detection of the enzyme. We have designed the required oligonucleotide probes and optimized the conditions of the membrane microarray-based hybridization analysis. Our method allows to identify 7 types of carbapenemase genes belonging to the molecular classes A, B, and D, and it also allows additional typing into genetic subgroups. The microarrays have been tested with the control strains producing the carbapenemase genes which have been characterized by sequencing. The developed method of hybridization analysis was employed to investigate clinical strains of Pseudomonas spp. and Acinetobacter spp., which produce carbapenemases of different classes based on phenotypic testing. All strains of Acinetobacter baumanii resistant to carbapenems were producers of two carbapenemase OXA-type genes (OXA-51, in combination with OXA-23 (1 strain), OXA-40 (5 strains), or OXA-58 (4 strains)). The metallo-β-lactamase VIM-2 type gene was detected in all Pseudomonas aeruginosa strains resistant to carbapenems. Testing of carbapenem-sensitive strains did not detect any carbapenemase genes. The microarray method for the identification of carbapenemase genes is very accurate and highly productive. It can be employed in clinical microbiological laboratories for the identification and study of carbapenemase epidemiology.
Acta Naturae. 2010;2(3):101-109
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New Test System for Serine/Threonine Protein Kinase Inhibitors Screening: E. coli APHVIII/ Pk25 design

Bekker O.B., Alekseeva M.G., Osolodkin D.I., Palyulin V.A., Elizarov S.M., Zefirov N.S., Danilenko V.N.


An efficient test system for serine/threonine protein kinase inhibitors screening has been developed based on the E. coli protein system APHVIII/Pk25. Phosphorylation of aminoglycoside phosphotransferase VIII (APHVIII) by protein kinases enhances resistance of the bacterial cell to aminoglycoside antibiotics, e.g. kanamycin. Addition of protein kinase inhibitors prevents phosphorylation and increases cell sensitivity to kanamycin. We have obtained modifications of APHVIII in which phosphorylatable Ser146 was encompassed into the canonical autophosphorylation sequence of Streptomyces coelicolor Pk25 protein kinase. Mutant and wild-type aphVIII were cloned into E. coli with the catalytic domain of pk25. As a result of the expression of these genes, accumulation of corresponding proteins was clearly observed. Extracted from bacterial lysates, Pk25 demonstrated its ability to autophosphorylate. It was shown that variants of E. coli containing both aphVIII and pk25 were more resistant to kanamycin than those carrying only aphVIII. Protein kinase inhibitors of the indolylmaleimide class actively inhibited Pk25 and reduced cell resistance to kanamycin. Modeling of APHVIII and Pk25 3D structures showed that pSer146 is an analog of phosphoserine in the ribose pocket of protein kinase A. Pk25 conformation was similar to that of PknB of Mycobacterium tuberculosis. Potential indolylmaleimide inhibitors were docked into the ATP-binding pocket of Pk25. The designed test system can be used for the primary selection of ATP-competitive small molecule protein kinase inhibitors.
Acta Naturae. 2010;2(3):110-121
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Individual Genome of the Russian Male: SNP Calling and a de novo Assembly of Unmapped Reads

Chekanov N.N., Boulygina E.S., Beletskiy A.V., Prokhortchouk E.B., Skryabin K.G.


A somatic cell genome was recently resequenced for a patient with renal cancer. The data were submitted to the NCBI Sequence Read Archive under the accession number SRA012240. Here, we have performed SNP calling for the genome and compared it with several published genomes. We have found 2, 921, 724 SNPs, including 1, 472, 679 newly described ones. Among them, 63, 462 SNPs have been mapped to the Y chromosome and, based on 18 markers, the genome has been ascribed to the R1a1a haplogroup predominant in Russian males. The mitochondrial haplogroup has been determined as U5a, which is also common in the European part of Russia. Short reads unmapped to the human genome were used for the de novo assembly of DNA sequences. This resulted in genome-specific contigs (more than 100 bp in length) with an overall length of 154 kbp (for GAII) and 4.7 kbp (for SOLiD).
Acta Naturae. 2010;2(3):122-126
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