Effect of heavy water on the growth, glucose assimilation and stability of Escherichia coli to freezing-thawing]

Growth and resistance to freezing--thawing of Escherichia coli B-1640 were investigated during cultivation in synthetic media prepared with H2O and D2O. It is found that during cultivation in D2O the maximum specific growth rate decreases and the duration of the exponential growth phase increases. During the growth in D2O the glucose consumption rate drops in the exponential growth phase, the lactate content in the culture liquid is lower by two orders than that in H2O; the resistance to freezing--thawing is lower than that in H2O. After leaving the exponential phase the culture in D2O restores specific growth rate, glucose consumption rate and resistance to freezing--thawing up to the values obtained during the growth in H2O. The translation ability of ribosomes isolated from cells grown in D2O and H2O is the same. We conclude that the culture adapts to D2O during the exponential growth phase. It is suggested that during the adaptation the second carbon source is used which compensates the consequences of the disturbances of glucose metabolism and transport caused by deuteration of the cell content in the adaptation to D2O.     

Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates

Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K⁺ and ATP:Mg²⁺] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K⁺ and PP_i:Mg²⁺] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K⁺ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PP_i releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.     

"Synthetic" maps of the Mari gene pool (from immunobiochemical polymorphism data)]

Models of geographic distribution of 33 alleles of 10 loci (AB0, TF, GC, PI, HP, AHS, F13B, ACP1, PGM1, GLO1) in the indigenous population of five raions (districts) of Marii El Republic were analyzed by cartographic statistical methods. Based on 33 maps for individual alleles, synthetic maps were constructed; they reflected the general characteristics of the spatial variability of the Mari gene pool. A map of reliability of the synthetic maps was also obtained. This study was the first to use estimates of the reliability of the gene-geographic prognosis for constructing and interpreting the maps of principal components. Synthetic maps of principal components reveal the geography of the main factors that determine the genetic diversity of the Maris. In the map of the first principal component (accounting for 25.5% of the total variation of the Mari gene pool), isolines clearly ran in the latitudinal direction; i.e., the variability exhibited a north-south gradient. The direction of changes reflects the characteristic features of the microevolution of the Mari gene pool, because it differs from the direction of the principal components of in the total Ural gene pool. The second principal component (24.3% of variation) also exhibited a latitudinal gradient in the western part of Marii El. In the eastern part of the republic, isolines drastically change their direction and display a marked west-east gradient. This longitudinal orientation of principal components is characteristic of the Maris in the synthetic maps of the Ural region. Contributions of individual genes in the variation of principal components were analyzed. In proceeding from the geographic space to the space of principal components, it was found that Highland Maris are separated from Meadow Maris not only geographically, but also genetically.     

Hemodynamic and motility disorders of the gastrointestinal tract in intramural ischemia

Angiotensometry and pulsomotorography were used to study ischemia in the hollow organs in dog experiments. Specific and nonspecific disturbances, criteria of compensation and decompensation were determined. Using different methods of stimulation, stable microhemodynamic signs of ischemia--lowered pulse and motor oscillations, intramural blood pressure elevations and transformation of impulse blood flow into continuous one--were found.     

Proteomics of wine additives: Mining for the invisible via combinatorial peptide ligand libraries

Combinatorial peptide ligand libraries (CPLLs) have been adopted for harvesting and identifying traces of casein (used as a fining agent) present in white wines. Although minute amounts (200 µL) of CPLL beads are added to the entire content of a wine bottle (750 mL), they are able to sequester with high efficiency (up to 80%) residual traces of casein, permitting a signal “amplification” of at least 5000-fold. It is here demonstrated that as little as 1 µg/L of casein can be efficiently detected in white wines, a major improvement over previous investigations in which the lower detection limit had been estimated at 100 µg/L. The fact that such very low levels of fining agents can still be detected in treated white wines should be taken into consideration by winemakers in labelling their products and by EC rulers in issuing proper regulations.     

The Role of Epibionts of Bacteria of the Genus <Emphasis Type="Italic">Pseudoalteromonas</Emphasis> and Cellular Proteasomes in the Adaptive Plasticity of Marine Cold-Water Sponges

It was found that cells of different color morphs of the cold-water marine sponges Halichondria panicea (Pallas, 1766) of the class Demospongiae differ in the content of epibionts of bacteria of the genus Pseudoalteromonas. The sponge cells with elevated levels of epibionts of bacteria of the genus Pseudoalteromonas showed an increased expression of Hsp70 proteins but had a reduced level of the proteasomal catalytic beta 5 subunit, which was accompanied by a change in their activity. Probably, epibionts of bacteria of the genus Pseudoalteromonas may affect the ubiquitin–proteasome system in the cells of cold-water marine sponges and, thereby, ensure their adaptive plasticity.     

Associating particulate essential fatty acids of the ω3 family with phytoplankton species composition in a Siberian reservoir

1. We studied variation in the composition of fatty acids in the seston of a small freshwater reservoir with changes in phytoplankton composition during four growth seasons. We focused on the dynamics of the ω3 fatty acids because of their potential importance for zooplankton nutrition. 2. Total diatoms were related to the 20:5ω3 fatty acid (eicosapentaenoic, EPA) content in seston. Among two dominant diatom genera, Cyclotella was not associated with EPA content. In contrast, there was a significant correlation between Stephanodiscus and the percentage contribution and content of EPA throughout the study. Hence, freshwater diatoms can differ strongly in content of the essential EPA. 3. We considered abundant cyanobacteria as a potential source of 18:3ω3 fatty acid (linolenic, ALA) to aquatic food webs. Among four dominant cyanobacteria species, two (Anabaena flos‐aquae and Planktothrix agardhii) showed significant correlation with the ALA content of the seston, while the other two (Aphanizomenon flos‐aquae and Microcystis aeruginosa) did not. 4. Dinophyta had a relatively high level of 22:6ω3 (docosahexaenoic, DHA) for freshwater species and can be also a source of EPA to aquatic food webs. 5. Our results show that various species of diatoms as well as cyanobacteria can be of contrasting nutritional value for zooplankton because of their different content of the essential PUFAs. Diatoms, which are low in EPA, could not be considered as a valuable food, while some field populations of cyanobacteria might be valuable sources of essential ALA.     

Reactive oxygen species and plant immunity

Reactive oxygen species (ROS) play a key role in plant defense mechanisms. They exert direct antimicrobial action, catalyze the mechanical strengthening of cell walls, function as secondary messengers in the superoxide synthase signal pathway and in triggering the hypersensitive response. Although recent studies have unraveled a nature and the mechanisms of the oxidative burst, many questions related to its mode of regulation, its modulation of signaling networks that control growth, development and defense responses remain unanswered.     

Local conformational changes in ferritins with variable iron content

Conformational changes were induced in human spleen ferritin by partial or complete removal of iron, and the immunoreactivity of the ferritin samples with variable iron content was analyzed. We established that a decrease in iron content resulted in bimodal changes in immunoreactivity of the epitopes recognized by the monoclonal antibodies G10 and F11. Immunoreactivity demonstrated a 3-6-fold decrease on lowering iron content from 800 to 40 atoms per protein molecule, followed by a sharp (4-14-fold) increase that was observed when low-iron ferritin was converted to iron-free apoferritin. These bimodal changes suggest the presence of more than two conformational states of ferritin with local alterations of the epitopes recognized by the monoclonal antibodies. The global conformation of ferritin, however, remained essentially unaltered, as demonstrated by ferritin interaction with polyclonal antibodies. Together, the results indicate that local conformational changes in the ferritin protein shell occur on progressive iron removal that results in low-iron and iron-free forms of ferritin. These changes are most clearly seen in apoferritin when compared to low-iron ferritin.