Significant Residue Features Revealed By Eigenvalue Decomposition Analysis Of Blosum Matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

On diagonal-Schur complements of block diagonally dominant matrices

It is known that the diagonal-Schur complements of strictly diagonally dominant matrices are strictly diagonally dominant matrices [J.Z. Liu, Y.Q. Huang, Some properties on Schur complements of H-matrices and diagonally dominant matrices, Linear Algebra Appl. 389 (2004) 365-380], and the same is true for nonsingular H-matrices [J.Z. Liu, J.C. Li, Z.T. Huang, X. Kong, Some properties of Schur complements and diagonal-Schur complements of diagonally dominant matrices, Linear Algebra Appl. 428 (2008) 1009-1030]. In this paper, we research the properties on diagonal-Schur complements of block diagonally dominant matrices and prove that the diagonal-Schur complements of block strictly diagonally dominant matrices are block strictly diagonally dominant matrices, and the same holds for generalized block strictly diagonally dominant matrices. (C) 2010 Elsevier Inc. All rights reserved.

Some new bounds on eigenvalues of the Hadamard product and the Fan product of matrices

Let A and B be nonsingular M-matrices. A lower bound on the minimum eigenvalue q(B circle A(-1)) for the Hadamard product of A(-1) and B, and a lower bound on the minimum eigenvalue q(A star B) for the Fan product of A and B are given. In addition, an upper bound on the spectral radius rho(A circle B) of nonnegative matrices A and B is also obtained. These bounds improve several existing results in some cases and the estimating formulas are easier to calculate for they are only depending on the entries of matrices A and B. (C) 2009 Elsevier Inc. All rights reserved.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

A comparison of silicon oxide and nitride as host matrices on the photoluminescence from Er3+ ions

This paper compares the properties of silicon oxide and nitride as host matrices for Er ions. Erbium-doped silicon nitride films were deposited by a plasma-enhanced chemical-vapour deposition system. After deposition, the films were implanted with Er3+ at different doses. Er-doped thermal grown silicon oxide films were prepared at the same time as references. Photoluminescence features of Er3+ were inspected systematically. It is found that silicon nitride films are suitable for high concentration doping and the thermal quenching effect is not severe. However, a very high annealing temperature up to 1200 degrees C is needed to optically activate Er3+ which may be the main obstacle to impede the application of Er-doped silicon nitride.

Calculation of the band structure of semiconductor quantum wells using scattering matrices

The transfer-matrix method widely used in the calculation of the band structure of semiconductor quantum wells is found to have limitations due to its intrinsic numerical instability. It is pointed out that the numerical instability arises from free-propagating transfer matrices. A new scattering-matrix method is developed for the multiple-band Kane model within the envelope-function approximation. Compared with the transfer-matrix method, the proposed algorithm is found to be more efficient and stable. A four-band Kane model is used to check the validity of the method and the results are found to be in good agreement with earlier calculations.

Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

Dendrimer films as matrices for electrochemical fabrication of novel gold/palladium bimetallic nanostructures

Electrodeposition of novel Au/Pd bimetallic nanostructures with dendrimer films as matrices has been reported. The dendrimers exhibited highly open structures arising from protonation of amines and this made them have good penetrability for solvent molecules. The unique properties of dendrimers obviously affected the morphologies and compositions of deposited bimetallic nanostructures compared with those from unmodified surfaces. Field-emitted scanning electron microscopy, energy dispersive spectroscopy, X-ray photoelectron spectroscopy and UV-vis spectroscopy were used to characterize these nanostructures.