Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

The scale dependent nuclear effects in parton distributions for practical applications

The scale dependence of the ratios of parton distributions in a proton of a nucleus A and in the free proton, , is studied within the framework of the lowest order leading-twist DGLAP evolution. By evolving the initial nuclear distributions obtained with the GRV-LO and CTEQ4L sets at a scale , we show that the ratios are only moderately sensitive to the choice of a specific modern set of free parton distributions. We propose that to a good first approximation, this parton distribution set-dependence of the nuclear ratios can be neglected in practical applications. With this result, we offer a numerical parametrization of for all parton flavours i in any , and at any and any for computing cross sections of hard processes in nuclear collisions. Received: 10 August 1998 / Published online: 27 April 1999     

Implementation of a medium-modified parton shower algorithm

We present a Monte Carlo implementation of medium-induced gluon radiation in the final-state branching process. Medium effects are introduced through an additive term in the splitting functions. We have implemented such modification within PYTHIA. We show the medium effects on the hump-backed plateau, and the transverse-momentum and angular distributions with respect to the parent parton. As expected, with increasing medium densities there is an increase (decrease) of partons with small (large) momentum fraction, and angular broadening is observed. The effects on the transverse-momentum distributions are more involved, with an enhancement of low- and intermediate-p _T partons and a decrease at large p _T, which is related to energy conservation, and to the lack of momentum exchange with the medium in our approach.     

Even-dimensional topological gravity from Chern–Simons gravity

It is shown that the topological action for gravity in 2n  -dimensions can be obtained from the (2n+1)$(2n+1)$-dimensional Chern–Simons gravity genuinely invariant under the Poincaré group. The 2n  -dimensional topological gravity is described by the dynamics of the boundary of a (2n+1)$(2n+1)$-dimensional Chern–Simons gravity theory with suitable boundary conditions.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

LC-DAD Determination of Fleroxacin in Bulk and Pharmaceutical Dosage Forms

Fleroxacin is a third generation fluoroquinolone with broad spectrum antibacterial activity. In this work an LC-DAD method for the analysis of fleroxacin was developed and validated using UV detection at 286 nm. The method was validated for linearity, precision, robustness, LOD, LOQ, specificity and accuracy at concentrations of 0.2–20.0 μg mL⁻¹ and r ² = 1. The LOD and LOQ were 0.059 and 0.197 μg, respectively, the recoveries were 99.92–102.0% and the CV was less than 2.0%. The LC-DAD validated method provided analytical sensitivity, specificity and reproducibility suitable for quality control analysis.     

Development of a Validated Stability-Indicating LC Assay and Stress Degradation Studies of Linezolid in Tablets

This paper describes the validation of an isocratic LC method for the assay of linezolid in tablets. Validation parameters such as linearity, precision, accuracy, specificity, limit of detection, limit of quantitation and robustness were determined. LC was carried out by reversed phase technique on an RP-18 column with a mobile phase composed of 1% acetic acid:methanol:acetonitrile (50:25:25, v/v/v). Linezolid and your combination drug product were exposed to acid, base, oxidation, dry heat and photolytic stress conditions. A linear response (r > 0.9999) was observed in the range of 8.0–20.0 μg mL⁻¹. The retention time of linezolid was 4.6 min. The method showed good recoveries and intra- and inter-day relative standard deviations were less than 1.0%. The LOD and LOQ were 0.21 and 0.63 μg mL⁻¹, respectively. The developed LC method for determination of related substances and assay determination of linezolid can be used to evaluate the quality of regular production samples. It can also be used to test the stability samples of linezolid.

     

Solid-state 2H NMR structure of retinal in metarhodopsin I

The structural and photochemical changes in rhodopsin due to absorption of light are crucial for understanding the process of visual signaling. We investigated the structure of trans-retinal in the metarhodopsin I photointermediate (MI), where the retinylidene cofactor functions as an antagonist. Rhodopsin was regenerated using retinal that was (2)H-labeled at the C5, C9, or C13 methyl groups and was reconstituted with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Membranes were aligned by isopotential centrifugation, and rhodopsin in the supported bilayers was then bleached and cryotrapped in the MI state. Solid-state (2)H NMR spectra of oriented rhodopsin in the low-temperature lipid gel state were analyzed in terms of a static uniaxial distribution (Nevzorov, A. A.; Moltke, S.; Heyn, M. P.; Brown, M. F. J. Am. Chem. Soc. 1999, 121, 7636-7643). The line shape analysis allowed us to obtain the methyl bond orientations relative to the membrane normal in the presence of substantial alignment disorder (mosaic spread). Relative orientations of the methyl groups were used to calculate effective torsional angles between the three different planes that represent the polyene chain and the beta-ionone ring of retinal. Assuming a three-plane model, a less distorted structure was found for retinal in MI compared to the dark state. Our results are pertinent to how photonic energy is channeled within the protein to allow the strained retinal conformation to relax, thereby forming the activated state of the receptor.     

Determination of soluble toxic arsenic species in alga samples by microwave-assisted extraction and high performance liquid chromatography-hydride generation-inductively coupled plasma-atomic emission spectrometry

A microwave-based procedure for arsenic species extraction in alga samples (Sargassum fulvellum, Chlorella vulgaris, Hizikia fusiformis and Laminaria digitata) is described. Extraction time and temperature were tested in order to evaluate the extraction efficiency of the process. Arsenic compounds were extracted in 8 ml of deionised water at 90 degrees C for 5 min. The process was repeated three times. Soluble arsenic compounds extracted accounted for about 78-98% of total arsenic. The results were compared with those obtained in a previous work, where the extraction process was carried out by ultrasonic focussed probe for 30 s. Speciation studies were carried out by high performance liquid chromatography-hydride generation-inductively coupled plasma-atomic emission spectrometry (HPLC-HG-ICP-AES). The chromatographic method allowed us to separate As(III), As(V), monomethylarsonic acid and dimethylarsinic acid in less than 13 min. The chromatographic analysis of the samples allowed us to identify and quantify As(V) in Hizikia sample and Sargasso material, while the four arsenic species studied were found in Chlorella sample. In the case of Laminaria sample, none of these species was identified by HPLC-HG-ICP-AES. However, in the chromatographic analysis of this alga by HPLC-ICP-AES, an unknown arsenic species was detected.     

Determination of gatifloxacin in bulk and tablet preparations by high-performance liquid chromatography

A sensitive, precise, and specific high-performance liquid chromatographic (HPLC) method was developed for the assay of gatifloxacin (GATX) in raw material and tablets. The method validation parameters yielded good results and included the range, linearity, precision, accuracy, specificity, and recovery. It was also found that the excipients in the commercial tablet preparation did not interfere with the assay. The HPLC separation was carried out by reversed-phase chromatography on a C18 absorbosphere column (250 x 4.6 mm id, 5 microm particle size) with a mobile phase composed of acetic acid 5%-acetonitrile-methanol (70 + 15 + 15, v/v/v) pumped isocratically at a flow rate of 1.0 mL/min. The effluent was monitored at 287 nm. The calibration graph for GATX was linear from 4.0 to 14.0 microg/mL. The interday and intraday precisions (relative standard deviation) were less than 1.05%.