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Register Now for the Protein Data Bank’s 40th Anniversary Symposium

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A special symposium marking the 40th anniversary of the Protein Data Bank (PDB) will be held this year at Cold Spring Harbor Laboratory in New York, October 28-30.

It’s quite fitting that the meeting is being held here. It was a 1971 symposium at the laboratory titled “The Structure and Function of Proteins at the Three-Dimensional Level” that led to the establishment of the PDB as a freely accessible portal for the experimentally determined structures of biological macromolecules. Since then, the PDB has grown into an international resource for structural biology, today containing nearly 75,000 structures of proteins, nucleic acids and complex assemblies.

Because it is such a vital resource for researchers, NIGMS and other parts of NIH, along with the National Science Foundation and Department of Energy, have helped fund the PDB’s operation for many years. NIGMS is also a sponsor of the symposium.

The October event, which is open to all, will include presentations by many prominent scientists who have been instrumental in the development of the PDB and the field of structural biology. Among the confirmed speakers are Michael Rossmann of Purdue University, an early advocate of the PDB; Wayne Hendrickson of Columbia University, a leader in solving the structures of membrane proteins; and Kurt Wüthrich of the Scripps Research Institute and the ETH Zürich, a pioneer in NMR structure determination techniques.

A limited number of travel awards to attend the symposium are available for students and early career scientists; applications are due by
August 1.

More information about the program, registration and travel is on the meeting Web site.

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Forging Ahead

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Under Jeremy Berg’s leadership, NIGMS has thrived and continued to support outstanding, cutting-edge research. I hope to maintain this momentum while serving as acting NIGMS director.

Many of you know me from the Division of Genetics and Developmental Biology, the part of NIGMS I’ve directed since 1988. Others know me from the NIH Director’s Pioneer and New Innovator Award programs, which I’ve led for a number of years, or from my role in chairing NIGMS’ strategic planning processes. Some may even recall when I previously served as acting NIGMS director (from May 2002, when Marvin Cassman left, to November 2003, when Jeremy arrived).

In this time of transition, we are managing a challenging budget situation and also pursuing several major activities. One is implementing action items from the training strategic plan. I am excited to see this effort come to fruition, as it will have a significant impact on both students in our training programs and those supported by regular research grants.

In addition, we are looking forward to marking the Institute’s 50th anniversary in 2012. Planning is already under way for activities at scientific meetings and on the NIH campus. We will post more details here in the coming months.

And of course we eagerly anticipate the selection of a new NIGMS director. The search committee is a terrific group of people who know the Institute well. I have a lot of confidence that they will find us a director who will continue NIGMS’ strong tradition of excellent leadership.

Part of Jeremy’s legacy at NIGMS is the Feedback Loop. Keeping open lines of communication has always been really important to us, and I welcome your input at any time.

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Farewell

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Today is my last day as Director of NIGMS. It is hard to believe that almost 8 years have passed since I was first offered this tremendous opportunity to serve the scientific community. It has been a privilege to work with the outstanding staff members at NIGMS and NIH, as well as with so many of you across the country.

As I write my final post, I find myself recalling a statement I heard from then-NIH Director Elias Zerhouni during my first few years here: It is very difficult to translate that which you do not understand. He made this comment in the context of discussions about the balance between basic and applied research, which certainly has applicability in this setting and is relevant in a broader context as well. In some ways, it has also been my mantra for the NIGMS Feedback Loop.

Early in my time at NIH, I was struck by how often even relatively well-informed members of the scientific community did not understand the underlying bases for NIH policies and trends. Information voids were often filled with rumors that were sometimes very far removed from reality. The desire to provide useful information to the scientific community motivated me and others at NIGMS to start the Feedback Loop, first as an electronic newsletter and, for the past 2 years, as a blog. Our goal was–and is–to provide information and data that members of the scientific community can use to take maximal advantage of the opportunities provided across NIH and to understand the rationales behind long-standing and more recent NIH policies and initiatives.

I chose the name Feedback Loop with the hope that this venue would provide more than just a vehicle for pushing out information. I wanted it to promote two-way communication, with members of the scientific community feeling comfortable sharing their thoughts about the material presented or about other issues of interest to them. In biology, feedback loops serve as important regulatory mechanisms that allow systems to adjust to changes in their environments. I hoped that NIGMS’ “feedback loop” would serve a similar role.

I am pleased with our progress toward this goal, but there is considerable room for further evolution. The emergence and success of similar blogs such as Rock Talk are encouraging signs. I know that NIGMS Acting Director Judith Greenberg shares my enthusiasm for communication with the community, and I hope that the new NIGMS Director will too. I encourage you to continue to play your part, participate in the discussions and engage in the sort of dialogue that will best serve the scientific community.

I plan to continue communicating with many of you in my new position as a member of the extramural scientific community. For the time being, you can reach me at jeremybergtemp@gmail.com.

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Meetings Help Develop a Diverse Scientific Workforce

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SACNAS National ConferenceAs part of our commitment to developing a diverse scientific workforce, we sponsor the Society for Advancement of Chicanos and Native Americans in Science (SACNAS) national conference Link to external web site and the Annual Biomedical Research Conference for Minority Students (ABRCMS) Link to external web site.

ABRCMS Seal

These conferences represent two of the largest gatherings of science and math undergraduate students from groups that are underrepresented in the biomedical and behavioral sciences. They are terrific opportunities for you to meet and recruit outstanding students. You also can volunteer to mentor students or judge their posters.

This year, SACNAS will meet in San Jose, CA, October 27-30, and ABRCMS in St. Louis, MO, November 9-12. For more information or to register, visit the meeting Web sites.

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Connecting at Lindau

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Greetings from Lindau, Germany, where I and my NIH colleagues, Irene Eckstrand and Katrin Eichelberg, are attending the 61st Lindau Nobel Laureate Meeting Link to external web site. This year’s meeting, focused on physiology and medicine, has brought together 23 Nobel laureates and 566 outstanding pre- and postdoctoral students, including 80 from the United States, to share their passion for science and their commitment to finding solutions to the world’s biggest problems.

Video remarks from NIH Director Francis Collins at the Lindau meeting. 

Video remarks from NIH Director Francis Collins at the Lindau meeting.

This is the third year that NIGMS has participated in the Lindau program, and the first year in which participation was NIH-wide.

Each morning, six Nobel laureates have given short lectures about the history of their science, their successes and failures, and their visions of the future. Among the NIGMS-funded laureates giving these talks are Elizabeth Blackburn, Oliver Smithies, Thomas Steitz, Roger Tsien and Ada Yonath. The afternoons are reserved for free-ranging discussions among the laureates and young researchers. It has been a delight to watch the two groups get to know each other and discuss important scientific problems of global interest and importance.

On the opening day, Countess Bettina Bernadotte, whose family has sponsored the meeting since its beginning, welcomed the assembly. Her enthusiasm for science and her commitment to the meetings was apparent in her introduction of the Lindau mission – “Educate. Inspire. Connect” – and her advice that we “never cease to be curious.” Expanding on this, Annette Schavan, the German Federal Minister of Education and Research, stressed that connections among the generations, such as those made at this meeting, are crucial to scientific progress.

The American delegation, which was sponsored by NIH, the Department of Energy, Oak Ridge Associated Universities and Mars Incorporated, organized a U.S.-themed International Day on Monday, June 27. This series of events truly jumpstarted the week.

As part of International Day, NIH-supported Nobel laureate Peter Agre explained his view of the scientist-citizen who uses his or her knowledge and talents to make the world a better place. The discoverer of aquaporins, Agre talked about applying his research to fighting malaria in Zambia. NIGMS’ Irene Eckstrand then spoke about using the power of computing to inform policies for the control and eradication of infectious diseases. An energetic discussion ensued between the highly engaged students and speakers, focusing on efforts to understand the epidemiology of malaria, approaches to reducing the number of deaths from the disease and the importance of collaborative research between developed and developing nations.

The International Day evening program included a very well-received video address from NIH Director Francis Collins on the strength of American medical science. His message about NIH’s commitment to global health aligned perfectly with the focus of earlier talks, including a presentation by Bill Gates, who was inducted into the Honorary Senate of the Lindau Foundation.

Irene, Katrin and I are all quite proud to have been a part of this effort and look forward to sharing more about our experiences here.

Post written by Donna Krasnewich, Irene Eckstrand and Katrin Eichelberg (NIAID)

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NIGMS Cell Repository Now Includes iPS Cell Lines

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The HGCR iPS cell lines undergo extensive characterization, including assessment of their capacity to differentiate into specialized cell types. The cell shown here was directed to differentiate into a nerve cell.As we anticipated last year, the NIGMS Human Genetic Cell Repository Link to external web site (HGCR) now offers human induced pluripotent stem cell lines that carry disease gene mutations. The first five lines to be made available were derived from individuals with Huntington’s disease, juvenile onset diabetes, severe combined immunodeficiency disease, muscular dystrophy and spinal muscular atrophy. The repository is developing more cell lines representing other diseases.

The iPS cell lines Link to external web site, along with more than 10,000 others in the repository, are comprehensively characterized to ensure their identity, stability and purity. This quality control makes the repository an excellent resource for researchers who need well-characterized, disease-specific cells.

You can order any of the repository’s cell lines via the HGCR catalog Link to external web site.

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At the Interface of Evolution and Medicine

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At last week’s Evolution and Medicine Symposium (link no longer available) at the Evolution 2011 meeting in Norman, Oklahoma, experts from around the country came together to discuss how evolutionary biology is influencing our understanding of human health and disease.

At the meeting, I talked about NIGMS’s commitment to funding research on the principles and dynamics of evolution and highlighted the importance of studying biological systems, such as infectious diseases and physiology, in their evolutionary context.

In preparing my remarks, I realized that the work of clinicians and evolutionary biologists could be highly synergistic. M.D.s know a great deal about individual variation and clinical presentation, while evolutionary biologists have a good grasp of variation at the population level. Both of these perspectives are very valuable to the field of personalized medicine, for example. The question now is: How do we create an opportunity for these two groups to work with each other?

The meeting featured many interesting talks, including:

  • Dyann Wirth of the Harvard School of Public Health explained that in the very near future we will have enough sequence data from Plasmodium, mosquitoes and humans to understand regional variation as well as co-evolution of the malaria pathogen and its hosts. We should be able to use this information to build computational models and evaluate intervention, eradication and elimination strategies. Wirth said these capabilities stem from advances in DNA sequencing technologies that are having a revolutionary effect on evolution research, including evolution and medicine.
  • Carl Bergstrom of the University of Washington spoke on the integration of mathematical modeling and evolution. He gave a real example of how to use antiviral drugs most effectively in an influenza outbreak. The question was how to deploy antivirals to reduce the likelihood of resistance and minimize illness and death. Bergstrom said that the answer is non-obvious unless you understand how phylogenies work and know a little bit of math.
  • Angela Hancock of the University of Chicago talked about recent data showing that human genetic variation that’s adaptive in one context will not be so in other contexts. Studying 61 populations from different parts of the world, she identified signals of selection in a variety of genes related to UV radiation, infection and immunity, and cancer.

This symposium came at the perfect time to describe two new NIGMS-related efforts. We previewed an NIH high school curriculum supplement on evolution and medicine that will be released this fall. Also, in conjunction with the National Science Foundation and the U.S. Department of Agriculture, we will be announcing later this summer a call for applications to study dynamic biological systems in their ecological and evolutionary contexts. I’ll share more details about these efforts in the near future.

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Acting Director Named

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Photo of Dr. Judith GreenbergAs I enter my final few weeks at NIGMS, I’m engaged in a lot of transition planning. One major aspect is the designation of an acting director, and I’m happy to tell you that Judith Greenberg has agreed to serve in this capacity after my departure early next month. She was acting director in 2002 and 2003, after Marvin Cassman left and before I arrived, and I know that she will once again do a fantastic job.

For more about Judith, see the news release we just issued.

 

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Productivity Metrics and Peer Review Scores, Continued

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In a previous post, I described some initial results from an analysis of the relationships between a range of productivity metrics and peer review scores. The analysis revealed that these productivity metrics do correlate to some extent with peer review scores but that substantial variation occurs across the population of grants.

Here, I explore these relationships in more detail. To facilitate this analysis, I separated the awards into new (Type 1) and competing renewal (Type 2) grants. Some parameters for these two classes are shown in Table 1.

Table 1. Selected=

Table 1. Selected parameters for the population of Type 1 (new) and Type 2 (competing renewal) grants funded in Fiscal Year 2006: average numbers of publications, citations and highly cited citations (defined as those being in the top 10% of time-corrected citations for all research publications).

For context, the Fiscal Year 2006 success rate was 26%, and the midpoint on the funding curve was near the 20th percentile.

To better visualize trends in the productivity metrics data in light of the large amounts of variability, I calculated running averages over sets of 100 grants separately for the Type 1 and Type 2 groups of grants, shown in Figures 1-3 below.

Figure 1. Running averages for the number of publications over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

Figure 1. Running averages for the number of publications over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

Figure 2. Running averages for the number of citations over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

Figure 2. Running averages for the number of citations over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

Figure 3. Running averages for the number of highly cited publications over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

Figure 3. Running averages for the number of highly cited publications over sets of 100 grants funded in Fiscal Year 2006 for Type 1 (new, solid line) and Type 2 (competing renewal, dotted line) grants as a function of the average percentile for that set of 100 grants.

These graphs show somewhat different behavior for Type 1 and Type 2 grants. For Type 1 grants, the curves are relatively flat, with a small decrease in each metric from the lowest (best) percentile scores that reaches a minimum near the 12th percentile and then increases somewhat. For Type 2 grants, the curves are steeper and somewhat more monotonic.

Note that the curves for the number of highly cited publications for Type 1 and Type 2 grants are nearly superimposable above the 7th percentile. If this metric truly reflects high scientific impact, then the observations that new grants are comparable to competing renewals and that the level of highly cited publications extends through the full range of percentile scores reinforce the need to continue to support new ideas and new investigators.

While these graphs shed light on some of the underlying trends in the productivity metrics and the large amount of variability that is observed, one should be appropriately cautious in interpreting these data given the imperfections in the metrics; the fact that the data reflect only a single year; and the many legitimate sources of variability, such as differences between fields and publishing styles.