Biomedical subjects

D F Hochstrasser

Publications and source records attributed to D F Hochstrasser.

17 recordsLinked to original sources

PubMed1992

Polypeptide marker and disease patterns found while mapping proteins in ascitis.

To assess the protein composition of ascitis, 28 samples of ascitic fluid were obtained from patients admitted to Geneva University Hospital. The samples were analysed randomly and blindly by high-resolution two-dimensional polyacrylamide gel electrophoresis. The final visual evaluation was compared with the discharged summary and diagnosis. The protein pattern of ascitis was, as expected, very similar to normal or diseased plasma, with the exception of two spots which were present in ascitic fluids but not in the 200 plasma samples analyzed in parallel. After microsequencing, they proved to be beta-fibrinogen fragments. Several diseases showed distinct patterns, especially acute pancreatitis. A group of intense spots with an apparent molecular mass between those of alpha 1-antitrypsin and beta-haptoglobin were found in all ascitic fluid from pancreatitis cases (six patients). These spots had isoelectric points similar to those of alpha 1-antitrypsin and beta-haptoglobin and microsequencing revealed that they were three different fragments of alpha 1-antitrypsin.

Acute Disease↗

PubMed1992

Clonality of cold agglutinins in patients with hemolytic anemia: an analysis by high-resolution two-dimensional gel electrophoresis.

High-resolution two-dimensional gel electrophoresis (2-DGE) was used to analyse plasma samples and partially purified cold agglutinins (CA) obtained from two selected patients. Both presented an acute hemolytic anemia with CA of high thermal amplitude, normal immunoglobulin levels, no detectable paraproteinemia, and no clinical evidence of a malignant B-cell disorder. The electrophoretograms of their plasma showed evident alternations of the "normal" protein profile, which were directly related to hemolysis (absence of the spots of haptoglobin and in one case of those of hemopexin), but no monoclonal gammopathy. The electrophoretograms of their purified CA revealed two clearly different spot patterns respectively corresponding to a monoclonal IgM and to polyclonal IgM. These results show that the clonality of CA associated with hemolytic anemia can be easily determined by 2-DGE. This technique may be very useful to discriminate chronic cold agglutinin disease in the early phase from "parainfectious" CA.

Adult↗

PubMed1992

Human liver protein map: a reference database established by microsequencing and gel comparison.

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.

Amino Acid Sequence↗

PubMed1992

Clonal imbalances of serum immunoglobulins after allogeneic bone marrow transplantation: an analysis by high-resolution two-dimensional gel electrophoresis.

The clonality pattern of immunoglobulins (Igs) produced after allogeneic bone marrow transplantation (BMT) was studied by high-resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of serum samples and purified Igs. With this technique, the light (L) chain of a monoclonal Ig usually appears as a single spot. Thus, the degree of clonal diversity of the functional B cells can be appreciated by the electrophoretic pattern of the serum L chains. Furthermore, 2D-PAGE allows a semi-quantitative determination of prominent Ig clones according to the size of L chain spots. We found that serum electrophoretograms of 8/19 patients after BMT (5-9 months) revealed L chain patterns which were similar to those of normal polyclonal Igs, that is, less than five distinguishable small spots among a cloud-like indiscrete L chain spots region ('polyclonal' pattern). A spectrum of clonal abnormalities was observed on the electrophoretograms of 11/19 patients: in five patients, multiple small L chain spots (corresponding to Ig concentrations between 0.2 and 2 g/l) were detected ('oligoclonal' pattern), whereas in six others, 'typical' monoclonal Igs (Ig concentrations > 2 g/l) were observed with (3/19 patients) or without (3/19 patients) multiple small clonal components. Sequential analysis of serum obtained from patients at different times after BMT revealed that imbalanced clonal reconstitution was transient and evolved towards apparently normal polyclonal Ig production. Our observations show that the development of clonal 'gammopathies' after BMT is a frequent, but not obligatory phenomenon. It may reflect a transient restriction of the B cell repertoire either through a limited outgrowth of precursor cells or through selective antigenic pressures.

Antibody Diversity↗

PubMed1992

Monoclonal gammopathy in a 30 weeks old premature infant.

The occurrence of monoclonal gammopathy in childhood is extremely rare. This report describes the presence of a monoclonal immunoglobulin in a 30 week old premature infant, incidentally discovered by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) during an ongoing study of the plasma/serum protein development. Comparative analysis of the electrophoretogram of the infant with 'reference' protein maps revealed the presence of an 'abnormal' immunoglobulin light chain spot. A spot having an identical apparent molecular weight and isoelectric point was also detected after 2D-PAGE of the mother's plasma and its Protein-A purified immunoglobulin fraction. The observation of a monoclonal gammopathy in a premature infant, most likely transmitted from his mother, highlights the potential usefulness of 2D-PAGE in the clinical laboratory.

Blood Protein Electrophoresis↗

PubMed1991

The MELANIE project: from a biopsy to automatic protein map interpretation by computer.

The goals of the MELANIE project are to determine if disease-associated patterns can be detected in high resolution two-dimensional polyacrylamide gel electrophoresis (HR 2D-PAGE) images and if a diagnosis can be established automatically by computer. The ELSIE/MELANIE system is a set of computer programs which automatically detect, quantify, and compare protein spots shown on HR 2D-PAGE images. Classification programs help the physician to find disease-associated patterns from a given set of two-dimensional gel electrophoresis images and to form diagnostic rules. Prototype expert systems that use these rules to establish a diagnosis from new HR 2D-PAGE images have been developed. They successfully diagnosed cirrhosis of the liver and were able to distinguish a variety of cancer types from biopsies known to be cancerous.

Biopsy↗

PubMed1991

LaboImage: a workstation environment for research in image processing and analysis.

Numerous images are produced daily in biomedical research. In order to extract relevant and useful results, various processing and analysis steps are mandatory. The present paper describes a new, powerful and user-friendly image analysis system: LaboImage. In addition to standard image processing modules. LaboImage also contains various specialized tools. These multiple processing modules and tools are first introduced. A one-dimensional gel analysis method is then described. The new concept of 'normalized virtual one-dimensional gel' is introduced, making comparisons between gels particularly easy. This normalized gel is obtained by compensating for the bending of the lanes automatically; no information loss is incurred in the process. Finally, the model of interaction in a multi-window environment is discussed. LaboImage is designed to run in two ways: interactively, using menus and panels; and in batch mode by means of user-defined macros. Examples are given to illustrate the potentialities of the software.

Algorithms↗

PubMed1991

High-resolution two-dimensional protein electrophoresis of pathological plasma/serum.

The potential usefulness of an optimalized high-resolution two-dimensional gel electrophoresis (2-DGE) protocol was studied by comparative analysis of plasma/serum obtained from apparently healthy individuals and from patients with a few selected known diseases. Despite their apparent complexity, patient electrophoretograms revealed readily detectable modifications of the 'reference' protein profile for those selected diseases (listed below). Abnormal profiles were characterized by presence or absence of particular spots, by reduction or enlargement of spot size, or by alterations of spot microheterogeneity. Combinations of several modifications enabled different 'disease-associated spot pattern' to be distinguished on the protein maps of patients with: monoclonal gammopathies, hypogammaglobulinemia, hepatic failure, chronic renal failure and hemolytic anemia. This study demonstrates that identification of plasma/serum protein alterations by 2-DGE allows a few selected diseases to be diagnosed solely on the basis of protein map modifications.

Agammaglobulinemia↗

PubMed1990

From biopsy to automatic diagnosis.

High resolution two-dimensional gel electrophoresis is a very powerful biochemical tool for analysis of complex protein mixtures. In well defined situations, protein maps, obtained from tissue biopsies or biological fluids by this technique, can be automatically analyzed by computer. Some polypeptide patterns are the fingerprints of diseases. Applying clustering algorithm and learning techniques, the prototype expert system MELANIE recognized patterns and associated the correct diagnosis to the specific pattern.

Diagnosis, Computer-Assisted↗

PubMed1988

Development of polyacrylamide gels that improve the separation of proteins and their detection by silver staining.

Background staining that is associated with silver detection of proteins and nucleic acids in polyacrylamide gels has been shown to be due mostly to the amide groups in methylenebisacrylamide, a commonly used gel crosslinker. In attempts to reduce this background staining, eight existing crosslinking agents were tested. All of these proved to be unsuitable. Six new crosslinking agents were synthesized and tested. Of these, diacrylylpiperazine provided increased physical strength, improved electrophoretic separation of proteins, and silver staining detection of proteins with reduced background stain.

Acrylamides↗

PubMed1988

Methods for increasing the resolution of two-dimensional protein electrophoresis.

A two-dimensional gel elctrophoresis protocol has been developed which provides for a 1.5-to 3-fold increase in the resolution of proteins compared to other frequently used methods. The major variations from previous protocols include increased pore size in the isoelectric focusing gels; cholamidopropyldimethylhydroxypropanesulfonate, a zwitterionic detergent, replaces most of the Nonidet P-40, a nonionic detergent, in the isoelectric focusing gels; no equilibration step is employed between the first and second dimensional separation. The use of a stacking gel in the second dimension has been eliminated; a more efficient and evenly distributed cooling system has been designed for the molecular mass separation, allowing faster migration with higher current. Finally, the crosslinker diacrylylpiperazine is employed which improves protein separation and detection with ammoniacal silver staining. Silver-stained two-dimensional gel electrophoretograms of human plasma and hamster brain tissues and autoradiographs of rat liver cells are compared to the results obtained from previous methods.

Animals↗

PubMed1988

'Catalysts' for polyacrylamide gel polymerization and detection of proteins by silver staining.

The crosslinker diacrylyl-piperazine produces polyacrylamide gels which display improved electrophoretic separation of proteins and better physical strength. It also produces gels with improved detection of proteins by ammoniacal silver staining by reducing the background. This reduced background provided us with an opportunity to investigate residual background staining caused by the catalytic reagents utilized in the polymerization of acrylamide gels. The commonly used catalyst system, tetramethyl-ethylenediamine and ammonium persulfate was shown to be responsible for the yellow staining background found after a prolonged development time with silver staining. An alternate catalyst system has been designed to decrease further the formation of this background staining. Dimethyl-piperazine or tetramethylethylenediamine, potassium or ammonium persulfate, and sodium thiosulfate are shown to provide for gels which have excellent mechanical and staining characteristics. These catalytic systems produce little background staining despite prolonged development time with the ammoniacal silver stain, and they reduce background staining with the dichromate silver stain.

Acrylic Resins↗

PubMed1988

Computerized classification of two-dimensional gel electrophoretograms by correspondence analysis and ascendant hierarchical clustering.

A powerful data processing methodology for analysis and classification of two-dimensional gels is introduced. The approach is based on correspondence analysis (CA) and ascendant hierarchical classification (AHC), and significantly differs from the more classical principal-component decomposition. Starting with a series of gels, each having a large number of spots, CA allows their representation in a factorial space of reduced dimension; classification into meaningful groups is then performed using AHC. Simultaneous representation of both spots and gels in the same space can be done. This precisely indicates the key spots pertinent for the classification, and therefore the characteristic proteins representative of a particular class of gels (i.e. of a particular disease or biological status). In addition, knowledge of these characteristic spots greatly simplifies the screening of future gels. After a brief overview of the Mélanie system for analyzing 2D gels, the theory of correspondence analysis and ascendant hierarchical classification is summarized. Equations are given that are easily ammenable to computation. How classification of two-dimensional gel electrophoretograms is accomplished is then detailed. Experimental results support the power of this approach.

Cluster Analysis↗

PubMedDate not supplied

Plasma protein map: an update by microsequencing.

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two-dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two-dimensional gel database.

Amino Acid Sequence↗

PubMedDate not supplied

Improving the detection of proteins after transfer to polyvinylidene difluoride membranes.

N-Terminal sequence analysis of proteins separated by two-dimensional polyacrylamide gel electrophoresis and transferred onto polyvinylidene difluoride (PVDF) membranes has become the method for molecular characterization of proteins contained in biological samples. However, the proteins of lower abundance cannot be sequenced directly, without improving the technique. We have studied a drying method on several PVDF membranes including Trans-Blott, Immobilon P and Problott. Using Amido Black, Coomassie Brilliant Blue R-250 and Ponceau S, we have obtained, in comparison with the non-dried membranes, an enormous increase in the number of detectable proteins.

Electrophoresis, Gel, Two-Dimensional↗

PubMedDate not supplied

Automatic learning strategies and their application to electrophoresis analysis.

Automatic learning plays an important role in image analysis and pattern recognition. A taxonomy of automatic learning strategies is presented; this categorization is based on the amount of inferences the learning element must perform to bridge the gap between environmental and system knowledge representation level. Four main categories are identified and described: rote learning, learning by deduction, learning by induction, and learning by analogy. An application of learning by induction to medical image analysis is then exposed. It consists in the classification of two-dimensional gel electrophoretograms into meaningful distinct classes, as well in their conceptual description.

Electrophoresis, Gel, Two-Dimensional↗

PubMedDate not supplied

A clinical molecular scanner: the Melanie project.

We developed an expert system to analyze and interpret protein maps. This system, Melanie (medical electrophoresis analysis interactive expert), can distinguish between normal and cirrhotic liver and identify various types of cancer on the basis of protein patterns in biopsy specimens. Our findings suggest that some diseases associated with toxic compounds or modifications of the human genome can be diagnosed by expert systems that analyze protein maps. The combination of protein mapping and computer analysis could result in a clinically useful "molecular scanner". The massive amount of information analyzed and stored in such studies requires new strategies, including centralized databases and image transmission over networks. Increased understanding of protein expression and regulation will enhance the importance of the human genome project in medicine and biology.

Computer Systems↗