Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input, HYDROID requires polyacrylamide gel electrophoresis (PAGE) images of HRF products and optionally can use a molecular model of the DNA-protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition, it can be applied to the analysis of RNA-protein complexes and free RNA or DNA molecules in solution. Compared with other methods reported to date, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available. The complete protocol takes ~3 h. Users should be familiar with the command-line interface, the Python scripting language and Protein Data Bank (PDB) file formats. A graphical user interface (GUI) with basic functionality (HYDROID_GUI) is also available.

SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit

The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10% polyacrylamide gel, 60-90 min at constant 900 V at 5 degrees C) resulted in a high polymorphism detection rate (95.3%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.

Modeling ssDNA electrophoretic migration with band broadening in an entangled or cross-linked network

We use a coarse-grained model proposed by Graham and Larson based on the temporary network model by Schieber et al.. [1] to simulate the electrophoretic motion of ssDNA and corresponding band broadening due to dispersion. With dimensionless numbers reflecting the experimental physical properties, we are able to simulate ssDNA behavior under weak to moderate electric field strengths for chains with 8-50 entanglements per chain ( approximately 1000-8500 base pairs), and model smoothly the transition from reptation to oriented reptation. These results are fitted with an interpolation equation, which allows the user to calculate dimensionless mobilities easily from input parameters characterizing the gel matrix, DNA molecules, and field strengths. Dimensionless peak widths are predicted from mobility fluctuations using the central limit theorem and the assumption that the mobility fluctuations are Gaussian. Using results from previous studies of ssDNA physical properties (effective charge xiq and Kuhn step length b(K)) and sieving matrix properties (pore size or tube diameter a), we give scaling factors to convert the dimensionless values to "real" experimental values, including the mobility, migration distance, and time. We find that the interpolation equation fits well the experimental data of ssDNA mobilities and peak widths, supporting the validity of the coarse-grained model. The model does not account for constraint release and hernia formation, and assumes that the sieving network is a homogeneous microstructure with no temperature gradients and no peak width due to injection. These assumptions can be relaxed in future work for more accurate prediction.

Model carbyne knots vs ideal knots

The structure and stability of model carbyne knots built from 60 to 120 carbon atoms with 0, 3, 4,., 7 crossings have been estimated by semiempirical AM1 calculations. The calculations have shown an increase of the knot-cycle energy difference (deltaE) with an increasing number of knot crossings and a decrease of deltaE with an increasing number of atoms constituting the molecule. The deltaE changes nonlinearly with the characteristics of the corresponding ideal knots such as the average crossing number (ACN) and the length-to-diameter ratio (L/D). The molecular mechanic strain energy of carbyne knots correlates similarly with ACN and L/D of ideal knots. The calculated energy of the model carbyne knots correlates also with the electrophoretic mobility or sedimentation coefficient of DNA knots. Thus, similarly to characteristics of ideal knots, the energy of carbyne knots is a rather easily available parameter which can be used for further correlations with some characteristics of DNA knots.

SDS-PAGE is underutilized as a tool for investigating renal patients

SDS-PAGE is an excellent single test for investigating proteinuria. It can provide much useful information on the underlying renal problem. Yet the literature hardly report a SDS-PAGE result in the management of renal patients. To examine how closely SDS-PAGE results may reflect biopsy findings, we investigated 11 patients scheduled for renal biopsy. Urine samples were taken at the same time for SDS-PAGE analysis using the PhastSystem (Pharmacia, Sweden). Comparing biopsy findings and SDS-PAGE results, the data show consistency in the revelation of tubular dysfunction and/or glomerular damage in all 11 patients. We concluded that the SDS-PAGE test is underutilized and suggest that its role for the management of renal patients be fully explored particularly in its potential for reducing the need for renal biopsy in certain patient groups.

Automated detection of differently expressed fragments in mRNA differential display

We present a novel method for the automated detection of fragments showing dissimilar expression in mRNA differential display. The analysis is based on aligning the numerical electrophoretic lane data in respect of a given distance function defined on a set of fragments, or signal peaks in general. We presume that significant dissimilarities between peaks result in extreme score values computed for aligned peak pairs. Whereas in sequence comparison, an overall sequence similarity score is conventionally used, the current method defines a special dissimilarity score for searching the peak pairs showing the largest relative differences between the lanes. The output of the analysis is a highly reduced list of peak pairs, along with a set of associated features extracted from the lanes. Only the peaks of this list need to be visually confirmed instead of the vast amount of peaks in the original electrophoretic results. The results obtained by the algorithm correlate well with results of visual evaluation of the same electropherograms. The current algorithm may be applied to the study of complex expression patterns in multiple lanes and, in general, to automated recognition of variously defined patterns of quantitative electrophoretic data.

The use of polyacrylamide gel electrophoresis in animal systematics, phylogeny, and ecophysiology

In the 1980s, the use of polyacrylamide gel electrophoresis (PAGE) was popular. But more recent developments in other electrophoretic techniques have resulted in this method being less widely used. However, it is adequate for the needs of naturalists for issues which do not require high-performance methods, such as in systematics, phylogeny, studies of intraspecific or clinal variability, ecology and ecophysiology. We illustrate the application of PAGE by the results of a research program on marine and terrestrial invertebrates which was conducted from 1979 to 1992, but which is still used to initiate graduate students to the research. Thus, issues faced by the zoologist can be clarified by this method, not yet obsolete and still useful in natural history despite considerable advances in other electrophoretic methods.

Identification of human lung and skin proteins conjugated with hexamethylene diisocyanate in vitro and in vivo

Diisocyanates are asthma-causing chemicals used in the commercial production of polyurethane. We have previously shown that human lung epithelial cell proteins can become conjugated with hexamethylene diisocyanate (HDI) and may be biologically important in diisocyanate-induced asthma. The objective of this study was to identify specific human lung and skin proteins that become conjugated with diisocyanate after in vitro and in vivo exposure. Following in vitro exposure of human airway epithelial cells (A549), keratin 18, the 78-kD glucose-regulated protein, trans-1, 2-dihyrobenzene-1,2-diol dehydrogenase, and actin were identified as prominent diisocyanate-conjugated proteins through use of a combination of immunocytochemical and mass spectrometric techniques. Following in vivo inhalation of an HDI aerosol, keratin 18 was also identified as the predominant diisocyanate-conjugated protein in human endobronchial biopsy samples, whereas albumin was the predominant diisocyanate-conjugated protein in bronchoalveolar lavage fluid. Keratin was also identified as a predominant diisocyanate-conjugated protein in human skin biopsy samples after epicutaneous exposure to liquid-phase HDI, although the major skin diisocyanate-conjugated protein (56-kD) differed from the predominant lung diisocyanate-conjugated keratin (47-kD). The data from this study identify keratin and other proteins as potential "carriers" for diisocyanates in vivo, and suggest that HDI conjugation of these proteins may play a role in the pathogenesis of diisocyanate-induced asthma.

[An assessment of the degree of chromophore photo damage to the heme and globin components in UV-irradiated molecules and electrophoretic fractions of human carboxyhemoglobin]

The contribution of hem and globin components of electrophoretic fractions of UV-irradiated human carboxyhemoglobin to photodestruction of the protein was studied. The changes observed are the result of summation of some processes unequal in intensity and direction that take place in microheterogeneous media of photomodified protein. Photosensitivity of hemoproteid in electrophoretic fraction depends on apoprotein condition, whereas the hem photoresistance cannot be the evidence of the photostability of the whole molecule.

Precipitation of specific proteins by freeze-thawing of human saliva

Frozen saliva samples demonstrate a variable amount of precipitate on thawing depending on the type of secretion [submandibular-sublingual (SML) greater than parotid]. This precipitate has been resuspended using EDTA or removed by centrifugation by some workers and others do not mention it. Yet others collect the salivas into EDTA or centrifuge them before freezing. To determine the adsorption of proteins to hydroxyapatite, prior treatment with EDTA would be disadvantageous. The aim here was to determine if the protein pattern in parotid and SML saliva as demonstrated by sodium dodecyl sulphate gel electrophoresis is affected by the formation of precipitates. Portions of parotid and SML saliva were thawed and treated in the following ways: (a) mixed vigorously with a vortex mixer; (b) centrifuged to remove the precipitate; (c) mixed with EDTA (1 and 5 mmol final concentration for parotid and SML samples, respectively) to resuspend the precipitate. The samples were loaded on to gradient (5-20%) SDS gels and, following electrophoresis, the gels were stained with Coomassie brilliant blue R-250. The protein patterns obtained for (a) and (c) were the same. The centrifuged samples demonstrated loss of a specific band of less than 14 kDa, although this was less obvious in the parotid samples. The SML samples also showed a reduction in other lower molecular-weight proteins. This study demonstrates that precipitates in thawed frozen salivas contain specific proteins and that these samples require careful handling to avoid any alteration in the overall protein composition.

[The genetic interpretation of the electrophoregrams of the helianthin in F1 sunflower seeds]

It has been shown, that in most cases the fertile plants of maternal line and F1 plants of respective hybrid are present among sterile plants of sunflower female lines in crossing plots. As a result, 16 various genotypes of seeds are ascertained in crossing plots at monogenic differences in marker trait. Only two classes are F1 seeds. In such cases specific share of 5 genotype groups may be distinguished by phenotypes of heliantin electrophoregrammes. Seeds of biological admixture may be attributed to the 6th distinguishing type.

[A comparison of the yield of Vi and O antigens during the adaptation of Salmonella typhi strains to cultivation under starvation conditions]

S. typhi strains Ty(2)4446 and Vi-1S underwent multiple passages in f synthetic liquid starvation culture medium consisting of water with salts and glucose added. In the process of the adaptation of the cultures to these stress conditions (starvation stress) the increasing yield of biomass from passage to passage was observed. Differences in the accumulation of Vi- and O-antigens were noted in two strains under study. In the cultures of strain Ty(2)4446 an insignificant increase in the antigen content from passage to passage was observed, while in the cultures of strain Vi-1S an increase in the content of Vi- and O-antigens was 4- to 5-fold. With the adaptation of the culture the Vi-antigen to O-antigen ratio changed from 1:57 to 1:20 for strain Ty(2)4446 and from 1:2.7 tp 1:2.2 for strain Vi-1S. Strain Ty(2)4446 had an advantage over strain Vi-1S with respect to the synthesis of Vi-antigen. These data are indicative of the expediency of using not only strain Ty(2)4446, but also strain Vi-1S for the preparation of typhoid vaccine, especially the one based on Vi-antigen.

Cysteine protease inhibitory activity and levels of salivary cystatins in whole saliva of periodontally diseased patients

The 3 human salivary cystatins S, SA and SN are multifunctional proteins that possess a cysteine protease inhibitory property, but their ability to act as such is very different (SN > SA >> S). One form, S, also appears to possess antibacterial properties towards the bacterium Porphyromonas gingivalis, often associated with periodontal diseases. In this study we measured the total cystatin inhibitory activity and the levels of each salivary cystatin in the whole saliva of 8 periodontally diseased patients and 2 groups of control subjects (n = 6 and n = 10). The total cystatin inhibitory activity and the total salivary cystatin concentration in the periodontally diseased patients were found to be lower than the controls (p < or = 0.005). The concentration of S was depleted to levels that would not allow it to be an effective antibacterial agent, and the concentration of SA, although depleted in some cases, was still present at sufficient levels to allow it to act as an effective physiological inhibitor of cathepsin L. The concentration of cystatin SN was also depleted in the periodontally diseased patients, but was still present in sufficient quantities to act as an effective physiological cysteine protease inhibitor of cathepsins H and L. In comparison, the concentration of all 3 salivary cystatins in the control subjects were sufficient to enable these proteins to be both effective physiological cysteine protease inhibitors and antibacterial agents.

Capsaicin induces cystatin S-like substances in submandibular saliva of the rat

Irritating dietary substances such as tannin and papain have been reported to alter the morphology of salivary glands and their secretions. Such alterations can be one line of protection from toxic or irritating substances in food. We investigated the effects of dietary capsaicin (a pungent ingredient of hot red pepper) on the rat submandibular gland and its secretions. Several groups of animals were offered either control diets or diets containing capsaicin (from 0.0001 to 0.1%) for seven days. Higher concentrations suppressed food consumption for two days, after which only the highest concentration continued to reduce intake. The relative weight of the salivary glands in capsaicin-diet groups increased in a dose-dependent fashion, and new proteins appeared in the submandibular saliva. Chromatographic and electrophoretic properties of these proteins were identical or similar to those of isoproterenol-induced proteins. After affinity chromatography of the new protein fraction on a Cm-papain Sepharose 4B column, SDS-electrophoresis of the eluate revealed three major bands (15,500, 16,500, and 28,000 kDa). Hydrolysis of N-benzoyl-D,L-arginine-p-nitroanilide by papain (a cysteine protease) decreased in the presence of the new protein fraction, suggesting that these proteins have cystatin-like activity (inhibition of cysteine protease). Denervation of the glossopharyngeal nerve suppressed induction of these proteins. The results suggest that dietary capsaicin induces cystatin S-like substances in submandibular saliva by stimulating the reflex arc involving the glossopharyngeal nerve. These proteins likely facilitate ingestion of diets containing the irritating substance.

Abnormal NF-kappa B activity in T lymphocytes from patients with systemic lupus erythematosus is associated with decreased p65-RelA protein expression

Numerous cellular and biochemical abnormalities in immune regulation have been described in patients with systemic lupus erythematosus (SLE), including surface Ag receptor-initiated signaling events and lymphokine production. Because NF-kappa B contributes to the transcription of numerous inflammatory genes and has been shown to be a molecular target of antiinflammatory drugs, we sought to characterize the functional role of the NF-kappa B protein complex in lupus T cells. Freshly isolated T cells from lupus patients, rheumatoid arthritis (RA) patients, and normal individuals were activated physiologically via the TCR with anti-CD3 and anti-CD28 Abs to assess proximal membrane signaling, and with PMA and a calcium ionophore (A23187) to bypass membrane-mediated signaling events. We measured the NF-kappa B binding activity in nuclear extracts by gel shift analysis. When compared with normal cells, the activation of NF-kappa B activity in SLE patients was significantly decreased in SLE, but not in RA, patients. NF-kappa B binding activity was absent in several SLE patients who were not receiving any medication, including corticosteroids. Also, NF-kappa B activity remained absent in follow-up studies. In supershift experiments using specific Abs, we showed that, in the group of SLE patients who displayed undetectable NF-kappa B activity, p65 complexes were not formed. Finally, immunoblot analysis of nuclear extracts showed decreased or absent p65 protein levels. As p65 complexes are transcriptionally active in comparison to the p50 homodimer, this novel finding may provide insight on the origin of abnormal cytokine or other gene transcription in SLE patients.

Multiple forms of the major phenylalanine specific protease in Treponema denticola

The 160, 190 and 270 kDa outer sheath proteases of Treponema denticola ATCC 35404 were found to be multiple forms of the major 91 kDa phenylalanine protease (PAP) by immunoblotting using anti-91 kDa specific antibodies. Multiple forms of the phenylalanine protease were also found in 2 other T. denticola strains studied, ATCC 33520 and the clinical isolate GM-1. Protein, proteolytic and Western blot analyses using antibodies against the PAP and the major outer sheath protein (MSP) indicated that the 190 and 270 kDa proteases were protein complexes formed by the MSP and the PAP. These complexes dissociated by storage in 0.3% or higher SDS concentrations. The purified PAP was found to completely degrade keratin, but was unable to degrade native actin either in its monomeric or polymerized form. The association of the MSP adhesin with a protease capable of degrading host native proteins may benefit the obtention of protein-based nutrients necessary to support the growth of these treponemes. These complexes may also play a role in the structural organization of T. denticola outer sheath.

Mobility of acetylated histones in sodium dodecyl sulfate-polyacrylamide gel electrophoresis

We describe an altered mobility for acetylated histone isoforms in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Isoforms of histones H3 and H4 with a higher acetylation degree have a slightly faster electrophoretic mobility. Since acetylation neutralizes the positive charge of the epsilon-amino group of lysine, without significantly changing the molecular mass of the protein, the acetylation-dependent mobility shift could be explained by the increase of the net negative charge of the SDS-histone complexes. A possible consequence of this differential mobility for the acetylation site determination by protein microsequencing from SDS gels is discussed.

Comparative evaluation of sensitivity of RNA-polyacrylamide gel electrophoresis and dot immunobinding assay for detection of bluetongue virus in cell culture

Bluetongue virus serotype 1 (Avikanagar isolate) was grown in BHK-21 cell line and titrated. The titre of the virus in BHK-21 cell line was 10(6) TCID50/ml. RNA-polyacrylamide gel electrophoresis (RNA-PAGE) and dot immunobinding assay (DIA) were performed on 10-fold serial dilutions of the sonicated cell culture material. The results indicated that the minimum limit of detection of the virus by RNA-PAGE and DIA was 10(5) TCID50/ml.

Antilactoferrin antibodies in autoimmune liver diseases

OBJECTIVE

Lactoferrin, an immunoregulatory protein in mucosal secretions, is one of the target antigens to perinuclear antineutrophil cytoplasmic antibodies (P-ANCAs). Circulating lactoferrin is cleared in the liver, but little is known about the implication of lactoferrin in hepatic inflammation. To evaluate the implication of immunological response to lactoferrin, we examined antilactoferrin antibodies in autoimmune liver diseases.

METHODS

Fourteen patients with primary biliary cirrhosis (PBC), 14 with autoimmune hepatitis (AIH), five with autoimmune cholangitis (AIC), six with chronic hepatitis C, and five with chronic hepatitis B were studied. We evaluated autoantibodies to lactoferrin in the sera of the patients by the Western Immunoblotting method.

RESULTS

Sera of five of the 14 patients (35.7%) with PBC, four of the 14 patients (28.6%) with AIH, and five of the five patients (100%) with AIC contained autoantibodies to human lactoferrin, but none with hepatitis B or C had them. The higher prevalence of serum antibodies to human lactoferrin was shown to be higher in patients with AIC than with hepatitis B (p < 0.01), hepatitis C (p < 0.01), PBC (p < 0.05), and AIH (p < 0.05).

CONCLUSION

Lactoferrin located in bile ducts and liver cells is one of the candidates of target antigens in autoimmune liver diseases, especially in AIC.

Mutation analyses of KRAS exon 1 comparing three different techniques: temporal temperature gradient electrophoresis, constant denaturant capillary electrophoresis and allele specific polymerase chain reaction

Mutations in the KRAS gene is a key event in the carcinogenesis of many human cancers and may serve as a diagnostic marker and a target for therapeutic intervention. In this study we have applied three different techniques for mutation detection of KRAS exon 1 mutations: Allele specific polymerase chain reaction (AS-PCR), temporal temperature gradient electrophoresis (TTGE) and constant denaturant capillary electrophoresis (CDCE). Samples from 191 sporadic colon carcinomas were analyzed. AS-PCR were performed with oligonucleotides specific for know mutations in codon 12 and 13 of the KRAS gene. In TTGE analyses, linear ramping of the temperature were performed during electrophoresis in a constant denaturant gel. CDCE analyses were performed using fluorescin labeled PCR-products. Separation was achieved under constant denaturing conditions using high temperature in a gel-filled capillary followed by laser detection. A mutated KRAS gene was found in 42/191 (22.0%) of the samples using AS-PCR, in 62/191 (32.5%) using TTGE and in 66/191 (34.6%) of the samples using CDCE. In the TTGE and CDCE analyses the sequence of the mutant were determined by comparing the electrophoretic pattern to that of known mutations or by mixing the sample with known mutations prior to reanalysis. In a titration experiment mixing mutant and wild-type alleles prior to PCR, the sensitivity for mutation detection was shown to be 10(-2) for TTGE and under optimized conditions 10(-3) for CDCE.

[The isolation and results of the study of the protein structure of spirochetes isolated from I. ricinus ticks in Byelarus]

Four hundred and eighty Ixodes ricinus (278 female and 202 male) samples collected in the natural biotopes of 13 administrative districts in southwest Byelarus were studied via DSK-H medium (Sigma) inoculation. Twenty-four spirochetes isolates (3, 2, 1, and 18 in the Brest, Gomel, Mogilev, and Grodno regions, respectively) were obtained on the territory of Byelarus. After adapted to the medium, most isolates (as many as 7 x 10(6)-5 x 10(7) microbial cells per ml) in the stationary phase. All the obtained isolates were cryoconserved at the level of 2-6 passages and after -70 degrees C storage during 4-6 months (a followup period) they were able to recover their initial reproductive activity in the fresh BSK-H medium. Proceeding from preidentification using a comparative electrophoretic analysis of the molecular mass of polypeptides, the pattern of their specific reactivity with polyclonal serum antibodies from the rabbit immunized with cultured Borrelia afzelii (Ip21 strain), in immunoblotting and indirect immunofluorescence assay, I. ricinus spirochetes were referred to Borrelia burgdorferi sensu lato isolates.

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.

Automated laser-induced fluorescence DNA sequencing: equalizing signal-to-noise ratios significantly enhances overall performance

We have significantly optimized the performance of the Perkin-Elmer/Applied Biosystems (PE/ABI) 373Stretch DNA sequencer. Best results were obtained using 19% less ddNTPs and 75% more dNTPs relative to the manufacturer's recommended reaction mixture. Other changes included 4.25% (instead of 4%) acrylamide gels run at 38 W (instead of 40 W). These variations produced a significant equalization of the signal-to-noise profile, resulting in longer reads. The overall accuracy improvement for unedited pGEM 1000-base sequences analyzed by the ABI100 basecaller was 8.2%. High accuracy gains were observed in the 501- to 850-base region (6.0%) and, most significantly, from that point to the end of the sequence (41.6%). A decrease in accuracy was also found for the first 30 bases, which usually correspond to vector sequence. Our study has focused primarily on double-stranded DNA (dsDNA) using the DyeDeoxy Terminator chemistry kit and 48-cm well-to-read (WTR) gels since, in our hands, such a combination represents the quicker, most accurate, versatile, and productive choice for large-scale DNA sequencing. Nevertheless, our findings could be also exploited in other sequencing strategies using ssDNA templates, the DyePrimer chemistry, alternative enzyme preparations, or different WTR lengths on the 373Stretch or other sequencing machines.

Characterization of proteinuria in primary glomerulonephritides. SDS-PAGE patterns: clinical significance and prognostic value of low molecular weight ("tubular") proteins

In 145 patients with focal segmental glomerulosclerosis (43), membranous glomerulonephritis (72), and membranoproliferative glomerulonephritis (30), 71% with normal renal function (NRF) and 63% with nephrotic syndrome (NS), the proteinuria was evaluated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and classified into four main patterns: physiological (termed 70 kd), pure glomerular (150 kd), mixed with low molecular weight (LMW) proteins as low as 23 kd (23 kd), and mixed with very LMW proteins (20 to 10 kd; termed 10 kd). The relative frequencies were 70 kd, 0.7%; 150 kd, 1.4%; 23 kd, 61%; and 10 kd, 37%. Therefore, only the two patterns characterized by LMW ("tubular") proteins were compared to determine whether they have different clinical and prognostic significance. The serum creatinine (sCr) values (P < 0.0001), the degrees of proteinuria (P = 0.007), and the tubulointerstitial damage (P = 0.015) were significantly different in the two subgroups of patients with 23-kd and 10-kd LMW proteinuria; the difference for tubulointerstitial damage was at the limit of statistical significance after Bonferroni correction. In 82 patients with NRF at entry (sCr, 1.00 +/- 0.22 mg/dL; range, 0.6 to 1.4 mg/dL) and a follow-up of 46 +/- 22 months (range, 12 to 84 months), the predictive value of the 23-kd and 10-kd SDS-PAGE patterns on functional outcome (chronic renal failure [CRF] or clinical remission) was evaluated. A total of 12.5% of 64 patients with mixed 23-kd proteinuria and 50% of 18 patients with mixed 10-kd proteinuria developed CRF. At this time, the difference between the survival curves was highly significant (P = 0.0001), as it also was after correction for NS (P = 0.0002). When the statistical analysis was limited to 69 patients with sCr < or = 1.2 mg/dL, the difference was still highly significant (P = 0.0016), as after correction for NS (P = 0.0064). Clinical remission developed in 30% of 64 patients with 23-kd proteinuria and in 33% of 18 patients with 10-kd proteinuria; this difference was not significant. In a retrospective analysis of 20 patients (13 focal segmental glomerulosclerosis and seven membranous glomerulonephritis; 10 with the 23-kd pattern and 10 with the 10-kd pattern) treated with steroids alone or with steroids and cyclophosphamide, 80% of the patients with the 23-kd pattern and 30% of the patients with the 10-kd pattern were responsive to treatment (P = 0.025). The SDS-PAGE patterns of 54 patients with NRF at entry were again evaluated after 48 +/- 22 months: 11 patients who developed clinical remission had changed from a prevalent (91%) 23-kd pattern to a prevalent physiological (55%) or glomerular (36%) pattern; eight patients who had developed CRF showed an increase from 37% to 100% of the 10-kd pattern. In 35 patients with normal and stable renal function (sCr from 1.08 +/- 0.20 mg/dL to 1.06 +/- 0.19 mg/dL) who had persistent proteinuria (20 patients) or NS (15 patients), the rate of the 10-kd pattern increased from 6% to 46% (72% in persistent NS), suggesting an impairment of tubular protein reabsorptive function even without a concomitant impairment of glomerular filtration rate, a phenomenon that can be hypothetically attributed to tubular toxicity of persistent proteinuria. The characterization of proteinuria by SDS-PAGE in primary progressive glomerulonephritis is a useful clinical tool: it can be used to identify the main pathophysiologic determinants of excretion of LMW proteins and it has a predictive value on CRF outcome in patients with NRF, reducing the unpredictability of clinical evolution. In focal segmental glomerulosclerosis and membranous glomerulonephritis, it seems to be of predictive value on responsiveness to therapy; monitoring the SDS-PAGE patterns over time may give some insights into the relationship between the persistent protein loss and the progression of the disease.

Simplified sizing of low-density lipoprotein using polyacrylamide gradient gel electrophoresis of plasma

Low-density lipoprotein (LDL) particles can be separated into subfractions according to size by non-denaturing polyacrylamide gradient gel electrophoresis. Established research methods require specialised equipment and are frequently unsuited to the clinical laboratory. In this study, we utilised a colour flat bed scanner in conjunction with shareware image analysis software to compare LDL particle diameters of isolated LDL with LDL in whole plasma. LDL was isolated by ultracentrifugation and electrophoresed on 3-13% gels (Gradipore; Sydney, Australia) for 2400 Volt-hours in parallel with plasma and molecular size standards. Coomassie Blue-stained gels were scanned in reflexive mode using a colour flat-bed scanner and Adobe Photoshop 3.0 software. Density traces of each lane were obtained using NIH Image software (public domain, USA). LDL particle diameters were determined from calibration curves of the log of molecular diameter of standards against migration distance. There was a good correlation between LDL particle diameters obtained using isolated LDL and whole plasma (r = 0.87, P < 0.001; n = 22). However, the group means (+/- S.D.) (24.7 +/- 0.6 and 24.8 +/- 0.5 nm respectively) were statistically different on the paired t-test (P < 0.05). It is unclear whether this numerically small difference is due to alterations in LDL during the longer preparative procedures for LDL, or to matrix effects during electrophoresis of plasma samples. In conclusion, plasma samples stained with Coomassie Blue and scanned with a colour flat bed scanner can conveniently be used for LDL particle sizing by non-denaturing polyacrylamide gradient gel electrophoresis.

Denaturing gradient gel electrophoresis to diagnose multiple endocrine neoplasia type 2

Multiple endocrine neoplasia type 2 (MEN 2) is an autosomal dominant cancer syndrome caused by mutations in the RET protooncogene. Others have already demonstrated the value of genetic testing in known MEN 2 kindreds. Previously described approaches to DNA-level diagnosis, particularly of index cases, are tedious. We developed appropriate denaturing gradient gel electrophoresis (DGGE) conditions for analysis of exons 10, 11, and 16 of this gene, where many of the pathogenic mutations map. We screened 16 members of a three-generation MEN 2 kindred by DGGE and found five affected but still asymptomatic patients, ranging in age from 5 to 67 years. We used DGGE to localize the pathogenic mutations and screen at-risk individuals in several other kindreds. DGGE--which requires no radioactive, fluorescent, or chemiluminescent labeling--is ideally suited to the diagnosis of MEN 2 because of the syndrome's dominant genetics and the rarity of clinically silent variants in the RET gene.

Time course analysis of serum and urinary proteins by SDS-PAGE in experimental nephrotic syndrome

Serum and urinary proteins from rats with nephrotic syndrome (NS) induced by puromycin aminonucleoside (PAN) were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Analysis was made on days 2, 4, 6, 8, 10, 12, 16, 20, and 30 after PAN injection. Data were compared with control rats (C). Rats developed proteinuria on days 4-30 and hypoproteinemia on days 4-16. Total protein concentration in serum and urine was similar on day 6. SDS-PAGE revealed that urinary albumin augmented on days 4-30 and serum albumin decreased markedly on days 4-20. Albumin concentration in serum and urine was similar on days 4-16. In addition, the study examined serum changes of 7 other proteins (designed as A, B, C, D, E, F, and G) which appeared or increased in urine, and whose molecular weights were higher (A, B, and C) or lower (D, E, F, and G) than that of albumin. In serum, protein A remained unchanged; protein B and G increased; proteins C, D, E, and F decreased. The qualitative pattern of urinary proteins remained essentially unchanged on days 4-30. During the intense proteinuria, the serum concentrations of protein B and albumin were similar and the urine concentrations of proteins C and D became comparable to that found in serum. These 7 serum proteins did not show the same behavior although all of them were excreted in urine. These data indicate that in PAN-nephrotic rats: (a) urinary proteins can be of low and high molecular weight, (b) serum proteins can be regulated independently of their urinary excretion and molecular weight, (c) the urine concentration of total protein and some specific proteins can reach values similar to that found in serum during the intense hypoproteinemia, and (d) the qualitative pattern of urinary proteins was unrelated to the magnitude of proteinuria.

[A genetic pool study of the population of the Republic of Tyva using genetic markers for the search for associations with tuberculosis]

Eighty three Tyvin patients with local pulmonary tuberculosis and 295 healthy donors of the same nationality were examined. They are resided in the central area of Tyva (in Kyzyl and its vicinities). In addition, 132 healthy Tyvin-Todjins were examined. Tuberculosis mortality was found to be associated with the antigen HLA-B15 in the Tyvins living in the central area of the Republic of Tyva (Kyzyl). The incidence of HLA antigens and polymorphic protein locus genotypes varies in different areas of the Republic of Tyva.

New types of large-pore polyacrylamide-agarose mixed-bed matrices for DNA electrophoresis: pore size estimation from Ferguson plots of DNA fragments

The average pore size value of gels containing polyacrylamide, covalently linked to agarose, was found to be 30% higher than the value of a regular N,N'-methylenebisacrylamide (Bis) cross-linked gel of the same %T. By increasing the agarose concentration (10% of the total amount of polyacrylamide), gels containing low amounts of acrylamide (1.5-2%) are reproducibly obtained; their pore sizes are 130% larger than the pore sizes of a 4%T, 3.3%C polyacrylamide gel. In general, mixed-bed matrices were found to be more elastic and mechanically stronger than classical polyacrylamide gels since an agarose-induced gelation process takes place during their polymerization.

PhosphorImager enhancement of sedimentation equilibrium-quantitative polyacrylamide gel electrophoresis: a highly sensitive technique for quantitation of equilibrium gradients of individual components in mixtures

The technique called sedimentation equilibrium-quantitative polyacrylamide gel electrophoresis (Darawshe et al. (1993) Anal. Biochem. 215, 236-242) has been extended to permit the quantitation and analysis of gradients of individual radiolabeled components in a mixture of radiolabeled solutes centrifuged to sedimentation equilibrium. Immediately following centrifugation, the contents of a sample tube are fractionated into aliquots corresponding to laminae of solution at different radial positions in the centrifuge. Following treatment with sodium dodecyl sulfate-containing buffer, a portion of each fraction is subjected to electrophoresis on a polyacrylamide gel. The gel is then incubated with a strong phosphor plate and subsequently scanned with a Molecular Dynamics PhosphorImage. The concentration of an individual radiolabeled component at a particular radial distance is proportional to the integrated intensity of the image of the radiolabeled band of that component in the fraction corresponding to that radial distance. Concentration gradients reconstructed in this fashion are interpreted in the context of conventional sedimentation equilibrium theory. The results of control experiments carried out with purified proteins of known molar mass and the measurement of the molar mass of a new, partially purified protein are reported.

Quantitative capillary gel electrophoresis assay of phosphorothioate oligonucleotides in pharmaceutical formulations

Quantitative capillary gel electrophoresis (QCGE) has been developed for the accurate quantitation of a 21-mer phosphorothioate oligonucleotide, ISIS 2922, and its degradation products in an intravitreal formulation. The electrokinetic mode of injection employed by CGE necessitates formulation of the external reference standard in a sample matrix similar to that of the drug product and the use of an internal standard for improved accuracy and precision. The analytical method detailed in this paper has demonstrated the necessary accuracy, precision, linearity, range, selectivity and ruggedness for use in routine drug product analysis and stability monitoring of phosphorothioate oligonucleotides.

High-speed and high-accuracy DNA sequencing by capillary gel electrophoresis in a simple, low cost instrument. Two-color peak-height encoded sequencing at 40 degrees C

A low-cost DNA sequencer was constructed based on a single helium-neon laser. The two-color peak-height encoded sequencing protocol, based on the use of T7 DNA polymerase in a manganese buffer, was used to generate samples. Two termination reactions were performed. In the first, a TAMRA (applied Biosystems)-labeled primer was extended in the presence of ddATP and ddCTP. The amounts of dideoxynucleotides were adjusted to produce a 3:1 peak height ratio. Similarly, a ROX (Applied Biosystems)-labeled primer was extended in the presence of ddGTP and ddTTP; the amounts of dideoxynucleotides was adjusted to produce a 3:1 peak height ratio. The pooled fragments were separated on a 4% T LongRanger gel operated at 39 degrees C. Over 500 bases of sequence were generated in 50 min.

Analysis of DNA restriction fragments and polymerase chain reaction products by capillary electrophoresis

Capillary electrophoresis (CE) is a new, high-resolution tool for the analysis of DNA restriction fragments and DNA amplified by the polymerase chain reaction (PCR). By combining many of the principles of traditional slab gel methods in a capillary format, it is possible to perform molecular size determinations of human and plant PCR amplification products and DNA restriction fragments. DNA restriction fragments and PCR products were analyzed by dynamic sieving electrophoresis (DSE) and capillary gel electrophoresis (CGE). As part of this study, sample preparation procedures, injection modes, and the use of molecular mass markers were evaluated. Optimum separations were performed using the uPage-3 (3% T, 3% C) CGE columns with UV detection at 260 nm. Membrane dialysis and ultrafiltration/centrifugation proved to be nearly equivalent methods of sample preparation. Reproducibility studies demonstrated that blunt-ended, non-phosphorylated markers (specifically allele generated markers) provide the most accurate calibration for PCR product analysis. This study demonstrates that CE offers a high-speed, high-resolution analytical method for accurately determining molecular size and/or allelic type as compared with traditional methodologies.

Abnormal expression of plasminogen activators in aortic aneurysmal and occlusive disease

PURPOSE AND METHODS

Aortic aneurysms are characterized by the destruction of the extracellular matrix of the media, whereas occlusive disease involves excess matrix accumulation within the intima. Plasmin degrades extracellular matrix directly and indirectly by activation of latent metalloenzymes. To determine the expression of tissue- and urokinase-type plasminogen activators, immunoassay, fibrin autography, Northern analysis, and immunohistochemistry were performed on specimens of aneurysmal (n = 12), occlusive (n = 8), and healthy (n = 6) aorta.

RESULTS

Immunoassay of tissue-type plasminogen activator revealed 8.7 +/- 0.9 ng tissue-type plasminogen activator/mg extracted protein in aneurysmal aorta, 5.7 +/- 0.3 ng/mg in normal aorta, and 2.5 +/- 0.3 ng/mg in occlusive aorta (p < 0.05 for comparisons between all groups). No urokinase-type plasminogen activator antigen was detected by urokinase-type plasminogen activator immunoassay. Fibrin autography exhibited lytic activity at 64 kDa and 54 kDa attributable to tissue-type plasminogen activator and urokinase-type plasminogen activator. The vast majority of fibrinolysis was secondary to free tissue-type plasminogen activator and was greatest in aneurysmal disease and least in occlusive disease. There was only a small amount of lysis secondary to urokinase-type plasminogen activator. Expression of tissue-type plasminogen activator and urokinase-type plasminogen activators mRNA was comparable in aneurysmal and occlusive aortas. In contrast to occlusive disease, aneurysms had an inflammatory cell infiltrate characterized by the expression of urokinase-type plasminogen activator by specific mononuclear cells. Tissue-type plasminogen activator expression was evident in the intima of normal and diseased aorta and in the media of diseased aorta.

CONCLUSION

Differential expression of plasminogen activators within the arterial wall may contribute to the unique pathogenesis of aneurysmal and occlusive aortic disease.

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.

Analysis of synthetic oligodeoxyribonucleotides by capillary gel electrophoresis and anion-exchange HPLC

Polyacrylamide slab gel electrophoresis has been traditionally used for the analysis of synthetic oligodeoxyribonucleotides. As the demand for oligonucleotides of high purity has increased, a need for additional high resolution analytical techniques has arisen. This report describes the principles and application of capillary gel electrophoresis and high-performance liquid chromatography for the analysis of synthetic DNA varying in base composition and length. From the results of a series of comparative experiments, the relative advantages and disadvantages of each technique are discussed.

[The embryonic brain-derived neuralizing factor (EBDNF): its partial purification by ion-exchange and affinity chromatography]

The data are presented about isolation from the brain of 7.5-day chick embryos of a factor capable of neuralizing effect on the early gastrula ectoderm of the grass frog Rana temporaria L. Earlier this factor was defined as embryonic brain-derived neuralizing factor (EBDNF) (Mikhailov, Gorgoliuk, 1989). The isolation procedure includes (1) extraction with deionized water at pH 9.0; (2) ion exchange chromatography on a column with DEAE-adsorbent at pII 8.0; (3) affinity chromatography on Heparin-Ultragel column. EBDNF-containing fraction is eluted from the Heparin-Ultragel column with 250 mM NaCl as a separate peak. Four bands are observed on SDS-electrophoregrams of this fraction, two more prominent ones having the molecular weight of 43 and 63 kDa. The yield of EBDNF-containing fraction is about 0.01-0.02% of the wet weight of the initial brain tissue.

Use of fluorogenic substrates to visualize trypsin and chymotrypsin inhibitors after electrophoresis

Fluorogenic substrates were tested as a means of increasing both the sensitivity and the selectivity of trypsin and chymotrypsin inhibitor detection after electrophoretic separation. Out of six substrates applied to cellulose acetate membranes, N alpha-benzyloxycarbonyl-L-arginine-4-methylcoumarinyl-7-amide (Z-Arg-MCA) and benzyloxycarbonyl-glycyl-glycyl-L-arginine-4-trifluoromethylcoumariny l-7-amide (Z-Gly-Gly-Arg-TFMCA) were found to be suitable for trypsin, and L-alanyl-L-alanyl-L-phenylalanine-4-methylcoumarinyl-7-amide (Ala-Ala-Phe-MCA) was suitable for chymotrypsin. A procedure to detect trypsin and chymotrypsin inhibitors, and to discriminate between them, was developed. After electrophoresis, slab gels were first incubated with the enzyme (bovine trypsin, bovine chymotrypsin, or human duodenal juice) at 37 degrees C, and then covered with the respective substrate membrane and incubated at room temperature while being observed under UV light. Dark blue inhibitor bands on a light-blue-fluorescent background were obtained with Z-Arg-MCA/trypsin and Ala-Ala-Phe-MCA/chymotrypsin, whereas Z-Gly-Gly-Arg-TFMCA/trypsin resulted in dark inhibitor bands on a fluorescent green background. The "inhibitor overlay membrane technique" (IOM technique) was used after polyacrylamide gel isoelectric focusing with carrier ampholytes and immobilized pH gradients, pore-gradient polyacrylamide gel electrophoresis, and sodium dodecyl sulfate pore-gradient polyacrylamide gel electrophoresis.

A program which automatically quantitates gel electrophoretic autoradiograms

The use of a computer-coupled film scanner to measure and analyze autoradiograms of gel electropherograms is described. A program has been written which fits Gaussian curves to the complex band pattern that constitutes a density profile without the need for estimated parameters in the input. The great majority of the fits are satisfactory. This program, which is written in FORTRAN, runs on a small, inexpensive computer. Another program which approximates a Gaussian least squares fit has been run for comparison; this procedure can also be used to refine occasional unsatisfactory fits. Finally, a program has been written which sums the density profile within specified limits, so that the integrated intensities of bands due to isolated protein components may be found.