Sulfate reduction, methanogenesis, and methane oxidation in the upper sediments of the Vistula and Curonian Lagoons, Baltic Sea

Microbiological, biogeochemical, and isotope geochemical investigations of the upper sediments of the Vistula and Curonian lagoons, Baltic Sea, were carried out. High content of organic matter in the sediments was responsible for the high numbers (over 10¹⁰ cells cm^?3) and activity of heterotrophic microorganisms. The calculated integral rates of dark CO₂ assimilation for the upper 30 cm of the sediments varied 12.5 to 38.8 mmol m^?2 day^?1 and were somewhat higher in the Curonian Lagoon than in the Vistula Lagoon. Integral rates of sulfate reduction were higher in the more saline Vistula Lagoon. Rapid consumption of sulfates of the pore water resulted in intensified methanogenesis, with significantly higher rates detected in the silts of the Curonian Lagoon. High rates of methanogenesis in the Curonian Lagoon correlated with higher methane levels in its upper sediments and near-bottom water. The highest rates of methane oxidation were detected in the uppermost sediment horizons (oxidized or slightly reduced), which was an indication of the barrier role of aerobic methanotrophic bacteria. The calculated methane flows from the sediments into the water column were 0.45 and 0.007 mmol m^?2 day^?1 for the Vistula and Curonian Lagoons, respectively. Low methane flow from the sediments of the Curonian Lagoon resulted probably from the specific weather (wind) conditions during sampling. The near-stormy conditions in the Curonian Lagoon caused sediment detachment, resulting in methane release into the water column.     

Kin groups in closely spaced capercaillie leks

We quantified the genetic structure among 58 capercaillie (Tetrao urogallus) from three closely spaced leks in boreal Russia using ten microsatellite loci. We did not find significant structuring with respect to lek membership in an overall analysis. However, all but one individual could be strongly assigned to one of two genetic clusters, which we interpret as reflecting different local lineages or extended family groups. There was evidence for structuring among some clusters within leks, and one smaller lek consisted of nine out of ten males from one cluster, which could reflect kin biasing of lek membership. One cluster was apparently outperforming the other, since nine out of ten juveniles sampled belonged to it.     

Evaluation of reasons of the MDR M. tuberculosis strains dissemination by analysis of the rifampicin and/or isoniazid resistant isolates

During the last years in Novosibirsk region of Russia the rate of TB patients infected by MDR strains of M. tuberculosis has been constantly increasing. This increase may occur as a result of the spontaneously mutated mycobacterium selection during treatment of patients or as a result of primary infection by the resistant M. tuberculosis, or also, as a result of both reasons in combination. If the main reason of MDR strain dissemination is selection of resistant bacterium during patient treatment, the equal apportionment of the dominated mutation into the mycobacterium genotypes would be observed. If the main reason is the primary infection by resistant M. tuberculosis, the unequal apportionment would be revealed. For deeper understanding of the main reasons of the fast MDR strains spreading in the region, the distribution of the main mutations over genotypes of strains in Novosibirsk (170 isolates) and Tomsk prison (51 isolates) was investigated. Mutations in rpoB gene associated with the rifampicin resistance and in katG (isoniazid resistance) were detected by biochips. M. tuberculosis genotypings were carried out by IS6110 PCR typing or MIRU typing, in the last method the twelve loci (MIRU 2, 4, 10, 16, 20, 23, 24, 26, 27, 31, 39, 40) have been used. The most frequent mutation in the rpoB gene was Ser531-->Leu (60-70% of the rifampicin resistant strains) and Ser315-->Thr in gene katG (80% of the isoniazid resistant M. tuberculosis). Both in Novosibirsk and in Tomsk prison the rates of clustered cases transmissions were high (69 and 63% respectively). Analysis of the distribution of the dominated mutations Ser531-->Leu (rpoB) and Ser315-->Thr (katG) revealed that all of them were detected in each clusters, but in Novosibirsk there were only two clusters, in which the percentage of strains, containing mutation Ser531-->Leu (rpoB) were higher (85.7% and 77.7% respectively, P < 0.05), then in others. Among the Tomsk prison's clusters it was revealed one in which the proportion of the Ser3 15-->Thr mutation in katGwas higher (96.4%, P < 0.05). The nonuniform distribution of the dominated mutations highlighted that the epidemic spread of drug-resistant strains of M. tuberculosis in region resulted from the selection of them during patient treatment and the subsequent transmission by TB patients.     

Evaluation of biochips for the rifampin resistance detection of M. tuberculosis in strains isolated at the Novosibirsk and Tomsk regions

Recently in Russia biochips for rifampin resistance detection of M. tuberculosis were developed. To investigate the conformity between rifampin resistance results determined both by the routinely used absolute concentration method and USING the biochips, 272 DNA samples of M. tuberculosis isolated from TB patients at Novosibirsk and Tomsk regions in 2000-2005 were analyzed. The biochip can detect 30 mutations in rpoB gene. The mutations were also tested using the single stranded conformational polymorphism method (SSCP). In addition, 60 DNAs were randomly sampled and sequenced. The results of rifampin resistance detection using biochip and absolute concentration methods were congruent in 86% cases, and were different when analyzed samples consisted of the susceptible and resistant strains of M. tuberculosis mixture. The most frequent mutations in the rpoB gene were S531 (76.2%), H526 (7%), D516 (5.6%), and L511 (5.6%). In 94% of rifampin resistant strains, there was also resistance to isoniazid. Therefore, in Siberia the rifampin resistance is the reliable marker for MDR strains of M. tuberculosis, and biochips can be used also for their detection. To hybridize with biochip the fluorescent-labeled single-stranded DNAs were routinely synthesized by two PCR, and intermediary product after the first PCR should be transferred into another tube. The last stage included high risk of cross-contamination. To exclude the risk, primer concentrations and temperature-time profile of PCR reactions were improved, and both PCR were combined in one tube. The two methods were congruent in 100%. The one tube method would be especially attractive for the routine PCR laboratory.     

Microbiological and biogeochemical processes in a pockmark of the Gdansk depression,Baltic Sea

Comprehensive microbiological and biogeochemical investigation of a pockmark within one of the sites of gas-saturated sediments in the Gdansk depression, Baltic Sea was carried out during the 87th voyage of the Professor Shtokman research vessel. Methane content in the near-bottom water and in the underlying sediments indicates stable methane flow from the sediment into the water. In the 10-m water layer above the pockmark, apart from methane anomalies, elevated numbers of microorganisms and enhanced rates of dark CO₂ fixation (up to 1.15 µmol C/(l day)) and methane oxidation (up to 2.14 nmol CH₄/(l day)) were revealed. Lightened isotopic composition of suspended organic matter also indicates high activity of the near-bottom microbial community. Compared to the background stations, methane content in pockmark sediments increased sharply from the surface to 40–60 ml/dm³ in the 20–30 cm horizon. High rates of bacterial sulfate reduction (SR) were detected throughout the core (0–40 cm); the maximum of 74 µmol S/(dm³ day) was located in subsurface horizons (15–20 cm). The highest rates of anaerobic methane oxidation (AMO), up to 80 µmol/dm³ day), were detected in the same horizon. Good coincidence of the AMO and SR profiles with stoichiometry close to 1: 1 is evidence in favor of a close relation between these processes performed by a consortium of methanotrophic archaea and sulfate-reducing bacteria. Methane isotopic composition in subsurface sediments of the pockmark (from ?53.0 to ?56.5‰) does not rule out the presence of methane other than the biogenic methane from the deep horizons of the sedimentary cover.     

First report on chitinous holdfast in sponges (Porifera)

A holdfast is a root- or basal plate-like structure of principal importance that anchors aquatic sessile organisms, including sponges, to hard substrates. There is to date little information about the nature and origin of sponges’ holdfasts in both marine and freshwater environments. This work, to our knowledge, demonstrates for the first time that chitin is an important structural component within holdfasts of the endemic freshwater demosponge Lubomirskia baicalensis. Using a variety of techniques (near-edge X-ray absorption fine structure, Raman, electrospray ionization mas spectrometry, Morgan–Elson assay and Calcofluor White staining), we show that chitin from the sponge holdfast is much closer to α-chitin than to β-chitin. Most of the three-dimensional fibrous skeleton of this sponge consists of spicule-containing proteinaceous spongin. Intriguingly, the chitinous holdfast is not spongin-based, and is ontogenetically the oldest part of the sponge body. Sequencing revealed the presence of four previously undescribed genes encoding chitin synthases in the L. baicalensis sponge. This discovery of chitin within freshwater sponge holdfasts highlights the novel and specific functions of this biopolymer within these ancient sessile invertebrates.     

Hormone resistance and neuroendocrine differentiation due to accumulation of genetic lesions during clonal evolution of prostate cancer

Progression of malignant tumors is largely due to clonal evolution of the primary tumor, clones acquiring different sets of molecular genetic lesions. Lesions can confer a selective advantage in proliferation rate or metastasis on the tumor cell population, especially if developing resistance to anticancer therapy. Prostate cancer (PCa) provides an illustrative example of clinically significant clonal evolution. The review considers the genetic alterations that occur in primary PCa and the mechanism whereby hormone-refractory PCa develops on hormone therapy, including mutations and alternative splicing of the androgen receptor gene (AR) and intratumoral androgen synthesis. Certain molecular genetic lesions determine resistance to new generation inhibitors (AR mutations that block the antagonist effect or allow other hormones to activate the receptor) or lead to neuroendocrine differentiation (repression of the AR signaling pathway, TP53 mutations, and amplification of the AURKA or MYCN oncogene). Multistep therapy based on the data about somatic mutations associated with progression and metastasis of the primary tumor can be expected to significantly improve the survival of patients with advanced PCa in the nearest future.     

Isolation and identification of chitin in the black coral Parantipathes larix (Anthozoa: Cnidaria)

Until now, there is a lack of knowledge about the presence of chitin in numerous representatives of corals (Cnidaria). However, investigations concerning the chitin-based skeletal organization in different coral taxa are significant from biochemical, structural, developmental, ecological and evolutionary points of view. In this paper, we present a thorough screening for the presence of chitin within the skeletal formations of a poorly investigated Mediterranean black coral, Parantipathes larix (Esper, 1792), as a typical representative of the Schizopathidae family. Using a wide array variety of techniques ((13)C solid state NMR, Fourier transform infrared (FTIR), Raman, NEXAFS, Morgan-Elson assay and Calcofluor White Staining), we unambiguously show for the first time that chitin is an important component within the skeletal stalks as well as pinnules of this coral.