[Protein families specific for plastoms in small taxonomy groups of algae and protozoa].

Protein clustering is useful for refinement of protein annotation as well as cluster finding by its phylogenetic profile. We performed clustering of plastid encoded proteins from Rhodophyta as well as other plastid containing species related to Rhodophyta branch on species tree. Data base for cluster finding by its phylogenetic profile is available on http://lab6.

[A fast algorithm to build a supertree with a set of gene trees].

Important desired properties of an algorithm to construct a supertree (species tree) by reconciling input trees are its low complexity and applicability to large biological data. In its common statement the problem is proved to be NP-hard, i.e.

[Attenuation regulation of amino acid and amino acyl-tRNA biosynthetic operons in bacteria: comparative genomics analysis].

We performed a large-scale search for attenuation regulation in bacteria based on two original computer programs modeling attenuation regulation and multiple alignment along a phylogenetic tree. The programs are available from http://lab6.iitp.

[Reconstructing genes evolution along a species tree].

A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups.

[Modeling evolution of regulatory signals for gene expression in bacteria].

A model of evolution of a regulatory signal along the phylogenetic tree of species taking into account the secondary RNA structure is suggested. Based on this model, an algorithm is presented. It inputs the extant primary structure of a signal for the leaves of the phylogenetic tree and computes the primary and secondary structures of all the nodes.

[Mechanism of manganese transport regulation based on the long RNA helix in Brucella].

It has been found that divalent cation transporters of the Nramp family in cell phagosomes and bacteria that parasitize on the cell compete for metals, which is crucial for bacterial survival. Long helices were determined by means of our algorithm for each mRNA in the 5'-untranslated region in Brucella. Conserved long RNA helices were found in mRNA that encode manganese transporters as well as Ni-dependent Glyoxalase I.

[Model of genes expression regulation in bacteria by means of formation of secondary RNA structures].

In this article a model, first, classical attenuation RNA regulation of gene expression by means of transcription termination is offered. The model bases on representation about a macrostate of secondary structure in RNA regulatory region between a ribosome and a RNA polymerase, on the formulas of a resonant type defining the value of deceleration of a RNA polymerase by a set of hairpins in the same region. The special attention is given to selection of parameters of model.

[Identification of ancestral genes untroducing incongruence between gene and species tree].

The article introduces two novel approaches to detect potential incongruence between the protein family tree and the species tree. The first approach implements substitution of a known mapping of gene tree G into species tree S with somewhat analogous multivalued G-into-S "mapping". The second approach is based on elementary concepts from the fuzzy-set theory.

[Search for conservative secondary structures of RNA].

We suggest a new algorithm to search a given set of the RNA sequences for conserved secondary structures. The algorithm is based on alignment of the sequences for potential helical strands. This procedure can be used to search for new structured RNAs and new regulatory elements.

[Computer analysis of regulating metabolism of glycerol-3-phosphate in proteobacteria genome].

Comparative computer-assisted analysis was used to study putative GlpR-regulons responsible for metabolism of glycerol and glycerol-3-phosphate in genomes of alpha-, beta-, and gamma-proteobacteria. New palindromic GlpR-binding signals were identified in gamma-proteobacteria; consensus sequences being TGTTCGATAACGAACA for Enterobacteriaceae, wTTTTCGTATACGAAAAw for Pseudomonadaceae, and AATGCTCGATCGAGCATT for Vibrionaceae. The signals in alpha- and beta-proteobacteria were also identified: they contained 3-4 direct TTTCGTT repeats separated by 3-4 nucleotide pairs.

[Search for alternative secondary structures of RNA, regulating expression of bacterial genes].

Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. The attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted.

[Identification of the horizontal gene transfer based on phylogenetic data].

We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees.

[Tree reconciliation: reconstruction of species evolution by phylogenetic gene trees].

It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a "consensus" tree best fitting the given set of gene trees.

[Algorithms for isolating regulatory signals in DNA sequences].

An algorithm is proposed for extracting regulatory signals from DNA sequences. The algorithm complexity is nearly quadratic. The results of testing the algorithm on artificial and natural sequences are presented.

[The microflora in suppurative-catarrhal endometritis in cattle].

Microflora isolated from cattle with acute postnatal pus-catarrhal endometritis has been studied. It is shown that the given pathology is caused by associations of different bacterial species. 284 strains isolated from the uterus content of 63 sick animals have been identified, their properties being studied.

[Determinaton of intracellular immunoglobulins by means of immunofluorescence. 1. The standardization of monospecific luminescent antisera against human G-, A- and M-class immunoglobulins in bone marrow preparations from patients with paraproteinemic hemoblastosis].

To assess the specificity and the activity of fluorescent antisera against human G-, A-, M-classes the authors used in the capacity of a substrate, containing specific antigen preparations, bone marrow cells of patients with paraproteinemic hemoblastosis. The method of making the preparations used permitted sufficiently objective assessment of the activity and specificity of the mentioned monospecific fluorescent conjugates. As revealed, the bone marrow preparations could be stored at -70 degrees C for over one year.