The protein disease database.
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Databases, Factual↗
Biomedical subjects
J E Myrick
Publications and source records attributed to J E Myrick.
Two-dimensional protein electrophoresis and multiple hypothesis testing to detect potential serum protein biomarkers in children with fetal alcohol syndrome.
Fetal alcohol syndrome (FAS) surveillance and intervention efforts are hampered by the lack of a specific biochemical test for diagnosis of the syndrome. Based on the hypothesis that abnormalities in growth and development (key features of FAS) involve altered protein metabolism, we analyzed serum proteins by two-dimensional gel electrophoresis and image analysis to search for potential protein biomarkers of FAS. Serum samples from 12 participants in whom FAS had been diagnosed and 8 sex- and age-matched participants whose mothers did not consume alcohol were analyzed in duplicate to determine whether the integrated intensities of matched proteins are significantly altered in children with FAS. Multiple hypothesis testing on 34 of the gels consisting of more than 1700 spots per gel revealed 21 proteins that we classified as potential protein biomarkers of FAS on the basis of significant t-test differences at p < 0.02. We classified 8 of the proteins as candidate biomarkers on the basis of significant concentration differences between case and control subjects at p < 0.01. One of the proteins is clearly an isoform of retinol binding protein; two appear in the area of the gel where alcohol dehydrogenase is expected to appear; one appears to be an isoform of alpha-1-antitrypsin; three appear to be isoforms of the beta-chain of haptoglobin; three may be forms of immunoglobulin light chains; and several others have not been associated with known proteins. No single protein differentiated all case subjects from control subjects, but stepwise canonical discriminant analyses revealed four groups of spots that distinguished between FAS case and control subjects with no misclassifications.(ABSTRACT TRUNCATED AT 250 WORDS)
Biomarkers↗
The protein disease database of human body fluids: I. Rationale for the development of this database.
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.
Body Fluids↗
The Protein Disease Database of human body fluids: II. Computer methods and data issues.
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.
Body Fluids↗
Comparison of the Bio Image Visage 2000 and the GELLAB-II two-dimensional electrophoresis image analysis systems.
To compare the Visage 2000 analysis system (Bio Image, Ann Arbor, MI, USA) with the GELLAB-II analysis system (National Cancer Institute, Frederick, MD, USA), we used each to perform image analysis of the same 29 silver-stained two-dimensional electrophoresis (2DE) gel image files from a study of urinary proteins in metal recovery plant workers who had confirmed body burdens of cadmium. Visage, aided by interactive analysis, detected an average of 890 +/- 177.6 spots per gel, or a total of 25,800 spots, whereas GELLAB-II detected 1971 +/- 198.5 spots per gel, or a total of 57,160 (a 222% increase over the Visage system), without operator intervention. Visage automatically quantified 52.5% (13,556) of the spots; 47.2% (12,173), consisting mostly of larger spots, had to be quantified interactively with an image editor, and 0.3% (71) were not quantified. GELLAB-II automatically quantified all detected spots. After we interactively assigned the maximum allowed number of landmarks (30 for Visage and 52 for GELLAB-II), we found that Visage matched 657 +/- 211.2 spots per gel, and GELLAB-II matched all detected spots and also extrapolated an average of 1269 virtual spots per gel. Plots of densities from the two systems on selected spots showed excellent agreement, and both systems showed high correlation between their measurements of the beta-2-microglobulin spot densities and an independent radioimmunoassay quantification of the original urine samples. By comparing the regression of the densities of all spots with urinary cadmium (UCD) levels, we found that several of the same detected spots from each system were highly correlated. The densities of four acidic proteins with relative molecular weights of approximately 112,000 Da (as quantified by GELLAB-II but not by Visage) were highly correlated with UCD concentrations. These proteins are new candidate biomarkers of cadmium toxicity. We compared the estimated labor costs of using each system to analyse a hypothetical 20-sample (60 gels) 2DE study and found that GELLAB-II was six times less expensive to use than Visage, primarily because of the operator time required to do interactive error correction with the Visage system.
Cadmium↗
Exploratory data analysis in two-dimensional electrophoresis.
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.
Blood Protein Electrophoresis↗
Quantitative two-dimensional electrophoretic detection of possible urinary protein biomarkers of occupational exposure to cadmium.
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.
Adult↗
Splitting merged spots in two-dimensional polyacrylamide gel electrophoresis gel images.
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.
Algorithms↗
Identification of haptoglobin alpha-2FF variants in mid-trimester maternal serum as potential markers for Down syndrome.
Exploratory protein analysis in mid-trimester maternal sera by 2-dimensional electrophoresis and image analysis was performed to determine the differences between mothers carrying fetuses with Down syndrome (DS) and control mothers. Nine haptoglobin alpha-1 and alpha-2 (Hp1 and Hp2) variants were detected. Three apparent isoforms of the Hp2FF protein having the same relative charge but different Mr's were detected, with the two smaller variants--Hp2FF (-0.7k) and Hp2FF (-1.3k)--believed to be first reported here. Ninety-two percent of the cases (n = 83) had the Hp2FF (-0.7k) protein, and 61% had Hp2FF (-1.3k). The geometric mean concentration of Hp2FF (Mr = 18.0 kd) was found to be significantly increased (P less than 0.01) in mid-trimester sera from cases (n = 27) compared to controls (n = 56). When the concentrations of the three Hp2FF isoforms were added, the cases had larger sums on average than controls (P less than 0.01).
Age Factors↗
Potential virulence factors of Haemophilus influenzae biogroup aegyptius in Brazilian purpuric fever. The Brazilian Purpuric Fever Study Group.
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Brazil↗
An improved radioimmunoassay of C-peptide and its application in a multiyear study.
A commercial radioimmunoassay (RIA) for human proinsulin C-peptide was modified to improve its ruggedness and specificity, to decrease the influence of specimen matrix, and to shorten "hands-on" time. In the new protocol, we prepare calibrators in a C-peptide-free serum pool, prepared by treatment with activated charcoal (biological matrix), instead of in a defined matrix. This yielded essentially 100% analytical recoveries for C-peptide concentrations up to 300 pmol/L, a broader analytical range. We also corrected calibrators and unknown samples for nonspecific binding (NSB). Decreasing the concentration of ethanol (from 950 to 880 mL/L) for differential precipitation of the antigen-antibody complex resulted in an NSB of less than 10%, while maintaining high bound/total count percentages for samples and calibrators. C-peptide is thermally unstable without aprotinin at -20 degrees C and with or without aprotinin at 4 degrees C or above, but multiple freeze-thaw cycles do not affect C-peptide in serum. The modified C-peptide assay was applied to plasma from a multiyear study (fasting and post-carbohydrate-challenge subjects). During the four years of the study CVs ranged from 1.9% to 8.6% for replicate analyses of C-peptide in samples with concentrations less than or equal to 500 pmol/L. Between-run CVs were 3.8% to 8.2%, total CVs 3.8% to 10.7%.
Buffers↗
High-density lipoprotein apolipoproteins in urine: I. Characterization in normal subjects and in patients with proteinuria.
A high-resolution two-dimensional electrophoretic method for protein, with silver staining, has been used to characterize and identify urinary high-density-lipoprotein apolipoproteins (HDL-Apos) and their isoforms in healthy subjects and in patients with kidney disease. Analytical techniques based on both molecular mass and ultracentrifugal flotation properties were used to isolate urinary lipoprotein particles with characteristics identical to those of HDL in plasma. HDL-Apos identified in urine of normal subjects and patients with glomerular proteinuria were Apos A-I, A-II, and C. Five isoforms of Apo A-I were present. Immunostaining of electroblotted proteins further confirmed the presence of HDL-Apos in urine. Creatinine clearance rate was decreased in the patients with proteinuria, and ranged from 32.5 to 40 mL/min. Concentrations of cholesterol and triglycerides in serum were greater in the patients' group, whereas mean HDL-cholesterol (0.68, SD 0.10 mmol/L) and Apo A-I (0.953, SD 0.095 g/L) were significantly (each P less than 0.01) lower. Results of this study suggest that measurement of urinary Apo A-I will reflect excretion of HDL in urine.
Apolipoprotein A-I↗
Effects of polybrominated biphenyls upon rat urinary protein patterns as detected by two-dimensional electrophoresis.
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Animals↗
Inflammatory mediators and modulators released in organ culture from rabbit skin lesions produced in vivo by sulfur mustard. III. Electrophoretic protein fractions, trypsin-inhibitory capacity, alpha 1-proteinase inhibitor, and alpha 1- and alpha 2-macroglobulin proteinase inhibitors of culture fluids and serum.
This is the third report in a series on the inflammatory mediators and modulators released in organ culture from skin lesions of various ages, which were produced in vivo in rabbits by the military vesicant, sulfur mustard (SM). It describes the electrophoretic protein fractions and trypsin-inhibitory capacities of the various culture fluids and the amounts of alpha 1-proteinase inhibitor and alpha-macroglobulin proteinase inhibitors in these fluids. With one-dimensional electrophoresis, the albumin and beta-globulin fractions of protein in culture fluids varied little with the development and healing of the SM lesions. These fractions proportionally resembled the corresponding fractions found in serum. The alpha 1-globulin fraction was proportionally smaller than the corresponding fractions of serum as the lesions healed. The alpha 2-globulin fraction was proportionally smaller than the corresponding fractions of serum at all stages of lesion development and healing. The gamma-globulin fraction was proportionally larger as the lesions healed. With two-dimensional electrophoresis, about 68%, 46%, and 35% of the protein spots in culture fluids from representative 1-day and 6-day SM lesions and normal skin, respectively, matched those from serum. In each case, the large, diffuse, serum albumin spot represented about two-thirds of the protein present. Thus, gravimetrically, in normal skin and in both developing and healing lesions, the extracellular proteins were 80-90% of serum origin. The trypsin-inhibitory capacity (TIC) per milligram protein in the culture fluids of healing lesions was markedly less than the TIC per milligram protein in the fluids of peak lesions. This decrease correlates well with the decrease found in the alpha 1-globulin fraction, which contains alpha 1-antiproteinase (alpha 1-PI) (and alpha 1-macroglobulin [alpha 1M] in rabbits). The alpha 1PI and the alpha 1M-alpha 2M proteinase inhibitors were identified in the culture fluids by means of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Western blots, specific antibodies, and the immuno-peroxidase technique. The levels of both free and proteinase-complexed alpha 1PI and alpha M inhibitors in the culture fluids decreased as the lesions healed. In both developing and healing lesions, at least half of the alpha 1PI and alpha M inhibitors seemed to be complexed with proteinases. Thus, serum seems to be a major source of unbounded extracellular protein within acute inflammatory lesions, and serum proteinase inhibitors seem to be the host's major defense against local damage by proteinases from serum, infiltrating leukocytes, and activated fibroblasts.
Aging↗