Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).     

Host genetic risk factors for West Nile virus infection and disease progression

West Nile virus (WNV), a category B pathogen endemic in parts of Africa, Asia and Europe, emerged in North America in 1999, and spread rapidly across the continental U.S. Outcomes of infection with WNV range from asymptomatic to severe neuroinvasive disease manifested as encephalitis, paralysis, and/or death. Neuroinvasive WNV disease occurs in less than one percent of cases, and although host genetic factors are thought to influence risk for symptomatic disease, the identity of these factors remains largely unknown. We tested 360 common haplotype tagging and/or functional SNPs in 86 genes that encode key regulators of immune function in 753 individuals infected with WNV including: 422 symptomatic WNV cases and 331 cases with asymptomatic infections. After applying a Bonferroni correction for multiple tests and controlling for population stratification, SNPs in IRF3 (OR 0.54, p?=?0.035) and MX1, (OR 0.19, p?=?0.014) were associated with symptomatic WNV infection and a single SNP in OAS1 (OR 9.79, p?=?0.003) was associated with increased risk for West Nile encephalitis and paralysis (WNE/P). Together, these results suggest that genetic variation in the interferon response pathway is associated with both risk for symptomatic WNV infection and WNV disease progression.     

Diagnostics of thyroid cancer: Limitations of the existing methods and perspectives for future developments

A novel approach to the development of a precise method of intraoperative diagnostics of thyroid cancer has been proposed on the basis of fundamental study of proteasomes in malignant tumors of mammals and human. The method is based on estimation of proteasome activity in small fragments of the tumor and adjacent tissues.     

Statistical analysis of DNA sequences in the neighborhood of splice sites

Prediction of gene sequences and their exon-intron structure in large eukaryotic genomic sequences is one of the central problems of mathematical biology. Solving this problem involves, in particular, high-accuracy splice site recognition. Using statistical analysis of a splice site-containing human gene fragment database, some characteristic features were described for nucleotide sequences in the splicing site neighborhood, the frequencies of all nucleotides and dinucleotides were determined, and those with frequencies increased or decreased in comparison to a random sequence were identified. The results can be used in sequence annotation, splicing site prediction, and the recognition of the gene exon-intron structure.     

Current trends in mathematical simulation of the function of semicircular canals

The review covers new trends in the simulation of the processes associated with the functioning of the semicircular canal (SC) system, i.e., the component of the vestibular apparatus responsible for the detection of angular movement of the head. The basic factor determining these trends is an increasing role of computers both in the research of mathematical models and in the direct simulation (imitation) of the SC structure, processes proceeding in SCs and conditions of the experiment. As shown by the analysis of the literature, at present, it is possible to distinguish the following trends in the development of SC simulation: (1) reconstruction models; (2) micro-simulation; (3) integrated models; (4) simulation models; (5) alternative models of SC functioning. Examples are given of publications presenting the present-day research in these fields.     

The Difference in Low-Temperature Tolerance of Arabidopsis thaliana Plants and Its Ethylene-Insensitive Mutants Is Related to Activities of Antioxidant Enzymes

Russian Journal of Plant Physiology - Arabidopsis thaliana Heynh. (L.) plants of the Columbia ecotype (Col-0) and its ethylene-insensitive etr1-1 (ethylene resistant 1) and ein2-1 (ethylene...     

The effect of dehydroepiandrosterone on inflammatory response of astroglial cells

An increased interest in neuroinflammation is conditioned by its involvement in various pathological processes in the brain. Astrocytes play an important role in neuroinflammation, participating in its regulation, throwing out a large number of signaling molecules. Steroid compounds, actively produced by astrocytes, are of interest with regards to the regulation of inflammatory processes in the central nervous system. In the present work the effect of dehydroepiandrosterone (DHEA) on astroglial cells (cultured primary rat astrocytes) in a model of inflammation was studied. The inflammatory response was stimulated with lipopolysaccharide (LPS). Expression levels of pro-inflammatory factor TNFα, antinflammatory interleukin IL-10, and both pro- and antiinflammatory protein COX-2 were measured. The expression of IL-10, COX-2, and TNFα mRNA was determined by real-time PCR, COX-2 protein level by immunoblotting method, TNFα and IL-10 release by enzyme immunoassay. The effect of short-term (30 min) and long-term (24 h) exposure to DHEA was evaluated. It was shown that DHEA potentiates LPS-stimulated (1) increase in the IL-10 mRNA level; (2) IL-10 release; (3) does not affect TNFα level, and (4) exerts a weak pulsating bidirectional effect on COX-2. Using trilostane, an inhibitor of 3β-hydroxysteroid dehydrogenase, a key enzyme of DHEA metabolism, it was shown that DHEA metabolites make the main contribution to its effect. Thus, DHEA is of interest as a stimulant of anti-inflammatory processes in the brain.     

Ultrastructural Changes in Chloroplasts of Cucumis sativus L. and Secale cereale L. during Low-Temperature Hardening

Russian Journal of Plant Physiology - Chloroplast ultrastructural changes were investigated in chilling-sensitive (cucumber, Cucumis sativus L.) and cold-tolerant (winter rye, Secale cereale L.)...