Determination of the vanadium content of protein solutions by electron paramagnetic resonance spectroscopy

A rapid and precise method of determining the vanadium content of protein solutions by electron paramagnetic resonance spectroscopy is reported The method is based on the linear relationship between the signal intensity of the first-derivative electron paramagnetic resonance signal and the concentration of the VO(H₂O)₅²⁺ species formed in acid solution. Six different proteins were investigated in the concentration range 10^?3-10^?5m. A precision of ±1%, an accuracy of ±3%, and a detection limit of 25ppb for vanadium was obtained. This analytical method was developed to aid in investigations of metal binding sites in proteins by vanadyl ion (VO²⁺) electron paramagnetic resonance spectroscopy.     

Large-scale extraction of gene regulation for model organisms in an ontological context

This paper presents an approach using syntactosemantic rules for the extraction of relational information from biomedical abstracts. The results show that by overcoming the hurdle of technical terminology, high precision results can be achieved. From abstracts related to baker's yeast, we manage to extract a regulatory network comprised of 441 pairwise relations from 58,664 abstracts with an accuracy of 83 - 90%. To achieve this, we made use of a resource of gene/protein names considerably larger than those used in most other biology related information extraction approaches. This list of names was included in the lexicon of our retrained partof- speech tagger for use on molecular biology abstracts. For the domain in question an accuracy of 93.6 - 97.7% was attained on Part-of-speech-tags. The method can be easily adapted to other organisms than yeast, allowing us to extract many more biologically relevant relations. The main reason for the comparable precision rates is the ontological model that was built beforehand and served as a guiding force for the manual coding of the syntactosemantic rules.     

New procedure for extraction of ammonium from natural waters for N isotopic ratio determinations

A new method for extracting ammonium from natural waters for N isotopic ratio determination is described. The method employs the conversion of the ammonium nitrogen into indophenol, which is then concentrated onto an octadecylsilane column. The method shows accuracy and precision comparable to those of other methods described in the literature. Some results from field experiments on the Swedish west coast are presented.     

Capillary electrophoresis with laser-induced fluorescence detection, an adequate alternative to high-performance liquid chromatography, for the determination of ciprofloxacin and its metabolite desethyleneciprofloxacin in human plasma

A method to determine plasma concentrations of ciprofloxacin and its metabolite desethyleneciprofloxacin (M1) by CE with HeCd laser-induced fluorescence detection is described. Following precipitation of proteins and centrifugation supernatant is injected hydrodynamically (10 s, 0.5 p.s.i.) into the capillary. Overall analysis time for the quantification of both analytes was 7 min. The total amount of plasma needed for multiple injections (n>5) was 10–20 μl. Data on accuracy and precision are presented. The assay performance is compared to the specifications of a validated HPLC method, which is routinely used for the quantification of ciprofloxacin and M1 in body fluids. Both methods showed comparable accuracy and precision for both analytes throughout the whole working range (inter-day precision <9%; inter-day accuracy 96–110%). The limit of quantification (LOQ) of 20 μg/l (M1 10 μg/l) for the CE procedure was slightly higher than for the HPLC method, where 10 μg/l (M1 2.5 μg/l) was determined. However, application of the methods to human plasma samples derived from a clinical study proved that comparable results are obtained and that the sensivity of the HPCE method was sufficient to fully describe typical plasma concentration timie profiles of ciprofloxacin and its metabolite M1. Both the adequate sensitivity and the required smaller sample volume compared to HPLC indicate that the method is feasible for clinical studies where sample amounts are limited, e.g., studies to investigate pharmacokinetics in pediatric patients. Preclinical studies form another possible application of this technique.     

New Procedure for Extraction of Ammonium from Natural Waters for 15N Isotopic Ratio Determinations

A new method for extracting ammonium from natural waters for ¹⁵N isotopic ratio determination is described. The method employs the conversion of the ammonium nitrogen into indophenol, which is then concentrated onto an octadecylsilane column. The method shows accuracy and precision comparable to those of other methods described in the literature. Some results from field experiments on the Swedish west coast are presented.     

A comparison of two methods for the microscopic determination of age at death.

The precision and accuracy of the Kerley and Ahlqvist-Damsten microscopic methods of age determination are compared. Both methods were applied to the same sample of 40 femoral thin sections of documented age at death. The results indicate that (1) both methods can be used with equal precision, as suggested by comparable observer errors; and (2) the Kerley method produces overall more accurate age estimates. The low previously published standard error of the Ahlqvist-Damsten method (6.71 years) apparently results from the uneven age distribution and small size (20) of their sample.     

Accurate and sensitive measurements of pO(2) in vivo using low frequency EPR spectroscopy: how to confer biocompatibility to the oxygen sensors

Within the last few years, there has been a significant amount of progress using EPR oximetry, which has resulted in the availability of instrumentation and paramagnetic materials capable of measuring pO(2) in tissues with an accuracy and sensitivity comparable to or greater than that available by any other method. While the results obtained with EPR so far indicate that criteria for the measurements of pO(2)-such as accuracy, sensitivity, repeatability, and noninvasiveness-can be met, some of the paramagnetic materials with optimum spectroscopic properties (i.e., strong simple signals which are appropriately responsive to changes in pO(2)) may have some undesirable interactions with tissues, causing reactions with and/or losing responsiveness to oxygen. In this paper, several approaches are discussed, such as encapsulation procedures, which can result in the availability of oxygen-sensitive materials in a suitable configuration for long-term studies (absence of toxicity and preservation of the responsiveness to oxygen).     

Rapid method for determining malondialdehyde as secondary oxidation product in palm olein system by Fourier transform infrared spectroscopy

A simple and rapid Fourier transform infrared (FTIR) spectroscopic method has been developed for the quantitative determination of malondialdehyde as secondary oxidation product in a palm olein system. The FTIR method was based on a sodium chloride transmission cell and utilised a partial least square statistical approach to derive a calibration model. The frequency region combinations that gave good calibration were 2900-2800, and 1800-1600 cm-1. The precision and accuracy, in the range 0-60 mumol malondialdehyde/kg oil, were comparable to those of the modified distillation method with a coefficient of determination (r2) of 0.9891 and standard error of calibration of 1.49. The calibration was cross-validated and produced an r2 of 0.9786 and standard error of prediction of 2.136. The results showed that the FTIR method is versatile, efficient and accurate, and suitable for routine quality control analysis with the result obtainable in about 2 min from a sample of less than 2 mL.     

Measurement of thin filament lengths by distributed deconvolution analysis of fluorescence images

The lengths of the actin (thin) filaments in sarcomeres directly influence the physiological properties of striated muscle. Although electron microscopy techniques provide the highest precision and accuracy for measuring thin filament lengths, significant obstacles limit their widespread use. Here, we describe distributed deconvolution, a fluorescence-based method that determines the location of specific thin filament components such as tropomodulin (Tmod) or probes such as phallacidin (a phalloidin derivative). Using Tmod and phallacidin fluorescence, we were able to determine the thin filament lengths of isolated chicken pectoralis major myofibrils with an accuracy and precision comparable to electron microscopy. Additionally, phallacidin fluorescence intensity at the Z line provided information about the width of Z lines. Furthermore, we detected significant variations in thin filaments lengths among individual myofibrils from chicken posterior latissimus dorsai and embryonic chick cardiac myocytes, suggesting that a ruler molecule (e.g., nebulin) does not strictly determine thin filament lengths in these muscles. This versatile method is applicable to myofibrils in living cells that exhibit significant variation in sarcomere lengths, and only requires a fluorescence microscope and a CCD camera.     

A model-free feature-based bi-planar RSA method for kinematic analysis of total knee arthroplasty

Fluoroscopic imaging is commonly used for assessing relative motions of orthopaedic implants. One limiting factor to in vivo model-based roentgen stereophotogrammetric analysis of total knee arthroplasty is the need for 3D models of the implants.The 3D models of the implant components must be reverse-engineered, if not provided by the company, which makes this method impractical for a clinical study involving many types or sizes of implants. This study introduces a novel feature-based methodology that registers the features at the implant-bone or implant-cement interface of the components that have elementary shapes. These features include pegs with hemispherical heads, and straight, circular or curved edges located on flat faces of the box of the femoral component or the stem geometry of the tibial component. Software was developed to allow easy registration of these features through a graphical user interface. The accuracy and precision of registration for multiple flexion angles from 0 to 120 deg was determined with reference to registered poses of the implants through experiments on bone replica models and also on a cadaver specimen implanted with total knee prostheses. When compared to an equivalent bi-planar model-based registration, the results were comparable: The mean accuracy of this feature-based method was 1.45 deg and 1.03 mm (in comparison to 0.95 deg and 1.32 mm for the model-based approach), and the mean precision was 0.57 deg and 0.26 mm (in comparison to 0.42 deg and 0.44 mm for the model-based approach).The methodology and the developed software can easily accommodate different design of implants with various fixation features. This method can facilitate in vivo kinematic analysis of total knee arthroplasty by eliminating the need for 3D models of the implant components.     

A quantitative electrochemiluminescence assay for Clostridium perfringens alpha toxin

Described is a rapid direct sandwich format electrochemiluminescence assay for identifying and assaying Clostridium perfringens alpha toxin. Biotinylated antibodies to C. perfringens alpha toxin bound to streptavidin paramagnetic beads specifically immunoadsorbed soluble sample alpha toxin which subsequently selectively immunoadsorbed ruthenium (Ru)-labeled detection antibodies. The ruthenium chelate of detection antibodies chemically reacted in the presence of tripropylamine and upon electronic stimulation emitted photons (electrochemiluminescence) that were detected by the photodiode of the detector. Elevated toxin concentrations increased toxin immunoadsorption and the specific immunoadsorption of Ru-labeled antibodies to alpha toxin, which resulted in increased dose-dependent electrochemiluminescent signals. The standardized assay was rapid (single 2.5-h coincubation of all reagents), required no wash steps, and had a sensitivity of about 1 ng/ml of toxin. The assay had excellent accuracy and precision and was validated in buffer, serum, and urine with no apparent matrix effects.     

Determination of uric acid in urine, saliva and calcium oxalate renal calculi by high-performance liquid chromatography/mass spectrometry

A very simple and direct method for determination of uric acid, in various biological matrices, based on high-performance liquid chromatography and mass spectrometry is described. Chromatographic separations were performed with a stationary phase Zorbax Sax Column, an anion exchange resin, with 50% sodium citrate 1 mM at pH 6.5 and 50% acetonitrile as mobile phase delivered at a flow rate of 1 ml/min. The detector counted negative ions by monitoring m/z 167.1, which corresponds to the urate anion. The method does not use an internal standard but quality control samples were used. Intra-day precision ranged between 1.1 and 1.5%, whereas inter-day precision was between 1.3 and 2.8% (n=5) working with some selected standards. Recovery tests of added standard have been successfully performed in urine and saliva samples, thus showing an appropriate accuracy of the method. The limit of quantitation found was 70 microg/l. Different urine and saliva samples were analyzed using an alternative analytical methodology based on an enzymatic reaction and photometric detection at 520 nm, resulting both methods comparable at a 95% confidence level. The method has been also applied to the determination of trace amounts of uric acid in the core of some selected calcium oxalate renal calculi.     

Striptease on glass: validation of an improved stripping procedure for in situ microarrays

Microarrays have rapidly become an indispensable tool for gene analysis. Microarray experiments can be cost prohibitive, however, largely due to the price of the arrays themselves. Whilst different methods for stripping filter arrays on membranes have been established, only very few protocols are published for thermal and chemical stripping of microarrays on glass. Most of these protocols for stripping microarrays on glass were developed in combination with specific surface chemistry and different coatings for covalently immobilizing presynthesized DNA in a deposition process. We have developed a method for stripping commercial in situ microarrays using a multi-step procedure. We present a method that uses mild chemical degradation complemented by enzymatic treatment. We took advantage of the differences in biochemical properties of covalently linked DNA oligonucleotides on in situ synthesized microarrays and the antisense cRNA hybridization probes. The success of stripping protocols for microarrays on glass was critically dependent on the type of arrays, the nature of sample used for hybridization, as well as hybridization and washing conditions. The protocol employs alkali hydrolysis of the cRNA, several enzymatic degradation steps using RNAses and Proteinase K, combined with appropriate washing steps. Stripped arrays were rehybridized using the same protocols as for new microarrays. The stripping method was validated with microarrays from different suppliers and rehybridization of stripped in situ arrays yielded comparable results to hybridizations done on unused, new arrays with no significant loss in precision or accuracy. We show that stripping of commercial in situ arrays is feasible and that reuse of stripped arrays gave similar results compared to unused ones. This was true even for biological samples that show only slight differences in their expression profiles. Our analyses indicate that the stripping procedure does not significantly influence data quality derived from post-primary hybridizations. The method is robust, easy to perform, inexpensive, and results after reuse are of comparable accuracy to new arrays.     

Supercritical fluid extraction of selected pharmaceuticals from water and serum

Selected drugs from benzodiazepine, anabolic agent and non-steroidal anti-inflammatory drug (NSAID) therapeutic classes were extracted from water and serum using a supercritical CO₂ mobile phase. The samples were extracted at a pump pressure of 329 MPa, an extraction chamber temperature of 45°C, and a restrictor temperature of 60°C. The static extraction time for all samples was 2.5 min and the dynamic extraction time ranged from 5 to 20 min. The analytes were collected in appropriate solvent traps and assayed by modified literature HPLC procedures. Analyte recoveries were calculated based on peak height measurements of extracted vs. unextracted analyte. The recovery of the benzodiazepines ranged from 80 to 98% in water and from 75 to 94% in serum. Anabolic drug recoveries from water and serum ranged from 67 to 100% and 70 to 100%, respectively. The NSAIDs were recovered from water in the 76 to 97% range and in the 76 to 100% range from serum. Accuracy, precision and endogenous peak interference, if any, were determined for blank and spiked serum extractions and compared with classical sample preparation techniques of liquid-liquid and solid-phase extraction reported in the literature. For the benzodiazepines, accuracy and precision for supercritical fluid extraction (SFE) ranged from 1.95 to 3.31 and 0.57 to 1.25%, respectively (n=3). The SFE accuracy and precision data for the anabolic agents ranged from 4.03 to 7.84 and 0.66 to 2.78%, respectively (n=3). The accuracy and precision data reported for the SFE of the NSAIDs ranged from 2.79 to 3.79 and 0.33 to 1.27%, respectively (n=3). The precision of the SFE method from serum was shown to be comparable to the precision obtained with other classical preparation techniques.     

Accuracy and precision of a method to study kinematics of the temporomandibular joint: combination of motion data and CT imaging

The purpose of the study was to test the precision and accuracy of a method used to track selected landmarks during motion of the temporomandibular joint (TMJ). A precision phantom device was constructed and relative motions between two rigid bodies on the phantom device were measured using optoelectronic (OE) and electromagnetic (EM) motion tracking devices. The motion recordings were also combined with a 3D CT image for each type of motion tracking system (EM+CT and OE+CT) to mimic methods used in previous studies. In the OE and EM data collections, specific landmarks on the rigid bodies were determined using digitization. In the EM+CT and OE+CT data sets, the landmark locations were obtained from the CT images. 3D linear distances and 3D curvilinear path distances were calculated for the points. The accuracy and precision for all 4 methods were evaluated (EM, OE, EM+CT and OE+CT). In addition, results were compared with and without the CT imaging (EM vs. EM+CT, OE vs. OE+CT). All systems overestimated the actual 3D curvilinear path lengths. All systems also underestimated the actual rotation values. The accuracy of all methods was within 0.5mm for 3D curvilinear path calculations, 0.05mm for 3D linear distance calculations and 0.2 degrees for rotation calculations. In addition, Bland-Altman plots for each configuration of the systems suggest that measurements obtained from either system are repeatable and comparable.     

Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.

A new approach to NMR solution structure refinement is introduced that uses paramagnetic effects on nuclear chemical shifts as constraints in energy minimization or molecular dynamics calculations. Chemical shift differences between oxidized and reduced forms of horse cytochrome c for more than 300 protons were used as constraints to refine the structure of the wild-type protein in solution and to define the structural changes induced by a Leu 94 to Val mutation. A single round of constrained minimization, using the crystal structure as the starting point, converged to a low-energy structure with an RMS deviation between calculated and observed pseudo-contact shifts of 0.045 ppm, 7.5-fold lower than the starting structure. At the same time, the procedure provided stereospecific assignments for more than 45 pairs of methylene protons and methyl groups. Structural changes caused by the mutation were determined to a precision of better than 0.3 A. Structure determination based on dipolar paramagnetic (pseudocontact) shifts is applicable to molecules containing anisotropic paramagnetic centers with short electronic relaxation times, including numerous naturally occurring metalloproteins, as well as proteins or nucleic acids to which a paramagnetic metal ion or ligand may be attached. The long range of paramagnetic shift effects (up to 20 A from the iron in the case of cytochrome c) provides global structural constraints, which, in conjunction with conventional NMR distance and dihedral angle constraints, will enhance the precision of NMR solution structure determination.     

Protein global fold determination using site-directed spin and isotope labeling

We describe a simple experimental approach for the rapid determination of protein global folds. This strategy utilizes site-directed spin labeling (SDSL) in combination with isotope enrichment to determine long-range distance restraints between amide protons and the unpaired electron of a nitroxide spin label using the paramagnetic effect on relaxation rates. The precision and accuracy of calculating a protein global fold from only paramagnetic effects have been demonstrated on barnase, a well-characterized protein. Two monocysteine derivatives of barnase, (H102C) and (H102A/Q15C), were 15N enriched, and the paramagnetic nitroxide spin label, MTSSL, attached to the single Cys residue of each. Measurement of amide 1H longitudinal relaxation times, in both the oxidized and reduced states, allowed the determination of the paramagnetic contribution to the relaxation processes. Correlation times were obtained from the frequency dependence of these relaxation processes at 800, 600, and 500 MHz. Distances in the range of 8 to 35 A were calculated from the magnitude of the paramagnetic contribution to the relaxation processes and individual amide 1H correlation times. Distance restraints from the nitroxide spin to amide protons were used as restraints in structure calculations. Using nitroxide to amide 1H distances as long-range restraints and known secondary structure restraints, barnase global folds were calculated having backbone RMSDs <3 A from the crystal structure. This approach makes it possible to rapidly obtain the overall topology of a protein using a limited number of paramagnetic distance restraints.     

Increase of the LC-MS/MS sensitivity and detection limits using on-line sample preparation with large volume plasma injection

Large volume injection (LVI) has systematically been studied to improve LC-MS/MS sensitivity (signal-to-noise ratio, or S/N) and detection limits. The method of LVI was combined with on-line solid phase extraction (on-line SPE) and LC-MS/MS detection for analysis of compounds directly in plasma. It was demonstrated that LVI of plasma with on-line SPE-LC-MS/MS allows for improvement of sensitivity and detection limits without compromising chromatographic peak shape and resolution and inducing significant matrix and signal suppression effects. Furthermore, sensitivity and detection limits improve linearly with the injection volume up to 100 microL. Quantification of the model compounds in plasma demonstrated comparable calibration curve statistics, precision and accuracy for 5, 50 and 100 microL plasma injections.     

Spatial interval discrimination in the presence of flanking lines

Spatial interval discrimination was studied in the absence or presence of distractors. In the latter case, two flanking lines surrounded two vertical lines delimiting the spatial interval. Using a temporal 2AFC technique with a method of constant stimuli we measured the accuracy of performance (discrimination thresholds) and biases (points of subjective equality) depending on the separations between the target and the flanking lines. For separations less than or comparable to the size of the spatial interval we found both a reduction of precision and the increase of perceived sizes of the spatial intervals: the discrimination thresholds were increased, the size of the spatial interval was overestimated. For larger separations, the size of the spatial interval was underestimated, but the precision of performance was not affected by the presence of flanking lines. We discuss the possible mechanisms underlying spatial interval discrimination in the presence of flanking lines.     

Accuracy of real-time MR temperature mapping in the brain: A comparison of fast sequences

PurposeTo compare magnetic resonance (MR) thermometry based on the proton resonance frequency (PRF) method using a single shot echoplanar imaging (ss EPI) sequence to both of the standard sequences, gradient echo (GRE) and segmented echoplanar imaging (seg EPI) in the in vivo human brain, at 1.5T and 3T.Material and methodsRepetitive MR thermometry was performed on the brain of six volunteers using GRE, seg EPI, and ss EPI sequences on whole-body 1.5T and 3T clinical systems using comparable acquisition parameters. Phase stability and temperature data precision in the human head were determined over 12 min for the three sequences at both field strengths. An ex-vivo swine skeletal muscle model was used to evaluate temperature accuracy of the ss EPI sequence during heating by high intensity focused ultrasound (HIFU).ResultsIn-vivo examinations of brain revealed an average temperature precision of 0.37 °C/0.39 °C/0.16 °C at 3T for the GRE/seg EPI/ss EPI sequences. At 1.5T, a precision of 0.58 °C/0.63 °C/0.21 °C was achieved. In the ex-vivo swine model, a strong correlation of temperature data derived using ss EPI and GRE sequences was found with a temperature deviation <1 °C.ConclusionThe ss EPI sequence was the fastest and the most precise sequence for MR thermometry, with significantly higher accuracy compared to GRE.