Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

An ESR and NMR study of the gamma radiolysis of a bisphenol-A based polycarbonate and a phthalic acid ester

A study of the gamma-radiolysis of the commercial polymers U-polymer, UP (Unitake) and polycarbonate, PC, (Aldrich) has been undertaken using ESR spectroscopy. The G-value of radical formation at 77 K has been found to be 0.31 +/- 0.01 for UP and 0.5 +/- 0.02 for PC. By using thermal annealing and spectral subtraction, the paramagnetic species formed on irradiation has been assigned. The effect of radiation on the chemical structure of UP and PC has been investigated at ambient temperature and at 423 K. The NMR results show that a new phenol type chain end is formed in the polymers on exposure to gamma-radiation. The G-value of formation of the new phenol ends was estimated to be 0.7 for PC (423 K) and 0.4 for UP (300 K). (C) 1998 John Wiley & Sons, Ltd.

Spin-glass dynamics

Spin glasses are magnetic systems with conflicting and random interactions between the individual spins. The dynamics of spin glasses, as of structural glasses, reflect their complexity. Both in experimental and numerical work the relaxation below the freezing temperature depends strongly on the annealing conditions (aging) and, above the freezing point, relaxation in equilibrium is slow and non-exponential, In this Forum, observed characteristics of the dynamics were summarized and the physical models proposed to explain them were outlined. (C) 1998 Elsevier Science B.V. All rights reserved.

Catalytic activities and coking characteristics of oxides-supported Ni catalysts for CH4 reforming with carbon dioxide

Catalytic activities and deactivation characteristics of oxides-supported nickel catalysts for the reaction of methane reforming with carbon dioxide were investigated. The dynamic carbon deposition on various nickel catalysts was also studied by a thermogravimetric method. Among the catalysts prepared, Ni/La2O3, Ni/alpha-Al2O3, Ni/SiO2, and Ni/CeO2 showed very high CH4 and CO2 conversions and moderate deactivation whereas Ni/MgO and Ni/TiO2 had lower conversions when the Ni reduction was conducted at 500 degrees C. When Ni/MgO catalyst was reduced at 800 degrees C, it exhibited not only comparable conversions of CH4 and CO2 with other active catalysts but also much longer period of stability without deactivation. The amount of carbon deposited in Ni-based catalysts varied depending on the nature of support and followed the order of Ni/La2O3 > Ni/alpha-Al2O3 > Ni/SiO2 > Ni/MgO > Ni/CeO2 at 700 degrees C. The carbons formed on the catalyst surface showed different structural and chemical properties, and these in turn affected the catalytic activity of the catalysts.

CO2 reforming of methane on Ni catalysts: Effects of the support phase and preparation technique

The effects of the support phase and catalyst preparation methods on catalytic activity and carbon deposition were systematically investigated over nickel catalysts supported on Al2O3, SiO2 and MgO for the reforming reaction of methane with carbon dioxide. It is found that the pore structure of the support and metal-support interaction significantly affected the catalytic activity and coking resistance. Catalyst with well-developed porosity exhibited higher catalytic activity. Strong interaction between metal and the support made the catalyst more resistant to sintering and coking, thus resulting in a longer time of catalyst stability. (C) 1998 Elsevier Science B.V.

Solution structure of methionine-oxidized amyloid beta-peptide (1-40). Does oxidation affect conformational switching?

The solution structure of A beta(1-40)Met(O), the methionine-oxidized form of amyloid beta-peptide A beta(1-40), has been investigated by CD and NMR spectroscopy. Oxidation of Met35 may have implications in the aetiology of Alzheimer's disease. Circular dichroism experiments showed that whereas A beta(1-40) and A beta(1-40)Met(O) both adopt essentially random coil structures in water (pH 4) at micromolar concentrations, the former aggregates within several days while the latter is stable for at least 7 days under these conditions. This remarkable difference led us to determine the solution structure of A beta(1-40)Met(O) using H-1 NMR spectroscopy. In a water-SDS micelle medium needed to solubilize both peptides at the millimolar concentrations required to measure NMR spectra, chemical shift and NOE data for A beta(1-40)Met(O) strongly suggest the presence of a helical region between residues 16 and 24. This is supported by slow H-D exchange of amide protons in this region and by structure calculations using simulated annealing with the program XPLOR. The remainder of the structure is relatively disordered. Our previously reported NMR data for A beta(1-40) in the same solvent shows that helices are present over residues 15-24 (helix 1) and 28-36 (helix 2), Oxidation of Met35 thus causes a local and selective disruption of helix 2. In addition to this helix-coil rearrangement in aqueous micelles, the CD data show that oxidation inhibits a coil-to-beta-sheet transition in water. These significant structural rearrangements in the C-terminal region of A beta may be important clues to the chemistry and biology of A beta(1-40) and A beta(1-42).

Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: Effects of solution environment on helicity

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha 3 beta 2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha 3 beta 2 interface. Here we describe the three-dimensional solution structure of MIT determined using 2D H-1 NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 Angstrom for the backbone atoms and 0.34 Angstrom for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha 3 beta 2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

Surface oxide and the role of magnesium during the sintering of aluminum

The effect of trace additions of magnesium on the sintering of aluminum and its alloys is examined. Magnesium, especially at low concentrations, has a disproportionate effect on sintering because it disrupts the passivating Al2O3 layer through the formation of a spinel phase. Magnesium penetrates the sintering compact by solid-state diffusion, and the oxide is reduced at the metal-oxide interface. This facilitates solid-state sintering, as well as wetting of the underlying metal by sintering liquids, when these are present. The optimum magnesium concentration is approximately 0.1 to 1.0 wt pet, but this is dependent on the volume of oxide and, hence, the particle size, as well as the sintering conditions. Small particle-size fractions require proportionally more magnesium than large-size fractions do.

Role of the 6-20 disulfide bridge in the structure and activity of epidermal growth factor

Two synthetic analogues of murine epidermal. growth factor, [Abu6, 20] mEGF4-48 (where Abu denotes amino-butyric acid) and [G1, M3, K21, H40] mEGF1-48, have been investigated by NMR spectroscopy. [Abu6, 20] mEGF4-48 was designed to determine the contribution of the 6-20 disulfide bridge to the structure and function of mEGF The overall structure of this analogue was similar to that of native mEGF, indicating that the loss of the 6-20 disulfide bridge did not affect the global fold of the molecule. Significant structural differences were observed near the N-terminus, however, with the direction of the polypeptide chain between residues four and nine being altered such that these residues were now located on the opposite face of the main beta-sheet from their position in native mEGF Thermal denaturation experiments also showed that the structure of [Abu6, 20] mEGF4-48 was less stable than that of mEGF. Removal of this disulfide bridge resulted in a significant loss of both mitogenic activity in Balb/c 3T3 cells and receptor binding on A431 cells compared with native mEGF and mEGF4-48, implying that the structural changes in [Abu6, 20] mEGF4-48, although limited to the N-terminus, were sufficient to interfere with receptor binding. The loss of binding affinity probably arose mainly from steric interactions of the dislocated N-terminal region with part of the receptor binding surface of EGF [G1, M3, K21, H40] mEGF1-48 was also synthesized in order to compare the synthetic polypeptide with the corresponding product of recombinant expression. Its mitogenic activity in Balb/c 3T3 cells was similar to that of native mEGF and analysis of its H-1 chemical shifts suggested that its structure was also very similar to native.

The use of crosslinking promoters in the gamma-radiolysis of poly(tetrafluoroethylene-co-perfluoromethylvinyl ether). I

Incorporation of 1 wt % of triallyl isocyanurate (TAIC) significantly enhanced the radiation crosslinking of the perfluoroelastomer, poly(tetrafluoroethylene-co-perfluoromethylvinyl ether) (TFE/PMVE). The dose for gelation was lowered by 70% with the presence of TAIC. The additive also improved the tensile properties of TFE/ PMVE both before and after crosslinking by irradiation. Higher radical yields were obtained with the presence of TAIC at 77 K, indicating the crosslinking promoter was acting as a radical trap. ESR studies showed that radiolysis of TAIC and subsequent photobleaching cleaved an allyl branch from the ring structure. Upon thermal annealing, an allyl radical on the TAIC molecule was observed. (C) 1999 John Wiley & Sons, Inc.

Flyash as support for Ni catalysts in carbon dioxide reforming of methane

A series of Ni catalysts supported on flyash treated by various chemical methods was tested for carbon dioxide reforming of methane. Ni catalyst on the flyash treated with CaO (Ni/Ash-CaO) shows high conversion and stability, being close to those of the well-reported Ni/Al2O3 and Ni/SiO2 catalysts with conversions approaching thermodynamic equilibrium levels.

An "openable," high-strength gradient set for orthopedic MRI

A novel three-axis gradient set and RF resonator for orthopedic MRT has been designed and constructed. The set is openable and may be wrapped around injured joints. The design methodology used was the minimization of magnetic field spherical harmonics by simulated annealing. Splitting of the longitudinal coil presents the major design challenge to a fully openable gradient set and in order to efficiently design such coils, we have developed a new fast algorithm for determining the magnetic field spherical harmonics generated by an are of multiturn wire. The algorithm allows a realistic impression of the effect of split longitudinal designs. A prototype set was constructed based on the new designs and tested in a 2-T clinical research system. The set generated 12 mT/m/A with a linear region of 12 cm and a switching time of 100 mu s, conforming closely with theoretical predictions. Preliminary images from the set are presented. (C) 1999 Academic Press.