Detection of carbapenem resistant bacteria (CRB) in Egypt

The emergence of resistant bacteria has become a worldwide threat. Multidrug resistant bacteria are globally spread. Several studies were performed to detect new resistant organisms and also the genes which are responsible for their resistance. Carbapenem resistance is considered the most dangerous resistance. In this study, we detect the presence of carbapenem resistant bacteria (CRB) in Egypt. This may cause un-treatable epidemic if its organization is neglected. This study distinguished the pathogens that are carbapenemase producing due to the presence of bla-NDM gene. The results detected the presence of CRB stains such as Klebsiella sp., Pseudomonas sp., Citrobacter sp., Enterobacter sp., Acinetobacter sp. and E. coli. As a result from this study, it is now proved that there are CRB in Egypt, thus it must be given a great consideration and must be managed. DOI: http://dx.doi.org/10.5281/zenodo.340876

Group theoretic methods applied to Burgers’ equation

AbstractIn this study, the group-theoretic methods for calculating the solution of Burgers’ equation with appropriate boundary- and initial-conditions is presented. The application of a one-parameter group reduces the number of independent variables by one, and consequently the governing partial differential equation with the boundary- and initial-conditions to an ordinary differential equation with the appropriate corresponding conditions. The obtained differential equation is solved analytically and the solution obtained in closed form, for a specific choice of boundary condition

BOUNDARY INTEGRAL METHODS AND FREE SURFACE PROBLEMS.

This dissertation is a study of boundary integral methods and free surface problems. An analysis is made for three problems, flow over an uneven bottom, flow from a uniform channel over shelf, and flow from a uniform channel over a sharp-crested weir. All problems studied here include the influence of gravity, under the assumptions that the motion is irrotational, the fluid is incompressible, inviscid, and the flow is two-dimensional and steady. The solutions are obtained by using conformal mapping theory, which maps the fluid region in the normalized complex-potential plane onto an upper half-plane, and Hilbert\u27s technique. Each problem has been programmed and run on a computer, and the computed results plotted and compared with different authors quoted in Chapter I, whenever possible.Dept. of Mathematics and Statistics. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis1981 .A234. Source: Dissertation Abstracts International, Volume: 42-08, Section: B, page: 3289. Thesis (Ph.D.)--University of Windsor (Canada), 1981

Molecular modeling of cation–π interactions and ammonium permeation in AmtB

Cation–π interactions are noncovalent interactions known to play various important roles in chemical and biological systems. In proteins, such interactions usually involve Phe, Tyr or Trp in contact with inorganic cations or positively charged amino acids (Arg and Lys). AmtB is a transmembrane protein that has a high affinity for ammonium and facilitates its transport across the membrane which provides a source of nitrogen for amino acid synthesis in bacteria. The amino acid residues that line the pore of the crystallographically-identified outer binding site, S1, of AmtB (Trp148, Phe107, and Phe103) are known to stabilize NH4+ through cation–π interactions. However, the nature of the transported species, NH3 or NH4+, and the permeation mechanism are not yet known. In this study, ab initio quantum mechanical calculations at the MP2/6-311++G(d,p) level of theory are performed on the interaction of Li+, Na+, K+ and NH4+ with benzene monomer, dimer, and trimer in order to measure the strength of cation–π interactions in these systems and to parameterize a polarizable force field for these interactions. The resulting force field is used to investigate cation–π interactions and their effect on π–π interactions in water. Polarizable potential models for NH3, Na+, K+, and NH4+ interacting with H2O and with model compounds of the amino acids found along the AmtB permeation pathway are also developed based on ab initio calculations on these interactions at the same level of theory. The resulting models are used to investigate the binding selectivity of S1 toward NH4+ and the biologically abundant monovalent ions Na+ and K+. The nature of the permeable species and possible permeation mechanisms are also investigated based on molecular dynamics free energy calculations

Symmetry analysis for steady boundary-layer stagnation-point flow of Rivlin–Ericksen fluid of second grade subject to suction

An analysis for the steady two-dimensional boundary-layer stagnation-point flow of Rivlin–Ericksen fluid of second grade with a uniform suction is carried out via symmetry analysis. By employing Lie-group method to the given system of nonlinear partial differential equations, the symmetries of the equations are determined. Using these symmetries, the solution of the given equations is found. The effect of the viscoelastic parameter k and the suction parameter R on the tangential and normal velocities, temperature profiles, heat transfer coefficient and the wall shear stress, have been studied. Also, the effect of the Prandtl number Pr on the temperature and the heat transfer coefficient has been studied

Molecular Modeling of Ions in Biological Systems

Ions are ubiquitous in biological systems. Metal ions contribute to biological function as counter ions, as triggers to cellular response, and as catalytic cofactors. They play structural roles and are part of the catalytic active site of metalloenzymes. NH4+ ions provide a source of nitrogen for amino acid synthesis in plants and bacteria and help maintaining the acid-base balance in mammals. The cationic side chains of amino acids Lys and Arg contribute to the stability of proteins and protein-DNA complexes through cation–π interactions with the π electrons of aromatic amino acids. Developing molecular models for ion-protein interactions is required to investigate and understand the various biological functions of ions and to complement and interpret experimental data. In this regard, the aims of this thesis are to: 1- Investigate the selectivity of alkali ions toward N, O, and S-containing ligands (a step toward understanding protein selectivity to metal ions). 2- Optimize new semiempirical quantum mechanical models for calcium and magnesium metalloproteins. 3- Study the strength and directionality of cation–π interactions involving inorganic and organic cations interacting with model compounds of aromatic amino acid side chains in both gas phase and aqueous solution. 4- Investigate the selectivity and binding affinity of AmtB and RhCG ammonium transport proteins toward various ions and study the function of amino acids that line the transport pathway of these proteins. Proteins bind metal ions through N, O, and S atoms from the side chains of the amino acids His, Asp, Glu, Ser, Tyr, Asn, Gln, Cys, and Met and from main chain carbonyl and amino groups. NH3, H2O, and H2S are used as minimal models for N, O, and S ligands to investigate the selectivity of alkali metal ions. Polarizable potential models for NH3 and H2S that accurately reproduce the experimental properties of the pure and aqueous liquids are developed. The models are used, together with a previously developed model for water, to study the solvation structures and solvation free energies of the ions in the pure liquids and to investigate the selectivity of alkali ions toward the three ligands. The models yield solvation structures and solvation free energies in good agreement with experiments and show a selectivity of alkali ions toward the three ligands that follows the order H2O > NH3 > H2S. Magnesium and Calcium are two of the most bioavailable metals and are known to play roles in signal transduction and in muscular contraction and are cofactors in many enzymes. Semiempirical models are optimized for the two metals based on the ab initio structures and binding energies of complexes formed between Mg2+ and Ca2+ with ligands that model binding groups in biological and chemical systems. Optimized models are tested on the ab initio properties of ~170 ion-ligand binary and ion-water-ligand ternary complexes. Optimized models of Mg underestimate the binding energies of S-containing complexes but give structures and binding energies of other complexes in agreement with ab initio data. Models for Ca reproduce the ab initio properties of all complexes, including S complexes. Cation–π interactions are common among protein structures and are believed to play key roles in stabilizing proteins and protein complexes with ligands and DNA. Polarizable potential models for the interaction of Rb+, Cs+, Tl+, ammonium, tetramethylammonium, and tetraethylammonium with aromatic amino acid side chains are calibrated based on the ab initio properties of the different cation–π complexes. The models are used to study the binding affinity and complexation geometry of the different pairs in water. Results are showing that cation–π interactions persist in aqueous solutions and are stronger than charge-dipole interactions (such as interactions of Rb+, Cs+, Tl+ with ethanol and acetamide). It is also found that cation–π complexes have geometries in aqueous solution similar to gas phase. In addition, results suggest that cation–π interactions influence the solubility of aromatic compounds in aqueous solutions. Proteins of the Amt/Mep/Rh family —ammonium transporters (Amt) in plants and bacteria, methylamine permease (Mep) in yeast, and rhesus (Rh) blood-group associated glycoproteins in animals— facilitate the permeation of ammonium across cell membranes. Crystal structures of AmtB and RhCG proteins reveal structural differences along the transport pathways. Amt proteins are selective toward NH4+ over Na+ and K+, yet their activity can be inhibited by ions such as Cs+ and Tl+. Polarizable potential models for NH3, NH4+, Na+, K+, Rb+, Cs+, and Tl+ interacting with model compounds to side chains of amino acids that line the transport pathway are optimized. The models are used to calculate the binding affinity of both proteins toward the various ligands and to study the functional roles of amino acids along the transport pathway. Results show that among the various ligands, only Cs+ and Tl+ can compete with NH4+ for binding the two proteins and hence inhibit the protein activity. Results also show that the large hydrophobicity of the pore lumen in RhCG protein destabilizes NH4+ and water molecules in the pore which suggests a net NH3 transport mechanism of the protein

Approximate solution of a flow over a ramp for large Froude number

AbstractAn approximate method is presented to solve the problem of steady free-surface flow of an ideal fluid over a semi-infinite ramp in the bottom. Schwartz-Christoffel transformation is used to map the region of flow, in the complex potential-plane, onto the upper half-plane. The Hilbert transformation as well as the perturbation technique are used as a basis for the approximate solution of the problem for large Froude number and small inclination angle of the ramp. General equations, in integral form, for any order of approximation are obtained. Solution up to first-order approximation is discussed and illustrated.Elevation of the free-surface for different ramp heights, different inclination angles of the ramp and different Froude numbers are plotted. An approximate formula of maximum elevation of the free-surface in terms of the ramp heights and its inclination angle is found

Nonlinear progressive internal gravity wave on fluid of trapezoidal bottom

AbstractIn the present paper we discuss a theoretical model for the interfacial profiles of progressive nonlinear waves which result from introducing a trapezoidal obstacle, of finite height, attached to the bottom below the flow of a stratified, ideal, two layer fluid, bounded from above by a rigid boundary. Assuming a very large horizontal length compared with the vertical height allows us to apply the shallow-water approximation theory, and, consequently, a nonlinear perturbation method is presented to construct per power series the analytical solution for the interfacial profiles of the progressive waves. The dependence of the interfacial profile on the trapezoidal obstacle size, as well as its dependence on some flow parameters, such as the ratios of depths and densities of the two fluids, have been studied and illustrated

Group theoretic approach for solving the problem of diffusion of a drug through a thin membrane

AbstractThe transformation group theoretic approach is applied to study the diffusion process of a drug through a skin-like membrane which tends to partially absorb the drug. Two cases are considered for the diffusion coefficient. The application of one parameter group reduces the number of independent variables by one, and consequently the partial differential equation governing the diffusion process with the boundary and initial conditions is transformed into an ordinary differential equation with the corresponding conditions. The obtained differential equation is solved numerically using the shooting method, and the results are illustrated graphically and in tables