Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition

Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call "nucleic acid-protein fingerprints". The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells - biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases - 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins

Unified Approach to KdV Modulations

We develop a unified approach to integrating the Whitham modulation equations. Our approach is based on the formulation of the initial value problem for the zero dispersion KdV as the steepest descent for the scalar Riemann-Hilbert problem, developed by Deift, Venakides, and Zhou, 1997, and on the method of generating differentials for the KdV-Whitham hierarchy proposed by El, 1996. By assuming the hyperbolicity of the zero-dispersion limit for the KdV with general initial data, we bypass the inverse scattering transform and produce the symmetric system of algebraic equations describing motion of the modulation parameters plus the system of inequalities determining the number the oscillating phases at any fixed point on the $x, t$ - plane. The resulting system effectively solves the zero dispersion KdV with an arbitrary initial data.Comment: 27 pages, Latex, 5 Postscript figures, to be submitted to Comm. Pure. Appl. Mat

Religiöse Identität: Individuelles und kollektives Selbstbewusstsein im postindustriellen Raum

Monografie in russischer und deutscher Sprache mit Begleitsbeiträge von Matthias Pulte, Andreas Püttmann, Lothar Roo

Master Robotic Net

The main goal of the MASTER-Net project is to produce a unique fast sky survey with all sky observed over a single night down to a limiting magnitude of 19 - 20mag. Such a survey will make it possible to address a number of fundamental problems: search for dark energy via the discovery and photometry of supernovas (including SNIa), search for exoplanets, microlensing effects, discovery of minor bodies in the Solar System and space-junk monitoring. All MASTER telescopes can be guided by alerts, and we plan to observe prompt optical emission from gamma-ray bursts synchronously in several filters and in several polarization planes.Comment: 10 pages, 8 figure

Geochemical evidence for seabed fluid flow linked to the subsea permafrost outer border in the South Kara Sea

Driven by rising bottom water temperatures, the thawing of subsea permafrost leads to an increase in fluid flow intensity in shallow marine sediments and results in the emission of methane into the water column. Limiting the release of permafrost-related gas hydrates and permafrost- sequestered methane into the global carbon cycle are of primary importance to the prevention of future Arctic Ocean acidification. Previous studies in the South Kara Sea showed that abundant hydro-acoustic anomalies (gas flares) induced by seafloor gas discharge into the water column occur in water whose depth is ≥20 m. This distribution of gas flares could indicate the outer extent to which continuous permafrost restricts upward fluid flow. This paper reports on a geochemical analysis of a 1.1 m long sediment core located in an area of shallow fluid flow off of the Yamal Peninsula coast (South Kara Sea) using high-resolution seismic data. Our results reveal a thin zone of Anaerobic Oxidation of Methane (AOM), a sharp shallow sulfate-methane transition (SMT) located at a sub-bottom depth of 0.3 m, and significant temporal variation in methane discharge confirmed by the pyrite (FeS2) distribution in the core sample. A concave up pore water chloride profile depicts upward fresh/brakish water advection in subsurface sediments. The terrestrial/fresh water genesis of methane from the sampled core is deduced from the stable isotopic signatures (δ13 C and δD). We propose two mechanisms for the observed fluid flow: i) convection of thaw water from subsea permafrost; and/or ii) lateral sub-permafrost ground water discharge marking the outer extent of continuous permafrost off of the central Yamal Peninsula coast at ˜45 m water depth

Remote sensing estimates of stand-replacement fires in Russia, 2002–2011

The presented study quantifies the proportion of stand-replacement fires in Russian forests through the integrated analysis of Landsat and Moderate Resolution Imaging Spectroradiometer (MODIS) data products. We employed 30 m Landsat Enhanced Thematic Mapper Plus derived tree canopy cover and decadal (2001–2012) forest cover loss (Hansen et al 2013 High-resolution global maps of 21st-century forest cover change Science 342 850–53) to identify forest extent and disturbance. These data were overlaid with 1 km MODIS active fire (earthdata.nasa.gov/data/near-real-time-data/firms) and 500 m regional burned area data (Loboda et al 2007 Regionally adaptable dNBR-based algorithm for burned area mapping from MODIS data Remote Sens. Environ. 109 429–42 and Loboda et al 2011 Mapping burned area in Alaska using MODIS data: a data limitations-driven modification to the regional burned area algorithm Int. J. Wildl. Fire 20 487–96) to differentiate stand-replacement disturbances due to fire versus other causes. Total stand replacement forest fire area within the Russian Federation from 2002 to 2011 was estimated to be 17.6 million ha (Mha). The smallest stand-replacement fire loss occurred in 2004 (0.4 Mha) and the largest annual loss in 2003 (3.3 Mha). Of total burned area within forests, 33.6% resulted in stand-replacement. Light conifer stands comprised 65% of all non-stand-replacement and 79% of all stand-replacement fire in Russia. Stand-replacement area for the study period is estimated to be two times higher than the reported logging area. Results of this analysis can be used with historical fire regime estimations to develop effective fire management policy, increase accuracy of carbon calculations, and improve fire behavior and climate change modeling efforts