Volume 4, Issue 30 August 2007
Rescuing Recorded Sound from Silence
Researchers Carl Haber and Vitaliy Fadeyev of Lawrence Berkeley National Laboratories working on IRENE. credit: LBNL
While listening to National Public Radio in 2000, Carl Haber learned that the Library of Congress had a big problem. The Library's audio collection, which spans the 130-year history of recorded sound, includes the soaring tenor of Enrico Caruso, the speeches of Teddy Roosevelt, and the voices of Native Americans from now-vanished tribes. These echoes of a bygone era were recorded on media such as wax cylinders and shellac and lacquer discs. But many are now too fragile to play in their original format; the pressure of a stylus or phonograph needle could cause irreversible damage. Others are too broken, worn or scratched to yield high-quality sound. The archivists needed a means to preserve the recordings without injuring them further.
A physicist with Lawrence Berkeley National Laboratory (LBNL), Haber was developing subatomic particle detectors to be used at CERN in Geneva, Switzerland. This involved using digital cameras and robots to place each delicate detector in precisely the right place. In a flash of insight, Haber realized that an optical scanning system could solve the Library's quandary.
Millions of historical sound recordings such as this wax cylinder are in need of preservation in the United States alone. credit: courtesy Carl Haber
"I had phonograph records as a kid, so I knew sound was stored in a mechanical profile. I realized that we could use images to figure out in detail what the groove actually looked like, and use a computer to calculate the sound. I thought that might be a way to get around the problem of things being delicate and damaged; you wouldn't have to touch them," Haber says.
Haber already had access to a machine that could make high-resolution digital scans. Postdoctoral fellow Vitaliy Fadeyev wrote a computer program to control the turntable and translate the images into sound.
Haber used a narrow beam of light to illuminate the record's surface. The flat bottoms of the grooves and the spaces between tracks appeared white; the sloped sides of the grooves, scratches and dirt looked black. The image was then analyzed by computer. The program found the edges of each groove by focusing on areas of high contrast. It could correct areas where scratches, breaks or wear made the groove wider or narrower than normal.
A digital scan of phonograph grooves taken by IRENE. The side-to-side wiggles of the groove contain the audio information. credit: Carl Haber
That first test was agonizingly slow. Forty minutes of scanning was required to obtain just one second of audio. But it provided what the scientists needed-proof of principle. And the scan played far more cleanly and clearly than the worn original disc.
Haber and Fadeyev wrote a paper describing the device and sent it, unsolicited, to the Library of Congress. The next thing Haber knew, he had an invitation to visit the Library to talk about the technique. By 2004, Haber and Fadeyev were developing ways to scan discs and cylinders more efficiently.
The two types of media presented very different problems. On antique monaural discs, sound is recorded in horizontal wiggles of the record groove. On cylinders, sound is recorded in the vertical plane-the depth of the groove.
The completed digital phonograph scanner, named IRENE, installed at the Library of Congress. It was developed with funds from the Library of Congress, the National Endowment for the Humanities, the National Archives, and the Mellon Foundation. credit: courtesy Carl Haber
"With discs, we used a camera to image them at high resolution in two dimensions. Once we understood how cylinders were recorded, we realized we had to measure the third dimension (3D) as well," Haber says.
In 2005, LBNL engineers Earl Cornell and Robert Nordmeyer joined the project. With the Library's urging, the team concentrated on producing a dedicated disc scanner. Dubbed IRENE (after the Weavers' "Good Night, Irene," the first disc the team scanned), the device was installed at the Library last summer for evaluation and needs just four seconds to scan one second of audio.
The group is now refining a device that scans in 3D. The device is based upon a type of confocal microscope. White light directed at the surface of a cylinder or disc passes through a lens. But the lens is imperfect by design; though it splits the light into its component colors, each color comes into focus at a different depth. The color of the reflected light reveals the height of the scanned point. The computer assembles these points into profiles for each groove and translates the data into sound.
A digital scan of phonograph grooves taken by IRENE. The side-to-side wiggles of the groove contain the audio information. credit: Carl Haber
The current 3D scanning process takes 20 hours to record one minute of sound. But a new version of the confocal scanner, developed for the dental industry, should reduce that to about 10 minutes.
A half-dozen physics and engineering undergraduates from UC Berkeley have been instrumental in speeding the project along. "Students can apply the kinds of techniques they learn in classes about statistics, mathematical analysis and signal processing to a project they can really get their arms around," Haber says. A Berkeley graduate student in linguistics is poised to join the project later this summer.
UC Berkeley's Phoebe Hearst Museum and Native Americans are among those who could benefit the most from IRENE and its sister 3D scanner. In the early 1900s, UC Berkeley anthropologist Alfred Kroeber and colleagues recorded the legends, songs, customs and voices of dozens of California Indians on some 3,000 one-of-a-kind wax cylinders. Many of these tribes and languages have since died out or are on the verge of extinction. The LBNL group is now collaborating with linguist Andrew Garrett and Victoria Bradshaw of the museum to digitize the Kroeber recordings. Remastering these cylinders could help new generations of native peoples study their ancestral customs and tongues—and help carry the sounds of the past into the future.
Sound Samples
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Genes to Grow On
All it takes to start a cancer is a single cell's mistake. That error-to proliferate and divide, again and again and again, ad infinitum-is the difference between normal, healthy growth and a potentially fatal tumor.
"The genes that regulate the normal growth of an organism to determine its final size are the same genes that are often mutated in human cancers," says Iswar Hariharan, a UC Berkeley professor of cell and developmental biology. Because these genes are so critical in both development and disease, he says, "We're trying to understand the cellular circuitry that regulates growth."
Hariharan first looked for genes that restrict tissue growth when he was a researcher at Harvard Medical School. There, his laboratory developed a fast and easy method to screen for growth-regulating genes. When these genes are mutated, cells grow better than their neighbors.
Iswar Hariharan gazes into fruit fly eyes to discover genes associated with growth restrictions. Left: a normal fly eye has equal amounts of normal (red) and mutated (white) tissues. Right: Flies with mutations in growth restriction genes have a larger proportion of white, mutated tissue than normal red tissue in their eyes. Photo credit: Iswar Hariharan
Hariharan conducts his research using a classic laboratory subject-the fruit fly-because it is easy to raise and has a well-studied genome. For the growth-gene screen, Hariharan mutates strains of flies, then observes the pattern of cells in each adult fly's retina. In these flies, mutant eye tissue is white, and normal tissue is red. Any fly with a disproportionate amount of white in its eyes must have a mutation in a growth-regulating gene.
Using the screen, Hariharan has identified about 35 genes that cause cell overgrowth. Many have links to human cancers. One gene, archipelago, is mutated in about 17 percent of endometrial cancers and 12 percent of colon cancers. Variants in the gene capicua have been identified in breast cancers.
Once he's identified a growth regulating gene, Hariharan can study what it does. "We're now piecing together the signaling pathways or circuits that cause growth," Hariharan says.
Some of the pathways Hariharan has found appear to detect the concentrations of nutrients inside cells, which might tell cells when they have enough resources to divide. Other pathways may help cells sense the nearness of their neighbors.
"We still have little information on how genes determine the eventual size of the organism or the size of individual organs," Hariharan says. The pathways involved in sensing crowdedness could represent the first genetic links between cell growth and overall organ size.
So far, Hariharan's laboratory has identified genes in at least five distinct pathways that regulate growth. Why these pathways are so numerous, and how they interact, remains unknown.
"In the cases we've tested, the pathways are not interchangeable, suggesting that they each do different things," Hariharan says. "It might be like baking a cake; you have to throw in your eggs and flour and sugar, and throwing in three times as much of one ingredient doesn't help you."
Since Hariharan returned to UC Berkeley as a professor in 2003 (he was a postdoctoral fellow here in the late 1990s), his laboratory has begun to study tissue regeneration.
If unchecked growth can spell disaster, controlled regrowth or regeneration can be a great boon. Understanding how lizards can regenerate their tails, for example, could be the first step in helping humans who have suffered heart attacks replace cardiac muscle.
Although fruit flies can't regenerate tissue as adults, they can, to a limited extent, do so as larvae. The tissue destined to become the fly's wings, known as the imaginal disc, can regrow missing portions if transplanted into a mature female fly's abdomen. Older imaginal discs seem less capable of regeneration. "The tissue has lost its plasticity and has become locked in place," Hariharan says. "We want to look at the growth regulating pathways and try to figure out what changes in them between when the disc can regenerate and when it cannot."
To study this phenomenon, Hariharan's laboratory has developed a strain of fly that can regenerate its imaginal discs without the need for transplantation surgery.
"If we find a gene that when mutated continues to allow regeneration to occur at an older age, that would be very interesting. It suggests there is a mechanism that actively keeps regeneration off," Hariharan says. Such a mechanism may also be present in mammals, as every other growth-regulating gene they've found so far in fruit flies has a mammalian counterpart.
Down the line, drugs targeting this mechanism could conceivably allow patients with severed spinal cords or injured hearts return to good health. Hariharan says, "This is our ultimate dream."
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Can't Cut This
Berkeley chemistry professor Jonathan Ellman is also affiliated with the California Institute for Quantitative Biosciences (QB3) and the Department of Cellular and Molecular Pharmacology at UC San Francisco.
When a malaria parasite lands in your blood, one of the first things it does is whip out its scissors. As fast as it can, this protozoan snips the hemoglobin in red blood cells to get the nutrients it needs to survive. Of course, the microbe behind this deadly disease doesn't actually deploy stainless-steel blades. Instead, it uses an array of biochemical scissors known as proteases.
Proteases are enzymes that snip proteins. They recognize certain strings of amino acids on a substrate protein, bind to this area, then break a nearby chemical bond. Proteases can destroy proteins by snipping them in half, as in malaria. They can also activate proteins by lopping off atoms covering a reactive site.
This versatility has made proteases critical to all manner of organisms, from viruses to plants to humans. Over the past 10 years, protease inhibitor drugs have become indispensable in the fight against AIDS, cardiovascular disease and diabetes.
But finding protease inhibitors is no picnic. Humans manufacture tens of thousands of proteins; figuring out which of these a protease targets is extremely challenging and time consuming.
However, "if you can identify the combination of side chains a protease cleaves, that can really help you figure out what its function is, and how to block it," says UC Berkeley Professor of Chemistry Jonathan Ellman.
Ellman has developed several methods to speed the matching of protease to substrate. His techniques to synthesize test molecules and detect good matches are now being used in the development of therapeutics against many diseases.
In collaboration with biochemist Charles Craik of UC San Francisco, Ellman first pioneered a method to create libraries of test molecules quickly and efficiently. Instead of mixing liquid chemicals and painstakingly purifying them again at each step, he attaches his precursor molecules to polystyrene beads resembling sand grains. To add more atoms to this chemical skeleton, he simply adds the beads to another chemical solution. "This allows you to make a lot of different side chains in substrates very rapidly, so you can synthesize many compounds in parallel," Ellman says.
Here, a protease inhibitor (stick figure) identified using Ellman's substrate activity screening method is bound to the protease cathepsin-S (surrounding 3D x-ray structure).
Initially, Ellman and Craik prepared and evaluated mixtures of substrates. This approach has been applied successfully to over 200 proteases. Since then, Ellman has developed a method to evaluate many individual substrates at once. To each substrate, he adds a reporter molecule that fluoresces when broken off. He then binds a dot of each type of substrate to a glass slide. A single slide can accommodate up to 10,000 different substrate droplets. A solution containing the protease gets poured on top. If a substrate is a match, the proteases do their snipping, and the severed pieces will fluoresce. The brightening fluorescent glow provides a clear signal that there is a hit.
"Once you've found a match, you can use a computer to scan the sequences of proteins encoded by the human genome to identify likely candidate targets. This can guide your efforts to better understand what that protease does," Ellman says.
Most new drugs are relatively large and complex, made up of hundreds of atoms. Trying to screen every possible arrangement of atoms in molecules of this size is impossible; the permutations are more numerous than there are molecules in the universe.
Ellman sidesteps this problem by working with molecules a third to two-thirds the size of most drugs. He creates fragments of drug-like substrates, then identifies those cleaved by a target protease. This technique, called substrate activity screening, increases the chances of identifying a match.
Because Ellman builds every substrate, he also knows exactly how the molecules are bound and cleaved by the protease. With this information, he can replace the bond that is normally cut with a more stable structure. The resulting inhibitor molecules act like decoys, keeping the protease occupied and reducing the damage to body proteins.
Ellman has developed a similar version of this assay for another class of enzymes called phosphatases. The bacterium that causes tuberculosis excretes two types of phosphatases into the body of its host. Their presence appears necessary for TB cases to worsen. Working with UC Berkeley Professor of Biochemistry and Molecular Biology Tom Alber, Ellman has identified two molecules capable of inhibiting these enzymes.
"Because these phosphatases are located outside the bacterium, they may be more accessible to drugs than typical bacterial drug targets, making it easier to kill off the bacteria," Ellman says. "By taking these enzymes out, we could provide an assist to the human immune system."
To date, Ellman's methods have been used in a wide variety of biomedical research. One company has employed them to understand why HIV develops resistance to protease inhibitors. Another is using them to develop proteases that could become a whole new class of drugs. And pharmaceutical giant Merck has used his methods to aid in the development of a new drug against type 2 diabetes. The drug was approved by the FDA just last year.
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