The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the a...

Inflammation is the basis of many diseases, with chronic wounds amongst them, limiting cell proliferation and tissue regeneration. Our previous preclinical study of flax fiber applied as a wound dressing and analysis of its components impact on the fibroblast transcriptome suggested flax fiber hydrophobic extract use as an anti-inflammatory and wound healing preparation. The extract contains ca...

A chloropropyl-functionalized silica (CP-silica) hybrid monolithic column was synthesized within the confines of a capillary via the sol-gel process using tetramethoxysilane (TMOS) and (3-chloropropyl)-trimethoxysilane (CPTMS) as the precursors. The resulting CP-silica hybrid monolith inside the capillary showed homogeneous macroporous morphology and was well attached to the inner wall of the c...

We demonstrate microscale spatial and chemical control of diffusion within protein matrixes created through the use of nonlinear multiphoton excited photochemistry. The mobility of fluorescent dyes of different mass and composition within controlled cross-linked environments has been measured using two-photon excited fluorescence recovery after photobleaching (FRAP). The diffusion times for sev...

The first successful approach to synthesizing ultrabright fluorescent mesoporous silica nanoparticles is reported. Fluorescent dye is physically entrapped inside nanochannels of a silica matrix created during templated sol-gel self-assembly. The problem of dye leakage from open channels is solved by incorporation of hydrophobic groups in the silica matrix. This makes the approach compatible wit...

In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a 20 × 20 matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we find that the MJ matrix can be accurately reconstructed from its first two principal component vectors as Mij = C0 + C1(qi + qj) + C2qiqj , with constant C’s, and 20...

Some properties of compounds in degrading bacteria are required for biodegradation of contaminants to higher performance. Those strains which have a high percentage of these features are more effective at biodegradation. The present experiments were designed to measure these parameters. In this study, measurement of cell surface hydrophobic-degrading bacteria was designed which oil was separate...

Pluronic/bile salt/phospholipid mixed micelles (Pluronic/BS/PS-MM) drug carrier system for solubilization hydrophobic drugs was developed. A typical hydrophobic compound, pyrene, was selected as a representative hydrophobic compound to model the hydrophobic drugs. Five Pluronics, F68, F88, F98, F108, and F127 with different PPO chain length were studied. CMC data and solubilization capacities w...

We present an amino map based on their inter-residue contact energies using the Miyazawa-Jernigan matrix. This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact energies imply the hydrophobic-hydrophilic nature of the amino acid residues. With the help of the map we are able to compare and draw inferences from unc...