Comparative bioinformatics analysis of prion proteins isolated from reptile, rodent, ruminant, and human species

Prion proteins (PrPs) are infectious pathogens that cause a group of invariably fatal, neurodegenerative diseases, including Creutzfeldt-Jakob disease, by means of an entirely novel mechanism. They are produced by various species, including reptile, rodent, ruminant and mammals, during normal metabolic processes, but they can be slowly changed into pathogenic isoforms upon contact with other infectious PrP isoforms. This transmission can occur across species barriers. In the present study, phylogram for each PrP sequence was generated by PAUP* 4.0 program using Neighbor-Joining method with 1,000 times bootstrapping process for the phylogenetic analysis. The molecular dynamics (MD) simulations were performed by the SANDER module in the AMBER 7 package using Amber 99 force field. All the simulation process was conducted in the IBM p690 Supercomputing System in Korea Institute of Science and Technology Information. To reduce the calculation time, we used the Generalized Born (GB) model. We compared the sequences and structural characteristics of normal and pathogenic (E200K) human PrPs with those of other reptile, rodent, ruminant and mammalian PrPs. Phylogenetic analysis revealed that, although the turtle PrP sequence is the most distinct of the PrPs analyzed, it nonetheless retains five conserved secondary structural elements that are similar to those found in the mammalian PrPs, suggesting that these elements have important functions in vivo. The RMS deviation between the normal and E200K human PrPs was larger than that between the normal human and bovine PrPs, and all of the beta-sheet structures in human E200K PrP were very stable during MD simulations.     

A highly efficient non-heme manganese complex in oxygenation reactions

A non-heme manganese(II) complex shows a high catalytic activity in the epoxidation of olefins by iodosyl benzene and in the oxidation of olefins, alcohols and alkanes by peracetic acid; a mechanism involving metal-based oxidants is proposed for the oxidation reactions.     

Fabrication of silica-coated magnetic nanoparticles with highly photoluminescent lanthanide probes

Bi-functional nanoparticles (NPs) that consist of silica-coated magnetic cores and luminescent lanthanide (Ln) ions anchored on the silica surface via organic linker molecules are reported. Compared to individual Ln ions, the hybrid NPs show a drastically enhanced photoluminescence due to the efficient ligand-to-metal energy transfer in the Ln-loaded NPs: the new bi-functional NPs could be used in a variety of biological applications involving magnetic separation and optical detection.     

Phonon softening in individual metallic carbon nanotubes due to the Kohn Anomaly

We have studied the line shape and frequency of the G band Raman modes in individual metallic single walled carbon nanotubes (M-SWNTs) as a function of Fermi level (epsilonF) position, by tuning a polymer electrolyte gate. Our study focuses on the data from M-SWNTs where explicit assignment of the G- and G+ peaks can be made. The frequency and line shape of the G- peak in the Raman spectrum of M-SWNTs is very sensitive to the position of the Fermi level. Within +/- variant Planck's over 2piomega/2 (where variant Planck's over 2piomega is the phonon energy) around the band crossing point, the G- mode is softened and broadened. In contrast, as the Fermi level is tuned away from the band crossing point, a semiconductinglike G band line shape is recovered both in terms of frequency and linewidth. Our results confirm the predicted softening of the A-symmetry LO phonon mode frequency due to a Kohn anomaly in M-SWNTs.     

EPR and HYSCORE investigation of the electronic structure of the model complex Mn(imidazole)6: exploring Mn(II)-imidazole binding using single crystals

The electronic structure of the Mn(II)-imidazole binding was studied by EPR spectroscopy using the model complex Mn(Im)(6) diluted in a single crystal of Zn(Im)(6)Cl(2).4(H(2)O). The second rank zero-field splitting (ZFS) tensor (D tensor) of the two sites, a and b, present in the crystal was determined by measuring the orientation patterns of the echo-detected EPR spectra in three different planes at 10K (D(a)=-106, D(b)=-118, E(a)=-17, E(b)=-22x10(-4)cm(-1). Euler angles with respect to the crystal habitus: alpha(a)=13 degrees , beta(a)=76 degrees , gamma(a)=108.5 degrees , alpha(b)=14 degrees , beta(b)=73.5 degrees , gamma(b)=103.5 degrees ). The contribution of cubic ZFS terms to the spectrum allowed us to determine the orientation of the N-Mn-N directions of the complex as well (Euler angles in the D tensor reference frame alpha=100 degrees , beta=23 degrees , gamma=0 degrees , both centers having the same orientation). The hyperfine interactions with (14)N were explored by HYSCORE spectroscopy. The correlation patterns and modulation amplitudes in the 2D experiments were studied for different electron spin transitions and orientations of the crystal. Signals of three different pairs of nitrogens were found. The results were analyzed considering that the N-Mn binding directions are principal directions of the hyperfine and nuclear quadrupole tensor of (14)N. All three pairs of nitrogens were found to be almost equivalent with an isotropic contribution of A(iso) approximately 3.2MHz and an almost axial anisotropic coupling of 2T approximately 1.1MHz along the N-Mn bonding direction. The nuclear quadrupole principal values are 1.5MHz along the bonding direction, -0.6MHz in the direction perpendicular to the imidazole plane, and -0.9MHz in the direction perpendicular to both.     

Reactivities of acridine compounds in hydride transfer reactions

Reactivities of acridine derivatives (10‐benzylacridinium ion, 1a ⁺, 10‐methylacridinium ion, 1b ⁺, and 10‐methyl‐9‐phenylacridinium ion, 1c ⁺) have been compared quantitatively for hydride transfer reactions with 1,3‐dimethyl‐2‐substituted phenylbenzimidazoline compounds, 2Ha–h . Reactions were monitored spectrophotometrically in a solvent consisting of four parts of 2‐propanol to one part of water by volume at 25 ± 0.1 °C. Reduction potentials have been estimated for acridine derivatives by assuming that the equilibrium constants for the reductions of 1a ⁺ –c ⁺ by 2Hb would be the same in aqueous solution and accepting ?361 mV as the reduction potential of the 1‐benzyl‐3‐carbamoylpyridinium ion. The resulting reduction potentials, E, are ?47 mV for 1a ⁺, ?79 mV for 1b ⁺, and ?86 mV for 1c ⁺. Each of acridine derivatives gives a linear Brønsted plot for hydride transfer reactions. The experimental slopes were compared with those obtained by Marcus theory. This comparison shows that the kinetic data are consistent with a one‐step mechanism involving no high‐energy intermediates. Copyright © 2007 John Wiley & Sons, Ltd.     

A note on interpolation in the Lumer's Nevanlinna class

A sufficient condition for free interpolation in the Lumer's Nevanlinna class in the unit ball of ⁿ is given in term of existence of pluriharmonic majorants.     

Application of the taraxerane–oleanane rearrangement to the synthesis of seco-oleanane triterpenoids from taraxerone

Synthetic oleananes and seco-oleananes form a group of promising anti-inflammatory and cancer chemopreventive agents with an excellent safety profile. These compounds are usually prepared by semi-synthesis from natural oleanane triterpenoids. Since a taraxer-14-ene was reported to be rearranged into an olean-12-ene under mild reaction conditions, a rapid synthesis of seco-oleananes from taraxerone, which is a readily available starting material, was explored by us. Treatment of taraxerone with m-chloroperoxybenzoic acid gave 14,15-epoxy lactones, which underwent the taraxerane–oleanane rearrangement leading to new seco-oleanane triterpenoids.     

Spatial and Temporal Bioactive Compound Contents and Chlorophyll Fluorescence of Kale (Brassica oleracea L.) Under UV-B Exposure Near Harvest Time in Controlled Environments

UV-B irradiation has been used to enhance the secondary metabolite content in plants, but its spatial effect on plants has not been considered. The objective of this study was to compare spatial photosynthetic traits and bioactive compound accumulation in kale (Brassica oleracea L. var Acephala) according to the distribution and length of UV-B exposure near harvest. Plants were exposed to UV-B of 0–3, 3–6 and 6–9 W m⁻² for 4 h per day at 5 days (Exp. 1) and 4.2 W m⁻² at 5, 4, 3, 2 or 1 days (Exp. 2) before harvest. In spatial distribution, the higher the UV-B intensity, the lower the mean F_v/F_m (maximal photochemical efficiency of PSII) and the higher the concentration of total flavonoid compound (TFC). With UV-B stress, F_v/F_m and fluorescence transient parameters decreased except for DI₀/CS (dissipated energy flux per cross section) and PI_abs (performance index of PSII). When exposed to UV-B radiation for 2 days before harvest, the total phenolic compounds and TFC per plant were highest, not always proportional to the local F_v/F_m but affected by dry weight. Short-term UV-B stress near harvest would be more efficient for the accumulation of bioactive compounds by minimizing the loss of plant weight.