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

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

We are developing a relational database to facilitate quantitative and qualitative comparisons of proteins in human body fluids in normal and disease states. For decades researchers and clinicians have been studying proteins in body fluids such as serum, plasma, cerebrospinal fluid and urine. Currently, most clinicians evaluate only a few specific proteins in a body fluid such as plasma when they suspect that a patient has a disease. Now, however, high resolution two-dimensional protein electrophoresis allows the simultaneous evaluation of 1,500 to 3,000 proteins in complex solutions, such as the body fluids. This and other high resolution methods have encouraged us to collect the clinical data for the body fluid proteins into an easily accessed database. For this reason, it has been constructed on the Internet World Wide Web (WWW) under the title Protein Disease Database (PDD). In addition, this database will provide a linkage between the disease-associated protein alterations and images of the appropriate proteins on high-resolution electrophoretic gels of the body fluids. This effort requires the normalization of data to account for variations in methods of measurement. Initial efforts in the establishment of the PDD have been concentrated on alterations in the acute-phase proteins in individuals with acute and chronic diseases. Even at this early stage in the development of our database, it has proven to be useful as we have found that there appear to be several common acute-phase protein alterations in the plasma and cerebrospinal fluid from patients with Alzheimer's disease, schizophrenia and major depression. Our goal is to provide access to the PDD so that systematic correlations and relationships between disease states can be examined and extended.

To increase the efficiency with which the phenotype of bacteriophage mutants is determined by gel electrophoresis, procedures are developed here for the preparation of the contents of bacteriophage plaques for gel electrophoresis. During the formation of plaques, the plaque-supporting upper layer gel is changed from the traditional agar gel to a gel made of a mixture of low-melt agaroses; the lower layer gel is eliminated. To extract particles from plaques, the plaque-supporting gel is disintegrated by both shaking and raising the temperature to 39-43 degrees C. During shaking, the gel is broken to domains that are 5-30 microns in diameter. After extraction, the contents of plaques are subjected to two electrophoretic analyses: (1) Nondenaturing agarose gel electrophoresis is performed after treatment with DNase. This procedure reveals both mature bacteriophage and immature capsids. (2) Nondenaturing agarose gel electrophoresis is performed after release of DNA from DNase-treated capsids. This latter procedure reveals both completely packaged (mature length) DNA and incompletely packaged (shorter than mature length) DNA. The amount of mature length DNA released per 2-3 mm plaque is 10-60 ng. In agreement with results previously obtained in liquid culture, most incompletely packaged DNA has the right, but not the left, mature T7 DNA end.

The HPGE-1000 apparatus (LabIntelligence, Menlo Park, CA) is a gel electrophoresis instrument with intermittent fluorescence scanning of the migration path and with preparative capability. An electroelution cup sealed with gel is placed onto the band of interest, identified and located under computer control, and the band is electroeluted into the cup at a right angle to the orientation of the resolving gel. The correct location of the eluted band and the degree of its recovery into the elution cup are then verified on the gel pattern, visualized on the computer screen. Using that procedure, SDS-conalbumin-FLUOS was electrophoresed at 5 V/cm in a discontinuous tricinate-chloride-Tris system at loads of 0.25 to 20 micrograms, using 5% agarose (MetaPhor, FMC), 0.03% SDS gel at 5 degrees C. The horizontal gel was partitioned at the sample loading slit between a gel in Tris-tricinate (prepared at the concentrations of an operative phase ZETA) and in Tris-chloride (prepared as phase BETA). The elution cup was sealed with the latter gel and overlayered with buffer of the composition of the former. This arrangement should provide for electroelution of the band as a highly concentrated stack. At electroelution times of 2, 3.5, 4-5, 12, 15 and 15 min at 15 V/cm yields were 58, 60, 54-76, 99, 99 and 84% for loads of 0.25, 0.5, 1, 4, 10 and 20 micrograms, respectively. At the most sensitive scale of detection (13), a full-scale peak was obtained at a load of 1.7 micrograms when the fluorophore (FLUOS, Boehringer-Mannheim) to protein ratio was 10:1. Similarly, homogeneous nucleosomal DNA (146 bp), electrophoresed in 0.2 x TBE buffer at a load of 5 micrograms, was near-quantitatively recovered into the same buffer by electroelution at 15 V/cm for 2.5 or 6 min.

We developed a simple, rapid and inexpensive method of DRB1 alleles genotyping by digestion of amplified DNA with allele-specific restriction fragments endonucleases. We took advantage of this protocol, initially described by Yunis et al. (1991) and called AFLP (Amplification Length Fragment Polymorphism) to standardise amplification procedure. Typing strategy was particularly studied to limit the number of restriction endonucleases. The determination of DRB1 allele was established on lysed fragments size which allows: (1) the absence of nonidentified allele and (2) a nonambiguous determination of each heterozygous allele. Six specific pairs of primers were chosen to amplify three generic groups: HLA DR 124 (DRB1 1, 2 and 4), HLA DR356810 (DRB1 3, 5, 6, 8 and 10) and DR79 (DRB1 7 and 9) with the same PCR protocol. Forty-eight from the 60 DRB1 alleles may be identified without any ambiguity. With our protocol, the three alleles associated with the most important autoimmune diseases (i.e., DRB1*02, *03 and *04) were totally subtyped. Our amplification procedure is reliable and extremely useful in routine-practice for the study of HLA-DRB1 genotyping of large series of samples and for the determination of DRB1 susceptibility factors involved in different autoimmune diseases.

The commercial automated gel electrophoresis apparatus (HPGE-1000 of LabIntelligence, Menlo Park, CA) allows one to recover the material migrating and visualized as a fluorescent-labeled band by electrophoresis into a collection cup located above the band at a right angle to the orientation of the separation path. The degree of recovery is a function of sample load (peak area), electrophoresis time at constant field strength, the mobility of the material and band width. Neglecting the latter, recovery of several SDS-proteins was measured as a function of the first three parameters. These measurements were used as a data base for a computer program capable of predicting, by interpolation of the experimental values, the time of electrophoresis needed to obtain a specified degree of recovery, or the degree of recovery obtained after a desired time of electrophoresis into the collection cup.

Electrophoresis in polymer solutions of a fluorescently labeled polystyrene carboxylate particle of 46.5 nm radius was carried out in a horizontal gel electrophoresis apparatus with intermittent scanning of the migration path. Polymers of the order of 10(6) (dextran, polyvinylpyrrolidone, polyacrylamide and polyethyleneglycol) and 10(5) (hydroxyethylcellulose, polyethyleneglycol) M(r) were used. In each application, bands formed, became symmetric and narrowed with increasing polymer concentration. The decrease in dispersion coefficients, D', with polymer concentration was sharpest with the polymers of M(r) 10(6); but significant differences in the effectiveness of polymers within that group also exist which are not accounted for. Provided that the demonstrated feasibility of banding in concentrated polymer solutions will allow for separations similar to those achieved at low polymer concentrations in CZE, the method promises to overcome the inherent shortcomings of capillary electrophoresis in polymer solutions with regard to inaccessibility of bands for immunological and affinity detection as well as to preparative scale and preparative instrumental complexity.

Toxicologic studies in rodents demonstrate that two-dimensional polyacrylamide gel electrophoresis of proteins (2DE) is very useful in the detection and evaluation of chemical toxicity by providing information regarding cellular status at the molecular level. Identification of a set of specific biomarkers of exposure or effect, with a proclivity for both a particular rodent and human target tissue, is required for development of an electrophoretically based testing system. In this regard, stress proteins, such as the heat shock and glucose-regulated proteins (Hsp and Grp), are appropriate candidates. The present investigation was undertaken to identify these stress proteins on conventional two-dimensional electrophoretic gel patterns of human and rat liver homogenates. The following stress proteins were identified, their x, y coordinate positions mapped, and abundances determined, and these data statistically analyzed and compared: Hsp25, Hsp32, Hsp60, Hsc70, Hsp70, Hsp90, Grp75, Grp78, Grp94, protein disulfide isomerase (PDI), and ER-60. With the exception of Hsp25 and Hsp32, the stress proteins examined were constitutively expressed at detectable levels in both unstressed human and rat liver; in virtually identical patterns. Based on our results, the human hepatic 2DE stress protein pattern seems well-suited to toxicologic screening particularly in in vitro applications and via extrapolations from rodent exposures.

Numerous abnormalities have been reported to exist in tissues outside the central nervous system in Alzheimer's disease (AD), supporting the conception of the illness as a systemic disorder. Two-dimensional (2-D) polyacrylamide gel electrophoresis with an immobilized pH gradient of 4-8 in the first dimension combined with computer-assisted image analysis was applied in investigation of extraneuronal proteins of blood cell origin in AD to search for extraneuronal markers. No qualitative protein changes specific for the condition could be observed. However, many statistically significant quantitative alterations were detected when AD and control 2-D patterns of extracts prepared from red blood cell membranes, platelets and lymphocytes were compared. One of these spots, with a marked change in mean intensity value, was identified as actin. The concentration of this protein was significantly reduced in AD platelets and lymphocytes.