Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.

Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.

Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions.

This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.

Enhanced multiresolution wavelet analysis of complex dynamics in nonlinear systems.

Multiresolution wavelet analysis (MWA) is a powerful data processing tool that provides a characterization of complex signals over multiple time scales. Typically, the standard deviations of wavelet coefficients are computed depending on the resolution level and such quantities are used as measures for diagnosing different types of system behavior. To enhance the capabilities of this tool, we propose a combination of MWA with detrended fluctuation analysis (DFA) of detail wavelet coefficients. We find that such an MWA&DFA approach is capable of revealing the correlation features of wavelet coefficients in independent ranges of scales, which provide more information about the complex organization of datasets compared to variances or similar statistical measures of the standard MWA. Using this approach, we consider changes in the dynamics of coupled chaotic systems caused by transitions between different types of complex oscillations. We also demonstrate the potential of the MWA&DFA method for characterizing different physiological conditions by analyzing the electrical brain activity in mice.

Extended detrended fluctuation analysis of electroencephalograms signals during sleep and the opening of the blood-brain barrier.

Detrended fluctuation analysis (DFA) is widely used to characterize long-range power-law correlations in complex signals. However, it has restrictions when nonstationarity is not limited only to slow variations in the mean value. To improve the characterization of inhomogeneous datasets, we have proposed the extended DFA (EDFA), which is a modification of the conventional method that evaluates an additional scaling exponent to take into account the features of time-varying nonstationary behavior. Based on EDFA, here, we analyze rat electroencephalograms to identify specific changes in the slow-wave dynamics of brain electrical activity associated with two different conditions, such as the opening of the blood-brain barrier and sleep, which are both characterized by the activation of the brain drainage function. We show that these conditions cause a similar reduction in the scaling exponents of EDFA. Such a similarity may represent an informative marker of fluid homeostasis of the central nervous system.

[Perspectives of improvement of the diagnosis of prostate cancer based on analysis of PCA3 gene expression].

Prostate cancer is the second leading cause of cancer death. The widespread introduction into the clinical practice of test for prostate specific antigen (PSA) led to an increase in the number of prostate biopsies performed. At the same time, a decrease in the threshold of age-specific PSA standards has resulted in an increase in the number of unnecessary biopsies. In this regard, a need has arisen for new prostate cancer biomarkers. PCA3 is a non-coding mRNA that is exclusively expressed by prostate cells. Currently, three generations of test diagnostic systems based on the quantitative analysis of the PCA3 mRNA in the urine or its cell sediment has already developed, and they differ in the type of material studied and the method for estimating the amount of PCA3 mRNA. Clinical studies of the developed test systems have shown that a high level of PCA3 expression in the patients urine correlates with the probability of detecting prostate cancer. PCA3 test has higher positive and negative predictive values than previously used PSA test. These data are repeatedly confirmed by studies conducted in different clinics. Thus, the introduction of the method of quantitative determination of PCA3 in clinical practice can significantly improve the efficiency of diagnosis of prostate cancer and reduce the number of unnecessary biopsies.

Characterizing scaling properties of complex signals with missed data segments using the multifractal analysis.

The scaling properties of complex processes may be highly influenced by the presence of various artifacts in experimental recordings. Their removal produces changes in the singularity spectra and the Hölder exponents as compared with the original artifacts-free data, and these changes are significantly different for positively correlated and anti-correlated signals. While signals with power-law correlations are nearly insensitive to the loss of significant parts of data, the removal of fragments of anti-correlated signals is more crucial for further data analysis. In this work, we study the ability of characterizing scaling features of chaotic and stochastic processes with distinct correlation properties using a wavelet-based multifractal analysis, and discuss differences between the effect of missed data for synchronous and asynchronous oscillatory regimes. We show that even an extreme data loss allows characterizing physiological processes such as the cerebral blood flow dynamics.

Characterization of the chaos-hyperchaos transition based on return times.

We discuss the problem of the detection of hyperchaotic oscillations in coupled nonlinear systems when the available information about this complex dynamical regime is very limited. We demonstrate the ability of diagnosing the chaos-hyperchaos transition from return times into a Poincaré section and show that an appropriate selection of the secant plane allows a correct estimation of two positive Lyapunov exponents (LEs) from even a single sequence of return times. We propose a generalized approach for extracting dynamics from point processes that allows avoiding spurious identification of the dynamical regime caused by artifacts. The estimated LEs are nearly close to their expected values if the second positive LE is essentially different from the largest one. If both exponents become nearly close, an underestimation of the second LE may be obtained. Nevertheless, distinctions between chaotic and hyperchaotic regimes are clearly possible.

Quantifying chaotic dynamics from integrate-and-fire processes.

Characterizing chaotic dynamics from integrate-and-fire (IF) interspike intervals (ISIs) is relatively easy performed at high firing rates. When the firing rate is low, a correct estimation of Lyapunov exponents (LEs) describing dynamical features of complex oscillations reflected in the IF ISI sequences becomes more complicated. In this work we discuss peculiarities and limitations of quantifying chaotic dynamics from IF point processes. We consider main factors leading to underestimated LEs and demonstrate a way of improving numerical determining of LEs from IF ISI sequences. We show that estimations of the two largest LEs can be performed using around 400 mean periods of chaotic oscillations in the regime of phase-coherent chaos. Application to real data is discussed.

Multiresolution analysis of pathological changes in cerebral venous dynamics in newborn mice with intracranial hemorrhage: adrenorelated vasorelaxation.

Intracranial hemorrhage (ICH) is the major problem of modern neonatal intensive care. Abnormalities of cerebral venous blood flow (CVBF) can play a crucial role in the development of ICH in infants. The mechanisms underlying these pathological processes remain unclear; however it has been established that the activation of the adrenorelated vasorelaxation can be an important reason. Aiming to reach a better understanding of how the adrenodependent relaxation of cerebral veins contributes to the development of ICH in newborns, we study here the effects of pharmacological stimulation of adrenorelated dilation of the sagittal sinus by isoproterenol on the cerebral venous hemodynamics. Our study is performed in newborn mice at different stages of ICH using the laser speckle contrast imaging and wavelet analysis of the vascular dynamics of CVBF. We show that the dilation of the sagittal sinus with the decreased velocity of blood flow presides to the stress-induced ICH in newborn mice. These morphofunctional vascular changes are accompanied by an increased variance of the wavelet-coefficients in the areas of endothelial and non-endothelial (KATP-channels activity of vascular muscle) sympathetic components of the CVBF variability. Changes in the cerebral venous hemodynamics at the latent stage of ICH are associated with a high responsiveness of the sagittal sinus to isoproterenol quantifying by wavelet-coefficients related to a very slow region of the frequency domain. The obtained results certify that a high activation of the adrenergic-related vasodilatory responses to severe stress in newborn mice can be one of the important mechanisms underlying the development of ICH. Thus, the venous insufficiency with the decreased blood outflow from the brain associated with changes in the endothelial and the sympathetic components of CVBF-variability can be treated as prognostic criteria for the risk of ICH during the first days after birth.

[Production of gaseous hydrocarbons by microbial communities of Lake Baikal bottom sediments].

Production of gaseous hydrocarbons by the microbial community of the Posolsky Bank methane seep bottom sediments (Southern Baikal) was studied at 4°C. Formation of both methane and a heavier gas- eous hydrocarbon, ethane, was detected in enrichment cultures. The highest methane concentrations (6.15 and 4.51 mmol L(-1)) were revealed in enrichments from the sediments from 55-cm depth incubated with-so- dium acetate and H2/CO2 gas mixture, respectively. A decrease in activity of aceticlastic methanogensand a decrease in methane concentration produced by hydrogenotrophic archaea occurred with depth. The highest concentration of ethane was revealed in enrichments from the microbial community of the layer close to gas hydrates (75 cm) incubated with CO2 as a substrate. According to analysis of the 16S rRNA gene fragments from the clone library, these enrichments were found to contain members of the phylum Crenarchaeota form- ing a separate cluster with members of the class Thermoprotei. The phylum Euryarchaeota was represented by nucleotide sequences of the organisms homologous to members of the orders Methanococcales, Methanosa- rcinales, and Thermoplasmatales.

[Effect of different calcium hypochlorite concentrations on the survival of potentially pathogenic microorganisms isolated from Baikal Lake].

The survival rate of bacteria of the genera Pseudomonas and Enterococcus isolated from Baikal Lake, exposed to different concentration of calcium hypochlorite used as a main agent for drinking water disinfection, was studied. Experimental studies have shown that chlorination was imperfect as this method is not always effective against Enterococci.

[Diversity of cultured aerobic microorganisms in the areas of natural oil seepage on Lake Baikal].

The diversity of cultured aerobic organisms collected from water samples and bottom sediment from two areas of natural oil seepage on Lake Baikal has been researched. Representatives of Alpha-, Beta-, and Gammaproteobacteria have been found in samples collected near the BolTshaya Zelenovskaya River mouth, while near Cape Gorevoi Utes Betaproteobacteria were absent. Most cultures are characterized by a sufficiently high homology level (96-100%) with nucleotide sequences from the international database.

The effect of L-NAME on intra- and inter-nephron synchronization.

Kidney autoregulation involves complicated intra- and inter-nephron synchronization phenomena among oscillatory modes produced, respectively, by the tubuloglomerular feedback (TGF) mechanism and by the myogenic regulation of the afferent arteriolar blood flow. The present study aims at examining to what extent these phenomena are reflected in the overall blood flow to the kidney and how they are affected by intravenous administration of nitro-l-arginine-methyl-ester (L-NAME), a potent NO synthesis inhibitor. Wavelet analysis is applied to detect rhythmic activity at the level of the renal artery and compare the observed fluctuations with blood flow variations recorded from efferent arterioles of individual nephrons. We show that administration of L-NAME increases the gain in both the TGF and the myogenic oscillations, and that both normotensive and hypertensive rats demonstrate reduced stability of the various rhythms. This implies that L-NAME, besides strengthening the gain in the individual feedback mechanisms, also causes more frequent transitions among the various synchronization states. In a broader perspective the purpose of the study is to demonstrate the significance of complex dynamic phenomena in the normal regulation of physiological systems as well as in their response to drugs.

[Microbial community of the water column of the Selenga River-Lake Baikal biogeochemical barrier].

The microbial communities of the estuarine zone and the mixing zone of river and lake waters in the Selenga River estuary were studied using the fluorescence in situ hybridization (FISH) method. The microorganisms belonging to the phylogenetic group Gammaproteobacteria were found to predominate in the river estuary, constituting up to 17% of the total bacterial community. Among cultivable microorganisms, organotrophic bacteria were predominant (2040 CFU/ml) in this zone, which results in high rates of microbial production (6.0 microg C/(1 day). The microbial community structure changed with distance from the river estuary; representatives of the Alpha-, Beta-, and Gammaproteobacteria were present in equal proportions; psychrotolerant and oligotrophic bacteria were numerous. The rate of heterotrophic carbon dioxide assimilation decreased to 3.8 microg C/(1 day). At 5-7 km from the river estuary, where the hydrologic, physical, and chemical conditions are similar to those of lake waters, members of the Betaproteobacteria, which are typical of the open waters of Lake Baikal, are the major representatives of planktonic microorganisms.

Characterizing multimode interaction in renal autoregulation.

The purpose of this paper is to demonstrate how modern statistical techniques of non-stationary time-series analysis can be used to characterize the mutual interaction among three coexisting rhythms in nephron pressure and flow regulation. Besides a relatively fast vasomotoric rhythm with a period of 5-8 s and a somewhat slower mode arising from an instability in the tubuloglomerular feedback mechanism, we also observe a very slow mode with a period of 100-200 s. Double-wavelet techniques are used to study how the very slow rhythm influences the two faster modes. In a broader perspective, the paper emphasizes the significance of complex dynamic phenomena in the normal and pathological function of physiological systems and discusses how simulation methods can help to understand the underlying biological mechanisms. At the present there is no causal explanation of the very slow mode. However, vascular oscillations with similar frequencies have been observed in other tissues.

[Study on the Lake Baikal microbial community in the areas of the natural oil seeps].

We studied the composition of a natural microbial community, the distribution of different groups of microorganisms (including those able to degrade oil hydrocarbons) within the areas of natural oil seeps in the Lake Baikal. It was revealed that, in the bottom sediments, the oil-degrading microorganisms dominating the community have included the bacteria of g. Bacillus, while in the water column, dominating microbes are presented by species of genera Rhodococcus Pseudomonas, and Micrococcus. Under the conditions of the model experiment, the potential activity of Baikal microbes towards utilization of n-alcanes has been assessed. Under such conditions it was shown that the concentration of n-alcanes decreases to 60% during 20 days of the experiment (the initial oil concentration was 0.5 mg/l, i.e., ten maximal permissible concentrations, MPC).

[Comparative characteristics of microbial communities in two regions of natural oil seepage in Lake Baikal].

Microbial communities and hydrocarbon contents have been studied in two regions of natural oil seepage in Lake Baikal: (1) opposite the Bol'shaya Zelenovskaya River mouth (studied previously) and (2) near Cape Gorevoi Utes (discovered in 2005). The abundance of both heterotrophic and hydrocarbon-oxidizing microorganisms is significantly higher in water samples from the first region, where the oil is biologically degraded. In the surface soil layer at stations located in the immediate vicinity of oil seepage site, the abundance of n-alkane-oxidizing microorganisms reaches 2000 cells/ml, and that of oil-oxidizing microorganisms reaches 2600 cells/ml. In water samples from near Cape Gorevoi Utes, the abundance of these groups of microorganisms does not exceed 190 and 500 cells/ml, respectively.

[Rexetin in the therapy of depressive states].

Rexetin was used in the dosage of 20-60 mg daily during 6 weeks in the treatment of 25 patients with depression. An efficacy of the therapy was evaluated by the Hamilton scales for Depression (HAM-D) and anxiety (HAM-A) and Montgomery-Asberg Scale (MADRS). Patients were considered as responders if they demonstrated the reduction of scores by 50%. Twenty-three responders (92.0%) were divided into 3 groups: the first--with immediate therapeutic response during 1-2 weeks (n = 8; 34.8%); the second--with positive dynamics at the 3rd week of the treatment (n = 9; 39.1%); the third group--with favorable results at the end of 5-6 week of the therapy (n = 6; 26.1%). The clinical predictors of different therapeutic responses during short-term therapy were as follows: severity of depressive episode, hypotimia of modality (anxiety, anxiety-sorrow); vitalization of verbal/ nonverbal sorrow affect; presentation of autonomic (somatic) appearances of generalized anxiety disorder; ranks of typical depressive symptoms in subjective perception of patients; character of sleep disorders, presence of atypical depressive symptoms, in particular a disturbance of interpersonal relations due to elevated irritability; localization and extent of generalization of pathological body sensations; dominant content of obsessive anxiety; a type of affective triad; panic attacks, with- or without agoraphobia, concomitant to depressive disorder. In the total group of responders, there was a simultant (harmonic) reduction of the total score on the depression and anxiety scales (65.2%) and the anticipating anxiolytic or thymoanaleptic effect of the drug was observed less often (34.8%).

[Degradation of bis(2-ethylhexyl)phthalate by microorganisms of water and sediments of the Selenga river and Baikal Lake under experimental conditions]. / Degradatsiia bis-(2-étilgeksil)ftalata mikroorganizmami vody i donnykh osadkov r. Selengi i oz. Baikal v usloviiakh model'nogo éksperimenta.

Degradation of bis-(2-ethylhexyl)phthalate (BEHP) by microbial associations of water and bottom sediments of the Selenga River and Lake Baikal and by pure cultures of microbial species belonging to various taxa isolated from the sediments under discussion has been studied. It has been shown that intense biological degradation occurs in both water and sediments. The degrees of conversion in experimental closed systems on minimal media are 46 and 24%, respectively. The most active of the organisms studied is a Micromironospora actinomycete. It degraded BEHP by 36% of its initial concentration. Spore-forming bacteria and microorganisms of the genus Pseudomonas were less active (17-23% and 7-11%).