Stimulus funds help Rice evolve
Researcher granted nearly $1 million to create
genome-analysis tools

BY MIKE WILLIAMS
Rice News staff

Things are quickly coming into focus for Nicholas Putnam, and a grant for nearly a million dollars certainly has helped that process along.

	JEFF FITLOW
	Evolutionary biologist Nicholas Putnam will use his nearly million-dollar grant to create computational tools to help researchers better understand the evolution of the genome.

Putnam, an evolutionary biologist who came to Rice last year, has received a National Science Foundation grant via the American Recovery and Reinvestment Act to pursue the creation of a set of tools to compare and interpret how genes are organized in the chromosomes of animals, including humans.

It’s no small matter when you’re talking about tracking down and comparing the genomes of species to find commonalities among lines that may go as far back as 750 million years, when the first multicelled animals got themselves organized.

But that’s Putnam’s passion. The assistant professor of ecology and evolutionary biology has been thinking about the need for these tools for a very long time, since his days as a postdoctoral fellow at Lawrence Berkeley National Laboratory and the University of California at Berkeley. The grant for the project, titled “Reconstructing 700 Million Years of the Evolution of Genome Organization: Tools and Community Resources,” will make them a reality.

Putnam said the computational tools would lead to a better understanding of why certain organizational features in the genomes of radically different species are essentially the same. Why would a sea anemone have gene groupings on its chromosomes similar to that of a human being, and what common purposes might they serve?

His previous work showed that living things have conserved some unexpected genomic features from some of the first multicelled animals. “This project is focused on a very specific feature of the genome,” said Putnam, whose group is settling into new headquarters in the Anderson Biological Laboratories. “We want to compare that feature between organisms and track it back in time. We want to understand how the arrangement of genes in the genome changes through evolution, specifically at a large scale.”

Putnam received a National Science Foundation grant for $933,526 via the American Recovery and Reinvestment Act.

The genome is the genetic code sequence stored within one set of chromosomes in the cells of each living being, and it generally determines how that being fits into the grand scheme of life. Evolutionary biologists find studying the genome useful in determining how species have diverged over eons.

Or, in particular ways, how they have not diverged at all. “It may not be possible to know with much precision when that first multicelled animal lived, but we can still, it turns out, learn a lot about its genome,” said Putnam. He was part of a groundbreaking study published in Science in 2007 that found thousands of protein-coding genes that ancient anemones share with all other living things, including humans, and several striking ways in which the human genome is more similar to that of the sea anemone than it is to more closely related animals such as fruit flies and nematode worms.

The ultimate goal is to create not only the software to compare genomes but also a Web-based resource that will help scientists gain a better understanding of evolution, biodiversity and the mechanisms species use to fight stress and disease. “There’s a whole range of analyses that people studying a particular gene or set of genes involved in the disease process can access — different types of comparative data and structural data. Our goal is to add another specific category of comparative data.”

Putnam has been planning the project for a long time. “It was at the top of my list when I came to Rice,” he said. But before coming to Houston, he had never before applied for a research grant.

“I wrote it in the first two weeks after I arrived last summer,” he said. “I think the deadline was Aug. 15, and it was very intense. I just said to myself, ‘This is my job right now, to learn how to apply for grants.’ So I thought I’d go for it.”

He credited his colleagues in evolutionary biology and in the Office of Sponsored Research for their helpful suggestions. “(Grants Coordinator) Linda Bird really gave me great support in the mechanics of submitting an NSF proposal,” he said.

“It’s likely that I was in the right place at the right time. I count myself as very lucky.”

Putnam is busy putting together his team. He plans to hire a scientific programmer, a postdoctoral student and a graduate student for the project’s three-year term.

The project won’t play a major role in the new course he’s teaching this semester, called Evolutionary Bioinformatics, but he expects it will become part of the course in future semesters, when the project’s tools are developed. “Next year, I’d love to use some of this data in examples and exercises for the class,” he said.