Synopsis
From skillful handling of the wide range of technologies to successful applications in drug discovery -- this handbook has all the information professional proteomics users need.
Edited by experts working at one of the hot spots in European proteomic research, the numerous contributions by experts from the pharmaceutical industry and public proteomics consortia to provide the necessary perspective on current trends and developments in this exciting field.
Following an introductory chapter, the book moves on to proteomic technologies, such as protein biochips, protein-protein interactions, and proteome analysis in situ. The section on applications includes bioinformatics, Alzheimer's disease, neuroproteomics, plasma and T-cell proteomics, differential phosphoproteome analysis and biomarkers, as well as pharmacogenomics.
Invaluable reading for medicinal and pharmaceutical chemists, gene technologists, molecular biologists, and those working in the pharmaceutical industry.
"synopsis" may belong to another edition of this title.
About the Author
All six editors are Researchers at the Medical Proteom-Center hosted by the University of Bochum (Germany). This international research center was established in 2002 under the leadership of Helmut E. Meyer, a co-founder of the Protagen AG. Professor Meyer is also initiator and coordinator of the Human Brain Proteome Project within the German National Genome Research Net (NGFN) as well as of the Brain Proteome Project within the Human Proteome Organisation (HUPO BPP).
From the Back Cover
By delving beyond the genomic information, proteomics can address problems that are inaccessible to conventional genomics studies. These new and powerful analytical techniques open up new possibilities for the investigation of drug action and for the development of new drugs.
From skillful handling of the wide range of technologies to successful applications in drug discovery -- this handbook has all the information professional proteomics users need.
Edited by experts working at one of the hot spots in European proteomic research, the numerous contributions by experts from the pharmaceutical industry and public proteomics consortia to provide the necessary perspective on current trends and developments in this exciting field.
Following an introductory chapter, the book moves on to proteomic technologies, such as protein biochips, protein-protein interactions, and proteome analysis in situ. The section on applications includes bioinformatics, Alzheimer's disease, neuroproteomics, plasma and T-cell proteomics, differential phosphoproteome analysis and biomarkers, as well as pharmacogenomics.
With its coverage of a wide range of technologies and areas of application, this book is invaluable for medicinal and pharmaceutical chemists, gene technologists, molecular biologists, and those working in the pharmaceutical industry.
From the Inside Flap
By delving beyond the genomic information, proteomics can address problems that are inaccessible to conventional genomics studies. These new and powerful analytical techniques open up new possibilities for the investigation of drug action and for the development of new drugs.
From skillful handling of the wide range of technologies to successful applications in drug discovery -- this handbook has all the information professional proteomics users need.
Edited by experts working at one of the hot spots in European proteomic research, the numerous contributions by experts from the pharmaceutical industry and public proteomics consortia to provide the necessary perspective on current trends and developments in this exciting field.
Following an introductory chapter, the book moves on to proteomic technologies, such as protein biochips, protein-protein interactions, and proteome analysis in situ. The section on applications includes bioinformatics, Alzheimer's disease, neuroproteomics, plasma and T-cell proteomics, differential phosphoproteome analysis and biomarkers, as well as pharmacogenomics.
With its coverage of a wide range of technologies and areas of application, this book is invaluable for medicinal and pharmaceutical chemists, gene technologists, molecular biologists, and those working in the pharmaceutical industry.
Excerpt. © Reprinted by permission. All rights reserved.
Proteomics in Drug Research
John Wiley & Sons
Copyright © 2006 Wiley-VCH Verlag GmbH & Co. KGaA, WeinheimAll right reserved.
ISBN: 978-3-527-31226-9
Chapter One
Administrative Optimization of Proteomics Networks for Drug DevelopmentAndr van Hall and Michael Hamacher
Abstract
Administrative structures are gaining more and more importance in the complex world of modern science. This article will define the terms administration and networking, describing the aims and tasks of project management. The analysis of neurodegenerative diseases with proteomics technologies will be looked at from the administrative point of view with a focus on the different phases of strategy development, human resources, project control and networking. The realization of these tasks is illustrated by short presentations of a national funded network, the German Human Brain Proteome Project (HBPP) within the National Genome Research Network (NGFN), as well as of the international Brain Proteome Project of the Human Proteome Organisation (HUPO BPP).
1.1 Introduction
In modern science, the importance of administration has increased steadily over the last few decades. Nevertheless, administrative work and its influence on the success of projects as well as on financial aspects (e.g., refunding) are still undervalued in the academic field. While industry recognized the importance of organizational aspects long ago, positions responsible for administrative tasks within scientific research groups (excluding administrative departments of the universities themselves) are rare. The number of operative relative to administrative personnel is still much higher in academia than in companies (at least in Europe). As a consequence, these tasks are often done by the coordinator of a given project or one of his coworkers, who are often overloaded with work, sometimes unmotivated and mostly untrained in this field. A picture of the typical administrative research scientist as being exhausted by research, teaching and organization is emerging. In addition, staff turnover in these positions is often high, resulting in loss of knowledge, lack of continuity, and commonly, a lack of perception as to where responsibility lies. At the same time, such positions could be extremely important for the overall success of the group, e.g., in the crosslinking of basic research and commercialization.
Owing to the increasing complexity of modern science, e.g., international networking and large consortia, and the urgent need to present scientific research to the public and to the governmental project management/advisory board, a department-spanning administration should be implemented. Most research efforts in the health sciences are extremely complex and are difficult to explain to nonscientists, which often leads to misunderstanding, antipathy or even hostility from the public (e.g., see stem cell discussion, gene technologies, etc.). As the last 20 years have clearly shown, the support of a common administrative staff leads to the scientific personnel being relieved of additional work to which they are not suited, to an optimization of the scientific output (increasing added value) and to a broader acceptance in society. The need for management expansion has also been recognized by the European Union and its advisory councils, as expressed by Ernst-Ludwig Winnacker, the president of the European Heads of Research Council, in an interview with The Scientist: "The networks of excellence are big enterprises that require a great deal of management, and these have not been appreciated by scientists as much as the smaller, short-term programs that are less complex to manage and that facilitate work with smaller partners." (The Scientist online, 25 August 2004: http://www.biomedcentral.com/). The reasons for this development will be shown in the next paragraphs.
1.2 Tasks and Aims of Administration
The following chapter will present a short overview about modern scientific administration, mainly focusing on the academic side of research. To set a common starting point of what "administration" is about, the following definition is used:
The act or process of administering, especially the management of a government or large institution.
The group of people who manage or direct an institution.
Simultaneously with the increasing complexity of life science, the tasks and aims of the administration have steadily grown and evolved to a much more active management role. Originally mainly involving finances and human resources, these tasks have been joined by numerous other duties and responsibilities. Many projects demand large groups or consortia resulting in network systems (see below), thus making the organization and the feedback of teamwork as well as facilitation of the flow of information within a network an essential part of work. Additionally, interactions between the network and other national as well as international research projects, research institutions and private enterprises have to be handled. This includes so-called lobby work, the discussion with and convincing of policy makers e.g., within the European Union, to support the kind of research one advocates as the most promising approach.
Further tasks required of an administration are the composition of progress reports/business plans and final reports on schedule, the organization and calling of coordination meetings, the coordination and active participation in public relations (conferences, seminars, TV, radio, journals, etc.). This includes the planning and realization of training courses concerning technologies and topics provided by the consortium members, and the publication of the subproject results obtained at the respective time points. Moreover, (existing) homepages should be improved and optimized steadily, so that they serve not only as an information platform, but also as an interchange and communication portal.
Taken together, the administration has to
build up a network offering fast and efficient information flow;
elaborate business plans, evaluate the progress of subprojects and co-ordinate efforts;
implement infrastructures (see evaluation, Section 1.4);
serve as a central contact and administration point (added value);
increase public knowledge and acceptance of proteomics;
implement a bioinformatics infrastructure that will serve as a basis for further data base projects.
The aims of the administration - particularly in universities - are obviously to optimize processes and workflows within the respective department or network. Though implementation of controlling and monitoring could be hard to adopt in academia (in regard to the strong group autonomy), both processes are inevitably mandatory, especially in times of decreasing budgets and funding, as a consequence of which some US universities have started to gather discarded or not-required high-tech equipment from local departments and offer it to all other groups for free, avoiding unnecessary investments and expenses.
There are several other domains that have to be carefully considered when aiming at successful projects, most notably in human resources, where the generation of job specifications and the consequent identification of adequate coworkers should not be underestimated. Qualified and motivated employees who fit into the group structure are the basic requirement for planning, performing and finishing work packages in a defined schedule. These have to be generated carefully and in regard to several questions, e.g., medical need, potential return of investment, proof of concept and commercialization.
Commercialization was more or less been ignored in academia until the 1980s, when more and more scientists came to the opinion that research and marketing do not necessarily exclude each other. Several processes around the world now show the increased importance of marketing. No application within the EU can be submitted to obtain grants without presenting utilization strategies. Scotland started a Proof of Concept Fund in 1999 to advance promising ideas from university to readiness for marketing (www.scottish-enterprise.com/proofofconceptfund). More than 140 projects have already been funded with [euro] 36 million, resulting in six existing and ten planned spin-offs. In Germany, universities and research organizations, e.g., the Fraunhofer Gesellschaft have implemented utilization departments specializing in regard to patents, licensing, consortia contracts, etc. The Ruhr University in Bochum, Germany, for example founded the Research and Collecting Society "RUBITEC - Society for Innovation and Technology" in March 1998 (http://www.ruhr-uni-bochum.de/rubitec/start.htm), consulting the numerous groups at the campus. The National Institutes of Health has elaborated a complex organization structure including the Office of Technology Transfer (http://ott.od.nih.gov) dealing with 341 invention disclosures and US$ 53.7 million in royalties in 2004. These centers offer competent help in realizing products and patents, but leave the initial efforts to the research groups. Scientists have to inform themselves about possible strategies and have to evaluate the putative success. An administrative coworker assuming this time-consuming job will function as a bridge between the groups and the central transfer departments. Thus, taken together, the optimal realization of these tasks will lead to the relief of the operative coworker, enabling the researcher to concentrate on the actual scientific work, to shorten the time from idea to output, and to commercialize his output successfully.
As already mentioned above, research efforts are more and more bundled in consortia and networks. Owing to the importance of this circumstance, it is necessary to discuss some theoretical aspects of networking and the consequences resulting from its nature.
1.3 Networking
Networks are an organizational structure with at least two independent entities being in a repetitive, long-lasting exchange/interaction status (see also Burt, 1980). Owing to the independency of the entities the network is more or less bound together by social relations, according to one or more motivations:
Necessity: interaction is initiated by law or regulatory prescription.
Asymmetry: to gain influence and control over the partner/its resources.
Reciprocity: to achieve bilateral aims and interests.
Efficiency: to gain higher input/output-ratio by utilize synergistic effects.
Stability: to reduce/absorb/predict uncertainties.
Legitimization: to gain or improve reputation, image or prestige.
The process of composing and inspiring a network can be divided into seven phases:
Self-analysis: what is the goal?
Specification: which resources are missing?
Preselection: who offers the lacking resources?
Partner analysis: does the new partner fit in the overall concept?
Definition of goals: what do the partners expect from each other?
Process modeling: how can the goals be reached?
Realization.
Industry is again on the cutting edge in establishing strategic alliances or regional clusters. In Switzerland more than 80% of all biotechnology companies are concentrated in the four regions Basel (Biovalley), Zurich (MedNet), Lake Geneva (bioalps) and Tessin (biopolo) (Veraguth, 2004), profiting from the "big pharma" industry that offers potential financiers, manpower and licensees.
In academia, the factors asymmetry, reciprocity, legitimization and efficiency probably have to be considered as the main motivation for building up networks. Nevertheless, most cooperative enterprises follow from personal relationships or historically derived projects that have been performed in the group several years ago. The need for combining synergistic resources is often unseen, sometimes hampered by ignorance of which potential partners are working in the same field or could offer complementary techniques. The identification of key players and potent partners is therefore an essential task in organizing a powerful network.
In addition to this selection mode, the management has to deal with regulation between the partners as well as between the consortium and external entities, with allocation concerning the access of given resources and with evaluation in regard to the output (profit, innovation, proof of concept). Problems within networks often evolve from the opportunistic behavior of one or more partners or due to different strategic targets, thus demanding complex agreements and interaction/communication right from the beginning to generate confidence between the partners. Throughout the whole project, several quality control steps concerning work packages, finances, etc., have to be performed.
1.4 Evaluation of Biomarkers
In general, the struggle for understanding and fighting e.g., neurodegenerative diseases, is intended to find either drug targets involved in the pathological processes or diagnostic markers that allow sensitive identification of disease stages (Zolg and Langen, 2004). Diagnostic markers can be subdivided into:
Screening markers: allow indication of the transit from health to disease [e.g., maternal serum invasive trophoblast antigen for Down syndrome during the second trimester (Palomaki et al., 2004)].
Prognostic markers: allow prediction of the disease process [e.g., survivin expression in pancreatic cancer patients (Kami et al., 2004)].
Stratification markers: allow prediction of the response to a medication strategy [NQO1 genotype in adenocarcinoma of upper gastrointestinal tract (Sarbia et al., 2003)].
Efficacy markers: allow monitoring of the efficacy of a given drug treatment [serum CYFRA 21-1 (cytokeratin-19 fragments) in breast cancer (Nakata et al., 2004)].
Before starting research, several questions have to be answered in a detailed business plan when aiming at a successful utilization concept in industry (Zolg and Langen, 2004), e.g.,
Do competitive markers already exist on the market?
Will the marker be easily accepted in the market?
Will the marker cover/exceed the research costs?
As academic research usually is much more philanthropic than industrial, these considerations are normally secondary for scientists in universities. Nevertheless, it is highly advisable to elaborate a business-plan-like approach concept dealing with pros and cons, work packages and possible contingency plans to increase efficacy and output.
The interconnection between the basic research and commercialization is structured most efficiently in an innovation process organized with clear stage gate decisions (see Chapter 17). An estimated 50% of all life science companies are using this structure. Here, product ideas originating from the research will be judged by a decision board in regard to economically relevant features (e.g., market need, competition, etc.). People and know-how will be transferred in several stages to the commercialization branch. This milestone-oriented process will be reviewed constantly by a board. After passing all criteria including concept, market attractiveness, competitive market position, competitive technology position, reward, and risk, the project will go into the next stage of the innovation process with clear planning for milestones and budgets. This phased project planning was developed by NASA in the early period of crewed spaceflights and propagated by product development experts such as R. G. Cooper (Cooper, 2001). Work is divided into sequential phases avoiding overlapping activities, but as every gate has to be carefully evaluated, it is inherent to the process that there will be a relatively long time from the idea to the market.
(Continues...)
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