Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society最新文献

{"title":"Electrophoresis of small DNA molecules in agaroses with different electroendosmotic properties.","authors":"A Pramatarova,&nbsp;C Hamelin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The migration rate of DNA standards in agaroses with different electroendosmotic (EEO) properties was compared in order to find an alternative to polyacrylamide slab gels for the separation of small restriction fragments by electrophoresis. Slower migration of DNA molecules only a few hundred of base pairs in length was observed after raising the concentration of unmodified low EEO agarose in gels up to 6%. Resolution of low-molecular-weight DNA fragments was best achieved, however, with hydroxyethylated agaroses showing high or low EEO properties. An immediate application of the above results was to confirm the presence of the human cytomegalovirus BamH I-P subgenomic fragment (7.2 kb) in a recombinant pAT153 plasmid by restriction endonuclease analysis.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"277-81"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19188912","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":"The molecular weights of twelve apolipoprotein(a) variants, determined using haptoglobin 2-2 polymer molecular weight standards.","authors":"W Y Craig,&nbsp;S E Poulin,&nbsp;A M DiGeorge,&nbsp;N R Forster,&nbsp;L M Neveux,&nbsp;T B Ledue,&nbsp;R F Ritchie","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Apolipoprotein(a) [apo(a)] variants were characterized in 398 sera by immunoblotting: (a) by molecular weight, using a haptoglobin 2-2 polymeric series as standards, and (b) by nomenclature, using serum pools containing previously characterized apo(a) variants as standards. The haptoglobin 2-2 standard curve (172-859 kDa) alleviates the necessity of obtaining molecular weights by extrapolation. Among the 398 sera, 40.2% had double apo(a) bands (54 phenotypes), 58.0% had a single apo(a) band and 1.8% were null (no bands observed). An inverse, though non-monotonic, relationship was observed between apolipoprotein(a) molecular weight and serum lipoprotein(a) [Lp(a)] concentration. Due to the large size of apo(a) and the relatively small increment between variants (15-16 kDa), molecular weight could not be used alone to characterize variants. Even with a CV of 3-4%, there was an overlap between variant molecular weight estimates. However, in combination with the identification of variants by comparison with standards, the haptoglobin 2-2 standard curve could be used to obtain mean molecular weight estimates for each variant. 12 distinct variants were identified among the sera, with apparent mean molecular weights of 314, 388, 410, 433, 454, 466, 503, 519, 528, 543, 553 and 572 kDa, respectively. These molecular weight estimates are consistent with the theoretical molecular weight range for apo(a) variants, calculated from sequence and carbohydrate analysis, of 238-643 kDa.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 5","pages":"241-6"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19207913","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":"Modulation of the activity of calpain II by phosphorylation--changes in the proteolysis of cyclic AMP-dependent protein kinase (peak II, DEAE).","authors":"W N Kuo,&nbsp;U Ganesan,&nbsp;D L Walbey,&nbsp;D L Davis,&nbsp;K Allen,&nbsp;L K McCall","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The proteolysis of the 32P-labeled holoenzyme of cyclic AMP-dependent protein kinase (A-PKII:DEAE, peak II fraction) was analysed by SDS-polyacrylamide gel electrophoresis and autoradiography. The contaminants of the A-PKII and calpain II apparently did not interfere with the accuracy of this highly sensitive analysis. Phosphorylation of calpain II by the catalytic subunit of cyclic AMP-dependent protein kinase (A-PK) greatly enhanced the proteolysis of A-PKII, whereas phosphorylation by protein kinase C (PK-C) or cyclic GMP-dependent protein kinase (G-PK) slightly altered the proteolysis.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"317-20"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19189491","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":"Quantitative two-dimensional electrophoretic detection of possible urinary protein biomarkers of occupational exposure to cadmium.","authors":"J E Myrick,&nbsp;S P Caudill,&nbsp;M K Robinson,&nbsp;I L Hubert","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>To search for new urinary protein biomarkers of cadmium toxicity, we used quantitative two-dimensional electrophoresis (2DE) and analysed urine samples from 18 male cadmium recovery plant employees whose mean age was 47 +/- 15.6 years (+/- 1 SD) and whose urine cadmium levels ranged from 0.14 microgram l-1 to 20.4 micrograms l-1 (0.06-37.1 micrograms g-1 creatinine). Image analysis of the silver-stained gels yielded intensity (concentration) values for a mean number, per person, of 825 +/- 184 urinary proteins (spots) and found 596 +/- 218 matched proteins (the same proteins in two or more gels) per person. Total urinary protein and the sum of all spot intensities were positively correlated (P = 0.0447 and P = 0.0616, respectively) with urinary cadmium (UCD), as measured by atomic absorption spectroscopy. The combined sum of the intensities of all acidic proteins with a relative molecular weight (M(r)) below 40 kDa was correlated with UCD (P = 0.0461), revealing a low M(r), acidic proteinuria as UCD increased. Multiple hypothesis testing by regression analysis of the intensities of matched proteins with UCD revealed 14 unidentified proteins that were considered candidates for biomarkers of cadmium exposure. The best two candidate proteins--those having M(r)s of less than 13.9 kDa and relative glyceraldehyde-3-phosphate dehydrogenase (G3PDHr) coordinates of -19.7 and -27.2--were excellently resolved in the 2DE gels, and their intensities increased by 323% and 857%, respectively, over the UCD range that was tested. Two other proteins with M(r)s of 23.9 kDa and 29.2 kDa and with acidic net charges were not as well resolved. Six very acidic proteins, with M(r)s ranging from 88.8 to 90.7 kDa and with intensities highly correlated with UCD, appeared to be related and were resolved as a 'charge train' (a group of related proteins, or isoforms, differing only by small changes in net charge). Four proteins appeared to increase only when the UCD concentration was above a threshold of 16 micrograms l-1.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"137-46"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19494977","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":"Single-stranded regions in yeast mitochondrial DNA revealed by pulsed-field gel electrophoresis.","authors":"R Maleszka","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Klenow fragment of E. coli DNA polymerase together with pulsed-field gel electrophoresis (PFGE) have been used to investigate the presence of single-stranded DNA (ssDNA) regions in yeast (Torulopsis glabrata) DNA. Electrophoretic profiles of total DNA from Rho+ (wild type) and Rho0 (no mitochondrial DNA) strains demonstrate that this method mediates the incorporation of labelled dATP into mitochondrial DNA (mtDNA), but not into chromosomal DNA. The majority of ssDNA (> 62%) has been found associated with the electrophoretically inert component, localized on the top of PFGE gels. Treatment with single-stranded nucleases allows the resolution of this immobile fraction into fast migrating, linear molecules of a heterogeneous size. The possibility that single-stranded tracts and their recombinogenic properties are responsible for the trapping of DNA in pulsed-field gels is discussed.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"259-63"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19188909","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":"Mechanical precision in two-dimensional electrophoresis can improve protein spot positional reproducibility.","authors":"M G Harrington,&nbsp;K H Lee,&nbsp;M Yun,&nbsp;T Zewert,&nbsp;J E Bailey,&nbsp;L Hood","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Current methods for high resolution two-dimensional electrophoresis (2DE) of proteins are capable of separating over 5000 protein spots in one procedure. Running and analysing such 2DE gels requires skilled technical work. However, the variable reproducibility of spot positions means that, even under the best circumstances, one gel cannot be overlain directly on another for precise comparison. Therefore, new and improved technologies that enhance gel-to-gel reproducibility are required. To this end, we have designed and built a research instrument to test whether a precise mechanical device could improve the gel-to-gel reproducibility by reducing the amount of distortion and positional variation between the first and second dimension gels. Other causes of poor reproducibility, including sample type and preparation, gel matrices and running conditions were not varied in order to limit this study to the mechanical variations inherent in current 2DE systems. We found that the sample standard deviation of pooled data for measured protein spot-to-spot distances in the prototype device was 1.3 mm as compared to 4.3 mm in a conventional 2DE system. These improvements support the possibility that greater automation of the multistep 2DE process will enhance reproducibility. This approach seems justified in order to achieve significantly better matching between gels and between results from different laboratories.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"347-53"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19189495","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":"Spectrophotometric quantitation of DNA on blots after ethanol-solubilization of the MTT-formazan from anti-digoxigenin-based detection of nucleic acids.","authors":"D J Colgan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The tetrazolium salt, 3-(4,5-dimethyl-thiazolyl-2)-2,5-diphenyl tetrazolium bromide (MTT) has recently been established as a substitute for Nitro-blue tetrazolium (NBT) in stain mixtures using antibody-conjugated alkaline phosphatase for the location of proteins on Western blots (Heegaard, 1990). Experiments reported here show that MTT is as sensitive as NBT in digoxigenin-labeled probe localization (on nucleic acid blots) utilizing alkaline-phosphatase-labelled, anti-digoxigenin antibodies. Moreover, as the formazan from MTT is soluble in ethanol, it is shown that spectrophotometric quantitation can be used to estimate the amount of target DNA on dot and Southern blots. For dot blotting, pBR328 was used as the probe and pBR322 as target. For Southern blots, human rDNA was used as the probe and total genomic calf DNA as the target. Staining response was linear over at least six twofold DNA dilutions in both types of blot.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 5","pages":"219-22"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"18695759","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":"Restriction sites as identification tags for the gene catalog: a 2D gel model.","authors":"J R Frey,&nbsp;J R Kettman,&nbsp;I Lefkovits","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In our effort to collect, organize and assemble data from lymphocyte cDNA libraries, we assign DNA restriction sites collectively to the spots on two-dimensional (2D) gel patterns. In order to test the efficiency and reliability of such an approach, we have modeled the restriction analysis of cDNA libraries with a panel of restriction endonucleases. The work has two parts. In the first, we have chosen 255 proteins from the EMBL data base and determined whether or not their coding sequences contain restriction sites for the enzymes of our choice. In order to apply a sufficient discriminatory power we decided to use a relatively large number of cleaving enzymes with low and high cutting frequencies. In total, 13 restriction enzymes were chosen, which could distinguish 2(13) or 8192 different restriction site combinations. We have compiled a table in which the absence or presence of restriction sites yields a pattern of 'zeros' and 'ones'. Such a restriction pattern can be read as a binary number. The binary numbers with maximally 13 digits would uniquely assign each of the 255 proteins if the nucleotide sequences would be truly at random. As the restriction sites are not randomly distributed, the 'typing' does not yield a unique assignment. The choice of sequences was not random either. In fact, there are some human nucleotide sequences which possess the same cut number (the decimal equivalent of the binary number representing the restriction pattern). In spite of this redundancy, 141 coding sequences could uniquely be distinguished by the above treatment. In the second part of the project we have used the above mentioned coding sequences to prepare two-dimensional maps (plots of charge vs size) of the same kind as one obtains from experimental 2D gels and submitted such a map together with 13 maps of restriction enzyme treated populations to a computer image analysis. Ideally, one would expect results (cut numbers) congruent to those obtained in the first part of the work. In the modeled system we were confronted with 2D maps which closely resembled the experimental situation (e.g. some spots were close together and overlapping) and instances of incorrect spot detection yielding 'false cut numbers'. From 255 proteins we were able to assign unequivocally 161 proteins. To implement the model in an actual experiment we will perform the digestion with the restriction enzymes in duplicate, and only spots assigned the same cut number upon the two independent treatments will be considered as carrying a valid restriction tag.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 6","pages":"283-96"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19188913","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":"Concanavalin A affinity immunoelectrophoresis of slowly migrating glycoproteins by chemical charge modification.","authors":"P M Heegaard,&nbsp;T C Bøg-Hansen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A method for the study of slowly migrating glycoproteins by lectin-affinity immunoelectrophoresis is described. The principle of the method is to modify chemically the polypeptide part of the glycoprotein in question to increase the net negative charge of the molecule without affecting the carbohydrate parts. In a model experiment, desialylated human alpha 1-acid glycoprotein is modified and it is shown by lectin affinity immunoelectrophoresis that glycan-bound sialic acid does not influence the binding of human alpha 1-acid glycoprotein to concanavalin A. Additionally, the method is used to study the carbohydrate-based microheterogeneity of slowly migrating mouse serum glycoproteins, and hitherto undetected microheterogeneity inherent in mouse transferrin and mouse haemopexin is detected and described in normal and inflammatory mice.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 5","pages":"213-7"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19207910","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":"Resolution of DNA in the presence of mobility modifying polar and nonpolar compounds by discontinuous electrophoresis on rehydratable polyacrylamide gels.","authors":"R C Allen,&nbsp;B Budowle,&nbsp;D J Reeder","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Ultrathin-layer rehydratable gels were surface loaded and run in the horizontal position to study effects of mobility modification of DNA. Mobility modification of DNA fragments was achieved by the addition of nonpolar monosaccharides and their corresponding sugar alcohols as well as with glycerol and ethylene glycol in the leading ion buffer. These compounds show little effect when included in the trailing ion buffer. Disaccharides show no mobility modification. Trailing ions such as serine and members of the Good buffer series reduced also the RF of double- or single-stranded DNA. While beta-alanine had no effect, serine and members of the Good buffer series, particularly MOPSO, showed a marked ability to decrease the RF; presumably due to changing the unstacking limits. Rapid separation of sequencing gels with high resolution was achieved with discontinuous buffer systems. The potential methodology for high-resolution scanning of gels as DNA zones unstack from the moving boundary is suggested.</p>","PeriodicalId":77007,"journal":{"name":"Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society","volume":"3 3-4","pages":"173-81"},"PeriodicalIF":0.0,"publicationDate":"1993-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19494981","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}