Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

Heuristic networks for space exploration

This paper reports new results from the development of Linguistic Geometry. This formal theory is intended to discover the inner properties of human expert heuristics, which have been successful in a certain class of complex control systems, and apply them to different systems. Linguistic Geometry relies on the formalization of search heuristics of high-skilled human experts, which allow for the decomposition of a complex system into a hierarchy of subsystems, and thus solve intractable problems by reducing the search. Currently, we investigate heuristics extracted in the form of hierarchical networks of paths. Employing Linguistic Geometry tools, the dynamic hierarchy of networks is represented as a hierarchy of formal attribute languages. This paper includes a formal survey of a Linguistic Geometry, and a new example of a solution of optimization problems for space robotic vehicles. This example includes the actual generation of the hierarchy of languages, with some details of trajectory generation, and it demonstrates the dramatic reduction of search in comparison with conventional search algorithms.     

330 GHz FMCW Image Sensor for Homeland Security Applications

A single-pixel imaging remote sensor operating at 330 GHz is described. It is based on a frequency modulated continuous wave (FMCW) and aimed at detection of concealed objects for ranges up to 40 m. The system consists of 2 horn-lens antennas integrated with a homodyne transceiver. The synthesized linear FMCW signal at X-band is multiplied by a factor of 32 to generate the transmitted signal. An intermediate frequency (IF) signal obtained in the output port of the 2-nd harmonic mixer is employed for image processing. Distance measurements were made by performing data acquisition unit based on LabView interface and resulting in a range resolution about 1 cm. Examples of 2D and 3D images reconstructed with this sensor are presented.     

Towards the integration of dark- and photo-fermentative waste treatment. 2. Optimization of starch-dependent fermentative hydrogen production

Eight natural microbial consortia collected from different sites were tested for dark, hydrogen production during starch degradation. The most active consortium was from silo pit liquid under mesophilic (37 °C) conditions. The fermentation medium for this consortium was optimized (Fe, NH₄⁺, phosphates, peptone, and starch content) for both dark fermentation and for subsequent purple photosynthetic bacterial H₂ photoproduction [Laurinavichene TV, Tekucheva DN, Laurinavichius KS, Ghirardi ML, Seibert M, Tsygankov AA. Towards the integration of dark and photo fermentative waste treatment. 1. Hydrogen photoproduction by purple bacterium Rhodobacter capsulatus using potential products of starch fermentation. Int J Hydrogen Energy 2008;33(23):7020–26], in the presence of the spent dark, fermentation effluent. The addition of Zn (10 mg L⁻¹), as a methanogenesis inhibitor that does not inhibit purple bacteria at this concentration, also did not inhibit dark, fermentative H₂ production. The influence of various fermentation end products at different concentrations (up to 30 g L⁻¹) on dark, H₂ production was also examined. Added lactate stimulated, but added isobutyrate and butanol strongly inhibited gas production. Under optimal conditions the fermentation of starch (30 g L⁻¹) resulted in 5.7 L H₂ L⁻¹ of culture (1.6 mol H₂ per mole of hexose) with the co-production mainly of butyrate and acetate.     

Femtosecond laser modification of an array of vertically aligned carbon nanotubes intercalated with Fe phase nanoparticles

Femtosecond lasers (FSL) are playing an increasingly important role in materials research, characterization, and modification. Due to an extremely short pulse width, interactions of FSL irradiation with solid surfaces attract special interest, and a number of unusual phenomena resulted in the formation of new materials are expected. Here, we report on a new nanostructure observed after the interaction of FSL irradiation with arrays of vertically aligned carbon nanotubes (CNTs) intercalated with iron phase catalyst nanoparticles. It was revealed that the FSL laser ablation transforms the topmost layer of CNT array into iron phase nanospheres (40 to 680 nm in diameter) located at the tip of the CNT bundles of conical shape. Besides, the smaller nanospheres (10 to 30 nm in diameter) are found to be beaded at the sides of these bundles. Some of the larger nanospheres are encapsulated into carbon shells, which sometime are found to contain CNTs. The mechanism of creation of such nanostructures is proposed.     

Morphological and adhesive properties of polypyrrole films synthesized by sonoelectrochemical technique

This paper presents electrochemical synthesis of polypyrrole films under high frequency sonication. The films are characterized in terms of adhesion and surface morphology. Comparison to classical electrosynthesized polypyrrole films is made. In particular, the use of high frequency sonication (500 kHz) during electrodeposition of polypyrrole on Si was reported for the first time. Chronocoulometry was used for polymer films electrosynthesis on Si substrates. Influence of polymer thickness on the rugosity, morphology and adhesion force properties was studied. Scanning Electron Microscopy and mechanical probe profiling showed that sonication led to less rough and more homogeneous surface structure. Adhesion force properties of polypyrrole films were also studied by means of force–distance curves obtained by atomic force microscopy. For polymer films obtained in the absence of sonication, adhesion forces decreases with increase in polymer thickness. On the contrary, for polymer films obtained under sonication, the adhesion of the films decreased when the polymer thickness decreased.     

Persönlichkeit 2.0

Online Social Networks (OSNs) wie MySpace, Facebook und StudiVZ sind inzwischen zu einem wichtigen Bestandteil des allt?glichen Miteinanders geworden. Entgegen der weit verbreiteten Meinung vermitteln Profile in OSNs kein verf?lschtes, selbstidealisiertes, sondern ein sehr genaues Bild von der Pers?nlichkeit der Profilbesitzer. Dies k?nnte ein wichtiger Grund für die Beliebtheit sozialer Netzwerke sein: Sie bieten eine Plattform für reale soziale Interaktionen und erm?glichen den Ausdruck der eigenen Pers?nlichkeit. Implikationen für den Datenschutz in OSNs werden diskutiert.     

ELECTROPORATION: BIO-ELECTROCHEMICAL MASS TRANSFER AT THE NANO SCALE

This article provides a brief review of the field of electroporation and introduces a new microdevice that facilitates studies to test theories, gain understanding, and control this important biomedical technology. Electroporation, a bio-electrochemical process whose fundamentals are not yet understood, is a means of permeating the cell membrane by applying a voltage across the cell and forming nano-scale pores in the membrane. It has become an important field in biotechnology and medicine for the controlled introduction of macromolecules, such as gene constructs and drugs, into various cells. It is viewed as an engineering alternative to biological techniques for the genetic engineering of cells. To study and control electroporation, we have created a low-cost microelectroporation chip that incorporates a live biological cell with an electric circuit. The device revealed an important behavior of cells in electrical fields. They produce measurable electrical information about the electroporation state of the cell that may enable precise control of the process. The device can be used to facilitate fundamental studies of electroporation and can become useful in providing precise control over biotechnological processes.     

Intermetallide catalysts for hydrogen storage on the basis of reversible aromatics hydrogenation/dehydrogenation reactions

New efficient intermetallide catalysts for hydrogen storage in reversible processes of aromatics hydrogenation and naphthene dehydrogenation were studied. These catalysts provide an enhanced activity in the dehydrogenation of saturated organic molecules, with no side reactions like cracking, hydrogenolysis, ring opening, or coke formation occurring on these catalysts. The use of intermetallides provides some hydrogen storage capacity in the low-temperature region, while their catalytic activity in the dehydrogenation affords the hydrogen supply in the high-temperature range.