Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

Motivation: Although a great deal of progress is being made in the development of fast and reliable experimental techniques to extract genome-wide networks of protein-protein and protein-DNA interactions, the sequencing of new genomes proceeds at an even faster rate. That is why there is a considerable need for reliable methods of in-silico prediction of protein interaction based solely on sequence similarity information and known interactions from well-studied organisms. This problem can be solved if a dependency exists between sequence similarity and the conservation of the proteins’ functions.Results: In this paper, we introduce a novel probabilistic method for prediction of protein-protein interactions using a new empirical probabilistic formula describing the loss of interactions between homologous proteins during the course of evolution. This formula describes an evolutional process quite similar to the process of the Earth’s population growth. In addition, our method favors predictions confi rmed by several interacting pairs over predictions coming from a single interacting pair. Our approach is useful in working with “noisy” data such as those coming from high-throughput experiments. We have generated predictions for fi ve “model” organisms: H. sapiens, D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae and evaluated the quality of these predictions

Defining Priorities for Innovation

The article considers a methodical approach to the determination of priority directions of innovation activity. The suggested methodical approach will allow to determine the branches of science and technology that are promising for commercialization of the created scientific and innovation reserve.Рассматривается методический подход к определению приоритетных направлений инновационной деятельности. Предлагаемый методический подход позволит определить отрасли науки и техники, которые являются перспективными для осуществления коммерциализации созданного научно-инновационного задела

Observation of crystallization slowdown in supercooled para-hydrogen and ortho-deuterium quantum liquid mixtures

We report a quantitative experimental study of the crystallization kinetics of supercooled quantum liquid mixtures of para-hydrogen (pH$_2$) and ortho-deuterium (oD$_2$) by high spatial resolution Raman spectroscopy of liquid microjets. We show that in a wide range of compositions the crystallization rate of the isotopic mixtures is significantly reduced with respect to that of the pure substances. To clarify this behavior we have performed path-integral simulations of the non-equilibrium pH$_2$-oD$_2$ liquid mixtures, revealing that differences in quantum delocalization between the two isotopic species translate into different effective particle sizes. Our results provide first experimental evidence for crystallization slowdown of quantum origin, offering a benchmark for theoretical studies of quantum behavior in supercooled liquids.Comment: 6 pages, 3 figure

Synthesis, local anaesthetic and antiarrhythmic activities of N-alkyl derivatives of proline anilides

We describe here the design, synthesis and evaluation of in vivo local anaesthetic and antiarrhythmic activities of a series of N-alkylproline anilides. Most of the compounds demonstrated surface anaesthetic activity higher than that of lidocaine, ropivacaine and bupivacaine. We established that the local anaesthetic activity was sensitive to structural variations in the substitution pattern at the aromatic ring and the type of alkyl group at the proline nitrogen atom. Some of the prepared N-alkylproline anilides possessed significant antiarrhythmic activity with higher therapeutic indexes than the reference drugs

Observation of the Efimov state of the helium trimer

Quantum theory dictates that upon weakening the two-body interaction in a three-body system, an infinite number of three-body bound states of a huge spatial extent emerge just before these three-body states become unbound. Three helium atoms have been predicted to form a molecular system that manifests this peculiarity under natural conditions without artificial tuning of the attraction between particles by an external field. Here we report experimental observation of this long predicted but experimentally elusive Efimov state of $^{4}$He$_{3}$ by means of Coulomb explosion imaging. We show spatial images of an Efimov state, confirming the predicted size and a typical structure where two atoms are close to each other while the third is far away

Experiments on microjets of undercooled liquid hydrogen

28th International Symposium on Rarefied Gas Dynamics 2012 (2012). AIP Conf. Proc.; 9 pags. ; 7 figs. ; 1 tab. ; PACS: 67.63.Cd, 33.20.Fb, 64.60.My, 64.70.dg, 47.60.KzNovel experiments on liquid microjets (filaments) of hydrogen and deuterium, carried out at the Laboratory of Molecular Fluid Dynamics of the IEM, are reported. These filaments, less than 10 microns in diameter, are an ideal medium to produce highly undercooled liquid samples and to investigate the homogeneous solidification process, free from wall effects. The filaments exit from cryogenic capillary nozzles into a vacuum chamber, to cool down very fast by surface evaporation. Finite size radius leads to a temperature gradient across the filament, determined by thermal conductivity, and, possibly, to a velocity gradient as well. The filaments are monitored by laser shadowgraphy, and analyzed by means of high performance Raman spectroscopy. Real-time measurements in the rotational and vibrational spectral regions reveal the structure and temperature along the filaments, allowing to track the crystal growth process. The high spatial resolution of Raman spectroscopy allows observing in situ the structural changes of the liquid microjets, with a time resolution of ∼ 10 ns. The filaments of pure para-H2 can be cooled down to 9 K (65% of its melting point at 13.8 K), while staying liquid, before eventually solidifying into a metastable polymorph. Crystallization kinetics revealed a growth rate of 33 cm/s, much higher than expected for a thermally activated process. The time and spatial control attained in these experiments offers new opportunities for investigating the processes of nonequilibrium phase transformations in undercooled fluids, as well as the propagation of liquid jets into a rarefied gas media. © 2012 American Institute of PhysicsThis work has been supported by the the Spanish Ministerio de Ciencia e Innovacion, through grants FIS2007-61430, FIS2010-22064-C02-01, and HD2008-0068, by the Helmholtz Gemeinschaft, through grant VH-NG-331, and by the German academic exchange service (DAAD) under reference Nr. 50025171.Peer reviewe

The interplay between ferroelectricity and electrochemical reactivity on the surface of binary ferroelectric Alx_xB1−x_{1-x}N

Polarization dynamics and domain structure evolution in ferroelectric Al$_{0.93}$B$_{0.07}$N are studied using piezoresponse force microscopy and spectroscopies in ambient and controlled atmosphere environments. The application of negative unipolar, and bipolar first-order reverse curve (FORC) waveforms leads to a protrusion-like feature on the Al$_{0.93}$B$_{0.07}$N surface and reduction of electromechanical response due to electrochemical reactivity. A surface change is also observed on the application of fast alternating current bias. At the same time, the application of positive biases does not lead to surface changes. Comparatively in a controlled glove box atmosphere, stable polarization patterns can be observed, with minuscule changes in surface morphology. This surface morphology change is not isolated to applying biases to free surface, a similar topographical change is also observed at the electrode edges when cycling a capacitor in ambient environment. The study suggests that surface electrochemical reactivity may have a significant impact on the functionality of this material in the ambient environment. However, even in the controlled atmosphere, the participation of the surface ions in polarization switching phenomena and ionic compensation is possible.Comment: 16 pages; 5 figure