The corrin moiety of coenzyme B12 is the determinant for switching the btuB riboswitch of E. coli

Riboswitches are regulatory elements in the 5'-untranslated region (5'-UTR) of bacterial mRNAs that bind certain metabolites with high specificity and affinity. The 202 nucleotide (nt)-long btuB riboswitch RNA of E. coli interacts specifically with coenzyme B12 and its derivatives thereby leading to changes in the RNA structure and hence to an altered expression of the downstream btuB gene. We report the investigations of the rearrangement of the three-dimensional structure of the btuB riboswitch upon binding to four different B12 derivatives: coenzyme B12, vitamin B12, adenosyl factor A and adenosyl-cobinamide. In-line probing experiments have shown that the corrin ring plays the crucial role in switching the three-dimensional riboswitch structure. Instead, the apical ligands influence only the binding affinity of the B12 derivative to the btuB riboswitch.     

Structural determination of individual chemical species in a mixed system by iterative transformation factor analysis-based X-ray absorption spectroscopy combined with UV-visible absorption and quantum chemical calculation

A multitechnique approach using extended X-ray absorption fine structure (EXAFS) spectroscopy based on iterative transformation factor analysis (ITFA), UV-visible absorption spectroscopy, and density functional theory (DFT) calculations has been performed in order to investigate the speciation of uranium(VI) nitrate species in acetonitrile and to identify the complex structure of individual species in the system. UV-visible spectral titration suggests that there are four different species in the system, that is, pure solvated species, mono-, di-, and trinitrate species. The pure EXAFS spectra of these individual species are extracted by ITFA from the measured spectral mixtures on the basis of the speciation distribution profile calculated from the UV-visible data. Data analysis of the extracted EXAFS spectra, with the help of DFT calculations, reveals the most probable complex structures of the individual species. The pure solvated species corresponds to a uranyl hydrate complex with an equatorial coordination number (CNeq) of 5, [UO2(H2O)5]2+. Nitrate ions tend to coordinate to the uranyl(VI) ion in a bidentate fashion rather than a unidentate one in acetonitrile for all the nitrate species. The mononitrate species forms the complex of [UO2(H2O)3NO3]+ with a CNeq value of 5, while the di- and trinitrate species have a CNeq value of 6, corresponding to [UO2(H2O)2(NO3)2]0 (D2h) and [UO2(NO3)3]- (D3h), respectively.     

Study of cell antigens and intracellular DNA by identification of element-containing labels and metallointercalators using inductively coupled plasma mass spectrometry

The enumeration of absolute cell numbers and cell proliferation in clinical samples is important for diagnostic and research purposes. Detection of cellular DNA with fluorescent dyes is the most commonly used approach for cell enumeration in cytometry. Inductively coupled plasma mass spectrometry (ICPMS) has been recently introduced to the field of protein and cell surface antigen identification via ICPMS-linked immunoassays using element-labeled affinity reagents such as gold and lanthanide-conjugated antibodies. In the present work, we describe novel methods for using metallointercalators that irreversibly bind DNA and low concentrations of rare earth metals added to cell growth media for rapid and sensitive measurement of cell numbers by mass spectrometry. We show that Ir- and Rh-containing metallointercalators are useful reagents for labeling cells and normalizing signals when studying antigen expression on different types and numbers of cells. Results are presented for solution analysis performed by conventional ICPMS and compared to measurements obtained on the novel flow cytometer mass spectrometer (FC-MS) instrument, designed to analyze multiple antigens and DNA simultaneously in single cells.     

Atmospheric turbulence profiling with SLODAR using multiple adaptive optics wavefront sensors

The slope detection and ranging (SLODAR) method recovers atmospheric turbulence profiles from time averaged spatial cross correlations of wavefront slopes measured by Shack-Hartmann wavefront sensors. The Palomar multiple guide star unit (MGSU) was set up to test tomographic multiple guide star adaptive optics and provided an ideal test bed for SLODAR turbulence altitude profiling. We present the data reduction methods and SLODAR results from MGSU observations made in 2006. Wind profiling is also performed using delayed wavefront cross correlations along with SLODAR analysis. The wind profiling analysis is shown to improve the height resolution of the SLODAR method and in addition gives the wind velocities of the turbulent layers.     

Microstructured Magnetic Calorimeter with Meander-Shaped Pickup Coil

In the last years metallic magnetic calorimeters (MMC) showed an energy resolution of a few eV for x-rays up to 10 keV. This makes MMCs a promising and powerful tool for many applications where photons or energetic massive particles have to be detected—like absolute activity measurements of radioactive isotopes, high resolution x-ray spectroscopy and x-ray fluorescence material analysis. However, in order to fulfill all requirements of these applications and to allow to reach the maximum resolving power a consequent micro-fabrication of the MMC detectors is needed. The micro-fabrication of metallic magnetic calorimeters requires reliable deposition and patterning processes for niobium structures with high critical currents and for paramagnetic sensors. As one result of our advances in microstructuring a fully microfabricated MMC which consists of a meander shaped niobium thin film pickup coil and a 3 μm thick sputter deposited paramagnetic Au:Er temperature sensor will be presented. Deposition of energy in the paramagnetic sensor causes a rise in temperature and results in a change of magnetization, which is measured by a low noise high bandwidth dc-SQUID. The sputter deposited Au:Er films we report on are working well and show thermodynamic properties close to the ones known from bulk material down to temperatures of 45 mK.      

Coercivity and domain structure of nanograined Fe–C alloys after high-pressure torsion

The microstructure and magnetic properties of binary hypo- and hyper-eutectoid Fe–C alloys were studied. The investigations have been carried out on the samples in the as-cast state, after a long annealing at 725 °C and on the specimens after the high-pressure torsion (HPT). The deformation was carried out at the ambient temperature and the pressure of 5 GPa. The grain size after HPT is in the nanometer range. Long annealing leads to a drastic decrease of the coercivity in comparison with the as-cast alloys. In all alloys the coercivity H _c increases with increasing carbon content. The distance L between pinning points for domain walls decreases with increasing carbon content. Increase of the coercivity and decrease of L are more pronounced below the eutectoid concentration. The coercivity of the nanostructured samples is higher than that of the as-cast alloys. Due to the pinning of domain walls by the cementite particles, the hysteresis loop in the coarse-grained alloys both in as-cast and annealed states has a narrowing near the zero magnetization.     

Growth and stability of Ga2O3 nanospheres

Gallium oxide thin films were prepared by thermal evaporation and deposition of Ga₂O₃ on NaCl(001) cleavage planes at varying substrate temperatures, oxygen pressures and deposition rates. The structure of the so-prepared thin films was checked by Transmission Electron Microscopy and Selected Area Diffraction and also characterized by X-ray Photoelectron Spectroscopy and Atomic Force Microscopy, both in the as-deposited state and after different oxidative and reductive treatments. The substrate temperature proved to be most crucial for the structure of the gallium oxide films, ranging from low-contrast amorphous structures at low substrate temperatures (298 K) to nanosphere structures at higher temperatures (580 K). The stability of the films was found to be mainly determined by the interaction of substrate temperature and deposition rate. Crystalline β-Ga₂O₃ structures were obtained after oxidative, reductive and annealing treatments at and beyond 773 K suggesting that the crystallization is mainly a thermal annealing effect.     

Anisotropic behaviour of the glass transition temperature in thin films of Langmuir-Blodgett deposited side chain polymers

Langmuir-Blodgett (LB) films of side chain polyamic acids were formed, deposited onto optical waveguides and imidized via heating to the corresponding polyimides on the optical waveguides. The LB film formation of the side chain polyamic acids, the imidization reaction and the glass transition behaviour of the polyimide thin films were investigated. Polarisation dependent waveguide mode spectroscopy was applied therefore. It was found that the glass transition temperature (Tg) of bulk and LB thin film samples of these polymers are identical and only depend on the spacer length between the side chain and backbone, not on film thickness. Our investigation shows that in the case of the ultrathin film geometry, the glass transition temperature exhibits an anisotropic behaviour. We find the classical kink in the temperature scan (a change in slope of the free volume vs. temperature plot) due to the thermal expansion change at Tg, in p-polarisation only, which is perpendicular to the main chain orientation. In the s-polarisation measurements (parallel to the main chains) no kink was found, only an offset in the vicinity of Tg. We attribute the anisotropic thermal behaviour to a transition, the freezing of segmental motion, in the side chains only.     

High-affinity, selective σ ligands of the 1,2,3,4-tetrahydro-1,4'-silaspiro[naphthalene-1,4'-piperidine] type: syntheses, structures, and pharmacological properties

The 1'-organyl-1,2,3,4-tetrahydrospiro[naphthalene-1,4'-piperidine] derivatives 1?a-4?a [for which organyl=benzyl (1?a), 4-methoxybenzyl (2?a), 2-phenylethyl (3?a), or 3-methylbut-2-enyl (4?a)] are high-affinity, selective σ? ligands. The corresponding sila-analogues 1?b-4?b (replacement of the carbon spirocenter with a silicon atom) were synthesized in multistep syntheses, starting from dichlorodivinylsilane, and were isolated as the hydrochlorides 1?b?HCl-4?b?HCl. Compounds 1?a?HCl-4?a?HCl and 1?b?HCl-4?b?HCl were structurally characterized by NMR spectroscopy (1H, 13C, 2?Si) in solution, and the C/Si analogues 3?a?HCl and 3?b?HCl were studied by single-crystal X-ray diffraction. These structural investigations were complemented by computational studies. The σ? and σ? receptor affinities of the C/Si pairs 1?a/1?b-4?a/4?b were studied with radioligand binding assays. The σ? receptor affinity of the silicon compounds 1?b-4?b is slightly higher than that of the corresponding carbon analogues 1?a-4?a. Because affinity for the σ? receptor is decreased by the C/Si exchange, the σ?/σ? selectivity of the silicon compounds is considerably improved, indicating that the C→Si switch strategy is a powerful tool for modulating both pharmacological potency and selectivity.     

Synthesis and functional characterization of tridegin and its analogues: inhibitors and substrates of factor XIIIa

Tridegin, a 66‐mer peptide isolated from the leech Haementeria ghilianii, is a potent inhibitor of the coagulation factor XIIIa. This paper describes the chemical synthesis of tridegin by two different strategies—solid‐phase assembly and native chemical ligation—both followed by oxidation in solution phase. Tridegin and truncated analogues were examined for their activity and revealed a particular importance of the C‐terminal region of the parent peptide. Based on these studies a minimal sequence required for factor XIIIa inhibition could be identified. Our data revealed that the glutamine residue at position 52 (Q⁵²) of tridegin most likely binds to the active site of factor XIIIa and was therefore suggested to react with the enzyme. The function of the N‐terminal region is also discussed, as the isolated C‐terminal segment of tridegin lost its inhibitory activity rapidly in the presence of factor XIIIa, whereas this was not the case for the full‐length inhibitor.