Genotyping of simple sequence repeats--factors implicated in shadow band generation revisited

PCR amplification of microsatellite sequences generates, besides the main product corresponding to allele size, also additional, undesired products usually shorter by multiples of the repeated unit. These extra products known as shadow bands or stutter products may complicate genotyping. The mechanism by which these artifacts are formed is not well understood and so no effective remedy has been found to cope with these spurious products. In this study, using the DNA templates containing the CAG/CTG repeats flanked by gene-specific sequences and universal priming sites, we analyzed the effects of many PCR variables on the shadow band generation. The most important result was that at the decreased temperature of the denaturation step during PCR cycling the shadow bands were either not formed or were strongly suppressed. Several possible sources of this effect are discussed.     

Car-parrinello molecular dynamics simulation of liquid formic acid

First-principles molecular dynamics has been used to investigate the structural, vibrational, and energetic properties of formic acid, formic acid-formate anion dimers, and liquid formic acid in a periodically repeated box with 32 formic acid molecules. We found that in liquid formic acid the hydrogen-bonded clusters mainly consist of linear branching chains. From our simulation, we got good agreement with the available structural and dynamical data. We also studied the proton transfer in the cis-formic acid-formate anion dimer, and we showed that this proton transfer does not have any potential barrier. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed.     

The E-normal structure of odd dimensional unitary groups

In this paper we define odd dimensional unitary groups ${\mathrm{U}}_{2n+1}(R,\mathrm{\Delta })$. These groups contain as special cases the odd dimensional general linear groups ${\mathrm{GL}}_{2n+1}(R)$ where R is any ring, the odd dimensional orthogonal and symplectic groups ${\mathrm{O}}_{2n+1}(R)$ and ${\mathrm{Sp}}_{2n+1}(R)$ where R is any commutative ring and further the first author's even dimensional unitary groups ${\mathrm{U}}_{2n}(R,\mathrm{\Lambda })$ where $(R,\mathrm{\Lambda })$ is any form ring. We classify the E-normal subgroups of the groups ${\mathrm{U}}_{2n+1}(R,\mathrm{\Delta })$ (i.e. the subgroups which are normalized by the elementary subgroup ${\mathrm{EU}}_{2n+1}(R,\mathrm{\Delta })$), under the condition that R is either a semilocal or quasifinite ring with involution and $n\ge 3$. Further we investigate the action of ${\mathrm{U}}_{2n+1}(R,\mathrm{\Delta })$ by conjugation on the set of all E-normal subgroups.     

Contents of the proceedings

Table of Contents

Contents of the proceedings     

Dynamics of money

We present a dynamical many-body theory of money in which the value of money is a time dependent "strategic variable" that is chosen by the individual agents. The value of money in equilibrium is not fixed by the equations, and thus represents a continuous symmetry. The dynamics breaks this continuous symmetry by fixating the value of money at a level which depends on initial conditions. The fluctuations around the equilibrium, for instance in the presence of noise, are governed by the "Goldstone modes" associated with the broken symmetry. The idea is illustrated by a simple network model of monopolistic vendors and buyers.     

Stability for Quadratic K1

The general quadratic group GQ _2n and its elementary subgroup EQ _2n are analogs in the theory of quadratic forms of the general linear group GL _n and its elementary subgroup E _n . This article proves that the stabilization map GQ _2n /EQ _2n GQ _2(n+1) /EQ _2(n+1) is an isomorphism whenever n +1 and S denotes the -stable rank of rings with anti-involution. As a corollary, a result is obtained which has been anticipated since the late 1960s: over rings of finite Bass–Serre dimension d, the stabilization map is an isomorphism whenever n d + 2.     

On an example concerning the Kobayashi pseudodistance

In this short note we calculate the Kobayashi pseudodistance for elementary Reinhardt domains in . They deliver us a number of examples giving a negative answer to a problem posed by S. Kobayashi.

     

GRID formalism for the comparative molecular surface analysis: application to the CoMFA benchmark steroids, azo dyes, and HEPT derivatives

Shape analysis is a powerful tool in chemistry and drug design, and molecular surface defines shape in the molecular scale. In the current publication we presented a novel formalism for the comparative molecular surface analysis (s-CoMSA). The method enables both quantitative modeling of 3D-QSAR and finding possible pharmacophoric sites. The method provides very predictive models for the CBG activity of the benchmark steroid series, tinctorial properties of the heterocyclic azo dyes and anti-HIV activity of the HEPT series.     

Charge mediation by ruthenium poly(pyridine) complexes in 'second-generation' glucose biosensors based on carboxymethylated β-cyclodextrin polymer membranes

Four different poly(pyridine) complexes of ruthenium, viz. Ru(II)(trpy)(phen)(OH(2))](2+) (1), trans-[Ru(III)(2,2'bpy)(2)(OH(2))(OH)](2+) (2), [(2,2'bpy)(2)(OH)Ru(III)ORu(III)(OH)(2,2'bpy)(2)](4+) (3), and [Ru(II)(4,4'bpy)(NH(3))(5)](2+) (4) (2,2'bpy=2,2'-bipyridine, 4,4'bpy=4,4'-bipyridine, trpy=2,2',2"-terpyridine, phen=1,10-phenanthroline), were tested as non-physiological charge mediators of 'second-generation' glucose biosensors. The membranes for these biosensors were prepared by casting anionic carboxymethylated beta-cyclodextrin polymer films (beta-CDPA) directly onto the Pt or glassy carbon (GC) disk electrodes. Simultaneously, glucose oxidase (GOD) was immobilized in the films by covalent bonding and the Ru complexes were incorporated both by inclusion in the beta-CD molecular cavities and by ion exchange at the fixed carboxymethyl cation-exchange sites. The leakage of the mediator from the polymer has been minimized by adopting a suitable pre-treatment procedure. The biosensors catalytic activities increased in the order 1<2<3<4, as established by linear sweep voltammetry. In case of complexes 2-4, the enzymatic glucose oxidation was mediated by the Ru complexes at their redox potentials. However, this oxidation was mediated by oxygen in case of complex 1 where H(2)O(2) was detected as the reaction product. The effectiveness of the mediators used in the presence of oxygen has been estimated using Pt and GC supports. The redox potential of the mediator does not depend on the support used, while the oxidation of H(2)O(2) proceeds on GC at much higher positive potentials than on Pt. The sensitivity and the linear concentration range of the biosensor studied varied significantly. For complex 4, which forms stable inclusion complex with beta-CD, the biosensor sensitivity was the highest and equal to 7.2 micro A mM(-1) cm(-2), detectability was as low as 1 mM, but the linear concentration range was limited only to 4 mM. In contrast, for complexes 2 and 3 the sensitivity was 0.4 and 3.2 micro A mM(-1) cm(-2), while the linear concentration range extended up to at least 24 and 14 mM glucose, respectively. Even though some common interfering substances, such as ascorbate, paracetamol or urea, are oxidized at potentials close to those of the Ru complex redox couples, their electro-oxidation currents at physiological concentrations are insignificant compared to those due to the biocatalytic oxidation of glucose. The biosensor response to glucose is reversible as demonstrated by the inhibition of GOD activity by Cu(II). That is, the Cu(II) concentration required to inhibit by half the response to glucose of the biosensor containing complex 2 was 1.0 mM. This inhibitory effect was fully reversed by addition of citrate, a ligand forming sufficiently stable complex with Cu(II).