Benthic zonation of the Eastern Gotland Basin, Baltic Sea

In this paper recent benthic biological studies in the Eastern Gotland Basin area of the Baltic Sea are summarised. A general pattern of vertical distribution of macrofauna is presented and special reference is made to sharp temporal changes in macrofauna of deeper, subhalocline areas of the basin. Information on faunal sediment reworking ability is compiled. The environmental factors driving benthic zonation are discussed and the vertical benthic zones are defined on the basis of their major biological and abiotic features. This analysis shows that due to sharp gradients in environment and clear differences in composition of macrofauna, the ecological functioning of the Eastern Gotland Basin benthic zones is clearly different. Therefore, in the biogeochemical models of benthic-pelagic interaction, these zones (together with water layers they underlie) should be treated separately, as different sub-systems.     

An ultrasensitive colorimetric method for the assay of endo-1,4-β-D-glucanase

Summary A colorimetric method for the assay of endo-1,4--D-glucanase from fungal cellulolytic systems which utilizes xyloglucan as substrate is described. The substrate forms a blue-green complex with I₂ which is lost upon its breakdown with the enzyme. The new assay is a simple one-step procedure and its sensitivity is comparable with that of viscometry.     

Isolation, fractionation and some properties of polysaccharides produced in a bound form by Azospirillum brasilense and their possible involvement in Azospirillum-wheat root interactions

Abstract It was shown that Azospirillum brasilense strains Sp7, Sp107, Sp245, and S17 when cultivated in a liquid synthetic malate medium to the end of the exponential phase of growth, produced at least two complex polysaccharide-containing components. The components were arbitrarily called lipopolysaccharide-protein complex and polysaccharide-lipid complex. These complexes were shown to interact with a wheat germ agglutinin. From polysaccharide-lipid complexes, acidic polysaccharides were isolated and their specific rotation, molecular masses, affinity for wheat germ agglutinin, and monosaccharide composition were determined. The polysaccharides of all strains contained rhamnose, galacturonic acid, and glucosamine, while the polysaccharides of strains Sp7 and S17 included additional fucose and mannose, respectively, and both had galactose. It is suggested that lipopolysaccharide-protein complexes, polysaccharide-lipid complexes, and polysaccharides may be involved in the process of interaction of azospirilla with wheat root surfaces.     

TERRA mimicking ssRNAs prevail over the DNA substrate for telomerase in vitro due to interactions with the alternative binding site

Telomerase is a key component of the telomere length maintenance system in the majority of eukaryotes. Telomerase displays maximal activity in stem and cancer cells with high proliferative potential. In humans, telomerase activity is regulated by various mechanisms, including the interaction with telomere ssDNA overhangs that contain a repetitive G‐rich sequence, and with noncoding RNA, Telomeric repeat‐containing RNA (TERRA), that contains the same sequence. So these nucleic acids can compete for telomerase RNA templates in the cell. In this study, we have investigated the ability of different model substrates mimicking telomere DNA overhangs and TERRA RNA to compete for telomerase in vitro through a previously developed telomerase inhibitor assay. We have shown in this study that RNA oligonucleotides are better competitors for telomerase that DNA ones as RNA also use an alternative binding site on telomerase, and the presence of 2′‐OH groups is significant in these interactions. In contrast to DNA, the possibility of forming intramolecular G‐quadruplex structures has a minor effect for RNA binding to telomerase. Taking together our data, we propose that TERRA RNA binds better to telomerase compared with its native substrate – the 3′‐end of telomere DNA overhang. As a result, some specific factor may exist that participates in switching telomerase from TERRA to the 3′‐end of DNA for telomere elongation at the distinct period of a cell cycle in vivo. Copyright © 2015 John Wiley & Sons, Ltd.     

The program Proteocat as a tool for planning of proteomic experiments

ProteoCat is a computer program that has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the unit of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases Asp-N and GluC). For peptides obtained after virtual hydrolysis or loaded from data files a number of properties important in mass-spectrometric experiments can be calculated and predicted; the resultant data can be analyzed or filtered (to reduce a set of peptides). The program is using new and improved modifications of own earlier developed methods for pI prediction, which can be also predicted by means of popular pKa scales proposed by other reseachers. The algorithm for prediction of peptide retention time has been realized similarly to the algorithm used in the SSRCalc program. Using ProteoCat it is possible to estimate the coverage of amino acid sequences of analyzed proteins under defined limitation on peptides detection, as well as the possibility of assembly of peptide fragments with user-defined minimal sizes of “sticky” ends. The program has a graphical user interface, written on JAVA and available at http://www.ibmc.msk.ru/LPCIT/ProteoCat.     

A simple method of prediction of visibility of peptides in mass spectrometry with electrospray ionization

A new method for selection of essential peptides applicable for protein detection and quantification analysis in the targeted positive electrospray mass spectrometry has been proposed. It is based on the prediction of the normalized abundance of the mass spectrometric peaks by using a linear regression model. This method has the following a priori restrictions: first selection of peptides must be arranged so that at pH 2.5 the tested peptides must be presented mainly as the 2⁺ and 3⁺ ions. Only peptides containing C-terminal lysine or arginine residues should be considered. The amino acid composition of the peptide, the peptide concentration, the ratio of the polar surface of peptide to common surface and ratio of the polar volume to the common volume are used as independent variables. Among several considered combinations of variables the best linear regression model had a determination coefficient in leave-one-out cross-validation procedure of 0.54. This model confidently discriminated peptides with high response ability and peptides with low response ability, and therefore it is applicable for selection of the most favorable peptides among peptides selected by means of simple criteria. This simple and fast screening method can be successfully applied to reduce the list of observed peptides.     

Expression of small RNAs of Mycobacterium tuberculosis in murine models of tuberculosis infection

The determination of the mechanisms contributing to the survival of pathogenic bacteria in the infected organism and the possible ways of their blocking is a promising approach to the development of new methods of affecting these bacteria. Among these mechanisms, the regulation of bacterial metabolism by small RNAs attracts particular interest since it has been found recently to play an important role in the bacterial pathogenesis. We have studied the expression of three most highly expressed small RNAs of Mycobacterium tuberculosis: MTS0997, MTS1338, and MTS2823 during tuberculosis progression in the strains of mice having different genetic resistance to the disease. It has been shown that the maximum expression of these small RNAs occurs at earlier stages of infection.     

Metagenomic Characterisation of the Viral Community of Lough Neagh,the Largest Freshwater Lake in Ireland

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.     

Evolution of ancient lake bivalves: the Lymnocardiinae (Cardiidae) of the Caspian Sea

The Caspian Sea as the largest continental water body in the world is known for its comparably high levels of biodiversity and endemism, also in mollusks. The evolution of a euryhaline taxon of cardiid bivalves, the Lymnocardiinae of the Ponto-Caspian region, remains unclear today. We studied material from the whole recent range of Lymnocardiinae (i.e., the Caspian, the Azov, and the Black Seas) using a LSU rDNA phylogeny aiming at (a) testing the monophyly of Lymnocardiinae and (b) determining the phylogenetic relationships within Cardiidae. Lymnocardiinae s.str. were monophyletic, i.e., a distinct group that included species of Hypanis, Didacna, and Monodacna. Lymnocardiinae as often understood, i.e., including Cerastoderma, are not monophyletic in our analysis and Cerastoderma should thus be transferred to Cardiinae. The Lymnocardiinae s.str. had a shallow tree topology and were poorly resolved. No clearcut biogeographical pattern could be derived from the phylogeny, i.e., species stemming from respective Ponto-Caspian regions, do not necessarily cluster together. We discuss a scenario of the evolutionary history and biogeographical (as well as taxonomic) implications. Given the complex history of the Ponto-Caspian region and the Caspian Sea in particular, the Lymnocardiinae would represent an interesting study object for addressing the consequences of environmental changes on biotic evolution at various spatial and temporal scales.