Microproteomics: analysis of protein diversity in small samples.

Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.

Evaluation of maximum likelihood procedures to estimate left censored observations.

The optimal procedure for estimating chemical levels below the limit of detection (LOD) remains a topic of interest when working with ultratrace analysis of environmental or clinical specimens. Unique to this investigation, we evaluated the performance of three maximum likelihood estimation (MLE) procedures to estimate the population mean and standard deviation from chemical data with 10-40% observations below the LOD. Randomly drawn observations from the normal distributions with these parameter estimates were used to replace censored observations. Final estimates of the mean and standard deviation (SD) were obtained from these full samples and compared to actual population mean mu and SD sigma. The study demonstrated that the average percent relative bias for both the mean and SD increased as the sample size decreased and the percent observations below the LOD increased. The MLE procedure with multiple imputations almost always had acceptable coverage rates for both the mean and the SD. These findings support earlier observations, and they suggest that MLE with multiple imputations is the preferred method to estimate mean and SD when the frequency of left censored observations in the population is < or =40%.

Microdetermination of fatty acids by gas chromatography and cardiovascular risk stratification by the "EPA+DHA level".

The therapeutic options for interfering with the electrical instability of a pathologically remodeled or ischaemic heart remain limited. Of increasing importance become interventions which target the fatty acid composition of blood and membrane lipids. In particular, the long-chain omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) provide parameters for stratification of risks associated with severe arrhythmia disorders and sudden cardiac death. Since EPA and DHA appear to have their anti-arrhythmogenic actions when present as free fatty acids, the parameters which determine a critical free fatty acid concentration are of great interest. In the present study, conclusions on EPA and DHA incorporation in blood lipids are derived from the administration of Omacor which contains highly purified (84%) EPA and DHA ethyl esters and reduced the risk of sudden cardiac death by 45% in post-myocardial infarction patients (GISSI-Prevention study). The "EPA+DHA level" is described as risk identifying parameter for severe arrhythmia disorders, particularly if they are associated with myocardial ischaemia. It appears essential not only to build up body stores for release of EPA and DHA but to provide also a sustained uptake of EPA and DHA in the form of ethyl esters. In contrast to more rapidly absorbed triacylglycerols from fish, ethyl esters are taken up slowly within 24 h. For the administration of 1 g/day Omacor to healthy volunteers, it is shown that in whole blood EPA is increased from 0.6% to 1.4% within 10 days while DHA is increased from 2.9% to 4.3%. After withdrawal, the EPA and DHA levels approach baseline values within 10 days. A gas chromatographic procedure was established which requires only 10 microl of whole blood for the identification of more than 30 fatty acids. Evidence is summarized strengthening the concept that a low "EPA+DHA level" presents a risk for severe arrhythmia disorders and sudden cardiac death. The administration of 840 mg/day of EPA and DHA ethyl esters raises the "EPA+DHA level" to approximately 6% that is associated with protection from sudden cardiac death. The pharmacological effects of ethyl esters are compared with the naturally occurring EPA and DHA triacylglycerols present in fish or fish oils which are of interest in primary prevention of cardiovascular disorders.

Comparison of methods for measurement of organic compounds at ultra-trace level: analytical criteria and application to analysis of amino acids in extraterrestrial samples.

The need for criteria to compare different analytical methods for measuring extraterrestrial organic matter at ultra-trace levels in relatively small and unique samples (e.g., fragments of meteorites, micrometeorites, planetary samples) is discussed. We emphasize the need to standardize the description of future analyses, and take the first step toward a proposed international laboratory network for performance testing.

Highly sensitive and selective surface plasmon resonance sensor for detection of sub-ppb levels of benzo[a]pyrene by indirect competitive immunoreaction method.

A surface plasmon resonance (SPR)-immunosensor for detection of benzo[a]pyrene (BaP) is developed by using a model BaP-hapten compound, BaP-bovine serum albumin conjugate (BaP-BSA), and an anti-BaP-BSA monoclonal antibody. BaP-BSA conjugate is immobilized on a gold thin-film sensor chip by means of simple physical adsorption. The number of BaP-hapten units in BaP-BSA conjugate is estimated to be 28 from the difference in molecular weight (MW) between BaP-BSA conjugate and BSA based on the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) measurement. Anti-BaP-BSA antibody on contact with the BaP-BSA conjugate immobilized sensor chip causes an increase in the incident angle of the sensor chip. Binding of anti-BaP-BSA antibody with surface-immobilized BaP-BSA conjugate is inhibited by the presence of BaP in analyte solution, because of the inhibition effect of BaP. The SPR immunosensor for BaP functioning with the indirect competitive immunoreaction of anti-BaP-BSA antibody between the analyte (BaP) in testing solution and the BaP-BSA conjugate immobilized on the sensor chip provides a rapid determination (response time: ca. 15 min) of BaP in the concentration range of 0.01-1000 ppb. The antibody anchored to the sensor chip by antigen-antibody binding is removed on treatment with a pepsin solution (pH 2.0) for few minutes. The SPR sensor chip is found to be reusable for more than 20 times with a little decrease (<7%) in the sensor response. Detection of BaP by direct competitive immunoreactions is also carried out by enzyme-linked immunosorbent assay (ELISA). The concentration of BaP could be determined as low as 0.01 ppb and 2 ppb using the SPR sensor and the ELISA method, respectively. The SPR sensor is found to detect BaP selectively in the presence of 2-hydroxybiphenyl (HBP); the incident angle shift of the SPR sensor for BaP is found to be same irrespective to the presence or the absence of a same concentration (as much as 30 ppb) of HBP together.

Single-nucleotide polymorphism analysis by allele-specific extension of fluorescently labeled nucleotides in a microfluidic flow-through device.

We describe a microfluidic approach for allele-specific extension of fluorescently labeled nucleotides for scoring of single-nucleotide polymorphism (SNP). The method takes advantage of the fact that the reaction kinetics differs between matched and mismatched configurations of allele-specific primers hybridized to DNA template. A microfluidic flow-through device for biochemical reactions on beads was used to take advantage of the reaction kinetics to increase the sequence specificity of the DNA polymerase, discriminating mismatched configurations from matched. The volume of the reaction chamber was 12.5 nL. All three possible variants of an SNP site at codon 72 of the p53 gene were scored using our approach. This work demonstrates the possibility of scoring SNP by allele-specific extension of fluorescently labeled nucleotides in a microfluidic flow-through device. The sensitive detection system and easy microfabrication of the microfluidic device enable further miniaturization and production of an array format of microfluidic devices for high-throughput SNP analysis.

Exploring nature's plasticity with a flexible probing tool, and finding new ways for its electronic distribution.

Concepts and results are described for the use of a single, but extremely flexible, probing tool to address a wide variety of genomic questions. This is achieved by transforming genomic questions into a software file that is used as the design scheme for potentially any genomic assay in a microarray format. Microarray fabrication takes place in three-dimensional microchannel reaction carriers by in situ synthesis based on spatial light modulation. This set-up allows for maximum flexibility in design and realization of genomic assays. Flexibility is achieved at the molecular, genomic and assay levels. We have applied this technology to expression profiling and genotyping experiments.

A BODIPY fluorescent microplate assay for measuring activity of calpains and other proteases.

The use of 4,4-difluoro-5,7-dimethyl-4-bora-3a, 4a-diaza-s-indacene-3-propionic acid (BODIPY-FL) labeled casein in autoquenching assays of proteolytic activity has been recently described, and we have adapted this assay to measurement of calpain activity. BODIPY-FL coupled to casein at a ratio of 8 mol of BODIPY-FL/mol of casein or higher produces a BODIPY-FL-casein substrate that can be used in an autoquenching assay of calpain proteolytic activity. This assay has a number of advantages for measuring calpain activity. (1) The procedure does not require precipitation and removal of undegraded protein, so it is much faster than other procedures that require a precipitation step, and it can be used directly in kinetic assays of proteolytic activity. (2) The BODIPY-FL-casein assay is easily adapted to a microtiter plate format, so it can be used to screen large numbers of samples. (3) Casein is an inexpensive and readily available protein substrate that more closely mimics the natural substrates of endoproteinases, such as the calpains, than synthetic peptide substrates do. Casein has K(m) values for micro- and m-calpain that are similar to those of other substrates such as fodrin or MAP2 that may be "natural" substrates for the calpains, and there is no reason to believe that calpain hydrolysis of casein is inherently different from hydrolysis of fodrin or MAP2, which are much less accessible as substrates for protease assays. (4) The BODIPY-FL-casein assay is capable of detecting 10 ng ( approximately 5 nM) of calpain and is nearly as sensitive as the most sensitive calpain assay reported thus far. (5) The BODIPY-FL-casein assay is as reproducible as the FITC-casein assay, whose reproducibility is comparable to or better than the reproducibility of other methods used to assay calpain activity. The BODIPY-FL-casein assay is a general assay for proteolytic activity and can be used with any protease that cleaves casein.

Fluorescent determination of chloride in nanoliter samples.

BACKGROUND: Measurements of Cl- in nanoliter samples, such as those collected during isolated, perfused tubule experiments, have been difficult, somewhat insensitive, and/or require custom-made equipment. We developed a technique using a fluorescent Cl- indicator, 6-methoxy-N-(3-sulfopropyl) quinolinium (SPQ), to make these measurements simple and reliable. METHODS: This is a simple procedure that relies on the selectivity of the dye and the fact that Cl-quenches its fluorescence. To measure millimolar quantities of Cl- in nanoliter samples, we prepared a solution of 0.25 mm SPQ and loaded it into the reservoir of a continuous-flow ultramicrofluorometer, which can be constructed from commercially available components. Samples were injected with a calibrated pipette via an injection port, and the resultant peak fluorescent deflections were recorded. The deflections represent a decrease in fluorescence caused by the quenching effect of the Cl- injected. RESULTS: The method yielded a linear response with Cl- concentrations from 5 to 200 mm NaCl. The minimum detectable Cl- concentration was approximately 5 mm. The coefficient of variation between 5 and 200 mm was 1.7%. Resolution, defined as two times the standard error divided by the slope, between 10 and 50 mm and between 50 and 200 mm was 1 mm and 2.6 mm, respectively. Furosemide, diisothiocyanostilbene-2,2'-disulfonic acid and other nonchloride anions (HEPES, HCO3, SO4, and PO4) did not interfere with the assay, whereas 150 mm NaBr resulted in a peak height greater than 150 NaCl. In addition, the ability to measure Cl- did not vary with pH within the physiological range. CONCLUSION: We developed an easy, accurate, and sensitive method to measure Cl- concentration in small aqueous solution samples.

Repeatability and reproducibility estimates from collaborative studies based on total concentration of trace analytes.

In the process of validating a given analytical method for the total concentration of a trace analyte, the precision indicators, repeatability and reproducibility, are obtained from a collaborative study of the method based on a standard one-way completely randomized model. This report discusses the shortcomings of the statistical models used in such studies, defines the component makeup for estimates of the repeatability and reproducibility variances based on these models, and considers suggestions offered as new policy regarding method performance based on total concentration.

The use of an automated microsampling system for the characterization of growth hormone pulsatility in newborn babies.

To overcome the difficulties of studying hormone pulsatility in the newborn, we have developed an automated microsampling system that permits the measurement of hormones in small prediluted samples of blood (40 microL) taken at 10-min intervals over 12 h. The system has been validated in adult volunteers, and the error attributable to the dilution was <4%. Using this method in 10 preterm babies, we have been able to describe pulsatile changes in GH and have demonstrated a clear postprandial elevation in GH levels peaking 60 min after a feed. Fourier transform analysis indicated a pulse periodicity of 180 min in babies who were appropriate for gestational age (n = 6), but faster, co-dominant pulse periodicities of 90-100 and 140 min in babies who were small for gestational age (weight and length below the 10th centile) (n = 4). There was no significant difference between mean, peak, and baseline GH levels between the two groups.

Specific quantitation of genomic DNA in the femtogram range by amplification of repetitive sequences.

An assay was developed to specifically quantitate concentrations as low as 50 fg/ml genomic DNA based on the amplification of repetitive sequences. Reliable results were obtained by using internal standard molecules which were coextracted, coamplified, and coanalyzed with the nucleic acids of interest. Amplification was performed by the polymerase chain reaction in the presence of fluorescent dye-labeled primers followed by quantitation of fluorescence derived from the reaction products after separation by PAGE. Based on the known amount of added internal standard molecules and the intensities of the fluorescence of the reaction products, the primary results of the assay were obtained as copies per milliliter of sample. These were converted into mass units of DNA by applying an experimentally determined conversion factor. Chicken DNA has been used as an example for genomic DNA, and the sequences amplified were CR1 repetitive elements. This type of assay may be applied in cases where a sensitive and precise quantitation of genomic DNA is required, such as in the quality control of biological products.

Micromethod for the determination of heparin in plasma after intravenous and subcutaneous administration.

A sensitive method has been developed for extracting and analyzing heparin from plasma after intravenous and subcutaneous administration in humans and rabbits. The glycosaminoglycans are precipitated from the biological fluid as cetylpyridinium salt, and heparin is cleaved with heparinase. The reaction products are analyzed by polyacrylamide gel electrophoresis and visualized by staining with Azure A/ammoniacal silver. With this method 12 ng of heparin can be detected.

Detection of minimal amounts of DNA by electron microscopy using simplified spreading procedures.

Electron microscopic examination of nucleic acids requires the use of special spreading techniques. The classical method was developed by Kleinschmidt and Zahn in 1959. Modifications of this method increased sensitivity to allow detection of a total amount of about 1 x 10(-3) micrograms of single-stranded DNA and 2 x 10(-5) micrograms of double-stranded DNA. Here we describe two rapid and simple procedures increasing sensitivity by 1-2 orders of magnitude to visualize at least 1 x 10(-5) micrograms of single- and/or double-stranded DNA.