Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes.

Background: RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded, the significance of the differences for rare mRNAs can be weakened by the presence of biological and technical noise.

Results: We have developed a method for cleaning RNA-seq data, which improves the detection of differentially expressed genes and specifically genes with low to moderate transcription.

Thermostable Lichenase from Clostridium thermocellum as a Host Protein in the Domain Insertion Approach.

Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.

Expression of Soluble Active Interferon αA in Escherichia coli Periplasm by Fusion with Thermostable Lichenase Using the Domain Insertion Approach.

A recombinant DNA in which the interferon αA (IFN-αA) gene sequence is integrated into a loop region of the gene coding thermostable lichenase was constructed. This approach of insertion fusion with thermostable lichenase is advantageous in terms of increasing the solubility, stability, and production of the fusion partner in soluble form in general and in the periplasm of bacterial cells in particular. Thus, the insertion of IFN-αA into the loop (53 a.

The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications.

The main specific features of β-1,3-1,4-glucanases (or lichenases, EC 3.2.1.

The Trametes hirsuta 072 laccase multigene family: Genes identification and transcriptional analysis under copper ions induction.

Laccases, blue copper-containing oxidases, ≿ an play an important role in a variety of natural processes. The majority of fungal laccases are encoded by multigene families that express closely related proteins with distinct functions. Currently, only the properties of major gene products of the fungal laccase families have been described.

Clostridium thermocellum thermostable lichenase with circular permutations and modifications in the N-terminal region retains its activity and thermostability.

The Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase) displays a high thermostability and specific activity and has a compact protein molecule, which makes it attractive, in particular, for protein engineering. We have utilized in silico analysis to construct circularly permuted (CP) variants and estimated the retained activity and thermostability. New open termini in the region of residues 53 or 99 in two lichenase CP variants (CN-53 and CN-99) had no effect on their activity and thermal tolerance versus another variant CP variant, CN-140 (cut in the region of residue 140), which displayed a dramatic decrease in the activity and thermostability.

[Range of Gene candidates involved in biosynthesis of laccase from basidiomycete Trametes hirsuta].

A comparative analysis of transcripts from the basidiomycota T. hirsuta grown with and without an inducer of the laccase biosynthesis was carried out. Methods of subtraction hybridization and massive parallel sequencing were used for this purpose.

[Expression of heterologous genes in plant systems: new possibilities].

The basic methods used in current practice for stable and transient expression of heterologous genes in plants are presented and compared. The key areas of research in the heterologous expression of genes in plants have been identified by analyzing literature and experimental data: modeling of metabolic pathways; creation of marker-free transgenic plants; the search for new regulatory elements and plant genes influencing the efficiency of expression of heterologous genes in plants; development of new methods for analyzing of transgenic plants and new approaches to the expression of heterologous genes in plants.

[Set of module vectors for stable or transient expression of heterologous genes in plants].

A set of module vectors for stable or transient gene expression in plants was constructed with regard to the majority of factors ensuring efficient heterologous gene expression in plants. The vectors are convenient to clone new regulatory elements and genes of interest via simple molecular cloning procedures. The vectors can be used to obtain transgenic plants with stable heterologous gene expression as well as to achieve transient expression because one vector includes the gene for the tomato bushy stunt virus p19 protein, which acts as a suppressor of posttranscriptional gene silencing.

[Efficiency of evaluating the carcinogenicity of chemical substances in short-term tests and the SAR model].

The efficiency of estimating the carcinogenic activity of chemical substances was compared for five short-term tests and structure-activity relationships (SAR) analysis. The sample included 84 substances with known biological testing results obtained by the Ames test, bacterial SOS chromotest (SOS), chromosome aberration (CA) cytogenetic test, sister chromatid exchange (SHE) test, and gene mutation (GM) test with mammalian cells in vitro and by carcinogenicity assays in rodents in vivo. Structural descriptors were selected using an original database, which included the structural formulas of substances with known carcinogenic activity in rodents.

[Dependence of the carcinogenicity of nitro compounds on their structural characteristics].

A new approach to the description of quantitative structure-activity relationships (QSAR analysis) based on compound descriptors has been used. The effect of the structural characteristics of nitric compounds on their carcinogenicity has been studied. It has been found that the carcinogenicity of nitric compounds is determined by the presence of furyl and/or azole heterocycles not condensed with benzene rings in their molecular structures.

[Use of ensemble structural descriptors for increasing the efficiency of QSAR study].

A new concept of describing the dependence of the mutagenic activity of a chemical substance on its structure (QSAR analysis) is presented. It involves ensemble descriptors, which are combinations of unrelated fragments of molecular structure. Software has been developed to generate various structural fragments of molecules and their combinations (ensembles) and select ensemble descriptors of statistical significance for the biological activity of a chemical.