Let’s start with a joke. “What are three Germans doing that you have put into one room? – Founding an association!” In Germany we have associations for everything in the smallest village. Associations of hen breeders, associations of stamp collectors, associations of local singers, associations of hobby gardeners, associations of wine drinkers, associations of The Kelly Family concert visitors, and so on. Since late 2001 we additionally have the German Society for Proteome Research (DGPF), whose very first founding charter was wrote down on a beer mat (well, we are in Germany, aren’t we). The foundation of the DGPF by scientists and industry representatives was a reaction on latest market and application movements towards protein research. Germany already has had strong Proteomics (& protein) research when others were still chasing the holy grail Genomics. But – to my impression – it was never really well communicated. So, one major aim of the DGPF will be to improve the international knowledge about the high level of German Proteomics. But why are researchers and the industry more and more focussed on Proteomics? One of the major disadvantages of Genomics approaches is the missing connection between a gene and its cellular function. The fact that a gene has been sequenced does not give us the cellular function of the gene product. That makes genomic results so difficult to interpret. Even the sequence analysis with bioinformatics tools does not yield the full picture. Additional problems arise through the organisation of the genetic information as well as the fact that only a subset of genes is active in a specific cell at a specific stage. So, scientists are moving to the functional level, to the gene products, to the proteins. And they developed the new term, “Proteomics”, for the complete set of proteins (functions) of a cell in a specific stage, in analogy to “Genomics” that addresses the complete set of genes (information) of a cell. Similar to other attempts with a large-scale option in industrial applications (drug discovery e.g.), it will depend on the technology developing and supplying industry if Proteomics will get its chance. When I was doing the research for this article I had the impression that some companies just stuck the Proteomics label onto their existing products. This is neither a solution nor does it really fit the researchers needs. But where are the bottlenecks and what has to be done? There is a dramatic increase of complexity while switching from the genetic to the functional level. A gene is a gene is a gene. There is slight variation caused by introns and foreign elements as well as expression control. But our scientific thinking is dominated by the “one gene – one protein” paradigm, even since the knowledge about posttranscriptional modifications has shown that it is not just that simple. With proteins one has to view every single candidate in the context of multi-functionality and networking. In many cases one protein is not just one function. It is part of a high-complex cellular network of interacting and cascading activities. The function of most regulatory proteins for example depends on environment (regarding ‘cellular clock’ and location), posttranslational modifications and interacting partners. As a result one protein might have a couple of functions depending on where, when and with whom it is. This puts Proteomics to trouble. At first, there are still no powerful technologies for many aspects in large-scale protein research available. Friedrich Lottspeich, head of the protein analysis group at the Max-Planck-Institute for Biochemistry in Munich and DGPF-chairman, said that recent methods exhibit great potential but are not yet ready for the industrial job, in drug discovery for example. There are only few suitable solutions for automation and high-throughput. Early stage MALDI-TOF applications work pretty well, in Structural Proteomics e.g.. But problems with high-throughput sample preparation, low abundant and hydrophobic proteins are unsolved. In Functional Proteomics automated interaction-screens based on the 2-Hybrid, SPR (surface plasmon resonance) or TAP (tandem affinity purification) technologies – that are essential to discover the networking aspect of proteins – are at its infancy. Antibody-based biochips already show the direction. At second, Proteome research results in huge amounts of data. Corresponding to the higher complexity, Proteomics causes exponentially more data than Genomics does. But drug discovery (and scientific research in common) is not just collecting data, even if one might suspect some scientists to think so. No, the scientific progress depends on results derived by the analysis and interpretation of collected data. And this is getting more and more difficult with increasing complexity. Finally, the complexity of protein functionality has to be taken into account while moving forward. An attempt to this is the field of Integrated Proteomics that considers various views by the combination of data coming from different approaches and sources. But . this again increases not only the total amount of data to be analysed but also the level of complexity. According to Thomas Franz, head of the Proteomics core facility at EMBL Heidelberg, existing bioinformatics solutions are not able to quantitatively and qualitatively analyse the produced data. This opinion is shared by a couple of colleagues working in the field. Scientific teams are analysing the data manually again because this is more effective and still yields the most meaningful results. The conclusion is an answer to my question what has to be done. There is a deep need for at least a) large-scale protein research technologies, b) suitable bioinformatics solutions and c) Proteomics-optimized devices. I am curious about the future development of Proteomics. It might be overrun by other “-omics” in public attention. But I am convinced that Proteomics will contribute important findings to our understanding of how a cell works. And for sure it is and will be a major market for technology suppliers and bioinformatics companies. Originally published in April 2002 by Inside-Lifescience, ISSN…

Well, honestly, things are on the move these days. Scientists and publishers are discussing new ways of publishing scientific results. EMBO starts an initiative to set up a platform that will provide services relating to access and retrieval of digital information in the life sciences, ranging from bibliographic or factual data to published full text – E-BioSci. Even database publishers draw nearer academic institutions to promote their content products. Last week scientists and information providers met at the 8th annual meeting of the German Information and Communication Initiative of the Learned Societies entitled “Open Systems for the Communication in Science and Research”. The conference wanted to discuss the latest national developments as well as strategies on how to improve the scientific information workflow. The talks and presentations concentrated on three major points: the future of scientific publication, current developments in information infrastructures, and multimedia in academic education and training. Not more!? To my opinion every single topic would have been enough for an own conference. But the organizers aimed at giving an overview and … bringing people from different disciplines together. I am sure you know the problem. For some reason communication between the academic disciplines often does not really exist but on the paper. Focusing on improving the supply of the scientific community with specialist information, we observe a variety of ‘island-solutions’. Young scientists are used to free internet information sources but are still completely inexperienced with using ‘valuable’ databases. How could they … there is no awareness of information with costs. The problem is well known. And now we are coming back to the lack of communication. Many scientific groups are developing strategies in parallel, to provide scientific labs with database information e.g.. Many solutions never really had a chance because they are redundant. Many resources are used in parallel without looking for synergies and if there could be a common way. Let’s think capitalistic … or evolutionary: The best(?) system will survive! OK. This works on the international information markets where one can observe concentration movements towards Thomson, Elsevier and some other players. But do our academic structures really have the resources – as regards time and money – to waste it in a try-and-error development? Would it not be better to coordinate international – at least national – efforts? Should we not move on with a common focus and thereby free money for other things? The first step in developing a common strategy is a vision, something that can be set as one’s goal. No ‘destination’ – no strategy. When you build a road you already know where you start from, but you also need to know where to go. Unfortunately my conclusion after this conference is that there are no true visions. Again we are developing strategies without a direction and wasting scientific resources and money. What we really need is more communication. Not only communication between information providers and academic users. Also, communication between the disciplines, communication between the scientists. And this conference was not the solution but a very first step. The results have to prove their worth in real life. Revised version of the article “Scientific information- where are the visions?”, originally published in March 2002 by Inside-Lifescience, ISSN…

In 2003 I had the opportunity to talk to Prof. Dr. Gottfried Schatz, at that time President of the Swiss Science and Technology Council, at the Handelsblatt-conference “Trends in Biotechnology” in Vienna, where Gottfried Schatz had held a lecture about research barriers within Europe. Gottfried Schatz offensively criticized that the European systems of university education and research funding hinder the development of scientific excellence. In his view, money for research – by working after the principle of discriminate all-round distribution – was too broadly scattered instead of promoting purposefully. Permanent academic positions and the rigid hierarchy structures at European universities were also a thorn in his flesh. Dr. Schatz was an enthusiastic advocate for the introduction of a tenure track system at European universities, and expected it to generate higher flexibility in science and education as well as to give highly qualified scientists clearer future prospects and better chances. 8 years have passed by.Did things change?Did the scientific systems really develop? Editor’s Note This is the English translation of an interview originally done in German language. Dr. Gottfried Schatz is President of the Science Council of the Institut Curie (Paris), Scientific Councillor of the Institut Pasteur (Paris), and President of the Swiss Science and Technology Council. After receiving his Ph.D. in Chemistry from the University of Graz in 1961, Gottfried Schatz joined the Biochemistry Department of the University of Vienna where he began his studies on the biogenesis of mitochondria and discovered mitochondrial DNA. From 1964 to 1966 he worked as a postdoctoral fellow with Efraim Racker at the Public Health Research Institute of the City of New York on the mechanism of oxidative phosphorylation. After a brief interlude back in Vienna, he emigrated to the USA in 1968 to join the staff of the Biochemistry Department at Cornell University in Ithaca, NY. Six years later, he moved to the newly created Biozentrum of the University of Basel where he and his group elucidated the mechanism of protein transport into mitochondria. Gottfried Schatz is a member of many scientific academies, including the National Academy of Sciences of the USA, the Royal Swedish Society, and the Netherlands Academy of Sciences, and has been awarded the Louis Jeantet Prize, the Marcel Benoist Prize, the Gairdner Award, the Krebs Medal, the Warburg Medal, the E.B. Wilson Medal, and many other honors. He has served as Secretary General of the European Molecular Biology Organization (EMBO), as Councillor of The Protein Society, and as Chairman of many Advisory Boards. Originally published on February 27, 2003 by Inside-Lifescience, ISSN…

In April 2009, a new line management of our team at Novartis asked for a new internal scientific information tool. The specification was  something like “PubMed … but much better!” (PubMed is a public search engine for bio-medical scientific literature, provided by none other than the US National Institutes of Health) The whole team met the spontaneous challenge, which came on top of concurrent pressure regarding resources as well as a quite high basic load regarding obligatory standard deliveries. I am still proud that I had the opportunity to be part of a real success story. After only 7 months for development and implementation we provided “iFind – the Novartis PubMed+” in December 2009. This great achievement was the result of a fantastic and highly motivated multidisciplinary team. And, by the way, the first time I had been exposed to and could practice agile methodology (here: SCRUM). My role with the development of iFind was to initially provide a vision … and subsequently more detailed specifications (URS), which met the needs of business and users. In parallel, I evaluated reasonable literature data sources for iFind. And I also contributed to the innovative usability concept and screen design of the iFind literature search & analysis tool. iFind highlights: CLIENT:Novartis Pharma AG(as an Novartis employee)PROJECT TIME FRAME: April – December…

I would like to share this article that was once published by Patrick Scholler in my former online journal Inside-Lifescience. I think it is worth not to be lost … Originally published in November 2001 by Inside-Lifescience, ISSN…

The fact that the 2001 Nobel Price in Medicine has been awarded to three Yeast researchers should not lead to the wrong conclusion that the Nobel committee appreciated the fight against alcoholism or overweight. In fact without the tasty products of Brewers or Bakers Yeast (Saccharomyces cerevisiae) our lives would be much more healthy but – honestly – less nicer. Coming to the point, the award really recognizes the contributions of Leland Hartwell, Paul Nurse and Timothy Hunt to the understanding the control mechanisms of the cell cycle, the molecular cell division management system. I myself did research on cell cycle regulation in Yeast in the late ’90s. As a Yeast guy in an innovative scientific environment that deals with frogs, mice and human cell lines you were always seen as an eccentric – and somehow funny – specialist (and it has always been a challenge to explain that my experiments are not related to a Yeast contamination in the cell culture lab). Later I was glad to have the opportunity to cooperate and to discuss my results with Gustav Ammerer and Kim Nasmyth in Vienna, two other great Yeast geneticists. Brewers Yeast – for example – is a budding organism (that is why it is also called Budding Yeast). Daughter cells are formed by small buds growing at the Yeast cell surface. This closely resembles the division of mammalian cells resulting in two daughter cells, e.g.. The key issue for the cell cycle now is to synchronize DNA replication with cell growth and division. And vice versa, the DNA replication needs to be reliably inhibited in the case that there is no division. So, the cell cycle is a series of cell functions controlling the whole life span of one cell generation. It starts over and over again until cell aging or other mechanisms stop the propagation. If the cell cycle does not work correctly cells either stop division or have improperly copied chromosomes or propagate uncontrolled. In humans the latter is connected to cancer. Here the medical relevance of research with Yeasts like S. cerevisiae and Schizosaccharomyces pombe comes in. Yeasts as model organisms for the understanding of common functions in eukaryotic cells. Yeast cells as easy to cultivate mini labs offering research opportunities as regards fundamental cell activities that are too difficult to study in higher cells with their much more complex regulation networks. Well, if we have learned something about cell cycle regulation in Yeast during the past years then that it is even pretty complex in this very simple organism. Today we know a tight network of internal and external signals including the cell metabolism as well as the cytoskeleton. It looks like that there is not just a simple ‘clock’ but a whole system of communicating proteins with checkpoints and feedback loops. We can use these findings in Yeast to look for homologies and similarities in higher organisms. By comparing functionally known Yeast genes and proteins with the human genome and proteome we will be able to identify new research objectives as well as putative pharmaceutical targets. To my view this “Nobel Prize for Yeast” is an appreciation of the role of model organisms in modern biomedical science. Understanding them leads to a faster understanding of the molecular basics of cellular malfunctions in humans. As a Yeastman still carrying small buds in my heart I congratulate the Nobel committee on its decision. Originally published in November 2001 by Inside-Lifescience, ISSN…