Diversity of the communities of acidophilic chemolithotrophic microorganisms in natural and technogenic ecosystems

The main representatives of acidophilic chemolithotrophs oxidizing sulfide minerals, ferrous iron, elemental sulfur, and reduced sulfur compounds and forming microbial communities in the natural and technogenic ecosystems with low pH values and high concentrations of heavy metal ions are listed. The species and strain diversity of the communities and environmental factors affecting their composition (temperature, pH value, energy substrate, mineralogical composition of sulfide ore concentrates, the presence of organic substances, and level of aeration) are analyzed. Involvement of mobile genetic elements (IS elements and plasmids) in the structural changes of the chromosomal DNA in the course of switching microbial metabolism to the oxidation of new energy substrates or under increased concentrations of metal ions is shown to be a probable mechanism responsible for the intraspecific genetic heterogeneity of the populations. Importance of determination of the dominant strains of different microbial species in the communities and of their physiological peculiarities for stabilization, optimization, and enhancement of efficiency of biotechnological processes for sulfide mineral oxidation is stressed.     

The plant cover of Russia in the area of the Braun-Blanquet syntaxonomy: the development of an approach and the results

Theoretical basis of ecologo-floristic classification according to Braun-Blanquet approach is discussed with the special attention to the contribution of Russian scientists. Principal results concern presentation of vegetation continuum in discrete classification units: polymodal conception of plant communities, principle of plural syntaxonomic decisions, pragmatic approach to classification, method of homological rows of plant communities, etc. Current ecologo-floristic classification of vegetation in Russia consists of 77 classes. This system is a good basement for estimation of rarity of plant communities and biodiversity protection. The first variant of "Red Book" of plant communities of Russia and other eastern European countries is discussed.     

Clinical and immunological effect produced by vaccination with "Pneumo 23" of children with atopic bronchial asthma

A total of 45 children aged 4-16 years with atopic bronchial asthma of different severity level-resulted from a past case of outhospital pneumonia, received vaccine "Pneumo 23" ("Aventis Pasteur", France). The vaccine was found to be well tolerated, no cases of the exacerbation of the atopic process were registered. A reliable Increased level of specific antibodies to the mixture of polysaccharides, contained in the vaccine "Pneumo 23", was found to occur. The tendency towards decreased level of serum IgE was established.     

In vitro maturation of cattle oocytes taken from ovaries with different morphofunctional states

We studied the capacity of cattle oocytes taken from ovaries with different morphofunctional state for development to metaphase 2 in vitro. A classification of ovaries has been proposed according to their morphofunctional state: (1) ovaries with a yellow body from the last cycle, without dominating follicle, with many follicles of varying diameter; (2) ovaries with a yellow body from the last cycle, with dominating follicle (from 10 mm in diameter); (3) ovaries with a large functioning yellow body and follicles of varying diameter; (4) ovaries with a follicular cystoid formation (more than 25 mm in diameter); (5) ovaries with a yellow body from past cycles and small (1-2 mm) follicles, supposedly with a weakened hormonal function. It was shown that the morphofunctional state of ovaries determined the total number of oocytes isolated from an ovary and number of morphologically normal oocytes feasible for cultivation. At the same time, no reliable differences in the capacity for extrusion of the first polar body between the oocytes from the ovaries of different types were found in the experiments on in vitro oocytes maturation. Since the coefficient of correlation between the extrusion of the first polar body and maturation to metaphase 2 was in 0.95, there is every reason to believe that the capacity for development to metaphase 2 does not depend on the morphofunctional state of ovaries.     

Nature of inhibition of the activity of macromolecular antibodies]

The presence in the organism of an inhibitory factor expressing its activity under conditions of increased macromolecular globulins production (of M-immunoglobulins in particular) was established experimentally. The inhibitory factor depressed the avidity of the macromolecular antibodies; its appearance preceded reduction of the macromolecular protein level in the blood serum. The inhibitory effect of the blood serum in blood letting and vaccination with bacterial antigen is connected with the blood serum albumins, and with increased cystein and sulfhydryl groups concentration.     

Oxidation of gold-antimony ores by a thermoacidophilic microbial consortium

Antimony leaching from sulfide ore samples by an experimental consortium of thermoacidophilic microorganisms, including Sulfobacillus, Leptospirillum, and Ferroplasma strains was studied. The ores differed significantly in the content of the major metal sulfides (%): Sb_S, 0.84 to 29.95; Fe_S, 0.47 to 2.5, and As_S, 0.01 to 0.4. Independent of the Sb_S concentration in the experimental sample, after adaptation to a specific ore and pulp compaction, the microorganisms grew actively and leached/oxidized all gold-antimony ores at 39 ± 1°C. The lower was the content of iron and arsenic sulfides, the higher was antimony leaching. For the first time the investigations conducted with the use of X-ray microanalysis made it possible to conclude that, in a natural high-antimony ore, Sb inhibits growth of only a part of the cell population and that Ca, Fe, and Sb may compete for the binding centers of the cell.     

Conversion from electrocardiosignals to equivalent electrical sources on heart surface

In biomarker discovery, applying domain knowledge is an effective approach to eliminating false positive features, prioritizing functionally impactful markers and facilitating the interpretation of predictive signatures. Several computational methods have been developed that formulate the knowledge-based biomarker discovery as a feature selection problem guided by prior information. These methods often require that prior information is encoded as a single score and the algorithms are optimized for biological knowledge of a specific type. However, in practice, domain knowledge from diverse resources can provide complementary information. But no current methods can integrate heterogeneous prior information for biomarker discovery. To address this problem, we developed the Know-GRRF (know-guided regularized random forest) method that enables dynamic incorporation of domain knowledge from multiple disciplines to guide feature selection. Know-GRRF embeds domain knowledge in a regularized random forest framework. It combines prior information from multiple domains in a linear model to derive a composite score, which, together with other tuning parameters, controls the regularization of the random forests model. Know-GRRF concurrently optimizes the weight given to each type of domain knowledge and other tuning parameters to minimize the AIC of out-of-bag predictions. The objective is to select a compact feature subset that has a high discriminative power and strong functional relevance to the biological phenotype. Via rigorous simulations, we show that Know-GRRF guided by multiple-domain prior information outperforms feature selection methods guided by single-domain prior information or no prior information. We then applied Known-GRRF to a real-world study to identify prognostic biomarkers of prostate cancers. We evaluated the combination of cancer-related gene annotations, evolutionary conservation and pre-computed statistical scores as the prior knowledge to assemble a panel of biomarkers. We discovered a compact set of biomarkers with significant improvements on prediction accuracies. Know-GRRF is a powerful novel method to incorporate knowledge from multiple domains for feature selection. It has a broad range of applications in biomarker discoveries. We implemented this method and released a KnowGRRF package in the R/CRAN archive.     

The Effect of I155T,K156Q,K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses

Molecular Biology - The continued circulation of influenza A virus subtype H5 may cause the emergence of new potential pandemic virus variants, which can be transmitted from person to person. The...     

Intensity of lipid peroxidation and antioxidant protection system indices during re-adaptation period after long-term space flights at the international space station

In the blood serum of seventeen members of crews which participated in 14 orbital expeditions to the International Space Station with the duration of 125 to 217 days, during the pre-flight period and on the day of landing on the 1st, 7th and 14th days of the rehabilitation period (RP) the content of LPO products was determined, namely diene conjugates (DC), malon dialdehyde (MDA), shiffbases (SB) and the main lipid oxidant - tocopherol (TP). The group of astronauts who made landing in the Space Shuttle spacecraft (8 persons) and the group of astronauts who accomplished space mission in the Soyus TM spacecraft (9 persons) demonstrated a decrease in DC and MDA levels with a rise in TF concentration in the course of the rehabilitation period. Changes in the group of the American spacecraft astronauts were more pronounced. LPO inhibition during the rehabilitation period is recognized [treated] as an adequate reaction to the stress caused by re-adaptation to the ground conditions. Also are discussed probable mechanisms of intergroup differencies in LPO intensity degree: biomembrane phase state changing under the influence of overloads during de-orbiting and stress response intensity during landing in different types of spacecraft.     

Viable nonsense mutants for the SUP45 gene in the yeast Saccharomyces cerevisiae are lethal at increased temperature

Nonlethal nonsense mutations obtained earlier in the essential gene SUP45 encoding the translation termination eRFI factor in the yeast Saccharomyces cerevisiae were further characterized. Strains carrying these mutations retain the viability, since the full-length eRF1 protein is present in these strains, although in decreased amounts as compared to wild-type cells, together with a truncated eRF1. All nonsense mutations are likely to be located in a weak termination context, because a change in the stop codon UGAA (in the case of mutation sup45-107) to UAGA (sup45-107.2) led to the alteration of the local context from a weak to strong and to the lethality of the strain carrying sup45-107.2. All nonsense mutations studied are characterized by thermosensitivity expressed as cell mortality after cultivation at 37 degrees C. When grown under nonpermissive conditions (37 degrees C), cells of nonsense mutants sup45-104, sup45-105. and sup45-107 display a decrease in the amount of the truncated eRF1 protein without reduction in the amount of the full-length eRF1 protein. The results of this study suggest that the N-terminal eRF1 fragment is indispensable for cell viability of nonsense mutants due to the involvement in termination of translation.