IU School of Medicine Deans' office updates and perspectives on IUSM research

The Wilkes Blog

Get ready to schedule the C1, Biomark and CyTOF

Filed under: Basic science,Research — Tags: , , , — David Wilkes on June 30, 2015 @ 11:21 am

Recently I talked about our acquisition of powerful new research tools, the CyTOF and three additional state-of-the art instruments that are being installed in the flow cytometry research facility in Walther Hall.

Along with the CyTOF for mass cytometry, we’ve purchased the Fluidigm C1 and Biomark Single-Cell Auto Prep and Analysis System, which does whole transcriptome analysis of individual cells, and the Fluidigm JUNO SNP genotyping system.

The good news is that installation of the C1 and Biomark is complete and they will be available for scheduling starting tomorrow. The Juno and the CyTOF will be on line soon thereafter.

As CyTOF core director Edward (Eddy) Srour says, “We’re definitely excited about this. You can ask more probing questions now, and it will definitely add to the arsenal for doing individualized medicine.”

However, he also advises that much preparation is needed to make a complete and successful run and you’ll want to make sure all your required reagents are in place for your assay.

For details contact Eddy at esrour@iupui.edu or Angelo Cardoso at aacardos@iu.edu.

26 new answers to the question, what brought people to the IU School of Medicine

Filed under: Faculty,Physician Scientist Initiative,Strategic Research Initiative — Tags: , , , , — David Wilkes on June 22, 2015 @ 11:17 am

Why do faculty choose to come to the IU School of Medicine? We recently asked that question of some of our newer faculty members to update the booklet “26 Answers to One Question.”

We published the first version a few years ago as a tool to help recruit new faculty to a school that needed to work harder to tell the world about its strengths. Who better to spread the word than those who had found reason to come here? It was time for an updated version and we’ve changed the brochure’s lineup significantly.

We’ve made a few print copies but our primary method of distribution is via PDF. If you could use some good news about the school to share with others, or if you just want to see what some of your new colleagues have to say about what brought them to IUSM, you can download the new version here.

Meet our new research friend, the CyTOF

Filed under: Basic science,Clinical research,Research — Tags: , , , , , , — David Wilkes on May 7, 2015 @ 10:36 am

Most of us have used, or at least know about flow cytometry: identifying properties in individual cells using lasers to “light up” fluorescently labeled antibodies. It’s highly useful technology, though the limits of the optical system make it impractical to identify more than a dozen or so antibody signals at once.

But now you can throw those limits out the window. The next generation, mass cytometry, is on its way. You can start making plans to head over to the third floor of Walther Hall, where the IU School of Medicine’s new CyTOF (Cytometry Time of Flight) Mass Cytometry System from Fluidigm is being installed.

Edward (Eddy) F. Srour, who has overseen the operations of the flow cytometry core, will also manage the CyTOF, which is being installed in the same lab. At the same time, we’re working out the cost and expense structure for using the system — but be reassured, we want people to use it.

We have joined a relative handful of leading academic research institutions to invest in this technology, one that probes more deeply into cellular activities, identifies more proteins, captures many more downstream events — in general lets us ask much more sophisticated research questions.

As Eddy says, the key is that the discovery process uses mass spectrometry to identify heavy metal tags, resulting in highly specific, narrow signals instead of the overlapping emissions of fluorescent tags. Think of being able to efficiently differentiate 32 signals — and someday as many as 100 — in one experiment.

Or think about cancer research asking whether inhibitor A more effectively shuts down a pathway in a particular cell type than does inhibitor B, and whether the two combined are more effective than either individually, all at the same time. This will be a major asset for our efforts in drug discovery and experimental therapeutics.

Along with the CyTOF, we’ve purchased the Fluidigm C1 and Biomark Single-Cell Auto Prep and Analysis System, which does whole transcriptome analysis of individual cells — 96 cells or more at a time.

Yes, this is one of the most expensive pieces of research equipment that we’ve ever bought. But its capabilities are scary. In a good way.

Have a big proposal? Get good advice from the P4PDT

Filed under: Basic science,Clinical research,Faculty,Grants,Research — Tags: , , , — David Wilkes on April 14, 2015 @ 2:03 pm

Are you working on, or considering developing, a program project grant with multiple PI’s and a hefty amount of funding? I want to remind you that we have a peer review committee to help you get the project developed and funded.

As many of you know we’ve put considerable effort into initiatives to support faculty research funding activities, with CTSI’s project development teams (PDTs) and subsequently the Peer Review and Mentoring Committees focused on getting grant resubmissions funded.

But our team to help with the larger proposals — the Multi-PI/Program Project Planning PDT — is seeking more proposals to review.

So this is your reminder about the P4PDT: This committee, chaired by Tom Callaghan, associate dean of VA research, was set up to help with multi-PI, multi-project grants with annual direct budgets of $500,000 or more.

The team can provide assistance with protocol development, cultivating collaborations and networking, project management, funds for mock site visits and dollars for pilot projects.

Applications don’t require a pilot funding request, but any such requests should be no more than $100,000 to be used over 24 to 36 months before the application is submitted for external funding.

How does this process work? Consider a recent proposal on bone healing from Todd McKinley and Melissa Kacena seeking $10 million over five years from the Department of Defense. The Defense Department accepted their letter of intent and an application was due Nov. 14, 2014.

Starting in mid-August Todd and Melissa worked with the P4 team, refining the application, streamlining some projects and getting recommendations for internal and external advisors with the aid of $25,000 from the committee. The P4 committee provided an extra $11,600 in October for additional experimental procedures that were included in the application.

The result? A highly competitive proposal that is scheduled to by reviewed by the DOD this month.

“Experience working with CTSI PDT team was very positive. They gave some harsh criticism and solid direction that helped us refocus our application into a stronger product,” says Melissa, recommending the process.

“Why not obtain peer-review from colleagues before submission to help identify holes you can fill in and make your application that much stronger.”

I certainly agree. To get more information, contact Tom Callaghan at jcallagh@iu.edu.

The TRI report card, part 3

This is the last in a series of blog posts about the Transforming Research Initiative, the faculty-developed strategic plan for research at IUSM that was completed in 2013.

The report listed six key goals for the research mission. We’ve covered four of them in the previous posts: research themes, team science, research communication and cores/centers/institutes. This week, recruitment and retention, and mentoring. (Once again, you can download the executive summary here.)

Goal 5: Recruitment and Retention

Recruiting and retention issues are with us always and we have instituted several initiatives to improve our efforts in this area. We continue to use funding from the Lilly Endowment-supported Physician Scientist Initiative to recruit accomplished researchers and to support projects such as the new centers for musculoskeletal and diabetes research.

Working with the Showalter Trust, we were able to add the Showalter Scholars program to our retention arsenal. Four young scientists are selected each year and receive $75,000 over three years to help fund their research.

Other efforts that support recruiting and retention include initiatives within the Office of Faculty Affairs and Professional Development, which now has four staffers specializing on recruitment and onboarding.

Goal 6: Mentoring

We’ve undertaken several initiatives to improve our mentoring efforts, starting with the Peer Review and Mentoring Committees. Those committees were created to provide investigators with advice from successful scientists to improve their grant proposals, both new and resubmissions. The committees also offer project management and biostatistics support. (For an account of how a grant application moved from the 54th to the 5th percentile after a PRMC review, see this inScope article.)

We also introduced the Independent Investigator Incubator, or I3, created and led by Aaron Carroll, now the associate dean for research mentoring at IUSM. This effort makes senior faculty “supermentors” available to younger researchers.

To encourage more applications for T32 awards to mentor pre- and post-doctoral trainees, we initiated annual support to PIs for new and competing renewal training grants.

All in all, I think we can feel good about the work that’s been accomplished in the last couple of years, effort that has made the TRI a working document. And like the TRI itself, these programs and successes have been the result of countless members of our research community pitching in to strengthen our research enterprise — efforts on which we can continue to build, because our work isn’t done.

The TRI report card, part 2

Last week I initiated a series of blog posts about the Transforming Research Initiative. The TRI is the faculty-developed strategic plan for research at IUSM that was completed in 2013, and it’s time to report back on how well we’re doing to implement it.

The report listed six key goals for the research mission. We covered two of them last time: research themes and team science. This week, two more (and again, you can download the executive summary here  .)

Goal 3: Research Communication

We’ve worked to improve both the internal and external communications about research. You’re reading the first one — we created the Wilkes Blog as a new method to get news to the research community at the school, hopefully in a way that’s both casual and authoritative.

Second, we have brought the school of communications office and staff back to the school, after several years in which they were part of a separate university organization, IU Communications.

Third, we’ve set the groundwork for improved communication with industry with the creation of the Industry Collaboration Portal, whose web site went live earlier this year.

We put together a list of 31 internal sources of funding for research projects and made it available via the IUSM research page at http://medicine.iu.edu/research/. Click on “Faculty Resources” then select “IUSM Pilot Funding Opportunities.”

And finally, we’re finishing work on a revision of the “26 Answers” brochure that tells IUSM’s story in the words of faculty members who have recently joined the school.

Goal 4: Cores/Centers/Institutes

Recognizing both a need and world-class expertise within the school, we are in the process of creating the Indiana Center for Musculoskeletal Health as well as assembling the pieces for a new Center for Diabetes and Metabolic Diseases. Development continues for the new Center for Chemical Biology and Experimental Therapeutics — key to our initiatives in translational research and personalized medicine.

Creating a new center involves a significant amount of work, but even more complex is our planning to reorganize our cores. In many instances the “recharge” model for core fees and services is not working and so we are exploring a centralized core management system.

Meanwhile, the Indiana CTSI is considering the development of “supercores” in genomics and proteomics that would incorporate capabilities at Purdue, Notre Dame and IU Bloomington.

Next week I’ll discuss how we’re progressing toward the remaining two goals, recruitment and retention, and mentoring.

The Transforming Research Initiative: A Report Card

About three years ago we started what became known as the Transforming Research Initiative at the IU School of Medicine.

It was an undertaking — by the faculty, not by me, not by the administration — to develop a new strategic plan for research in response to the changing environment for research, particularly a growing emphasis on team science projects with multiple PIs, and the ever-tightening belt applied to NIH funding.

After more than a year of effort, a final report listed six research goals. Now it’s time to describe what’s been done to prevent the TRI from becoming just another report gathering dust. I’ll go through it goal by goal, and if you need a refresher on the TRI report, you can download the executive summary here .

Goal 1: Research Themes

The TRI planning identified seven initial research themes: cancer, cardiovascular, neuroscience, obesity/metabolism, personalized medicine, health services research, and regenerative medicine.

Cancer, cardiovascular and neuroscience continue to receive substantial attention as the initial focus areas of the Strategic Research Initiative partnership with IU Health.

We’ve seen personalized medicine initiatives develop in several areas, notably at the Krannert Institute of Cardiology (with SRI funding), the IU Simon Cancer Center and a major project about to begin at Eskenazi Health. The planned Center for Chemical Biology and Drug Discovery will support the personalized medicine theme.

Health services research and the school’s emphasis on population health is represented by the creation of the Center for Health Innovation and Implementation Science, and continues to build on such strengths as the Regenstrief Institute and the Children’s Health Services Research team.

Supporting the obesity/metabolism theme is the new Center for Diabetes and Metabolic Diseases, headed by Raghu Mirmira, while the new Indiana Center for Musculoskeletal Health advances the regenerative medicine theme.

Goal 2: Team Science

Reflecting the increasing emphasis on team science in biomedical research, the IUSM Standards of Excellence in Research for Promotion and Tenure were updated last year to include “excellence in research through contributions that have helped shape collaborative projects.” (See the “About Promotion and Tenure” page on the Office of Faculty Affairs web site.)

Increasingly, we are also making school space allocation decisions with research themes and team science in mind — recent examples include the musculoskeletal and diabetes centers, and on a larger scale, the IU Neuroscience Research Building.

Don’t forget about ReSEARCH Connect, our powerful tool to find research collaborators.

Next time, I’ll cover two more goals: research communications and cores, centers and institutes.

Our friends at IACUC have eased reporting requirements

Filed under: IACUC,Research — Tags: , , , , — David Wilkes on February 9, 2015 @ 2:24 pm

Good news for most of you who use animals in research: You have one less report to prepare.

Starting March 1, most annual research protocols will no longer be required to go through the annual continuation process and so investigators will no longer need to complete the annual review form.

The change was implemented by the IUSM Institutional Animal Care and Use Committee after evaluating the annual continuation requirements from both the U.S. Department of Agriculture and the NIH Office of Laboratory Animal Welfare.

There are some protocols that will still need to go through the annual continuation review process:

  • VA studies
  • Protocols with USDA covered species
  • Protocols with Pain Category E
  • Other protocols at the discretion of the veterinarian or the IACUC

And, as before, protocols are approved for 36 months and if activities will continue after that, a new approved protocol is required.

So if you are not in one of the exception categories, make good use of your new free time!

Meet Tricia Wright, director of the Office of Postdoctoral Affairs

Filed under: Faculty,Graduate education,Postdocs,Research — Tags: , , , — David Wilkes on January 28, 2015 @ 3:45 pm

Here at the IU School of Medicine we employ approximately 200 postdoctoral scholars, early career scientists gaining research experience, expertise and, hopefully, some publications too.

The school and mentoring faculty benefit from the work our postdocs perform, and we have an obligation to ensure that they receive the training and guidance needed to help them pursue independent careers, whether in academic medicine, in private industry or elsewhere.

To help ensure that, we have recruited Tricia Wright to be the director of the IUSM Office of Postdoctoral Affairs.

Dr. Wright, who was awarded her doctorate in genetics and molecular biology from the University of North Carolina at Chapel Hill, comes to IU from Duke University, where she completed a postdoc performing breast cancer related research in the Department of Pharmacology and Cancer Biology. She was chair of professional development for the Duke University Postdoctoral Association and co-founder of the Duke Diversity Postdoc Alliance.

She has a long list of services and activities planned for the office, starting with establishing an IUSM Postdoctoral Association, creating an Office of Postdoctoral Affairs advisory committee consisting of faculty and postdocs to further develop and refine policies and commonly used documents. In addition, she plans to host postdoc orientations and professional development programs for postdocs.

If you have suggestions or questions, Tricia can be reached at trmwrigh@iu.edu.

You have a reprieve, but you still need to prepare for the new NIH biosketch

Filed under: Basic science,Faculty,Grants,Research,Team science/collaboration — Tags: , , — David Wilkes on December 17, 2014 @ 8:25 am

Like it or not, a new format for the NIH biosketch is still on the way, despite the postponement of the deadline from January 25 to May 25 when it will become mandatory for proposals.

Fundamentally, the new format is meant to provide a better description of the quality of the applicant’s research by describing “up to five of their most significant contributions to science, along with the historical background that framed their research.” That information goes into section C, which no longer asks for “Selected Peer-Review Publications,” but wants “Contribution to Science” instead.

For each of those significant contributions that you list you’ll include the central findings, the impact “on the progress of science” or the application to health or technology, your role in the work and more — including up to four peer-reviewed publications and/or other “non-publication research products” such as video products, patents, software, educational aids and many others. You’ll also need to provide an Internet URL link to a full list of your publications residing in a digital database.

In section A, the personal statement, you’re now invited to list up to four publications relevant to your qualifications for the proposal as well as specific contributions to science that are in addition to (i.e., different from) those in section C.

Oh, and the new biosketch can be five pages, up from four.

For some perspective and history on the new format you can read the “Rock Talk” blog posts by Sally Rockey, deputy director for extramural research at the NIH. I’ve listed the relevant posts among the resources at the end of this item. The often harsh comments at the end of the blog posts indicate some of the controversy about the format, which I’m not going to rehash here. (Keep in mind that people with strongly negative views are much more likely to post in these forums than others.)

Will this new format mean more work for investigators? I’m sure it will, at least initially. (Note that researchers are encouraged to use the SciENcv service as a way to create and update biosketches.) Will it improve the grant review process? To me, that’s hard to say. The new format may make it easier for applicants to report important contributions in this era of team science.

I’ve only scratched the surface here; you really need to acquaint yourself with the details. May 25 will be here soon, and you can use the new format sooner if you want. Here are some linked documents to help:

Guide Notice for the new biosketch: NOT-OD-15-032

New biosketch instructions and sample

Rock Talk, May 22, 2014: Changes to the Biosketch

Rock Talk, Nov. 26, 2014: Implementing the Modified NIH Biosketch Format

Rock Talk, Dec. 9, 2014: Following Up on the Biosketch Implementation

Science Experts Network Curriculum Vitae (SciENcv)





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