Hyperbaria and stress

Performed on rats was study of the cause of appearance of stress reaction at action of hyperbaria upon organism. It was established that at the 5-h long action of gas mixtures (oxygen—nitrogen and oxygen—argon) under pressure of 0.35 and 0.5 MPa and partial pressure of oxygen of 0.02–0.03 MPa in camera 300 l in volume there was clearly realized stress confirmed by the corresponding markers. The appearance of stress was connected with density of gas mixture, which amounted to 6 g/l, that mechanically makes breathing difficult. On the other hand, use for respiration mixtures of elegas (SF6) with density of 6 g/l at normal pressure produces pronounced stress. At equal density, no difference was revealed in action of nitrogen, argon or elegas. Thus, use of high pressures requires light gases (helium, hydrogen, neon) that have low density.     

A Causal Role for V5/MT Neurons Coding Motion-Disparity Conjunctions in Resolving Perceptual Ambiguity

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QuartetS: a fast and accurate algorithm for large-scale orthology detection

The unparalleled growth in the availability of genomic data offers both a challenge to develop orthology detection methods that are simultaneously accurate and high throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence in the accumulated sequenced genomes. Here, we report a novel orthology detection method, termed QuartetS, that exploits evolutionary evidence in a computationally efficient manner. Based on the well-established evolutionary concept that gene duplication events can be used to discriminate homologous genes, QuartetS uses an approximate phylogenetic analysis of quartet gene trees to infer the occurrence of duplication events and discriminate paralogous from orthologous genes. We used function- and phylogeny-based metrics to perform a large-scale, systematic comparison of the orthology predictions of QuartetS with those of four other methods [bi-directional best hit (BBH), outgroup, OMA and QuartetS-C (QuartetS followed by clustering)], involving 624 bacterial genomes and >2 million genes. We found that QuartetS slightly, but consistently, outperformed the highly specific OMA method and that, while consuming only 0.5% additional computational time, QuartetS predicted 50% more orthologs with a 50% lower false positive rate than the widely used BBH method. We conclude that, for large-scale phylogenetic and functional analysis, QuartetS and QuartetS-C should be preferred, respectively, in applications where high accuracy and high throughput are required.     

Proteome sequence features carry signatures of the environmental niche of prokaryotes

Background  

Prokaryotic environmental adaptations occur at different levels within cells to ensure the preservation of genome integrity, proper protein folding and function as well as membrane fluidity. Although specific composition and structure of cellular components suitable for the variety of extreme conditions has already been postulated, a systematic study describing such adaptations has not yet been performed. We therefore explored whether the environmental niche of a prokaryote could be deduced from the sequence of its proteome. Finally, we aimed at finding the precise differences between proteome sequences of prokaryotes from different environments.     

K<Superscript>+</Superscript>/Na<Superscript>+</Superscript> in the animal extracellular fluid at weathering of granitoids and problem of the origin of life

Leaching of granitoids of the paleoproterozoic age was performed from several seconds to 360 days in water solutions (pH < 6.0) in the oxygen or argon medium. Under these conditions the entrance of K⁺ into the solution has been shown to occur at the higher rate than that of Na⁺. The obtained data are considered as evidence in favor of a possibility of the existence at the earlier stages of the Earth geologic history of water reservoirs with predominance of K⁺ over Na⁺. The K⁺/Na⁺ ratio exceeding 1 has been shown in prokaryotes, in cells and tissues of the free living and parasitic species of invertebrate and vertebrate animals. At the same time, in the extracellular fluid of the fresh water, marine, and terrestrial animals, in which the Na+ concentration varies from 13 to 482 mmol/l, the K⁺/Na⁺ ratio is preserved at the level of 0.034 ± 0.001. These results are discussed in relation to the problem of origin of protocells and of concentration ratios of monovalent cations in water phases of multicellular organisms.     

Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases

In this article, we present a new method termed CatFam (Catalytic Families) to automatically infer the functions of catalytic proteins, which account for 20-40% of all proteins in living organisms and play a critical role in a variety of biological processes. CatFam is a sequence-based method that generates sequence profiles to represent and infer protein catalytic functions. CatFam generates profiles through a stepwise procedure that carefully controls profile quality and employs nonenzymes as negative samples to establish profile-specific thresholds associated with a predefined nominal false-positive rate (FPR) of predictions. The adjustable FPR allows for fine precision control of each profile and enables the generation of profile databases that meet different needs: function annotation with high precision and hypothesis generation with moderate precision but better recall. Multiple tests of CatFam databases (generated with distinct nominal FPRs) against enzyme and nonenzyme datasets show that the method's predictions have consistently high precision and recall. For example, a 1% FPR database predicts protein catalytic functions for a dataset of enzymes and nonenzymes with 98.6% precision and 95.0% recall. Comparisons of CatFam databases against other established profile-based methods for the functional annotation of 13 bacterial genomes indicate that CatFam consistently achieves higher precision and (in most cases) higher recall, and that (on average) CatFam provides 21.9% additional catalytic functions not inferred by the other similarly reliable methods. These results strongly suggest that the proposed method provides a valuable contribution to the automated prediction of protein catalytic functions. The CatFam databases and the database search program are freely available at http://www.bhsai.org/downloads/catfam.tar.gz.     

Peculiarities of development in the marine brown alga <Emphasis Type="Italic">Alaria angusta</Emphasis> Kjellman, 1889 (Alariaceae: Ochrophyta) under laboratory-controlled conditions

This paper describes the formation of gametophytes and the early stages of the development of sporophytes in the kelp seaweed Alaria angusta from Kamchatka. To establish laboratory cultures we used zoospores obtained from A. angusta sporophytes collected on October 29, 2014. The gametophytes were grown under different conditions: at 6–7°С and natural light and at 10°С and illumination with cool white fluorescent bulbs, 30 μmol photon m^–2 s^–1, 12: 12 h L: D cycle. In the first case (natural light, 6–7°С), the vegetative growth of male and female gametophytes lasted for more than 4 months; maturation of sexual products occurred 144 days after germination of the embryospores. In the second case (artificial light, 10°С), rapid development of the gametophytes occurred; the first juvenile sporophytes appeared on the 10th day after the zoospores settled onto the substrate. Our data contribute to understanding of the regulatory effect of temperature and light on the peculiarities of species vegetation in the natural environment and formation of the age structure of the species population, one particular feature of this process is the continuous appearance of juvenile sporophytes in the warm period of the year.     

Thyroid activity in patients with major depression

Hypothalamus-pituitary-thyroid (HPT) axis dysfunction has been associated with pathophysiology of major depression. The aim of the study was to determine serum levels of total 3,5,3'-triiodothyronine (T3), total thyroxine (T4) and thyroid-stimulating-hormone (TSH) in patients with major depression and healthy controls. The study included 53 medication-free patients with depression and 49 healthy controls. Exclusion criteria for patients was: other axis-I and axis-II diagnoses, intensive psychotherapy or electroconvulsive therapy, prior clinical and/or laboratory evidence of hypo- or hyperthyroidism, alcohol or nicotine dependence, pregnancy, hormone supplement therapy, somatic illnesses (diabetes, renal or hepatic disorders), infections or autoimmune diseases, recent surgical treatment or significantly changed body weight. For controls: the presence of psychiatric disorders and/or thyroid dysfunctions. The diagnosis of major depression was made using structured clinical interview based on DSM-IV criteria. The results showed significantly lower T3 and TSH levels in patients compared to controls. There was no significant difference in T4 values between patients with depression and control subjects. The results showing altered levels of thyroid hormones in depression indicate that further research on thyroid hormone activity can contribute to the better understanding of the biological basis of depression. Based on the high frequency of the subtle neuroendocrine disorders coexisting with depression, the association of thyroid abnormalities and depression should not be underestimated. Future research should identify different behavioral endophenotypes characteristic for depression, which would greatly facilitate delineating the biological phenomena associated with this psychiatric illness.     

Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions

MOTIVATION: Data that characterize primary and tertiary structures of proteins are now accumulating at a rapid and accelerating rate and require automated computational tools to extract critical information relating amino acid changes with the spectrum of functionally attributes exhibited by a protein. We propose that immunoglobulin-type beta-domains, which are found in approximate 400 functionally distinct forms in humans alone, provide the immense genetic variation within limited conformational changes that might facilitate the development of new computational tools. As an initial step, we describe here an approach based on Support Vector Machine (SVM) technology to identify amino acid variations that contribute to the functional attribute of pathological self-assembly by some human antibody light chains produced during plasma cell diseases. RESULTS: We demonstrate that SVMs with selective kernel scaling are an effective tool in discriminating between benign and pathologic human immunoglobulin light chains. Initial results compare favorably against manual classification performed by experts and indicate the capability of SVMs to capture the underlying structure of the data. The data set consists of 70 proteins of human antibody kappa1 light chains, each represented by aligned sequences of 120 amino acids. We perform feature selection based on a first-order adaptive scaling algorithm, which confirms the importance of changes in certain amino acid positions and identifies other positions that are key in the characterization of protein function.     

Are endogenous clustered DNA damages induced in human cells?

Although clustered DNA damages are induced in cells by ionizing radiation and can be induced artifactually during DNA isolation, it was not known if they are formed in unirradiated cells by normal oxidative metabolism. Using high-sensitivity methods of quantitative gel electrophoresis, electronic imaging, and number average length analysis, we found that two radiosensitive human cell lines (TK6 and WI-L2-NS) accumulated Fpg-oxidized purine clusters and Nth-oxidized pyrimidine clusters but not Nfo-abasic clusters. However, four repair-proficient human lines (MOLT 4, HL-60, WTK1, and 28SC) did not contain significant levels (<5/Gbp) of any cluster type. Cluster levels were independent of p53 status. Measurement of glycosylase levels in 28SC, TK6, and WI-L2-NS cells suggested that depressed hOGG1 and hNth activities in TK6 and WI-L2-NS could be related to oxybase cluster accumulation. Thus, individuals with DNA repair enzyme deficiencies could accumulate potentially cytotoxic and mutagenic clustered DNA damages. The absence of Nfo-detected endogenous clusters in any cells examined suggests that abasic clusters could be a signature of cellular ionizing radiation exposure.