QCD with dynamical Wilson fermions. II

We present results for the QCD spectrum and the matrix elements of scalar and axial-vector densities at β=6/g2=5.4, 5.5, 5.6. The lattice update was done using the hybrid Monte Carlo algorithm to include two flavors of dynamical Wilson fermions. We have explored quark masses in the range ms≤mq≤3ms. The results for the spectrum are similar to quenched simulations and mass ratios are consistent with phenomenological heavy-quark models. The results for matrix elements of the scalar density show that the contribution of sea quarks is comparable to that of the valence quarks. This has important implications for the pion-nucleon σ term.

Kaon B parameter with Wilson fermions

We calculate the kaon B parameter in quenched lattice QCD at beta=6.0 using Wilson fermions at kappa=0.154 and 0.155. We use two kinds of nonlocal (''smeared'') sources for quark propagators to calculate the matrix elements between states of definite momentum. The use of smeared sources yields results with much smaller errors than obtained in previous calculations with Wilson fermions. By combining results for p=(0,0,0) and p=(0,0,1), we show that one can carry out the noperturbative subtraction necessary to remove the dominant lattice artifacts induced by the chiral-symmetry-breaking term in the Wilson action. Our final results are in good agreement with those obtained using staggered fermions. We also present results for B parameters of the DELTAI = 3/2 part of the electromagnetic penguin operators, and preliminary results for B(K) in the presence of two flavors of dynamical quarks.

Characterization of RNA polymerase III transcription factor TFIIIC from the mulberry silkworm, Bombyx mori

Fractionation of nuclear extracts from posterior silk glands of mulberry silkworm Bombyx mori. resolved the transcription factor TFIIIC into two components (designated here as TFIIIC and TFIIIC1) as in HeLa cell nuclear extracts. The reconstituted transcription of tRNA genes required the presence of both components. The affinity purified TFIIIC is a heteromeric complex comprising of five subunits ranging from 44 to 240 kDa. Of these, the 51-kDa subunit could be specifically crosslinked to the B box of tRNA(1)(Gly). Purified swTFIIIC binds to the B box sequences with an affinity in the same range as of yTFIIIC or hTFIIIC2. Although an histone acetyl transferase (HAT) activity was associated with the TFIIIC fractions during the initial stages of purification. the HAT activity, unlike the human TFIIIC preparations, was separated at the final DNA affinity step. The tRNA transcription from DNA template was independent of HAT activity but the repressed transcription from chromatin template could be partially restored by external supplementation of the dissociated HAT activity. This is the first report on the purification and characterization of TFIIIC from insect systems.

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

An association and Wilson activity coefficient model for solubilities of aromatic solid pollutants in supercritical carbon dioxide

The solubilities of various solid pollutants in supercritical carbon dioxide were investigated. The intermolecular interactions play a significant role in determining the solubilities of solids in supercritical carbon dioxide. A new model equation was derived by using the concepts of association and activity coefficient model to correlate the solubilities of solids. The model equation combines the association and Wilson activity coefficient models and includes the interaction potentials between the molecules, which are useful in understanding the behavior of the solid solutes in SCCO2. The new model equation involves five adjustable parameters to correlate the solubilities of solids by incorporating the interactions between the molecules. The equation correlated 75 solid systems with an average AARD of around 9%, which was better than the correlations obtained from standard models such as Mendez Santiago-Teja (MT) model and association model. (C) 2012 Elsevier B.V. All rights reserved.

An estimate of the number of tropical tree species

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between similar to 40,000 and similar to 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of similar to 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of similar to 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.