ALBERT

Notes: Equilibrium adsorption studies on Escherichia coli and Saccharomyces sp. revealed the capacity and affinity of these organisms for the surfaces of powdered charcoal and nickel. In simple salt solutions both organisms readily adsorbed to each solid with an affinity and maximum loading capacity individual to each cell-solid combination. In the presence of common growth media (lab-lemco, nutrient broth, peptone, and yeast extract, individually at a concentration of 1.3%), each medium substantially inhibited adsorption. Each medium contained a protein-aceous constituent as determined by ultraviolet (UV) analysis. The degree of inhibition was relative to medium concentration present during assay. Cell wall extracts from whole-yeast cells also effectively inhibited adsorption. Cells adsorbed in the presence of sodium chloride solutions were susceptible to subsequent desorption by nutrient broth.

Notes: The white-rot fungus Phanerochaete chrysosporium produces extracellular peroxidases (ligninase and Mn-peroxidase) believed to be involved in lignin degradation. These extracellular enzymes have also been implicated in the degradation of recalcitrant pollutants by the organism. Commercial application of ligninase has been proposed both for biomechanical pulping of wood and for wastewater treatment. In vitro stability of lignin degrading enzymes will be an important factor in determining both the economic and technical feasibility of application for industrial uses, and also will be critical in optimizing commercial production of the enzymes. The effects of a number of variables on in vitro stability of ligninase and Mn-peroxidase are presented in this paper. Thermal stability of ligninase was found to improve by increasing pH and by increasing enzyme concentration. For a fixed pH and enzyme concentration, ligninase stability was greatly enhanced in the presence of its substrate veratryl alcohol (3,4-dimethoxybenzyl alcohol). Ligninase also was found to be inactivated by hydrogen peroxide in a second-order process that is proposed to involve the formation of the unreactive peroxidase intermediate Compound III. Mn-peroxidase was less susceptible to inactivation by peroxide, which corresponds to observations by others that Compound III of Mn-peroxidase forms less readily than Compound III of ligninase.

Notes: The direct microbial conversion (DMC) process for the production of ethanol from lignocellulosic biomass is limited by low volumetric ethanol production rates due to the low cell densities of Clostridium thermosaccharolyticum which is a key organism for ethanol production in this process. Hence, this study focuses on the use of a continuous- culture cell recycle system to improve the volumetric ethanol productivity and yield of the fermentation of xylose by C. thermosaccharolyticum. Early experiments with the continuous-culture cell recycle system showed a two-fold improvement in volumetric ethanol productivity. However, the ethanol yield at the higher dilution rates suffered because of the large amount of lactate produced. The manipulation of two environmental parameters - iron concentration in the nutrient medium and the N2 purge rate of the fermentor headspace - allowed a dramatic reduction in the lactate production and a simultaneous improvement in the ethanol titer and yield. Under the improved conditions of increased iron concentration (12.5 mg/L FeSO4 · 7H2O) and decreased N2 purge rate (0.1 L/min), a continuous culture of C. thermosaccharolyticum operating at a dilution rate of 0.24 h-1 and 50% cell recycle produced 8.6 g/L ethanol and less than 1 g/L each of acetate and lactate. The volumetric ethanol productivity was 2.2 g/L/h, which is 8 times larger than obtained for a continuous culture operated with no cell recycle and the same specific growth rate.

Notes: We have designed and constructed an automated, computer-controlled, nucleic acid hybridization analysis system (Electrophoresis 1987, 8, 255-261). The system performs 9 simultaneous experiments, beginning with submarine electrophoretic separation of the restriction fragments and including microwave fixation of the separated fragments, denaturation, neutralization, prehybridization, hybridization, washing and drying. The final step is electronic detection of the hybridization pattern. The detector system consists of 90 Geiger-Mueller detectors arranged to simultaneously sample the 9 hybridizations at 10 positions each. The hybridization matrix is moved across the detectors by a robot arm in increments preprogrammed by the operator and the entire length of the matrix can be counted. The results are printed out as a plot of radioactive counts vs. distance from the origin of electrophoresis. We describe here the characteristics of the detection system.

Notes: The existence of two radii of each charged particle - a geometric and electrokinetic radii, is supposed. The mathematical relationship between them in the four possible combinations of an ion and its counterion is analyzed: (i) at equal geometric radii and, in absolute values, equal valencies; (ii) at equal geometric radii and, in absolute values, different valencies; (iii) at different geometric radii and, in absolute values, equal valencies; (iv) at different geometric radii and, in absolute values, different valencies. One of the equations worked out can be used to define the relationship between the geometric and electrokinetic radii of a polyion. All the equations are used in working out precise calculations.

Notes: In its most useful form a cellular protein database should be genomically based, because it is the genome which determines both the total number of proteins a cell can make and the particular ones that will be made under any given condition. Such a database should trace each protein back to its structural gene, and should account for every structural gene of a cell. Recent advances in molecular biology greatly facilitate the construction of such gene-protein databases. The mapping of genes of unidentified proteins resolved from total cell extracts on two-dimensional gels can now be accomplished by largely biochemical methods, without the necessity of isolating mutants or performing genetic crosses. Other techniques permit one to search gels for the product of any newly discovered gene (or open reading frame) suspected of encoding a protein. Consequently, gene-protein indices can be built independently and simultaneously from either direction - deducing the genetic map from the protein pattern, or finding the protein pattern from information encoded in the genome. A database of this sort is being constructed for the bacterium, Escherichia coli. Given the current pace of DNA nucleotide sequencing, the development of total gene-protein indices for a variety of cells can be anticipated in the near future.

Notes: As part of our continuing studies into the biochemical basis of long-term changes in neuronal function in Aplysia, we have developed a simple method for obtaining amino acid sequence information from proteins isolated on two-dimensional gels. Proteins isolated on preparative two-dimensional gels are digested in situ with Staphylococcus, aureus V8 protease, and the resulting peptides electrophoresed, transferred to a polyvinylidene difluoride membrane, and sequenced in a gas-phase sequencer. The method is simple and should be applicable to a variety of other systems where the development of a two-dimensional gel database is underway.

Notes: In this paper, techniques are demonstrated for unambiguously mapping phosphoproteins and glycoproteins into a protein database of unfractionated fibroblast proteins. These methods allow for precise registration of subsets of proteins with the image of total proteins. The methods are also applicable to database mapping of antigens identified by indirect immunodetection methods and receptor molecules identified with photoaffinity ligands.

Notes: An apparatus for fully automated capillary isotachophoresis was constructed. A commercial apparatus (Shimadzu IP-2A) was modified in the electrolyte pumping system and the flow lines were simplified. An automatic sampler was used for sequential sampling. The equipment, pumps, the sampler, a high-voltage DC power supply, and a recorder, were controlled by a system controller which comprises a microcomputer and a BASIC program for time-control of the equipments. The apparatus was successfully used for the automated sequential analysis of human serum proteins. Forty serum samples were analyzed within 17 h without manual operation and for each sample the serum proteins were resolved into about twenty UV peaks or shoulders.

Notes: A multi-chamber apparatus for preparative isoelectric focusing is described. The apparatus is constructed of 32 separation chambers and 2 electrode chambers, all separated by uncharged porous membranes. The total volume of the 32 separation chambers is 660 mL. A cooling system and a stirring system are built in. Human serum proteins were separated by isoelectric focusing in a natural pH gradient. The fractionation was monitored by fused rocket immunoelectrophoresis. The number of fractionation was monitored by fused rocket immunoelectrophoresis. The number of proteins in each fraction was monitored by crossed immunoelectrophoresis. The apparent pI values of IgG. transferrin and alpha-1-antitrypsin are as found in the literature. Orosomucoid (alpha-1-acid glycoprotein) (pI = 1.8) is concentrated at the acid end of the pH gradient.

Notes: Optimal conditions for isotachophoretic separation of carboxymethyl-D-glucoses formed by acidic depolymerization of carboxymethylcellulose were found. 6-O-car-boxymethyl-D-glucose, 2-O-carboxymethyl-D-glucose and 3-O-carboxymethyl-D-glucose were identified and determined in the reaction mixture after carboxy-methylcellulose hydrolysis. Relative reactivity of hydroxy groups in the glucopyranose unit of cellulose decreased in the following order: O(6)H〉O(2)H〉 〉O(3)H. This was found to be in agreement with the data published by other authors.

Notes: An affinity method was developed to investigate the interaction between protease and protease inhibitor by incorporating a protease incubation step into a two-dimensional electrophoretic separation of the plasma protease inhibitory proteins. This involved the application of the isoelectric focusing gel to filter paper saturated in the protease of choice before being placed on the second-dimensional polyacrylamide electrophoresis gel. General protein staining or immunoblotting was used to detect the protein or ligand in the complex. An in situ oxidation method was developed using the reagent ligand in the complex. An in situ oxidation method was developed using the reagent chloramine T to investigate the effect of this reagent on the complexing abilities and inhibitory activities of the protease inhibitory proteins. Oxidation was performed either after electrophoresis prior to staining for enzyme inhibition or during two-dimensional electrophoresis prior to the aforementioned protease incubation. The latter allowed the effect of oxidation on complex formation to be examined. Whole plasmas were utilized as the sources of protease inhibitory proteins with the human and mouse being used as models. The equine protease inhibitory system was examined by the two methods and shown to consist of three classes of inhibitory proteins based on their susceptibilities to oxidation and abilities to form complexes with various proteases.

Notes: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis without a stacking gel minimizes lateral spreading of protein when samples are applied in agarose wells and allows high sample throughput (6 samples/cm gel width). The method is simple and convenient to use and gives comparable resolution to the standard method with 4-20% or 6-30% polyacrylamide gradient gels. Best results are obtained when the upper zone of the separating gel is of low polyacrylamide concentration. This indicates a need for the molten agarose to penetrate and anneal with the separating gel.

Notes: Two-dimensional (2-D) polyacrylamide gel electrophoresis can detect thousands of polypeptides, separating them by apparent molecular weight (Mr) and isoelectric point (pI). Thus it provides a more realistic and global view of cellular genetic expression than any other technique. This technique has been useful for finding sets of key proteins of biological significance. However, a typical experiment with more than a few gels often results in an unwieldy data management problem. In this paper, the GELLAB-II system is discussed with respect to how data reduction and exploratory data analysis can be aided by computer data management and statistical search techniques. By encoding the gel patterns in a “three-dimensional” (3-D) database, an exploratory data analysis can be carried out in an environment that might be called a “spread sheet for 2-D gel protein data”. From such databases, complex parametric network models of protein expression during events such as differentiation might be constructed. For this, 2-D gel databases must be able to include data from other domains external to the gel itself. Because of the increasing complexity of such databases, new tools are required to help manage this complexity. Two such tools, object-oriented databases and expert-system rule-based analysis, are discussed in this context. Comparisons are made between GELLAB and other 2-D gel databases analysis systems to illustrate some of the analysis paradigms common to these systems and where this technology may be heading.

Notes: Polyacrylamide gel electrophoresis in linear pore gradients (4.8 to 48 %T, 5 %CBis) provides for migration arrest, in a practical sense, after about 5000 Vh for proteins of 290 and 450 kDa, but not for smaller proteins over 20 000 Vh. The arrest is not due to inadequate field strength nor is it caused by water redistribution within pore gradien gels. The possibility is being discussed that exponential pore gradients, and a higher or a lower degree of crosslinking suggested by the literature may be remedies for the present failure to arrest the migration of smaller proteins.

Notes: The submaxillary gland esteroproteases were separated by two-dimensional polyacrylamide gel electrophoresis, and their súbstrate specificities were determined by histochemical staining procedures using cellulose acetate membranes. Twenty-one proteolytically active enzymes were classified into four groups based on substrate specificities on benzoyl-arginine-ethylester (BAEE), N-α-benzoyl-DL-arginine-p-nitroanilide (BAPNA), and poly-L-lysine. These types were further divided into eight subgroups by their sensitivity to inhibitors and androgen dependence. These results suggest that eight groups of esteroproteases are present in the submaxillary gland of male mice.

Notes: A program in BASIC suitable for personal computers is described which is applicable to gel electrophoresis conducted in a single (continuous) buffer. The curve fitting is to a polynomial function, allowing for an objective selection of the most appropriate curve type and order - linear, convex or concave - in the particular application. Results do not differ significantly from previous programs for evaluation of linear Ferguson plots or of curve fitting to an exponential function for evaluating convex plots, executed on mainframe computers such as the DEC-10 (Digital) and IBM 370 computers. Thus, the program combines original versatility with, for the first time, the possibility for widespread application of Ferguson plot analysis on personal computers.

Notes: R-Form lipopolysaccharides of Acinetobacter calcoaceticus could be incorporated into polyacrylamide gels in an immobile form by adding it directly to the acrylamide-N, N′-methylenebisacrylamide polymerization mixture. The separation of A. calcoaceticus 69 V outer membrane proteins in these affinity gels demonstrated a specific interaction with the lipopolysaccharide ligand for one of the proteins. This protein is heat-modifiable and has an Mr of about 18 000. By incorporation of varying concentrations of lipopolysaccharide, a dissociation constant of the protein-lipopolysaccharide complex of 0.5 mM could be determined. In comparison, for another A. calcoaceticus strain, CCM 5593, a higher dissociation constant (1.0 mM) - indicative of lower affinity - was obtained.

Notes: The influence of a soluble anionic polymer on electrophoresis of proteins was studied in relation to the nonspecific ionic effect of an affinophore on application to affinophoresis. Zone electrophoresis of proteins was carried out in agarose gel in the presence of succinyl-poly-L-lysine (degree of polymerization, 120) by using three electrophoresis buffers differing in ionic strength (0.06, 0.12 and 0.18) and pH (7.0 and 7.9). Proteins migrated as distinct single bands even in the presence of the polymer. The mobility of cationic proteins towards the cathode was first decreased and then increased towards the anode as the polymer concentration increased, while that of anionic proteins was not affected. The dependence of the apparent mobility changes of the proteins on the concentration of the polymer was treated quantitatively in the same way as affinity electrophoresis. The extent of the ionic interaction between a cationic protein and the polymer could be estimated as an apparent dissociation constant. It greatly depended on the ionic strength of the electrophoresis buffer. Except for the extremely cationic proteins such as lysozyme, the ionic interaction with up to 0.1 mM of the polymer could be practically suppressed by the use of 0.1 M sodium phosphate buffer (pH 7.0).

Notes: Sodium dodecyl sulphate-polyacrylamide gel electrophoresis has been used to determine the metacercariae (Mc) total body protein band profiles of different Diplostomum spp. Four species of fish were investigated, roach (Rutilus rutilus) infected with D. spathaceum Mc, gywniad (Coregonus laveratus) infected with D. coregonus Mc, ruff (Gymnocephalus cernua) infected with a Diplostomum species related to D. gasterostei Mc, and perch (Perca fluviatilis) infected with D. gasterostei Mc. The four species of Diplostomum Mc were distinguished by three different bands of molecular weight, Mr 55 500, 53 500 and 52 000. A homology of polypeptide component distribution was evident for D. gasterostei Mc, from P. fluviatilis, and D. coregonus Mc, from C. laveratus, the latter showing reduced protein concentrations between bands Mr 32 000-40 000. Critical analysis of Mc polypeptide patterns showed no evidence of contamination with lens, retina or vitreous humour host eye protein. Gross morphological data for the parasites was also considered in relation to different band profiles obtained for the Diplostomum spp. Mc. Band profile analysis in conjunction with other taxonomic tests proved to be a useful tool in the identification of unknown species.

Notes: The binding of Coomassie Brilliant Blue R-250 to several species of bovine pancreatic ribonuclease is affected by the presence of a carbohydrate moiety in the enzyme molecule. Enzymic deglycosylation of several chromatographic fractions of ribonuclease, which have different degrees of glycosylation, results in increased staining by Coomassie Brilliant Blue R-250. Ovalbumin and other glycoproteins tested show similar behavior. The results indicate that carbohydrate moieties may represent a common hindrance to the binding of Coomassie Brilliant Blue dyes to glycoproteins.

Notes: Viral polypeptides were prepared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by copper staining and electroelution from gel slices. Poliovirus capsid polypeptide VP 1 isolated by this procedure induced monospecific antibodies in rabbits, i. e., antisera reacting only with the homologous polypeptide. Our results demonstrate the applicability of the described copper staining method as a rapid visualization step for preparing viral proteins after SDS-PAGE.

Notes: A soluble protein of unknown function was shown, by two-dimensional polyacrylamide gel electrophoresis, to be present in Neisseria gonorrhoeae at significantly higher concentrations than in the other related bacteria tested. The data indicate the possibility of this protein being specific to Neisseria gonorrhoeae. This protein was designated as NG 8.4 and purified. A radioimmunoassay was developed for the measurement of this protein and subsequently used to determine the degree of cross reaction exhibited by a number of species of bacteria. Of the bacteria tested only those of the genus Neisseria gave a significant reaction in the assay.

Notes: From the cerebrospinal fluid of 32 patients with different neurological diseases immune complexes were isolated using protein A-Sepharose. The isolated heavy and light chains and their constituents were analyzed by two-dimensional gel electrophoresis. In addition to immunoglobulins, some proteins such as albumin, apolipo-protein A-I and a number of unknown proteins were detected in all preparations. A complex consisting of three proteins with molecular masses between 52-55 kDa reacted slightly with polyclonal antibodies to glial fibrillary acidic protein, Whether the linkage between these antigens and the Ig is due to the Fab region or the Fc region remains unknown in our study. In some immune complexes of neurological diseases such as amyotrophic lateral sclerosis, astrocytoma and multiple sclerosis, differences are easily recognizable in the gel pattern.

Notes: Cerebrospinal fluid (CSF) proteins were separated into three main fractions by size exclusion-high performance liquid chromatography (SE-HPLC). Subsequent analysis of each fraction by two-dimensional gel electrophoresis (2-DE) facilitated the detection of trace components in CSF and additionally provided more information about the native properties of various proteins. Certain proteins are present in a polymeric form and appear in the high molecular weight SE-HPLC fraction. In the middle molecular weight SE-HPLC fraction we found a CSF-specific transthyretinrelated protein by immunoblotting with polyclonal antibodies to transthyretin. Possible interpolypeptide disulfide bonds of such polymeric proteins were studied using a nonreducing 2-DE system. This procedure revealed that all apolipoprotein E monomers in CSF, which are synthesized in astrocytes, are linked by disulfide bonds. In the CSF from a patient with clinically definite multiple sclerosis (MS), novel proteins appeared in the high molecular weight SE-HPLC fraction, which are obscured by other proteins if total CSF is analyzed.

Notes: The method of isoelectric focusing proteins on cellulose acetate membranes has been improved by the introduction of: (i) plastic-backed membranes, (ii) a commercially available Mini-IEF cell and (iii) sensitive colloidal gold staining. The improved methodology is described with applications for clinical laboratories.

Notes: The polymorphism of alpha-1-antitrypsin (PI) has been studied by hybrid isoelectric focusing in miniaturized immobilized pH gradient gels, with an interelectrode distance of 55 mm, in two narrow ranges of pH 4.35-4.75 and 4.35-4.55, following rehydration with pH 4.2-4.9 carrier ampholytes. The use of the separator N-(2-acetamido)-2-aminoethanesulfonic acid (ACES) in combination with carrier ampholytes for gel rehydration has been shown to enhance PI band sharpness. The influence of different additives (sucrose, sorbitol and glycerol) on the PI band pattern has also been evaluated. Glycerol has been shown to be responsible for the change in the relative mobility of the M3 band. The analysis of the minor M-7 isoprotein zone by hybrid isoelectric focusing followed by silver staining has permitted a more reliable classification of PIM subtypes. A population study carried out with 164 unrelated individuals living in Spain is also presented.

Notes: The preparation of 0.45 mm thin polyacrylamide gels, containing urea, for horizontal micro isoelectric focusing of milk proteins with PhastSystem is described. Isoelectric focusing in the small gels, stained either with Coomassie Brilliant Blue R-250 or with the more sensitive silver stain, affords a fast and sensitive procedure for an analysis of milk and cheese proteins. The procedure can be effectively exploited in detecting adulteration in ovine cheese with bovine milk.

Notes: Native Hemophilus influenzae polysaccharide-protein conjugate particles were analyzed by a two-dimensional agarose electrophoresis procedure. In view of their preparation by random chemical crosslinking, the conjugates necessarily exhibit a polydisperse two-dimensional gel pattern which varies depending on the conditions of the particular preparation. The polydisperse patterns were interpreted with regard to the size and surface net charge density of the conjugate on the basis of the extended Ogston model. Data processing was performed by a new program, designated ZWEIDI.DO, written in the language of M-LAB (modeling laboratory). The program computes particle and gel fiber specific parameters from the positions of standards and unknown(s) on the two-dimensional gel using a simultaneous linear least-square curve fitting routine. Based on these calculations, the program serves to compute a nomogram of iso-size and iso-free-mobility profiles. Superimposing these profiles on the gel patterns, the size and free mobility range of the polydisperse conjugate mixtures is obtained. Potentially, the procedure could serve as a tool for quality control in the production of conjugates as vaccines and for the physical characterization of polydisperse subcellular particles and vesicles.

Notes: A multiple immunoblotting technique was developed to positively identify up to three different antigens on a single nitrocellulose replica of a two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel. Three highly sensitive immunoblot assays were selected, including: horseradish peroxidase/luminescence, alkaline phosphatase, and silver-enhanced immunogold. As a major advantage, the method permits a simultaneous detection of up to three different antigens without eluting the antibody-dye complex between staining of single polypeptides, thus providing a highly accurate identification of closely migrating components. The staining procedure is summarized in a flow chart. In addition to the multiple immunoblot staining, some suggestions are provided for a sensitive protein staining.

Notes: Electrophoresis of monomeric actin (G-actin) on 8-25 % acrylamide Pharmacia PhastGels was carried out using gels and agarose buffer strips preequilibrated in buffer containing adenosine triphosphate (ATP), calcium ions (Ca2+) and dithiothreitol. On these gels G-actin ran as a sharp band at an apparent molecular mass of 45 kDa relative to standard proteins which is slightly greater than its actual molecular mass of 42 kDa. Electrophoresis in the absence of these solutes led to denaturation and aggregation of the protein, as reflected by a long streak. Filamentous actin (F-actin) did not enter the gel. The actin monomer-binding protein, deoxyribonuclease I, (DNase I) forms a binary complex with G-actin. The purity and apparent molecular mass 74 kDa of this complex were determined by native gel electrophoresis. By the simple procedure of preequilibrating both gel and buffer strips with appropriate ligands, this technique could be extended to investigate interactions between actin and other G-actin-binding proteins and other proteins whose stability is ligand dependent.

Notes: Premeiotic and meiotic whole testes from grasshoppers were compared for the presence of meiosis associated proteins using one- and two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis. One-dimensional sodium dodecyl sulphate-polyacrylamide gels detected differences between premeiotic and meiotic samples but two-dimensional gels gave more precise results. Isoelectric focusing revealed only one meiosis-associated protein, while nonequilibrium pH gradient electrophoresis detected five more. It is not known whether these proteins relate to the nuclear aspects of meiosis, or associated cellular changes. These proteins have been electrophoretically purified and monoclonal antibodies are being prepared.

Notes: A mixture of the nonionic detergent Triton X-100, the zwitterionic detergent 3-[(cholamidopropyl)dimethylammonio]-1-propanesulphonate (CHAPS), 9M urea and carrier ampholytes was found comparable to media containing sodium dodecyl sulfate in the capacity for solubilization of myelin proteins, including the highly hydrophobic proteolipid protein. The solubilized sample was incorporated into the polymerization mixture before moulding an ultrathin gel, with heat convection characteristics allowing a high wattage to be applied, thus allowing fast separation with high resolving power. Since the most basic protein in myelin focuses at a pH 〉 10, fast separation is essential in order to minimize decay of the cathodic end of the pH gradient.

Notes: Commercial preparations of streptavidin, a bacterial biotin-binding protein, were analyzed by isoelectric focusing combined with an affinity-based protein blot using biotinylated, protein-saturated nitrocellulose. The colorimetrical detection of strep-tavidin with biotinylated alkaline phosphatase allows the selective visualization of streptavidin molecules with at least two active biotin-binding sites. Dependent on the preparation, seven to sixteen streptavidin forms were found with isoelectric points ranging from 5 to 8. Molecular weight analysis of the subunits of streptavidin showed that the observed heterogeneity was mainly due to limited proteolysis, which does not destroy the biotin-binding activity. The preparations differed also in the nonspecific reactivity of streptavidin with single-stranded DNA, bovine serum albumin and Tween 20. No relationship was observed between heterogeneity and non-specific binding activity. Data obtained from protein blots onto nitrocellulose saturated with single-stranded DNA showed that it cannot be excluded that streptavidin with only a single active biotin-binding site is mainly responsible for the nonspecific reactivity of some streptavidin preparations.

Notes: Two acute-phase proteins have been identified in very low density (VLDL)- and high density lipoproteins (HDL) of patients after acute myocardial infarction. Both proteins have a relative molecular weight of 11 000 and isoelectric points pI 6.08 and 6.27, and do not contain cysteine or sugar residues. Polyclonal antibodies to these acute phase reactants did not cross-react with other serum apolipoproteins. Evidence is given that both proteins are polymorphic forms of the human serum amyloid A protein.

Notes: A method for the determination or 4-methylimidazole in caramel color, based on cationic separation of the sample by capillary isotachophoresis, is described. No pretreatment of the sample is necessary and the detection limit was found to be 5 ppm.

Notes: A model system for studies of mechanisms governing the alterations of glycosylation of plasma glycoproteins was developed. The system employs two human hepatoma cell lines, Hep 3B and Hep G2, as target cells and agarose affinity electrophoresis with lectins for studies of microheterogeneity of α1-protease inhibitor (PI), a model glycoprotein synthesized by hepatocytes. As an example for the application of the system, the effect of cytokines on major microheterogeneity of plasma proteins is demonstrated. The results indicate that interleukin 6, transforming growth factor β1 and, to some extent, tumor necrosis factor α are directly involved in regulating the pattern of glycosylation of plasma proteins in vitro, but the major effect is obtained by using combinations of interleukin 6, transforming growth factor β1, tumor necrosis factor a and interleukin 1. In addition, the results underline the dissociation between alteration of gene expression and the changes in the pattern of plasma protein glycosylation.

Notes: In contrast to the conventional combination of physical, chemical and enzymatic methods used for a structural analysis of glycans in glycoproteins, alternative methods involve affinity electrophoresis as a tool for the detection, characterization, and quantitation of glycoproteins and their carbohydrate moiety, owing to interactions with lectins. Two major approaches involve (i) crossed affino-immunoelectrophoresis and variations thereof, whereby lectin/glycoprotein interactions occur during the electrophoretic runs, or (ii) affino-blotting, where the glycoproteins are electrophoretically separated and then immobilized onto a solid support prior to their interaction with lectins. A critical comparison of these two series of techniques is the scope of the present paper. These techniques are of high interest by virtue of their ability at differentiating a classical glycan structure from unusual oligosaccharide side chains. The former structures will usually be qualitatively and quantitatively described with the easy and fast procedures as well as the simple equipment required for crossed affino-immunoelectrophoresis or affino-blotting, whereas the latter will be good candidates for further structural analyses.

Notes: By means of two-dimensional lectin affinity electrophoresis of human α-fetoprotein (AFP) from different sources, AFP bands separated with erythroagglutinating phytohemagglutinin (E-PHA) were further characterized with other lectins of known oligosaccharide specificities. The results with a cord serum AFP revealed that not only AFP-P2 (E-PHA-nonreactive) but also AFP-P4 and P5 (E-PHA-reactive) had affinities for Concanavalin A (Con A) and Allomyrina dichotoma lectin (allo A), indicating that the cord serum AFP has nonbisected biantennary complex-type oligosaccharides with the terminal galactose on Man α1 → 6 residue sialylated at the C-6, but not C-3, position. On the other hand, the results with a hepatoblastoma (HUH-6 C1-5 cell line) AFP showed that not only AFP-P5 but also AFP-P1 (E-PHA-nonreactive) and P3 (E-PHA-less reactive) had Con A-nonreactive AFP and that AFP-P1 had AFP-A1 (allo A-nonreactive) and AFP-A2 (allo A-less reactive), and AFP-P3 and P4 had AFP-A1s (allo A-nonreactive), as main components, in addition to the spots of cord serum AFP. Most of the E-PHA-dependent bands of AFP were further subdivided with Lens culinaris agglutinin (LCA-A) into LCA-A-reactive, weakly reactive and nonreactive spots. Similar results were obtained with AFP preparations from hepatocullular carcinomas and other malignancies, indicating that the bisected bi-(or tri-and tetra-) antennary sugar chains with the exposed terminal galactose of the Man α 1 → 6 arm as well as those with the C-3 sialylated galactose residues could be expressed in AFP upon malignant transformation. The two-dimensional lectin affinity electrophoresis thus proves useful for further characterization of lectin-dependent AFP bands.

Notes: An affinity electrophoresis system is described to allow determination of dissociation constants of lipopolysaccharide (LPS)-protein complexes. The LPS ligand is incorporated into polyacrylamide gels by addition to the polyacrylamide-N, N′-methyl-enebisacrylamide polymerization mixture. Quantitative evaluation revealed formation of immobile protein-ligand complexes. The method was applied both to R- and S- form LPS from Acinetobacter calcoaceticus. For a heat-modifiable outer membrane protein with Mr 18 000 from strain 69V the dissociation constant was determined to be 0.5 mM (EDTA-salt extracted R-LPS) and 0.3 mM (phenol-chloroform-petrolether extracted R-LPS). In comparison, for another A. calcoaceticus strain, CCM 5593, a higher dissociation constant of 1.0 mM (phenol-chloroform-petrolether extracted R-LPS) - indicative of lower affinity - was obtained. When S-LPS from A. calcoaceticus 69V was incorporated into the affinity gels, a dissociation constant of 0.02 mM was determined which indicates much stronger interactions than those exerted by R-LPS forms.

Notes: A natural sulfated polysaccharide (agaropectin), contained in crude agar, can be used as a medium for electrophoretic separation of hemoglobin mutants, constituting a particular class of protein-ligand interactions. Mutations which either modify the electrostatic charge at the surface of the hemoglobin molecule or not, have been studied according to their putative interaction with the medium. Using conformational specificities of the hemoglobin molecule, we have also demonstrated that isoelectric focusing on a polyacrylamide gel in the absence of heme ligands represents a useful, convenient and rapid procedure for isolating silent Hb variants in their native form, provided that they exibit an abnormal Bohr effect.

Notes: The electrophoretic separation of DNA molecules can be controlled by the use of contour-clamped homogeneous electric fields (CHEF). This paper describes an improved CHEF apparatus with negligible distortion in the electric fields. When the electric field was periodically reoriented, DNA molecules up to 2 megabases were resolved in a highly uniform manner. Furthermore, when the field strength was changed with orientation, topological variations of conventional-sized DNA molecules were resolved.

Notes: Chromosome-size DNA molecules can now be separated using a variety of pulsd field gel electrophoresis techniques. In this article, we study the predictions of the biased reptation model concerning the effect of two pulsed fields, making an arbicray angle, on the power of separation of gel electrophoresis. Separation is predicted to be largely enhanced for obtuse angles, in agreement with experiments. Interestingly very large molecules, which are not separated by pulsed fields, are predicted not to migrate along the gel diagonal for fairly long periods of time. Finally, we discuss the optimization of these techniques using the results of the theory, and the limitations of the latter when fluctuations and intramolecular modes probably dominate the system.

Notes: We apply the concepts of tube and reptation to the pulsed electrophoresis of DNA, considering both biased reptation and “breathing” modes (internal modes of the chain). Using suitable preaveraging approximations, analytical expressions are derived which relate displacement in crossed field electrophoresis to molecular weight, field strength, field period, pore size of the gel, and the angle between the field. These expressions provide scaling laws for the change of mobility when one (or more) of the parameters is varied as well as “universal” velocity versus molecular weight versus pulse time curves. These results are quantitatively compared with experiments. At some point which depends on field angle, field strength and chain length, however, we predict a failure of this model due to symmetry breakdown and loss of ergodicity. Qualitatively, this should lead to considerable band spreading and/or splitting of the highest DNA bands into two bands migrating sideways from the diagonal. The case of field inversion is also investigated. It is shown that only breathing modes can explain the strong differences in mobility experienced by chains of different length when opposite fields of equal amplitude are applied: the “trapping” of chains in conformations of low mobility is associated with an antiresonance-like coupling between the external field and the internal modes.

Notes: High resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) in combination with computer-assisted densitometry was used to analyze 800-1000 silver stained postmitochrondrial and 600-800 cytosolic polypeptides extracted from malignant and nonmalignant human breast tissues. The 2D-PAGE patterns of polypeptides from malignant and normal tissues were similar, although both qualitative and quantitative polypeptide differences were noted. Six cytosolic poly peptides (pI/ molecular mass X 10-3), 5.20/80, 5.75/43, 6.20/40, 5.43/35, 5.46/34.5, and 5.50/34 were detected exclusively in malignant tissues. One constitutive poly peptide, p52 (7.25/52), was not detected in tumor samples. Marked quantitative differences in spot density were noted in polypeptides localized mainly in the molecular weight ranges of 22-40 kDa and pI of 5.65-7.00. An overall increase in polypeptide expression was noted in this region of 2D-PAGE gels of malignant tissues as compared to normal. Twenty-two acidic and 19 polypeptides separated under nonequilibrium isoelectric focusing conditions were significantly increased in tumor samples while one polypeptide was decreased. One polypeptide, p24 (6.15/24), was expressed in greatest concentrations in tumors which also expressed the greatest estrogen receptor content. Expression of p24 was markedly reduced in normal tissue and in malignant tissues expressing low levels of estrogen and progesterone receptors. No significant differences in the expression of the Yb and Ya subunits of glutathione S-transferases (GST)-A, -B and ligandin were observed between normal and malignant breast tissue. None of the Yp subunits of the placental isoform of GST were detected in either normal or malignant breast tissues.

Notes: During the last decade several strategies have been developed to identify proteins which could serve as markers in tumor biology. One avenue of great promise to detect such proteins seems to be the separation of prefractionated organelles from tumor cells by high resolution two-dimensional electrophoresis. Using detergent-lysed nuclei from several human tumor cell lines, especially from brain tumors, and two-dimensional electrophoresis, we analyzed the nuclear protein pattern obtained after sequential salt extraction of tumor cell nuclei. In addition to proteins occurring in all tumor cell lines, the pattern of different tumor cell lines exhibits considerable differences when proteins were visualized by silver staining, thus emphasizing the specificity of nuclear proteins with respect to the cell type. Even quantitative variations of the nuclear phosphoproteins 23/4 were detectable, indicating a potential correlation between their synthesis/phosphorylation and the proliferation behavior of tumor cells. The data indicate that nuclear proteins with their distinct heterogeneity and tissue specificity may represent a powerful source in determining tumor-specific proteins. The extent of chromosomal protein heterogeneity may be additionally increased by their covalent modification by nuclear kinases; therefore, tumor-specific nuclear proteins may occur as quantitative and qualitative variations.

Notes: Serum proteins associated with acute myocardial infarction (AMI) have been monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and high resolution two-dimensional electrophoresis (2-DE) under nonreducing conditions. Proteins a, b, c (Mr 13 000; pI 6.2, 6.7 and 7.5, respectively) and e (Mr 27 000; pI 5.2) appear simultaneously ∼ 30 h after infarction, reach maximum intensity after 48 h and progressively decline thereafter. Protein d (Mr 15 000; pI 7-8.5; identified as hemoglobin) sometimes appears within 18 h of infarction. Proteins a-c are not detected in the 2-DE patterns of healthy myocardium, infarcted myocardium, pectoral muscle or tongue, but e is present in all and tentatively identified as myosin light chain. Other myocardial proteins which are either reduced in amount following infarction or more specifically associated with myocardium than pectoral muscle are not detected in the serum of AMI patients. Analysis of unconcentrated urine by SDS-PAGE and silver staining does not reveal proteins specific to AMI.

Notes: Aldehyde dehydrogenase (ALDH) consists of four different isozymes (I, II, III, IV). Among these, ALDH I shows genetic polymorphism (normal and deficient) in a population of Mongoloid origin. The significantly lower frequency of ALDH I deficiency was found in alcoholic patients compared with healthy controls. ALDH I deficiency is one of the important genetic factors in regulating alcohol consumption and plays a protective role against alcoholism. Population genetic studies on ALDH I deficiency in different ethnic groups indicate that ALDH deficiency was found only in Mongoloid population groups.

Notes: Agarose isoelectric focusing followed by blotting with nitrocellulose, nylon or polyvinylidene difluoride membranes, and immunochemical detection of cerebrospinal fluid IgG with various combinations of antisera, was evaluated. Polyvinylidene difluoride proved to be an easy-to-handle and reliable membrane for protein blotting. Among immunochemical visualization reactions, the most sensitive employed biotinylated goat anti-human IgG followed by streptavidin colloidal gold conjugate and silver enhancement in 20% w/v urea, allowing a sensitivity of less then 1 picogram IgG/band.

Notes: Isoelectric points and subunit sizes of catalases in human blood and human cultured skin fibroblasts from acatalasemic and normal subjects were analyzed by isoelectric focusing in agarose gel and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively, followed by electroblotting to polyvinylidene difluoride membranes for immunodetection. The results indicated that the isoelectric point of residual catalase in the C fraction prepared from acatalasemic erythrocytes was identical with that of catalase prepared from normal erythrocytes. The residual catalase in homogenates of acatalasemic cultured skin fibroblasts also reacted with anticatalase rabbit serum and had an isoelectric point identical with that of normal catalase. Sub-unit sizes of normal and acatalasemic catalases in the C fractions of erythrocytes were also found to be identical on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, followed by electroblotting and immunoenzymatic amplification. The results indicated no substantial difference in molecular size and charge of catalase proteins between normal and acatalasemic erythrocytes and fibroblasts.

Notes: In order to increase the pathway of the light inside a gel (or autoradiogram) during scanning, it is placed on top of a mirror and the densitometry is performed in a vertical reflection mode. As the light passes the gel a second time after being reflected by the mirror, the absorbance is nearly doubled. This increase in absorbance results in higher sensitivity and resolution.

Notes: Standard mixtures of proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Polynomial regression analysis was used to fit curves to the data, points obtained by plotting log10 of protein molecular weight versus electrophoretic mobility. Polynomials with orders ranging from 1 to 4 were generated. The coefficients of each equation were analyzed for statistical significance. It was found that a third order polynomial was the hightest-order equation in which all coefficients contributed significantly to the prediction of molecular weights. Using this equation, it was possible to estimate the molecular weights of known proteins in the range from 97 400 to 14 400 with a maximum error of 1 %, compared with a maximum error of 17 % when a first-order equation was used to describe the migration of the standarads.

Notes: An algorithm for automatic evaluation of nucleic acid sequencing gel antoradiographs is described which is simple and fast, with a low level error rate.

Notes: The representative β-hydroxyethylmorpholinium-chloride-bicinate moving boundary with a trailing ion net mobility relative to Na+ of 0.41, detected by precipitation of chloride with silver nitrate, exhibits a decreasing chloride mobility at increasing polyacrylamide gel concentrations from 3.5 to 45 %T, 5 %CBis. This decrease, largely due to an increase of field strength at constant current, is described by a convex plot of log (mobility) vs. %T (Ferguson plot) and signifies that chloride/bicinate are sieved by the gel. In agarose gels, the same plot of mobility vs. gel concentration is constant below 7 % gel concentration, since in those gels field strength and migration rate remain the same within that gel concentration range. Both in polyacrylamide and in agarose gels the displacement rate of the chloride-bicinate boundary as a function of the time of electrophoresis or distance migrated remains invariant within 15 %. The plot of log(mobility) vs. gel concentration extrapolated to 0 %T is 5.85 and 5.41 (10-5 cm2 s-1V-1) for polyacrylamide and for agarose (SeaKem HGT-P, FMC) gels, respectively. The slightly decreased mobility intercept at 0 %T for agarose is presumably due either to the electroendosmotic properties of agarose HGT-P and/or failure to Sufficiently take into account the flattening of the Ferguson plot in the polyacrylamide concentration range below 3 % in which a transition from a gel to a fluid (sol) medium takes place.

Notes: A method was developed for the preparation of completely intact plant DNA embedded in agarose, and suitable for restriction enzyme digestion. Digestion with restriction enzyme was carried out according to modified protocols of Anand [1] and Kenwrick et al. [2]. The new method of DNA isolation allows the separation of high molecular weight plant DNA by pulsed field gel electrophoresis.

Notes: Horizontal two-dimensional gel electrophoresis with immobilized pH gradients in the first dimension resulted in excellent patterns of porcine erythrocyte lysate proteins. The overwhelming excess of hemoglobin was removed by chloroform-ethanol extraction and the number of spots further increased by acetone precipitation, revealing considerably more protein spots than detected by analyzing the untreated sample. A total of 430 protein spots have been reproducibly obtained for further analysis of genetic variations. A number of enzyme systems have been identified by visual inspection and comparison with previous results. The existence of further multiple forms for other enzymes is also apparent.

Notes: Proteins from nuclear plasma of mouse liver and brain and from the nuclear membranes of mouse liver were separated by two-dimensional electrophoresis. For the purpose of comparison, liver cytosol proteins were also investigated. The protein samples were prepared from two inbred strains of the mouse (DBA/2J, C57BL/6J) and their hybrids. The patterns obtained were compared with regard to the composition and genetic variability (qualitative and quantitative variants) of proteins from different nuclear fractions and organs. The percentage (〉 30 %) of spots common to different organs (liver, brain), but from the same nuclear fraction (plasma) was greater than the percentage (〈 20 %) of spots common to different cell and nuclear fractions (cytosol, nuclear plasma and nuclear membranes) of the same organ (liver). Quantitative genetic variants occurred much more frequently than qualitative genetic variants (5.1 % vs. 0.2 %; liver nuclear plasma). The incidence of genetic variants was much higher in liver (5.3 %) than in brains (0.0 %), and higher in solubilized nuclear proteins (5.3 %) than in structure-bound nuclear proteins (2.1 %).

Notes: Electrophoretic light scattering has been used to investigate the interaction of ricin, a vegetal toxin, with cells. This technique allowed measurements in the presence of free ligand and proved particularly useful for the study of a system with low affinity. The electrophoretic mobility of erythrocytes and oligodendrocytes was found equal to 2.08 × 10-8 and 2.35 × 10-8m2s-1 V-1, respectively. Upon ricin binding, these values decreased significantly. This change was related to the saturation of the binding sites. The specificity of the interaction was demonstrated by conducting the experiments in the presence of lactose. This specific inhibitor fully prevented the ricin-cell interaction.

Notes: Following polyacrylamide gel electrophoresis in an acetic/formic acid buffer, pH 2.0, in fabric reinforced gels, amino acids and oligopeptides could successfully be fixed in the gel by freeze-drying. Lyophilization of the fabric reinforced polyacrylamide gel after electrophoresis resulted in a dry film which absorbed ninhydrin solution quickly and uniformly, thus improving the detection limit for amino acids and oligopeptides with molecular weights ranging from 189-1045. Most amino acids were detected with a sensitivity of 0.1-0.25 μg and for oligopeptides the detection limit was found to be 0.5-5 μg.

Notes: Transparency of nitrocellulose membranes can be realized by simply impregnating the filters with concentrated Triton X-114. Within a few seconds, protein blots become transparent and can be photographed by transillumination or scanned on a densitometer. Removal of the detergent is possible and the recovered filters can further be used for immunodetection purposes. This procedure is particularly well-suited where extensive investigation of a single separated protein sample is required.

Notes: β-1,3-Glucanase (laminarinase) activity was detected after polyacrylamide gel electrophoresis under native conditions by using laminarin as substrate. Following incubation of gels, laminarin was stained with Aniline Blue. Under UV illumination, lysis zones appeared as dark bands against a fluorescent background. As low as 0.001 unit of commercial Penicillium laminarinase could be observed after incubating the polyacrylamide gel for 45 min at pH 5.0. Extracts of commercial Penicillium laminarinase exhibited four bands with lytic activity towards laminarin. Analysis of intercellular fluid extracts of tobacco mosaic virus-infected tobacco leaves revealed four β-1,3-glucanases corresponding to three acidic pathogenesis-related proteins, b4 (2), b5 (N) and b6b (0), and one basic protein. The presence of laminarin in gels retarded the migration of some proteins with β1, 3-glucanase activity. This change in electrophoretic mobility could be used as a complementary affinity test for identifying proteins with β-1,3-glucanase activity.

Notes: A theory for discontinuous electrophoresis in a polyacrylamide gel is presented for one buffer at two pH values. It is shown that polyions stack between identical leading and trailing ions, and resolve in a gel of constant polyacrylamide concentration. The theory is illustrated by the separation of serum protein polyions in a Tris-glycinate buffer of pH 8.19 in the well-forming gel, and pH 9.16 in the resolving gel. The selected concentrations and electrolyte ionization degrees of Tris and glycine have values at which the serum protein polyions stack between the resolving and electrode buffers, followed by separation in the resolving gel.

Notes: Isolated metaphase chromosomes of several fibroblastoid cell lines (Chinese hamster, Chinese hamster × human hybrid) were subjected to free flow electrophoresis (FFE) to study their electrophoretic mobility (EM). The morphology and stability of the chromosomes were unaffected by FFE as examined by cytogenetic methods and flow cytometry. The chromosomes of the complement all showed similar EM under most of the conditions applied. At neutral pH the EM of the chromosomes had the same sign as free DNA and about 2/3 of its magnitude. The variation of EM with buffer parameters such as ionic strength, valence of counterions, buffer capacity and dielectric constant of the solvent were investigated. Thermal denaturation increased the EM of the chromosomes by 20 %. Partial denaturation might offer a possibility to separate or enrich large amounts of chromosomes by FFE.

Notes: The electrophoretic titration curves of complex mixtures of vitamin K-dependent human blood proteins and proteins of Bothrops asper venom were investigated. In both protein mixtures some curves exhibited marked distortions such as additional maxima and minima when Pharmalyte 3-10 carrier ampholytes were used for isoelectric focusing in agarose gels. The distortions result from an unspecific interactions-between some carrier ampholyte constituents with particular proteins. The interacting carrier ampholyte components could be completely removed by binding to albumin and ultrafiltration through a UM-2 Amicon membrane with resultant regular titration curves. The interacting carrier ampholyte species were only partially removed by ultrafiltration through a UM-2 membrane without incubation with albumin.

Notes: The methodology for conventional radiofluorography of two-dimensional gels, followed by rehydration of the gel and subsequent silver staining, is described. The image obtained by radiofluorography is referred to as biosynthetic image, and the image obtained by silver staining as constitutive image. Since the two images are already in close register (the same gel), reliable identification of polypeptides by the two different assays is possible, and the comparison provides valuable information on the catabolism of each entity. The utility of this procedure is illustrated in experiments involving a labeling with L-[35S] methionine of an entire mouse. Both serum and tissue samples were analyzed by two-dimensional gel electrophoresis with the aim of determining several categories of polypeptides in terms of their biosynthetic rates and their composition.

Notes: A procedure was developed for casting thin-layer multistrip polyacrylamide gels and using them for the simultaneous gel electrophoresis at several gel concentrations (Ferguson plot analysis) at the sub-microgram load level, using silver staining, autoradiography and, potentially, blotting for detection. The lower viscosity of polymerization mixtures, compared to agarose gelation mixtures, required the redesign of the multistrip cassette with separation of channels by rubber gaskets and the application of a cassette press. The lowered viscosity also required addition of 35% sucrose and an increased rate of polymerization in application to multistrip gels formed on a common NetFix backing. The present design allows one to obtain Ferguson plots exemplified by those of 32P-labeled DNA followed by autoradiographic detection.

Notes: A method is described for the determination of the triazine herbicides prometryne, desmetryne, terbutryne, OH-atrazine and OH-simazine in purified extracts of milk using analytical capillary isotachophoresis. The reproducibility of isotachophoretic analyses was 3.5% and the detection sensitivity reached 2 ng. Recovery of triazines from fortified samples of homogenized full milk (0.05 mg/L) was about 65%.

Notes: The Pharmacia PhastSystem equipment has been used for crossed immunoelectro-phoresis combined with a technique for immunoblotting with monoclonal antibodies. This miniaturized gel system is compared to the conventional approach using platelet membrane receptor proteins as a model. Whereas in the conventional system the electrophoretic procedure takes place within 20 h, 3 h are adequate for the small gel system. Because of the short second-dimensional electrophoresis, and only one over-night incubation, the total electrophoretic and blotting procedure could be reduced from about 48 h to 24 h. The amount of antiserum used during the second-dimensional electrophoresis could be reduced roughly by a factor of 5. The examples with electrophoresis and immunoblotting using platelet extracts in 1 % Triton X-100 demonstrate that membrane receptor proteins can be studied even when present as noncovalent complexes. The immunoblotting can be used with monoclonal antibodies that do not function in Western blotting.

Notes: Distribution and cellular levels of retinol-binding protein and retinoic acid-binding protein, involved in the molecular action of retinoids, were analyzed in rat testis and liver. Both binding proteins of cytosolic extracts were separated by linear-polyacryl-amide gradient gel electrophoresis and following electrophoretic separation, could be visualized by complementary identification tests such as autoradiography and marker proteins. The concentrations of the binding proteins were evaluated by scanning the polyacrylamide gradient gels and the resulting data were found to be in accordance with those obtained by counting radioactivities. Polyacrylamide gradient gel electrophoresis appears suitable to detect and quantitatively evaluate cytosolic retinol- and retinoic acid-binding proteins.

Notes: Plasma protein and lipoprotein fractions of five patients were analyzed on day 1, 5, and 15 after severe head injury by combining three types of two-dimensional electrophoresis (2-DE) to obtain information on lipoprotein and apolipoprotein composition. On analysis under nondenaturing conditions in both dimensions on day 5, the samples show modifications of isoelectric point (pI) and molecular weight (Mr) properties of the high density lipoprotein (HDL) fraction in addition to an increase in inflammatory proteins and a return to a normal pattern on day 15. In the second type of 2-DE the samples were analyzed employing isoelectric focusing without denaturant in the first dimension, followed by sodium dodecyl sulfate (SDS) in the second dimension in order to study the protein composition of lipoprotein fractions. On day 5, a decrease of the apolipoproteins apo A-I, apo A-II, and apo C were noted, with simultaneous appearance of an unidentified protein with Mr 12 000 and pI 6.0. In the third type of 2-DE, employing urea and Nonidet P-40 in the first and SDS in the second dimension, the plasma polypeptide composition was studied. The presence of an unidentified polypeptide could be confirmed on day 5, tending to disappear there-after. This Mr 12 000 component consists of two major spots at pI 5.7 and 6.0 and four minor ones between pI 6.0 and 8.0. These properties suggest that this protein corresponds to serum amyloid A apolipoprotein.

Notes: The application of a small format two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) system to the study of protein heterogeneity among group B coxsackie virus (CVB) isolates is described. Under the conditions of electrophoresis developed during this study, protein samples could be processed within 7 h and up to 300 intracellular proteins were resolved from uninfected HEp-2 cell lysates. 2D-PAGE was used to characterise the intracellular proteins of clinical CVB isolates of serotypes 4 and 5. Intracellular proteins from virus-infected cells were radiolabelled using a pulse-chase protocol under conditions which promoted inhibition of cellular protein synthesis. Depending on the CVB serotype up to 11 intracellular virus proteins were identified, ranging in molecular weight between 14 000 and 54 000. Although the overall two-dimensional protein profiles were characteristic for the two CVB serotypes, within a CVB serotype there was some heterogeneity of the virus proteins, mainly affecting the proteins' net charge. The sensitivity of 2D-PAGE in detecting subtle differences in virus proteins combined with the convenience of the small gel format makes this a suitable approach for the study of the molecular epidemiology of human virus pathogens.

Notes: Formulations are given both for narrow (〈2 pH units) and for wide range (up to 8 pH units) immobilized pH gradients, spanning between pH 2.5 and pH 11. The contribution from water to the buffering power (β) at these pH extremes requires the recipes to be optimized (in terms of gradient linearity) for each desired level of βav.

Notes: A high resolution two-dimensional affinity electrophoresis has been developed, using capillary isoelectric focusing as the first electrophoresis and slab gel affinity electrophoresis as second electrophoresis. By this method 1-2 μg of anti-dinitrophenyl antibodies have been separated completely into several hundred homogeneous IgG spots. They are grouped into a number of families which are composed of several IgG spots of the same affinity to the hapten but of a different pI. It is suggested that each individual family is derived from one monoclonal antibody producing cell line.

Notes: The development of rocket enzyme activity electrophoresis for the detection and quantification of various proteinases, lipases and pectinases is presented. Rocket enzyme activity electrophoresis is more sensitive than the radial diffusion assay and often enables distinction between qualitatively different enzymes present in the same samples, whereas the radial diffusion assay only provides information on the overall enzyme activity. However, calibration and optimization of the enzyme activity electrophoretic assay have to be performed for each new enzyme-substrate system to be analyzed. Some of the common pitfalls in the development of new enzyme activity electrophoretic assays are presented. Enzyme activity electrophoresis can be applied in combination with other electrophoretic assays. Particularly the combination of enzyme activity electrophoresis with various immunoelectrophoretic methods can provide detailed information on the enzymes studies.

Notes: The migration of a series of supercoiled plasmids ranging in size from 4 to 91 kilobases (kb) has been analyzed by orthogonal-field-alternation gel electrophoresis (OFAGE). These circular DNAs enter OFAGE gels and are resolved over the same region of the gel as linear DNAs from 260 to 2200 kb. Furthermore, a distinct triphasic migration pattern was observed for the supercoiled DNAs. The migration of plasmids between 6 and 20, and 60 and 91 kb is inversely proportional to size, whereas the mobilities of plasmids between 20 and 60 kb increase with size. Unlike linear DNA molecules, the relative mobilities of these plasmids are constant over a broad range of pulse times, from 10 to 120 s. Electrophoresis of supercoiled, relaxed, and nicked open circular forms as well as topoisomers of small plasmids shows that the extent of supercoiling has a dramatic effect on plasmid migration on OFAGE. Several practical applications for exploiting the different migration properties of circular and linear DNA molecules on OFAGE are presented.

Notes: The mobility of linear DNA during field-inversion gel electrophoresis was measured as a function of molecular weight Mr, pulse time t, and field strength E. Values of Mr between 48.5 and 194 kilobase pairs (kb), E from 5 to 14 V/cm and pulse times of 0.3 to 12 s were used. The data are presented as three-dimensional surfaces of mobility: E:t for fixed Mr or graphs of mobility: Mr:t for fixed E. The surfaces are not smoothly increasing functions of E, Mr, or t but instead show a valley with minimum mobility and a steep rise in mobility as t increases. For a field of 10 V/cm, 1 % agarose gels, and 3:1 ratio of forward: back pulse time, the forward switching time t* at which the mobility changes most rapidly is given by t* =(0.034 ± 0.003) Mr for Mr in kb and t* in seconds. The data and equations delineate the best conditions to achieve a particular separation.

Notes: The maximum length of DNA molecules that can be separated by gel electrophoresis can be increased greatly by periodically altering the direction of the electric field with respect to the gel by an angle that exceeds 90°. One method involves rotating the gel by the desired angle in alternate directions periodically during electrophoresis. We describe a modification of the rotating gel electrophoresis apparatus developed by Serwer (Electrophoresis 1987, 8, 301-304) that uses a pneumatic rotary actuator instead of a stepping motor, hence reducing the cost by about 50 %. Other advantages of our design are a lower center of gravity that makes the apparatus more stable and the removal of all electrical power from beneath the fluid-filled electrophoresis chamber. We present data demonstrating the separation of chromosomal length DNA molecules from Saccharomyces cerevisiae strain 334 into 14 resolved bands in parallel lanes.

Notes: Curved DNA fragments have a reduced electrophoretic mobility in polyacrylamide gels. The retardation in gels is extremely sensitive to small structural variations which influence the DNA helix axis. This gel assay can also be used to detect very small structural variations in DNA sequences which are not curved: The noncurved seguences of interest can be combined with curved stretches in phase with the helix turn. Using such sequence constructions, even subtle influences on the DNA helix axis can be detected. Experiments of this kind allow the determination of a relative order of sequence-specific DNA twist and wedge angles.

Notes: Transient electric birefringence has been used as an analytical tool to study the orientation of DNA in agarose gels, and to study the orientation of the matrix alone. The sign of the birefringence of DNA oriented in an agarose gel is negative, as observed in free solution, indicating that the DNA molecules orient parallel to the direction of the electric field. If the median pore diameter of the gel is larger than the contour length of the DNA molecule, the DNA effectively does not see the matrix and the birefringence relaxation time is the same as observed in free solution. However, if the median pore diameter of the gel is smaller than the contour length of the DNA, the DNA molecule becomes stretched as well as oriented. For DNA molecules of moderate size (≤ 4 kb), stretching in the gel causes the birefringence relaxation times to increase to the values expected for fully stretched molecules. Complete stretching is not observed for larger DNA molecules. The orientation and stretching of DNA molecules in the gel matrix indicates that end-on migration, or reptation, is a likely mechanism for DNA electrophoresis in agarose gels.When the electric field is rapidly reversed in polarity, very little change in the orientation of the DNA is observed if the DNA molecules were completely stretched and had reached their equilibrium orientation before the field was reversed in direction. Hence completely stretched, oriented DNA molecules are able to reverse their direction of migration in the electric field with little or no loss of orientation. However, if the DNA molecules were not completely stretched or if the equilibrium orientation had not been reached, substantial disorientation of the DNA molecules is observed at field reversal. The forced rate of disorientation in the reversing field is faster than the field-free rate of disorientation. Complicated patterns of reorientation can be observed after field reversal, depending on the degree of orientation in the original field direction.The effect of pulsed electric fields on the orientation of the agarose gel matrix itself was also investigated. If very short pulses of high amplitude (e.g. 1-10 kV/cm in amplitude and 10-1000 μs in duration) were applied to the gel, the sign of the birefringence was small and positive, the Kerr law was obeyed, and the birefringence decayed to zero after the removal of the electric field with a relaxation time varying from 10-220 μs, depending on the length of the orienting pulse. These results indicate that individual agarose chains or bundles of chains, or dangling ends of the matrix, could be oriented by very short pulses of high amplitude. However, when smaller electric fields were used (e.g., 10-100 V/cm applied to the gel for 0.5-2 s), the amplitude of the birefringence of the gel matrix increased markedly and the signal passed through an extremum several seconds after removal of the electric field before decaying slowly to zero. These slow time-dependent effects indicate that domains in the agarose matrix were being oriented by the longer pulses used at the lower electric field strengths. The sign of the birefringence of the agarose gel could be reversed from positive to negative, or vice versa, by reversing the direction of the applied electric field, indicating that the domains apparently change their direction of orientation from parallel to perpendicular (or vice versa) after field reversal. Orientation and reorientation of microdomains of the matrix in alternating pulsed electric fields would increase the fluidity of the matrix, making it easier for very large DNA molecules to migrate through the gel during electrophoresis.

Notes: Studies of orosomucoid (α1-acid glycoprotein) in human serum have revealed that orosomucoid is a mixture of molecules with differences in the glycan chains. This microheterogeneity has been studied using crossed affinoimmuno-electrophoresis with the lectin concanavalin A which binds to biantennary glycans. The relative proportions of the three orosomucoid subtypes are altered in various pathological conditions independently of the total serum orosomucoid concentration. There are reproducible differences in microheterogeneity patterns between some pathological conditions: Acute tissue injury or inflammation results in a high proportion of orosomucoid with biantennary glycans. Conditions with increased estrogen levels are associated with a high proportion of orosomucoid with tri- or tetraantennary glycans and a low total serum orosomucoid concentration. Chronic inflammation also seems to be associated with a high proportion of orosomucoid with tri- or tetraantennary glycans but with a high total serum concentration of orosomucoid. Other diseases, such as cancer, can not be associated with any specific microhetero-geneity pattern. The microheterogeneity pattern in these conditions seems to be determined by disease activity and unspecific inflammation in surrounding tissues.

Notes: An affinity electrophoresis procedure is described for the separation and quantification of the bone- and liver-derived fractions of alkaline phosphatase in plasma. Separation is carried out on cellulose acetate membrane pre-soaked with buffer containing wheat germ lectin. The electrophoretic mobility of the bone enzyme is preferentially retarded by the lectin and this fraction is well separated from the liver fraction. After separation, enzyme activity is demonstrated by staining using an indigogenic alkaline phosphatase substrate incorporated in agar gel, and the stained fractions quantified by densitometry. The procedure has low imprecision, good linearity, and the activities of the bone and liver fractions correlate well with values obtained using nonelectrophoretic quantification methods. The procedure is especially suitable for use in the diagnostic laboratory.

Notes: For the detection of the cystic fibrosis protein (CFP) in serum of cystic fibrosis (CF) carriers, thin-layer polyacrylamide gel isoelectric focusing proved inappropriate as diagnostic test, but was useful for screening fractions on purification of CFP by chromatofocusing on a Mono P column. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis an Mr 12 000 protein (P 12) was found in most CFP-positive sera, indicating good correlation between these two CF-associated proteins. Detection of the P 12 protein by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was well reproducible and less delicate than IEF. The technique was also used to purify P 12 from serum by two successive preparative electrophoresis steps in a 7.5-15 % gradient and 15 % homogeneous gel. The use of silver staining revealed that P 12 which was present in all sera of CF patients and carriers with variable intensities, was also present in trace amounts in normal sera.

Notes: Several genetic variants and also isoforms of transferrin differing in carbohydrate structure can be separated by polyacrylamide or agarose gel isoelectric focusing. Numerous blood plasma or serum samples can be analyzed in parallel in each gel. Studies of the heterogeneity of transferrin have already revealed many results of importance to different fields of human medicine. Gene typing can give important and useful information for paternity determination and in forensic medicine. The gene type C 2 seems to have increased frequency in certain malfunctions. Furthermore, functional abnormalities of liver cells can be revealed by determination of the concentrations of transferrin isoforms differing mainly in their carbohydrate parts. The isoforms can be quantified with zone immunoelectrophoresis assay. Thus valuable information can be obtained about important modulated regulations of cell and membrane functions, even when these are disturbed by disease and xenobiotics. The information may be useful e.g. in the detection of individuals suffering from toxic effects, to identify toxic agents and exposure conditions. Studies of house painters revealed that exposure to different types of paints had an effect on transferrin. Determination of the concentration of the isotransferrin with pI 5.7 in blood samples from alcoholics can be used as a marker for the detection of liver dysfunction and for the monitoring of therapy treatments. In addition, by analyzing the isotransferrins a rare genetic abnormality can be detected.

Notes: Mitochondrial inner membrane proteins extracted from beef heart tissue were examined for reactivity to antimitochondrial antibody (AMA) present in sera of patients with primary biliary cirrhosis (PBC) by an immunoblotting technique. Four proteins, which reacted with AMA, had molecular masses of 70 kDa, 50 kDa, 47 kDa and 40 kDa, as defined by their relative mobility (Rf) in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All sera of 114 PBC patients were positive with at least one and as many as four of the mitochondrial proteins. The major antigenic proteins of mitochondrial inner membrane to which AMA reacts were the 70 kDa and 47 kDa proteins. All PBC sera containing antibodies to the 50 kDa and/or 40 kDa proteins reacted with 70 kDa as well. The isolation of antigen reacting with AMA of PBC is important to warrant further study of AMA and the cause of the disease. The isolation of responsible antigens had been difficult because the four antigens were insoluble. However, the antigen newly found by us, the 36 kDa fragment, obtained by partial trypsin digestion, is soluble. Using several procedures, the antigenic protein target of AMA was purified from mitochondria for the first time. We determined the N-terminal sequence of the soluble 36 kDa fragment, 25 residues in length. Until now the N-terminal sequence of the 36 kDa protein has not shown significant homology with any known protein. The present results of antigen purification would contribute to the elucidation of the epitopes of AMA antigen.

Notes: We have recently devised an improved procedure for the rapid electrophoretic separation of multiple forms of serum gamma-glutamyltransferase (GGT). This procedure is based on the separation on cellulose acetate strips, usually employed for lipoprotein electrophoresis, followed by visualization with a fluorescent reagent. The method is highly sensitive and the fractions are more clearly resolved than with other, procedures. Reference intervals have been evaluated in the sera from 142 healthy subjects and the patterns (two GGT forms comigrating with alpha1 and alpha2-globulin) are reproducible. In 150 sera from patients with various hepatobiliary diseases (including neoplasias), acute pancreatitis and non liver-involving neoplasias, we observed some disease-specific GGT forms: an albumin comigrating enzyme (Alb-GGT) specific of liver neoplasia; a gamma-globulin comigrating GGT (gamma-GGT) and a nonmigrating isoform (dep-GGT) both specifically associated to extrahepatic jaundice. Multiple lipoprotein fraction precipitation showed that beta-gamma- and dep-GGT are complexes between GGT and low density lipoprotein and very low density lipoproteins (LDL + VLDL), and that some of the alpha1-GGT from cirrhotic patients is a complex between GGT and high density lipoprotein (HDL). GGT fractions from normal subjects and Alb-GGT from patients with liver neoplasia do not appear to be complexed with lipoproteins. The amount of GGT complexed with LDL + VLDL differs in various hepatobiliary diseases, and using a cutoff of 20 U/L it is possible to use this test to distinguish non-cholestatic diseases from liver malignancies (i. e. in monitoring cirrhotics and other high risk groups of patients as to the possible evolution to liver cancer, in patients with gastrointestinal tumor which frequently metastasizes to the liver). Furthermore, treatment of GGT with neuraminidase confirms the association of sialic acid with all the GGT fractions, although Alb-GGT is more sensitive to this treatment than is beta-GGT. Our study, indicating the existence of clinical biochemistry correlations between isoenzyme patterns of serum GGT and diseases of hepatobiliary nature including neoplasias, opens up the possibility of enlarging the vocabulary of biochemical signals in these disorders. Furthermore, the lipoprotein-precipitated fractions of serum GGT are an additional test for discriminating hepatocarcinoma from noncholestatic chronic hepatitis and cirrhosis.