Features of structural organization and expression regulation of malate dehydrogenase isoforms from <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis> strain 2R

Two isoforms of malate dehydrogenase (MDH), dimeric and tetrameric, have been found in the purple non-sulfur bacterium Rhodobacter sphaeroides strain 2R, devoid of the glyoxylate shunt, which assimilate acetate via the citramalate cycle. Inhibitory analysis showed that the 74-kDa protein is involved in tricarboxylic acid cycle, while the 148-kDa MDH takes part in the citramalate pathway. A single gene encoding synthesis of the isologous subunits of the MDH isoforms was found during molecular-biological investigations. The appearance in the studied bacterium of the tetrameric MDH isoform during growth in the presence of acetate is probably due to the increased level of mdh gene expression, revealed by the real-time PCR, the product of which in cooperation with the citramalate cycle enzymes plays an important role in acetate assimilation.     

The comparison of gastroprotective properties of Semax and its metabolites

Semax (MEHFPGP) was shown to increase gastric mucosal homeostasis to the action of such ulcerogenic factors as ethanol and stress. In the case of the stress model of ulcer formation, Semax and its two metabolites—HFPGP and FPGP—at the wide range of doses (0.06–3.7 μmol/kg) have demonstrated protective antiulcerogenic properties. In the case of ethanol model of ulcer formation, only Semax in two used doses (0.06 and 0.37 μmol/kg) reported reliable protective antiulcerogenic property. It was supposed that Semax’s gastroprotective activity directed to peripheral mechanisms of ulcerogenesis did not depend on its metabolites’ activities. On the contrary, Semax’s gastroprotective activity directed to the central mechanisms of ulcerogenesis might be also caused by gastroprotective activities of HFPGP and FPGP metabolites.     

Changes in plasma and IgG N-glycome during childhood and adolescence

Despite the importance of protein glycosylation in all physiological and pathological processes and their potential as diagnostic markers and drug targets, the glycome of children is still unexplored. We analyzed N-linked plasma and IgG glycomes in 170 children and adolescents between 6 and 18 years of age. The results showed large biological variability at the population level as well as a large number of associations between different glycans and age. The plasma N-glycome of younger children was found to contain a larger proportion of large complex glycan structures (r = -0.71 for tetrasialylated glycans; r = -0.41 for trisialylated glycans) as well as an increase in disialylated biantennary structures (r = 0.55) with age. Core fucosylation and the level of agalactosylated plasma and IgG glycans decreased while digalactosylated glycans increased with age. This pattern of age-dependent changes in children differs from changes reported in adult population in both, direction and the intensity of changes. Also, sex differences are much smaller in children than in adults and are present mainly during puberty. These important observations should be accounted for when glycan-based diagnostic tests or therapeutics are being developed or evaluated.     

A new strategy to reduce allelic bias in RNA-Seq readmapping

Accurate estimation of expression levels from RNA-Seq data entails precise mapping of the sequence reads to a reference genome. Because the standard reference genome contains only one allele at any given locus, reads overlapping polymorphic loci that carry a non-reference allele are at least one mismatch away from the reference and, hence, are less likely to be mapped. This bias in read mapping leads to inaccurate estimates of allele-specific expression (ASE). To address this read-mapping bias, we propose the construction of an enhanced reference genome that includes the alternative alleles at known polymorphic loci. We show that mapping to this enhanced reference reduced the read-mapping biases, leading to more reliable estimates of ASE. Experiments on simulated data show that the proposed strategy reduced the number of loci with mapping bias by ≥63% when compared with a previous approach that relies on masking the polymorphic loci and by ≥18% when compared with the standard approach that uses an unaltered reference. When we applied our strategy to actual RNA-Seq data, we found that it mapped up to 15% more reads than the previous approaches and identified many seemingly incorrect inferences made by them.     

The effect of natural clinoptilolite on the serotonergic receptors in the brain of mice with mammary carcinoma

The ex vivo effect of tribomechanically micronized zeolite (MZ) on the binding of 3H-8-OH-DPAT to 5-HT(1A) and 3H-5-HT to 5-HT(1B) receptors was investigated in the brain of nontumorous (control) and mammary carcinoma bearing female mice. During 14 and 28 days mice were fed with standard food, standard food supplemented with 25% of MZ, or standard food supplemented with 25% of non tribomechanically micronized zeolite (non-MZ). A reduced binding of 3H-8-OH-DPAT to 5-HT(1A) receptors in mammary carcinoma bearing mice was found when compared to control mice fed with standard food for 28 days, suggesting a time dependent alteration of 5-HT(1A) receptors in mammary carcinoma. The addition of MZ for 28 days in these mice abolished the decrease in 5-HT(1A) receptors binding, indicating a possible beneficial effect of MZ, at least on 5-HT(1A) receptors in mammary carcinoma bearing mice. The preliminary data show that MZ administered as a food supplement (25%) for 14 days induced a transient decrease in the binding of 3H-5-HT to brain 5-HT(1B) receptors only in control, but not in tumor-bearing mice, that disappeared after 28 days of MZ-supplemented food administration. The mechanism of the indirect action of MZ on the brain serotonergic receptors might be achieved by the alterations in the electrolytes balance, and/or by the regulation of the immune system.     

Low levels of endogenous oxidative damage cluster levels in unirradiated viral and human DNAs

Ionizing radiation induces bistranded DNA damage clusters-two or more oxidized bases, abasic, sites or strand breaks on opposing strands within a few helical turns-but it is not known if clusters are also formed in unirradiated DNA in solution or in unirradiated cultured human cells. The frequencies of endogenous oxidized purine clusters (recognized by Escherichia coli Fpg protein), oxidized pyrimidine clusters (recognized by Nth protein), and abasic clusters (cleavage by Nfo protein) were determined using quantitative gel electrophoresis, electronic imaging, and number average length analysis. Methods of DNA isolation and storage were found to affect cluster levels significantly. In bacteriophage T7 DNA prepared using stringent conditions, the frequencies of these clusters were <1/Mbp. In DNA from unirradiated human 28SC monocytes, the levels of such clusters were, at most, a few per gigabase pair.     

Axillary meristem development in the branchless Zu-0 ecotype of Arabidopsis thaliana

Axillary meristems form in the leaf axils during post-embryonic development. In order to initiate the genetic dissection of axillary meristem development, we have characterized the late-flowering branchless ecotype of Arabidopsis thaliana (L.) Heynh., Zu-0. The first-formed rosette leaves of Zu-0 plants all initiate axillary meristems, but later-formed leaves of the rosette remain branchless. Alteration in the meristem development is axillary meristem-specific because the shoot apical and floral meristems develop normally. Scanning electron microscopy, histology and RNA in situ analysis with SHOOTMERISTEMLESS ( STM), a marker for meristematic tissues, show that a mound of cells form and STM mRNA accumulates in barren leaf axils, indicating that axillary meristems initiate but arrest in their development prior to organizing a meristem proper. Expression and retention of the STM RNA in barren leaf axils further suggests that STM expression is not sufficient for the establishment of the axillary meristem proper.     

Antibiotic prophylaxis of postoperative suppurative complications in surgical urology

Preoperative sanation of the urinary tracts is an obligatory condition for lowering the risk of severe infectious complications. When there is no bacteriuria it is recommended in the cases subject to short-term surgical interventions without subsequent drainage of the urinary tracts to perform single or one-day prophylaxis with cephalosporins or semi-synthetic penicillins in the routine doses. The same principle is applicable to transurethral operations, endourological manipulations and lithotripsy. When there are urinary fistulas preventing complete sanation of the urinary tracts before operations it is advisable to use combinations of aminoglycosides with carbenicillin. The treatment terms in such cases amount to 7 to 10 days. Antibiotics of the reserve group, i.e. amikacin, sisomicin and ureidopenicillins should not be used prophylactically in such cases.     

Determination of the biological activity of antibiotics by using dry nutrient media

The possibility of using available dry nutrient media Nos. 5 to 12 in assays of antibiotic biological activity with the agar diffusions method was studied with respect to benzylpenicillin, gramicidin S, kanamycin sulfate, kanamycin B, oleandomycin, novobiocin, tetracycline and erythromycin. The dry media were used instead of the respective media prepared with meat hydrolyzate. Optimal conditions of the assays on such media were determined.     

State of the Ichthyoplankton Community along the Crimean Peninsula in August 2011

Data on species composition, spatial distribution of ichthyoplankton, and feeding of fish larvae in August 2011 are presented for the shelf and the open waters along the Crimean Peninsula from Kerch Strait to Karkinit Bay. In the ichthyoplankton, fish eggs and larvae represented 19 species from 16 families. The average egg abundance was 111 egg/m² and larvae abundance was 22 ind./m². The elimination ratio of the European anchovy Engraulis encrasicolus, which dominates in the plankton from the final stages of development to the prelarvae in 2011, was similar to that observed in 1957. The high number of larvae of the older age group in the western halistatic zone is explained by the peculiarities of the hydrological regime. Decrease in the pressure of predatory jelly macroplankton and an fodder zooplankton (zooplankton abundance) contribute to the survival of the fish larvae.