Ali El-Lakkani

Characteristics of low-angle x-ray scattering from some biological samples.

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.

An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation

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.

Study of the radiation protection effect of selenium-methionine by determining the paramagnetic properties of liver tissues of mice

The paramagnetic properties of the liver tissues were observed after the change which took place during 3, 18 and 24 hours following the administration of s-methionine or alternatively of se-methionine and subsequent irradiation. The signals recorded were those characteristic of P-450 citochrome, free radicals of the semichinon type, Mo-protein and Fe-s-protein. Spectra of these paramagnetic centres generally show the changes in activity of the ferments characteristic for the tissue, which is closely related to the increased or decreased functional activity of the liver tissues [1,2].We showed that in irradiated animals which contained ordinary methionine the functional activity of the hepocites drops with the increase of doses. In animals treated with se-methionine, however, the functional activity was found to be significantly larger in comparison with the control group of animals which had not been protected. This is believed to be due to the radiation protective effect of se-methionine.

An efficient method for measuring the similarity of protein sequences

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.

A method to improve prediction of secondary structure for large single RNA sequences

The function of a particular RNA molecule within an organic system is principally determined by its structure. The current physical methods available for structure determination are time consuming and expensive. Hence, computational methods for structure prediction are often used. The prediction of the structure of a large single sequence of RNA needs a lot of research work. In the present work, a method is introduced to improve the prediction of large single sequence RNA secondary structure obtained by Mfold program using the concept of minimum free energy. The Mfold program contains a constraint option that allows forcing some helices in the predicted structure. In our method, some of the firstly formed hairpins that are expected, by a statistical study, to be present in the real structure are forced in the Mfold predicted structure. The results show improvement, toward the real structure, in the Mfold predicted structure and this gives evidence to the RNA kinetic folding.

Transient conductivity change in purple membrane suspension during the photocycle

During the photocycle of bacteriorhodopsin in the purple membrane of Halobacteria halobium protons are pumped through the membrane. In purple membrane suspension the release and uptake of protons cause a transient electric conductivity change. This change is measured in AC electric field oriented purple membrane suspension. The signal is strongly and nonlinearly orientational dependent. The time course of the electric signal is analyzed and it is shown that proton release coincides with the decay of the M-state and the proton uptake with the decay of theO-state.