Approach to spot overlapping problem in 2D-PAGE revealed clinical and functional significance of RKIP and MnSOD in renal cell carcinoma
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Noriyuki Hosoya , Marimu Sakumoto , Yoshihiko Tomita , Tadashi Kondo Previously, we identified protein spots with differential intensity between normal and tumor tissues of renal cell carcinoma (RCC) using 2D-DIGE. Here, we further examined two proteins, raf-1 kinase inhibitory protein (RKIP) and manganese superoxide dismutase (MnSOD), identified in one protein spot. Western blotting demonstrated that RKIP and MnSOD exhibited opposite expression patterns in normal and tumor tissues. Immunohistochemisry showed that MnSOD level signific...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Proteome profiling illustrated by a large-scale fed-batch fermentation of Penicillium chrysogenum
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Michaela Helmel , Andreas Posch , Christoph Herwig , Günter Allmaier , Martina Marchetti-Deschmann Filamentous fungi are employed for the large-scale production of value-added products, including organic acids, enzymes, and antibiotics and bioprocess characterization is essential for production optimization but relies on empiricism-based strategies. Protein expression profiles in an industrial scale, 180h fed-batch fermentation of Penicillium chrysogenum are presented. The biomass of P. chrysogenum, as well as the specific penicilli...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Synovial fluid protein adsorption on polymer-based artificial hip joint material investigated by MALDI-TOF mass spectrometry imaging
This study investigates in vitro protein adsorption on gamma-irradiated and Vitamin E doped UHMW-PE using synovia as modeling system. SDS-PAGE and MALDI-TOF mass spectrometry imaging showed adsorption of high abundance proteins in a mass range between 2 and 200kDa. Protein layer formation was observed on planar UHMW-PE material, whereas morphologically modified UHMW-PE regions were highly affected by protein aggregation. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Comparative proteomic analysis reveals molecular mechanism of seedling roots of different salt tolerant soybean genotypes in responses to salinity stress
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Hongyu Ma , Liru Song , Zhigang Huang , Yan Yang , Shuang Wang , Zhankui Wang , Jianhua Tong , Weihong Gu , Hao Ma , Langtao Xiao Salinity stress is one of the major abiotic stresses that limit agricultural yield. To understand salt-responsive protein networks in soybean seedling, the extracted proteins from seedling roots of two different genotypes (Lee 68 and Jackson) were analyzed under salt stress by two-dimensional polyacrylamide gel electrophoresis. Sixty-eight differentially expressed proteins were detected and identified...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Proteomic insights into non-small cell lung cancer: New ideas for cancer diagnosis and therapy from a functional viewpoint
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Johannes Linxweiler , Laxmikanth Kollipara , René P. Zahedi , Pavel Lampel , Richard Zimmermann , Markus Greiner We recently characterized SEC62 as an oncogene in non-small-cell lung cancer (NSCLC). Here we aimed to gain further insight into the molecular mechanisms of the cancer-related functions of this oncogene. We performed 2D-DIGE proteome analysis of tumor material from patients with NSCLC and of HEK293 cells stably overexpressing plasmid-encoded SEC62, combined with investigation of the Sec62 interactome. Furthermore, we ana...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
In situ activity-based protein profiling of serine hydrolases in E. coli
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Dmitry Shamshurin , Oleg V. Krokhin , David Levin , Richard Sparling , John A. Wilkins A fluorophosphonate based alkyne activity probe was used for the selective labeling of active serine hydrolases in intact Escherichia coli cells. A biotin-azide tag was subsequently attached to the alkyne functionality of the probe with copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Comparison of proteins from in-cell and lysate labeled preparations suggested qualitatively similar patterns of reactivity in both preparations. Approxim...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Arivusudar Marimuthu , Tai-Chung Huang , Lakshmi Dhevi N. Selvan , Santosh Renuse , Raja Sekhar Nirujogi , Praveen Kumar , Sneha M. Pinto , Sudha Rajagopalan , Akhilesh Pandey , H.C. Harsha , Aditi Chatterjee miRNAs regulate gene expression by binding to cognate mRNAs causing mRNA degradation or translational repression. Mass spectrometry-based proteomic analysis is being widely used to identify miRNA targets. The miR-200b miRNA cluster is often overexpressed in multiple cancer types, but the identity of the targets remains elu...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
The membrane complexome of a new Pseudomonas strain during growth on lysogeny broth medium and medium containing glucose or phenol
In this study, we have performed a systematic analysis of Pseudomonas sp. strain phDV1 membrane protein complexes by growing the strain in lysogeny broth medium, and medium containing glucose or phenol as sole carbon sources. In order to study the membrane complexome, we developed an approach for the extraction and the analysis of the membrane protein complexes in native conditions. Our strategy involves (a) enrichment of the membrane proteome from Pseudomonas sp. strain phDV1 by two washing steps; (b) solubilization using n-dodecyl-β-maltoside; (c) a combination of BN-PAGE with Tricine-SDS-PAGE; and (d) protein identific...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Biomarker discovery in asthma and COPD: Application of proteomics techniques in human and mice
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Steven Haenen , Elke Clynen , Benoit Nemery , Peter H.M. Hoet , Jeroen A.J. Vanoirbeek The use of advanced proteomics approaches in the search for biomarkers in chronic lung diseases, such as asthma and COPD, is rather limited. Asthma and COPD are complex disorders, which can be subdivided into several phenotypes. This results in a heterogeneity of differential expressed biological molecules. Furthermore, genetic differences between animals and humans make ‘translation’ of possible biomarkers challenging. Yet, the improved sensit...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): A. Saskia Venne , René P. Zahedi More than 450 post-translational modifications (PTMs) are known, however, currently only some of those can be enriched and analyzed from complex samples such as cell lysates. Therefore, we need additional methods and concepts to improve our understanding about the dynamic crosstalk of PTMs and the highly context-dependent regulation of protein function by so-called ‘PTM codes’. The mere focus on affinity-based enrichment techniques may not be sufficient to achieve this ambitious goal. However, the c...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
A proteomics approach for the development of sarcoma biomarkers
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Tadashi Kondo , Akira Kawai Sarcomas are rare and clinically diverse malignancies, and treatment optimization requires the development of suitable biomarkers. In earlier research employing proteomics analysis, we identified peroxiredoxin 2 as a biomarker of osteosarcoma (OS) that can predict response to neoadjuvant chemotherapy and verified its functional significance in the resistance of OS cells to chemotherapeutic drugs. In addition, in gastrointestinal stromal tumor (GIST), we identified pfetin as a prognostic biomarker and validate...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Bertrand Fabre , Thomas Lambour , David Bouyssié , Thomas Menneteau , Bernard Monsarrat , Odile Burlet-Schiltz , Marie-Pierre Bousquet-Dubouch Protein complexes are the main molecular machines that support all major cellular pathways and their in-depth characterization are essential to understand their functions. Determining the stoichiometry of the different subunits of a protein complex still remains challenging. Recently, many label-free quantitative proteomic approaches have been developed to study the composition of protein c...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Towards automated discrimination of lipids versus peptides from full scan mass spectra
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Piotr Dittwald , Trung Nghia Vu , Glenn A. Harris , Richard M. Caprioli , Raf Van de Plas , Kris Laukens , Anna Gambin , Dirk Valkenborg Although physicochemical fractionation techniques play a crucial role in the analysis of complex mixtures, they are not necessarily the best solution to separate specific molecular classes, such as lipids and peptides. Any physical fractionation step such as, for example, those based on liquid chromatography, will introduce its own variation and noise. In this paper we investigate to what extent ...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
The emergence of peptides in the pharmaceutical business: From exploration to exploitation
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 Author(s): Thomas Uhlig , Themis Kyprianou , Filippo Giancarlo Martinelli , Carlo Alberto Oppici , Dave Heiligers , Diederik Hills , Xavier Ribes Calvo , Peter Verhaert This minireview touches upon the challenges and opportunities peptides experience on the track to become an approved pharmaceutical. Peptide attributes originally considered troublesome with respect to drug development may now turn out to be more convenient rather than unfavourable. Besides characteristic high target affinity, biological peptides often exhibit higher than exp...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
News from the EuPA Liaison committee: Contributing to shaping the HUPO-iMOP initiative
Publication date: September 2014 Source:EuPA Open Proteomics, Volume 4 (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
