A new neomycin phosphotransferase II solid phase assay in combination with polyacrylamide sodium dodecylsulphate gel electrophoresis

A new general method for the determination of neomycin phosphotransferase (NPT) II (EC 2.7.1.95) activity in cell extracts after separation in SDS-polyacrylamide gels is described. The enzymatic activity of NPT II is restored after SDS-polyacrylamide gel electrophoresis by incubating the gel for 3 h (20 mM Tris-HCl buffer, pH 7.4). The enzymatic activity is determined by in situ phosphorylation of aminoglycoside antibiotics bound to solid supports and brought into direct contact with the gel surface. A novel, mechanically stable, negatively charged matrix was synthesized for use in this solid phase enzyme assay and compared to phosphocellulose and carboxymethylcellulose paper. This new method allows the easy and exact determination of the molecular weight of any fusion protein with NPT II by assaying the position of the enzymatic activity in the gel and a consecutive immunological reaction following protein transfer onto nitrocellulose membranes.     

An automated spectrophotometric flow-injection procedure for the determination of cellulase activity in bioreactor preparations.

A spectrophotometric procedure for the determination of cellulase activity in precipitated bioreactor preparations and culture filtrates is described. It is based on the determination of reducing sugar produced by the action of the enzyme on carboxymethylcellulose. The reducing sugar is derivatized with p-aminobenzoyl-hydrazide and permits a limit of detection of 0.1 U ml-1 cellulase in the presence of background sugar, with a sampling rate of 5 h-1. The method can readily be applied to the determination of any carbohydrase acting on soluble substrates and producing reducing sugars, e.g. amylase, dextranase, xylanase, glucanase and polygalacturonase.     

Assay of aminoglycoside phosphotransferase in situ

A method for the evaluation of the aminoglycoside phosphotransferase activity in bacterial colonies directly is described. The method is based on the ability of the enzyme to modify the substrate immobilized on carboxymethylcellulose paper. The sensitivity and accuracy of the method were tested by comparing the results of the present assay to those obtained with conventional procedures. The method seems to be particularly useful for the detection within a bacterial population producing aminoglycoside phosphotransferase of those cells which do not make the enzyme and for rapid determination of the relative levels of enzyme produced by different clones.     

Electrochemical assay of endo-depolymerase activity of cellulases

A method for determination of endo-1,4-beta-D-glucanase activity of cellulase samples based on the indirect measurement of decrease in viscosity of a carboxymethylcellulose solution in an electrochemical cell in the presence of an electron carrier was developed. A rotating disk electrode is used as the working electrode. When two reactions (enzymatic and electrochemical) proceeded in the cell simultaneously, the limiting diffusion current at a constant applied potential increases as the viscosity of the solution decreases. Conditions where the initial rate of change of diffusion current (dI/dt) is proportional to the enzyme concentration were found. A good correlation between the new method and a previously known viscometric method for determination of endoglucanase activity was observed.     

A colorimetric method for the enzymatic analysis of gases: the determination of ethanol and formaldehyde vapors using solid alcohol oxidase

A novel enzymatic approach to the direct determination of ethanol vapors in the gas phase is described. The system is composed of alcohol oxidase, peroxidase, and the color indicator 2,6-dichloroindophenol dispersed on microcrystalline cellulose (avicel). Simple devices are developed for the semiquantitative determination of ethanol in the breath. The devices are optimized to produce a sharp color change at a set time of 1 min for ethanol concentrations above the legal limit for driving (kinetic method) or a stable final color after 5 min (equilibrium method). Such color changes are detectable by simple visual observation. Using TLC plastic sheets and a transmittance densitometer, the system can also be used as a quantitative method for the determination of ethanol or formaldehyde vapors. Dehydrated enzymes may be useful for the analysis of hazardous gases.     

Sequencing of rat liver cytosolic proteins by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry following electrophoretic separation and extraction

A new technique is described that enables the direct determination of the complete or partial amino acid sequence of cytosolic proteins separated by gel electrophoresis and allows for the further observation of disease- or drug-induced posttranslational modifications. The procedure uses a two-phase extraction strategy (ethyl acetate/ammonium bicarbonate) for the efficient separation of proteins/peptides from an electrophoretic matrix and subsequent sequence analysis by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry. The method was tested using hepatocyte cytosolic proteins and compared to a complementary approach using direct solvent extraction from in-gel digests. Although the latter procedure identified the proteins, it did not enable complete amino acid sequence determination. In contrast, high sequence coverage was obtained using the peptide extraction procedure, without any apparent dependence on protein size. The technique minimized the chemically inconsistent modifications generated from in-gel digestion, thus aiding mass spectrometric interpretation and valid protein sequence identification.     

Molecular mass determination by sedimentation velocity experiments and direct fitting of the concentration profiles.

A new method for the direct molecular mass determination from sedimentation velocity experiments is presented. It is based on a nonlinear least squares fitting procedure of the concentration profiles and simultaneous estimation of the sedimentation and diffusion coefficients using approximate solutions of the Lamm equation. A computer program, LAMM, was written by using five different model functions derived by Fujita (1962, 1975) to describe the sedimentation of macromolecules during centrifugation. To compare the usefulness of these equations for the analysis of hydrodynamic results, the approach was tested on data sets of Claverie simulations as well as experimental curves of some proteins. A modification for one of the model functions is suggested, leading to more reliable sedimentation and diffusion coefficients estimated by the fitting procedure. The method seems useful for the rapid molecular mass determination of proteins larger than 10 kDa. One of the equations of the Archibald type is also suitable for compounds of low molecular mass, probably less than 10 kDa, because this model function requires neither the plateau region nor a meniscus free of solute.     

Direct determination of total soil carbohydrate content

A direct procedure for the determination of total soil carbohydrate content and a classic determination after acid hydrolysis, both employing the phenol-sulphuric acid method, are compared. The direct procedure enables simultaneous determination of mono-, oligo- and polysaccharides without prior hydrolysis. This procedure is reproducible and takes only a short period of time. The correlation between the proposed method and the classic one with hydrolysis was high (r²=0.9843; n=11; p=0.05).     

Fluctuation Simulations and the Calculation of Mechanical Partial Molar Properties

Abstract

A method for the direct calculation of partial molar volumes, energies, and enthalpies in multicomponent mixtures in which all species have finite concentrations is presented. The approach, which is based on fluctuation theory, allows the simultaneous determination of the properties of all components in the mixture. The advantages and limitations of the method are illustrated through the (N, U, V) molecular dynamics calculation of the mechanical partial molar properties of two binary Lennard-Jones mixtures.     

Direct haplotyping of kilobase-size DNA using carbon nanotube probes

We have implemented a method for multiplexed detection of polymorphic sites and direct determination of haplotypes in 10-kilobase-size DNA fragments using single-walled carbon nanotube (SWNT) atomic force microscopy (AFM) probes. Labeled oligonucleotides are hybridized specifically to complementary target sequences in template DNA, and the positions of the tagged sequences are detected by direct SWNT tip imaging. We demonstrated this concept by detecting streptavidin and IRD800 labels at two different sequences in M13mp18. Our approach also permits haplotype determination from simple visual inspection of AFM images of individual DNA molecules, which we have done on UGT1A7, a gene under study as a cancer risk factor. The haplotypes of individuals heterozygous at two critical loci, which together influence cancer risk, can be easily and directly distinguished from AFM images. The application of this technique to haplotyping in population-based genetic disease studies and other genomic screening problems is discussed.     

Determination of the degree of substitution and its distribution of carboxymethylcelluloses by capillary zone electrophoresis

A method based on capillary zone electrophoresis (CZE) has been developed to determine the degree of substitution (DS) of carboxymethylcellulose (CMC). Separations were performed with borate buffer (pH 9, ionic strength 20 mM) as background electrolyte in capillaries of 75 microm ID, with an applied voltage of 10 kV, and for detection UV absorption at 196 nm was measured. The use of an internal standard (phthalic acid) to correct for mobility variations resulted in a strong improvement of the precision of the DS determination. Experiments with indirect UV detection indicated that the peak widths obtained actually reflect the variation in mobility, and with that of the DS value, of CMC samples. With the proposed method not only the average DS value but also its dispersity could be established for technical CMC samples. A small but definite effect of the polymeric size on the mobilities was observed. Therefore, DS calibration curves will have to be determined for a specific MM range. Since the size effect is small, a classification of CMCs as low-, middle-, or high MM will be sufficient to obtain accurate data on the DS distribution.     

A novel thermoacidophilic cellulase from Alicyclobacillus acidocaldarius

A novel cellulase was isolated from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius ATCC27009 grown in medium containing carboxymethylcellulose. The enzyme is a glycosylated monomer of 56.2 kDa, relatively thermostable, with optimal pH and temperature of 4.0 and 65 degrees C, respectively. Enzymatic assays on several polysaccharides demonstrated that CelG was specific for carboxymethylcellulose.     

Direct haplotyping of bi-allelic SNPs using ARMS and RFLP analysis techniques

Haplotype analysis of single nucleotide polymorphisms (SNPs) is an important and rapidly growing approach for association studies. In recent years, statistical procedures to haplotype determination from genotypic information have employed in population studies. These procedures, even though some advantages for estimation of haplotype frequencies in large population samples, have limitations in the accuracy of the analysis. In this study, we have designed a reliable method for direct haplotyping of polymorphic sites using the amplification refractory mutation system (ARMS) and restriction fragment length polymorphism (RFLP) analysis techniques. We applied the method to determination of haplotypes composed of three SNPs within the paraoxonase1 gene promoter and found the approach can be used in many studies in population and in a variety of clinical settings.     

Radii of gyration of sodium carboxymethylcellulose in aqueous and mixed solvent media from viscosity measurement

The viscosities of three sodium carboxymethylcellulose samples with molecular weights of 90,000 [degree of substitution (DS): 0.7], 250,000 (DS: 0.9), and 700,000 (DS: 0.9) have been reported in water and methanol–water mixtures in salt-free and salt-containing solutions at 35 °C. The results were analyzed in terms of a phenomenological approach for the viscosity of polymer solutions to determine the intrinsic viscosities [η] of the polyelectrolyte samples. This contribution presents a new and convenient method for the determination of the root-mean-square radii of gyration of the polyion chains using the [η] values obtained as a function of the added salt concentration. The polyion coils are found to expand at low ionic strength and these collapse drastically with increasing ionic strength. Addition of methanol to the medium in which these samples are dissolved causes a contraction of the polyion chains, although this influence is less pronounced than that of the added salt.     

Functional nodes in dynamic neural networks for bioprocess modelling

This contribution presents a novel method for the direct integration of a-priori knowledge in a neural network and its application for the online determination of a secondary metabolite during industrial yeast fermentation. Hereby, existing system knowledge is integrated in an artificial neural network (ANN) by means of 'functional nodes'. A generalized backpropagation algorithm is presented. For illustration, a set of ordinary differential equations describing the diacetyl formation and degradation during the cultivation is incorporated in a functional node and integrated in a dynamic feedforward neural network in a hybrid manner. The results show that a hybrid modelling approach exploiting available a-priori knowledge and experimental data can considerably outperform a pure data-based modelling approach with respect to robustness, generalization and necessary amount of training data. The number of training sets were decreased by 50%, obtaining the same accuracy as in a conventional approach. All incorrect decisions, according to defined cost criteria obtained with the conventional ANN, were avoided.     

Recovery of erythropoietin from anemic sheep plasma

A method is described for the large-scale preparation of erythropoietin from anemic sheep plasma. DEAE-cellulose and carboxymethylcellulose column chromatography was used to prepare Step II erythropoietin. A total of 168 sheep yielded 499 liters of plasma from which 323,000 IU of Step II erythropoietin was obtained.     

3D-structure determination of fluorescent proteins by homology modeling combined with mass spectrometry

A method for the 3D-structure generation of GFP-like fluorescent proteins is presented. The method is based on a combination of homology modeling for the overall spatial structure determination and mass spectrometry for the chromophore structure identification. The proposed approach can be applied to the spatial structure determination ofnoncrystalizable GFP homologs.     

Spectrophotometric determination of rifampicin S in the presence of rifampicin O]

The limits of the use of the methods of direct photometric and differential spectrophotometric determination of rifamycin S containing rifamycin O as an admixture were discussed. The method of direct photometry did not provide determination of rifamycin S in the presence of rifamycin O since instability of the latter under the analysis conditions. A possibility of using the differential-spectrophotometric method for determination of rifamycin S in the presence of not more than 5 per cent of rifamycin O was shown.     

Direct quantification of dimethylsulfoniopropionate (DMSP) in marine micro- and macroalgae using HPLC or UPLC/MS

A simple method for the direct quantification of dimethylsulfinopropionate (DMSP) using HPLC or UPLC coupled to UV and/or MS detection is introduced. The protocol is applied for the determination of DMSP from marine micro- and macroalgae. The method is based on the derivatisation of DMSP using 1-pyrenyldiazomethane followed by reversed phase HPLC or UPLC separation. The detection limit is 590 nM, corresponding to 1 ng DMSP per injection. Using a combination of UV and MS detection the calibration curves were linear in the range of 2.93 microM to 11.7 mM concentrations. We show that direct determination of DMSP is possible from macroalgal tissue and microalgal cultures if DMSP-lyase activity is suppressed during work-up.     

Experimental determination of flux control distribution in biochemical systems: in vitro model to analyze transient metabolite concentrations

Determination of the control coefficients allows the identification of rate-controlling steps in a reaction system. However, the measurement of the flux control coefficients in a biochemical system is not a trivial task, except for some special cases. We have developed a theoretical basis for the direct determination of these coefficients from dynamic responses. In order to show the validity of this methodology experimentally, the dynamic approach is applied to an in vitro reconstituted partial glycolytic pathway to determine the flux control coefficients of hexokinase and phosphofructokinase. It is shown that the dynamic approach gives consistent results, which agree well with values obtained by the direct enzyme titration method. The detailed procedure and potential applications to other systems, such as immobilized enzyme or cell reactors, are discussed. (c) 1993 Wiley & Sons, Inc.