Natalia Ivanova

The metabolic pathway collection: an update

The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways. The current collection contains 2180. Metabolic reconstructions for the first completely sequenced organisms-Haemophilus influenzae,Mycoplasma genitalium,Saccharomyces cerevisiaeandMethanococcus janaschii-are all included in the current release. All of the pathways in the collections are available as ASCII files in the form generated by the main curator, Evgeni Selkov. In addition, we are offering a more structured encoding of a subset of the collection; our initial release of this subcollection includes all of the pathways inMycoplasma genitalium, and we ultimately intend to offer the entire collection in this form as well.

Factors Limiting Distribution of the Rare Lichen Species Lobaria pulmonaria (in Forests of the Kologriv Forest Nature Reserve)

The distribution patterns and coenotic confines of the epiphytic lichen Lobaria pulmonaria have been studied. The factors limiting the habitat of this rare lichen species in the Kologriv Forest Nature Reserve (southern taiga subzone) have been revealed. It has been shown that L. pulmonaria is attracted to forest areas, which are less affected by humans and characterized by better light conditions than other communities. It has been found that L. pulmonaria is able to colonize trees at various ontogenetic states, beginning from virginal ones.

Spatial distribution features of the root biomass of some tree species (Picea abies, Pinus sylvestris, Betula sp.)

The effect of intra- and interspecific competition on the spatial distribution of the biomass and mortmass of woody plant roots in mixed tree stands has been studied. It has been found that the mass of roots in the samples from tree pairs of different species is higher than in the samples from monospecific pairs. Species-specific differences in the vertical distribution of roots and the effect of intra- and interspecific competition on the spatial structure of biomass have been shown. It has been noted that the proportion of dead roots increases almost linearly with depth.

Changes in Vegetation and Earthworm Populations under Free Grazing European Bison (Bison bonasus) in Broad-Leaved Forests of the Kaluzhskie Zaseki State Nature Reserve

This paper studies the impact of a free-ranging bison population on the vegetation and soil fauna in spatially adjacent biotopes (meadow-transition zone-surrounding forest) in the Kaluzhskie Zaseki State Nature Reserve. It is noted that bison maintains meadows in the absence of haymaking. Analysis of phytosociological relevés shows that the forest vegetation has been significantly transformed by bison over 10–15 years, as evident from (1) differences in the ecological-coenotic structure of the vegetation in the different biotopes, (2) a larger ecological-coenotic diversity of communities in the transition zones in comparison with surrounding forests, and (3) an increase in the participation of nitrophilous species in the vegetation. A fairly high earthworm species diversity (a total of seven species in the biotopes) is found; Aporrectodea caliginosa dominates in the earthworm density and biomass. The total earthworm density and biomass became lower in the transition zone than in neighboring forests and meadows, and the differences in earthworm density between the transition zone and the meadows were statistically significant.

Additional file 1: of High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains

Major protein profiles of P. fulva DSM 17717T, P. parafulva DSM 17004T and P. cremoricolorata DSM 17059T type strains. The intensity value was determined as an average from all spectra containing that peak and the relative intensities with respect to the base peak in percentage are indicated within parenthesis. (m/z: mass to charge ratio; + and -: presence or absence of the corresponding protein). (PDF 99 kb)

Additional file 2: Table S2. of High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

Nodulation and N2 fixation properties of E. medicae WSM244 on selected Medicago spp. Data compiled from [3, 6, 8]. Note that ‘+’ and ‘-’ denote presence or absence, respectively, of nodulation (Nod) or N2 fixation (Fix). (DOCX 15xa0kb)