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Henning Hermjakob, European Bioinformatics Institute, UK
Biomolecular pathways are a key tool to put proteomics results into context, and pathway databases are often the first port of call to make sense of long lists of identifications and quantitations. Reactome (https://reactome.org)  is an open source, open data knowledge base of curated human pathways. While Reactome employs full time curators, we depend critically on voluntary domain experts who provide their time and knowledge to ensure quality and coverage of the pathways annotated in the database. Similar to manuscript reviewers, these essential community contributors are hard to attract, and the Reactome team would like to reach out to the HUPO community to contribute to the extension and validation of Reactome content. Recently, we have added features that allow to search for contributors by name, and for them to claim their contributions to their ORCID (https://orcid.org/) profile with a few clicks , contributing to efforts to provide credit for open data.
So, if you have a favorite pathway, please check if it’s already perfect in Reactome, and if not, click on https://reactome.org/community/collaboration to provide your expertise, and to support your future pathway analysis!
When you give presentations please disseminate this important message- using the slides included here.
Example of a Reactome pathway overview diagram (free to download as vector graphic).
1: Jassal B, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.
2: Viteri G, et al. Reactome and ORCID-fine-grained credit attribution for community curation. Database (Oxford). 2019 Jan 1;2019. pii: baz123. Doi: 10.1093/database/baz123. PubMed PMID: 31802127.
Sanjeeva Srivastava, IIT Bombay, India
On February 5 – 7, 2019 the Continuing Education Programmes (CEP) at IIT Bombay hosted a Proteomics course titled “Proteomics: Sample Preparation, Mass Spectrometry and Data Analysis”. Participants prepared their own samples for protein identification, label-free quantification and iTRAQ-based quantitative proteomics analysis. While the participants learnt new techniques, the proteomics team from IIT did meta data analysis, results for coverage and reproducibility in assays. Click here to view the event photos.
A Message from hPOP - Assay Invite
The hPOP project to profile people from around the world has been highly successful in the sample collection. We have collected samples from each of the three regions: Boston (Pilot n = 31 individuals), Taipei (N = 106), Dublin (n = 115), Orlando (n = 84). Plus to increase North American numbers we have collected samples from the Bay area (n = 40).
We are now ready for the analyses. On a google spread sheet we list possible assays. We are looking for volunteers to help carry them out. Feel free to suggest additional assays. Our goal is to get these assays done in the next 2-3 months and then analyze the data and present the results at the next HUPO meeting in Australia. The analyses will take some time because there is lots to do we need to do age correction, BMI, etc. We suggest discussing results/analyses on consortium calls starting in January. Note the Snyder lab signed up for many assays but if there are volunteers to take over some of them that would be fine (we want to make sure that a basic set of analyses is done).
We are also building an interactive database to get the data back to participants.
1. Please sign up for assays on the google spread sheet here.
2. Send any and all comments to us at email@example.com.
Let us know if you would like to participate in any of the consortium calls. This is a very unique project and open access resource-we hope to get a high profile paper out of this.
Norman Anderson passed away November 22, 2018 after a short illness, five months before his 100th birthday. He is known both for visionary Big Science projects (the Molecular Anatomy Program, the Human Protein Index, and Rapid Response to Viral Pandemics) and for a series of widely-used bioanalytical inventions (the zonal ultracentrifuge, the centrifugal fast analyzer, large scale 2-D electrophoresis, and virus purification, which was his creative focus late in life). His career spanned military service in World War II (US Navy), advanced degrees (Duke University), National Laboratories (Oak Ridge and Argonne), commercial biotechnology (Large Scale Biology Corp), and non-profit foundations (Viral Defense Foundation), producing more than 250 publications and 35 patents.
Norman Anderson was raised in a religious family of St. Paul MN, in which his father, brother and both sisters pursued careers in the Norwegian Lutheran church. Joining the Navy during World War II, work in underwater photography, eye movement tracking during instrument flight, and on submarines and blimps, expanded his horizons and allowed him to develop novel equipment and ideas. During the war, he met and rapidly married Mary Lloyd Glidewell, daughter of a prominent lawyer in Reidsville, NC, who provided the genial southern atmosphere that sustained him for their 77 years together. Mary Lloyd encouraged him to follow his scientific interests as a graduate student at Duke, instead of accompanying his Navy friends to Hollywood as a photographer, and after a PhD in cell physiology, Norman accepted a fellowship at Oak Ridge National Laboratory where he remained for 20 years. At Oak Ridge, he developed a plan for the complete fractionation of human cells, and to this end developed the zonal ultracentrifuge (including systems for large scale influenza virus purification still used to produce safe vaccines today), the centrifugal fast analyzer (subsequently commercialized by multiple companies for clinical laboratory testing), and high-pressure liquid chromatography systems.
After a brief interlude at the Medical University of South Carolina, Dr. Anderson moved to Argonne National Laboratory near Chicago, where, together with his son Leigh Anderson, he pioneered the use of large-scale 2-D electrophoresis to catalog the human proteins. The potential of this technology led them to start Large Scale Biology Corp. (LSBC), leading to the complete automation of 2-D electrophoresis and the creation of protein databases, as well as development of a large-scale centrifugal oligonucleotide synthesizer (PCOS). After merging with a California-based protein expression company, LSBC completed a highly successfully IPO in 2000.
Over the past 15 years Dr. Anderson focused his attention on the problem of detecting newly emerging viruses and rapidly creating vaccines to prevent their spread as epidemics. His vision of a Manhattan Project-style approach to this existential challenge to civilization highlighted the differences between modern mechanisms of grant-based scientific research and the scale, commitment and speed possible in the context of a World War.
Dr. Anderson received a number of awards including the Distinguished Clinical Chemist Award from the International Federation for Clinical Chemistry (1990); the 1983 Pittsburgh Analytical Chemistry Award (1983) for work in high resolution two-dimensional electrophoresis (shared with N. Leigh Anderson); an Docteur Honoris Causa, University of Nancy, France; the John Scott Medal and Award for the invention of the zonal ultracentrifuge (1972); the Atomic Energy Commission Citation and Gold Medal for the invention and development of the K-II vaccine-purification ultracentrifuge (1972); the Preis für Biochemische Analytik, awarded by the Deutsche Gesellschaft für Klinische Chemie for the invention of the centrifugal fast analyzer (1972); and a U.S. Navy Special Citation for outstanding work as a combat photographic officer in the submarine service in the Pacific during WWII (1946).
Norman Anderson is survived by his son (Leigh Anderson), with whom he collaborated in proteomics research for more than 40 years, Leigh’s wife Constance Seniff, and his daughter (Beth Anderson, successively a ballerina, rock musician, scientific instrument builder and science animator), and her husband Douglas Huff. Mary Lloyd died six months before him, which was a great blow. Norman is fondly remembered by a host of co-workers, students and neighbors in whom his perpetual enthusiasm excited a profound interest in science.
Following an international search, the Human Proteome Organization (HUPO; www.hupo.org) has recently selected cancer researcher Mark Baker from Macquarie University, Australia as the incoming Chair of the Human Proteome Project. Effective January 2019, Mark will succeed pioneering physician-scientist Gilbert (Gil) Omenn from the University of Michigan, USA who led this emerging global collaborative project since launch in 2010.
The Human Proteome Project brings together an impressive array of research teams from around the globe, focused on achieving highly-confident detection and identification of all the expressed proteins that are predicted to be coded by the human genome. The Human Proteome Project then aims to characterize the proteome’s sequence, splice and chemical modifications that alter locations, function and interaction. The Human Proteome Project is cooperating with the broader scientific community to annotate biological, chemical, cellular and disease aspects of the human proteome using rapidly-evolving technologies.
One outcome will be a comprehensive “map” of protein pathways and networks that will demonstrate the indispensable role our proteomes play in precision medicine - because we know it is impossible to predict these dynamic, structural and functional details of biology just by sequencing our genomes.
Sustained progress through the Human Proteome Project will noticeably enhance our understanding of human biology at the molecular level, lay solid foundations for monitoring health and the development of new preventive, diagnostic, prognostic and therapeutic interventions in disease, and increase our biological understanding of what it means to be human.
Contacts for Comment:
Professor Mike Snyder - HUPO President, Stanford University, USA firstname.lastname@example.org
Ms Chelsea Prangnell - Manager, Human Proteome Organization email@example.com
Dear HUPO members,
The 2018 HUPO General Assembly of Members will take place in Orlando, Florida at the 17th Human Proteome Organization World Congress on:
Date: Tuesday, October 2, 2018
Location: Loews Royal Pacific Resort; located in the innovation stage area of the exhibit hall
Join us for free drinks and updates on the HUPO organization. If you are attending HUPO 2018 we hope you will join us for this annual meeting of HUPO members.
The HUPO 2018 Council election opens on September 5. You will receive an email from Simply Voting containing your unique voting ID and password. If you don’t receive an email from Simply Voting in your inbox on September 5 please check your spam/junk folder.
Last year only 40% of HUPO members voted and we’d like to see this number increase significantly. The voting process is easy, fast and anonymous so please participate. Every vote counts!
We look forward to seeing you in Orlando!
The Nominations and Elections Committee of the Human Proteome Organization presents the official slate of candidates for the 2018 HUPO Council election. HUPO would like to thank all candidates standing for Council election for a three-year term beginning in January 2019 (2019-2021). The election period for HUPO Council is September 5 - September 30, 2018.
In September, all active HUPO members will receive an email containing online voting instructions with a secure election ID code. Electors will simply click on the link provided to cast their anonymous votes.
The slate of candidates is now available here. We encourage you to review the slate of candidates prior to the election opening date on September 5, 2018.
Chair, HUPO Nominations and Elections Committee
Deadline January 14, 2018: Institut Pasteur has launched an international call for junior candidates wishing to establish new independent research groups in the cutting edge interdisciplinary environment of its campus in Paris, France. This year the call will be focused on the topics associated with the INstitut Convergence entitled “Emergence of Pathologies Through Individuals and populatiONs” (INCEPTION program). Read on here.
Mark HUPO 2018 in Orlando, Florida on your calendar now! Congress dates are September 30 - October 3, 2018. We are pleased to announce there will be an HPP Post-Congress Day on October 4, 2018. Attendees may also look forward to a complete roster of pre-congress activities (workshops and short courses) on Sunday, September 30 before the official congress opening on Sunday evening.
All congress sessions and special hotel guest room block will be at Loews Royal Pacific located on the grounds of Universal Studios. The congress hotel guest room rate of $189 per night will be available three days pre- and post-congress (based on availability) should you wish to plan some “fun time” at the Universal Studios parks (includes the Harry Potter attraction).
Visit www.HUPO2018.org on January 15, 2018 for the following:
You might have noticed our promotion at HUPO 2017 in Dublin where we invited “Wizards in Training” to take a photo dressed a la Harry Potter. We look forward to seeing these wizards (and a few more) in Orlando next September.
HUPOST: Can you tell us what this prize, which is referred to as the Dutch Nobel Prize, means for you, and for the field?
Heck: The Spinoza prize is the most prestigious Dutch science award, and is given annually to three to four researches, selected from all disciplines of science.
It is of course an enormous honour to be awarded this prize, and while it’s known as the Dutch Nobel Prize, it evidently does not compare to the real Nobel. Nevertheless, it comes with a 2.5 million euro budget, to be spend freely for research, so it is a very strong driver for creativity and innovation.
Although a personal prize, I think this award is also an award for my group and the field, because the prize is an implicit recognition for the importance and impact of analytical chemistry, biomolecular mass spectrometry and proteomics.
HUPOST: You have your own Wikipedia page, and a list of prestigious awards to your name. What would be your advice to young researchers who want to make a difference?
Heck: If you want to make a difference, evidently you should keep up with the literature, so you know what lives in the field, but that knowledge should not stop you from doing the unexpected and you should always look for unexpected findings. In my view, these are the key to innovation and succes. And I try to encourage everyone not to be a follower; try doing something different than the other labs in your field. When you have a keen eye for the unexpected, and do original work, then you will be able to contribute unique findings and can make a difference. And find the right environment, as good mentors are way more important than a good lab-infrastructure.
HUPOST: When a researcher pursues something different, the research can also fail. Do you have any tips on how to deal with such setbacks?
Heck: We should not fear failure. In fact, most scientific experiments end in failure. There’s no satisfaction to be had from planning an experiment for which the outcome is already known. And never forget: after you encounter a few failures, the next success will taste so much sweeter!
HUPOST: If you were a starting scientist today, what topic would you choose?
Heck: My main driver is very broad: understanding how life works at the molecular level. Of course, ‘life’ is very diverse, and there’s much to study. But right now, I would love to look more into how the brain works at the molecular level. This is an area we still understand so little about.
In general, I strongly believe that everybody needs to find something that strongly attracts their interest, as it is very important in science to work on a topic you really care about.
HUPOST: Your lab has also produced very nice short movies to introduce science to the general public; how important is this outreach?
Heck: I think it is very important and exciting to outreach to the general public. But I have also learned that you need to have a strategy for these movies, so that they hit their mark. Importantly, it is also very much fun to make such movies. Overall, I believe that if you study proteins, and are excited about proteins, as I am, that you should also spread this excitement! And because the general public will not read our papers in Nature and Science, such movies are a great way to bring our research to a broader audience. It is particularly rewarding to see that some of our movies are featured in the Washington Post, but these are used in classrooms as well. If you make a movie, try to make them as multi-purpose as possible.
HUPOST: While on the subject of classrooms, do you believe that knowledge about proteomics should move into classrooms?
Heck: Yes, of course, although I would prefer a more overall view: we should be teaching more insight into life at the molecular level in the classrooms, and this should be based on knowledge of the entire cast of macromolecules (DNA, RNA, proteins) that feature in this grand spectacle we call live.
I also think that the progress of scientific knowledge in the life sciences are taking too long to reach the classrooms, and that is a pity. All the more so because the knowledge is so interesting and inspiring. A great example is the gene transcription machinery, which is not only a fundamental process in all life, but it also combines proteins, DNA, and RNA in a fascinating molecular machine.
HUPOST: Which of your contributions to the field gave you the most satisfaction?
Heck: That’s a difficult question. It’s like being asked to pick the favourite child amongst your children. But I really enjoy technology development. This because there is great satisfaction in receiving mails from other researchers that write to let you know that your technology has helped them do their research. Science is all about sharing after all, and when people pick up technologies that you’ve developed, and it works for them, that is extremely motivating.
In addition, new technologies often lead to breakthrough findings in biology. For instance, the EThcD technology we developed has led to the discovery of widespread proteasomally spliced HLA peptides, which shook up the field of immunology. So I really like the ability of technological breakthroughs to lead to a new understanding of biology, which is, after all, the goal!
Paper reference: http://science.sciencemag.org/content/354/6310/354
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