Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization.

Oligonucleotide microchips are manufactured by immobilizing presynthesized oligonucleotides within 0.1 x 0.1 x 0.02 mm or 1 x 1 x 0.02 mm polyacrylamide gel pads arranged on the surface of a microscope slide. The gel pads are separated from each other by hydrophobic glass spacers and serve as a kind of 'microtest tube' of 200 pl or 20 nl volume, respectively. Fractionation of single-stranded DNAs is carried out by their hybridization with chip pads containing immobilized 10mers. DNA extracted separately from each pad is transferred onto a sequencing chip and analyzed thereon. The chip, containing a set of 10mers, was enzymatically phosphorylated, then hybridized with DNA and ligated in a site-directed manner with a contiguously stacked 5mer. Several cycles of successive hybridization-ligation of the chip-bound 10mers with different contiguously stacked 5mers and hybridized with DNA were carried out to sequence DNA containing tetranucleotide repeats. Combined use of these techniques show significant promise for sequence comparison of homologous regions in different genomes and for sequence analysis of comparatively long DNA fragments or DNA containing internal repeats.     

Persistence factors of Helicobacter pylori

Isolates of H. pylori from patients with chronic gastritis and peptic ulcer, were found to be capable of inactivating lysozyme and intercide (the bactericidal component of human leukocytic interferon). The expression and penetration capacity of their antilysozyme activity (ALA) and antiintercide activity was determined. The wide spread of ALA among H. pylori clinical isolates associated with inflammatory changes in bioptic specimens, confirmed the leading role of this microorganism in the pathogenesis of the gastric mucosal lesions. The retrospective analysis of clinical cases made it possible to recommend the use of the ALA sign as one of the criteria for choosing the scheme of eradication therapy even at the stage of the initial diagnostics of H. pylori infection.     

Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle

The tRNA tertiary core region is important for both tRNA stability and activity in the translation elongation cycle. Here we report the effects of mutating each of two highly conserved base pairs in the tertiary core of Phe-tRNA(Phe), 18-55 and 19-56, on rate and equilibrium constants for specific steps of this cycle, beginning with formation of aminoacyl-tRNA.EF-Tu.GTP ternary complexs and culminating with translocation of A-site-bound peptidyl-tRNA into the P-site. We find that codon-dependent binding of aminoacyl-tRNA to the A/T-site and proofreading of near-cognate tRNA are sensitive to perturbation of either base pair; formation of the ternary complex and accommodation from the A/T to the A-site are sensitive to 18-55 perturbation only, and translocation of peptidyl-tRNA from the A- to P-site is insensitive to perturbation of either. These results underline the importance of the core region in promoting the efficiency and accuracy of translation, and they likely reflect different requirements for structural integrity of the core during specific steps of the elongation cycle.     

Effect of Lighting Conditions on the Reproductive Success of Cypripedium calceolus L. (Orchidaceae,Liliopsida)

Biology Bulletin - Abstract—The influence of lighting conditions on the reproductive characteristics of Cypripedium calceolus L. was studied on the territory of the Komi Republic, where the...     

Influence of cycloferon on the biological properties of bacterial intracellular pathogens

The influence of cycloferon on some biological properties of pathogenic (Shigella spp., Salmonella spp., Francisella tularensis, Brucella spp.) and opportunistic (Escherichia coli, Staphylococcus spp.) microorganisms has been experimentally determined in vitro. As revealed in these experiments, the preparation used at concentrations under study considerably suppresses the antilysozyme and anticomplementary activity of Gram-negative intracellular parasites (shigellae, salmonellae, F. tularensis, Brucella). These data reveal one of the possible mechanisms of the action of cycloferon on intracellular parasites in acute and chronic bacterial infections.     

Analysis of Reproductive Parameters of Urban and Rural Population of Chuvashia

Genetic and demographic characteristics for urban and rural population of the Chuvash Republic (Chuvashes and Russians) were calculated based on 1122 questionnaires. The sibship sizes for Chuvashes were 2.05 (urban) and 2.78 (rural). For Russians these indices were 1.75 (urban) and 2.00 (rural), respectively. Crow’s index and its components were I _m = 0.04; I _f = 0.18; and I _tot = 0.22 for urban, and I _m = 0.07; I _f = 0.27; and I _tot = 0.36 for rural Chuvashes, respectively; and I _m = 0.04; I _f = 0.30; and I _tot = 0.35 for urban, and I _m = 0.03; I _f = 0.29; and I _tot = 0.33 for rural Russians, respectively.__________Translated from Genetika, Vol. 41, No. 6, 2005, pp. 850–854.Original Russian Text Copyright © 2005 by El’chinova, Zinchenko, Kirillov, Abrukova.     

Phototropic response features for different systematic groups of mesoplankton under adverse environmental conditions

Current trends in the application of bioindication methods are related to the use of submersible tools that perform real‐time measurements directly in the studied aquatic environment. The methods based on the registration of changes in the behavioral responses of zooplankton, in particular Crustaceans, which make up the vast majority of the biomass in water areas, seem quite promising. However, the multispecies composition of natural planktonic biocenoses poses the need to consider the potential difference in the sensitivity of organisms to pollutants.This paper describes laboratory studies of the phototropic response of plankton to attracting light. The studies were carried out on a model natural community that in equal amounts includes Daphnia magna, Daphnia pulex, and Cyclops vicinus, as well as on the monoculture groups of these species. The phototropic response was initiated by the attracting light with a wavelength of 532 nm close to the local maximum of the reflection spectrum of chlorella microalgae. Standard potassium bichromate was used as the model pollutant.The largest phototropic response value is registered in the assemblage. The concentration growth rate of crustaceans in the illuminated volume was 4.5 ± 0.3 ind (L min)⁻¹. Of the studied species, the phototropic response was mostly expressed in Daphnia magna (3.7 ± 0.4 ind (L min)⁻¹), while in Daphnia pulex, it was reduced to 2.4 ± 0.2 ind (L min)⁻¹, and in Cyclops vicinus, it was very small—0.16 ± 0.02 ind (L min)⁻¹. This is caused by peculiar trophic behavior of phyto‐ and zoophages. The addition of a pollutant, namely potassium bichromate, caused a decrease in the concentration rate of crustaceans in the attracting light zone, while a dose‐dependent change in phototropic responses was observed in a group of species and the Daphnia magna assemblage.The results of laboratory studies showed high potential of using the phototropic response of zooplankton to monitor the quality of its habitat thus ensuring the early diagnostics of water pollution. Besides, the paper shows the possibility of quantifying the phototropic response of zooplankton using submersible digital holographic cameras (DHC).