R H Kelly, A B Carpenter, K S Sudol, S P Jagarlapudi, S Manzi
{"title":"Complement C3 fragments in urine: detection in systemic lupus erythematosus patients by western blotting.","authors":"R H Kelly, A B Carpenter, K S Sudol, S P Jagarlapudi, S Manzi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We characterized urinary excretion of C3 fragments among patients with systemic lupus erythematosus (SLE) as a possible indicator of renal involvement. 28 patients, representing a broad range of disease activity were admitted to our study. Urinary proteins were separated on 4-20% gradient SDS-PAGE gels, under reducing conditions, and transblotted to nitrocellulose. Western blots were developed with a polyvalent goat-anti-human C3d antiserum, and an alkaline phosphatase-conjugated rabbit anti-goat IgG. Three patterns were obtained: 1) no bands detected; 2) bands suggesting the presence of intact C3; and 3) samples with additional low molecular (< 4 x 10(4)) bands. The 12 patients with no C3 bands had minimal disease activity (e.g. fatigue, arthralgia, arthritis, rash, oral ulcers). The seven patients with intact C3 patterns also had minimally active disease. Their primary clinical findings included fatigue, pleurisy, renal disease which had been treated, hemolytic anemia, and arthritis. Patients with low molecular weight C3 fragments in their urine formed two sub-sets, based upon their presenting features. The first group had severe disease and contained all patients with active lupus nephritis (n = 4), while the second consisted of non-renal patients with primary clinical findings of moderate disease activity (e.g. thrombocytopenia, pneumonitis, arthritis). Our results suggest urinary excretion of low molecular weight C3 fragments correlates with active renal disease, but is a variable finding among SLE patients with non-renal manifestations of disease activity.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"265-9"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19188910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wave packets analysis of two-dimensional protein maps: a new approach to study the diversity of immunoglobulins.","authors":"A Zahnd, J D Tissot, D F Hochstrasser","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This report describes a mathematical approach for classifying two-dimensional (2D)-protein maps without spot detection or pattern matching. Analysis of electrophoretograms was performed using wave packet decompositions of the signals. The scanned images were automatically decomposed into a set of sub-images organized in a tree structure. Each sub-image contained relevant information such as its energy, or entropy. Moreover the node position itself of the sub-image reflected a frequency localization. A distance was then defined using the tree repartition of these quantities. Finally a statistical clustering on the tree structures was performed, terminating with a classification of the images according to their repartition frequencies. The algorithm has been applied to classify immunoglobulin (Ig) light chain patterns and proved useful to automatically detect monoclonal, oligoclonal or polyclonal Igs.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"321-8"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19189492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Capillary electrophoresis to measure sulfoesterase activity on chondroitin sulfate and heparin derived disaccharides.","authors":"A Pervin, K Gu, R J Linhardt","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Capillary electrophoresis was used to assay sulfoesterase activity on sulfated disaccharides derived from chondroitin sulfate, dermatan sulfate and heparin. The three sulfoesterases studied were chondro-4-O-sulfatase (EC 3.1.6.9) and chondro-6-O-sulfatase (EC 3.1.6.10) from Proteus vulgaris and heparo-2-O-sulfatase from Flavobacterium heparinum. Capillary electrophoresis was used to analyse sulfated disaccharide before and after sulfoesterase treatment and a change in migration time was indicative of the presence of sulfoesterase activity. This assay was used both on purified sulfoesterases and on minor sulfoesterase contaminants present in other enzyme preparations. The high sensitivity of capillary electrophoresis permits the elimination of 35S-radiolabeled substrates normally required to assay sulfoesterases. The high resolution of capillary electrophoresis allows the use of this assay on impure enzyme preparations containing high protein concentrations.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"297-303"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19189489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploratory data analysis in two-dimensional electrophoresis.","authors":"S P Caudill, J E Myrick, M K Robinson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The use of computerized matching of proteins in the analysis of multiple two-dimensional electrophoresis (2DE) gels creates volumes of data that are readily accessible for exploratory analysis. When these data are used in health-effects studies or in studies to identify factors associated with particular diseases, hundreds or even thousands of hypotheses can be tested. Interpreting so many hypothesis tests requires some preliminary statistical evaluations of the data. In addition, prior to the preliminary statistical evaluations and subsequent hypothesis tests, accurate protein quantification and correct protein matching must be verified. In this report we present an approach used at the Centers for Disease Control to address these issues. This approach consists of a randomized experimental design incorporating replicate gels for each specimen, gel image analysis, protein matching, editing, Boolean unions of all gels to obtain correspondences and contradictions of match identification numbers, resolution of correspondences and contradictions, statistical tests to identify outliers, and finally an assessment of statistical and practical significance to focus attention on the proteins most likely to be associated with the effects under study. We illustrate our approach with data from an exploratory exposure-response study.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"133-6"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19494976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M J Doktycz, W A Gibson, H F Arlinghaus, R C Allen, K B Jacobson
{"title":"Use of resonance ionization spectroscopy to detect DNA bands on ultrathin spin-coated gels.","authors":"M J Doktycz, W A Gibson, H F Arlinghaus, R C Allen, K B Jacobson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Development of alternative electrophoresis procedures are necessary for large volume sequencing and mapping studies. The use of stable isotopes as DNA labels and ultrathin gels promises to greatly increase the rate of sequencing. Spin coating is presented as an alternative method for producing ultrathin polyacrylamide gels. The technique has the potential of producing gels of micron to submicron thicknesses by varying the viscosity of the acrylamide solution and the spinning speed. Thirty micron thick 6% (weight %) gels were produced in this manner. Tin-labeled DNA oligomers were electrophoresed and detected using sputter-initiated resonance ionization spectroscopy (SIRIS). The usefulness of SIRIS and laser atomization RIS (LARIS) to sample the surface and deeper layers of 240 microns thick gels was investigated. With LARIS, whole cross-sections of the gel can be atomized, possibly allowing complete sampling of labels.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"157-62"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19494979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Non-isotopic detection of single-stranded conformation polymorphisms using ethidium bromide/UV light.","authors":"W G Ballhausen, C Kraus","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In the course of searching for single base substitutions resulting in polymorphisms or point mutations within the adenomatous Polyposis coli (APC) gene we established an alternative non-radioactive procedure to detect single-stranded conformation polymorphisms (SSCP) of polymerase chain reaction (PCR) products. A fast and inexpensive SSCP assay system is described in detail with general application allowing the non-isotopic identification of single base alterations of PCR products. This was achieved by combining heat denaturation of PCR products resulting in a high yield of single-stranded DNA and ethidium bromide staining of separated DNA strands in non-denaturing polyacrylamide vertical standard gels. The validity of the non-radioactive procedure described here is demonstrated by the identification of allele-specific SSCP patterns derived from intragenic polymorphisms of the APC gene.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"129-31"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19495061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A new method of scaling up free flow electrophoresis.","authors":"P Painuly, M C Roman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Free flow electrophoresis (FFE) has been utilized for the separation of proteins and cells for many years and has evolved into the most promising method of continuous separation of biomolecules. One of the major drawbacks inherent in FFE in the past, however, is the thermal convection caused by joule heating which occurs whenever a current is applied across a conducting liquid medium. To provide efficient heat dissipation, the cross-section of traditional FFE units is restricted to approximately 1 mm, which limits sample throughput. A new continuous FFE apparatus, which internally cools the separation unit by passing water through aligned capillary tubes, has been developed. This innovation allows scale-up of the separation without thermal convection. Results of separations of dyes and proteins are presented.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"119-27"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19375094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K Srinivasan, S C Morris, J E Girard, M C Kline, D J Reeder
{"title":"Enhanced detection of PCR products through use of TOTO and YOYO intercalating dyes with laser induced fluorescence--capillary electrophoresis.","authors":"K Srinivasan, S C Morris, J E Girard, M C Kline, D J Reeder","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Recent developments in the chemical synthesis of DNA-binding dyes have enhanced detection of polymerase chain reaction (PCR) products by capillary electrophoresis. These dyes are dimers of thiazole orange (TOTO) or oxazole orange (YOYO) and have a very high binding affinity for DNA (Haugland, 1992). These dyes show enhanced fluorescence signals when they bind to double-stranded DNA and their fluorescence in the unbound state is almost zero, making them extremely useful in detecting minute (fg) quantities of DNA. We report here the utility of these dyes in DNA typing applications using a laser-induced fluorescence detector in conjunction with a capillary electrophoresis system.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 5","pages":"235-9"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19207912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Strategies for pH gradients' optimization.","authors":"F C Celentano, E Gianazza","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A few problems arising when optimizing the composition of the mixtures to be used for IPG casting with a two chambers mixer are discussed. The behavior in the composition space of a number of objective functions is described by simulation. This allows the formalization of rules to be followed for finding the initial guess required to start the optimization algorithm and for directing and limiting the search of the objective's minimum. the results of the simulation show that a fully automatic gradient computation and optimization is possible.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 5","pages":"191-201"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19207937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Splitting merged spots in two-dimensional polyacrylamide gel electrophoresis gel images.","authors":"P F Lemkin, J E Myrick, K M Upton","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We describe a heuristic computer algorithm using boundary analysis for improving spot finding and spot quantitation of large saturated or near-saturated spots in two-dimensional polyacrylamide electrophoresis gels. This spot quantitation is done using spot segmentation, which consists of spot finding and subsequent quantification steps. Occasionally, clusters of large saturated spots may become merged during spot finding. To correct this, the merged spots must be cut apart before quantitation. It is generally obvious from viewing the merged spot's border where they should be cut--at opposing saddlepoints (concavities in the boundary). The algorithm uses an analysis of the missegmented spot's boundary when a saturated spot is detected. If a near-saturated spot is larger than a given size, the spot segmenter program attempts to merge saturated fragments. When merging occurs, the segmenter program analyses the boundary to see if the spot should be split. The new algorithm first finds all robust concavities and then tries to match complementary ones. These paired concavities are then used to guide cutting of the missegmented spot into two or more separate spot regions. Finally, control is returned to the segmenter program to reprocess the data as a set of smaller separated spots.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"163-72"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19494980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}