A cell biologist in Massachusetts aims to “rediscover” a forgotten organelle, while a biochemist and chemist explore the “epigenetics of RNA” in Illinois. In New York and California, a team of geneticists are examining functional genomics within individual stem cells.
These recipients of the National Institutes of Health (NIH) Exceptional, Unconventional Research Enabling Knowledge Acceleration (EUREKA) grants couldn’t agree more: this atypical funding opportunity has provided them with research prospects that no traditional funding mechanism may ever have.
The EUREKA grants, distributed through various branches of the NIH―primarily the National Institute of General Medical Sciences (NIGMS), which supports basic research to increase understanding of life processes―total up to $67.4 million. Fifty-six grants were awarded to individuals who are the most likely to achieve capacious scientific gains by taking substantial research risks.
“EUREKA awards reflect the NIH’s continued commitment to funding transformative research, even if it carries more than the usual degree of scientific risk,” NIH director Francis S. Collins said in a press release. “The grants seek to elicit those ‘eureka moments’ when scientists make major theoretical or technical advances.”
Each EUREKA researcher will receive up to $200,000 per year for up to four years to test unconventional ideas and tackle methodological challenges, according to the NIH web site.
BioTechniques caught up with some 2009 EUREKA grant recipients to talk about their forthcoming work in genomics, cell biology, and molecular biology.
Rediscovery of the nucloelinus
“Typically, when you say to somebody ‘nucleolinus’ you’ll get a few reactions,” Mark Alliegro, senior research scientist at the Marine Biological Laboratory in Woods Hole, MA, told BioTechniques. “The largest percentage of people haven’t [heard of it]…and they think you’re nuts. Then you get a small percentage of people who say they have [heard of the organelle]…but the conversation ends there.”
Alliegro is on a mission to rediscover this little-known organelle that has captured his interest since working on his master’s thesis in graduate school. It was distinguished as a distinct organelle within the nucleuolus in 1857 by Louis Agassiz, but no paper detailing the cellular component has been published since 1971. Alliegro is determined not only to re-establish the nucleolinus’ status as an organelle, but also to show that it may play a critical role in cell division.
Alliegro and his research team’s focus lies primarily in cellular motility and functional genomics. They are poised to investigate the nucleolinus’ involvement in cell division using a set of novel techniques they’ve developed specifically for isolating the nucleolinus from surf clam (Spisula solidissima) oocytes.
One such technique employs a Hamilton-Thorne XYClone laser system used on an upright microscope. Alliegro has been able to knock out the nucleolinus using this mechanism. Alternatively, he and his team have also isolated the organelle via a sucrose gradient.
“Fortunately for us, [nucleolinuses are] extremely dense,” Alliegro said. “They’re like driveway gravel. We can spin them at 500× g in a tabletop centrifuge and they pellet in about eight minutes. They’re like marbles; they come out nice and clean.”
In laser-targeted cells, where the nucleolinus has been eradicated, Alliegro and his colleagues have seen “definite cell division effects,” particularly in microtubule organization and the creation of mitotic centrosomes. Their first paper on the topic is in the pre-publication stage.
Alliegro asserts that the preliminary data he submitted as part of the EUREKA application was too sparse and indeterminate to have qualified for a traditional R01 grant. “There’s no way that a regular study function would have accepted this work at the stage that I submitted it,” he said. “It was too preliminary and too risky.”
“This EUREKA mechanism came along at an absolutely perfect time for the lab because we’ve gotten to the point where we’re no longer interested in incremental, run-of-the-mill research,” he said. “We were really poised to try something different.”
Discovering the epigenetics of RNA modifications
Meanwhile, in Chicago, Tao Pan and Chuan He are pioneering an effort to explore the “epigenetics of RNA,” a term that Pan effectively coined along with co-investigator Alfonso Mondragon in 2006 as part of a Chicago Biomedical Consortium grant. While it’s known that post-transcriptional modifications, such as methylation, occur in RNA, Pan and He are examining whether or not they are chemically reversible.
Both of the University of Chicago, Pan, a biochemistry and molecular biology professor, and He, an associate professor of chemistry, are studying the methylation of transfer RNA (tRNA) using one—or several—of nine candidate enzymes thought to carry out reversible modifications.
“Nobody really talks about the epigenetics of RNA,” Pan told BioTechniques. “We’ve known about post-transcriptional RNA modification for over 50 years, but never simply asked the question [whether] perhaps these modifications can be removed for a purpose.”
Pan and He are examining radioactively labeled tRNAs for reversible methylations under a wide range of physiological conditions, by performing micro-detections on gels. Their methods are detailed in the paper, “Innate immune and chemically triggered oxidative stress modifies translational fidelity,” published in the Nov. issue of Nature.
“tRNA in humans carry 13 modifications per molecule,” Pan said. “Out of the thirteen, three on average are methylations. Perhaps some of these modifications can be reversible under certain conditions as a function of stress response.”
In applying for the funding, Pan and He proposed to use various genomic techniques in order to discover possible novel functionalities of tRNA, an otherwise well-studied molecule. Pan said that the EUREKA grant offered the team a unique opportunity to “think outside of the box.”
“We would not have done this work without [EUREKA],” he said. This type of exploratory research “clearly would not fly in a regular grant.”
Single-cell functional genomics
A bicoastal collaboration among experts on genetics and aging seeks to investigate genomic activity within individual stem cells—rather than among a population of cells, which several studies have already done.
Jan Vijg, professor and chair of the department of genetics, and a professor in the department of ophthalmology and visual sciences at the Albert Einstein College of Medicine in New York City, and Judith Campisi, a professor at the Buck Institute for Age Research in Novato, CA, and staff scientist in the division of life sciences at the Lawrence Berkeley National Laboratory in Berkeley, CA, aim to “develop new, single-cell approaches for looking at cellular information machinery as a whole.”
Specifically, this project averts the “tendency to look at cells not individually, but as mixtures,” Vijg told BioTechniques. The researchers hope to discover the extent to which heterogeneity exists among the genome, epigenome, and transcriptiome in stem cell populations.
Vijg and Campisi are using amplification technology to multiply the genome in order to investigate all of the global mRNA present in a single cell. They are developing a procedure to identify the patterns of DNA methylation therein. The goal is to correlate specific genetic changes with the functional decline of a cell, measured by use of fluorescent imaging technology.
It’s a risky project, Vijg said, considering the multiple genetic analysis techniques they’re using within a single cell. He said that without EUREKA, it’s likely that only parts of their research would have been funded through more conventional mechanisms.
”The grant will force us to break both of our heads over the problem much more systematically than we would have otherwise done,” Vijg said. “We realize that not all that we want will actually work out the way we planned it. However, if only a fraction can be realized, it would be worth it.”
The NIH makes decisions about whether to reissue the EUREKA initiative on a year-by-year basis, according to its web site. If EUREKA is reissued next year, the funding opportunity announcement will appear in the NIH Guide 2010 during late summer/early fall.