Western Blotting Using In-Gel Protein Labeling as a Normalization Control: Advantages of Stain-Free Technology

Western blotting is one of the most used techniques in research laboratories. It is popular because it is an easy way of semiquantifying protein amounts in different samples. In Western blotting, the most commonly used method for controlling the differences in the amount of protein loaded is to independently quantify housekeeping proteins (typically actin, GAPDH or tubulin). Another less commonly used method is total protein normalization using stains, such as Ponceau S or Coomassie Brilliant Blue, which stains all the proteins on the blots. A less commonly used but powerful total protein staining technique is stain-free normalization. The stain-free technology is able to detect total protein in a large linear dynamic range and has the advantage of allowing protein detection on the gel before transblotting. This chapter discusses the theory, advantages, and method used to do total protein quantification using stain-free gels for normalization of Western blots.

Benchmarking of protein carbonylation analysis in Caenorhabditis elegans: specific considerations and general advice

Oxidative stress has been extensively studied due to its correlation with cellular disorders and aging. In proteins, one biomarker of oxidative stress is the presence of carbonyl groups, such as aldehyde and ketone, in specific amino acid side chains such as lysine, proline, arginine and threonine, so-called protein carbonylation (PC). PC study is now a growing field in general and medical science since PC accumulation is associated with various pathologies and disorders. At present, enzyme-linked immunosorbent assays (ELISA) seem to be the most robust method of quantifying the presence of carbonyl groups in proteins, despite having some recognised caveats. In parallel, gel-based approaches present cross-comparison difficulties, along with other technical problems. As generic PC analyses still suffer from poor homogeneity, leading to cross-data analysis difficulties and poor results overlap, the need for harmonisation in the field of carbonyl detection is now widely accepted. This study aims to highlight some of the technical challenges in proteomic gel-based multiplexing experiments when dealing with PC in difficult samples like those from Caenorhabditis elegans, from protein extraction to carbonyl detection. We demonstrate that some critical technical parameters, such as labelling time, probe concentration, and total and carbonylated protein recovery rates, should be re-addressed in a sample-specific way. We also defined a procedure to cost-effectively adapt CyDye™-hydrazide-based protocols to specific samples, especially when the experimental interest is focused on studying differences between stimulating conditions with a maximised signal-to-noise ratio. Moreover, we have improved an already-existing powerful solubilisation buffer, making it potentially useful for hard-to-solubilise protein pellets. Lastly, the depicted methodology exemplifies a simple way of normalising carbonyl-related signal to total protein in SDS-PAGE multiplexing experiments. Within that scope, we also proposed a simple way to quantify carbonyl groups by on-gel spotting diluted dye-containing labelling buffer. Proof of the robustness of the procedure was also highlighted by the high linear correlation between the level of carbonyls and the ultraviolet exposure duration of whole worms (R²=0.993). Altogether, these results will help to standardise existing protocols in the growing field of proteomic carbonylation studies.

Quality control and stability studies with the monoclonal antibody, trastuzumab: application of 1D- vs. 2D-gel electrophoresis

Recombinant monoclonal antibodies (rmAbs) are medicinal products obtained by rDNA technology. Consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. The aim of this work was to study the suitability of gel electrophoresis for the assessment of charge heterogeneity, post-translational modifications and the stability of the therapeutic, recombinant monoclonal antibody, trastuzumab. One-dimensional, SDS-PAGE, under reducing and non-reducing conditions, and two-dimensional gel electrophoresis were used for the determination of molecular mass (Mr), the isoelectric point (pI), charge-related isoform patterns and the stability of trastuzumab, subjected to stressed degradation and long-term conditions. For the assessment of the influence of glycosylation in the charge heterogeneity pattern of trastuzumab, an enzymatic deglycosylation study has been performed using N-glycosidase F and sialidase, whereas carboxypeptidase B was used for the lysine truncation study. Experimental data documented that 1D and 2D gel electrophoresis represent fast and easy methods to evaluate the quality of biological medicinal products. Important stability parameters, such as the protein aggregation, can be assessed, as well.

Characterization of glycoprotein biopharmaceutical products by Caliper LC90 CE-SDS gel technology

Over the last decade, science has greatly improved in the area of protein sizing and characterization. Efficient high-throughput methods are now available to substitute for the traditional labor-intensive SDS-PAGE methods, which alternatively take days to analyze a very limited number of samples. Currently, PerkinElmer(®) (Caliper) has designed an automated chip-based fluorescence detection method capable of analyzing proteins in minutes with sensitivity similar to standard SDS-PAGE. Here, we describe the use and implementation of this technology to characterize and screen a large number of formulations of target glycoproteins in the 14-200 kDa molecular weight range.

Resolution-enhanced native acidic gel electrophoresis: a method for resolving, sizing, and quantifying prion protein oligomers

The formation of β-sheet-rich prion protein (PrP(β)) oligomers from native or cellular PrP(c) is thought to be a key step in the development of prion diseases. To assist in this characterization process we have developed a rapid and remarkably high resolution gel electrophoresis technique called RENAGE (resolution-enhanced native acidic gel electrophoresis) for separating, sizing, and quantifying oligomeric PrP(β) complexes. PrP(β) oligomers formed via either urea/salt or acid conversion can be resolved by RENAGE into a clear set of oligomeric bands differing by just one subunit. Calibration of the size of the PrP(β) oligomer bands was made possible with a cross-linked mouse PrP(90-232) ladder (1- to 11-mer) generated using ruthenium bipyridyl-based photoinduced cross-linking of unmodified proteins (PICUP). This PrP PICUP ladder allowed the size and abundance of PrP(β) oligomers formed from urea/salt and acid conversion to be determined. This distribution consists of 7-, 8-, 9-, 10-, and 11-mers, with the most abundant species being the 8-mer. The high-resolution separation afforded by RENAGE has allowed us to investigate distinctive size and population changes in PrP(β) oligomers formed under various conversion conditions, with various construct lengths, from various species or in the presence of anti-prion compounds.

Counterion dye staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and tryptic gel digestion of stained protein for mass spectrometry

A fast and matrix-assisted laser desorption/ionization mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet, to form an ion-pair complex. The protocol, including fixing, staining, and quick washing steps, can be completed in 1-1.5 h, depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

A single-step simultaneous protein staining procedure for polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis

A simple method for staining of proteins simultaneously on sodium dodecyl sulfate (SDS) polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis is described. A 5% solution of Alta, a commercially available cosmetic preparation, is added in the upper tank buffer during electrophoresis. On completion of electrophoresis, the gel is washed in distilled water and viewed on a white light plate and a transilluminator to photograph the protein profiles. The gel is processed for western blot transfer of proteins onto a nitrocellulose membrane, and upon completion, the protein profiles on the membrane are viewed and photographed as stated above. The membrane can then be processed for immunostaining as per the standard procedure. Thus, the staining procedure using Alta is simple, rapid (without any need of destaining), and cost-effective.

Silver staining of 2D electrophoresis gels

Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It -combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. For its use in proteomics, two important additional features must be considered, compatibility with mass spectrometry and quantitative response. Both features are discussed in this chapter, and optimized silver staining protocols are proposed.

Coomassie-Brilliant Blue staining of polyacrylamide gels

Over the past, a series of staining procedures for proteins were published. The most commonly used staining dye for proteins is still Coomassie-Brilliant Blue. The major reason is Coomassie-Brilliant Blue staining is simple, fast, and sensitive. As Coomassie-Brilliant Blue is almost insoluble in water, a series of procedures including colloidal aqueous procedures were described.

Tricine-SDS-PAGE

Tricine-sodium dodecyl sulphate-polyacrylamide gel electrophoresis (tricine-SDS-PAGE) is an efficient way of separating low-molecular-mass proteins. However, the standard system is quite complicated and specifically may not be useful when the separated proteins require to be recovered from the gel for quantitative analysis. Here, we describe a simplified system whereby these smaller proteins can be resolved in comparatively low-percentage gels which have high compatibility with modern detectors such as UV and inductively coupled plasma mass spectrometry (ICP-MS).

Accelerated Coomassie Blue staining and destaining of SDS-PAGE gels with application of heat

Coomassie Brilliant Blue is commonly used for the detection of proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, owing to its reliability and simplicity. Here, we report dramatically decreased protein staining and destaining time, as well as significantly increased detection sensitivity with the application of enhanced heat. The staining time was 5 min at 55, 62.5, or 70°C for a 1.5-mm gel, while it took 45, 45, and 20 min, respectively, for destaining. The staining time could be reduced to 1 min for a 0.8 mm gel stained at 65°C, to 2 min at 60°C and 5 min at 55°C. The destaining of proteins analyzed on a 0.8 mm gel could be accomplished in 8, 15, and 20 min at 65, 60, and 55°C, respectively. Application of heat, thus, enables proteins to be stained and destained rapidly, as well as enhancing detection sensitivity.

Diagonal electrophoresis for the detection of protein disulfides

Cysteines are one of the most rarely used amino acids in proteins, therefore when conserved in proteins they usually play critical roles in structure, function, or regulation of the protein. These cysteines or thiols can be reversibly oxidised to sulfenic acid (-SOH), thiyl radicals (-S) or nitrosothiols (-SNO) or form both inter-and intra-disulfide bridges (PSSP). The protein thiol groups PSSPs, represent a larger active redox pool than glutathione and are likely to be directly involved in cellular defence against oxidative stress. Diagonal electrophoresis is a relatively simple technique to analyze the formation of protein disulfides by sequential non-reducing/reducing electrophoresis. Proteins that do not form disulfides, electrophorese identically in both dimensions and form a diagonal after the second dimension, proteins that contained intra-chain disulfides lie above this diagonal, while those that formed inter-disulfides fall below the diagonal. This technique therefore allows for the detection and identification of protein disulfides.

International Conference on Harmonisation; Guidance on Q4B Evaluation and Recommendation of Pharmacopoeial Texts for Use in the International Conference on Harmonisation Regions; Annex 10 on Polyacrylamide Gel Electrophoresis General Chapter; availability. Notice

The Food and Drug Administration (FDA) is announcing the availability of a guidance entitled "Q4B Evaluation and Recommendation of Pharmacopoeial Texts for Use in the ICH Regions; Annex 10: Polyacrylamide Gel Electrophoresis General Chapter. The guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The guidance provides the results of the ICH Q4B evaluation of the Polyacrylamide Gel Electrophoresis General Chapter harmonized text from each of the three pharmacopoeias (United States, European, and Japanese) represented by the Pharmacopoeial Discussion Group (PDG). The guidance conveys recognition of the three pharmacopoeial methods by the three ICH regulatory regions and provides specific information regarding the recognition. The guidance is intended to recognize the interchangeability between the local regional pharmacopoeias, thus avoiding redundant testing in favor of a common testing strategy in each regulatory region. In the Federal Register of February 21, 2008 (73 FR 9575), FDA made available a guidance on the Q4B process entitled "Q4B Evaluation and Recommendation of Pharmacopoeial Texts for Use in the ICH Regions."

Evaluation of Schistosoma haematobium 27-29 kDa antigen for immunodiagnosis of schistosomiasis haematobium

The study demonstrated the immunodiagnostic potential of differrent Egyptian human Schistosoma haematobium antigens. ELISA was used to measure the levels of total immunoglobulin G (IgG) and IgG4 antibodies (Abs) against S. haematobium adult worm antigens (Ags) (SAWA), excretory/secretory Ags (E/S) and cysteine proteinase Ag (27-29 kDa) for diagnosis of schistosomiasis. SDS-PAGE profiles of S. haematobium Ags showed several bands for SAWA, E/S and 27-29 kDa Ags which are characteristic of infections with Schistosoma spp. Purified protein fraction showed a single homogenous band of 27-29 kDa. For summarizing the potency of S. haematobium Ags, sensitivety rate, negative predictive value and diagnostic efficacy were calculated between data of 40 human patients in ELISA. SAWA Ag recorded 85.0 %, 77%, 90.0% with total IgG & 90.0 %, 83% and 93.3% with IgG4 isotype, respectively. While, E/S recorded 87.5%, 80%, 92.0% with total IgG and 92.5%, 87%, 95.0% with IgG4 isotype, respectively. Purified 27-29 kDa Ag presents the higher significant (P<0.01) results recording 90.0%, 83%, 93.3% with total IgG and 97.5%, 95%, 98.3% with IgG4 isotype, respectively. The results proved that combining the detection of IgG4 isotype using the 27-29 kDa Ag in sera of schistosomiasis haematobium patients in ELISA test could represent an effective immunodiagnostic tool for detecting infection in low worm burden population. This test could be useful in sero-epidemiolocal studies in low endemic areas and in diagnosis of infection in travelers to schistosomiasis endemic areas.

Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.

Improved protein identification through the use of unstained gels

In this work, a method for improved protein identification of low-abundance proteins using unstained gels, in combination with robotics and matrix-assisted laser desorption/ionization tandem mass spectrometry, has been developed and evaluated. Omitting the silver-staining process resulted in increased protein identification scores, an increase in the number of peptides observed in the MALDI mass spectrum, and improved quality of the tandem mass spectrometry data.

Precision and variance components in quantitative gel electrophoresis

The error in quantitative gel electrophoresis/Western blotting was investigated considering the purity testing of erythropoietin. The overall error was over 35% relative standard deviation. However, an analysis of variance elucidated that the interoperator variability was the dominant error source, which already explained almost 80% of the total variance. Careful compilation and investigation of the possible error sources strongly indicates that the immunoreaction after blotting and the subsequent color reaction are the major error sources in this case.

Replaceable Cross-Linked Polyacrylamide for High Performance Separation of Proteins

An alternative sieving matrix, replaceable cross-linked polyacrylamide (rCPA), was developed for sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) separation of proteins. This rCPA could be conveniently pressurized into separation capillaries under a pressure of 80 psi. SDS-CGE separations using this matrix generated high resolutions for a wide range (approximately 4 kD to approximately 300 kD) of proteins. When compared to the most frequently used sieving matrixes, the rCPA permitted the highest resolutions with comparable or increased separation speed for protein separations.

Improved method for making nondenaturing composite gradient gels for the electrophoretic separation of lipoproteins

Nondenaturing gradient gel electrophoresis continues to be used widely for resolution and characterization of lipoprotein subclasses. Methods for making such gels in the laboratory have been published, but occasionally samples do not display uniform mobilities for all lanes in a laboratory-made gel. To help overcome this limitation, we recommend a modification

A systematic investigation into the recovery of radioactively labeled proteins from sodium dodecyl sulfate-polyacrylamide gels

We report the results of a systematic investigation designed to optimize a method for quantifying radioactivity in proteins in sodium dodecyl sulfate-polyacrylamide gels. The method involves dissolving appropriately sized pieces of gel in hydrogen peroxide and heating to 70 degrees C overnight followed by liquid scintillation counting. H(2)O(2) had no effect on the count rates of [(14)C]bovine serum albumin (BSA) when counted in a conventional liquid scintillation system, and the count rates remained stable for several days. Temperatures below 70 degrees C resulted in incomplete extraction of radioactivity from gels containing [(14)C]BSA, but there was also a significant reduction in count rates in samples incubated at 80 degrees C. At 70 degrees C recovery was not affected by the amount of sample loaded onto the gel or by the staining procedure (Coomassie Brilliant Blue or SYPRO Ruby). Recoveries were in the range of 89-94%, and the coefficient of variation for five replicate samples was 5-10%. This method offers a reliable way of measuring the amount of radioactivity in proteins that have been separated by electrophoresis. It may be useful, for example, in quantitative metabolic labeling experiments when it is necessary to know precisely how much tracer has been incorporated into a particular protein.

Highly sensitive and simple fluorescence staining of proteins in sodium dodecyl sulfate-polyacrylamide-based gels by using hydrophobic tail-mediated enhancement of fluorescein luminescence

Fluorescein has an extremely low luminescence intensity in acidic aqueous media. However, when it was bound to proteins, subsequent increase of luminescence intensity took place. Furthermore, when a hydrophobic tail, such as aliphatic hydrocarbons, was introduced to fluorescein, more dramatic increase of luminescence intensity was observed upon binding to proteins. In the present study, by utilizing this luminescence enhancement, three hydrophobic fluorescein dyes (5-dodecanoyl amino fluorescein, 5-hexadecanoyl amino fluorescein, and 5-octadecanoyl amino fluorescein) were examined as noncovalent fluorescent stains of protein bands in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Effective incorporation of the dyes to proteins in gels was accomplished either simply by adding dyes at the protein fixation step, or by treating gels with a staining solution after the fixation. The sensitivity of this staining method using the fluorescein derivatives was approximately 1 ng/band for most proteins. For some cases, protein bands containing as low as 0.1 ng were successfully visualized. In addition, the detection sensitivity showed much less protein-to-protein variation than silver staining. This new staining method was also successfully applied to two-dimensional electrophoresis of rat brain proteins. Its overall sensitivity was comparable to that of silver staining.

Ultrathin-layer sodium dodecyl sulfate disc electrophoresis of proteins in the range from 10 to 220 kDa in homogeneous, low-concentrated polyacrylamide gels

This study describes an ultrathin-layer sodium dodecyl sulfate (SDS) disc electrophoresis in polyacrylamide gels of a thickness of only 150 microm. By use of 2-amino-2-methyl-1,3-propanediol/glycine instead of traditional Tris/HCl buffer in the resolving phase of the gel, proteins with a wide range of molecular sizes (10 kDa to over 220 kDa) are separated in unusually low-concentrated gels (4%T, 3.3%C). 2-Amino-2-methyl-1,3-propanediol in the resolving part of the gel contributes to stabilization of the pH value at 8.8, while glycine improves destacking as well as separation of small proteins from the bulk of stacked SDS. This method combines both the advantages of conventional slab-gel electrophoresis and capillary gel electrophoresis. It is easy to apply and well suited for all further miniaturization attempts.

A general approach to the analysis of errors and failure modes in the base-calling function in automated fluorescent DNA sequencing

We describe the analysis of errors and failure modes in the base-calling function in automated DNA sequencing, on instruments in which fluorescently-labeled Sanger dideoxy-sequencing ladders are detected via their times of migration past a fixed detector. A general approach entails the joint use of: (i) well-defined control samples such as M13mp18, and (ii) mathematical simulation of sequencing electropherograms, with the deliberate introduction of different types of distortion and noise. An algorithm, the electrophoretic trace simulator (ETS), is used to calculate electrophoresis traces corresponding to the output data stream of an automated fluorescent DNA sequencer. The ETS accepts a user-defined sequence of nucleotide bases (A, C, G, T) as input, and employs user-adjustable functions to compute the following critical parameters of an electropherogram: peak intensity, peak spacing, peak shape as a function of base number; background, noise, and spectral cross-talk correction (for a sequencer using multiple dyes). We use a combination of M13mp18 controls and simulated electropherograms to analyze two problems of considerable practical importance: (i) variation in electrophoretic migration rates between different lanes of a gel, and (ii) variation in signal intensity due to user-dependent loading artifacts. The issue of base-calling errors and failure modes, for electropherograms that contain noise and distortion, is addressed.

Increasing the sensitivity of single-strand conformation polymorphism analysis of the LDLR gene mutations in brazilian patients with familial hypercholesterolemia

Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), one of the most common single gene disorders. It is thought that FH affects approximately 1 of 500 individuals in most populations. Single-strand conformation polymorphism (SSCP) analysis is widely used to detect mutations in the LDLR gene. However, several factors such as temperature, pH, running time, gel composition and size of the DNA fragments can influence its sensitivity. We have optimized the electrophoretic conditions to screen mutations in the promoter region and exons 1-18 of the LDLR gene by varying temperature (5 degrees C, 8 degrees C, 12 degrees C and 15 degrees C), voltage (300 to 600 V), and running time (1 to 4 hours) in the semi-automated GenePhor system (Amersham Biosciences). The efficiency of the method was evaluated by using 30 positive controls (DNA samples with mutations and polymorphisms in the LDLR gene, previously characterized) and DNA samples from 90 Brazilian patients with FH. Our results show that the use of two temperatures (5 degrees C and 15 degrees C) in combination with other optimized conditions resulted in high mutation detection rate (97%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for the diagnosis of genetic disorders, cancer, and for pharmacogenetic studies.

Ammonium dodecyl sulfate as an alternative to sodium dodecyl sulfate for protein sample preparation with improved performance in MALDI mass spectrometry

Sodium dodecyl sulfate (SDS) is a strong surfactant that is widely used in protein sample preparation. While protein and peptide samples containing up to approximately 1% SDS can be analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) using a two-layer matrix/sample deposition method, the presence of SDS in a protein sample generally degrades mass resolution and mass measurement accuracy. This degradation in performance is found to be related to the formation of sodium-protein adducts in the MALDI process. If the instrument resolving power is insufficient to separate these adduct peaks from the protonated molecular ion peak, peak broadening is observed in the protein molecular ion region, and as a result, the peak centroid shifts to a higher mass. In this work, we present a method using ammonium dodecyl sulfate as a viable alternative to SDS for protein sample preparation with much improved MALDI MS performance. Three non-sodium-based dodecyl sulfate surfactants, ammonium dodecyl sulfate (ADS), hydrogen dodecyl sulfate, and tris(hydroxymethyl)aminomethane dodecyl sulfate were investigated. Of the three surfactants tested, it is found that ADS gives the best performance in MALDI. For proteins with moderate molecular masses (i.e., up to approximately 25 kDa), the presence of ADS in a protein sample does not result in significant degradation in mass resolution and accuracy, and the protonated molecular ion peak is the dominant peak in the MALDI spectrum. The ammonium adduct ions dominate the MALDI spectra when the protein mass exceeds approximately 25 kDa; however, ADS still gives better results than SDS. The behavior of ADS in gel electrophoresis was also investigated. It is shown that cell extracts dissolved in ADS can be separated by normal SDS-polyacrylamide gel electrophoresis by simply mixing them with the SDS sample buffer. The application of ADS as the surfactant for protein solubilization with improved performance in MALDI analysis is demonstrated in the study of a detergent insoluble fraction from a Raji/CD9 B-cell lymphocyte lysate.

Standardization of denaturing gradient gel electrophoresis for mutant screening of influenza A (H3N2) virus samples

Because of the extensive genetic variability of the influenza viruses, new virus mutants arise worldwide. In the human population, some strains may become potentially epidemic after evading the immune response of the host. At present, molecular methods have made it possible to identify these variants. However, if a large number of samples need to be analyzed the identification of randomly mutated nucleotides cannot be achieved by sequencing analysis or restriction fragment length polymorphism (RFLP). In order to improve this process, a denaturing gradient gel electrophoresis (DGGE) protocol capable of discriminating between reference strains representative of different influenza seasons, some mutant strains, and five clinical isolates was standardized Ribonudeic acid (RNA) was isolated and submitted to a one-step RT-PCR that amplified the region codifying for the globular domain of the Haemagglutinin (HA) molecule. The amplicons were analyzed by electrophoresis in 6% polyacrylamide gel at 60 degreeC/150 V for 8 h, using a 31--41% urea--formamide gradient. This method was able to distinguish between closely related nucleotide sequences, confirming its suitability as screening methodology for the analysis of influenza virus epidemiology, by allowing a faster and more extensive evaluation of a large number of the variant strains detected in a specific region of the world.

Effects of high-molecular-mass substrates on protein migration during sodium dodecyl sulfatepolyacrylamide gel electrophoresis

Substrate-sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has become a popular procedure for the separation and identification of active fractions present in enzyme mixtures due to its relative simplicity. Procedures including high-molecular-mass substrates within the gel, such as starch for identification of amylase activity, and protein substrates, including gelatin, casein, and collagen, for revealing protease activity, have been described. SDS-PAGE separation under denaturing conditions is dependent on the molecular mass of the proteins and on the effective pore size of the gels, the last factor being affected by the inclusion of high-molecular-mass substrates into the polyacrylamide matrix. In order to quantify the effect of the addition of increasing concentrations of such substrates on protein migration, starch, gelatin, and casein were included in gels in which polyacrylamide concentration was kept constant. High-molecular-mass substrates decreased migration of proteins ranging from 6.5 to 205 kDa, although the migration pattern, and thereby the accuracy of the assignation of relative molecular masses to proteins separated on those gels, was practically unaffected. The substitution of glycine, as the carrying ion, by Tricine in denaturing electrophoresis buffer systems resulted in an improvement of the migration of proteins in substrate-containing gels. Results suggested that zymograms including substrates remain a valuable procedure for the separation and the relative molecular mass assignation of active enzyme fractions.

Evaluation of peptide electropherograms by multivariate mathematical-statistical methods. I. Principal component analysis

Depository effects in slowly metabolised proteins, typically glycation or the estimation of products arising from the reaction of unsaturated long-chain-fatty acid metabolites (possessing aldehydic groups) are very difficult to assess owing to their extremely low concentration in the protein matrix. In order to reveal such alterations we applied deep enzymatic fragmentation resulting in a set of small peptides, which, if modified, are likely to change their electrophoretic properties and can be visualised on the resulting profile. Peptide maps of collagen (a mixture of collagen types I and III digested by bacterial collagenase) were applied as the model protein structure for detecting the nonenzymatic posttranslational changes originating during various physiological conditions like high fructose diet and hypertriglyceridemic state. Capillary electrophoresis in acidic media (sodium phosphate buffer, pH 2.5) was used as the separation method capable of (partial) separation of over 60 peptide peaks. Two to 13 changes were revealed in the profiles obtained reflecting the physiological conditions of the animals tested. Combination of peptide profiling with subsequent t-test evaluation of individual peak areas and principal component analysis based on cumulative peak areas of individual sections of the electropherograms allowed to determine in which section (part) of the electropherogram the physiological state indicating changes occurred. Simultaneously it was possible to reveal the qualitative differences between the four physiological regimes investigated (i.e., which regime affects the collagen molecules most and which affects them least). The approach can be used as guidance for targeted preseparation of the very complex peptide mixture.

Improvement of base-calling in multilane automated DNA sequencing by use of electrophoretic calibration standards, data linearization, and trace alignment

We present a new method for the linearization and alignment of data traces generated by multilane automated DNA sequencing instruments. Application of this method to data generated with the Visible Genetics Open Gene DNA sequencing system (using MicroCel 700 gel cassettes, with a 25 cm separation distance) allows read lengths of > 1,000 nucleotides to be routinely obtained with high confidence and > 97% accuracy. This represents an increase of 10-15% in average read length, relative to data from this system that have not been processed in the fashion described herein. Most importantly, the linearization and alignment method allows usable sequence to be obtained from a fraction of 10-15% of data sets which, because of original trace misalignment problems, would otherwise have to be discarded. Our method involves adding electrophoretic calibration standards to the DNA sequencing fragments. The calibration standards are labeled with a dye that differs spectrally from the dye attached to the sequencing fragments. The calibration standards are identical in all the lanes. Analysis of the mobilities of the calibration standards allows correction for both systematic and random variation of electrophoretic properties between gel lanes. We have successfully used this method with two-dye and three-dye DNA sequencing instruments.

RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month.

Urine protein analysis by gel electrophoresis and laser densitometry after chemotherapy in pediatric cancer patients

A common side effect of chemotherapy is reversible or nonreversible nephrotoxicity. SDS polyacrylamide gel electrophoresis combined with laser densitometry was evaluated as a suitable method to analyze pathologic urine proteins. A total of 52 pediatric patients were followed during and 63 patients were followed after therapy. During therapy renal damage was recorded in 43% of the leukemia patients, in 56% of nephroblastoma patients, and 75% of patients with other tumors. Three or more months after therapy pathologic patterns were seen in 25% of acute lymphoblastic leukemia patients, in 35% of patients with nephroblastoma, and in 62% of other patients. Patients with persistent complete tubular proteinuria and mixed glomerular/tubular proteinuria were found to have a high risk for irreversible renal damage and should be controlled periodically. This method permits a rapid and reliable analysis of urine proteins and is suitable for follow-up tests of renal function during and after chemotherapy.

SDS-electrophoresis of unconcentrated urine samples using a semi-automatic method

The study of urinary proteins is an important tool in the screening and diagnosis of patients with renal impairment. Quantification of total proteins, although useful, can provide only limited information. Gel electrophoresis of urine samples may provide more detailed information.

Preparative application of commercial automated gel electrophoresis apparatus to subcellular-sized particles: sequential isolations, fractions re-run, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, yield and purity

The analytical and preparative potential of automated gel electrophoresis apparatus with intermittent fluorescence scanning of the migration path, the HPGE-1000 apparatus (LabIntelligence, Belmont, CA) was further developed in application to subcellular-sized particles. Resolution between two rat liver microsome components in agarose (MetaPhor) gel electrophoresis was found to increase with decreasing agarose concentration to 0.04%. It was less, even in an agarose solution at that low concentration, than that in laterally aggregated 4% polyacrylamide gel. The three components of the microsomal preparation were sequentially isolated from 0.6 and 0.8% agarose gel electropherograms. One fraction when re-electrophoresed was found to exhibit the original mobility and did not give rise to the other components. Yields of each component were near-quantitative after one or two electroelution steps. Based on protein content, no impurities could be detected in two of the microsome fractions; the third fraction contained 2% of nonmicrosome impurity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of all three microsome fractions were indistinguishable from one another and from that of the unfractionated microsome preparation.

Standardization of procedures of Plasmodium falciparum antigen preparation for serologic tests

The objective of the present study is to standardize the technical variables for preparation and storage of Plasmodium falciparum and of antigen components extracted with the amphoteric detergent Zwittergent. P. falciparum obtained from in vitro culture was stored at different temperatures and for different periods of time. For each variable, antigen components of the parasite were extracted in the presence or absence of protease inhibitors and submitted or not to later dialysis. Products were stored for 15, 30 and 60 days at different temperatures and immunological activity of each extract was determined by SDS-PAGE and ELISA using positive or negative standard sera for the presence of IgG directed to blood stage antigens of P. falciparum. Antigen extracts obtained from parasites stored at -20 degrees C up to 10 days or at -70 degrees C for 2 months presented the best results, showing well-defined bands on SDS-PAGE and Western blots and presenting absorbance values in ELISA that permitted safe differentiation between positive and negative sera.

Standardization and clinical management of lipoprotein(a) measurements

The present article proposes personal suggestions to improve determinations and clinical interpretation of results of lipoprotein(a) assays. Methods and procedures for sampling and quantification of the various isoforms of lipoprotein(a) in serum, plasma and urine are reviewed with the aim of improving the reliability and reproducibility of results and reinforcing the clinical utility of lipoprotein(a) measurements.

High-efficiency blotting of proteins of diverse sizes following sodium dodecyl sulfate-polyacrylamide gel electrophoresis

High-molecular-weight proteins often blot onto nitrocellulose membranes poorly following sodium dodecyl sulfate-polyacrylamide gel electrophoresis, resulting in low levels of detection on immunoblots, and hence difficulty in analyzing rare proteins. Moreover, optimizing conditions for the transfer of high-molecular-weight proteins to nitrocellulose frequently results in the inefficient transfer or loss of lower molecular weight proteins. This problem is particularly vexing during the analysis of large proteins which may be processed to one or more smaller biologically active forms. Using radiolabeled protein standards and phosphorimaging technology, we have quantitated the efficacy of many different protein gel electrophoresis and blotting protocols. Here we report novel gel and blotting conditions which significantly improve the transfer and retention of high-molecular-weight proteins, without sacrificing the efficient transfer of lower molecular weight proteins. Using this newly described procedure, we have detected a rare 500-kDa protein in immunoblots which was previously not detectable with any of the commonly used blotting procedures. Since the improved conditions offer increased sensitivity across a spectrum of protein sizes, they should be widely applicable.

Development and standardization of solid phase assays for the detection of anti-neutrophil cytoplasmic antibodies (ANCA). A report on the second phase of an international cooperative study on the standardization of ANCA assays

Anti-neutrophil cytoplasmic antibodies (ANCA) are diagnostic markers for systemic vasculitis. They are classically detected by an indirect immunofluorescence test using normal donor neutrophils as substrate. This assay lacks antigenic specificity and is not quantitative. The 'EC/BCR Project for ANCA Assay Standardization' is an international collaboration study with the aim to develop and standardize solid phase assays for ANCA detection. In this part of the study the isolation and characterization of proteinase-3 and myeloperoxidase, the two main target molecules for ANCA, and the development and standardization of ELISAs with these antigens are described. Six laboratories successfully isolated purified proteinase-3 preparations that could be used. Three of these preparations, together with one myeloperoxidase preparation, were subsequently used for ANCA testing by ELISA. The ELISA technique was standardized in two rounds of testing in the 14 participating laboratories. The coefficient of variation of these new assays decreased from values of approx. 50% in the first round to approx. 20% in the second round. We conclude that purified proteinase-3 and myeloperoxidase can be used in standardized ELISAs for ANCA detection. Whether such procedures offer advantages over the IIF test will be determined in a prospective clinical study.

Subtyping of Bacillus cereus by total cell protein patterns and arbitrary primer polymerase chain reaction

Bacillus cereus is a ubiquitous sporeforming Gram-positive rod that is associated with foodborne outbreaks as well as several opportunistic infections. Inspite of the prevalence of B. cereus associated foodborne outbreaks, subtyping of the species using molecular typing assays was not attempted. In this study we have recovered 58 B. cereus isolates from natural and clinical sources and initially characterized them, along with a B. cereus strain (ATCC 14579) and B. thuringiensis natural isolate, by biotyping, antibiotic susceptibility testing, and SDS-PAGE of total cell proteins. Our data have shown the existence of 1 biotype, 3 anti-biograms and 22 (38%) total cell protein patterns among the 58 B. cereus isolates. B. thuringiensis had a different protein pattern. SDS-PAGE of total cell proteins data denote clonal heterogeneity within B. cereus. Protein pattern 4 (pp4) was the most predominant with 13 isolates of B. cereus showing this pattern. Eight out of the 13 isolates with pp4 and one B. cereus strain (ATCC 14579) were further subtyped by using the arbitrary primer polymerase chain reaction (AP-PCR) assay. Eight (88.8%) different PCR patterns out of the 9 B. cereus isolates were obtained. Patterns obtained by SDS-PAGE of total cell proteins and AP-PCR were reproducible. These results indicate that SDS-PAGE of total cell proteins allows the differentiation among species within Bacillus and of strains within B. cereus. The typability of the method was 100% and the simpson's discrimination index of diversity was 98%. The utility of SDS-PAGE of total cell proteins in a pilot epidemiologic study was assessed and results obtained demonstrate its typing potential. AP-PCR allows further subtyping of the species. Both methods if used in conjunction may be useful for further clinical and epidemiologic studies of the spectrum of diseases caused by B. cereus.

DNAOPT: a computer program to aid optimization of DNA gel electrophoresis and SDS-PAGE

Several methods and computer programs have been developed for estimating the size of DNA fragments from gel electrophoresis. However, methods are lacking that may facilitate in optimization of gel conditions. In this article, a computer program called DNAOPT is described, which was developed to assist researchers in tuning the gel conditions of gel electrophoresis. The DNAOPT program fits the reciprocal of the migration distance vs. the size of the DNA fragments using the hyperbolic regression method and computes the hyperbolic parameters such as signal, flatness and capacity (optimization parameters). The program further manipulates these parameters obtained by running gel electrophoresis under various conditions (i) to determine the relationship between the gel conditions (temperature, buffer concentration, electric field strength, etc.) and optimization parameters; (ii) to demonstrate gel electrophoresis curves and optimization parameters graphically; and (iii) to represent the optimizing parameters at different gel conditions in tabular form. The above-mentioned program options aid the users in selecting optimum gel conditions by running the gel repeatedly under various conditions in which the agarose concentration, electric field strength, temperature, buffer concentration and so on are varied in a systematic way for each set of gel conditions. Similarly, this program can also be used to optimize gel conditions of sodium dodecyl sulfate polyacrylamide gel electrophoresis.

Multiple fluorescence-based PCR-SSCP analysis

Multiple fluorescence-based polymerase chain reaction single-strand conformation polymorphism (MF-PCR-SSCP) was developed. The target sequence was amplified by PCR using forward and reverse primers labeled with two different fluorescent dyes at their 5' ends. The amplified products were then heat-denatured, mixed with internal standard DNA markers labeled with a third fluorescent dye and applied to a temperature-controlled gel in an automated DNA sequencer, with a gel-temperature-controlling system. Mutations were detected as positional shifts of two-colored peaks in the electrophoretogram. The image data were analyzed by the computer program GENESCAN 672. The peak positions were standardized to internal DNA size markers. MF-PCR-SSCP analysis of 7 human tumor cell lines with 7 different single base mutations of the human K-ras oncogene detected all mutations even under the same electrophoresis conditions. Complete loss of heterozygosity was detected in two cell lines simultaneously. A gel temperature at 20 degrees C and polyacrylamide concentration of 10% gave the best separation. MF-PCR-SSCP is superior to the current PCR-SSCP in several ways: it does not involve radioactivity, migration patterns are standardized to internal standard DNA markers, there is a strict temperature-controlling system and the higher percentage of the gel enables better separation with resultant 100% detection of mutations most likely under one set of electrophoresis conditions.

Our obsession with high resolution in gel electrophoresis: does it necessarily give the right answer?

Poor resolution of protein zones in an electrophoretic pattern may not necessarily be the result of poor technique. The example is given of the 'streak material', extracted from wheat flour, now recognised to be aggregated subunits of glutenin. The size distribution of the aggregated glutenin 'streak' is the key to elucidating the functional properties of wheaten dough. A stepped-layer gel technique has been devised to quantitate the proportions of aggregated glutenin in specific size groupings.

Electrophoretic artifacts arising from the use of thiol-containing reagents

Thiol reagents migrate as a curtain behind the salt front when loaded with the sample solution onto disc-electrophoresis gels. In immobilized pH gradients (IPG) the same compounds are driven by electrophoresis and electroosmosis from the alkaline to the neutral and acidic regions of the gradients. In either case, a dose-dependent sideways spreading results in spurious reduction between adjacent lanes if samples with and without reducing agent are loaded side by side.

Preliminary treatment of urinary proteins improves electrophoretic analysis and immunodetection

Analysis of urinary protein composition is an important tool in studies on renal physiology and physiopathology. Urine is, however, a complex mixture containing, besides protein, a variety of compounds such as salts, peptides, oligosaccharides, and glycosaminoglycans. Some of these compounds interfere with the electrophoretic migration of protein in sodium dodecyl sulfate-polyacrylamide gels and prevent correct analysis of the protein pattern. We describe a simple method for extracting urinary proteins that considerably improves their electrophoretic migration and subsequent immunodetection. This treatment involves ammonium sulfate fractionations (for precipitating proteins), EDTA (for inhibiting protein aggregation), and HCl hydrolysis (for removing glycosylaminoglycans). Recovery during extraction was found to be almost quantitative for total protein and three representative proteins: albumin, alpha 1-glycoprotein acid, and beta 2-microglobulin.

pMCT 118 (D1S80): a new allelic ladder and an improved electrophoretic separation lead to the demonstration of 28 alleles

Population data studies carried out on caucasians from Northwest Germany (n = 218) using the AMPFLP system pMCT 118 (D1S80). The method used in a previous study (Rand et al. 1992) for pMCT 118 could be improved by increasing the electrophoretic separation length from 10 to 20 cm and by using an extended allelic ladder which allowed the distinction of 8 additional alleles (a total of 28 alleles). Out of the 8 additional alleles 5 could be differentiated which differed within the 16 bp repeat sequence. The allele frequencies found were compared to population data from American caucasians, Hispanics and black Americans (Eisenberg and Maha 1991). All populations with the exception or black Americans, showed good agreement.