Evaluation of automated analysis of 15N and total N in plant material and soil

Simultaneous determination of ¹⁵N and total N using an automated nitrogen analyser interfaced to a continuous-flow isotope ratio mass spectrometer (ANA-MS method) was evaluated. The coefficient of variation (CV) of repeated analyses of homogeneous standards and samples at natural abundance was lower than 0.1%. The CV of repeated analyses of ¹⁵N-labelled plant material and soil samples varied between 0.3% and 1.1%. The reproductibility of repeated total N analyses using the automated method was comparable to results obtained with a semi-micro Kjeldahl procedure. However, the automated method gave results which were 3% to 5% higher than those obtained with the Kjeldahl procedure. Since only small samples can be analysed, careful sample homogenization and fine grinding are very important. Evaluation of a diffusion method for preparing nitrate and ammonium in solution for automated ¹⁵N analysis showed that the recovery of inorganic N in the NH₃ trap was lower when the N was diffused from water than from 2 M KCl. The results also indicated that different proportions of the NO₃ ^- and the NH₄ ⁺ in aqueous solution were recovered in the trap after combined diffusion. The method is most suited for diffusing either NO₃ ^- or NH₄ ⁺ alone, but can be used for combined diffusion of the two ions.     

Modification of Lofland's colorimetric semiautomated serum triglyceride determination, assessed by an enzymatic glycerol determination

Erroneously high values for serum triglyceride levels obtained with the semiautomated method of Lofland were found to be due to contamination of the isopropanol extracts with glucose or other carbohydrate. Treatment of the isopropanol extracts with a mixture of copper sulfate and calcium hydroxide removed the contaminating glucose. Analysis of the glucose-free extracts by either the semiautomated or manual colorimetric method gave values in good agreement with each other and with those obtained by a new specific enzymatic method. The simple modification described in this paper obviates the necessity for the more expensive automated fluorometric apparatus.     

Evaluation of an on-line solid-phase extraction method for determination of almokalant, an antiarrhythmic drug, by liquid chromatography

A fully automated liquid chromatographic method based on a Prospekt solid-phase extraction unit is described for determination of the antiarrhythmic drug almokalant in plasma. The assay comprises solid-phase extraction on a C₂ phase and separation on a C₁₈ column with fluorometric detection. In the original procedure 40 samples a day could be run unattended but by modifying the sequence in the solid-phase extraction process it was possible to increase this number to 70. The method gives an absolute recovery of 92% and a repeatability (C.V.) of 2.9% at 75 nmol/1 of plasma. The limit of quantitation is 2 nmol/1 of plasma (C.V. < 20%). As regards accuracy and precision the performance of the method is as good as the manual method based on liquid-liquid extraction. The Prospekt method is, above all, faster and requires far less manual effort.     

Comparison of manual and automated methods for identifying target sounds in audio recordings of Pileated, Pale-billed, and putative Ivory-billed woodpeckers

ABSTRACT.   Although offering many benefits over manual recording and survey techniques for avian field studies, automated sound recording systems produce large datasets that must be carefully examined to locate sounds of interest. We compared two methods for locating target sounds in continuous sound recordings: (1) a manual method using computer software to provide a visual representation of the recording as a sound spectrogram and (2) an automated method using sound analysis software preprogrammed to identify specific target sounds. For both methods, we examined the time required to process a 24-h recording, scanning accuracy, and scanning comprehensiveness using four different target sounds of Pileated Woodpeckers ( Dryocopus pileatus ), Pale-billed Woodpeckers ( Campephilus guatemalensis ), and putative Ivory-billed Woodpeckers ( Campehilus principalis ). We collected recordings from the bottomland forests of Florida and the Neotropical dry forests of Costa Rica, and compared manual versus automated cross-correlation scanning techniques. The automated scanning method required less time to process sound recordings, but made more false positive identifications and was less comprehensive than the manual method, identifying significantly fewer target sounds. Although the automated scanning method offers a fast and economic alternative to traditional manual efforts, our results indicate that manual scanning is best for studies requiring an accurate account of temporal patterns in call frequency and for those involving birds with low vocalization rates.     

Manual gas-phase isothiocyanate degradation

We describe a manual gas-phase isothiocyanate degradation procedure for the primary structure determination of proteins and peptides. The proteins and peptides are applied to a polybrene-coated glass fiber filter wedged into a small glass column. The phenylisothiocyanate is directly pipetted onto the filter disk. The coupling and cleavage reactions are performed in small desiccators containing trimethylamine and trifluoroacetic acid vapors, respectively. The wash and extraction steps are performed by allowing the suitable solvents to percolate through the filter disk. The extracted anilinothiazolinone is then converted to the phenylthiohydantoin and identified by any one of a number of described methods. Our results show that this method is very sensitive and that the reactions proceed faster than those of the published automated procedure. No expensive equipment is required and the manual degradation can be performed by a laboratory assistant. A large number of samples can be simultaneously subjected to the degradation under identical conditions, making this an ideal method for physicochemical investigations into the isothiocyanate degradation. We also use this method to screen HPLC fractions after enzymatic protein fragmentation. Manually sequenced glass filters can be transferred to the automated instrument for more extended degradations.     

Automated microanalysis of adenosine phosphates, phosphocreatine, creatine, and lactate in muscle

An automated enzymatic procedure suitable for determination of ATP, ADP, AMP, phosphocreatine, creatine, and lactate in needle biopsies of human skeletal muscle (ca. 30 mg dry wt) using a fast centrifugal analyzer (Multistat III, Instrumentation Laboratory Inc.) is presented. Coefficients of variation ranged from 0.7 to 4.2% for multiple determinations of ATP, ADP, phosphocreatine, and creatine; from 6 to 24% for lactate; and from 9 to 20% for AMP. The procedure should be usable, with appropriate modification, with other tissues and with other fast centrifugal analyzers. Muscle samples are collected into liquid freon, lyophilized, and extracted with 600 microliter of 0.65 M perchloric acid. Neutralized supernatants can be stored for up to 3 years at -80 degrees C with no significant deterioration. The procedure takes much less time than similar manual procedures and gives better reproducibility, particularly for ADP and AMP.     

Automated analysis of the pyridinium crosslinks of collagen in tissue and urine using solid-phase extraction and reversed-phase high-performance liquid chromatography.

A fully automated method for assaying the collagen crosslinking amino acids, pyridinoline and deoxypyridinoline, in human urine samples or tissue hydrolysates is described. Samples were processed using a Gilson ASPEC system with solid-phase extraction of the crosslinks on columns containing 100 mg of microgranular cellulose. Introduction of an additional solvent step during sample preparation allowed direct analysis by reversed-phase HPLC and elimination of the drying step used previously in a manual method. Use of a synthetic pyridinoline derivative as internal standard enabled accurate quantification of the crosslinks by correcting for recoveries through the whole assay. Samples were analyzed in sequential mode with a total assay time of 30 min. The automated assay showed close correlation with the manual method for both free and total crosslink determinations in human urine (r > 0.97). Reproducibility was improved, as seen from replicate analyses of human urine (CV < 3% for automated pyridinoline measurement compared with 8-12% previously observed for the manual method). Crosslink excretion is the most useful marker of collagen degradation in metabolic bone diseases and arthritic disorders. The automated assay which has been developed is rapid, convenient, and reliable and will greatly facilitate the monitoring of urinary collagen crosslinks and their tissue levels in clinical investigations.     

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses

Studies on host-associated microbial communities using faecal samples has been providing important insights into the health, ecology and evolution of various animals. Many gut microbiome studies currently use manual kit-based DNA extraction methods, yet new methods that allow high-throughput sample processing are in demand. In this study, we evaluated magnetic cellulose bead-based DNA extraction methods, which can be automated in a work station, using mouse, Mus musculus (Linnaeus), and bovine, Bos taurus (Linnaeus), faeces as a model. Our data showed that those methods can provide good quantity and quality of extracted DNA suitable for 16S-rRNA-based microbiome analyses for a wide variety of samples, comparable to or more efficiently than the widely used standard method. The automated extraction requires less time and fewer manual steps, which makes these methods suitable for high-throughput faecal microbiome analyses.     

Encephalitozoon cuniculi: Quantitation of Parasites and Evaluation of Viability1

Two methods (manual and automated) for quantitation of viable versus dead Encephalitozoon cuniculi are reported. The manual method uses ethidium bromide and acridine orange to stain dead and viable organisms, respectively. The stained organisms are visually differentiated with the aid of a fluorescence microscope. The automated method uses propidium iodide to stain dead parasites, which are differentiated from viable unstained parasites with the aid of a flow cytometer. An automated cell counter (Coulter Counter) was used to count rapidly large numbers of samples and to improve the sensitivity of counting low concentrations of parasites. These methods will enhance investigators' abilities to conduct quantitative experiments on host defense mechanisms against E. cuniculi.     

Evaluation of an automated fluorescent antibody procedure for detection of Salmonella in foods and feeds.

A prototype automated system using fluorescent antibody (FA) was evaluated for rapid detection of salmonellae in foods. Samples were enriched in selenite cystine and tetrathionate broths. After incubation, both were transferred into fresh selenite cystine for a 4-h "post-enrichment" to dilute possible background fluorescence from product. These cultures were then analyzed automatically, and results were compared with those obtained by the methods of the Association of Official Analytical Chemists (AOAC). Initially, 167 samples of milk powder, dried yeast, and imported frog legs were examined. The AOAC and automated FA methods correlated well with all samples but frog legs. Difficulty with the latter was caused by procedural and mechanical problems coupled with high numbers of competing microorganisms in post-enrichment cultures. Modification of procedure and partial redesign of equipment corrected these difficulties, and excellent correlation was obtained with another 116 frog leg samples. All 89 AOAC-confirmed positives were also detected by the automated FA method, and there were only 4% false FA positives. The system shows potential for screening products for salmonellae; however, all positives should be confirmed by manual biochemical and serological methods.     

Comparative study between two laser scanning cytometers and epifluorescence microscopy for the detection of Cryptosporidium oocysts in water.

BACKGROUND: Cryptosporidium detection in water and environmental samples has increased during the last years, largely due to an increase in the number of reported waterborne outbreaks of cryptosporidiosis and the implementation of new regulations about Cryptosporidium monitoring in water supplies. The aim of this study was to validate and compare the capacity of two laser scanning cytometers commercially available (LSC and ChemScanRDI), against manual microscopic enumeration of Cryptosporidium oocysts in surface water and reference material samples. METHODS: Reference material and surface water samples were analysed by two laser scanning cytometers methodologies and by manual epifluorescence microscopy. Two mAbs from commercial suppliers were used to evaluate background reduction. RESULTS: Highly significant correlations were obtain between both cytometers (R(2) = 0.99) and with manual microscopy (R(2) = 0.98), showing that oocysts counts made by cytometers were equivalent to those obtained with conventional methods. We observed a variability in oocysts counts when different antibodies where used with laser scanning cytometers and manual microscopy. CONCLUSIONS: This study showed the efficacy of the laser scanning technology (LSC and ChemScanRDI), as an automated and a more standardized alternative to manual epifluorescence microscopy examination, for Cryptosporidium detection in water samples. High quality antibodies are needed for automated enumeration as well as for manual microscope observations.     

Effect of cellulose physical characteristics, especially the water sorption value, on the efficiency of its hydrolysis catalyzed by free or immobilized cellulase

Cellulase, an enzymatic complex that synergically promotes the degradation of cellulose to glucose and cellobiose, free or adsorbed onto Si/SiO₂ wafers at 60 °C has been employed as catalyst in the hydrolysis of microcrystalline cellulose (Avicel), microcrystalline cellulose pre-treated with hot phosphoric acid (CP), cotton cellulose (CC) and eucalyptus cellulose (EC). The physical characteristics such as index of crystallinity (I_C), degree of polymerization (DP) and water sorption values were determined for all samples. The largest conversion rates of cellulose into the above-mentioned products using free cellulase were observed for samples with the largest water sorption values; conversion rates showed no correlation with either I_C or DP of the biopolymer. Cellulose with large water sorption value possesses large pore volumes, hence higher accessibility. The catalytic efficiency of immobilized cellulase could not be correlated with the physical characteristics of cellulose samples. The hydrolysis rates of the same cellulose samples with immobilized cellulase were lower than those by the free enzyme, due to the diffusion barrier (biopolymer chains approaching to the immobilized enzyme) and less effective contact between the enzyme active site and its substrate. Immobilized cellulase, unlike its free counterpart, can be recycled at least six times without loss of catalytic activity, leading to higher overall cellulose conversion.     

Development of an automated micrometeorological method for measuring the emission of mercury vapor from wetland vegetation

The ability of green plants to act as conduits to enhance the transport ofHg from soils to the atmosphere is now established, but the data base isseverely limited. The potential role of this process in mobilizing Hg inglobal and regional cycles makes it imperative that automated methods bedeveloped to increase our capability to measure and understand the processin a variety of ecosystems. We previously published a tower-basedmicrometeorological gradient method for measuring gas-phase Hg^°fluxes in terrestrial systems based on the Modified Bowen ratio (MBR)approach. The method relied on demanding and time-consuming manualsampling of Hg gradients. Automated Hg sampling methods now exist, andwe describe here applications of the Tekran Hg analyzer to automatednear-real-time measurements of Hg gradients over wetland vegetation. Weuse these data with MBR to compute fluxes of Hg from those of othertrace gases. From 1996 to 1998 we sampled Hg fluxes over emergentmacrophytes in the Florida Everglades, beginning with manual methods, butlater deploying automated methods for most of the study to collect morethan 500 30-min fluxes over 2 y. The limitations of the manual methodresulted in considerable uncertainly in our earlier observations, even to theextent that we initially doubted that vegetation emissions were real. However, the automated method allowed us to quantify the actualdevelopment of Hg emission gradients over wetland vegetation. Followingsunrise Hg fluxes show diel patterns similar to those of CO₂ andH₂O, providing information on the possible mechanisms of Hgemission. Our data suggest mean daytime emission rates of Hg over thesewetlands on the order of 30 ng m^-2 h^-1. Fluxes wereinfluenced by temperature, solar radiation, and atmospheric turbulence. There exists a significant biotic re-emission of Hg^° from the oceans,and our data provide the first direct evidence of a similar process insubtropical wetlands.     

The impact of sampling frequency and sampling times on chamber-based measurements of N2O emissions from fertilized soils

An automated closed‐chamber system was developed to measure N₂O fluxes in the field. It was deployed at two N‐fertilized grassland sites in two successive years, together with replicated manual chambers, to investigate the spatial and temporal variability in fluxes, and the likely impact of sampling frequency on cumulative flux values. The automated system provided flux data at 8‐h intervals, while manual sampling was conducted at intervals of 3–7 days. The autochambers showed fluctuations in emissions not detected by manual sampling. However, integrated flux values based on the more intensive measurements were on average no more than 14% greater than those based on data from the autochambers that were obtained at the same time as manual sampling. This difference was not significant and well within the spatial variability determined with manual chambers. If daily sampling intervals were used immediately after fertilization, the agreement was closer still, increasing the confidence that can be placed in manual procedures. Diurnal variations in temperature and flux were small, and results from sampling at mid‐day were not significantly different from those based on early morning or evening sampling. Where diurnal fluctuations in temperature and flux are likely to be much larger, the autochamber/sampler system could prove very useful to quantify the effect.     

Improved automated method for determining vitamin C in plasma and tissues.

An improved automated method for determining vitamin C in plasma and tissues is described. Total vitamin C was determined after oxidation to dehydroascorbic acid by reaction with 2,4-dinitrophenylhydrazine. The recovery of ascorbic acid added to plasma was 98 to 101% with a coefficient of variation of 1.8%. Interaction between samples with low, medium, and high concentrations was 1% and the coefficient of variation on 60 replicate analyses of plasma was 2.0%. In the analysis of 16 samples of rat plasma, results obtained by the automated method were essentially the same as those obtained by the original manual method. It was possible to determine vitamin C in 0.15 ml of plasma containing as little as 1.2 μg/ml. Vitamin C was also measured in extracts of rat heart, spleen, kidneys, adrenals, liver, and brain.     

Automation of a Hemagglutination-Inhibition Test for Parainfluenza 3 Antibodies in Bovine Sera

An automated hemagglutination-inhibition (HI) test for the "shipping fever" strain (SF-4) of parainfluenza 3 antibody in bovine sera was developed and compared to manual tube and microtiter test procedures. The automated system operating at 60 samples per hr provided the most test results per specified time period, and the manual tube test provided the least. The manual microtiter test and the automated system at 40 samples per hr, falling between the two above procedures, were comparable in the number of sera that could be titrated in 1 day by one technician. There was little difference between automated and manual test reproducibility when measured at the twofold titer one-dilution difference level. However, the automated system titrated a higher number of sera at the same titer on repeat runs than either of the manual test procedures. The automated one-quartile difference reproducibility (each twofold dilution subdivided into 4 units-"quartiles") was equal to the manual test one-dilution difference reproducibility. The standard deviation of the per cent variation from the mean of paired serum titers for 40-sample-per-hr runs ranged from +/-3.49 to +/-5.36%. The manual and automated systems were of comparable sensitivity in their detection of negative sera.     

Simultaneous loading of 200 sample lanes for DNA sequencing on vertical and horizontal, standard and ultrathin gels.

We have developed a simple and efficient technique for automated parallel loading of >/=200 lanes on a 30 cm-wide gel in automated DNA sequencing, using porous filter materials and an associated manual or robotic system. The samples are loaded onto the teeth of a comb made of the porous material. The comb, with samples, is inserted directly above the straight edge of the polymerized gel. The samples are driven from the comb into the gel by the applied electrical field. A particularly advantageous aspect of this method is the elimination of the thin gel walls separating the sample wells in the standard gel loading technique. The time for sample loading is significantly reduced to a few minutes. The loading technique is applicable to horizontal or vertical systems, with standard or ultrathin gels.     

Automated fluorescent in situ hybridization (FISH) analysis of t(9;22)(q34;q11) in interphase nuclei.

BACKGROUND: For chronic myeloid leukemia, the FISH detection of t(9;22)(q34;q11) in interphase nuclei of peripheral leukocytes is an alternative method to bone marrow karyotyping for monitoring treatment. With automation, several drawbacks of manual analysis may be circumvented. In this article, the capabilities of a commercially available automated image acquisition and analysis system were determined by detecting t(9;22)(q34;q11) in interphase nuclei of peripheral leukocytes. METHODS: Three peripheral blood samples of normal adults, 21 samples of CML patients, and one sample of a t(9;22)(q34;q11) positive cell-line were used. RESULTS: Single nuclei with correctly detected signals amounted to 99.6% of nuclei analyzed after exclusion of overlapping nuclei and nuclei with incorrect signal detection. A cut-off value of 0.84 mum was defined to discriminate between translocation positive and negative nuclei based on the shortest distance between signals. Using this value, the false positive rate of the automated analysis for negative samples was 7.0%, whereas that of the manual analysis was 5.8%. Automated and manual results showed strong correlation (R(2) = 0.985), the mean difference of results was only 3.7%. CONCLUSIONS: A reliable and objective automated analysis of large numbers of cells is possible, avoiding interobserver variability and producing statistically more accurate results than manual evaluation.     

Reticulocyte quantification by flow cytometry, image analysis, and manual counting.

Reticulocyte counting by flow cytometry with thiazole orange was compared to manual or automated counting of new methylene blue stained blood smears. Forty-nine samples were compared for manual counting from randomly chosen clinical samples. Two hundred and eighty-nine samples from bone marrow transplant patients were compared during the period before and through chemo-irradiation and engraftment. The slopes of correlation plots were less than 1 when flow cytometric data were the dependent variable, suggesting that thiazole orange is less sensitive than new methylene blue. In a third study, 407 samples from bone marrow transplant patients were compared after increasing the thiazole orange concentration. The reticulocyte fluorescence distribution was divided into four groups of the brightest (youngest) 40, 60, 80, and 100% of reticulocytes. The slopes from regression analysis were 0.25, 0.49, 0.78, and 1.14, respectively. This demonstrates that thiazole orange is more sensitive than new methylene blue because the window of analysis includes an increased fraction of mature reticulocytes. In addition, the precision of each assay as measured. The rank order of precision from high to low was flow cytometry > image analysis > manual counting.     

A method for the rapid,automated filtration of protein hydrolyzates

A method for the automated filtration of protein hydrolyzates prior to amino acid analysis is described. Minor modification of a Technicon Sampler II enables it to function simultaneously as a sampler and a filtrate collector. Samples are drawn from cups in the sampler tray and are forced through a Teflon filter (pore size, 0.2 μm) in a Millipore Swinnex filter holder by a variable-speed Technicon proportioning pump. The filtrates are collected in cups in the sampler tray opposite those containing unfiltered hydrolyzates. Using this technique, 12 hydrolyzates can be filtered in 25 min compared to the approximately 2 h of technician time required for their manual filtration. Aliquots from each of 48 samples representing different proteins and hydrolysis conditions are filtered manually and by the automated technique. Analysis of variance of the resulting recoveries of each amino acid indicate little likelihood of effects due to filtration method.