Carbohydrate analysis of bacterial polysaccharides by high-pH anion-exchange chromatography and online polarimetric determination of absolute configuration

A significant problem in structure determination of complex carbohydrates, especially for bacterial polysaccharides, is determination of the absolute configuration of the component monosaccharides. A number of analytical methods have been used for this purpose but, as a result of the wide variety of chemical properties of sugars found in complex polysaccharides, no single method is universally applicable. High-resolution gas chromatography of volatile derivatives with chiral reagents is the most widely used method. Optical activity, although direct and simple, lacks sensitivity generally requiring a large quantity of pure monosaccharide. We report a combination of high-performance anion-exchange chromatography (HPAEC) with combined electrochemical pulsed amperometric detection and in-line detection of optical rotation with an in-line laser polarimeter for analysis of a number of sugars found in complex polysaccharides. We show that application of the method for analysis of capsular polysaccharides of several gram-positive and gram-negative pathogenic bacteria provides useful information simultaneously on carbohydrate composition and the enantiomeric configuration of component sugars.     

Determination of reducing sugars in the nanomole range with tetrazolium blue

Addition of sodium potassium tartrate to basic solutions of tetrazolium blue [(2,2',5,5'-tetraphenyl-3,3'-dimethoxy 4,4'-biphenylene) ditetrazolium chloride] greatly improved their efficacy as colorimetric reagents for reducing sugar determination. This modification increased sensitivity and decreased reaction time. The modified reagent can determine as little as 1 nmol of neutral sugars as well as 2-amino and N-acetyl amino sugars.     

实时荧光定量PCR方法快速检测转基因大豆

针对转基因大豆中普遍含有的35S启动子进行引物设计,以双链DNA染料SYBR GreenⅠ为荧光标记物,利用实时荧光定量PCR方法对大豆样品进行检测。该法检测转基因大豆的检测低限为0.005 nmol/L的35S启动子,线性范围达3个数量级,可快速区分转基因大豆和非转基因大豆,具有快速、简便、灵敏、安全、高通量、低成本等优点,可推广用于转基因植物产品的快速定量检测。     

Reevaluation of the Griess method for determining NO/NO2- in aqueous and protein-containing samples.

Nitric oxide (NO) is an important intracellular and extracellular signal substance. Nitrite is one product of the oxidative metabolism of NO. The purpose of this study was to establish a simple method of determining nitrite (NO2-) to provide a means of estimating the endogenous formation of NO or NO2-. A flow injection analysis (FIA) based on the Griess reaction was developed for this purpose. Using a standard additive method, it is possible to eliminate matrix effects such as those that can occur in samples containing protein. This measuring method is suitable for measurements in effluates or protein-rich cellular supernatants. The sensitivity of the method is 2 nmol/L for samples in aqueous phases and 8 nmol/L for protein-containing phases. The two-point discrimination is 2 nmol/L. A linear correlation between nitrite and signal level can be demonstrated over a range of 0.002-5 micromol/L. Reproducibility, including sample preparation and analysis, can be specified with a coefficient of variation (C.V.) of 6.7%. Day-to-day variability for identical samples 0.8% (C.V.). This study presents examples of the application of this method (measurements in blood samples and in isolated perfused hearts) and compares them to established methods of measuring NO and NO2. We found the FIA method to be equally sensitive as NO measurement by means of oxyhemoglobin assay. The FIA method is seven times more sensitive than HPLC methods, and its design is significantly simpler. Compared to the traditional Griess method, its sensitivity is higher by a factor of 500. With its high sensitivity, high reproducibility, and its unsurpassed low susceptibility to interference, this method of analysis provides a means of reliably determining nitrite concentration as a marker of NO formation in various matrices. Therefore, it can be a valuable instrument in experimental and clinical studies to determine the physiologic and pathophysiologic relevance of NO.     

Long oligonucleotide arrays on nylon for large-scale gene expression analysis

To date, most studies of multigenic expression patterns by long DNA array have used DNA fragments as probes. These probes are usually obtained as PCR products, and this represents a time-consuming and error-prone approach, requiring strict quality control. The present study examines the use of 40- and 70-mer synthetic oligonucleotides as probes for DNA array analysis with radioactive labeled targets. Design, spotting onto nylon filters, and hybridization conditions were determined and optimized. In this approach, the sensitivity and the specificity of the hybridization appear comparable to the conventional long DNA probes assay, permitting the analysis of small samples of approximately 1 microg total RNA. The long oligonucleotide array thus provides a very convenient method for the analysis of gene expression patterns in biological specimens and in clinical research.     

High-performance liquid chromatographic measurement of exogenous thiosulfate in urine and plasma

A simple technique using reverse-phase ion-pair liquid chromatography for measurement of exogenous thiosulfate is described. Accurate measurement of thiosulfate in plasma and urine was permitted by precolumn derivatization with monobromobimane, a substance that readily yields fluorescent compounds upon reaction with a variety of biologically important nucleophiles including glutathione, cysteine, and sulfite. Using an injection volume of 50 microliters, as little as 0.16 nmol of thiosulfate was reliably measured. The interassay precision of the method was reflected by a coefficient of variation of 7.7% while the coefficient of variation for interassay analysis was 2.6%. Recovery of thiosulfate from plasma was 96.9 +/- 3.2% and greater than 98% from urine. The simplicity, sensitivity, and precision of the method make it ideal for the study of thiosulfate and other important nucleophiles in body fluids.     

Assay of reducing sugars in the nanomole range with 2,2'-bicinchoninate

The photometric assay of reducing sugars with 2,2'-bicinchoninate was improved and its conditions were optimized. Optical density is linear between 1 and 25 nmol sugar/sample, and the assay is not affected by borate, phosphate, or other buffer anions. The molar extinction coefficients produced by the standard procedure with the 12 most common monosaccharides occurring in carbohydrates and conjugated glycocompounds are listed.     

Micropipette suction for measuring piconewton forces of adhesion and tether formation from neutrophil membranes.

A new method for measuring piconewton-scale forces that employs micropipette suction is presented here. Spherical cells or beads are used directly as force transducers, and forces as small as 10-20 pN can be imposed. When the transducer is stationary in the pipette, the force is simply the product of the suction pressure and the cross-sectional area of the pipette minus a small correction for the narrow gap that exists between the transducer and the pipette wall. When the transducer is moving along the pipette, the force on it is corrected by a factor that is proportional to the ratio of its velocity relative to its drag-free velocity. With this technique, the minimum force required to form a membrane tether from neutrophils is determined (45 pN), and the length of the microvilli on the surface of neutrophils is inferred. The strength of this technique is in its simplicity and its ability to measure forces between cells without requiring a separate theory or a calibration against an external standard and without requiring the use of a solid surface.     

A modified tetramethylbenzidine method for measuring lipid hydroperoxides

A simple and sensitive spectrophotometric method for measuring lipid peroxides and peroxides in general is described. The method was developed by modifying an existing method based on the peroxidase activity of hemoglobin with tetramethylbenzidine as the electron donor. The modifications resulted in much improved sensitivity and reproducibility. With the modified method lipid peroxides as low as 2 nmol can be measured, a high sensitivity compared with other spectrophotometric methods. The absorbance is linear over a wide range of concentrations. It is suggested that this modified method in combination with the commonly used thiobarbituric acid method will give a better quantitation of lipid peroxidation.     

The initial phosphate burst in ATP hydrolysis by myosin and subfragment-1 as studied by a modified malachite green method for determination of inorganic phosphate

The Malachite Green method for determination of inorganic phosphate (Pi) (Itaya K. & Ui, M. (1966) Clin. Chim. Acta 14, 361-366) was modified to measure Pi in the range of 0.2-15 nmol per ml of ATPase reaction mixture. An ATPase reaction mixture is quenched with an equal volume of 0.6 M PCA; the supernatant after centrifugation is mixed with an equal volume of the Malachite Green/molybdate reagent containing 2 g of sodium molybdate, 0.3 g of Malachite Green and 0.5 g of Triton X-100 or Sterox SE in 1 liter of 0.7 M HCl, and the absorbance at 650 nm is then measured after a 35-40 min incubation at 25 degrees C. Owing to the high sensitivity and simplicity of the modified method, the slow time course of myosin ATP hydrolysis in the presence of Mg2+ and the size of initial phosphate burst can be determined accurately using relatively low concentrations of native myosin and its subfragment-1. The phosphate burst size varied with changes in pH, ionic strength, and temperature. A typical value was 0.8-0.9 mol per site in 0.1 M KCl, 10 mM MgCl2, pH 8.0 at 25 degrees C for fresh enzyme preparations.     

Chromatographic analysis of sugars in physiological fluids by postcolumn reaction with cuprammonium: a new and highly sensitive method

A new highly sensitive method of high-performance liquid chromatographic analysis has been used to separate mono-, di-, and oligosaccharides present in jejunal aspirates from experimentally perfused animals. The sugars in the column eluant are detected at 280 to 310 nm after reaction with cuprammonium. No reaction coil is required between the column and uv detector because the reaction is virtually instantaneous. This technique is more sensitive than differential refractometry, so that it is possible to detect 2.5 nmol (450 ng) of glucose routinely, compared to a minimum detection limit of 100 nmol (18 micrograms) using a commercial refractive index detector. Using a suitable postcolumn pump, the technique is not sensitive to changes in solvent composition, as with gradient elution, and is applicable to analysis of other cis-cis glycols.     

Improved method of analysis of biomass sugars using high-performance liquid chromatography

The precise quantitative analysis of biomass derived sugars is a very important step in the conversion of biomass feedstocks to fuels and chemicals. However, the most accurate method of biomass sugar analysis is based on the gas chromatography analysis of derivatized sugars either as alditol acetates or trimethylsilanes. The derivatization method is time-consuming but the alternative HPLC method cannot resolve most sugars found in biomass hydrolysates. We have demonstrated for the first time that by careful manipulation of the HPLC mobile phase, biomass monomeric sugars (arabinose, xylose, fructose, glucose, mannose, and galactose) can be analyzed quantitatively and there is excellent baseline resolution of all the sugars. This was demonstrated for both standard sugars and corn stover hydrolysates. Our method can also be used to analyze dimmeric sugars (cellobiose and sucrose).     

A radioassay for nonoxidized methionine in peptides. A method for identifying (after isoelectric focusing) and for estimating biologically active forms of corticotropin and other hormones

A radioassay for nonoxidized methionine in peptides is described; it has advantages over other methods currently used because of its simplicity, sensitivity, accuracy, and applicability to individual peptide components in mixtures and to many samples at a time. Methionyl residues were S-carboxymethylated with iodo[2-14C]acetic acid; iodo[2-3H]acetic acid did not provide a stable radioactive tracer. The labeled peptide was isolated by carboxymethylcellulose chromatography or by isoelectric focusing (IEF) or electrophoresis in polyacrylamide gel, and its radioactivity measured. The assay was applied to corticotropins, alpha-melanotropin, bombesin, glucagon, substance P, parathormone, and calcitonin. Twenty-four to thirty samples were conveniently analyzed at a time with a lower detection limit of less than 1 nmol of methionine per sample. The accuracy of the assay, assessed also by reverse-phase high-performance liquid chromatography, is a consequence of its precision, the specificity of the reaction with iodoacetic acid, and the use of an appropriate standard of the peptide being assayed. Methionine was identified, and could be estimated, in individual peptide components of a mixture by using IEF to separate simultaneously the labeled peptide from iodo[2-14C]acetic acid and from other peptide and protein components. This was facilitated by a convenient method for detecting and quantifying these peptides after IEF. The assay is particularly useful for several peptide hormones whose biological activity depends on their sole methionine residue being in a nonoxidized state. It can be used for monitoring their isolation or synthesis and their stability during processing and storage, as well as for evaluating differences in biological potency between preparations and analogues.     

Fluorometric determination of sialic acids using malononitrile in weakly alkaline media and its application to postcolumn labeling in high-performance liquid chromatography

A sensitive method for determination of sialic acids by monitoring the fluorescence produced with malononitrile in borate buffer has been established. Measurement of the fluorescence intensity of the reaction mixture at 430 nm with irradiation at 360 nm allowed determination of 3-60 nmol of sialic acids with high reproducibility. A few amino sugars and deoxy sugars, as well as catecholamines reacted with this reagent; however other carbohydrates, amino acids, amines, aldehydes, and carboxylic acids including alpha-keto acids, etc., showed little reactivity. This method was successfully applied to postcolumn fluorescence labeling of sialic acids in high-performance liquid chromatography.     

Measurement of microgram quantities of protein by a generally applicable turbidimetric procedure

A modified turbidimetric method for protein determination which involves the use of trichloroacetic acid as the precipitating agent is described. Maximal turbidity develops in less than 30 min and is stable for at least 120 min. A linear relationship between turbidity at 340 nm and protein concentration is observed between 2 and 40 micrograms protein. Sodium dodecyl sulfate is added to avoid the interference by nonionic and cationic detergents and lipids and to decrease the protein-to-protein variation. The use of cetyltrimethyl ammonium bromide provides a two-step procedure to correct for the contribution of contaminating nucleic acid. Many compounds which interfere with other protein quantitation methods have no effect on this system. The interference of commonly used reagents as sucrose and urea can be easily corrected. This procedure compared favorably with the most widely used protein quantitation methods in simplicity, sensitivity, and specificity.     

Stripping interfering sugars from samples using adapted bacteria.

Bacteria adapted to individual sugars quickly remove targeted sugars--stripping them--from samples in which unwanted sugars interfere. Adapted bacteria are equivalent to specific reagents for removal of sugars down to bacterial Km values, micromolar to submicromolar concentrations. Bacterial stripping is a simple method, useful when background sugars in micro-to millimolar concentrations (or larger) interfere with analysis of sought-for sugars. Bacteria such as Escherichia coli and Klebsiella are easily adapted to individual sugars such as lactose, fructose, etc., by growing the bacteria on them. Hence one can easily create (and store) many kinds of cells ready to sponge up or strip out unwanted compounds. E. coli specifically remove several sugars from samples containing 100-500 nmol of sugars, using 1-5 mg of adapted cells, and 25 degrees C temperatures. Stripping requires 1-5 min and consists of mixing cells and sample, spinning down the cells, and withdrawal of stripped supernate. A 1-5 min interval is adequate for uptake and stripping, but far too short for cells to metabolize the sugars that were taken up. Hence the cells do not leak metabolites, but act as specific adsorbants without injection of appreciable byproducts into the sample.     

Analyzing complicated protein folding kinetics rapidly by analytical Laplace inversion using a Tikhonov regularization variant

Kinetic experiments provide much information about protein folding mechanisms. Time-resolved signals are often best described by expressions with many exponential terms, but this hinders the extraction of rate constants by nonlinear least squares (NLS) fitting. Numerical inverse Laplace transformation, which converts a time-resolved dataset into a spectrum of amplitudes as a function of rate constant, allows easy estimation of the rate constants, amplitudes, and number of processes underlying the data. Here, we present a Tikhonov regularization-based method that converts a dataset into a rate spectrum, subject to regularization constraints, without requiring an iterative search of parameter space. This allows more rapid generation of rate spectra as well as analysis of datasets too noisy to process by existing iterative search algorithms. This method's simplicity also permits highly objective, largely automatic analysis with minimal human guidance. We show that this regularization method reproduces results previously obtained by NLS fitting and that it is effective for analyzing datasets too complex for traditional fitting methods. This method's reliability and speed, as well as its potential for objective, model-free analysis, make it extremely useful as a first step in analysis of complicated noisy datasets and an excellent guide for subsequent NLS analysis.     

A fluorimetric Morgan-Elson assay method for hyaluronidase activity

Despite their physiological importance, hyaluronidases (HAases) have long been "neglected enzymes," due, presumably, in part to the lack of rapid, sensitive assays. Currently, the colorimetric Morgan-Elson assay method, which is based upon the generation of a new reducing N-acetyl-D-glucosamine terminus with each cleavage reaction, is most widely employed but is yet insensitive. We, therefore, reinvestigated the colorimetric method and established the fluorimetric Morgan-Elson assay for HAase activity, with the optimized tetraborate reagent. The fluorimetric assay, requiring neither specialized reagents nor a long time to perform, provided high sensitivity, nearly comparable to that of enzyme-linked immunosorbent assay (ELISA)-like assays, with a detection limit of 5 x 10(-3)NFU/ml of bovine testicular HAase after 1-h incubation. The increased sensitivity permitted rapid measurement of low HAase activity in biological samples such as human and rabbit serum HAases, the latter of which has not been detected either by an ELISA-like assay or by zymography. Human serum HAase was easily characterized it along with its optimum pH and kinetic parameters.     

Optimized microplate β-1,3-glucanase assay system for Trichoderma spp. screening

β-1,3-glucanase is an important cell wall-degrading enzyme involved in mycoparasitism by Trichoderma spp. during antagonism against phytopathogenic fungi. A simple microplate-based method to assay β-1,3-glucanase activity is described here as an alternative to an expensive tube-assay method. The reaction volume of the micro-assay was reduced to 130 µl from the 1150 µl used in the standard β-1,3-glucanase macro-assay. Statistical analyses showed significant difference in sensitivity between the micro- and the macro-assay. The micro-method was optimized using the Response Surface Quadratic Model. The sensitivity of the optimized micro-method was shown to be four-fold greater than the macro-assay and two-fold higher than the micro-assay. The optimized micro-assay was significantly more sensitive in all of the twenty examined isolates during Trichoderma spp. β-1,3-glucanase screening. We conclude that this modified and optimized method is more convenient, faster, cheaper and more reproducible than the traditional tube-assay.