Comparison of the quick Gram stain method to the B&M modified and favor methods

The Gram stain is an established method for bacterial identification, but the time needed to carry out this stain is 2-3 min. We attempted to shorten this time and stained a total of 70 clinical specimens isolated from using the Bartholomew & Mittwer (B&M) modified or Favor methods with a 3 s duration for washing and staining steps. Results were plotted and analyzed using a Hue Saturation Intensity (HSI) model. The range based on a plot of the two methods with the HSI model was presented as a reference interval. Our results indicated that 100% (35/35) of strains were Gram positive and 97.1% (34/35) were Gram negative for the quick B&M modified method. In the quick Favor method, 80.0% (28/35) were Gram positive and 68.6% (24/35) of strains were Gram negative. We propose that the quick B&M modified method is equivalent to the standard Gram staining method and is superior to the quick Favor method.     

Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection

An ultraperformance LC (UPLC) method for the separation of different lipid molecular species and lipid isomers using a stationary phase incorporating charged surface hybrid (CSH) technology is described. The resulting enhanced separation possibilities of the method are demonstrated using standards and human plasma extracts. Lipids were extracted from human plasma samples with the Bligh and Dyer method. Separation of lipids was achieved on a 100 × 2.1 mm inner diameter CSH C₁₈ column using gradient elution with aqueous-acetonitrile-isopropanol mobile phases containing 10 mM ammonium formate/0.1% formic acid buffers at a flow rate of 0.4 ml/min. A UPLC run time of 20 min was routinely used, and a shorter method with a 10 min run time is also described. The method shows extremely stable retention times when human plasma extracts and a variety of biofluids or tissues are analyzed [intra-assay relative standard deviation (RSD) <0.385% and <0.451% for 20 and 10 min gradients, respectively (n = 5); interassay RSD <0.673% and <0.763% for 20 and 10 min gradients, respectively (n = 30)]. The UPLC system was coupled to a hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometer, equipped with a traveling wave ion-mobility cell. Besides demonstrating the separation for different lipids using the chromatographic method, we demonstrate the use of the ion-mobility MS platform for the structural elucidation of lipids. The method can now be used to elucidate structures of a wide variety of lipids in biological samples of different matrices.     

Freezing of bovine embryos: Effects of a one-step addition of 1.4 M glycerol

The effects of a one-step addition of 1.4 M glycerol (method A) upon morphological appearance and developmental capacity of frozen/thawed day 7 bovine embryos were investigated and compared to a standard stepwise addition of 1.0 M glycerol (method B). With method A, the percentage of intact embryos (classified as excellent, good and poor) was 95.3% (61 out of 64) without differences between morulae (96.5%) and blastocysts (94.4%). With method B, the percentage of intact embryos was 83.0% (44 out of 53). The percentage was similar for blastocysts (89.2%) and significantly (p < 0.05) lower for morulae (68.8%) when compared to method A. The percentage of embryos with a damaged zona pellucida was considerably increased with method A (26.6%) when compared to method B (13.2%). The proportion of embryos with excluded blastomeres was similar in both methods (21.9% method A, 17.0% method B). With method A, pregnancy rates after nonsurgical transfer were 51.0% (25 out of 49) and were better than with method B (40.5%; 15 out of 37). Embryos with a damaged zona pellucida resulted in a high pregnancy rate of 66.7% (8 out of 12). A pregnancy rate of 52.9% (10 out of 17) was obtained with embryos showing some excluded blastomeres. Thus, a one-step addition of 1.4 M glycerol facilitates and accelerates the process of embryo cryopreservation and is compatible with high pregnancy rates. Damage of the zona pellucida does not impair further development of frozen/thawed bovine embryos provided blastomeres are intact.     

Determination of pramipexole (U-98,528) in human plasma and urine by high-performance liquid chromatography with electrochemical and ultraviolet detection

A sensitive and selective high-performance liquid chromatographic (HPLC) method was developed for the determination of pramipexole in human plasma and urine. Plasma/urine is made alkaline before pramipexole and BHT-920 (internal standard) are extracted by ethyl ether and back-extracted with a solution that contains heptanesulfonic acid. Separation is achieved by ion-pair chromatography on a Zorbax Rx C₈ column with electrochemical detection at 0.6 V for plasma and ultraviolet detection at 286 nm for urine. The retention times of pramipexole and internal standard are approximately 14.4 and 10.7 min, respectively. The assay is linear in concentration ranges of 50 to 15 000 pg/ml (plasma) and 10 to 10 000 ng/ml (urine). The correlation coefficients are greater than 0.9992 for all curves. For the plasma method, the analysis of pooled quality controls (300, 3000, and 10 000 pg/ml) demonstrates excellent precision with relative standard deviations (R.S.D.) (n=18) of 1.1%, 2.3%, and 6.8%, respectively. For the urine method, quality control pools prepared at 30, 300, and 3000 ng/ml had R.S.D. values (n=18) of 2.9%, 1.7%, and 3.0%, respectively. The plasma and urine controls were stable for more than nine and three months, respectively. The mean recoveries for pramipexole and internal standard from plasma were 97.7% and 98.2%, respectively. The mean recoveries for pramipexole and internal standard from urine were 89.8% and 95.1%, respectively. The method is accurate with all intra-day (n=6) and overall (n=18) mean values for the quality control samples being less than 6.4 and 5.8% from theoretical for plasma and urine, respectively.     

A novel method for dose distribution registration using fiducial marks made by a megavoltage beam in film dosimetry for intensity-modulated radiation therapy quality assurance

PurposePhotographic film is widely used for the dose distribution verification of intensity-modulated radiation therapy (IMRT). However, analysis for verification of the results is subjective. We present a novel method for marking the isocenter using irradiation from a megavoltage (MV) beam transmitted through slits in a multi-leaf collimator (MLC).MethodsWe evaluated the effect of the marking irradiation at 500 monitor units (MU) on the total transmission through the MLC using an ionization chamber and Radiochromic Film. Film dosimetry was performed for quality assurance (QA) of IMRT plans. Three methods of registration were used for each film: marking by irradiating with an MV beam through slits in the MLC (MLC-IC); marking with a fabricated phantom (Phantom-IC); and a subjective method based on isodose lines (Manual). Each method was subjected to local γ-analysis.ResultsThe effect of the marking irradiation on the total transmission was 0.16%, as measured by a ionization chamber at a 10-cm depth in a solid phantom, while the inter-leaf transmission was 0.3%, determined from the film. The mean pass rates for each registration method agreed within ±1% when the criteria used were a distance-to-agreement (DTA) of 3 mm and a dose difference (DD) of 3%. For DTA/DD criteria of 2 mm/3%, the pass rates in the sagittal plane were 96.09 ± 0.631% (MLC-IC), 96.27 ± 0.399% (Phantom-IC), and 95.62 ± 0.988% (Manual).ConclusionThe present method is a versatile and useful method of improving the objectivity of film dosimetry for IMRT QA.     

Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria

The identification of mycobacteria is essential because tuberculosis (TB) and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA) that was designed for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria.     

Classification of human and zoonotic group hepatitis E virus (HEV) using antigen detection

Hepatitis E virus (HEV) is one of the major pathogens that cause acute viral hepatitis. The human (genotypes 1 and 2) and zoonotic (genotypes 3 and 4) groups of HEV present different epidemiology and clinical features. In this study, we developed a classification method for rapidly classifying HEV into human or zoonotic groups that combines a general antigen test with a zoonotic group-specific antigen test. Evaluation of serial samples from HEV-infected rhesus monkeys indicated that HEV antigen-positive samples can be classified using the antigen-based classification method. The antigen-based classification method was evaluated further on 55 genotyped samples from acute hepatitis E patients, including 9 human and 46 zoonotic groups. The novel method was completely consistent with the sequencing results: 9/9 for the human groups (100%, 95% confidence interval [CI] 66.4–100%) and 46/46 for the zoonotic groups (100%, 95% CI 92.3–100%). This method was also successfully used for the clustering of some samples that could not be clustered by sequencing. Compared with the sequencing-based method, this method is less time-consuming, less expensive, and less technically complex and is therefore ideal for large numbers of samples. In conclusion, this study provides a convenient and sensitive method for classifying different groups of HEV, and it has potentially important public health applications, especially in underdeveloped areas that cannot afford the high cost of nucleic acid testing.

     

Reliability, repeatability and accuracy of the falling head method for hydraulic conductivity measurements under laboratory conditions

The aim of this study was to verify under lab conditions the reliability, repeatability and accuracy of the falling head method (FHM) for hydraulic conductivity measurements. The FHM is a reliable procedure that has slight variations (less than 10%) in repeated measurements and turns out to be a reliable technique to record the hydraulic conductivities typically described for clogged and unclogged subsurface-flow constructed wetlands (from 4 to ca. 360 m/day). The accuracy of the method is acceptable considering difficulties in the measurement of hydraulic conductivity in highly conductive media. Accordingly, results show measurement deviations of 20% when compared with a laboratory constant head method for highly conductive media (higher than 250 m/day), and 80% for media with low hydraulic conductivity (lower than 50 m/day). The main conclusion of the present paper is that of the FHM is a reliable and repeatable technique for hydraulic conductivity measurements and it is accurate enough for on-site clogging assessment in full-scale constructed wetlands.     

Clinical application of the SurePath liquid-based Pap test in cytological screening of bronchial brushing for the diagnosis of lung cancer

The SurePath liquid-based Pap test (LPT) is successfully and widely used to assess sputum cytology. This study aimed to compare the cytological findings and diagnostic sensitivity of LPT with those of the conventional Pap smear (CPS) method for diagnosing lung cancer. Bronchial brushing specimens from 204 patients diagnosed with lung cancer were studied. LPT slides showed decreased areas of cell monolayers, a clearer background and distinct, stereoscopic cytological features. The LPT had a significantly higher diagnostic sensitivity for lung cancer (71.6%) than the CPS method (57.8%, p < 0.05), particularly for small cell lung carcinoma and >2 cm lesions (p < 0.05). Combination of the LPT with the CPS method showed obviously higher diagnostic sensitivity for the detection of adenocarcinoma (63.6%), central lesions (85.0%) and >2 cm lesions (81.4%) compared with the CPS method alone (p < 0.05, p < 0.01). Thus, LPT is a useful and easily performed technique that can be widely applied, and is suitable for the early diagnosis of lung cancer.     

Analysis of clozapine and norclozapine by high-performance liquid chromatography

A simple and reliable method for analyzing the concentrations of clozapine and its biologically active metabolite, norclozapine, in human serum or plasma has been developed. This method is based on reversed-phase high-performance liquid chromatography (HPLC) with automated solid-phase extraction (SPE). For HPLC analysis, samples and standards are prepared with an ASPEC automatic sample preparator using 100 mg Bond-Elut C₁₈ SPE columns. The HPLC assay is an isocratic method with a mobile phase of acetonitrile-methanol-10 mM dipotassium hydrogenphosphate, pH 3.7 (30:2:100, v/v/v) at a flow-rate of 1.5 ml/min with a C₁₈ reversed-phase column. Detection is performed with a diode array detector set at 220 nm and with peak purity analyses at 210–365 nm. The absolute recovery varied from 85 and 95%. The intra-assay coefficients of variation (C.V.s) were from 4.2 and 8.0% and the inter-assay C.V.s were from 1.1. to 9.3% at therapeutic drug concentrations. The detection limit is 15 nmol/l. The method has been developed for use in a clinical laboratory for therapeutic drug monitoring.     

An effective calibration technique for radiochromic films using a single-shot dose distribution in Gamma Knife®

PurposeA method of calibrating radiochromic films for Gamma Knife^® (GK) dosimetry was developed. The applicability and accuracy of the new method were examined.MethodsThe dose distribution for a sixteen millimeter single-shot from a GK was built using a reference film that was calibrated using the conventional multi-film calibration (MFC) method. Another film, the test film, from a different set of films was irradiated under the same conditions as the reference film. The calibration curve for the second set of films was obtained by assigning the dose distribution of the reference film to the optical density of the test film, point by point. To assess the accuracy of this single-film calibration (SFC) method, differences between gamma index pass rates (GIPRs) were calculated.ResultsThe SFC curves were successfully obtained with estimated errors of 1.46%. GIPRs obtained with the SFC method for films irradiated using a single-shot showed differences less than one percentage point when dose difference criterion (ΔD) was 2% and the distance to agreement criterion (Δd) was 1 mm. The GIPRs of the SFC method when the films were irradiated following a virtual target treatment plan were consistent with the GIPRs of the MFC method, with differences of less than 0.2 percentage points for ΔD = 1% and Δd = 1 mm.ConclusionThe accuracy of the SFC method is comparable to that of conventional multi-film calibration method for GK film dosimetry.     

Comparison of methods for the identification of coagulase-negative staphylococci

Coagulase-negative staphylococci (CNS) species identification is still difficult for most clinical laboratories. The scheme proposed by Kloos and Schleifer and modified by Bannerman is the reference method used for the identification of staphylococcal species and subspecies; however, this method is relatively laborious for routine use since it requires the utilization of a large number of biochemical tests. The objective of the present study was to compare four methods, i.e., the reference method, the API Staph system (bioMérieux) and two methods modified from the reference method in our laboratory (simplified method and disk method), in the identification of 100 CNS strains. Compared to the reference method, the simplified method and disk method correctly identified 100 and 99% of the CNS species, respectively, while this rate was 84% for the API Staph system. Inaccurate identification by the API Staph method was observed for Staphylococcus epidermidis (2.2%), S. hominis (25%), S. haemolyticus (37.5%), and S. warneri (47.1%). The simplified method using the simple identification scheme proposed in the present study was found to be efficient for all strains tested, with 100% sensitivity and specificity and proved to be available alternative for the identification of staphylococci, offering, higher reliability and lower cost than the currently available commercial systems. This method would be very useful in clinical microbiology laboratory, especially in places with limited resources.     

A Low Complexity Rapid Molecular Method for Detection of Clostridium difficile in Stool

Here we describe a method for the detection of Clostridium difficile from stool using a novel low-complexity and rapid extraction process called Heat Elution (HE). The HE method is two-step and takes just 10 minutes, no specialist instruments are required and there is minimal hands-on time. A test method using HE was developed in conjunction with Loop-mediated Isothermal Amplification (LAMP) combined with the real-time bioluminescent reporter system known as BART targeting the toxin B gene (tcdB). The HE-LAMP-BART method was evaluated in a pilot study on clinical fecal samples (tcdB ⁺, n =  111; tcdB ⁻, n  = 107). The HE-LAMP-BART method showed 95.5% sensitivity and 100% specificity against a gold standard reference method using cytotoxigenic culture and also a silica-based robotic extraction followed by tcdB PCR to control for storage. From sample to result, the HE-LAMP-BART method typically took 50 minutes, whereas the PCR method took >2.5 hours.In a further study (tcdB ⁺, n =  47; tcdB ⁻, n  = 28) HE-LAMP-BART was compared to an alternative commercially available LAMP-based method, Illumigene (Meridian Bioscience, OH), and yielded 87.2% sensitivity and 100% specificity for the HE-LAMP-BART method compared to 76.6% and 100%, respectively, for Illumigene against the reference method. A subset of 27 samples (tcdB ⁺, n =  25; tcdB ⁻, n  = 2) were further compared between HE-LAMP-BART, Illumigene, GeneXpert (Cepheid, Sunnyvale, CA) and RIDA®QUICK C. difficile Toxin A/B lateral flow rapid test (R-Biopharm, Darmstadt, Germany) resulting in sensitivities of HE-LAMP-BART 92%, Illumigene 72% GeneXpert 96% and RIDAQuick 76% against the reference method. The HE-LAMP-BART method offers the advantages of molecular based approaches without the cost and complexity usually associated with molecular tests. Further, the rapid time-to-result and simple protocol means the method can be applied away from the centralized laboratory settings.     

The estimation of micro-algal protein content and its meaning to the evaluation of algal biomass I. Comparison of methods for extracting protein

The spectrophotometric evaluation of micro-algal protein needs a prior extraction from cells in order to liberate protein for measurement. The conditions of extraction (temperature, duration, normality of sodium hydroxide, pretreatment) which yield optimal protein content are tested with three algal cultures (Scenedesmus, Synechococcus, Asterionella). A standard method of extraction is presented. Comparison of this method with nine published methods reveals markedly lower protein yields for easy extractable (43–100%) and hard extractable (5–75%) algal species, relative to this method, depending on ease of cell wall breakage. The application of this standard method to field investigations is demonstrated and compared to other biochemical parameters. The advantages of this method over other protein extraction methods, with respect to field material, are discussed.     

Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected nonhomologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for αhelix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For Β-strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method.     

HPLC analysis of asymmetric dimethylarginine,symmetric dimethylarginine,homoarginine and arginine in small plasma volumes using a Gemini-NX column at high pH

There is increasing recognition of the clinical importance of endogenous nitric oxide synthase inhibitors in critical illness. This has highlighted the need for an accurate high performance liquid chromatography (HPLC) method for detection of asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) in small volumes of blood. Here, the validation of an accurate, precise HPLC method for the determination of ADMA, SDMA, homoarginine and arginine concentrations in plasma is described. Solid phase extraction is followed by derivatisation with AccQ-Fluor™ and reversed phase separation on a Gemini-NX column at pH 9. Simultaneous detection by both UV–vis and fluorescence detectors affords extra validation. This solid phase extraction method gives absolute recoveries of more than 85% for ADMA and SDMA and relative recoveries of 102% for ADMA and 101% for SDMA. The intra-assay relative standard deviations are 2.1% and 2.3% for ADMA and SDMA, respectively, with inter-assay relative standard deviations of 2.7% and 3.1%, respectively. Advantages of this method include improved recovery of all analytes using isopropanol in the solid phase extraction; sharp, well-resolved chromatographic peaks using a high pH mobile phase; a non-endogenous internal standard, n-propyl l-arginine; and accurate and precise determination of methylated arginine concentrations from only 100 μL of plasma.     

Rapid determination of the anti-cancer drug chlorambucil (Leukeran™) and its phenyl acetic acid mustard metabolite in human serum and plasma by automated solid-phase extraction and liquid chromatography–tandem mass spectrometry

A bioanalytical method for the determination of the anticancer drug chlorambucil (Leukeran™) and its phenyl acetic acid mustard metabolite in human serum and plasma is described. Automated solid-phase extraction of the analytes is carried out with C₁₈ sorbent packed in a 96 well format microtitre plate using a robotic sample processor. The extracts are analysed by isocratic reversed-phase liquid chromatography using pneumatically and thermally assisted electrospray ionisation (TurboIonspray) with selected reaction monitoring. The method is specific and sensitive, with a range of 4–800 ng/ml in human serum and plasma for both parent drug and metabolite (sample volume 200 μl). The method is accurate and precise with intra-assay and inter-assay precision (C.V.) of <15% and bias <15% for both analytes. The automated extraction procedure is significantly faster than manual sample pre-treatment methods, a batch of 96 samples is extracted in 50 min allowing for faster sample turnaround. The method has been used to provide pharmacokinetic support to biocomparability studies of Leukeran™ following single doses of oral tablet formulations.     

Fiber background rejection and crystal over-response compensation for GaN based in vivo dosimetry

For dosimetric measurements using an implantable optical fiber probe with GaN (Gallium Nitride) scintillator as radioluminescence (RL) transducer, a bi-channel method is proposed to reject the background contribution of the irradiated fiber segment. It is based on spectral differences between the narrow-band light emission from GaN and the large-band background from the irradiated optical fiber. Experimental validation of this method using 6 MV photon beam has shown that the remaining background contribution after subtraction is below 1.2% for square field sizes ranging from 3 cm to 20 cm. Furthermore, a compensation method for the over-response of GaN is also proposed, since GaN is not tissue equivalent. The over-response factor of GaN exhibits a linear increase with square field aperture and depends on depth from phantom surface. This behaviour is modelled to allow compensation in specific conditions. The proposed method has been evaluated and has shown a maximum deviation of 3% for a 6 MV photon beam and 1% for an 18 MV photon beam at a depth beyond the build-up region.     

High-throughput analysis of fatty acid composition of plasma glycerophospholipids

Plasma FA composition, a marker of FA status and dietary intake, is associated with health outcomes on a short- and long-term basis. Detailed investigation of the relationships between plasma FA composition and health requires the analysis of large numbers of samples, but manual sample preparation is very cumbersome and time consuming. We developed a high-throughput method for the analysis of FAs in plasma glycerophospholipids (GPs) with increased sensitivity. Sample preparation requires two simple steps: protein precipitation and subsequent base catalyzed methyl ester synthesis. Analysis of GP FAs is performed by gas chromatography. Coefficients of variation for FAs contributing more than 1% to total FAs are below 4%. Compared with the established reference method, results of the new method show good agreement and very good correlations (r > 0.9). The new method reduces the manual workload to about 10% of the reference method. Only 100 µl plasma volume is needed, which allows for the analysis of samples from infants. The method is well suitable for application in large clinical trials and epidemiological studies.