Use of denaturing gradient gel electrophoresis to detect mutation in VS2 of the 16S-23S rDNA spacer amplified from Staphylococcus aureus isolates

To develop a double gradient denaturing gradient gel electrophoresis (DG-DGGE) based typing method that rapidly and accurately types clinical isolates of Staphylococcus aureus, the VS2 region of the 16S-23S rRNA spacer region (ISR) was chosen because of its potential high variation. The VS2 region was amplified with a 40-mer GC-clamp attached to the 5'-end of the reverse primer. The 145 bp PCR product was then separated by DG-DGGE using denaturant concentrations of 25-40% and polyacrylamide concentrations of 6-12%. Of the five mutations identified in 336 S. aureus isolates, one mutation was found to be highly specific for 161/171 (94%) of methicillin-resistant S. aureus (MRSA) isolates from different geographic locations and isolation times. This same mutation was found in 15/160 (9%) of penicillin- or methicillin-sensitive S. aureus isolates. In some isolates two mutations occured together in the one genome suggesting some S. aureus isolates have two copies of VS2. In these 336 isolates nine genotypes with different combinations of the five mutations were identified. In 18 coagulase-negative staphylococci (CNS), the MRSA-specific mutation was found along with two other mutations in all isolates demonstrating consistent differences in the presence of these mutations between CNS and S. aureus. The marked differences in VS2 sequences found between MRSA, methicillin- or penicillin-sensitive S. aureus (SSA), and CNS by DGGE in the present study may be useful in evolutionary studies and in the development of a specific assay for MRSA from clinical specimens.     

Dipolar interactions and origin of spin ice in ising pyrochlore magnets

Recent experiments suggest that the Ising pyrochlore magnets Ho2Ti2O7 and Dy2Ti2O7 display qualitative properties of the nearest-neighbor "spin ice" model. We discuss the dipolar energy scale present in both these materials and discuss how spin-ice behavior can occur despite the presence of long-range dipolar interactions. We present results of numerical simulations and a mean field analysis of Ising pyrochlore systems. Based on our quantitative theory, we suggest that the spin-ice behavior in these systems is due to long-range dipolar interactions, and that the nearest-neighbor exchange in Dy2Ti2O7 is antiferromagnetic.     

Exact scalar field cosmologies in a higher derivative theory

We obtain exact cosmological solutions of a higher derivative theory described by the Lagrangian L=R+2αR ² in the presence of interacting scalar field. The interacting scalar field potential required for a known evolution of the FRW universe in the framework of the theory is obtained using a technique different from the usual approach to solve the Einstein field equations. We follow here a technique to determine potential similar to that used by Ellis and Madsen in Einstein gravity. Some new and interesting potentials are noted in the presence of R ² term in the Einstein action for the known behaviours of the universe. These potentials in general do not obey the slow rollover approximation.     

Denaturing gradient gel electrophoretic multilocus sequence typing of Staphylococcus aureus isolates

To obviate the need for multilocus sequencing, a method using denaturing gradient gel electrophoresis (DGGE) was developed for the multilocus sequence typing (MLST) of Staphylococcus aureus isolates. Sequence types (STs) were obtained on the basis of sequences of polymerase chain reaction (PCR) products from seven housekeeping genes and compared to the reference MLST database. The melt curves, sequences and DGGE profiles were compared for 100 STs (i) to determine PCR conditions with 40-mer GC-clamps attached to the forward and reverse primers; (ii) to choose single restriction enzyme sites for digestion of PCR products into two fragments each with a GC-clamp attached and (iii) to optimize DGGE conditions. When the DGGE types (DT) were analyzed, the majority of DTs (76/100) were accurately classified into one ST (95% of nucleotide changes were detected), 10 DTs were classified into one of two STs corresponding to a single nucleotide ambiguity and 14 DTs were classified into 3 or 4 STs corresponding to 4 or 5 nucleotide ambiguities. A combination of STs and DTs were used to obtain septuplet sets of STs (7-ST) for 25 S. aureus isolates. When compared to the reference MLST database, one methicillin-resistant S. aureus (MRSA) isolate had the same genotype as the first MRSA clone. The DGGE-MLST method can be used as a rapid, accurate and 20-fold less expensive method than DNA sequencing for the detection of all sequence types. This combined laboratory and in silico approach could have wide applicability not only to MLST methods for other bacteria but to the screening of multilocus nucleotide differences deposited in other mutation databases.     

On the applicability of CNDO indices for the prediction of chemical reactivity

A series of CNDO/2 molecular orbital properties were evaluated to determine their utility in parameterizing chemical reactivities. Some of these indices were used previously for only electron methods and were extended here to include the framework. Theoretical rationales were given for this extension to the semi-empirical all valence electron methods. Four systems, the aromatic hydrocarbons, the benzene derivatives, the substituted benzoic acids, and the substituted phenyl amines, were studied to test how well these indices can parameterize chemical reactivities. This study focused on reactions involving both and electrons where the reactive site is not necessarily on the aromatic framework. For the nonplanar and heteropolar systems, these indices performed as well as the Hückel method did for the classical aromatics. These CNDO indices should perform effectively in multivariable regressions to parameterize the reactivities for more complicated problems such as those encountered in quantitative structure activity relationships of drugs.     

Orbital Angular Momentum in Scalar Diquark Model and QED

We compare the orbital angular momentum of the ‘quark’ in the scalar diquark model as well as that of the electron in QED (to order α) obtained from the Jaffe–Manohar decomposition to that obtained from the Ji relation. We estimate the importance of the vector potential in the definition of orbital angular momentum.     

An efficient one-pot synthesis of coumarin-amino acid derivatives as potential anti-inflammatory and antioxidant agents

Abstract

A series of seven coumarinyl-amino acid ester conjugates have been synthesized and characterized by NMR (¹H and 13C) and mass spectra. Further, the compounds were investigated for their therapeutic applications such as anti-inflammatory and antioxidant activities. Among the synthesized compounds most of the analogs showed good efficiency compared with the standard.     

Use of double gradient denaturing gradient gel electrophoresis to detect (AT)n polymorphisms in the UDP-glucuronosyltransferase 1 gene promoter associated with Gilbert's syndrome.

Gilbert's syndrome, due to reduced hepatic bilirubin glucuronidation is associated with the presence of two extra nucleotides (TA) in the promoter region of the UDP-glucuronosyltransferase 1 (UGT1A1) gene. A rapid method was developed to detect this genetic polymorphism, using double gradient denaturing gradient gel electrophoresis (DG-DGGE). The promoter region of the UGT1A1 gene was amplified with a 40-mer GC-clamp attached to the 5'-end of the reverse primer. The polymerase chain reaction (PCR) product was then separated by DG-DGGE using denaturant concentrations of 15-25% and polyacrylamide concentrations of 6-12%. The (TA)6/(TA)6 homozygotes were clearly distinguished from both (TA)7/(TA)7 homozygotes and (TA)6/(TA)7 heterozygotes. The (TA)7 allele frequency was consistent with that previously reported and elevated bilirubin levels correlated with the presence of the (TA)7 allele. The DG-DGGE method described will make detection for this polymorphism fast, simple, nonradioactive and suitable for a clinical routine diagnostic laboratory, helping to establish the role of this polymorphism in individuals with jaundice due to multiple causes.