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      Sizing up models of heart failure: Proteomics from flies to humans

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          Abstract

          Cardiovascular disease is the leading cause of death in the western world. Heart failure is a heterogeneous and complex syndrome, arising from various etiologies, which result in cellular phenotypes that vary from patient to patient. The ability to utilize genetic manipulation and biochemical experimentation in animal models has made them indispensable in the study of this chronic condition. Similarly, proteomics has been helpful for elucidating complicated cellular and molecular phenotypes and has the potential to identify circulating biomarkers and drug targets for therapeutic intervention. In this review, the use of human samples and animal model systems (pig, dog, rat, mouse, zebrafish, and fruit fly) in cardiac research is discussed. Additionally, the protein sequence homology between these species and the extent of conservation at the level of the phospho-proteome in major kinase signaling cascades involved in heart failure are investigated.

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          Most cited references96

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          Update on activities at the Universal Protein Resource (UniProt) in 2013

          The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
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            A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila.

            In Drosophila, enhancer trap strategies allow rapid access to expression patterns, molecular data, and mutations in trapped genes. However, they do not give any information at the protein level, e.g., about the protein subcellular localization. Using the green fluorescent protein (GFP) as a mobile artificial exon carried by a transposable P-element, we have developed a protein trap system. We screened for individual flies, in which GFP tags full-length endogenous proteins expressed from their endogenous locus, allowing us to observe their cellular and subcellular distribution. GFP fusions are targeted to virtually any compartment of the cell. In the case of insertions in previously known genes, we observe that the subcellular localization of the fusion protein corresponds to the described distribution of the endogenous protein. The artificial GFP exon does not disturb upstream and downstream splicing events. Many insertions correspond to genes not predicted by the Drosophila Genome Project. Our results show the feasibility of a protein trap in Drosophila. GFP reveals in real time the dynamics of protein's distribution in the whole, live organism and provides useful markers for a number of cellular structures and compartments.
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              Proteomics of early zebrafish embryos

              Background Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.
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                Author and article information

                Journal
                Proteomics Clin Appl
                Proteomics Clin Appl
                prca
                Proteomics. Clinical Applications
                Wiley-VCH Verlag GmbH & Co (Oxford, UK )
                1862-8346
                1862-8354
                October 2014
                08 October 2014
                : 8
                : 9-10
                : 653-664
                Affiliations
                [1 ]Department of Medicine, Division of Cardiology, The Johns Hopkins University Baltimore, MD, USA
                [2 ]Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center Los Angeles, USA
                Author notes
                Correspondence: Dr. Jennifer E. Van Eyk, The Johns Hopkins University School of Medicine, Mason F. Lord Bldg, Center tower, Room 602, Baltimore, MD 21224, USA, E-mail: jvaneyk1@ 123456jhmi.edu , Fax: +1-410-550-8512

                These authors contributed equally to this work.

                Article
                10.1002/prca.201300123
                4282793
                24723306
                efb9469b-d3ea-41a2-aed4-7a27e1332021
                © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

                This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 21 November 2013
                : 31 January 2014
                : 03 April 2014
                Categories
                Reviews

                Molecular biology
                animal models,heart failure,posttranslational modifications
                Molecular biology
                animal models, heart failure, posttranslational modifications

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