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Results for “proteome mapping”

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At least 469 records · Page 26Linked to original sources
PubMed2006

Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics.

The accurate mass and time tag mass spectrometry method and clustering analysis were used to compare the abundance change of 992 Yersinia pestis proteins under four contrasting growth conditions (26 and 37 degrees C, with or without Ca2+) that mimicked growth states in either a flea vector or mammalian host. Eighty-nine proteins were observed to have similar abundance change profiles to 29 known virulence associated proteins, providing identification of additional biomarker candidates. Eighty-seven hypothetical proteins, which clustered into 5 distinct clusters of like-protein abundance change, were identified as unique biomarkers related specifically to growth condition.

Bacterial Proteins↗
PubMed2006

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.

Animals↗
PubMed2003

Proteomic study of human umbilical vein endothelial cells in culture.

The endothelium is a single layer of cells lining the inside face of all blood vessels. It constitutes a major metabolic organ which is critically involved in the generation and the regulation of multiple physiological and pathological processes such as coagulation, hemostasis, inflammation, atherosclerosis, angiogenesis and cancerous metastasis dissemination. In order to increase our knowledge about the protein content and the main biological pathways of human vascular endothelial cells, we have undertaken the proteomic analysis of the most explored present endothelial cell model, i.e. primocultures of human umbilical vein endothelial cells (HUVECs). Using low levels of protein loads (~ 30 nug), the association of two-dimensional electrophoresis with matrix-assisted laser desorption/ionization-time of flight mass spectrometry, liquid chromatography-tandem mass spectrometry and database interrogations allowed us to identify 53 proteins of suspected endothelial origin in quiescent HUVECs. Beside cytoskeletal proteins such as actin, tubulin, tropomyosin and vimentin, we identified various proteins more especially implicated in cellular motility and plasticity (e.g. cofilin, F-actin capping protein and prefoldin), in regulation of apoptosis and senescence (protease inhibitor 9, glucose related proteins, heat shock proteins, thioredoxin peroxidase, nucleophosmin) as well as other proteins implicated in coagulation (annexin V, high mobility group protein), antigen presentation (valosin containing protein and ubiquitin carboxyl terminal hydrolase isozyme L1) and enzymatic capabilities (glutathione-S-transferase, protein disulfide isomerases, lactate deshydrogenase). The presented annotated 2-D maps of HUVECs will be soon available on the web at http://www. huvec.com.

Cells, Cultured↗
PubMed2006

Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A new methodology for quantitative analysis of proteins is described, applying stable-isotope labeling by small organic molecules combined with one- or two-dimensional electrophoresis and MALDI-TOF-MS, also allowing concurrent protein identification by peptide mass fingerprinting. Our method eliminates fundamental problems in other existing isotope-tagging methods requiring liquid chromatography and MS/MS, such as isotope effects, fragmentation, and solubility. It is also anticipated to be more practical and accessible than those LC-dependent methods.

Animals↗
PubMed2002

Comparative analysis of protein interaction networks.

Recent advances in proteomics and computational biology have lead to a flood of protein interaction data and resulting interaction networks (e.g. (Gavin et al., 2002)). Here I first analyse the status and quality of parts lists (genes and proteins), then comparatively assess large-scale protein interaction data (von Mering et al., 2002) and finally try to identify biological meaningful units (e.g. pathways, cellular processes) within interaction networks that are derived from the conservation of gene neighborhood (Snel et al., 2002). Possible extensions of gene neighborhood analysis to eukaryotes (von Mering and Bork, 2002) will be discussed.

Animals↗
PubMed2004

Identification of specific oxidatively modified proteins in chicken muscles using a combined immunologic and proteomic approach.

Muscle proteins are generally believed to be key players in free radical processes that eventually lead to oxidative deterioration or modifications of meat proteins resulting in alterations in functionality, for example, gel-forming ability, emulsification properties, and water-binding capacity. This study addresses protein oxidation in chicken muscles using a combined immunologic and proteomic approach and identifies specific proteins that contain carbonyls and/or 3-nitrotyrosine (3-NT). Whereas alpha-enolase was the predominant carbonyl-reactive species among the water-soluble muscle proteins, several other proteins (actin, heat shock protein 70, and creatine kinase) contained carbonyls and/or 3-nitrotyrosine. Finally, this approach was used to demonstrate differential susceptibility of water-soluble muscle proteins toward oxidation in chickens fed a low-antioxidant diet compared with chickens fed a diet supplemented with antioxidant-rich fruits/vegetables.

Animals↗
PubMed2005

Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients: toward dissecting the molecular circuitry of epithelial-adipocyte stromal cell interactions.

It has become clear that growth and progression of breast tumor cells not only depend on their malignant potential but also on factors present in the tumor microenvironment. Of the cell types that constitute the mammary stroma, the adipocytes are perhaps the least well studied despite the fact that they represent one of the most prominent cell types surrounding the breast tumor cells. There is compelling evidence demonstrating a role for the mammary fat pad in mammary gland development, and some studies have revealed the ability of fat tissue to augment the growth and ability to metastasize of mammary carcinoma cells. Very little is known, however, about which factors adipocytes produce that may orchestrate these actions and how this may come about. In an effort to shed some light on these questions, we present here a detailed proteomic analysis, using two-dimensional gel-based technology, mass spectrometry, immunoblotting, and antibody arrays, of adipose cells and interstitial fluid of fresh fat tissue samples collected from sites topologically distant from the tumors of high risk breast cancer patients that underwent mastectomy and that were not treated prior to surgery. A total of 359 unique proteins were identified, including numerous signaling molecules, hormones, cytokines, and growth factors, involved in a variety of biological processes such as signal transduction and cell communication; energy metabolism; protein metabolism; cell growth and/or maintenance; immune response; transport; regulation of nucleobase, nucleoside, and nucleic acid metabolism; and apoptosis. Apart from providing a comprehensive overview of the mammary fat proteome and its interstitial fluid, the results offer some insight as to the role of adipocytes in the breast tumor microenvironment and provide a first glance of their molecular cellular circuitry. In addition, the results open new possibilities to the study of obesity, which has a strong association with type 2 diabetes, hypertension, and coronary heart disease.

Adipocytes↗
PubMed2001

Proteome analysis of the common human pathogen Helicobacter pylori.

The common human pathogen Helicobacter pylori is the major cause of gastric and duodenal ulcers. Based on the complete genome sequences of two independent isolates more than 1800 protein species have been resolved by two-dimensional gel electrophoresis and more than 200 of them have been identified (http://www.mpiib-berlin.mpg.de/2D-PAGE). Using these data, a large range of research areas including strain fingerprinting, protein composition and subcellular localization, gene regulation, and pathogen-host interactions have been investigated. The results that have been obtained led to a more detailed understanding of the Helicobacter biology and pathology and open further interesting fields for future work.

Bacterial Proteins↗
PubMed2005

Identification of fibrosis-relevant proteins using DIGE (difference in gel electrophoresis) in different models of hepatic fibrosis.

Proteomics became a more and more important technique for the large-scale analysis of proteins during the last years. Two-dimensional (2D) electrophoresis as a major tool of proteomics is a powerful method to compare two different biological stages (e. g. healthy and diseased tissue) and to find differences in their protein pattern. One major problem in proteomics is the gel to gel variation of two-dimensional gel electrophoresis, which could cause artefacts in the detection of expression differences. The "difference in gel electrophoresis" (DIGE) technique allows the separation of two proteomes in the same gel. The protein pools were labelled with different fluorescent dyes and equal amounts of protein were separated in the same gel. Another advantage of DIGE is the possibility to separate an internal standard labelled with a third dye in the same gel to allow quantitative expression analysis. We compared proteomes of three different fibrosis models with the appropriate control (tissue inhibitor of metalloproteinases-1 (TIMP-1) overexpressing HepG2 cells in comparison to a HepG2 control, freshly isolated HSC in comparison to activated HSC and healthy mouse liver in comparison to fibrotic mouse liver). Among the differentially expressed proteins several were already found to be relevant for fibrosis but we also detected some proteins like the selenium binding protein 2 which might be relevant for hepatic fibrosis.

Animals↗
PubMed2005

Algorithms for alignment of mass spectrometry proteomic data.

MOTIVATION: The analysis of biological samples with high-throughput mass spectrometers has increased greatly in recent years. As larger datasets are processed, it is important that the spectra are aligned to ensure that the same protein intensities are correctly identified in each sample. Without such an alignment procedure it is possible to make errors in identifying the signals from peptides with similar molecular weight. Two algorithms are provided that can improve the alignment among samples. One algorithm is designed to work with SELDI data produced from a Ciphergen instrument, and the other can be used with data in a more general format. RESULTS: The two algorithms were applied to samples drawn from a common pool of reference serum. The results indicate substantial improvement in consistently identifying peptide signals in different samples.

Algorithms↗
PubMed2005

Effect of all-trans-retinoic acid on mRNA binding protein p62 in human gastric cancer cells.

p62 is a cancer-associated antigen binding to mRNA encoding insulin-like growth factor II that was isolated by immunoscreening a cDNA expression library with autoantibodies from patients with hepatocellular carcinoma (HCC). In the present study, multiple methods including flow cytometry, confocal laser-scanning microscope, electron microscope were used to characterize the effect of ATRA on BGC-823 cells, which presented two phenotypes of differentiation and apoptosis in cells treated with 1.0 and 50 microM ATRA, respectively. Interestingly, we found that p62 was cytoplasmic in location, but it significantly decreased in cytoplasm and appeared in nucleus of cells when the cells were treated with 50 microM all-trans retinoic acid (ATRA) for 5 days. Furthermore, proteomics approach on differential nucleus proteins showed that the up-regulation and/or down-regulation of cell cycle proteins and IGF binding proteins were involved in the apoptosis of BGC-823 cells induced by ATRA. These results suggest that there is a significant association between expression and distribution of p62 and the growth arrest of tumor cells, in which p62 is associated with cell apoptosis induced by ATRA.

Apoptosis↗
PubMed2003

Novel therapeutic targets in Helicobacter pylori.

The failure of current regimens to treat the gastric pathogen Helicobacter pylori is a growing problem. Responsible for gastritis and peptic ulcer disease, and designated as a Class 1 carcinogen, its presence in up to 90% of the population of the developing world makes its treatment a primary concern. The use of genomic, proteomic and transcriptomic data to determine essential gene products as targets for novel therapeutic agents is of key interest in this research. This review describes how such data can be obtained, evaluated and eventually used as a basis for the development of both vaccine and novel anti-helicobacter agents. It indicates both past successes and possible new avenues to exploit the increased availability of such data, whilst also examining the limitations of such approaches.

Animals↗
PubMed2004

Initial peptide mass fingerprinting analysis of proteins obtained by lysis of Coxiella burnetii cells.

Whereas the complete genome of Coxiella burnetii (C.b.), the etiological agent of Q-fever, has recently been published (Seshadri et al., Proc. Natl. Acad. Sci. USA. 100, 5455-5460, 2003), the C.b. proteome is still under study. Using the bioinformatic approach, we found in total 309 proteins on two dimensional electroctrophoretic images of C.b. whole cell lysates. Eighteen major protein species were subjected to peptide mass fingerprinting and identified as the products of 6 known open reading frames (ORFs): the chaperone DnaK (heat shock 70 K protein), chaperonin 60 K (GroEL protein, heat shock protein B), DnaJ-like protein djlA (mucoidy activation protein mucZ), elongation factor Ts (EF-Ts), ribosomal protein L7/L12, and chaperonin 10 K (GroES protein, heat shock protein A).

Bacteria↗
PubMed2006

Layered expression scanning: multiplex molecular analysis of diverse life science platforms.

With the advent of the genomic era, there is an increasing use of high-throughput techniques to generate transcriptome- and proteome-based profiles of biological specimens. Each of these methodologies offers a unique window into the inner workings of cell and tissue samples. Often, these studies generate large data sets and provide investigators with a substantial number of candidate dysregulated genes and pathways. Follow-up studies are then undertaken to independently validate the original findings and to extend the study to additional samples or more quantitative measurements. Although there are several methods available for these validation efforts, they are often tedious and laborious to perform; thus, additional tools that enable this task are needed. One such approach is layered expression scanning (LES), a new technique developed via a cooperative research and development agreement (CRADA) between the National Cancer Institute and 20/20 GeneSystems, Inc. The technique is based on the movement of biomolecules from a two-dimensional life science platform (histological tissue section, electrophoresis gel, multi-well plate, etc.) through a set of analysis membranes while maintaining the original distribution pattern of the molecules. Each membrane measures one analyte and the data are then mapped back to the original specimen, permitting each component of the life science platform to be studied in detail. LES can be configured in several different ways depending on the goals of the study. In this review, we summarize the use of the LES technique for a variety of biological applications.

Membranes, Artificial↗
PubMed2005

Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling.

Chemical genomics aims to discover small molecules that affect biological processes through the perturbation of protein function. However, determining the protein targets of bioactive compounds remains a formidable challenge. We address this problem here through the creation of a natural product-inspired small-molecule library bearing protein-reactive elements. Cell-based screening identified a compound, MJE3, that inhibits breast cancer cell proliferation. In situ proteome reactivity profiling revealed that MJE3, but not other library members, covalently labeled the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1), resulting in enzyme inhibition. Interestingly, MJE3 labeling and inhibition of PGAM1 were observed exclusively in intact cells. These results support the hypothesis that cancer cells depend on glycolysis for viability and promote PGAM1 as a potential therapeutic target. More generally, the incorporation of protein-reactive compounds into chemical genomics screens offers a means to discover targets of bioactive small molecules in living systems, thereby enabling downstream mechanistic investigations.

Antineoplastic Agents↗
PubMed2006

Proteomic characterization of acid stress response in Synechocystis sp. PCC 6803.

A comparative proteomic analysis using 2-DE coupled with MALDI-MS and LC-MS/MS was performed in Synechocystis sp. PCC 6803 to identify protein candidates involved in acid stress response in cyanobacteria. Comparison of soluble proteins from the cytoplasmic fraction of cells grown on media set at pH 7.5 and 5.5 using 2-DE identified four proteins, which showed significant changes in the abundance. Surprisingly, several general stress proteins, either the heat shock family proteins or chaperonins, did not show perceptible fold changes in response to acidity. Compared to the cytoplasmic proteome, the periplasmic proteome showed remarkable changes as a function of external pH. Protein expression profiling at different external pH, i.e., 9.0, 7.5, 6.0 and 5.5, allowed classifying the periplasmic proteins depending on their preferential expression patterns towards acidity or alkalinity. Among the acid- and base-induced proteins, oxalate decarboxylase and carbonic anhydrase were already known for their role in pH homeostasis. Several unknown proteins from the periplasm, that showed significant changes in response to pH, provide ideal targets for further studies in understanding pH stress response in cyanobacteria. This study also identified 14 novel proteins, hitherto unknown from the periplasmic space of Synechocystis.

Bacterial Proteins↗
PubMed2003

Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT).

The chemically-coded affinity tag (CCAT) method combines standard electrophoresis protocols with MALDI-TOF-MS analysis to identify and quantify protein abundances in complex samples in one step. This method is designed to fit into the workflow of SDS-PAGE or two-dimensional electrophoresis (2-DE) only requiring basic proteome laboratory equipment. Prior to electrophoresis two protein samples are separately labelled with a heavy or a light version of the CCAT reagent via reduced cysteines in the proteins. Equal amounts are then combined and electrophoretically separated. Proteins can then be excised from the gel to obtain their peptide mass fingerprint by mass spectrometry. This fingerprint enabled not only identification, but also quantification by comparing relative peak intensities of CCAT-labelled peptides. In this article, we display how the CCAT method can be used to analyse two protein samples in one gel and that the peak intensities of labelled peptides reflect the abundance of a protein in it.

Affinity Labels↗
PubMed2003

Integrating 'omic' information: a bridge between genomics and systems biology.

The availability of genome sequences for several organisms, including humans, and the resulting first-approximation lists of genes, have allowed a transition from molecular biology to 'modular biology'. In modular biology, biological processes of interest, or modules, are studied as complex systems of functionally interacting macromolecules. Functional genomic and proteomic ('omic') approaches can be helpful to accelerate the identification of the genes and gene products involved in particular modules, and to describe the functional relationships between them. However, the data emerging from individual omic approaches should be viewed with caution because of the occurrence of false-negative and false-positive results and because single annotations are not sufficient for an understanding of gene function. To increase the reliability of gene function annotation, multiple independent datasets need to be integrated. Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology.

Computational Biology↗