[Show abstract][Hide abstract] ABSTRACT: Isolation of newmicroalgal strainswith unique and valuable properties fromdiverse environmental conditions is an important starting point for the establishment of high quality feedstock for biofuel production. In this study, we have isolated twelve strains of microalgae, belonging to the genera Chlorella, Botryococcus, Scenedesmus, Nannochloris and Bracteacoccus from samples obtained from various natural sources by flow cytometry. Five of them were selected for further evaluation, as lipid producers on the basis of Nile Red fluorescent microscopy screening. Analysis of the biomass in the exponential and stationary phases of growth showed that the strain Scenedesmus abundans A1175 has the highest specific growth rate (0.20 ± 0.01 d-1), biomass productivity (73.82 ± 4.53 mg L-1 d-1) and lipid content (44.4 ± 2.7%) in nitrogen depleted conditions. Strains Chlorella vulgaris A1123 and S. abundans A1175 have a high total content of saturated (SFA) and monounsaturated (MFA) fatty acids (67.0% and 72.8% respectively). S. abundans A1175 also had low polyunsaturated fatty acid (PUFA) content that would allow for its use as a source of high quality biofuels.
[Show abstract][Hide abstract] ABSTRACT: The influence of polymorphic variations of the gene encoding serotonin transporter (5-HTT) on individual characteristics of cerebral hemodynamics (detected by means of functional magnetic resonance imaging (fMRI) under conditions of the performance of the tasks of the “Stop–Signal” experimental paradigm) was studied in the work. The 5-HTT gene polymorphic variants were determined by means of allelespecific PCR with DNA isolated from the blood of subjects as a matrix. Altogether, 24 subjects (eight individuals with the LL genotype, eight with the LS genotype, and eight with the SS genotype) were studied. In the experiments, the subjects either push a button after the appearance of a target stimulus (Go condition) or suppressed already prepared movement (Stop condition). Differences associated with the genotype were observed in hemodynamic responses registered in areas of the cuneus (occipital lobe of the cerebral cortex), as well as medial frontal and inferior frontal gyri (frontal lobes of the cerebral cortex). The SS genotype carriers demonstrated a significantly larger contrast between fMRI responses under Go and Stop conditions as compared with the LL and LS genotype carriers (which can be interpreted as an index of a greater intensity of the activation processes in them and a decreased capacity for the suppression of inadequate movements). Theoretically, individuals with the SS genotype have an advantage over individuals with LL and LS genotypes when making a decision with a lack of time; however, they deal worse with situations requiring the suppression of inadequate behavioral responses.
No preview · Article · Nov 2015 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: Over 10000 scientific studies have been dedicated to mathematical modeling and simulations of biologic systems at all levels of their organization. At the Institute of Cytology and Genetics, Novosibirsk, software tools are being developed for the analysis of the propagation of ideas/opinions in social systems with regard not only to social but also biological (genetic, physiological, and psychological) factors. The consideration of more factors in these models allows better analysis of social processes, more precise predictions, and smarter strategies for process control. Agent-based modeling is an approach that is widely used for these tasks. In the present study, the simple model introduced by Bonabeau (2002) is considered and extended. In the original model, the complex behavior of the system arises on the basis of two different strategies of agent behavior. The extended sociobiological model describes more sophisticated agents with additional characteristics. It allows social and biological submodels to be combined within a common software tool. As the number of agent parameters (dissatisfaction, enmity, and mobility) increases, the dynamic variability of the model increases manifold times. The addition of the dissatisfaction parameter enables an agent to compare his success with other agents, which may be interpreted as self-esteem. The model can be further improved by the addition of various mechanisms of idea and opinion transmission, which will make it possible to model the dissemination of ideas within populations (and, in addition, the spread of diseases, rumors, and any sort of information), to model a heterogeneous distribution of parameters within population, and to consider different topologies of social networks. Nevertheless, even now the “aggressor–defender” model can simulate many social and biological phenomena.
Full-text · Article · Nov 2015 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: Modern trends in the use of DNA in nanotechnology and biotechnology are aiming to develop new methods of analysis of DNA molecules based on the developing instrument base. We have developed a method of mild nondestructive ablation to transfer DNA molecules into an aerosol phase using terahertz radiation. In this paper, the size of DNA nanoparticles in the gas phase was measured using the diffusion aerosol spectrometer. The changes taking place with DNA in the gas phase were visualized using the atomic force microscopy (AFM). A comparison of the measurements of the diffusion sizes of the plasmid pUC18 aerosol particles with measurements using AFM gives grounds to assume that the process of condensation of the DNA molecules takes place in the gas phase. A model was constructed according to modern concepts of the process of DNA condensation and formation of globules. The theoretical calculations are in good agreement with the experimental results. The experimentally estimated persistence length of the DNA in the gas phase was about 0.5 nm, which indicates the absence of a distributed charge on the surface of the DNA in the gas phase and the nonionizing nature of terahertz radiation. The study of DNA conformation in the gas phase will expand knowledge of DNA compaction in natural and artificial conditions.
Full-text · Article · Aug 2015 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: The development of in vitro technologies has produced new experimental information on protein binding onto DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent in vitro selected sequences reflect the actual structures of the real transcription factor (TF) binding sites. The Kullback–Leibler divergence has been applied to the comparison of frequency matrices of TF binding sites constructed on sets of artificially selected sequences and real sites. The similarity of core sequences of real and artificial sites has been observed for 80% of all TFs studied. For 20% of TFs, in vitro selected binding site sequences have a broader range of permissible significant nucleotides not found in real sites. The optimal lengths of DNA sequences containing real binding sites, at which the sites are recognized most accurately, are estimated by the weight matrix method. For approximately 80% of the TFs studied, the optimal binding site length notably exceeds the lengths of the core sequences, as well as the lengths of in vitro selected sites. The detected features of in vitro selected TF binding sites impose constraints on their use in the development of computer-assisted methods of the recognition of candidate sites in genomic sequences.
Full-text · Article · Jul 2015 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: The review describes integrated experimental and computer approaches to the investigation of the mechanisms of transcriptional regulation of the organization of eukaryotic genes and transcription regulatory regions. These include (a) an analysis of the factors affecting the affinity of TBP (TATA-binding protein) for the TATA box; (b) research on the patterns of chromatin mark distributions and their role in the regulation of gene expression; (c) a study of 3D chromatin organization; (d) an estimation of the effects of polymorphisms on gene expression via high-resolution Chip-seq and DNase-seq techniques. It was demonstrated that integrated experimental and computer approaches are very important for the current understanding of transcription regulatory mechanisms and the structural and functional organization of the regulatory regions controlling transcription.
[Show abstract][Hide abstract] ABSTRACT: The review describes combined experimental and computational approaches to the investigation of the mechanisms of transcriptional regulation of eukaryotic genes and organization of transcription regulatory regions. These include (a) an analysis of the factors affecting the affinity of TBP (TATA-binding protein) for the TATA box; (b) research on the patterns of chromatin mark distributions and their role in the regulation of gene expression; (c) a study of 3D chromatin organization; (d) an estimation of the effects of polymorphisms on gene expression via high-resolution ChIP-seq and DNase-seq techniques. It was demonstrated that combined experimental and computational approaches are very important for the current understanding of transcription regulatory mechanisms and the structural and functional organization of the regulatory regions controlling transcription.
No preview · Article · Apr 2015 · Russian Journal of Genetics
[Show abstract][Hide abstract] ABSTRACT: The adaptation of subterranean rodents, which dig passages with their front teeth, to underground life presumes the formation of protection mechanisms against inhaling dust particles of different size when digging. One such mechanism can be a specific pattern of air-flow organization in the nasal cavity. To verify this assumption, we conducted a comparative study of the geometry and aerodynamics of nasal passages of a typical representative of subterranean rodents, the mole vole, and a representative of ground rodents, the house mouse. Numerical modeling of air flows and the deposition of micro- and nanoparticle aerosols indicate that sedimentation of model particles over the whole surface of the nasal cavity is higher in the mole vole than in the house mouse, while, on the contrary, particle deposition on the surface of the olfactory epithelium is much less in the burrowing rodent as compared to the ground rodent. The adaptive significance of the latter was substantiated by an experimental study on the inflow of hydrated manganese oxide MnO · (H2O)
and Mn ion nanoparticles from the nasal cavity into brain. It has been shown with use of magnetic resonance tomography (MRT) that there is no difference between the studied species with respect to the inflow of particles or ions by the olfactory bulb when they are introduced intranasally. Meanwhile, when inhaling a nanoparticle aerosol of MnCl2, the Mn deposition in the house mouse’s olfactory bulbs significantly exceeds that in the mole vole’s bulbs. Thus, the morphology of nasal passages as a factor determining the aerodynamics of upper respiratory tract ensures more efficient protection of both the lungs and brain against inhaled aerosols for burrowing rodents than for ground ones.
[Show abstract][Hide abstract] ABSTRACT: Terahertz (THz) radiation was proposed recently for use in various applications, including medical imaging and security scanners. However, there are concerns regarding the possible biological effects of non-ionising electromagnetic radiation in the THz range on cells. Human embryonic stem cells (hESCs) are extremely sensitive to environmental stimuli, and we therefore utilised this cell model to investigate the non-thermal effects of THz irradiation. We studied DNA damage and transcriptome responses in hESCs exposed to narrow-band THz radiation (2.3 THz) under strict temperature control. The transcription of approximately 1% of genes was subtly increased following THz irradiation. Functional annotation enrichment analysis of differentially expressed genes revealed 15 functional classes, which were mostly related to mitochondria. Terahertz irradiation did not induce the formation of γH2AX foci or structural chromosomal aberrations in hESCs. We did not observe any effect on the mitotic index or morphology of the hESCs following THz exposure.
Full-text · Article · Jan 2015 · Scientific Reports
[Show abstract][Hide abstract] ABSTRACT: An association of the level of personal anxiety with polymorphic variants of the gene encoding serotonin transporter (5-HTT) in 57 Russian residents of Siberia and 62 Tuvinians was studied. The 5-HTT gene polymorphic variants were determined be means of allele-specific PCR with DNA isolated from the blood of subjects as a matrix. The level of explicit anxiety was established by means of Spielberger–Khanin questionnaire; implicit anxiety was established by means of associative test. Indices of aggressiveness, impulsiveness, behavioral activation and inhibition systems (BAS and BIS) were additionally determined in each subject. The 5-HTT gene S-allele was significantly more frequently found in the Tuvinians, while the L allele was more common in Russians. The implicit and explicit anxiety levels were lower in carriers of the LL genotype than in carriers of the SS genotype; LS heterozygotes demonstrated intermediate values of anxiety. The sex and ethnicity factors were associated with the level of explicit (but not implicit) anxiety. Tuvinian men with the SS genotype demonstrated a low explicit anxiety level, while Russian men with this genotype demonstrated high anxiety level. No intergroup differences were found in women with the SS genotype. An association of 5-HTT gene polymorphic variants with BAS indices and an inclination to verbal aggression was also detected. The data can be interpreted as an index of differences in the direction of anxiety in different cultures. Theoretically, genetically highly anxious Tuvinian men are afraid to show fear, since manifestation of fear is condemned in their social environment.
No preview · Article · Dec 2014 · Journal of Genetics and Breeding
[Show abstract][Hide abstract] ABSTRACT: Inhalation of air-dispersed sub-micrometre and nano-sized particles presents a risk factor for animal and human health. Here, we show that nasal aerodynamics plays a pivotal role in the protection of the subterranean mole vole Ellobius talpinus from an increased exposure to nano-aerosols. Quantitative simulation of particle flow has shown that their deposition on the total surface of the nasal cavity is higher in the mole vole than in a terrestrial rodent Mus musculus (mouse), but lower on the olfactory epithelium. In agreement with simulation results, we found a reduced accumulation of manganese in olfactory bulbs of mole voles in comparison with mice after the inhalation of nano-sized MnCl2 aerosols. We ruled out the possibility that this reduction is owing to a lower transportation from epithelium to brain in the mole vole as intranasal instillations of MnCl2 solution and hydrated nanoparticles of manganese oxide MnO · (H2O)x revealed similar uptake rates for both species. Together, we conclude that nasal geometry contributes to the protection of brain and lung from accumulation of air-dispersed particles in mole voles.
Full-text · Article · Oct 2014 · Proceedings of the Royal Society B: Biological Sciences
[Show abstract][Hide abstract] ABSTRACT: Purpose of the study was to track permanent proteins of urine proteome in the 520-day isolation experiment at the IBMP Ground-Based Test Facility with controlled environmental parameters. Object of the investigation was urine sampled from 6 normal male subjects at the age of 25 to 37 years. Second morning aliquots were gathered during baseline data collection, on days 50, 93, 124, 153, 180, 251, 274, 303, 330, 371, 400 and 427 of isolation, and in 7 days after its completion. Samples were subject to chromatography-mass spectrometry; results were analyzed with the help of bioinformatics resources. The following 7 permanent proteins were observed in urine over the entire length of the investigation: epidermal growth factor, polymer immunoglobulin receptor, plasma serine protease inhibitor, protein AMBP, keratin, type II cytoskeletal 1, collagen alpha-1 (vi) chain, serum albumin.
No preview · Article · Jul 2014 · Aviakosmicheskaia i ekologicheskaia meditsina = Aerospace and environmental medicine
[Show abstract][Hide abstract] ABSTRACT: We describe development and application of the new SNP–MED modular software system, designed to examine the influence of singlenucleotide polymorphisms (SNPs) on the function of genes associated with the risk of socially significant diseases. The SNP–MED system includes Genomics, Proteomics, and Gene Networks’ software components, and the Information Resource Database.
Full-text · Article · Jun 2014 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: The TATA-binding protein (TBP) is a key part of the transcription complex of RNA polymerase II. Alone or as a part of the basal transcription factor TFIID, TBP binds the TATA box located in the core region of the TATA-containing promoters of class II genes. Previously, we studied the effects of single nucleotide polymorphisms (SNPs) on TBP/TATA-box interactions using gel retardation assay. It was demonstrated that most SNPs in the TATA boxes of some human gene promoters cause a 2- to 4-fold decrease in TBP/TATA affinity, which is associated with an increased risk of hereditary diseases, such as β thalassemias of diverse severity, hemophilia B Leyden, myocardial infarction, thrombophlebitis, lung cancer, etc. In this work, the process of TBP/TATA complex formation has been studied in real time by a stopped-flow technique using recombinant human TBP and duplexes, which were identical to the TATA box of the wild-type and a SNP-containing triosephosphate isomerase gene promoter and were fluorescently labeled by the Cy3/Cy5 FRET pair. It has been demonstrated for the first time that real-time binding of TBP to the TATA box of the TPI gene promoter is complete within 10 s and is described by a single-stage kinetic model. The complex formation of TBP with the wild-type TATA box occurs 5.5 times faster and the complex dissociation occurs 31 times slower compared with the SNPcontaining TATA box. Within the first seconds of the interaction, TBP binds to and simultaneously bends the TATA box. Importantly, the TATA box of the wild-type TPI gene promoter requires lower TBP concentrations compared to the TATA box containing the -24T → G SNP, which is associated with neurological and muscular disorders, cardiomyopathy, and other diseases.
[Show abstract][Hide abstract] ABSTRACT: Approaches are considered for the search for novel sources of non-food, renewable raw materials for third-generation biofuel production, namely, microalgae strains inhabiting natural systems of Western Siberia. This regional biodiversity survey is of great interest in connection with the vast habitat areal and the limited research on the properties of microalgae. During the work, a number of strains was isolated; one of them, Chlorella spp. A1125, has the necessary characteristics for cultivation in a pilot photobioreactor, including a maximum lipid productivity of 0.081 g/L (23% of the dry cell weight) with growth in minimal media. The strain is characterized by the content of both saturated fatty acids C16:0 (25%) and unsaturated fatty acids C16:2 (16%) and C18:2 (27%), making it a promising candidate for the third-generation biofuel production.
No preview · Article · Nov 2013 · Russian Journal of Genetics: Applied Research
[Show abstract][Hide abstract] ABSTRACT: The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are relevant to predict the efficacy of potential drugs against virus or host targets. One of the promising targets for development of new drugs is the viral NS3 protease. Here we developed a stochastic model of the subgenomic HCV replicon replication in Huh-7 cells and in the presence of the NS3 protease inhibitors. Along with consideration of the stochastic nature of the subgenomic HCV replicon replication, the model takes into account the existence and generation of main NS3 protease drug resistant mutants, namely BILN-2061 (A156T, D168V, R155Q), VX-950 (A156S, A156T, T54A) and SCH-503034 (A156T, A156S, T54A). The model reproduces well the viral RNA kinetics in the cell from the moment of the subgenomic HCV replicon transfection to steady state, as well as the viral RNA suppression kinetics in the presence of NS3 protease inhibitors BILN-2061, VX-950 and SCH-503034. We showed that the resistant mutants should be taken into account for the correct description of biphasic kinetics of the viral RNA suppression. The mutants selected in the presence of different inhibitor concentrations have maximal replication capacity in the given inhibitor concentration range. Our model can be used to interpret the results of the new anti-HCV drug testing in replicon systems, as well as to predict the efficacy of new potential drugs and optimize the mode of their use.