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Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W. Proceedings of the EuBIC developer's meeting 2018. J Proteomics 2018; 187:25-27. [PMID: 29864591 DOI: 10.1016/j.jprot.2018.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
Abstract
The inaugural European Bioinformatics Community (EuBIC) developer's meeting was held from January 9th to January 12th 2018 in Ghent, Belgium. While the meeting kicked off with an interactive keynote session featuring four internationally renowned experts in the field of computational proteomics, its primary focus were the hands-on hackathon sessions which featured six community-proposed projects revolving around three major topics: Here, we present an overview of the scientific program of the EuBIC developer's meeting and provide a starting point for follow-up on the covered projects.
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Affiliation(s)
- Sander Willems
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - David Bouyssié
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS, Toulouse, France
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Viktoria Dorfer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Marie Locard-Paulet
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS, Toulouse, France
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Julian Uszkoreit
- Medizinisches Proteom-Center, Ruhr University Bochum, Bochum, Germany
| | - Dirk Valkenborg
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium; Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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2
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Affiliation(s)
- Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
- * E-mail:
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3
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Abstract
This study focuses on the 5-year Protein 3000 Project launched in 2002, the largest biological project in Japan. The project aimed to overcome Japan's alleged failure to contribute fully to the Human Genome Project, by determining 3000 protein structures, 30 percent of the global target. Despite its achievement of this goal, the project was fiercely criticized in various sectors of society and was often branded an awkward failure. This article tries to solve the mystery of why such failure discourse was prevalent. Three explanatory factors are offered: first, because some goals were excluded during project development, there was a dynamic of failed expectations; second, structural genomics, while promoting collaboration with the international community, became an 'anti-boundary object', only the absence of which bound heterogeneous domestic actors; third, there developed an urgent sense of international competition in order to obtain patents on such structural information.
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4
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Ferguson SM. Commercial considerations for immunoproteomics. Methods Mol Biol 2013; 1061:361-367. [PMID: 23963949 DOI: 10.1007/978-1-62703-589-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The underlying drivers of scientific processes have been rapidly evolving, but the ever-present need for research funding is typically foremost amongst these. Successful laboratories are embracing this reality by making certain that their projects have commercial value right from the beginning of the project conception. Which factors to be considered for commercial success need to be well thought out and incorporated into a project plan with similar levels of detail as would be the technical elements. Specific examples of commercial outcomes in the field of Immunoproteomics are exemplified in this discussion.
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Affiliation(s)
- Scott M Ferguson
- Human Health Therapeutics Portfolio, National Research Council Canada, Ottawa, ON, Canada
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5
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Wilson DS, Fang B, Dalton WS, Meade C, Koomen JM. An ET-CURE pilot project supporting undergraduate training in cancer research, emerging technology, and health disparities. J Cancer Educ 2012; 27:418-27. [PMID: 22528637 PMCID: PMC3439555 DOI: 10.1007/s13187-012-0362-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The National Cancer Institute's Center to Reduce Cancer Health Disparities has created pilot training opportunities under the "Continuing Umbrella of Research Experiences" program that focus on emerging technologies. In this pilot project, an 18-month cancer biology research internship was reinforced with: instruction in an emerging technology (proteomics), a transition from the undergraduate laboratory to a research setting, education in cancer health disparities, and community outreach activities. A major goal was to provide underrepresented undergraduates with hands-on research experiences that are rarely encountered at the undergraduate level, including mentoring, research presentations, and participation in local and national meetings. These opportunities provided education and career development for the undergraduates, and they have given each student the opportunity to transition from learning to sharing their knowledge and from being mentored to mentoring others. Here, we present the concepts, curriculum, infrastructure, and challenges for this training program along with evaluations by both the students and their mentors.
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Affiliation(s)
- Danyell S. Wilson
- Health Outcomes and Behavior, Moffitt Cancer Center
- Molecular Oncology, Moffitt Cancer Center
| | - Bin Fang
- Proteomics, Moffitt Cancer Center
| | | | - Cathy Meade
- Health Outcomes and Behavior, Moffitt Cancer Center
| | - John M. Koomen
- Molecular Oncology, Moffitt Cancer Center
- Experimental Therapeutics, Moffitt Cancer Center
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6
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Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CAJ, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DTF, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH. The Scottish Structural Proteomics Facility: targets, methods and outputs. ACTA ACUST UNITED AC 2010; 11:167-80. [PMID: 20419351 PMCID: PMC2883930 DOI: 10.1007/s10969-010-9090-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 12/19/2022]
Abstract
The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
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Affiliation(s)
- Muse Oke
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Lester G. Carter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Stanford Synchrotron Radiation Light Source, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025 USA
| | - Kenneth A. Johnson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Xuan Yan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Melina Kerou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Nadine D. Weikart
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Faculty of Chemistry, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- Present Address: Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG UK
| | - Md. Arif Sheikh
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stefan Schmelz
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Mark Dorward
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Division of Signal Transduction Therapy, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Michal Zawadzki
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, RG42 6EY UK
| | - Christopher Cozens
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Helen Falconer
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Institute of Structural and Molecular Biology, Edinburgh University, Kings Buildings, Edinburgh, EH9 3JR UK
| | - Helen Powers
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Ian M. Overton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
- Present Address: MRC Human Genetics Unit, Crewe Road South, Edinburgh, EH4 2XU UK
| | - C. A. Johannes van Niekerk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Xu Peng
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Prakash Patel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Roger A. Garrett
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Peter J. Coote
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - David T. F. Dryden
- EaStChem School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JJ UK
| | - Geoffrey J. Barton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | | | - Garry L. Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
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7
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Markley JL, Aceti DJ, Bingman CA, Fox BG, Frederick RO, Makino SI, Nichols KW, Phillips GN, Primm JG, Sahu SC, Vojtik FC, Volkman BF, Wrobel RL, Zolnai Z. The Center for Eukaryotic Structural Genomics. J Struct Funct Genomics 2009; 10:165-79. [PMID: 19130299 PMCID: PMC2705709 DOI: 10.1007/s10969-008-9057-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/12/2008] [Indexed: 10/29/2022]
Abstract
The Center for Eukaryotic Structural Genomics (CESG) is a "specialized" or "technology development" center supported by the Protein Structure Initiative (PSI). CESG's mission is to develop improved methods for the high-throughput solution of structures from eukaryotic proteins, with a very strong weighting toward human proteins of biomedical relevance. During the first three years of PSI-2, CESG selected targets representing 601 proteins from Homo sapiens, 33 from mouse, 10 from rat, 139 from Galdieria sulphuraria, 35 from Arabidopsis thaliana, 96 from Cyanidioschyzon merolae, 80 from Plasmodium falciparum, 24 from yeast, and about 25 from other eukaryotes. Notably, 30% of all structures of human proteins solved by the PSI Centers were determined at CESG. Whereas eukaryotic proteins generally are considered to be much more challenging targets than prokaryotic proteins, the technology now in place at CESG yields success rates that are comparable to those of the large production centers that work primarily on prokaryotic proteins. We describe here the technological innovations that underlie CESG's platforms for bioinformatics and laboratory information management, target selection, protein production, and structure determination by X-ray crystallography or NMR spectroscopy.
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Affiliation(s)
- John L Markley
- Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
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8
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Abstract
The Spanish National Network of Proteomic Facilities--ProteoRed has been created as an initiative for the coordination, integration and development of the proteomics facilities and laboratories distributed throughout Spain. ProteoRed's main objective is to give support to the scientific community allowing them wide access to emerging proteomics technologies and thus encouraging the science of proteomics. In addition, standardization of protocols and robustness of workflows are addressed by multi-centric laboratory activities. Educational, training and dissemination issues are part of the core activities of ProteoRed. To reach these objectives, specific activities have been developed through six working groups (WG1-WG6) covering functional, technical, educational and scientific aspects of proteomics.
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Affiliation(s)
- Alberto Paradela
- Proteomics Facility, National Center for Biotechnology, Madrid, Spain.
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9
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Norvell JC, Berg JM. [Protein structure initiative]. Tanpakushitsu Kakusan Koso 2008; 53:655-657. [PMID: 18409559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- John C Norvell
- National Institute of General Medical Sciences, National Institutes of Health, USA
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10
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Iavindrasana J, Lo Iacono L, Müller H, Periz I, Summers P, Wright J, Friedrich CM, Dach H, Gattermayer T, Engelbrecht G, Benkner S, Hofmann-Apitius M, Dunlop R, Arbona A, Rajasekaran H, Fingberg J, Chiarini A, Moore B, Bijlenga P, Hose RD, Frangi AF. The @neurIST project. Stud Health Technol Inform 2008; 138:161-164. [PMID: 18560117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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12
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Kasper CE. Genomics and proteomics methodologies for vulnerable populations research. Annu Rev Nurs Res 2007; 25:191-217. [PMID: 17958293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This chapter describes common genomic and proteomic methods and their application to the study of vulnerable population groups. The International HapMap project is discussed in relation to unique Haplotype single nucleotide polymorphisms (htSNPs) in population groups. In addition, studies, which have used these methods to investigate aging, ethnic, and racial specific conditions, as well as psychiatric diseases, are reviewed. Advantages and limitations of various genomic and proteomic approaches are discussed in relation to population admixture and sample selection.
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Affiliation(s)
- Christine E Kasper
- Uniformed Services University of the Health Sciences, Graduate School of Nursing, Bethesda, Maryland, USA
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13
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Abstract
As Europe is rolling out its seventh Framework Program for funding research with some emphasis on post-genomics, initiatives are burgeoning in the community to establish a comprehensive resource of protein-affinity reagents. Will funding priorities and community-based efforts meet?
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14
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Abstract
To avoid duplication of effort, slow adoption and inefficiency in development, those developing biological standards need to communicate more with each other, attract help from experts in the ontology/standards communities and keep focused on needs of users.
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Affiliation(s)
- Catherine A Ball
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305-5307, USA.
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15
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Puri M, Robin G, Cowieson N, Forwood JK, Listwan P, Hu SH, Guncar G, Huber T, Kellie S, Hume DA, Kobe B, Martin JL. Focusing in on structural genomics: The University of Queensland structural biology pipeline. ACTA ACUST UNITED AC 2006; 23:281-9. [PMID: 17097918 DOI: 10.1016/j.bioeng.2006.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/22/2006] [Accepted: 09/25/2006] [Indexed: 10/24/2022]
Abstract
The flood of new genomic sequence information together with technological innovations in protein structure determination have led to worldwide structural genomics (SG) initiatives. The goals of SG initiatives are to accelerate the process of protein structure determination, to fill in protein fold space and to provide information about the function of uncharacterized proteins. In the long-term, these outcomes are likely to impact on medical biotechnology and drug discovery, leading to a better understanding of disease as well as the development of new therapeutics. Here we describe the high throughput pipeline established at the University of Queensland in Australia. In this focused pipeline, the targets for structure determination are proteins that are expressed in mouse macrophage cells and that are inferred to have a role in innate immunity. The aim is to characterize the molecular structure and the biochemical and cellular function of these targets by using a parallel processing pipeline. The pipeline is designed to work with tens to hundreds of target gene products and comprises target selection, cloning, expression, purification, crystallization and structure determination. The structures from this pipeline will provide insights into the function of previously uncharacterized macrophage proteins and could lead to the validation of new drug targets for chronic obstructive pulmonary disease and arthritis.
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Affiliation(s)
- Munish Puri
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
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Hamacher M, Marcus K, van Hall A, Meyer HE, Stephan C. The HUPO Brain Proteome Project – No need to hurry? J Neural Transm (Vienna) 2006; 113:963-71. [PMID: 16835694 DOI: 10.1007/s00702-006-0510-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2005] [Accepted: 04/05/2006] [Indexed: 10/24/2022]
Abstract
The HUPO Brain Proteome Project (HUPO BPP) is dedicated to the analysis of the brain proteome and has initiated two pilot studies in order to elaborate a standardised system for data collection and reprocessing. Samples of mouse brains (different developmental stages) and human brain tissue (biopsy and post-mortem samples) were shipped to different laboratories in Europe, Asia and the US that were invited to identify as many proteins as possible using their own approaches. In addition, a centralised data reprocessing strategy has been elaborated in an iterative way to generate highly reliable lists of identified proteins. This consortium could be a good example for a standardized proteomics workflow.
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Affiliation(s)
- M Hamacher
- Medical Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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17
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Wang BC, Adams MWW, Dailey H, DeLucas L, Luo M, Rose J, Bunzel R, Dailey T, Habel J, Horanyi P, Jenney FE, Kataeva I, Lee HS, Li S, Li T, Lin D, Liu ZJ, Luan CH, Mayer M, Nagy L, Newton MG, Ng J, Poole FL, Shah A, Shah C, Sugar FJ, Xu H. Protein production and crystallization at SECSG -- an overview. ACTA ACUST UNITED AC 2006; 6:233-43. [PMID: 16211524 DOI: 10.1007/s10969-005-2462-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2004] [Accepted: 02/15/2005] [Indexed: 11/27/2022]
Abstract
Using a high degree of automation, the Southeast Collaboratory for Structural Genomics (SECSG) has developed high throughput pipelines for protein production, and crystallization using a two-tiered approach. Primary, or tier-1, protein production focuses on producing proteins for members of large Pfam families that lack a representative structure in the Protein Data Bank. Target genomes are Pyrococcus furiosus and Caenorhabditis elegans. Selected human proteins are also under study. Tier-2 protein production, or target rescue, focuses on those tier-1 proteins, which either fail to crystallize or give poorly diffracting crystals. This two tier approach is more efficient since it allows the primary protein production groups to focus on the production of new targets while the tier-2 efforts focus on providing additional sample for further studies and modified protein for structure determination. Both efforts feed the SECSG high throughput crystallization pipeline, which is capable of screening over 40 proteins per week. Details of the various pipelines in use by the SECSG for protein production and crystallization, as well as some examples of target rescue are described.
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Affiliation(s)
- Bi-Cheng Wang
- Southeast Collaboratory for Structural Genomics, University of Georgia, Athens, GA 30602, USA
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Hondermarck H. [Proteomics of breast cancer: From differential to functional analysis]. J Soc Biol 2006; 200:199-202. [PMID: 17151556 DOI: 10.1051/jbio:2006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
From differential analysis to identify biomarkers, to functional analysis for finding new therapeutic targets, proteomics bring new comprehensive information for a better understanding of the molecular basis of oncology and new perspectives for the clinic. However the major limitation of proteomic investigations, more generally of post-genomic approaches, remains the molecular and cellular complexity of the mammary gland that is still a major challenge.
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Affiliation(s)
- Hubert Hondermarck
- JE 2488 ERI-8 INSERM Signalisation des facteurs de croissance dans le cancer du sein, IFR-118, Université des Sciences et Technologies de Lille, 59650 Villeneuve d'Ascq.
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Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK. New York-Structural GenomiX Research Consortium (NYSGXRC): A Large Scale Center for the Protein Structure Initiative. ACTA ACUST UNITED AC 2005; 6:225-32. [PMID: 16211523 DOI: 10.1007/s10969-005-6827-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 05/02/2005] [Indexed: 11/27/2022]
Abstract
Structural GenomiX, Inc. (SGX), four New York area institutions, and two University of California schools have formed the New York Structural GenomiX Research Consortium (NYSGXRC), an industrial/academic Research Consortium that exploits individual core competencies to support all aspects of the NIH-NIGMS funded Protein Structure Initiative (PSI), including protein family classification and target selection, generation of protein for biophysical analyses, sample preparation for structural studies, structure determination and analyses, and dissemination of results. At the end of the PSI Pilot Study Phase (PSI-1), the NYSGXRC will be capable of producing 100-200 experimentally determined protein structures annually. All Consortium activities can be scaled to increase production capacity significantly during the Production Phase of the PSI (PSI-2). The Consortium utilizes both centralized and de-centralized production teams with clearly defined deliverables and hand-off procedures that are supported by a web-based target/sample tracking system (SGX Laboratory Information Data Management System, LIMS, and NYSGXRC Internal Consortium Experimental Database, ICE-DB). Consortium management is provided by an Executive Committee, which is composed of the PI and all Co-PIs. Progress to date is tracked on a publicly available Consortium web site (http://www.nysgxrc.org) and all DNA/protein reagents and experimental protocols are distributed freely from the New York City Area institutions. In addition to meeting the requirements of the Pilot Study Phase and preparing for the Production Phase of the PSI, the NYSGXRC aims to develop modular technologies that are transferable to structural biology laboratories in both academe and industry. The NYSGXRC PI and Co-PIs intend the PSI to have a transforming effect on the disciplines of X-ray crystallography and NMR spectroscopy of biological macromolecules. Working with other PSI-funded Centers, the NYSGXRC seeks to create the structural biology laboratory of the future. Herein, we present an overview of the organization of the NYSGXRC and describe progress toward development of a high-throughput Gene-->Structure platform. An analysis of current and projected consortium metrics reflects progress to date and delineates opportunities for further technology development.
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Affiliation(s)
- Jeffrey B Bonanno
- Structural GenomiX, Inc., 10505 Roselle Street, San Diego, CA 92121, USA
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Abstract
The Danish Breast Cancer Cooperative Group (DBCG) was established in 1977 with the aim to ensure optimal breast cancer diagnostics and therapeutic modalities on a nationwide basis. DBCG was organized in such a way so it represents a broad interdisciplinary collaboration with established clinical databases and biobanks. This review summarizes the infrastructures, such as those of the DBCG, that are required to facilitate translational research studies aiming at further diagnostic and therapeutic improvements through interactions directed at prevention, early diagnosis, and treatment of primary breast cancer.
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Affiliation(s)
- Henning T Mouridsen
- Danish Breast Cancer Cooperative Group, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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MESH Headings
- Drug Design
- Drug Industry/instrumentation
- Drug Industry/methods
- Drug Industry/trends
- Electrophoresis, Gel, Two-Dimensional/instrumentation
- Electrophoresis, Gel, Two-Dimensional/methods
- Electrophoresis, Gel, Two-Dimensional/trends
- Europe
- Isotope Labeling/instrumentation
- Isotope Labeling/methods
- Isotope Labeling/trends
- Mass Spectrometry/methods
- Proteins/chemistry
- Proteins/classification
- Proteins/genetics
- Proteomics/instrumentation
- Proteomics/methods
- Proteomics/organization & administration
- Proteomics/trends
- Sequence Analysis, Protein/methods
- Technology, Pharmaceutical/instrumentation
- Technology, Pharmaceutical/methods
- Technology, Pharmaceutical/trends
- United States
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27
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Affiliation(s)
- Ruedi Aebersold
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA.
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