The Messages in Marmots

by Kathleen M. Wong

We've all heard the news—climate change is altering the world as we know it. Seas are set to rise and glaciers to melt, drought to parch some lands and scorching temperatures to desiccate others. The effects on us humans are grimly predictable. We'll have to scramble to develop new cars to drive, lands to farm, and sources of water to drink.

But the fate of the birds and beasts who share our planet remains an open question. Will chipmunks and salamanders weather this latest shift in habitat and climate conditions by adapting, or might they fade into extinction? How did they respond to climate change over past millennia, and what can we learn from this?

Craig Moritz, UC Berkeley professor of Integrative Biology and director of the university's Museum of Vertebrate Zoology (MVZ), is uniquely positioned to help answer that question. By combining traditional systematics – the study of animal specimens collected from the wild – with new molecular and computing tools, he and his staff are analyzing how shifts in climate and habitat have affected animals in epochs past. At the same time, they might help forecast how species will react to climate change in the future.

"The business of the whole museum is understanding the patterns of speciation, extinction, and range change that gave rise to patterns of diversity we see today," Moritz says.

Much of that work begins with the museum's vast collection. Each of the more than 710,000 animal specimens, including stuffed storks, grizzly pelts, and pickled amphibians, is associated with a species name, the date and location where it was collected, and often genetic and photographic information as well.

After Moritz joined the museum as director in 2001, he developed the museum's Biodiversity Informatics laboratory. Since then, staff have painstakingly put the information associated with every specimen online, along with thousands of photos and images of the museum's first fifty years of field notes. Much of that information has been entered into databases containing information about birds, mammals, and reptiles and amphibians from collections around the world.

"We're not a public display museum. But through bioinformatics, we can get the collection out of the cabinets and let people know what we have. Anyone can download the data and do what they want with it. Until now, we weren't able to get that information out," Moritz says.

The new format has revolutionized how scientists and others work with the collection. Now able to compare data from more specimens from a wider geographic range, researchers can also overlay spatial information such as annual precipitation and temperature, elevation, vegetation type, and other data collected via satellite. The resulting maps give researchers a new way to evaluate what factors influence a species' range over time.

For example, one of Moritz's specialties is tropical rainforest ecology in Queensland, Australia. "We have a fairly good idea from the fossil record about what temperature and rainfall was like under glacial conditions tens of thousands of years ago. We can ask using modeling where rainforests were likely to have persisted. Then we can use patterns of genetic data we've recovered from our specimens to estimate where species have persisted and how their populations have changed."

Moritz also studies the spatial dynamics of vertebrates in California. Here, he follows in the footsteps of the museum's first director, Joseph Grinnell. In 1908, Grinnell began a 30-year survey of animal populations at more than 700 sites across California. Moritz and the MVZ are re-sampling those same areas 100 years later as part of the ten-year Grinnell Project. By comparing the two sets of specimens, the researchers hope to understand how native species respond to major climate and land use change.

"What we've seen already with our work in the Yosemite area has been quite dramatic," Moritz says. "The ranges of a lot of high elevation species like the pika, alpine chipmunks, and Belding's ground squirrels are contracting upwards" where it's cooler. But other high elevation species, such as marmots and Lyell's shrew, seem to be holding their own. "We've seen enough to know that simplistic notions like all high-elevation species or predators will do one thing isn't backed up by our data," Moritz says. "Now we have to think more like ecologists and say, what is it about these organisms – what they eat or where they live or their hibernation patterns – is causing these changes."

Answering those questions is particularly pertinent today, as severe climate change is forecast to occur across California and the West over the next century. "We're trying to determine what species are going to be really hammered by climate change and habitat fragmentation, and which are going to be resilient. If we know that, we can more efficiently target our conservation strategies," Moritz says. Data from Grinnell's collection will allow the scientists to validate their hypotheses against the previous 100 years of climate change in the state.

In addition, California State Parks has asked Moritz and the museum to help identify areas in the state where rapid speciation and evolution is occurring so these places can be protected as new parks. The agency also wants information about patterns of evolution in existing parks that can be highlighted in brochures and educational programs.

"Natural history museums are just at the beginning of some really exciting science. They have a very proud record, but as these new tools come on board, I think Berkeley's well placed to maintain the leadership position," Moritz says.

Related Web Sites

• Craig Moritz Research Group
• Department of Integrative Biology—Craig Moritz
• Museum of Vertebrate Zoology

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Crystals Reveal Earth's Hidden History

by Kathleen M. Wong

Rudy Wenk studies crystals. But you shouldn't get the wrong idea. A UC Berkeley professor of geology, Wenk is not interested in the sparkly gems revered in alternative healing classes. His crystals have a far more serious job: revealing the structure of the earth hundreds of miles beneath our feet.

Wenk's research centers around a property of crystals and rocks known as anisotropy. When earthquakes rumble through the planet, scientists have observed that they propagate faster in some directions than in others. This is due to the crystalline structure of rocks within the Earth. At these high pressures the atomic lattice of crystals within rocks will deform and align in a preferred direction, much the way tugging on a sagging tennis net will create an orderly, directional grid of cells. A crystal's alignment affects how fast seismic waves can pass through it. In some directions, a seismic wave may be slowed by a factor of two relative to other directions. The degree to which crystals are aligned in a rock determines this response.

"We can use the anisotropy seismologists observe and interpret from that how the material within the Earth has been deformed," Wenk says.

Scientists have already used seismic wave data to confirm the general structure of the Earth. So far, studies suggest it consists of a thin crust; a slightly thicker and mostly solid upper mantle; a viscous lower mantle that makes up about 70 percent of Earth's volume; and an iron core that is liquid on the outside and crystalline on the inside.

Now scientists would like to improve the resolution of their deep earth images. Doing so would essentially allow them to peer into the mantle and witness the processes underlying mountain building, basin sinking, and the rise of islands such as Hawaii. "The lower mantle is the largest volume of the Earth. Whatever happens there has an impact on the structures which we observe on the surface," Wenk suggests.

This is where Wenk's research comes in. He studies crystal deformation and alignment under deep earth conditions. By doing so, he hopes to gain a better understanding of how to interpret both seismic wave data and surface rock samples. "If you take a rock sample from a mountain and look at the alignment of crystals within it, this tells us something about the history of how those rocks were deformed. This information can help us unravel the deformation history of the mountain range," Wenk says.

Wenk simulates conditions in Earth's interior by using a contraption called a diamond anvil cell. The cell consists of two gem-grade diamonds placed on either side of a sealed chamber. Wenk then fills the chamber with crystals he'd like to study under deep earth conditions, and squeezes the diamonds together. The anvil can produce more than 360 gigapascals of pressure – equivalent to conditions in the center of the Earth. As the cell is squeezed, Wenk bombards it with powerful synchotron x-rays to watch the crystals deform.

"We can get an idea of the changes in the anisotropy pattern in the earth as material gets subducted into the lower mantle by observing deformation in the laboratory under extreme conditions," Wenk says.

He and his students are now developing a means to heat the interior of diamond anvil cells using lasers at the Advanced Light Source at Lawrence Berkeley Laboratories. They are able to cook their samples to 2,000 Kelvin, approximating the infernal temperatures found in Earth's interior.

Wenk also approaches the problem from the other direction, by analyzing the crystal orientation patterns of rocks samples thought to originate from the deep earth. With this method, he can use a small sample of rock to get an idea of the larger geological processes at work in an entire region.

By combining the experimental results, sample analysis, seismic results and information about large-scale convection, Wenk can model how anisotropy develops. For example, in one recent paper he follows the crystalline deformation likely to occur as a slab of rock sinks toward the core-mantle boundary, and upwells toward the surface again in a cycle that takes hundreds of millions of years. In the process, Wenk is revealing the dynamics of hidden subterranean earth.

Related Web Sites

• Professor Wenk's homepage
• Texturing of rocks in the Earth's mantle

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Proteins as Shape-Shifters

by Kathleen M. Wong

The devil is in the details, or so the old adage goes. Jhih-Wei Chu understands that better than anyone. A UC Berkeley professor of chemical engineering and QB3 faculty affiliate, Chu models the behavior of proteins atom by painstaking atom. By understanding how proteins interact with other molecules, as well as larger structures in the cell, he is developing a new way to target medicines, design novel materials, and ultimately improve our understanding of cell behavior.

"More than ninety percent of the work in biology is done by proteins," Chu says. The majority function like nanoscale Rube Goldberg machines. When the appropriate target molecule, or ligand, floats by, the active site of a protein will envelop it like a hand closing over a ball. The act of binding then triggers another part of the protein to change shape. Such conformational changes, scientists believe, is how proteins communicate with other proteins and cell elements.

Chu studies how these conformational changes occur. His findings could help develop a more targeted generation of medicines. "A lot of ligands are common from one protein family to another. If you design a drug to target a protein where the ligand binds, you might bind many other proteins as well. This leads to side effects," Chu says. "We'd like to design molecules that don't target active sites but modulate the protein's conformational change instead."

Chu's computer models can track between 30,000 and 1,000,000 atoms, including the protein itself, water molecules, and target substrates. Following that many particles produces an incredibly detailed picture of protein behavior. The tradeoff, however, is that atomistic simulations require massive amounts of processing power. For example, one recent simulation of 100 nanoseconds (ten millionths of a second) took Chu a month and a half to complete.

If designed carefully, 100 nanoseconds is sufficient to watch a protein binding and closing around one ligand. Chu can even hurry the process along by pushing and pulling on different portions of the protein with precise amounts of force. But Chu wants to understand how those conformational changes affect the cell and its external environment. And these processes can require microseconds to milliseconds to occur. Running an atomistic model of such behaviors could occupy a year an a half of computer time.

To sidestep this problem, Chu uses an approach called multiscale modeling. He uses information obtained from finer-grained models to set the parameters of more coarse-grained simulations. Though not as detailed as atomistic models, these larger-scale simulations can follow longer reactions and involve structures such as cell membrane molecules – without taking months to complete.

"The approach we're taking will enable us to transfer the most important pieces of information to models at other scales. Only then can we correctly characterize the behavior of the system," Chu says. "Can there be a systematic way of doing such a transfer of information? If we have a successful methodology for one application, maybe there's a way to generalize that and apply it to many cases."

Chu's simulations have already yielded many useful insights into protein behavior. For example, proteins are often capable of twisting into several different poses, or conformations, while completing a reaction. Chu's models can not only identify which reaction pathway is most likely, but help him analyze how best to modulate that conformational change. Such drugs could prevent one portion of the protein from closing around the ligand, accelerate its gripping behavior, or block the process altogether.

While scientists have a fairly good understanding of how single proteins function, they remain more mystified at how protein assemblages work in concert. "Once they're linked together, proteins can walk, pull things from one place to another. How do different proteins get together to form a machine? How do these molecules communicate with each other at the molecular level? We think conformational change is a part of this," Chu says.

Chu has already found this to be true for actin molecules, which help muscles contract and cells move. In order to link into a long filament, individual actin molecules must "burn" a unit of chemical energy known as ATP. Using molecular simulations, Chu found that this reaction causes a coiled portion of each actin protein to loosen, transforming the structure of each molecule from rigid to floppy, and short to long. This relaxation is what allows actin to move.

"I'm a chemical engineer. We're very good at breaking big problems into small ones, understanding each step very carefully, and at the end putting things together to form a factory. So if we understand how the different units of a cell work, and how they connect to each other, we can try to understand the cell itself–the most efficient factory," Chu says.

Related Web Sites

• Chu Group
• Department of Chemical Engineering—Jhih-Wei Chu
• "Jhih-Wei Chu joins chemical engineering department," (College of Chemistry—News and Publications, Fall 2006)

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ScienceMatters@Berkeley is published online by the College of Letters and Science at the University of California, Berkeley. The mission of ScienceMatters@Berkeley is to showcase the exciting scientific research underway in the College of Letters and Science and the College of Chemistry.

Last updated January 22, 2007.

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