ABSTRACT
An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
Subject(s)
Sequence Analysis, Protein/methods , Amino Acid Sequence , Amino Acids/chemistry , Animals , Baculoviridae/chemistry , DNA Helicases/chemistry , Electron Transport Complex I/chemistry , Humans , Protein Subunits/chemistry , Species Specificity , Transferrin/chemistry , Vertebrates , Viral Proteins/chemistryABSTRACT
A new two-dimensional graphical representation of protein sequences is introduced. Twenty concentric evenly spaced circles divided by n radial lines into equal divisions are selected to represent any protein sequence of length n. Each circle represents one of the different 20 amino acids, and each radial line represents a single amino acid of the protein sequence. An efficient numerical method based on the graph is proposed to measure the similarity between two protein sequences. To prove the accuracy of our approach, the method is applied to NADH dehydrogenase subunit 5 (ND5) proteins of nine different species and 24 transferrin sequences from vertebrates. High values of correlation coefficient between our results and the results of ClustalW are obtained (approximately perfect correlations). These values are higher than the values obtained in many other related works.
Subject(s)
Sequence Analysis, Protein/methods , Amino Acid Sequence , Amino Acids/chemistry , Animals , Computational Biology , Computer Graphics , Humans , NADH Dehydrogenase/chemistry , Protein Subunits/chemistry , Species Specificity , Transferrin/chemistry , VertebratesABSTRACT
The dielectric properties of two freshly excised mice tissue samples (kidney, skeletal muscle) and also freshly excised Ehrlich solid tumor were measured in the frequency range from 20 Hz to 100 kHz using RLC bridges. The data were fitted to a summation of multiple Cole-Cole dispersion and also to the constant power law which is related formally to the fractal geometries of tissues using a genetic algorithm for optimization developed by the author. The data were in good agreement with the Cole-Cole equation for the three samples.
Subject(s)
Carcinoma, Ehrlich Tumor/physiopathology , Electric Conductivity , Electricity , Kidney/physiology , Muscle, Skeletal/physiology , Animals , Male , MiceABSTRACT
Design of medical imaging devices based on the detection of low-angle coherent scattering is a subject of increasing interest. The technique is based on the differences in the distribution of photons coherently scattered from different body tissues. Coherent scattering is also useful in monitoring changes that may occur in a healthy tissue (e.g. carcinoma). In this work, low angle scattering properties of some tissues and tissue-equivalent materials are studied. Special care is given to the possibility of distinguishing between tissues of similar water content (e.g. muscle and blood). For this purpose, a Monte Carlo simulation is updated, introducing molecular form factor data, which include molecular interference effects. This program is used to simulate the angular distribution of scattered photons from two tissue-equivalent materials (lucite and water) and three biological samples (muscle, fat and blood). Simulation results agree well with previously measured angular distributions of scattered photons at 59.54 keV. Scattering from water and lucite is also measured at 8.047 keV. The effects of scattering geometry, sample thickness, incident photon energy and tissue type on the angular distribution of scattered photons are investigated. Results reveal the potential of measuring the full width at half maximum (FWHM) of the scattered photon distribution for tissue characterization. Energies up to 13 keV and sample thickness of 0.3 cm reported maximum differences between investigated samples. These conditions are expected to maximize the potential of using coherent scattering set-ups to monitor changes in biological samples even if their water contents are similar. Present results may act as a guide for the optimization of coherent scattering imaging systems.
