Volume 1, Issue 2
The Cellular Mechanic
In 2001, Carlos Bustamante was selected by Time magazine as one of "America's Best" in science and medicine. He is professor of molecular and cell biology, physics, and chemistry and is affiliated with the California Institute for Quantitative Biomedical Research (QB3). (courtesy Howard Hughes Medical Institute)
Carlos Bustamante is a mechanic. He tinkers with machines to see what makes them tick. He talks a lot about torque and force, compression and tension. Bustamante is not an engineer though. He's a UC Berkeley professor of molecular and cell biology, physics, and chemistry. And the devices he studies are the microscopic machines behind life itself--cells, proteins, molecular motors, and DNA.
Bustamante is a pioneer in the field of mechanochemistry, devising miraculous methods to manipulate and study individual molecules of proteins, DNA, and RNA. By pulling, prodding, and twisting these molecules, Bustamante furthers our understanding of how cells and microorganisms work.
"Until recently, biochemists and biophysicists did not think of cell processes using mechanical terms," says Bustamante, who is also a Howard Hughes Medical Institute researcher and faculty scientist at Lawrence Berkeley National Laboratory. "Now we have the methods to directly detect and measure the mechanical forces of biochemical reactions at the level of individual molecules."
Most recently, Bustamante and his research group showed that certain proteins essential to compacting DNA for cell division work as "molecular Velcro," helping the double helix of DNA stay bunched up in a well-defined structure. Previously, other researchers determined that if the gene for the proteins, called condensins, was knocked out, the chromosomes failed to segregate properly. Still, the actual mechanics of the condensins were a mystery. To see what was happening, Bustamante created an experiment to measure the force required to yank apart a compacted DNA molecule that had been treated with condensins.
The biomolecular portal motor of bacteriophage PHI-29 (yellow) compresses the coiled DNA into the viral capsid at 6,000 times its normal pressure. The Bustamante group made the measurement by pulling on the DNA with optical tweezers while it was being packed. (courtesy the researchers)
"When we pulled the molecule apart, we saw it extend in a sawtooth pattern of force, like the click-click-click of Velcro unzipping," he says.
After the researchers pulled and relaxed the molecule dozens of times, they proposed a theory about how the condensin proteins create the Velcro-like effect. Each condensin protein, Bustamante explains, attaches sequentially to the DNA. But it also binds less strongly to its neighboring condensin protein. With each attachment, the DNA scrunches closer together into a condensed structure.
The work was published in a June issue of Science Express, a Web site that provides rapid electronic publishing of selected papers that will appear in the journal Science. While the results of the experiment were exciting, the science behind the assay is equally innovative.
"All of these measurements are only now possible to measure because we can grab single molecules and play tug-of-war," Bustamante says.
Over the last decade, Bustamante and his colleagues have advanced various methods to manipulate single molecules, from atomic force microscopes to "optical tweezers." The latter, most recently used to measure the dynamics of DNA's compression, involves the attachment of tiny plastic beads to both ends of a molecule. In this case, the bead at one end of the DNA strand was held in place with suction from a micropipette. The other bead was captured in an "optical trap" created from the radiation pressure of a laser beam. Grasping the bead with the optical tweezers enables the researchers to move or tug the molecule with precise and measurable force.
In 2001, the researchers examined the folding of three types of RNA substructures, including this "hairpin."
In previous experiments, Bustamante and his frequent collaborator, chemistry professor Ignacio Tinoco, used optical tweezers to unfold and refold single RNA molecules. The way nucleic acids and proteins fold into three-dimensional shapes is critical to their function, Bustamante says. Later, the researchers measured the power of the molecular motor that packs a virus's DNA so tightly that it can be injected into a hijacked cell at ten times the pressure of a cork shooting out of a champagne bottle.
"The cell is really like a tiny industrial city with many factories that all perform different functions," Bustamante says. "In the future, perhaps we could go into the cell and play around with those components in vivo."
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An Explosive Theory About Volcanoes
The hulking steel volcano simulator in UC Berkeley professor Michael Manga's laboratory is a far cry from the baking soda-and-vinegar science fair projects of our youth. Of course, that's to be expected. What's unusual is that Manga, a professor of earth and planetary science, is trying to answer the same question posed by the quintessential science class experiment: Why do volcanoes erupt?
Michael Manga is also part of a NASA-funded project to analyze Mars's natural history and the possibility that the planet could have supported life. Five of the 10 team members are professors in UC Berkeley's Department of Earth and Planetary Sciences.
More specifically, Manga's research explains why volcanoes sometimes erupt by oozing lava and other times violently burst ash into the air. Understanding what makes magma erupt in these two very different ways, sometimes from the same volcano, could help scientists determine how hazardous a particular volcano may be.
"Many people live on volcanoes," Manga says. "Knowing when a volcano may be dangerous could help us warn people appropriately. It's way too expensive to tell people to evacuate if nothing ends up happening."
The two types of volcanic eruptions are known as explosive and effusive. Mount Saint Helens' 1980 explosive eruption caused the death of 58 people and more than $1.2 billion in property damage. The slow creep of lava from Hawaii's Kilauea volcano is effusive--visitors flock to the area to watch the honey-like flow.
For many years, scientists believed that explosive eruptions are caused when rising magma breaks as it moves. To demonstrate, Manga grabs a hunk of Silly Putty.
"Silly Putty and magma are similar," he says, tugging on the rubbery substance. "If you deform it slowly enough, it flows. But if you pull it hard, it breaks."
Inside a volcano, the breakage of magma, known as fragmentation, releases gas bubbles trapped in the liquid. The pressure of the escaping gas was thought to propel the fragmented magma, in the form of ash, out of the volcano much like soda squirts from a soft drink bottle if you shake it before popping the top.
But in November, Manga and graduate student Helge Gonnermann published a hypothesis in the journal Nature proposing that fragmentation is also evident in effusive eruptions. According to their report, fragmentation is not the sole cause of explosive eruptions. In fact, they wrote, if the magma repeatedly fragments as it rises to the surface, the steady escape of the gas pressure prevents an explosive eruption. Volcanoes, they went on to say, only explode when the magma rises so quickly that the pressure builds faster than it's released.
"Whether a volcano erupts explosively or not depends on the amount of bubbles inside the magma and how much, or how quickly, the pressure changes," Manga says.
The Little Glass Mountain obsidian flow, the result of late Holocene eruptive activity on the eastern flanks of northern California's Medicine Lake shield volcano, the largest volcano in the Cascade Range. Mt. Shasta, an active volcano, is in the background. (courtesy Helge Gonnermann)
The researchers first realized that fragmentation may be universal across eruptions while studying obsidian created by an effusive eruption at California's Big Glass Mountain volcano. The multi-colored bands visible in the rock hinted that the magma had fragmented, reannealed, and deformed as it ascended.
A 2-cm wide slice through a piece of banded obsidian from Big Glass Mountain in northern California. The bands, which contain different concentrations of microcrystals of the mineral pyroxene, are created by shear forces as the magma rises under the volcano and as it flows on the surface. (courtesy Helge Gonnermann)
Currently, Manga and Atsuko Namiki, a post-doctoral researcher in the laboratory, are using the volcano simulator to test their theories and models about how and why magma fragments. A corn syrup-like liquid is held in the machine's sample chamber, separated from the vacuum chamber by diaphragms. Decreasing the pressure in the vacuum chamber causes the diaphragms to break. Once exposed to the pressure change, the sample liquid expands and blows out the top. A high-speed video camera captures 2,000 frames per second, enabling the researchers to analyze the liquid fragmentation.
"These kinds of experiments help us predict whether something like a big landslide at Mount Saint Helens, for example, would change the pressure enough to cause an explosive eruption," Manga says.
Along with volcano simulators, Manga and his colleagues build unusual models of various planets' entire geological systems. Massive plexiglass vats of corn syrup are heated and cooled from the top and bottom to provide insight into how rock melts and moves through a planet's mantle. In just one day, the researchers can simulate billions of years of Earth's geophysical history. Gaining a better understanding of geophysical fundamentals such as how fluids carry heat through a planet's mantle, Manga says, is important to all of their research efforts.
Post-doctoral research Atsuko Namiki with a volcano simulator. She mixes the various syrupy fluids used in the experiment herself so that they exhibit desired properties.
"Kids have been doing science fair projects about these things forever," he says. "But there are so many simple questions that we just can't answer yet."
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The Mathematics of High-Tech Highways
John Rice is also involved in the Taiwanese American Occultation Survey (TAOS), an effort to detect comets in the Kuiper Belt beyond Neptune.
How long 'til we get there? That question is at the tip of every child's tongue during long road trips. The answer is squarely in the realm of probability and statistics. Just ask John Rice, a UC Berkeley professor of statistics searching for meaning in masses of traffic data.
Rice and his colleagues across campus in the College of Engineering are developing a system that taps California's pre-existing freeway sensor network for data to intelligently deal with congestion. The Freeway Performance Measurement System (PeMS) is a repository for real-time traffic data that streams into the California Department of Transportation from thousands of loop detectors, hexagon-shaped wire sensors in the pavement that count cars and measure average speed. Rice devised the statistical algorithms that convert the raw loop data into "news you can use."
Loop detectors on California freeways provide data for Rice's statistical analysis. (Bill Stone/PATH photo)
Already, travelers who log on to the PeMS Web site can be informed of expected travel times at that moment along many common routes. Eventually, the system will be optimized for mobile phone use. PeMS was also designed to help traffic managers make informed decisions about ramp-metering lights and message boards and aid city planners in the study of long-term traffic trends when considering capital improvements.
Creating an accurate picture of a chaotic system like California's freeways is no easy task though. A model is only as good as the data that's fed into it, and, according to Rice, "a lot of the loop detector data is bad."
"There is a great deal of intermittent malfunction and noise in the system," he says.
Basically, the loop detectors are prone to occasional failure. As a result, the two gigabytes of data streaming into PeMS each day is of wildly varying quality. Cleaning that data--identifying bad data and inferring what may be missing--is a matter of statistics.
It's difficult to identify a broken detector based on a single abnormal measurement, Rice explains. However, by comparing a day's worth of measurements from a single detector with the measurements from many other detectors, the software can "easily distinguish bad behavior from good." Once the bad data is removed, those holes must be filled through "imputation," statistical guesses based on historical data or measurements from neighboring loop detectors.
Of course, what a driver really wants to know is how long it will take to get from one place to another at some time in the future. For example, say you have a meeting across town in two hours. Ideally, you would visit the PeMS Web site right away and enter your origin, destination, and desired time of arrival. The system would then suggest a departure time and the fastest route. To that end, Rice and his colleagues have developed novel prediction algorithms.
One of their predictive techniques is based on a statistical model called "linear regression," a term borrowed from the phrase "regressing towards the average." Essentially, the algorithm works on the assumption that if current congestion is especially bad compared to historical data, it's likely to improve and vice versa. Based on the current state of the freeway, an equation then forecasts the total travel time between two points.
The Berkeley Highway Laboratory is a 2.7 mile section of Interstate 80 that's observable with a bank of video cameras. (courtesy ITS)
To improve the quality of the predictions, Rice and his collaborators are now exploring the use of video cameras to complement existing loop detectors. A few miles south of the Berkeley campus, adjacent to the San Francisco-Oakland Bay Bridge, more than a dozen video cameras mounted high above the freeway keep a constant vigil on surrounding traffic conditions. The surveillance cameras are part of the Berkeley Highway Laboratory, an Institute of Transportation Studies test-bed for traffic monitoring systems.
"Cameras provide better spatial coverage than loop detectors and are easy to replace if they break," Rice says. "The problem with video though is that it's very difficult for computers to spot cars and track them to accurately measure speed and congestion."
Indeed, machine vision is one of computer science's toughest challenges. The difficulty is compounded by the fact that the cameras are mounted relatively far away atop a building, resulting in low-resolution video. So instead of honing in on particular vehicles, the technique devised by Rice and graduate student Young Cho represents each lane in a video frame as a multi-colored "intensity profile." When the profiles are stacked, an "intensity flow" across time and space becomes visible. These stripes, known as moving peaks, contain information about the aggregate behavior of the vehicles and are easily analyzed by a computer.
"By looking at how the images evolve, we can use our algorithm to abstract useful information like local speed estimates," Rice says.
Indeed, while Rice's formulas, graphs, and algorithms may resemble hieroglyphics to the uninitiated, his research is actually a bridge between a somewhat esoteric science and everyday life.
"I've always been attracted to statistics because it sits between math and the physical world," Rice says.
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Berkeley's Scientific Legacy
1948: Wendell Meredith Stanley and the birth of biochemistry at UC Berkeley
Wendell M. Stanley (courtesy Bancroft Library)
Wendell Meredith Stanley (1904-1971) was the father of Berkeley biochemistry. Away from campus though, he's perhaps better known for sharing a Nobel Prize in Chemistry in 1946 for his research on the tobacco mosaic virus. In 1935, Stanley, then at the Rockefeller Institute for Medical Research, and his colleagues crystallized the tobacco mosaic virus, transforming the study of viruses as large molecules. During World War II, Stanley 's insight into viruses as the cause of infectious disease informed the development of an influenza vaccine.
Shortly after the war, Stanley's drive to understand the secrets of viral structures led him to UC Berkeley where he founded the Virus Laboratory. Upon arrival, he spearheaded the construction of the Biochemistry and Virology Laboratory Building that would eventually be renamed in honor of Stanley himself. An innovative administrator, Stanley purposely combined the two units to encourage the sharing of ideas, a precursor to the cross-disciplinary research essential to today's bioscience and bioengineering efforts.
A diseased leaf from Stanley's research archives (courtesy Bancroft Library)
In 1954, Stanley and his collaborators made another biochemical breakthrough that helped save millions of lives. For the first time, an animal virus--specifically, polio--was crystallized for study. Understanding the structure of the virus for polio helped enable researchers to develop a vaccine against it. The following decade, Stanley's research group coalesced into what would ultimately become the current Department of Molecular and Cell Biology.
Last year, the original Stanley Hall was demolished to make room for the 185,000 square foot, state-of-the-art Stanley Biosciences and Bioengineering Facility. Scheduled for completion in 2006, the new building will house the California Institute for Quantitative Biomedical Research (QB3), a cooperative effort between UC Berkeley, UC San Francisco, and UC Santa Cruz. As a hub of Berkeley's Health Science Initiative, the new facility will bring together biologists, computer scientists, chemists, physicists, and engineers to foster novel research and education while promoting the development of new technologies to improve human health.
Indeed, the objective of the Stanley Biosciences and Bioengineering Facility is not so different than the goal first set when Wendell Meredith Stanley joined the Berkeley faculty more than fifty years ago: "Every effort will be made to develop this (department) into the foremost center for biochemical research in the world."
Stanley with other 1946 chemistry Nobelists, John N. Northrup and James B. Sumner. (courtesy Bancroft Library)