This paper describes the SNP-MED modular computer-based information system for estimation of the influence of single nucleotide polymorphisms (SNPs) on the function of genes associated with the risk of socially significant diseases. The system includes software components Genomics, Proteomics, Gene networks and the Information resource database (BDIR).

Six regulatory SNPs (single nucleotide polymorphisms) of two human APC and MLH1 genes (rs75996864, rs76241113, rs78037487, rs80112297, rs80313086 and rs1800734) were evaluated by the previously developed rSNP_Guide method to compute the significance of the changes for binding of the SNP region with 40 transcription factors. For each SNP, all analyzed proteins were ranged according to the significance of the changes for protein binding to the alleles evaluated by Student’s t-test. We found that rs75996864, rs76241113, rs78037487, rs80112297, and rs80313086 of APC, as well as rs1800734 of MLH1 in humans concerned to the greatest extent the binding of transcription factors NF-Y, NFkB, c-Myb, RAR, YY-1, and Sp-1, which are known to be involved in colon cancer development. Our results substantiate investigation of associations of rs75996864, rs76241113, rs78037487, rs80112297, and rs80313086 in the APC gene with colon cancer by using commonly accepted medical and genetic protocols.

Web-service SNP_TATA_Comparator has been developed for using experimentally proven in silico evaluation of in vivo biochemical manifestations of SNPs in the core promoter regions of human genes associated with diseases on the base of the TBP/TATA complex equilibrium equation (TBP is TATA binding protein). Data of individual deviations from the reference human genome (Ensembl, rel. 68, i.e. the variant of human genome commonly accepted as datum in comparison analysis) are accessible for free in the real-time mode. Also, data from the GENCODE database (rel. 17) are automatically invoked. The reported Web service SNP_TATA_Comparator is designed for personalized medicine using individual genomes in diagnosis, monitoring, prevention, and treatment.

We present the BioUniWA system for automatic generation of web services for unified access to resources in the field of bioinformatics. The BioUniWA system was originally designed as the BioInfoWF development system to support access to computing modules and pipelines through web services. BioUniWA can automatically generate web-based applications for computational modules and pipelines whose formal descriptions are defined by a language based on XML. In the future, one will be able to use these web-based applications in a variety of bioinformational systems, such as Taverna or Galaxy, as well as directly in the source code of applications to be developed. We have designed a tool that greatly simplifies the annotation of computing modules and schemes of pipelines, as well as their publication via Internet.

BioUniWA is distributed under a free GNU general public license. The distribution package and user documentation are available at BioUniWA http://bioinfowf.bionet.nsc.ru.

We present a computer package for analyzing the structure-functional organization and evolution of biological, social and other networks. The programs allows investigation of not only the global network architecture, but also its local properties, revealing key regulators and structure-functional modules. Also, the network evolution can be traced. The package has been tested with two gene networks: the co-authorship network of biomedical papers and the biomedical term network.

Neuronal synaptic contacts are among the basic elements that determine the plasticity of the nervous system. Changes in the efficiency of synaptic transmission mediate sensation, conduction of excitation, learning, and memory. Dendritic spines are the postsynaptic part of excitatory synapses in higher divisions of mammalian brains. Protein–protein networks of spine microdomains form the functional system of neuronal synapses. Reconstruction of the conceptual model of molecular interactions has been performed. The model represents activity-dependent changes of the synaptic transmission efficiency, integration of excitation in the local dendritic network of a neuron, and prolonged maintenance of the new level of neurotransmission.

The scope of neurobiological studies has been greatly expanded in the last years. It is accompanied by accumulation of a huge body of experimental data on the structure, function and evolution of the nervous system at different hierarchical levels of its organization. High-throughput sequencing technologies and microarray tests permit the expression of thousands of genes to be analyzed with regard to cell location in the brain. Methods of gene expression analysis are briefly reviewed in the context of brain research. We have analyzed specific features of genes differentially expressed in brain cells. Some genes overexpressed in brain tissues are associated with neurological diseases. The numbers of exons and active transcripts in genes differentially expressed in different organs are considered. Statistically significant difference in such parameters is shown for genes intensely expressed in the brain and other organs. Examples of such differentially expressed genes associated with neurological deceases are presented.

Evaluation of gene expression efficiency in different organisms is a vital task of modern biology. Microorganisms that feed on humans and pets are particularly interesting. In this work, bioinformatical analysis of 62 Mycoplasma strains is performed. It has been shown that translation efficiency in these organisms depends on the number of potential secondary structures in genes and does not depend on codon compositions. Several species with low concentrations of local inverted repeats in genes have been found. Phylogenetic analysis shows that this feature may be associated with their environment. High concentrations of local inverted repeats, not typical of other Mycoplasma species, have been found in the translation start regions of M. haemofelis genes.

We have studied properties of bacterial strains isolated from hot springs in the Northern Baikal region, Baikal Rift Zone, known to have a wide range of growth conditions (pH, temperature, and carbon sources). The phylogenetic analysis and microbiological studies show that thermophilic strains belonging to the Geobacillus stearothermophilus,Anoxybacillus flavithermus, and Thermoactinomyces vulgaris species express lipolytic activity. The isolated Geobacillus stearothermophilus strains grow at up to 70 °С in a wide pH range (5–10). The isolates of the Anoxybacillus genus can grow at 60–70 °С and рН ≤ 11. Thermoactinomyces vulgaris Gus-2-1 has a narrower growth condition range: 50–60 °С and рН 7–10. Of the strains with lipolytic activity isolated in this study, Geobacillus stearothermophilus is the most promising for further studies of secreted lipases.

A new strain, Geobacillus stearothermophilus 22 was isolated from the Garga hot spring in the Bargusin Valley, Baikal Region, Russia. The morphology and biochemistry of the strain were analyzed, and the  genomewide sequencing was conducted. The sequence was subjected to bioinformatic analysis. Nucleotide sequences (contigs) of the strain were found to be similar to the genome of the thermophilic strain G. kaustophilus Y412MC52. The proteome of the new strain was analyzed. Fragments associated with hemicellulases (endoxylanase, beta xylosidase, and arabinofuranosidase) and the endoxylanase enzyme were detected.

Properties of thermostable lipases from Geobacillus bacteria are considered. The enzymes are divided into groups with regard to their thermostability. Coordinated amino acid substitutions are demonstrated in the highly thermostable group (half-inactivation time > 1000 min); V198A, Q203E, V204I, Q217E; and V294I, P306A, T307A, D312S, R313H, E316G, V324I, S334N, A343T. The hydrophilic moment of α helices, correlating with the charge and polarity of amino acid in the region, exerts the most significant influence on enzyme thermostability. Most thermostable lipases are characterized by structural stabilization of the lid domain in the 198А-217Е region.

Thermophilic bacteria are extensively used in biotechnology. Species of the genus Geobacillus rank among the most promising ones. Current methods of the genetic and metabolic engineering of these microorganisms are considered. Examples of their use in various branches of biotechnology are presented.

A mathematical model of the ethanol and lactic acid biosynthesis in the cells of Geobacillus spp. developed and adapted to the available experimental data is presented. It is shown that the mathematical model allows in silico design of genetic engineering experiments with the Geobacillus spp. bacterium and prediction of the dynamics of changes in synthesized ethanol and lactic acid concentrations depending on the molecular manipulations with the activity of enzymes of the metabolic system.

This paper introduces classes of segregation models, which describe the inheritance of a quantitative trait, in extended diallelic recombinant inbred crosses. The distinctive feature of the method is usage of the multiple-QTL approach and incorporation of epistatic interactions of loci groups. Solutions that would describe experimental data set to an accuracy of environmental variance are sought in the constructed classes of models. Then linkage analysis is performed: model loci positions of the found solutions are mapped on chromosomes. The search procedure and linkage analysis have been tested with real data on cerebellum weight in laboratory mice as a quantitative trait. The developed software is briefly described.

One way to study the variability of biologic objects is their geometrization: the objects are presented by points in a multidimensional space in such a way that the distances between the points would be best consistent with the dissimilarities between objects. If the dissimilarities between the objects are Euclidean distances, this task (up to translation, rotation and reflection) is solved by metric scaling. We consider the metric properties of some well-known evolutionary distances of nucleotide sequences. It is shown that the Jukes-Cantor and Kimura distances are not metrics. We introduce a new Kimura distance analog, the PQdistance. It is shown that the p and PQ distances are the squares of Euclidean metrics named Ep-distance and EPQ-distance, respectively. The applicability of the EPQ distance is illustrated by the example of a cytochrome b sequence set of 12 rodent species from West Siberia and Altai, taken from the GenBank, and compared with the results of the use of the LogDet-distance.

This is a short review of the COMSOL Multiphysics package. Model building in COMSOL and methods of biophysical problem specification are demonstrated. Examples of the investigation of several problems in plant biomechanics and morphodynamics are considered.

The experimental data obtained to date provided grounds for certain concepts of the stem cell niche regulation in shoot apical meristem. Mathematical modeling is used for checking their consistency and coherence with experimental evidence. In this paper, we summarize mathematical models of stem cell niche regulation offered by different authors, analyze the experimental base and working hypotheses formalized in these models, and identify methodological differences in the approaches to the construction of these models.

Rapid and accurate methods of microorganism identification are essential in various human activities. They include primarily clinical diagnostics. In addition, they are in demand in environment monitoring, harmacology, food industry, research, etc. There are diverse approaches to microbe identification: phenotyping, genotyping, chemotaxonomy, direct protein profiling, etc. In this work, the effects of various growth conditions, such as temperature, growth time, and nutrition medium, on the reproducibility of microbe identification by MALDI-TOF mass spectrometry are considered by the example of three Geobacillus stearothermоphilus strains.

Identification of microorganisms from their protein profiles, or direct protein profiling, has been extensively used in the last decade. Being sufficiently accurate and specific, this method is fast and inexpensive. In this review, current notions of the potential of this method are considered and it is compared with other approaches to microorganism identification.

Miscanthus cv. Soranovskii was registered as a state breeding achievement in 2013. On the base of phenotyping and DNA sequencing, the new crop was identified as Miscanthus sacchariflorus. The development of methods for converting its biomass to sugar-containing substrate for biotechnological use is in progress. Effects of mechanical and chemical treatments combined with enzymatic hydrolysis on sugar production from Miscanthus biomass have been studied. The best procedure includes grinding to ~100 μm particles followed by treatment with calcium hydroxide. Enzymatic hydrolysis of such materials yields substrates containing 10 to 15 g/L reducing sugars.