Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding

The aa(3)-type cytochrome c oxidases from mitochondria and bacteria contain a cation-binding site located in subunit I near heme a. In the oxidases from Paracoccus denitrificans or Rhodobacter sphaeroides, the site is occupied by tightly bound calcium, whereas the mitochondrial oxidase binds reversibly calcium or sodium that compete with each other. The functional role of the site has not yet been established. D477A mutation in subunit I of P. denitrificans oxidase converts the cation-binding site to a mitochondrial-type form that binds reversibly calcium and sodium ions [Pfitzner, U., Kirichenko, A., et al. (1999) FEBS Lett. 456, 365-369]. We have studied reversible cation binding with P. denitrificans D477A oxidase and compared it with that in bovine enzyme. In bovine oxidase, one Ca(2+) competes with two Na(+) for the binding, indicating the presence of two Na(+)-binding sites in the enzyme, Na(+)((1)) and Na(+)((2)). In contrast, the D477A mutant of COX from P. denitrificans reveals competition of Ca(2+) (K(d) = 1 microM) with only one sodium ion (K(d) = 4 mM). The second binding site for Na(+) in bovine oxidase is proposed to involve D442, homologous to D477 in P. denitrificans oxidase. A putative place for Na(+)((2)) in subunit I of bovine oxidase has been found with the aid of structure modeling located 7.4 A from the bound Na(+)((1)) . Na(+)((2)) interacts with a cluster of residues forming an exit part of the so-called H-proton channel, including D51 and S441.     

Soybean lectin as a component of a composite biopreparation involving Bradyrhizobium japonicum 634b

The effects of the composite biopreparation Bralec (involving the soybean-specific root nodule bacterium Bradyrhizobium japonicum strain 634b and soybean lectin at concentrations of 500, 50, and 5 μg/ml as major components) on the development and functional activity of soybean-rhizobium symbiosis (development phases of one leaf, four true leaves, and budding) was studied. It was demonstrated that pretreatment of seed with this preparation stimulated the development of both the macro-and microsymbionts. The experimental plants displayed an active accumulation of biomass (4–42% higher compared with the variant with inoculation), development of root nodules (the number increased by 11–110% and the weight by 27–157%), and elevated nitrogen-fixing activity (by 45–204%). The soybean yield increased by 8–10% upon treatment with Bralec 500 and Bralec 5 as compared with the traditional seed bacterization with root nodule bacteria.     

Diversity and distribution of leaf mining insects on birches (<Emphasis Type="Italic">Betula</Emphasis> spp.) in Siberia

The diversity and distribution of leaf mining insects developing on birches (Betula spp.) in Siberia were reviewed based on published records and our observations. Analysis of the literature revealed 52 species of leaf miners recorded as feeding on different Betula species in Siberia. Among them, three species were listed under different names and six species were erroneously recorded as birch consumers. Thus, the revised list of birch leaf miners contains 44 species. Five moth and four sawfly species are mentioned in the literature as pests of Betula. Four sawflies are known to be invasive in North America. Our collections comprised 25 species, including the micro-moth Stigmella continuella (Lepidoptera, Nepticulidae), a new species for Siberia found in Novosibirsk. Immature stages of 15 species were identified using DNA barcoding. Twenty species were recorded from several regions of Siberia for the first time. The dominant group is Lepidoptera (31 species), followed by Coleoptera (7), Hymenoptera (5), and Diptera (1). Two-thirds of all the known leaf miners develop exclusively on birches; the remaining species also colonize alders (Alnus, Betulaceae), some Rosaceae, Salicaceae, and Ulmaceae. In our observations, the majority of insects (96%) developed on B. pendula. About half of them were also observed on the East Asian birches B. dahurica, B. divaricata, B. costata, B. ermanii, and B. gmelinii; five species were found on the North American birches B. occidentalis and B. papyrifera. All the leaf mining species listed in our paper for Siberia also occur in Europe. The similarity between the miner faunas of these regions is discussed and it is warned about possible errors in diagnostics of the Siberian species using the keys and catalogues for the European fauna. The importance of DNA barcoding in the study of the local insect faunas of poorly explored regions is also emphasized.     

The lime leafminer Phyllonorycter issikii in Western Siberia: Some ecological characteristics of the population of the recent invader

The detection of the lime leafminer Phyllonorycter issikii in Novosibirsk in 2008–2009 is reported. Mines of this pest have been found on the small-leaved lime Tilia cordata and the Siberian lime T. sibirica, but not on the Amur lime T. amurensis (common host plant of moth). Leaves of T. cordata carried 2–3 times more mines than T. sibirica. On both host plants, the parasitism of mature larvae and pupae did not exceed 7%. Lack of control by local parasitoids can give the pest an opportunity to increase population density and spread further in Western Siberia.     

sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics

Gene-based association analysis is an effective gene-mapping tool. Many gene-based methods have been proposed recently. However, their power depends on the underlying genetic architecture, which is rarely known in complex traits, and so it is likely that a combination of such methods could serve as a universal approach. Several frameworks combining different gene-based methods have been developed. However, they all imply a fixed set of methods, weights and functional annotations. Moreover, most of them use individual phenotypes and genotypes as input data. Here, we introduce sumSTAAR, a framework for gene-based association analysis using summary statistics obtained from genome-wide association studies (GWAS). It is an extended and modified version of STAAR framework proposed by Li and colleagues in 2020. The sumSTAAR framework offers a wider range of gene-based methods to combine. It allows the user to arbitrarily define a set of these methods, weighting functions and probabilities of genetic variants being causal. The methods used in the framework were adapted to analyse genes with large number of SNPs to decrease the running time. The framework includes the polygene pruning procedure to guard against the influence of the strong GWAS signals outside the gene. We also present new improved matrices of correlations between the genotypes of variants within genes. These matrices estimated on a sample of 265,000 individuals are a state-of-the-art replacement of widely used matrices based on the 1000 Genomes Project data.     

Variability of Microbiota under Diverse Conditions of Soil Moistening

According to data on the abundance of taxonomic, physiological, and ecotrophic microbial groups, analysis of the seasonal changes in their composition under conditions of artificial (irrigation) and natural (wet land formation) soil moistening was carried out. It was revealed with statistical reliability that the greatest response to changes caused by different soil moistening modes was observed in the numbers of aerobic cellulose-degrading microorganisms, denitrifiers, and fungi. An increase in erosion resistance of steppe soils during irrigation is explained by the combined effect of physicochemical and biological processes, and by higher numbers of algae, fungi, aerobic cellulose-degrading microorganisms, and oligonitrophiles, in particular.     

The comprehensive diagnosis of changes in the stomach and small intestine in patients with chronic colitis

Combined investigation of 121 patients with chronic colitis (CC) has shown chronic gastroduodenitis in 90.9% and the intestinal malabsorption syndrome in all the patients. Comparison of the frequency of intestinal malabsorption symptoms has shown that they are less marked in CC than in chronic enterocolitis with predominant intestinal lesion.     

Specific Features of Phosphate Transformation on Rhodobacter sphaeroides Chromatophores

ATP production has been shown to take place on illumination of Rhodobacter sphaeroides chromatophores by a single light flash, i.e., in the absence of a proton gradient (which would form as a result of electron transport should a second flash occur). ATP synthesis was accompanied by H₂O₂ formation. Simultaneous formation of ATP and H₂O₂ is indicative of oxidative activation of phosphate during ATP synthesis, as in model systems with isolated chlorophyll. These data provide a theoretical background for selecting illumination parameters in laboratory and industrial photobioreactors used for cultivation of photosynthetic bacteria in biotechnological processes.