ActaNaturae

Forum

The Intellectual Property of Scientific Organizations and Rights to It

One of the most acute problems inhibiting the establishment of innovative economics in our country is the im-perfection 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.

VAK: Protecting High Standards in Science

On the role played by the High Attestation Commission of the Russian Federation (VAK) of Russia in manag-ing 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.

Living Systems in Russia are Evaluated in Terms of the Number of Scientific Publications Related to the Subject

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 different states.

The 50th Anniversary of the M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

By Academician V.T. Ivanov, Director of the Institute Under the February 20, 1959, Resolution of the Presidium of the USSR Academy of Sciences, the Institute for Chemistry of Natural Products was founded within the Academy’s Chemical Sciences Division. The institution would go on to play an important part in the development of Russian physical and chemical biology. The founding of the Institute was brought about by the rapid developments in the chemistry of bioactive compounds, the natural products among them, and reflected the growing importance of this field in understanding the mechanisms of biological processes and in development of new medicinal preparations.

The Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of the Russian Academy of Sciences (until 2003 the Novosibirsk Institute of Bioorganic Chemistry)

Rewiews

Modern Technologies for Creating Synthetic Antibodies for Clinical Application

Abstract—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); Fc?R (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).

Life and Death Decisions in the CD95 System: Main Pro-and Anti-Apoptotic Modulators

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 apoptosis of the death effector domain (DED)-containing proteins: pro-apoptotic protein procaspase-8 and anti-apoptotic protein c-FLIP. Gaining insights into these processes will improve our understanding of the pathogenesis of diseases such as cancer, autoimmunity and AIDS, and will open new approaches to rational treatment strategies.

Catalytic Bioscavengers Against Toxic Esters, an Alternative Approach for Prophylaxis and Treatments of Poisonings

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.
Key-words: bioscavengers, carbamates, cocaine, enzyme engineering, enzymotherapy, organophosphorus compounds
Abbreviations: AChE, acetylcholinesterase; BChE, butyrylcholinesterase; CaE, carboxylesterase; ChE, cholinesterase; DFPase, diisopropylfluorophosphate hydrolase; GMP, good manufacturing practice; GMP, good manufacturing practice, GST, glutathione S-transferase; OP, organophosphorus compound; OPAA, organophosphoric acid anhydrolase; OPAH, organophosphorus acid anhydride hydrolase; PEG, polyethylene glycol; PON1, paraoxonase 1; PTE, phosphotriesterase

The Regulation of Telomerase in Oncogenesis

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 (dominant-negative 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).

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical–molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers. Keywords: green fluorescent protein, molecular modeling, molecular dynamics, molecular mechanics Abbreviations: QM/MM - combined methods of quantum and molecular mechanics, MD - molecular dynamics, TD-DFT - the method of density functional theory depending on time

Research articles

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

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 GFR?1 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. Key words: embryonic stem cells, glial-derived neurotrophic factor, transfection, proliferation, immunocitochemistry, emroid bodies.

Analysis of Myelin Basic Protein Fragmentation by Proteasome

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.

Direct Matrix-Assisted Laser Desorption–Ionisation (MALDI) Mass-Spectrometry Bacteria Profiling for Identifying and Characterizing Pathogens

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. Key words: MALDI mass spectrometry, bacteria profiling, Neisseria gonorrhoeae, Helicobacter pylori.

The Interaction between the RNA-Dependent RNA-Polymerase of the Hepatitis Virus and RNA Matrices

Hepatitis C is one of the most dangerous and widespread viral diseases. Currently, the World Health Organization estimates that about 170 million people are infected with the hepatitis C virus (HCV), the causative agent of infection, in almost every country in the world. The RNA-dependent RNA-polymerase (R-RNAP, virus nonstructural protein) is a key fragment that carries out HCV genome replication. R-RNAP is about 65 kDA in molecular weight and localized on the endoplasmic reticulum membrane of infected hepatic cells by the C-tail ?-spiral transmembrane domain (21 a.r.).

The Genes of Antimicrobial Peptides for the Therapy of Intracellular Infections

Resistance to antibiotics is of great social and economic importance and is regarded as a threat to the national security of any country and the global community as a whole. Among the bacterial agents of different infections, resistance to some antibiotics can reach 98%. Infections caused by antibiotic-resistant strains are distinguished by their significant duration, they often require hospitalization, they increase the length of hospi-tal stay, and they often worsen the prognosis for a disease [1]. If the chosen medicines turn out to be ineffective, the doctors have to use second- or third-order medicines, which are often rather expensive, less safe, and not always available. All these facts increase direct and indirect eco-nomic expenditures, as well as cause a risk of antibiotic-resistant strain propagation. Causative agents of intracellular infections such as my-coplasmas and chlamydiae are characterized by high antibiotic resistance. Treating mycoplasmosis and clamidiosis with a wide range of antibiot-ics is almost ineffective due to the quick formation of resistance to these medicines, and, as a result, the development of virus persistence in the organism.