SLIDESHOW: A Walk Through Gloria Coruzzi’s Plant Genome Wonderland

Coruzzi poses among the greenhouse’s rice plants. Members of her team studying nitrogen in use in plants are comparing rice gene networks with those of the simple Arabidopsis plant. Because rice and Arabidopsis are far apart on the evolutionary tree, Coruzzi explains, genes involved in nitrogen use that are common to both must be important.

Coruzzi’s research has shed light on enigmas that have troubled evolutionary scientists for more than a century. Charles Darwin himself was intrigued by what he called the “abominable mystery” behind the rapid appearance of some 250,000 species of flowering plants in the fossil record. He’d probably be thrilled by Coruzzi’s BigPlant tree, which identifies the genes that underlie the divergence of flowering plants, or angiosperms, from the gymnosperms that preceded them.

Many of the plants in this room are species that have been around since dinosaurs walked the earth. For the biodiversity project, Coruzzi and her team are focusing on cyads, the world’s most primitive living gymnosperms, or seed plants.

Coruzzi tells us about her ambitious biodiversity project, a collaboration between NYU, the New York Botanical Garden, the American Museum of Natural History, and Cold Spring Harbor Laboratory. She and her colleagues are sequencing the genomes of 50 long-neglected species of plants, with the goal of learning about the gene networks that control the production of seeds.

Though we might not see much of ourselves in these weeds, the methods used to compare their genes are essentially the same as those used by scientists studying the body. “You take humans who have a disease and humans who don’t and then you look at the differences in sequences (SNPs) between those populations,” Coruzzi explains. “The students in my lab are taught about the methodology of genomics, and that transcends whether you’re a plant or human. Many of our students go on to med school.”

Arabidopsis is a weed; it can grow almost anywhere. Coruzzi and her team are taking advantage of the natural variations between strains of the plant grown in different environments in their study of nitrogen use. By comparing the DNA sequences of the different strains and looking for single nucleotide polymorphisms (SNPs), they can identify the genes that allow strains growing in a habitat with poor soil, say, to use nitrogen more efficiently.

Inside an environmentally controlled growth chamber, Coruzzi admires Arabidopsis seedlings. “Aren’t they beautiful?” she asks.

After leading us down to the basement of the building, Coruzzi pokes around in search of Arabidopsis plants being grown from seed. Because the chambers here are shared by scientists studying all six kingdoms of life, you never know what you might find growing behind these doors.

Coruzzi shows us a basement classroom outfitted with laptops for each student. The genome revolution, she explains, has turned biology into a quantitative science—and biologists, in a sense, into computer scientists.

Arabidopsis was chosen as the first plant species to have its genome sequenced because it has a relatively small amount of DNA, and only two copies of each chromosome (other plants have six). As a bonus, it reproduces in just 4 to 5 weeks, so researchers can quickly learn the results of a genetic cross.

The next stop on our tour is the center’s top floor, home to the Irene Rose Sohn Zegar Memorial Greenhouse, which Coruzzi calls “the jewel in the crown of the building.” Here, thanks to the contributions of donors, researchers can apply what they’ve learned in the lab to the study of living plants, including a range of crops and biodiverse species.

Coruzzi shows us a chip that holds 27,000 plant genes. Each experiment in her lab is replicated three times—which, when multiplied by 27,000, amounts to a whole lot of data. That’s why the researchers turn to computers to help organize and analyze their results.

These tiny containers, called Eppendorf tubes, are designed to hold very small experimental samples. Each one has a lid that can be snapped shut and labeled.

In the lab, Coruzzi and her team take genes from a “model plant,” the humble weed Arabidopsis, and inject them into the cells of more useful plants such as corn and rice in sample tests. The goal is to see whether genes that control nitrogen use in the simple weed can function in crop cells, and to target these genes in transgenic plants to boost the growth of crops. Several commercial field trials are underway for corn and other crops.

Our tour begins in the shared open-air lab space where members of Coruzzi’s team study the plant genes that control nitrogen use efficiency. Why is nitrogen so important? It’s the essential nutrient that limits plants’ growth—so crops that use it most efficiently are a boon to farmers, producing a high yield without much fertilizer. And because nitrates in fertilizer can make groundwater unsafe, using less of it is in everyone’s best interest.

NYU’s Center for Genomics and Systems Biology has been a model for other institutions building similar facilities. On this efficiently designed floor, scientists enjoy natural light and a view of the city. “Because we’re in the heart of New York,” Coruzzi says, “we use every inch of space.”

Here, Coruzzi tells us about the center’s fluorescence-activated cell sorter, a sophisticated machine that uses a laser beam to detect cells that express the DNA she’s interested in. These cells are then sorted into a vial for further study of their RNA profile.

These shiny metal beads are used to heat samples in the lab. They distribute heat more evenly than a warm-water bath would—and because no liquid is involved, there’s no risk of leaking or mildew.

Budding scientists at every level, from high school students to postdocs, have a role in Coruzzi’s lab. Here, undergraduate Becky Grinberg works with an RNA sample from a live plant.

Recent high-school graduates Angela Fan (left) and Jenny Yeoh-Wang work in the lab as their mentors, Coruzzi and postdoctoral fellow Ulises Rosas, look on. Each year, the center hosts pre-college students who work on research projects with NYU scientists.

Meeting the President—that’s one way to kick off a career. While still students at Stuyvesant High School, Mimi Yen (front row, second from right) and Angela Fan (in beige, left of Obama) were among 40 winners of the international INTEL Science Talent Search competition for 2012. Both received the honor for projects they worked on at the Center for Genomics and Systems Biology—Yen in Assistant Professor Matt Rockman’s lab; Fan in Coruzzi’s.

In the center’s bioinformatics suite, where biologists use computer programs to study gene networks, postdoctoral researcher Kranthi Varala shows us how to browse the BigPlant phylogenomic tree for groups of genes shared among different species. This software, developed by NYU in collaboration with the American Museum of Natural History, is available online for use by scientists around the world.

Back in the lab, a student takes a steady hand to an experiment involving about 2,000 tiny Arabidopsis seeds, some of which have acquired a modified “transgene.”

Searching for a single gene that, say, causes a disease is an old way of thinking about genetics, Coruzzi explains. Nowadays, scientists focus on understanding how groups of genes interact. This diagram, generated by computers in her lab, shows the connections between plant genes in a vast network.