Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods

We present a web resource MEM (Multi-Experiment Matrix) for gene expression similarity searches across many datasets. MEM features large collections of microarray datasets and utilizes rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. Unique features of MEM include automatic detection, characterization and visualization of datasets that includes the strongest coexpression patterns. MEM is freely available at .     

The influence of repetitive thermal stresses on the dominance of reef-building Acropora spp. (Scleractinia) on coral reefs of the Maldive Islands

The distribution and size-age structure of Acropora corals were studied in two Maldivian atolls that differ in their geographic position and sea surface temperature regimes. The frequency and strength of thermal anomalies for the last 2 decades had a significant influence on the abundance, mortality rates, and age structures of acroporid communities. The long-term temperature amplitude was higher and the maxima were more pronounced in the northernmost Ihavandippolu Atoll than those in the equatorial South Huvadhoo Atoll. These differences resulted in a 10.4% mean cover of Acropora at Ihavandippolu Atoll, whereas the Acropora cover in the South Huvadhoo Atoll reached 59.5%. In the northern atoll, the coral mortality rate after the 2010 thermal anomaly was 3 times higher than that in the southern atoll. Younger acroporid colonies (up to 2 years old) dominated the northern atoll reefs, while the southern atoll showed a high proportion of older mature colonies. In both atolls, healthy table colonies of Acropora cytherea with a disk diameter greater than 2 m were observed that apparently survived three thermal anomalies since 1998. The mechanisms of acclimatization of Acropora and the prospects for its dominance in the Maldives under changing environmental conditions are discussed.     

Cold adaptation in the phytopathogenic fungi causing snow molds

Snow molds are psychrophilic or psychrotrophic fungal pathogens of forage crops, winter cereals, and conifer seedlings. These fungi can grow and attack dormant plants at low temperatures under snow cover. In this review, we describe the biodiversity and physiological and biochemical characteristics of snow molds that belong to various taxa. Cold tolerance is one of the important factors related to their geographic distribution, because snow molds develop mycelia under snow cover and because they should produce intra- and extracellular enzymes active at low temperatures for growth and infection. Basidiomycetous snow molds produce extracellular antifreeze proteins. Their physiological significance is to keep the extracellular environment unfrozen. The psychrophilic ascomycete Sclerotia borealis shows normal mycelial growth under frozen conditions, which is faster than that on unfrozen media at optimal growth temperature. This fungus does not produce extracellular antifreeze proteins, but osmotic stress tolerance enables the fungus to grow at subzero temperatures. In conclusion, different taxa of snow molds have different strategies to adapt under snow cover.     

Participation of putrescine in the antiport mechanism of potassium transport inEscherichia coli

Alkalinization of culture medium is accompanied by a considerable increase in the putrescine production byEscherichia coli and its efflux, in the environment. Existence of the reversible putrescine⁺²/2K⁺ exchange was shown under conditions of inhibition and energy limitation of the main potassium transport systems. It is assumed that this exchange serves as an alternative mechanism of potassium transport for providing continuous functioning of K⁺/H⁺ antiporter.     

Formation and dynamics of plasma layers formed on the foil surface under the action of a high-current pulse

Results are presented from studies of the possibility of using a thin metal foil for recyclable vacuum transmission lines with magnetic insulation in a conceptual fusion reactor based on high-voltage high-current electromagnetic generators. Numerical simulations and experiments in the Angara-5-1 facility were carried out to determine both the threshold for the explosion of a foil heated by a current pulse and the parameters of the plasma layer formed at the foil surface. It was found experimentally that an additional plasma current channel forms on the surface of a 120-μm stainless-steel foil at a linear current density of 0.25–0.5 MA/cm, which corresponds to a magnetic field of 0.3–0.6 MG. For the same conditions, one-dimensional computer simulations of the foil heating were performed in an MHD model by using a wide-range semiempirical equation of state for stainless steel. The calculated threshold for plasma generation on the foil surface is compared with the experimental data. The main parameters of the plasma layer are also calculated at linear current densities of 2–10 MA/cm, which far exceed the threshold current density. The plasma layer parameters as functions of the linear current density are determined for the case of an iron foil.     

The expression of Fc gamma receptors on the surface of macrophages activated by a vaccinal strain of Yersinia pestis

The expression of Fc gamma R on the surface of macrophages in the process of antiplague immunity formation is analyzed. The stud is performed on the alveolar and peritoneal macrophages obtained from intact and immunized guinea pigs in different periods after vaccination (the 1st, 7th, 14th and 21st day). It is established that during the formation of the antiplague immunity there occurs activation of macrophages which is accompanied by an increase of the Fc gamma R expression on the outer surface of the membrane both of peritoneal and alveolar macrophages and the pattern of response of these cells to the interaction with the vaccine strain of the plague microbe changes. The Fc gamma R expression heterogeneity of certain macrophage populations is revealed both in an intact and in immune organism as well as different pattern of the intact alveolar and peritoneal macrophage response during the interaction with the vaccine strain of the antiplague microbe. These differences are levelled in the process of the antiplague immunity formation.     

Inhibition of glucose in Zajdela hepatoma by 6-phosphogluconate; the role of 3-phosphoglycerate

Influence of 6-phosphogluconate and 3-phosphoglycerate have been studied for their effect on the fructose-6-phosphate glycolytic transformation reactions in homogenates of the Zajdela hepatoma cells. It is established that 6-phosphogluconate inhibits formation of lactate from fructose-6-phosphate and increases the ratio: dioxyacetone-phosphate/lactate. The influence of 6-phosphogluconate on the formation of lactate from the fructose-1,6-bisphosphate is similar. 3-phosphoglycerate removes the effect of 6-phosphogluconate, its content being unchanged in samples, which indicates rather the regulatory, than the substrate role of 3-phosphoglycerate. Analogous experiments with homogenates of the rat liver show that 6-phosphogluconate inhibits hexosephosphate isomerase, but almost all the introduced substrate (fructose-6-phosphate) is transformed into glucose. Processes of fructose-6-phosphate consumption in the hepatoma and liver are opposite.     

Etiological structure and resistance to antibacterial drugs of causative agents of cross infection in Donetsk

Tests for hemocultures were performed in 51 patients with clinical diagnoses of sepsis treated in a reanimation unit. Microbial cultures were isolated from 30 patients (58.9 per cent). Staphylococci in pure cultures and associations were the causative agents of sepsis in 26 patients (86.4 per cent). The cultures of E. coli, Y. enterocolitica and Streptococcus faecalis were isolated from 2, 1 and 1 patients, respectively. Pus specimens from 111 patients with postinjection suppuration were tested and staphylococci in pure cultures and associations were detected in 90 patients (81.8 per cent). The cultures of P. vulgaris, Streptococcus pyogenes, E. coli, Str. faecalis, Enterobacter spp. and Pseudomonas aeruginosa were isolated from 10, 5, 3, 1, 1 and 1 patients, respectively. The results showed that Staphylococci played the leading role in development of the hospital infections. Treatment of such patients should be performed with an account of antibioticograms since many strains are resistant to various antibiotics.