Rapid genotyping of CYP2D6, CYP2C19 and TPMT polymorphisms by primer extension reaction in a dipstick format

In recent years an increasing amount of interest has been directed at the study and routine testing of polymorphisms responsible for variations in drug metabolism. Most of the current methods involve either time-consuming electrophoresis steps or specialized and expensive equipment. In this context, we have developed a rapid, simple and robust method for genotyping of CYP2D6*3, CYP2D6*4, CYP2C19*2, CYP2C19*3 and TPMT*2 single nucleotide polymorphisms (SNP). Genomic DNA is isolated from whole blood and the segments that span the SNP of interest are amplified by PCR. The products are subjected directly (without purification) to two primer extension (PEXT) reactions (three cycles each) using normal and mutant primers in the presence of biotin-dUTP. The PEXT primers contain a (dA)₃₀ segment at the 5′ end. The PEXT products are detected visually by a dry-reagent dipstick-type assay in which the biotinylated extension products are captured from immobilized streptavidin on the test zone of the strip and detected by hybridization with oligo(dT)-functionalized gold nanoparticles. Patient samples (76 variants in total) were genotyped and the results were fully concordant with those obtained by direct DNA sequencing.     

Theoretical investigation on the electronic and geometric structure of GaN2+ and GaN4+

The electronic and geometric structures of gallium dinitride cation, GaN2+ and gallium tetranitride cation, GaN4+ were systematically studied by employing density functional theory (DFT-B3LYP) and perturbation theory (MP2, MP4) in conjunction with large basis sets, (aug-)cc-pVxZ, x = T, Q. A total of 7 structures for GaN2+ and 24 for GaN4+ were identified, corresponding to minima, transition states, and saddle points. We report geometries and dissociation energies for all the above structures as well as potential energy profiles, potential energy surfaces, and bonding mechanisms for some low-lying electronic states. The calculated dissociation energy (De) of the ground state of GaN2+, X1Sigma+, is 5.6 kcal/mol with respect to Ga+(1S) + N2(X1Sigmag+) and that of the excited state, ?3Pi, is 24.8 kcal/mol with respect to Ga+(3P) + N2(X1Sigmag+). The ground state and the first excited minimum of GaN4+ are of 1A1(C2v) and 3B1(C2v) symmetry with corresponding De of 11.0 and 43.7 kcal/mol with respect to Ga+(1S) + 2N2(X1Sigmag+) for X1A1 and Ga+(3P) + 2N2(X1Sigmag+) for 3B1.     

Investigation of the local composition enhancement and related dynamics in supercritical CO2-cosolvent mixtures via computer simulation: the case of ethanol in CO2

The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.     

On the Convergence of Newton’s Method for Polynomial Equations and Applications in Radiative Transfer

 Newton’s method is used to approximate a locally unique zero of a polynomial operator F of degree in Banach space. So far, convergence conditions have been found for Newton’s method based on the Newton-Kantorovich hypothesis that uses Lipschitz-type conditions and information only on the first Fréchet-derivative of F. Here we provide a new semilocal convergence theorem for Newton’s method that uses information on all Fréchet-derivatives of F except the first. This way, we obtain sufficient convergence conditions different from the Newton-Kantorovich hypothesis. Our results are extended to include the case when F is a nonlinear operator whose kth Fréchet-derivative satisfies a H?lder continuity condition. An example is provided to show that our conditions hold where all previous ones fail. Moreover, some applications of our results to the solution of polynomial systems and differential equations are suggested. Furthermore, our results apply to solve a nonlinear integral equation appearing in radiative transfer in connection with the problem of determination of the angular distribution of the radiant-flux emerging from a plane radiation field. Received 9 December 1997 in revised form 30 March 1998     

On the applicability of two Newton methods for solving equations in Banach space

In this study we examine the applicability of Newton’s method and the modified Newton’s method for approximating a locally unique solution of a nonlinear equation in a Banach space. We assume that the Newton-Kantorovich hypothesis for Newton’s method is violated, but the corresponding condition for the modified Newton method holds. Under these conditions there is no guarantee that Newton’s method starting from the same initial guess as the modified Newton’s method converges. Hence, it seems that we must always use the modified Newton method under these conditions. However, we provide a numerical example to demonstrate that in practice this may not be a good decision.     

Quantization of Discretized Spacetimes and theCorrespondence Principle

An algebraic quantization procedure for discretized spacetime models is suggestedbased on the duality between finitary substitutes and their incidence algebras.The provided limiting procedure that yields conventional manifold characteristicsof spacetime structures is interpreted in the quantum algebraic framework as acorrespondence principle.     

Dodekahydro‐closo‐dodekaborate der schweren Erdalkalimetalle aus wäßriger Lösung: Ca(H2O)7[B12H12] · H2O,Sr(H2O)8[B12H12] und Ba(H2O)6[B12H12]

Dodecahydro‐ closo ‐dodecaborates of the Heavy Alkaline‐Earth Metals from Aqueous Solution: Ca(H₂O)₇[B₁₂H₁₂] · H₂O, Sr(H₂O)₈[B₁₂H₁₂], and Ba(H₂O)₆[B₁₂H₁₂] The crystalline hydrates of the heavy alkaline earth metal dodecahydro‐closo‐dodecaborates (M[B₁₂H₁₂] · n H₂O, n = 6–8; M = Ca, Sr, Ba) are easily accessible by reaction of an aqueous (H₃O)₂[B₁₂H₁₂] solution with an alkaline earth metal carbonate (MCO₃). By isothermic evaporation of the respective aqueous solution we obtained colourless single crystals which are characterized by X‐ray diffraction at room temperature. The three compounds Ca(H₂O)₇[B₁₂H₁₂] · H₂O (orthorhombic, P2₁2₁2₁; a = 1161.19(7), b = 1229.63(8), c = 1232.24(8) pm; Z = 4), Sr(H₂O)₈[B₁₂H₁₂] (trigonal, R3; a = 1012.71(6), c = 1462.94(9) pm; Z = 3) and Ba(H₂O)₆[B₁₂H₁₂] (orthorhombic, Cmcm; a = 1189.26(7) pm, b = 919.23(5) pm, c = 1403.54(9) pm; Z = 4) are neither formula‐equal nor isostructural. The structure of Sr(H₂O)₈[B₁₂H₁₂] is best described as a NaCl‐type arrangement, Ba(H₂O)₆[B₁₂H₁₂] rather forms a layer‐like and Ca(H₂O)₇[B₁₂H₁₂] · H₂O a channel‐like structure. In first sphere the alkaline earth metal cations Ca²⁺ and Sr²⁺ are coordinated by just seven and eight oxygen atoms from the surrounding water molecules, respectively. A direct coordinative influence of the quasi‐icosahedral [B₁₂H₁₂]^2– cluster anions becomes noticeable only for the Ba²⁺ cations (CN = 12) in Ba(H₂O)₆[B₁₂H₁₂]. The dehydratation of the alkaline earth metal dodecahydro‐closo‐dodecaborate hydrates has been shown to take place in several steps. Thermal treatment leads to the anhydrous compounds Ca[B₁₂H₁₂], Sr[B₁₂H₁₂] and Ba[B₁₂H₁₂] at 224, 164 and 116 °C, respectively.     

Direct and Indirect Chemiluminescence: Reactions,Mechanisms and Challenges

Emission of light by matter can occur through a variety of mechanisms. When it results from an electronically excited state of a species produced by a chemical reaction, it is called chemiluminescence (CL). The phenomenon can take place both in natural and artificial chemical systems and it has been utilized in a variety of applications. In this review, we aim to revisit some of the latest CL applications based on direct and indirect production modes. The characteristics of the chemical reactions and the underpinning CL mechanisms are thoroughly discussed in view of studies from the very recent bibliography. Different methodologies aiming at higher CL efficiencies are summarized and presented in detail, including CL type and scaffolds used in each study. The CL role in the development of efficient therapeutic platforms is also discussed in relation to the Reactive Oxygen Species (ROS) and singlet oxygen (¹O₂) produced, as final products. Moreover, recent research results from our team are included regarding the behavior of commonly used photosensitizers upon chemical activation under CL conditions. The CL prospects in imaging, biomimetic organic and radical chemistry, and therapeutics are critically presented in respect to the persisting challenges and limitations of the existing strategies to date.