Vol 1, No 1 (2009)


To the readers of the first issue of Acta Naturae

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Acta Naturae. 2009;1(1):1-1
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Dear Colleagues!

Bilenkina I.P.
Acta Naturae. 2009;1(1):2-2
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VAK: Protecting High Standards in Science

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On the role played by the High Attestation Commission of the Russian Federation (VAK) of Russia in managing domestic science, criteria, and professional selection, as well as the role the of scientific periodicals in this process; Acta Naturae talked to the president of this commission, academician Mikhail Kirpichnikov of the Russian Academy of Sciences.
Acta Naturae. 2009;1(1):6-11
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The Intellectual Property of Scientific Organizations and Rights to It

Gordeeva M.I.


One of the most acute problems inhibiting the establishment of innovative economics in our country is the imperfection of the legislation regulating the production of marketable goods on the basis of new technologies. Many specialists—both scientists and representatives of business entities—are certain that the current laws cannot effectively influence the creation of innovative chains. It is not an exaggeration to say that the current laws are not focused on building a knowledge‑oriented economy. It could be said that the problem of nascent intellectual property rights is the most important problem of the day. Who should be the proprietors of these rights? The scientists, business, or the state? And to what extent? Let’s try to debate this situation and consider herein the rights of scientific organizations to the results of intellectual property obtained within the framework of their activity.
Acta Naturae. 2009;1(1):12-18
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Living Systems in Russia are Evaluated in Terms of the Number of Scientific Publications Related to the Subject

Sychev V.V., Kolesnichenko A.V.


Those fields within science in which there is continuous development need to be objectively evaluated in order to determine the efficiency of work being conducted by those working in that field. Different criteria provide an estimate of this efficiency at both the level of individual scientists as well as that of entire scientific institutions. Moreover, it is possible to obtain an estimate of the rate of progress in research activities within
Acta Naturae. 2009;1(1):19-31
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Modern Technologies for Creating Synthetic Antibodies for Clinical Application

Deyev S.M., Lebedenko E.N.


The modular structure and versatility of antibodies enables one to modify natural immunoglobulins in different ways for various clinical applications. rational design and molecular engineering make it possible to directionally modify the molecular size, affinity, specificity, and immunogenicity and effector functions of an antibody, as well as to combine them with other functional agents. this review focuses on up-to-date methods of antibody engineering for diagnosing and treating various diseases, particularly on new technologies meant to refine the effector functions of therapeutic antibodies. Key words: monoclonal antibodies, humanized antibodies, single-chain antibodies, multivalency, bispecificity, target-specific delivery, barnase:barstar module, and immunodibarnase. Abbreviations: ADcc (antibody-dependent cellular cytotoxicity); cDc (complement-dependent cytotoxicity); MAb (monoclonal antibodies); cH and cL (constant domains of antibody heavy and light chains); СНО cells (chinese hamster ovary cells); eGFr (Her1) (epidermal growth factor receptor, cancer marker); Fab (antigen-binding fragment of antibody); Fc (constant (crystallizable) antibody fragment); Fcγr (cell receptor of antibody Fc-fragments); Fcrn (neonatal receptor of antibody Fc-fragments); Her1 and Her2/neu (cancer markers of tyrosine kinase receptor group); IgA, IgG, IgD, Ige, IgM (A, G, D, e, M immunoglobulins (antibodies of the A, G, D, e, M classes)); scFv (single chain fragment variable); PSMA (prostate-specific membrane antigen); VeGF (vascular endothelial growth factor); VH and VL (variable domains of heavy and light antibody chains).
Acta Naturae. 2009;1(1):32-50
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The Regulation of Telomerase in Oncogenesis

Skvortzov D.A., Rubzova M.P., Zvereva M.E., Kiselev F.L., Donzova O.A.


Telomerase is a complex ribonucleoprotein that completes the telomeres' ends in eukaryotic cells which shorten due to DnA underreplication. the core enzyme consists of a protein catalytic subunit—telomerase reverse transcriptase (tert)—and telomeric rnA (telomerase rnA (tr)); a small region of this rnA serves as a template for the telomeric repeats synthesis. Apart from rare exceptions, telomerase is not active in the somatic cells and tissues of the human body. However, the activation of telomerase activity in cancer cells was shown for certain in 80–90 % of cases. understanding the mechanism of telomerase functioning and the mechanisms of its regulation could be used in oncodiagnostics. telomerase itself and its regulators could be important targets for anticancer therapy. the activity of telomerase in a cell is affected by proteins with multiple functions, and this influence is not necessarily specific. there are also cases when telomerase regulators act together or when several regulators are organised in the cascade. the aim of this review is to generalize and systemize data about the regulation of telomerase in ontogenesis. Key words: telomerase, telomerase reverse transcriptase, telomerase rnA, regulation, cancer. Abbreviations: 5azadc (5-aza-2'-deoxicitidine), AV (adenoviruses), HBV (Hepatitis B Virus) HIV (Human Immunodeficiency Virus), HPV (Human papillomavirus), eBV (epstein–Barr Virus), np (nucleotide pair), OB-motive (oligonecleotide/oligosaccharide binding motive), rt (reverse transcription), Pcr (polymerase chain reacion), rnAse (ribonuclease), tert (telomerase reverse transcriptase), htert (human tert), mtert (mouse tert), Dn-htert (dominantnegative mutated htert), erβ (estrogen β receptor), HtLV-I (Human t-lymphotropic virus), tr (telomerase rnA), trAP (telomeric repeat Amplification Protocol), PHA (phytohemagglutinin), Hre (Hypoxia response element), neS (nuclear export signal).
Acta Naturae. 2009;1(1):51-67
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Catalytic Bioscavengers Against Toxic Esters, an Alternative Approach for Prophylaxis and Treatments of Poisonings

Masson P., Rochu D.


Bioscavengers are biopharmaceuticals that specifically react with toxicants. thus, enzymes reacting with poisonous esters can be used as bioscavengers for neutralization of toxic molecules before they reach physiological targets. Parenteral administration of bioscavengers is, therefore, intended for prophylaxis or pre-treatments, emergency and post-exposure treatments of intoxications. these enzymes can also be used for application on skin, mucosa and wounds as active components of topical skin protectants and decontamination solutions. Human butyrylcholinesterase is the first stoichiometric bioscavenger for safe and efficient prophylaxis of organophosphate poisoning. However, huge amounts of a costly enzyme are needed for protection. thus, the bioscavenger approach will be greatly improved by the use of catalytic bioscavengers. catalytic bioscavengers are enzymes capable of degrading toxic esters with a turnover. Suitable catalytic bioscavengers are engineered mutants of human enzymes. efficient mutants of human butyrylcholinesterase have been made that hydrolyze cocaine at a high rate. Mutants of human cholinesterases capable of hydrolyzing OPs have been made, but so far their activity is too low to be of medical interest. Human paraoxonase a promiscuous plasma enzyme is certainly the most promising phosphotriesterase. However, its biotechnology is still in its infancy. Other enzymes and proteins from blood and organs, and secondary biological targets of OPs and carbamates are potential bioscavengers, in particular serum albumin that reacts with OPs and self-reactivates. Lastly, non-human enzymes, phosphotriesterases and oxidases from various bacterial and eukaryotic sources could be used for external use against OP poisoning and for internal use after modifications for immunological compatibility.
Acta Naturae. 2009;1(1):68-79
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Life and Death Decisions in the CD95 System: Main Proand Anti-Apoptotic Modulators

Lavrik I.N., Krammer P.H.


Apoptosis is common to all multicellular organisms. Apoptosis can be triggered by the extrinsic (death receptor (DR)) or the intrinsic (mitochondrial) death pathways.CD95 (APO-1/Fas) is a prototypic member of the DR family. This review is focused on the mechanisms of CD95 (APO-1/Fas)-mediated apoptosis and the role in the apoptosisof the death effector domain (DED)-containing proteins: pro-apoptotic protein procaspase-8 and anti-apoptotic protein c-FLIP. Gaining insights into these processes willimprove our understanding of the pathogenesis of diseases such as cancer, autoimmunity and AIDS, and will open new approaches to rational treatment strategies.
Acta Naturae. 2009;1(1):80-83
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Analysis of Myelin Basic Protein Fragmentation by Proteasome

Bacheva A.V., Belogurov A.A., Ponomarenko N.A., Knorre V.D., Govorun V.M., Serebryakova M.V., Gabibov A.G.


The proteasome is a high molecular protein complex whose purpose is specific protein degradation in eukaryotic cells. One of the proteasome functions is to produce peptides, which will then be presented on the outer cell membrane using main histocompatibility complex (MHc) molecules of the first or second class. there are definite reasons to believe that proteasome directly takes part in the specific degradation of myelin basic protein (MBP), which make up to 30% of all proteins in the myelin sheath of neuronal axons. the details of the proteasomal degradation of MBP are still unclear. In this work, the features of specific MBP degradation by proteasome were studied. It was demonstrated that MBP (non-ubiquitinated) is a good substrate for 20S and for the 26S proteasome. this is the first work on detecting the sites of MBP proteolysis by proteasome from brains of SJL/J/J and Balb/c mice’s lines. Substantial differences in the degradation pattern of this neuroantigen were found, which could indicate the better presentation MBP parts on MHc molecules in the case of mice predisposed to the development of experimental autoimmune encephalomyelitis.
Acta Naturae. 2009;1(1):84-87
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The Interaction between the RNA-Dependent RNA-Polymerase of the Hepatitis Virus and RNA Matrices

Konduktorov K.A., Lyudva G.S., Ivanov A.V., Tunitskaya V.L., Kochetkov S.N.
Acta Naturae. 2009;1(1):88-90
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Studying of Membrane Localization of Recombinant Potassium Channels in E.coli

Nekrasova O., Tagway A., Ignatova A., Feofanov A., Kirpichnikov M.


The effective expression of recombinant membrane proteins in E.coli depends upon the targeting and insertion of proteins into the cellular membrane, as well as on those proteins adopting the correct spatial structure. A significant technological problem involves the design of approaches for detecting the location of target proteins within a host cell. Using a hybrid potassium channel KcsA-Kv1.3 as a model, we developed a technological scheme which is suitable for the study of membrane localization in E.coli cells of recombinant proteins containing voltage-gated eukaryotic potassium channels as the functional active site. The scheme involves both biochemical and fluorescent methods for detecting target proteins in the cytoplasmic membrane of E.coli, as well as the study of the ligand-binding activity of membrane-embedded proteins.
Acta Naturae. 2009;1(1):91-95
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Cell-free Production of the Extracellular Domain of the Nicotinic Acetylcholine Receptor

Lyukmanova E.N., Kopeina G.S., Shulepko M.A., Shenkarev Z.O., Arseniev A.S., Dolgikh D.A., Kirpichnikov M.P.
Acta Naturae. 2009;1(1):96-98
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Complete Sequencing of the Mitochondrial Genome of Opisthorchis felineus , Causative Agent of Opisthorchiasis

Mordvinov V.A., Mardanov A.V., Ravin N.V., Shekhovtsov S.V., Demakov S.A., Katokhin A.V., Kolchanov N.A., Skryabin K.G.


Opisthorchis felineus, a hepatic trematode, is the causative agent of opisthorchiasis, a dangerous disease in both human beings and animals. Opisthorchiasis is widespread in Russia, especially Western Siberia. The purpose of the present study was to determine the complete mitochondrial DNA sequence of this flatworm. Two parallel methods were employed: (1) capillary electrophoresis to sequence the mitochondrial genome fragments obtained through specific PCR amplification, and (2) high throughput sequencing of the DNA sample. Both methods made possible the determination of the complete nucleotide sequence of the O. felineus mitochondrial genome. The genome consists of a ring molecule 14,277 nt in length that contains 35 genes coding 2 rRN A, 22 tRN A, and 12 proteins: 3 subunits of cytochrome-C-oxidase, 7 subunits of NADH-dehydrogenase, B apocytochrome, and subunit 6 of ATP-synthetase. Like many other flatworms, O. felineus is characterized by the absence of the ATP-synthetase subunit 8 gene. Nineteen out of the 22 tRN As have a typical “clover leaf” structure. The tRN A(AGC) and tRN A-Cys genes lack DHU-loops, while the tRN A-Ser(UC A) has 2 alternative structures: one with a DHU-loop, and one without it. Analyzing the results obtained from the high throughput sequencing revealed 45 single-nucleotide polymorphisms within the mitochondrial genome. The results obtained in this study may be used in the development of molecular diagnostic methods for opisthorchiasis. This study shows that high throughput sequencing is a fast and effective method for decoding the mitochondrial genome of animals.
Acta Naturae. 2009;1(1):99-104
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The Organization in Micro-Loops of an Extended Fragment of Chicken Chromosome 14, Including the Alpha Globin Gene Cluster in the Erythroid Cells

Philonenko E.S., Gavrilov A.A., Ravin S.V., Iarovaia O.V.


It has been shown that the activation of tissue-specific gene transcription during the course of cell differentiation is associated with a spatial reorganization of the genomic domains harboring those specific genes. This reorganization consists of the relocation to the nuclear matrix of the whole genomic domain containing one or more of the genes being transcribed. However, it remains unclear whether, during this process, extended areas of the genome also become attached to the nuclear matrix. We studied the genome´s pattern of interaction with the nuclear matrix in both erythroid and non-erythroid cells of chickens, using a 220Kb region of chromosome -14, which contains the alpha-globin gene cluster and some surrounding house-keeping genes. The results show that in erythroid cells, the fragment of the genome containing the alpha-globin gene domain became spatially arranged into micro-loops which could not be detected by mapping experiments.
Acta Naturae. 2009;1(1):105-108
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The Production and Characteristics of a Mouse’s Embryonic Stem Cell Lineage, Transfected by the Glia Neurotrophic Factor and Gene Fused with the Green Fluorescent Protein Gene

Arsenieva E.L., Kuzmin I.V., Manuilova E.S., Novosadova E.V., Murkin E.V., Pavlova G.V., Tarantul V.Z., Grivennikov I.A.


The influence that the expression of the human (glial-derived neurotrophic factor (GDNF)) neurotrophic factor has on the morphology and proliferative activity of embryonic stem cells (SC) of a mouse with R1 lineage, as well as their ability to form embroid bodies (EB), has been studied. Before that, using a PCR (polymerase chain reaction) coupled with reverse transcription, it was shown that, in this very lineage of the embryonic SC, the expression of the receptors’ genes is being fulfilled for the neurotropfic RET and GFRα1 glia factor. The mouse's embryonic SC lineage has been obtained, transfected by the human GDNF gene, and has been fused with the “green” fluorescent protein (GFP) gene. The presence of the expression of the human GDNF gene in the cells was shown by northern hybridization and the synthesis of its albuminous product by immunocitochemical coloration with the use of specific antibodies. The reliable slowing-down of the embriod-body formation by the embryonic SC transfected by the GDNF gene has been shown. No significant influence of the expression of the GDNF gene on the morphology and the proliferative activity of the transfected embryonic SCs has been found when compared with the control ones.
Acta Naturae. 2009;1(1):109-114
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Direct Matrix-Assisted Laser Desorption– Ionisation (MALDI) Mass-Spectrometry Bacteria Profiling for Identifying and Characterizing Pathogens

Ilina E.N.


This study examines the features and limitations of direct Matrix-Assisted Laser Desorption–Ionisation (MALDI) mass-spectrometry profiling of bacterial cells for investigating a microbial population. The optimal laboratory protocol, including crude bacteria lyses by a solution of 50% acetonitrile, 2.5% trifluoroacetic acid, and using α-cyano-4-hydroxy cinnamic acid as the MALDI matrix, has been developed. Two different bacteria species were under investigation, and representative mass spectra from 278 strains of Neisseria gonorrhoeae and 22 strains of Helicobacter pylori have been analyzed. It’s known that both bacteria demonstrate a variable degree of polymorphism. For N. gonorrhoeae, the MALDI mass spectra that was collected possessed about 70 peaks, 20 of which were good reproducible ones. In spite of the fact that three peaks were found with differing spectra in some strains, little diversity in the N. gonorrhoeae population was revealed. This fact indicates the prospects in using direct MALDI mass-spectrometry profiling for gonococcus identification. In the case of H. pylori strains, the variety in the collected mass-spectra was shown to be essential. Only five peaks were present in more than 70% of strains, and a single mass value was common for all spectra. While these data call into question the possibility of the reliable species identification of H. pylori using this approach, the intraspecies differentiation of strains was offered. Good association between MALDI profile distributions and the region of strain isolation have been found. Thus, the suggested direct MALDI mass-spectrometry profiling strategy, coupled with special analysis software, seems promising for the species identification of N. gonorrhoeae but is assumed insufficient for H. pylori species determination. At the same time, this would create a very good chance for an epidemiological study of such variable bacteria as H. pylori.
Acta Naturae. 2009;1(1):115-120
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The Role of Stacking Interactions in Complexes of Proteins with Adenine and Guanine Fragments of Ligands

Pyrkov T.V., Pyrkova D.V., Balitskaya E.D., Efremov R.G.
Acta Naturae. 2009;1(1):124-127
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Contributors’ Guidelines

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Acta Naturae. 2009;1(1):128-128
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