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PubMed2004

PEDRo: a database for storing, searching and disseminating experimental proteomics data.

BACKGROUND: Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. RESULTS: This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. CONCLUSIONS: The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation.

Animals↗
PubMed2004

Expressional patterns of chaperones in ten human tumor cell lines.

BACKGROUND: Chaperones (CH) play an important role in tumor biology but no systematic work on expressional patterns has been reported so far. The aim of the study was therefore to present an analytical method for the concomitant determination of several CH in human tumor cell lines, to generate expressional patterns in the individual cell lines and to search for tumor and non-tumor cell line specific CH expression.Human tumor cell lines of neuroblastoma, colorectal and adenocarcinoma of the ovary, osteosarcoma, rhabdomyosarcoma, malignant melanoma, lung, cervical and breast cancer, promyelocytic leukaemia were homogenised, proteins were separated on two-dimensional gel electrophoresis with in-gel digestion of proteins and MALDI-TOF/TOF analysis was carried out for the identification of CH. RESULTS: A series of CH was identified including the main CH groups as HSP90/HATPas_C, HSP70, Cpn60_TCP1, DnaJ, Thioredoxin, TPR, Pro_isomerase, HSP20, ERP29_C, KE2, Prefoldin, DUF704, BAG, GrpE and DcpS. CONCLUSIONS: The ten individual tumor cell lines showed different expression patterns, which are important for the design of CH studies in tumor cell lines. The results can serve as a reference map and form the basis of a concomitant determination of CH by a protein chemical rather than an immunochemical method, independent of antibody availability or specificity.

Journal Article↗
PubMed2005

Proteome analysis of a recombinant Bacillus megaterium strain during heterologous production of a glucosyltransferase.

A recombinant B. megaterium strain was used for the heterologous production of a glucosyltransferase (dextransucrase). To better understand the physiological and metabolic responses of the host cell to cultivation and induction conditions, proteomic analysis was carried out by combined use of two-dimensional gel electrophoresis and mass spectrometry (2-DE/MS) for protein separation and identification. 2-DE method was optimized for the separation of intracellular proteins. Since the genome of B. megaterium is not yet available, peptide sequencing using peptide fragment information obtained from nanoelectrospray ionization quadrupole-time-of-flight tandem mass spectrometry (ESI-QqTOF MS/MS) was applied for protein identification. 167 protein spots were identified as 149 individual proteins, including most enzymes involved in the central carbon metabolic pathways and many enzymes related to amino acid synthesis and protein synthesis. Based on the results a 2-DE reference map and a corresponding protein database were constructed for further proteomic approaches on B. megaterium. For the first time it became possible to perform comparative proteomic analysis on B. megaterium in a batch culture grown on glucose with xylose induction for dextrasucrase production. No significant differences were observed in the expression changes of enzymes of the glycolysis and TCA cycle, indicating that dextransucrase production, which amounted to only 2 % of the entire protein production, did not impose notable metabolic or energetic burdens on the central carbon metabolic pathway of the cells. However, a short-term up-regulation of aspartate aminotransferase, an enzyme closely related to dextransucrase production, in the induced culture demonstrated the feasibility to use 2-DE method for monitoring dextransucrase production. It was also observed that under the cultivation conditions used in this study B. megaterium tended to channel acetyl-CoA into pathways of polyhydroxybutyrate production. No expression increases were found with cytosolic chaperones such as GroEL and DnaK during dextransucrase production and secretion, whereas a strong up-regulation of the oligopeptide-binding protein OppA was observed in correlation with an increased secretion of dextransucrase into the culture medium.

Journal Article↗
PubMed2005

Coxiella burnetii whole cell lysate protein identification by mass spectrometry and tandem mass spectrometry.

The whole cell lysate of Coxiella burnetii strain RSA 493 was separated by two-dimensional electrophoresis and more than 500 protein spots were found on silver-stained reference map. Spots from the gels were subjected to identification based on peptide mass fingerprinting (PMF). In order to identify additional proteins, tandem mass spectrometry (MS/MS) using electrospray and matrix-assisted laser desorption/ionization techniques was applied. The three independent approaches resulted in the identification of 197 open reading frames (ORFs). Fifty-two proteins were identified by PMF and at least with one of the MS/MS methods, 37 proteins with both MS/MS instruments, and 19 proteins with all three techniques applied. All predicted C. burnetii ORFs were compared with the Clusters of Orthologous Groups database. The data related to identified proteins were stored and indexed in a file that can be read and searched using Microsoft Access.

Bacterial Proteins↗
PubMed2007

The proteome and secretome of human arterial smooth muscle cell.

Smooth muscle cells (SMCs) play a crucial role in cardiovascular diseases. Proteomic analysis using two-dimensional gel electrophoresis (2DE) associated with mass spectrometry allows characterization of the proteome and secretome of human smooth muscle. The presence of a distinct SMC population in the arterial wall implies that under normal conditions, SMCs are phenotypically heterogeneous. Intracellular and secreted proteins from a primary culture of SMCs obtained from patients undergoing coronary bypass surgery were analyzed using 2DE in order to determine their specific features. The 2D reference maps show that SMCs are involved in a wide range of biological functions. They could constitute a useful tool for a wide range of investigators involved in vascular biology, allowing them to investigate SMC protein changes associated with cardiovascular disorders or environmental stimuli.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2026

The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration.

Rare coding variants can have large effects on disease risk and provide direct routes from human genetics to disease mechanisms and therapeutic targets, but their discovery is constrained by sample size, particularly for low-prevalence diseases. Here we establish the Biobank Rare Variant Analysis (BRaVa) consortium, a global rare variant association resource that integrates sequencing and linked health-record data from ten biobanks and cohorts comprising over 1.2 million individuals across diverse ancestries. We performed gene-based meta-analyses of rare coding variation across 33 clinical endpoints and 11 quantitative traits. Aggregating evidence across biobanks and ancestries identified 514 gene-trait associations, including 31 not previously reported in prior studies or curated association resources following systematic literature review. Notably, 36.1% of gene-level associations were undetectable in any individual biobank, and 91 emerged only through cross-ancestry meta-analysis, demonstrating that federated integration enables discovery beyond the reach of single cohorts. Similar gains were observed at the variant level, where 25.0% of phenotype-locus associations were detectable only through meta-analysis. Effect size estimates were correlated across ancestries with concordant directions of effect, supporting the generalizability of rare variant associations. The identified signals implicate pathways involved in transcriptional and epigenetic regulation, metabolism, vascular and epithelial biology, and immune function, highlighting rare coding variation as an engine for biological discovery across medical record phenotypes. For example, damaging variation in ANKRD12 implicates inflammatory transcriptional dysregulation in asthma and chronic obstructive pulmonary disease, and ultra-rare predicted loss-of-function variants in NAA15 link protein acetylation processes to type 2 diabetes risk. BRaVa establishes a scalable framework and freely available community resource for rare variant meta-analysis across global biobanks. Public release of gene- and variant-level association summary statistics provides a reference map of rare coding variant associations to support disease gene discovery, biological interpretation, and therapeutic target prioritization as sequencing-linked health-record resources continue to expand.

Journal Article↗
PubMed2006

[Establishment of protein expression profile of human normal colonic epithelia].

OBJECTIVE: To establish a protein expression profile of human normal colonic epithelia. METHODS: Two-dimensional gel electrophoresis (2-DE) was applied to separate the total proteins of 20 human normal colonic epithelial tissues. The expression proteins in the human normal colonic epithelia were identified by both matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and electrospray ionization tandem mass spectrometry (ESI-Q-TOF), and the biological function and subcellular locations of the identified proteins were analyzed by bioinformatics. RESULTS: A 2-DE reference map of human normal colonic epithelium was established. On the 2-DE map, 1020+/-50 protein spots were detected, 204 protein spots representing 162 non-redundant proteins were identified, and 37 proteins had posttranslational modification. The identified proteins were categorized into several protein groups according to their functions or subcellular locations, whose data were available at our website (http://www.xyproteomics.org). CONCLUSION: A protein expression profile of human normal colonic epithelia is established for the first time, which provides useful information for investigating the physiological functions and pathologic process of colonic epithelia.

Adult↗
PubMed1986

Comparative studies on tree pollen allergens. XIII. Partial characterization of the alder (Alnus incana) pollen extract by two-dimensional IEF/SDS-PAG electrophoresis combined with electrophoretic transfer and immunoautoradiography.

Horizontal isoelectric focusing (IEF) and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2-D SDS-PAGE) combined with electrophoretic transfer (ET) and immunoautoradiography (IAR) were used to characterize the crude alder (Alnus incana) pollen extract (AI crude) and fraction AI 34. IEF resolved AI crude and AI 34 into 34 and 39 distinct protein bands, respectively, when stained with Coomassie brilliant blue. The band patterns were similar and the majority of bands were located in the pH region 4.0-7.0. After ET and IAR, the distribution of antigenic reactivities was similar to that of the protein stain. Allergenic reactivity was detected in the pH region 4.6-5.2 only, where two bands at pH 4.9 demonstrated dominating IgE-binding properties. The 2-D reference maps of AI crude and AI 34 consisted of 40 and 45 protein spots, respectively. The autoradiogram of AI crude demonstrated 35 spots capable of binding rabbit IgG. The main IgE-binding zone was located at pH 4.6-5.2 and 20 kilodaltons with an area of weaker autoradiographic signals at pH 4.6-5.2 and 40 kilodaltons. ET from polyacrylamide gels to nitrocellulose (NC) membranes was quantitative and IAR gave significant radiostaining of spots containing 0.01 and 0.1 microgram of AI crude in the IgG and IgE systems, respectively. For the characterization of the alder pollen extract, horizontal 2-D SDS-PAGE combined with ET and IAR provided a powerful supplement to conventional crossed immuno- and radioimmunoelectrophoretic techniques (CIE/CRIE).

Animals↗
PubMed1994

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.

Blotting, Western↗
PubMed1995

High resolution two-dimensional electrophoresis: technique and potential applicability to the study of inner ear disease.

Technologic progress in two-dimensional polyacrylamide gel electrophoresis (2-D Page), in combination with immunoblotting, amino acid sequencing, and computer-assisted image analysis, allowed establishment of human body fluid and tissue "reference maps," which in turn enabled meaningful comparison of data from various clinical and research centers. Altered protein profiles have been observed in plasma/serum, cerebrospinal fluid, urine, and other body fluids in numerous systemic or localized pathologic entities. Human perilymph, obtained during ear surgery or post mortem, exhibits a protein profile differing from plasma in several ways. Most interesting are the extremely high levels of high density lipoprotein-associated proteins, a group of proteins thought to play a role in atherosclerosis, nerve damage/regeneration, chronic inflammation, and Alzheimer's disease, among others. A technique is described for collection and analysis of human perilymph, using a state-of-the-art standardized 2-D Page technique. It is expected that, as in other body fluids, disease-specific protein patterns will be identified. With the possible exception of presumed perilymphatic fistula, it is not envisioned that analysis of perilymph will be used for diagnostic purposes but rather as an aid for the elucidation of the mechanisms underlying inner ear disease, whether localized or as part of systemic alterations.

Adult↗
PubMed1997

[Coronary angiography: 1st or 2nd-line test?].

Coronary angiography, although now performed extremely frequently, remains an invasive and expensive examination, whose place, as first-line diagnostic method, must be discussed; Its main advantage is to provide a definitive diagnosis of coronary atherosclerosis as well as simple prognostic indicators (single vessel, two-vessel or three-vessel disease; concomitant evaluation of left ventricular function by associated radiological ventriculography). However, it is unable to precisely assess the degree of coronary wall disease and, more importantly, cannot evaluate the functional repercussions of stenosis. Under these conditions, only cases in which myocardial revascularization is expected to provide a definite clinical benefit (presence of frank angina symptoms) probably justify first-line coronary angiography. In all other cases, coronary angiography is a useful examination to provide reference "mapping" of the coronary lesions, but an obvious clinical benefit for the patient cannot be expected from systematic use of this technique. In particular, in such situations, coronary angiography should not be the only element on which the decision to perform myocardial revascularization should be based: the "oculostenotic reflex" must always be avoided.

Angina Pectoris↗
PubMedDate not supplied

The reference problem and mapping of coherence: a simulation study.

Four techniques are applied to record EEG signals: bipolar recording, referential recording, common average reference recording and source derivation. For the interpretation of EEG parameter maps knowledge of the properties of the applied recording technique is essential. Bipolar recordings are not discussed in this paper. The application of reference and common average reference recording has the disadvantage of an unknown reference potential. This disadvantage is much larger with the use of source derivation because every electrode signal has its particular reference signal. This must be taken into consideration when coherence estimations are made. With actual EEG records the influence of the reference cannot be determined unambiguously. However, simulation studies enable some essential conclusions. In this paper by means of autoregressive processes EEG signals with given power and coherence properties were simulated and different recording situations using the same data set were reconstructed. The essential result is that computation and mapping of coherences yield the most reliable results when reference recording is used. However, measures to ensure a low reference signal must be taken.

Brain Mapping↗
PubMed2005

Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.

OBJECTIVE: To investigate the indirect alignment of two anatomical ontologies through a reference ontology and to compare it to direct alignment between these two ontologies. The ontologies under investigation are the Adult Mouse Anatomical Dictionary (MA) and the NCI Thesaurus (NCI). The Foundational Model of Anatomy serves as reference ontology. METHODS: The direct alignment employs a combination of lexical and structural similarity. The indirect alignment simply derives mappings from direct alignments to the reference ontology. RESULTS: The indirect MA-NCI alignment yielded 703 mappings and the direct alignment 715, 654 of which are common to both. The mappings specific to one approach were analyzed. CONCLUSIONS: When a reference ontology exists, indirect alignment of multiple ontologies through a reference represents a valid, cost-effective alternative to pairwise alignment.

Anatomy↗
PubMed1997

Standardized characterization of gene expression in human colorectal epithelium by two-dimensional electrophoresis.

New diagnostic and prognostic markers are needed in colorectal cancer. They can be found by differential analysis at DNA, RNA or protein level. The accuracy of phenotypic comparisons of tumor and normal tissues depends on the purity of the samples. We present an effective method to identify and isolate proteins that are differentially expressed under altered conditions, and a two-dimensional reference protein map of the normal human colonic epithelium. Normal colonic mucosa, primary tumors and liver metastases were prepared in the operating room. After washing in an ice-cold medium containing protease inhibitors, crypts were isolated by mechanical preparation without using metalloproteinases. Epithelial cells were then selected using Ber-EP4 Dynabeads. The samples were denaturated before processing for immobilized pH gradient two-dimensional polyacrylamide gel electrophoresis according to SWISS-2DPAGE standards. The samples contained more than 95% epithelial cells as confirmed by fluorescence-activated cell sorting using pan-anticytokeratin antibodies. Cell surfaces were not damaged, as assessed by scanning electronic microscope. A protein reference map of the normal colonic epithelium was defined. Using gel matching, N-terminal sequencing and/or immunoblotting techniques, 60 polypeptides - including proteins specifically expressed in colorectal epithelium - have now been identified. This reproducible method of sample preparation permits the comparison of protein patterns found in various pathological states with the present reference map (http://www.expasy.ch). Some of these patterns might provide diagnostic or prognostic markers, or even molecular targets for therapy in the future.

Colorectal Neoplasms↗