Contents of Volume 18 (2000)

Volume Contents

Contents of Volume 18 (2000)     

A physical model of laser-assisted blocking of blood flow: I. Rectangular radiation pulses

A method for the calculation of blocking blood flow upon treatment of vessel pathologies by laser irradiation at a wavelength of 530 nm are considered. The model is based on the assumption that blood-vessel occlusion is a consequence of preceding photothermal coagulation of internal layers of the vessel wall. The irradiation regimes are determined that provide homogeneous coagulation of the vessel wall at a minimal energy consumption and high selectivity of action upon irradiation by rectangular laser pulses.     

Application of splines for determining the velocity characteristic of a medium from a vertical seismic survey

A method for solving the inverse kinematic problem of determining the velocity characteristic of a medium from a vertical seismic survey, is proposed. It is based on the combined use of the eikonal equation and spline methods of approximation for multivariable functions. The problem is solved by assuming a horizontally stratified medium; no assumptions about the number of layers and their thickness are made. First, using the data of the first arrival times of the seismic signal from several shotpoints, which are registered by detectors located in the vertical borehole, a spline approximating the function of first arrival time of the signal from source points to any point in the Earth subsurface is constructed. Then with the help of the eikonal equation, the characteristic of the medium around the borehole is determined. Numerical experiments on the model and the real data show high efficiency of the proposed method.     

Dynamic vortex-antivortex interaction in a single cross-tie wall

A fascinating property of micromagnetism comes from the possibility to control the domain and vortex configuration through the sample shape and size. For instance, in a rectangular platelet a configuration containing a stable combination of vortices and an antivortex can be created. Such a single cross-tie wall can be understood as being a coupled micromagnetic system with three static solitons. Here we report on its magnetization dynamics including the vortex-antivortex interactions. The spectrum of eigenmodes is investigated as well as the effect of different vortex core orientations. We show that the vortex dynamics can be used to identify the core configuration, which is not directly accessible to x-ray microscopy because of its limited spatial resolution.     

Capturing the interaction potential of amyloidogenic proteins

Experimentally derived static structure factors obtained for the aggregation-prone protein insulin were analyzed with a statistical mechanical model based on the Derjaguin-Landau-Verwey-Overbeek potential. The data reveal that the protein self-assembles into equilibrium clusters already at low concentrations. Furthermore, striking differences regarding interaction forces between aggregation-prone proteins such as insulin in the preaggregated regime and natively stable globular proteins are found.     

Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction

Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such complexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies.     

Determination of the absolute configurations of pharmacological natural products via density functional theory calculations of vibrational circular dichroism: the new cytotoxic iridoid prismatomerin

A new highly cytotoxic iridoid has very recently been isolated from Prismatomeris tetrandra and shown to have the structure 3, similar to that of the iridoid oruwacin, 2. We report the determination of the absolute configuration (AC) of the new iridoid, prismatomerin, using vibrational circular dichroism (VCD) spectroscopy. The VCD spectrum of the acetate derivative of 3, 4, is analyzed using the Stephens theory of VCD and density functional theory (DFT). The AC of the naturally occurring 3 is shown to be 1R,5S,8S,9S,10S, identical to that of the naturally occurring iridoid plumericin, 1, also determined using VCD spectroscopy. The [alpha]D values of the natural products 3 and 1 are negative and positive, respectively. Since the ACs of 3 and 1 are identical, it follows that the AC of 3 cannot be correctly determined by empirical comparison of the signs of the [alpha]D values of 3 and 1.     

Preparation and characterization of standard reference material 3276, carrot extract in oil

The National Institute of Standards and Technology (NIST), the Food and Drug Administration (FDA) Center for Drug Evaluation and Research (CDER) and Center for Food Safety and Applied Nutrition (CFSAN), and the National Institutes of Health (NIH), Office of Dietary Supplements (ODS) are collaborating to produce a series of standard reference materials (SRMs) for dietary supplements. Standard reference material (SRM) 3276 Carrot Extract in Oil is one in this series, with values assigned for trans-alpha-carotene, trans- and total beta-carotene, delta- and gamma-tocopherol, and twelve fatty acids. Results for carotenoids and tocopherols were obtained by use of combinations of liquid chromatography (LC), on columns of differing selectivity, with absorbance and mass spectrometric (MS) detection. Fluorescence detection also was used for the tocopherols. Results for fatty acids were obtained by use of gas chromatography (GC) with both flame-ionization and mass-spectrometric detection. This material is intended for use as a primary control material when assigning values to in-house (secondary) control materials and for validation of analytical methods for measurement of these analytes in similar matrices.     

Chip-based nano-LC-MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device

Although the proteome of each organism is unambiguously coded in its genome, the proteome shows the real biology in action in each particular organism. New powerful tools are being developed for biochemists and biologists to analyze complex biological samples for studying the complete protein supplement of the genome, i. e., the proteome. There are several methods available for proteome analysis including 2-DE and several forms of MS. In recent years, technologies such as microfluidics and array-based systems have appeared in the field of analysis, identification, and quantification of proteins. These novel approaches might help in solving current technical challenges in proteomics. This paper presents a practical application of the first commercially available microfluidic nano-ESI device coupled with nano-LC (i. e., HPLC-chip) for the analysis of samples of some biological protein mixtures.