Ferritin: A Biomarker Requiring Caution in Clinical Decision

OBJECTIVES

To determine the ferritin inter-assay differences between three "Conformité Européenne" (CE) marked tests, the impact on reference intervals (RI), and the proportion of individuals with iron deficiency (ID), we used plasma and serum from healthy blood donors (HBD) recruited in three different Switzerland regions.

DESIGN AND METHODS

Heparinized plasma and serum from HBD were obtained from three different transfusion centers in Switzerland (Fribourg, Geneva, and Neuchatel). One hundred forty samples were recruited per center and per matrix, with a gender ratio of 50%, for a total of 420 HBD samples available per matrix. On both matrices, ferritin concentrations were quantified by three different laboratories using electrochemiluminescence (ECL), latex immunoturbidimetric assay (LIA), and luminescent oxygen channeling immunoassay (LOCI) assays, respectively. The degree of agreement between matrices and between the three sites/methods was assessed by Passing-Bablok and we evaluated the proportion of individuals deemed to have ID per method.

RESULTS

Overall, no difference between serum and heparinized plasma ferritin values was observed according to Passing-Bablok analyses (proportional bias range: 1.0-3.0%; maximum constant bias: 1.84 µg/L). Significant median ferritin differences (p < 0.001 according to Kruskal-Wallis test) were observed between the three methods (i.e., 83.6 µg/L, 103.5 µg/L, and 62.1 µg/L for ECL, LIA, and LOCI in heparinized plasma, respectively), with proportional bias varying significantly between ±16% and ±32% on serum and from ±14% to ±35% on plasma with no sign of gender-related differences. Affecting the lower end of RI, the proportion of ID per method substantially varied between 4.76% (20/420) for ECL, 2.86% (12/420) for LIA, and 9.05% (38/420) for LOCI.

CONCLUSIONS

Serum and heparinized plasma are exchangeable for ferritin assessment. However, the order of magnitude of ferritin differences across methods and HBD recruitment sites could lead to diagnostic errors if uniform RI were considered. Challenging the recently proposed use of uniform ferritin thresholds, our results highlight the importance of method- and region-specific RI for ferritin due to insufficient inter-assay harmonization. Failing to do so significantly impacts ID diagnosis.

High-sensitive cardiac troponin T as a marker of hemorrhagic complications in elderly patients anticoagulated for non-massive pulmonary embolism

BACKGROUND

Recent data have raised concerns about the risk/benefit ratio of thrombolysis in non-high risk pulmonary embolism patients due to increased serious bleeding events. Whether cardiac biomarkers could be of help for bleeding risk stratification in this setting remains elusive.

OBJECTIVES

To determine the prognostic accuracy of hs-cTnT, NT-proBNP, RIETE and PESI score for the occurrence of clinically relevant bleeding (CRB) in elderly patients under conventional anticoagulation therapy for non-massive pulmonary embolism (NMPE).

METHODS

We evaluated 230 elderly patients with available blood sample taken within one day from diagnosis. The primary study endpoint was CRB at 1, 3 and 24 months. Prognostic accuracies and associations were determined using C-statistics and subhazard ratios (SHR), respectively.

RESULTS

hs-cTnT displayed the highest discriminatory power at 1 month (C-statistics: 0.77, 95% CI: 0.68-0.88) which remained stable over time. Although C-statistics comparison indicated that hs-cTnT was not statistically superior to RIETE score (0.77 vs 0.67, p = 0.11), adding hs-cTnT to RIETE score significantly improved the C-statistics from 0.67 to 0.78 (p = 0.02). SHRs indicated that for each hs-cTnT log-unit increase, there was a 58% increase in the risk of CRB independently of the RIETE score (adjusted SHR: 1.58, 95% CI: 1.31-1.92). At the pre-specified cut-off of 14 ng/l, the negative predictive value of hs-cTnT was 96.9% (95% CI: 91.4-99.0) and 94.9 (95%CI: 88.6-97.8) at 1 and 3 months, respectively.

CONCLUSION

In elderly, hs-cTnT provides incremental prognostic information over the RIETE score and could represent a valuable tool to identify NMPE patients at low risk of bleeding.

CRP-Based Cardiovascular Risk Assessment: New Conventional CRP Assay Fit for Purpose?

BACKGROUND

Subclinical inflammation was shown to play a role in the context of cardiovascular disorder processes. American College of Cardiology/American Heart Association guidelines on cardiovascular risk assessment in specific clinical contexts recommend the use of C-reactive protein (CRP) measurement with high sensitive (hs)-CRP assays that meet the precision requirements for values <2 mg/L. Until now, only hs-CRP assays reached the required limit of quantification. However, new regular CRP assays allow measuring CRP down to 0.6 mg/L.

METHODS

A multisite comparative study between hs-CRP and a new conventional CRP assay (Tina-quant) was performed to evaluate the possibility of using regular CRP assays for cardiovascular risk assessment.

RESULTS

A satisfactory concordance was observed between regular CRP assays and the hs-CRP assay. Both assays met the analytical precision requirements at the different cutpoints tested (1.00, 2.00, and 3.00 mg/L).

CONCLUSION

These results suggest that this new regular CRP assay can be used for cardiovascular risk assessment, which is expected to provide substantial operational and financial advantages when compared with hs-CRP assays.

Sharing of Worldwide Spread Knowledge Using Hypermedia Facilities & Fast Communication Protocols (Mosaic and World Wide Web): The Example of ExPASy

The sharing of knowledge worldwide using hypermedia facilities and fast communication protocols (i.e., Mosaic and World Wide Web) provides a growth capacity with tremendous versatility and efficacy. The example of ExPASy, a molecular biology server developed at the University Hospital of Geneva, is striking. ExPASy provides hypermedia facilities to browse through several up-to-date biological and medical databases around the world and to link information from protein maps to genome information and diseases. Its extensive access is open through World Wide Web. Its concept could be extended to patient data including texts, laboratory data, relevant literature findings, sounds, images and movies. A new hypermedia culture is spreading very rapidly where the international fast transmission of documents is the central element. It is part of the emerging new “information society”.

Impact of long distance rowing on biological health: A pilot study

OBJECTIVES

To determine the impact of long distance rowing (160km, nonstop) on standard biological parameters and to study the relation between inflammation, myocardial necrosis, lipid profile, heart rate and energy expenditure.

METHODS

Electrolytes, lipid profile, C-reactive protein (CRP), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), procalcitonin (PCT), high-sensitive troponin T (hs-cTnT), and N-terminal pro-brain natriuretic peptide (NT-proBNP), were measured on non-fasting venous blood samples collected 8h before and after the rowing race on five healthy competitors. Heart rate and energy expenditure were measured using sporting self-measurement devices.

RESULTS

After 16.5h of race, significant increases in median CRP (+25.2mg/l; p=0.04), IL-6 (+1.85pg/ml; p=0.04), TNF-α (+1.2pg/ml; p=0.04) and NT-proBNP levels (+88.8pg/ml; p=0.04) were observed, and a close to significant elevation for hs-cTnT(+6ng/l; p=0.06) and PCT (+0.14μg/l; p=0.07). On the other hand, significant decrease in median total cholesterol (-0.5mmol/l; p=0.04), triglycerides (-0.7mmol/l; p=0.04) were observed. Furthermore, significant correlations between the maximal heart rate reached during the race and CRP (r=0.90; p=0.03), IL-6 (r=0.90; p=0.03), and NT-proBNP (r=0.90; p=0.03) were observed, whereas no such associations were retrieved with median heart rate, the percentage of time passed over 70% of maximal heart rate or energy expenditure during the race. There was no association between PCT, NT-proBNP, hs-cTnT, inflammatory biomarkers, lipid profile or heart rate parameters.

CONCLUSIONS

Long distance rowing induces inflammation and myocardial strain related to the maximal effort generated during the race, but has a favourable effect on lipid profile.

Allopurinol, oxidative stress and intestinal permeability in patients with cirrhosis: an open-label pilot study

BACKGROUND

Cirrhosis is associated with intestinal barrier failure, related in part to enterocytes oxidative damage via xanthine oxidase overactivity. Experimentally, allopurinol, a xanthine oxidase inhibitor, reduces enterocytes' damage and bacterial translocation.

AIM

To assess the short-term effects of allopurinol on intestinal permeability, oxidative stress and endotoxin-dependent cytokines in patients with cirrhosis.

METHODS

Nineteen patients with cirrhosis, in a stable condition (age: 56 years; Child A/B/C: 6/7/6; ascites: 12; alcoholic cirrhosis: 16/19; abstinence >2 weeks), were included. At baseline and day 10 of allopurinol 400 mg/day, intestinal permeability [lactulose/mannitol (Lac/Man) ratio test], oxidative stress (serum malondialdehyde), as well as TNF-soluble receptor-1, IL-6 and lipopolysaccharide-binding protein (which reflects exposition to endotoxin) were measured.

RESULTS

Malondialdehyde decreased significantly (-23%, P<0.05), whereas no effects were seen on intestinal permeability and the endotoxin-associated systemic inflammatory response. At baseline, portal pressure correlated to the Lac/Man ratio (r=0.55, P<0.02). At day 10, changes in malondialdehyde correlated to changes in the Lac/Man ratio (r=0.51, P<0.05).

CONCLUSIONS

A 10-day course of allopurinol in patients with cirrhosis is associated with a significant reduction in oxidative stress but no effect on intestinal permeability and inflammatory markers. Whether intestinal damage in cirrhosis can be accessible to antioxidant therapy requires further study.

MODULAR ANALYTICS: A New Approach to Automation in the Clinical Laboratory

MODULAR ANALYTICS (Roche Diagnostics) (MODULAR ANALYTICS, Elecsys and Cobas Integra are trademarks of a member of the Roche Group) represents a new approach to automation for the clinical chemistry laboratory. It consists of a control unit, a core unit with a bidirectional multitrack rack transportation system, and three distinct kinds of analytical modules: an ISE module, a P800 module (44 photometric tests, throughput of up to 800 tests/h), and a D2400 module (16 photometric tests, throughput up to 2400 tests/h). MODULAR ANALYTICS allows customised configurations for various laboratory workloads. The performance and practicability of MODULAR ANALYTICS were evaluated in an international multicentre study at 16 sites. Studies included precision, accuracy, analytical range, carry-over, and workflow assessment. More than 700 000 results were obtained during the course of the study. Median between-day CVs were typically less than 3% for clinical chemistries and less than 6% for homogeneous immunoassays. Median recoveries for nearly all standardised reference materials were within 5% of assigned values. Method comparisons versus current existing routine instrumentation were clinically acceptable in all cases. During the workflow studies, the work from three to four single workstations was transferred to MODULAR ANALYTICS, which offered over 100 possible methods, with reduction in sample splitting, handling errors, and turnaround time. Typical sample processing time on MODULAR ANALYTICS was less than 30 minutes, an improvement from the current laboratory systems. By combining multiple analytic units in flexible ways, MODULAR ANALYTICS met diverse laboratory needs and offered improvement in workflow over current laboratory situations. It increased overall efficiency while maintaining (or improving) quality.

Web applications for total quality management

Total quality management involves the consideration of many quality subjects as part of the management, such as quality processes, quality education, quality assurance, quality planning, quality results and quality document management. But crucial quality elements are also communication, data management and information sharing. Web applications and other associated computer communication applications such as E-mail and newsgroups, for example, offer to the laboratory environment the best tools to achieve proper communication and data management/sharing. These applications, enabling the set-up of Internet and Intranet sites, are used to share the information in the form of simple text pages or of completely interactive pages, which could comprise audio and video files, web page formulae and web data management applications. These applications are being associated to several applications and also being integrated into the laboratory information system (LIS).

Renal cell carcinoma and normal kidney protein expression

Renal cell carcinoma (RCC), a human kidney cancer from the proximal tubular epithelium, accounts for about 3% of adult malignancies. Molecular and cytogenetic analysis have highlighted deletions, translocations, or loss of heterozygosity in the 3p21-p26, a putative RCC locus, as well as in 6q, 8p, 9pq, and 14pq. Studies on phenotypic expression of human kidney tissue and on post-translational modifications in RCC have not yet provided a marker for early renal cell carcinoma diagnosis. Current diagnostic methods do not help to detect the tumor before advanced stages. We therefore used two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) to study normal and tumor kidney tissues in ten patients suffering from RCC. A human kidney protein map in the SWISS-2DPAGE database accessible through the ExPASy WWW Molecular Biology Server was established. Of 2789 separated polypeptides, 43 were identified by gel comparison, amino acid analysis, N-terminal sequencing, and/or immunodetection. The comparison between normal and tumor kidney tissues showed four polypeptides to be absent in RCC. One of them was identified as ubiquinol cytochrome c reductase (UQCR), whose locus has elsewhere been tentatively assigned to chromosome 19p12 or chromosome 22. A second polypeptide was identified as mitochondrial NADH-ubiquinone oxido-reductase complex I whose locus is located on chromosome 18p11.2 and chromosome 19q13.3. These result suggest that the lack of UQCR and of mitochondrial NADH-ubiquinone oxidoreductase complex I expression in RCC may be caused by unknown deletions, or by changes in gene transcription or translation. It might indicate that mitochondrial disfunction plays a major role in RCC genesis or evolution.

Translationally controlled tumor protein: a protein identified in several nontumoral cells including erythrocytes

The translationally controlled tumor protein (TCTP) is a growth-related protein which is regulated at the translational level. It is present in mammals, higher plants and Saccharomyces cerevisiae. This study was undertaken to localize and further characterize the TCTP in human cell lysates using two-dimensional gel electrophoresis, monoclonal antibodies, and 45Ca-gel overlay. TCTP was found in several healthy and tumoral cells including erythrocytes, hepatocytes, macrophages, platelets, keratinocytes, erythroleukemia cells, gliomas, melanomas, hepatoblastomas, and lymphomas. It could not be detected in kidney and renal cell carcinoma (RCC). A monoclonal antibody raised against TCTP detected three isoforms likely due to post-translational modifications. A calcium binding property was found as well as heat stability and cytoplasmic localization. The high degree of homology from plants to man and its expression in many tissues suggests that TCTP most likely has a cell housekeeping function.

Large-scale amino-acid analysis for proteome studies

Amino-acid analysis is a relatively new method for identification of proteins separated by two-dimensional gel electrophoresis and blotted onto polyvinylidene difluoride (PVDF) membranes. This article describes modified amino-acid analysis methods for this purpose. Streamlined sample handling is a key feature of the process. To minimise sample manipulation, a single vial is used for hydrolysis and the protein hydrolysate on PVDF membrane is extracted by a one-step procedure. The hydrolysate should not be stored for long periods before analysis. Applications of the technique are presented to demonstrate the identification procedure. This approach is the most cost-effective and time-effective first step in mass protein screening for a large-scale proteome project.

Rapid protein identification using N-terminal "sequence tag" and amino acid analysis

Proteins can be identified by amino acid analysis and database matching, but it is often desirable to increase the confidence in identity through the use of other techniques. Here we describe a rapid protein identification method that uses Edman degradation to create a 3 or 4 amino acid N-terminal "sequence tag," following which proteins are subjected to amino acid analysis protein identification procedures. Edman degradation methods have been modified to take only 23 min per cycle, and rapid amino acid analysis techniques are used. The Edman degradation and amino acid analysis is done on a single PVDF membrane-bound protein sample. A computer database matching program is also presented which uses both amino acid composition and "sequence tag" data for protein identification. This method represents the most inexpensive, accurate, and rapid means of protein identification, which is ideal for the screening of proteomes separated by 2-D gel electrophoresis. The creation of N-terminal Edman degradation "sequence-tags" prior to peptide mass fingerprinting of samples should also be useful.

The yeast SWISS-2DPAGE database

The systematic sequencing of the yeast genome will soon be completed. A new challenge has been launched by the EUROFAN (European Functional Analysis) project whose goal is to elucidate the physiological and biochemical function of newly discovered open reading frames (ORF) from yeast. One of the approaches is to use protein-based technologies such as two-dimensional gel electrophoresis and protein identification in order to establish a yeast reference map. Modified protein patterns can be compared to the reference map which hopefully will help identify changes related, for example, to growth processes or developmental events. This paper describes the yeast SWISS-2DPAGE database in which charge separation was obtained using immobilized pH gradient (IPG). Proteins identified by gel comparison, amino acid composition analysis and/or microsequencing are recorded and described in an accessible uniform format. We have identified more than one hundred polypeptides, several of which were newly mapped. In addition, the yeast SWISS-2DPAGE database can be freely accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server.

Identification of proteins by their amino acid composition: an evaluation of the method

Expression of different genomes can be studied by high-resolution two-dimensional electrophoresis (2-D PAGE). To help these studies, two-dimensional reference maps of different biological tissues and fluids have been built and can be found in the SWISS-2DPAGE database, accessible via the World Wide Web network on the ExPASy molecular biology server. Different techniques were used to identify the polypeptides. At the present time, the method considered to be the fastest and the most cost-effective is amino acid composition analysis (AAC). Proteins, transferred onto polyvinylidene (PVDF) membranes, were submitted to vapor-phase hydrolysis, derivatized with 9-fluorenylmethyl chloroformate (FMOC) and separated on an ODS-Hypersil column. Identification was obtained by using the program 'AACompIdent' available from ExPASy. In this work, different experimental parameters, such as contamination, reproducibility and accuracy, have been assessed. First, it has been found that a major source of contamination was human keratin. Next, amino acids have been classified into 'reliable' and 'nonreliable'. Accordingly, 'bias' and 'weights' were defined for each amino acid, which could be set in the 'AACompIdent' program. Finally, examples of identification, including the use of Edman degradation sequence tagging, are described.

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis

Separation and identification of proteins by two-dimensional (2-D) electrophoresis can be used for protein-based gene expression analysis. In this report single protein spots, from polyvinylidene difluoride blots of micropreparative E. coli 2-D gels, were rapidly and economically identified by matching their amino acid composition, estimated pI and molecular weight against all E. coli entries in the SWISS-PROT database. Thirty proteins from an E. coli 2-D map were analyzed and identities assigned. Three of the proteins were unknown. By protein sequencing analysis, 20 of the 27 proteins were correctly identified. Importantly, correct identifications showed unambiguous "correct" score patterns. While incorrect protein identifications also showed distinctive score patterns, indicating that protein must be identified by other means. These techniques allow large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states. The computer program described here is accessible via the World Wide Web at URL address (http:@expasy.hcuge.ch/).

Characterization of human plasma glycoproteins separated by two-dimensional gel electrophoresis

Purification of protein isoforms for the characterization of post-translational modifications, such as glycosylation, can be laborious and demanding. We report a means of determining monosaccharide composition and the identity of glycoproteins from a single spot on a two-dimensional (2-D) gel. The sensitivity of the method depends on the degree of glycosylation of the protein. We show that bovine fetuin can be analyzed and identified at the level of 100 pmol. 2-D reference maps enable quick identification of glycoprotein isoforms, and the nature of glycosylation differences. Human sera glycoforms were isolated by micropreparative 2-D PAGE using a narrow-range immobilized pH gradient. Single spots excised from one polyvinylidene difluoride blot of a 2-D gel were used sequentially for sialic acid analysis, neutral and amino sugar analysis, and finally amino acid analysis. The glycosylation variations in isoforms of human fetuin and alpha-1-antitrypsin were determined. The amino acid composition, in conjunction with protein pI and MW, successfully identified the glycoproteins.

The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995

SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (Saccharomyces cerevisiae) and Escherichia coli origin, as well as virtual entries for each of the protein sequences in the SWISS-PROT database.

Human blood platelet protein map established by two-dimensional polyacrylamide gel electrophoresis

Two-dimensional (2-D) maps of cytosol and enriched-membrane platelet proteins has allowed the identification of more than 25 spots by three different methods: matching of the platelet gels with other 2-D reference maps, immunoblotting with chemiluminescence detection, and N-terminal sequencing. Different G protein (guanosine triphosphate-binding protein) subunits, cytoskeletal proteins, and proteins common to the human liver, red blood cells and plasma were identified. The two platelet protein maps presented here contribute to the project of identification of human cell and body fluid proteins. They may serve as working tools since platelets are popular models for the study of central nervous system neurotransmitter systems and stimulus-response coupling mechanisms.

Rapid detection of the main human plasma glycoproteins by two-dimensional polyacrylamide gel electrophoresis lectin affinoblotting

Glycoprotein modifications in the glycan moiety can occur in diseases such as cancers, inflammatory processes and alcoholism. We combined high-resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) with lectin affinoblotting in order to establish the normal human plasma glycoprotein map. Human plasma proteins were separated by mini 2-D PAGE (7 x 9 cm), transferred onto polyvinylidene difluoride membranes and incubated with biotinylated lectins. We focused our study on lectins binding sialic acid and galactose residues. Known plasma glycoproteins such as alpha 1-antitrypsin, alpha 1-antichymotrypsin, alpha 2-HS glycoprotein, alpha 1-acid glycoprotein, haptoglobin beta-chain and transferrin were easily detected in ng amounts. This protocol was adequate to establish a normal plasma glycoprotein map and will allow the study of glycoproteins in diseases.

Inside SWISS-2DPAGE database

Several two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) databases have been established and updated for more than 15 years. Only recently have developments of computer networks and high-speed transfer protocols provided the required tools for sharing comprehensive and hypermedia 2-D PAGE databases. This publication describes the SWISS-2DPAGE database structure. Proteins present in samples of human tissue, cells, cell lines and body fluids are assembled and described in an accessible uniform format. SWISS-2DPAGE can be freely accessed through the World-Wide Web (WWW) network on the ExPASy molecular biology server.

Phenotyping of apolipoprotein E using immobilized pH gradient gels for one-dimensional and two-dimensional separations

Apolipoprotein E (apo E) is a normal component of several classes of plasma lipoproteins. Apo E phenotypes are closely related to total cholesterol, low density lipoprotein (LDL)-cholesterol and apo B concentration. The apo E 2/2 phenotype is related to the type III hyperlipoproteinemia due to the defective binding of apo E-2 to the hepatic receptors. The apo E 4/4 phenotype has been reported to be present in most elderly people suffering from the Alzheimer disease, and is associated with increased risk of coronary heart disease and Creutzfeld-Jakob disease. Therefore, apo E phenotyping is essential. The method described here uses a precast immobilized pH gradient, avoids time-consuming separation of lipoproteins from plasma, needs no pretreatment with neuraminidase and involves highly sensitive enhanced chemiluminescence for visualization. Therefore it has many advantages over previously published methods.

Spermatocytes and round spermatids of rat testis: protein patterns

Spermatogenesis is a process in the testis that involves meiotic cell division and spermiogenesis. The mechanisms of regulation and its associated proteins are mostly unknown. This publication shows the two-dimensional (2-D) gel electrophoresis protein map obtained from rat testis using nonlinear 3.5-10 immobilized pH gradients for the first-dimensional separation. Eighteen proteins were successfully identified in the SWISS-PROT protein database using amino acid analysis of proteins recovered from polyvinylidene difluoride (PVDF) membranes and verified for one of them by comparison with Anderson's rat liver reference map. Fourteen new polypeptides were identified and four were previously known. Two of these new proteins were closely related to the spermatogenetic process. T-complex protein 1 is expressed in large amounts in germ cells. Androgen-dependent sperm-coating glycoprotein is secreted by epididymal cells. In order to detect changes in protein expression during meiosis and spermiogenesis, spermatocytes and round spermatid cell populations were purified by centrifugal elutriation and compared. In this way several proteins not found in the spermatocyte 2-D images could be high-lighted. The sperm-coating glycoprotein was thus shown to be present in large amounts in round spermatids.

Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy

The sharing of knowledge worldwide using hypermedia facilities and fast communication protocols (i.e., Mosaic and World Wide Web) provides a growth capacity with tremendous versatility and efficacy. The example of ExPASy, a molecular biology server developed at the University Hospital of Geneva, is striking. ExPASy provides hypermedia facilities to browse through several up-to-date biological and medical databases around the world and to link information from protein maps to genome information and diseases. Its extensive access is open through World Wide Web. Its concept could be extended to patient data including texts, laboratory data, relevant literature findings, sounds, images and movies. A new hypermedia culture is spreading very rapidly where the international fast transmission of documents is the central element. It is part of the emerging new "information society".

The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis

SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of Geneva in collaboration with the Department of Medical Biochemistry of Geneva University. The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition.

Analysis of glycoproteins separated by two-dimensional gel electrophoresis using lectin blotting revealed by chemiluminescence

The carbohydrate structures of blotted glycoproteins can be analyzed by probing with lectins. The objective of the present work was to optimize the lectin blotting of human plasma glycoproteins separated by two-dimensional gel electrophoresis and the detection by the sensitive chemiluminescence method. The proposed detection method was found to be ten times more sensitive than a standard colorimetric reaction. Furthermore, the generated signals are detected on a X-ray film and provide a permanent record. The method is also very reliable when compared to the colorimetric detection. The present procedure for glycoprotein analysis is particularly well suited for screening changes in glycosylation of proteins in biological samples.

SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images

This publication presents the SWISS-2DPAGE database which gathers data on proteins identified on various two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps. Each SWISS-2DPAGE entry contains data on one protein, including mapping procedures, physiological and pathological data and bibliographical references, as well as several 2-D PAGE images showing the protein location. Links are also provided to other databases such as SWISS-PROT, EMBL, PROSITE and OMIM. The database has been set up on a server which may be accessed from any computer connected to the internet and it also makes it possible to display the theoretical location of proteins, the positions of which are not yet known on the 2-D PAGE.

Plasma and red blood cell protein maps: update 1993

This publication updates the reference plasma and red blood cell protein maps obtained with immobilized pH gradients. Seventeen polypeptide spots or chains were partially characterized by direct N-terminal sequencing or by sequencing of peptides obtained from enzymatic digestion. Additional new polypeptides and previously known proteins are listed in a table and/or labeled on the protein maps, thus providing the 1993 update of the human plasma and red blood cell two-dimensional gel SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Determination of human alcohol dehydrogenase and acetaldehyde dehydrogenase genotypes by single strand conformation polymorphism in discontinuous buffer electrophoresis

Under appropriate conditions single strand conformation polymorphism (SSCP) analysis of polymerase chain reaction (PCR) products allows the detection of single base mutations in a given DNA fragment. We adapted this method for the routine determination of allele variants of human alcohol and acetaldehyde dehydrogenase without radioisotopic labeling. After PCR amplification of the selected exon, the DNA fragments were heat-denatured and loaded on a polyacrylamide gel containing glycerol. For electrophoresis a discontinuous buffer system was used with sulfate as leading ion and borate as trailing ion. The DNA bands were revealed by silver staining. Acrylamide concentrations, ionic strength and electrophoresis temperature were systematically investigated for each DNA fragment. The polymorphisms detected by SSCP were identical to those found by hybridization with 32P-labeled allele-specific oligonucleotides. This method avoids the use of radioactivity, is less expensive and simpler than the allele-specific oligonucleotide (ASO) methodology and thus particularly suited for routine analysis.