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Objective: Proteomics is the large-scale study of localization, identification, structure, and function of the proteome. A proteome is the complete set of proteins expressed and modified by an organism under a specific set of environmental conditions. This study was undertaken to investigate the novel protein biomarkers that play a role in breast cancer under inflammatory condition. Methods: The two-dimensional gel electrophoresis (2-DE) was applied in the context of the breast cancer model system to investigate the effect of interferon-gamma (IFN-γ) on the differential protein expression in breast cancer-derived cell lines CAMA-1 and 3,4-methylenedioxyamphetamine (MDA)-MB-231. Whole cell lysates were prepared from IFN-γ-stimulated and non-stimulated CAMA-1 and MDA-MB-231 cells for 2-DE to obtain information for potential differential protein expression. Protein spots in the gels were visualized by silver staining and analyzed by Progenesis SameSpot. Gels were then scanned using the Epson image scanner with LabScan 6.0 software. The ExPASy tool was used to identify and quantify breast cancer cell membrane proteins expressed in response to IFN-γ. Results: In the present proteomics study, a series of differentially expressed proteins were analyzed in IFN-γ-stimulated CAMA-1 and MDA-MB-231 cells. While results obtained from this analysis can be used as preliminary data to identify differences between untreated and IFN-γ-treated samples, they were not used for further mass spectrometry analysis. Conclusion: The data described and discussed here can be utilized for further data validation projects and could assist in the discovery of new breast cancer-related proteins and molecular pathways.

Heat treatment of milk may cause whey proteins and caseins to form aggregates. These soluble and micellar aggregates and their other properties (size, composition, shape, etc.) can affect the techno-functionalities to the milk, conferring interesting or negative features depending on the application in dairy industries. In this study, we propose a new approach to characterise those protein aggregates. SDS-agarose electrophoresis is followed by the calculation of a retention factor (Rf) for each protein spot. Rf allows milk aggregates to be compared qualitatively under the same conditions. This method could be transposed to the dairy industry for a better knowledge of the milk subsequent to heat treatment.

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 significantly correlated with shorter progression-free survival. Gene-silencing assay demonstrated that RKIP and MnSOD had suppressive and promotive effects on tumor cell proliferation and invasion, respectively. Our findings reveal biological and clinical significance of RKIP and MnSOD in RCC.

The Binder of SPerm 1 (BSP1) protein is involved in the fertilization and semen cryopreservation processes and is described to be both beneficial and detrimental to sperm. Previously, the relationship of BSP1 with freezability events has not been completely understood. The objective of this work was to determine the differential abundance of the forms of the BSP1 protein in cryopreserved seminal plasma of Bos taurus indicus bulls with different patterns of semen freezability using proteomics. A wide cohort of adult bulls with high genetic value from an artificial insemination center was used as donors of high quality, fresh semen. Nine bulls presenting different patterns of semen freezability were selected. Two-dimensional gel electrophoresis showed differential abundance in a group of seven protein spots in the frozen/thawed seminal plasma from the bulls, ranging from 15 to 17 kDa, with pI values from 4.6 to 5.8. Four of these spots were confirmed to be BSP1 using mass spectrometry, proteomics, biochemical, and computational analysis (Tukey's test at P

2D-gel electrophoresis (2DGE) is an important technique in proteomics for analyzing the protein expressions. However, the analysis of 2DGE images is still a cumbersome and tedious task. One of the main reasons is the presence of a large amount of the inhomogeneities in the foreground and the background intensities. In this paper, we have proposed a novel approach of segmentation of the protein spots in the non separable wavelet domain. It utilizes the inter-scale relationship among enhanced wavelet coefficients, which can easily distinguish the different features of the image the interior region of spots, the edges and the background. This technique is based on a single threshold and is independent of the gray value of the image. It copes with the inhomogeneities in the 2DGE images up to a great extent, which is helpful for finding the protein spots accurately. The artifacts are further removed using a non-threshold based method comprising a weighted Gaussian energy distribution model. Experimental results show that our method outperforms the available commercial software and previously reported works. (C) 2015 Elsevier Ltd. All rights reserved.

International audience; Cotyledonary somatic embryos (SEs) of maritime pine are routinely matured for 12 weeks before being germinated and converted to plantlets. Although regeneration success is highly dependent on SEs quality, the date of harvesting is currently determined mainly on the basis of morphological features. This empirical method does not provide any accurate information about embryo quality with respect to storage compounds (proteins, carbohydrates). We first analyzed SEs matured for 10, 12 and 14 weeks by carrying out biological (dry weight, water content) and biochemical measurements (total protein and carbohydrate contents). No difference could be found between collection dates, suggesting that harvesting SEs after 12 weeks is appropriate. Cotyledonary SEs were then compared to various stages, from fresh to fully desiccated, in the development of cotyledonary zygotic embryos (ZEs). We identified profiles that were similar using hierarchical ascendant cluster analysis (HCA). Fresh and dehydrated ZEs could be distinguished, and SEs clustered with fresh ZEs. Both types of embryo exhibited similar carbohydrate and protein contents and signatures. This high level of similarity (94.5 %) was further supported by proteome profiling. Highly expressed proteins included storage, stress-related, late embryogenesis abundant and energy metabolism proteins. By comparing overexpressed proteins in developing and cotyledonary SEs or ZEs, some (23 proteins) could be identified as candidate biomarkers for the late, cotyledonary stage. This is the first report of useful generic protein markers for monitoring embryo development in maritime pine. Our results also suggest that improvements of SEs quality may be achieved if the current maturation conditions are refined.

Two species of microcolonial fungi – Cryomyces antarcticus and Knufia perforans - and a species of black yeasts–Exophiala jeanselmei - were exposed to thermo-physical Mars-like conditions in the simulation chamber of the German Aerospace Center. In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis. Despite of the expectations, the fungi did not express any additional proteins under Mars simulation that could be interpreted as stress induced HSPs. However, up-regulation of some proteins and significant decreasing of protein number were detected within the first 24 hours of the treatment. After 4 and 7 days of the experiment protein spot number was increased again and the protein patterns resemble the protein patterns of biomass from normal conditions. It indicates the recovery of the metabolic activity under Martian environmental conditions after one week of exposure.

Background Natural microbial communities are extremely complex and dynamic systems in terms of their population structure and functions. However, little is known about the in situ functions of the microbial communities. Results This study describes the application of proteomic approaches (metaproteomics) to observe expressed protein profiles of natural microbial communities (metaproteomes). The technique was validated using a constructed community and subsequently used to analyze Chesapeake Bay microbial community (0.2 to 3.0 μm) metaproteomes. Chesapeake Bay metaproteomes contained proteins from pI 4–8 with apparent molecular masses between 10–80 kDa. Replicated middle Bay metaproteomes shared ~92% of all detected spots, but only shared 30% and 70% of common protein spots with upper and lower Bay metaproteomes. MALDI-TOF analysis of highly expressed proteins produced no significant matches to known proteins. Three Chesapeake Bay proteins were tentatively identified by LC-MS/MS sequencing coupled with MS-BLAST searching. The proteins identified were of marine microbial origin and correlated with abundant Chesapeake Bay microbial lineages, Bacteroides and α-proteobacteria. Conclusion Our results represent the first metaproteomic study of aquatic microbial assemblages and demonstrate the potential of metaproteomic approaches to link metagenomic data, taxonomic diversity, functional diversity and biological processes in natural environments.