SOFTWARE WATCH | Map Protein Interactions

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When Laurent Cocea lost his job in 2002, he immediately set to work creating his own company to solve a problem he had while still employed at Amgen in Toronto. "We had a team of students who spent six weeks mapping protein interactions," he says. "Once they did it, they couldn't edit it."

Now, thanks to "Dynamic Signaling Maps," a program Cocea designed, any researcher can map complex protein interactions in minutes, rather than weeks. And the best part is that, for the near future, the tool is available for free on the Web (www.hippron.com/hippron/index.html). Cocea hopes to lure researchers into using the product through the free Web site (he's attracted more than 200 registered users so far) and eventually to charge their institutions, primarily biotechnology firms, to pay for licenses. Several other firms have developed similar software, but most of it is based on proprietary, often expensive database technology.

As a browser-based system, scientists can utilize the Maps software on any computer. And best of all, a user can import the final map into almost any graphics program, including Microsoft PowerPoint, and edit it further. That means that the user can quickly integrate new information, even while en route to a conference.

--Sam Jaffe

GADGET WATCH | A Cooler Cooler

Courtesy of Eppendorf

Any researcher performing manual PCR is familiar with the low-tech method of keeping tubes cold: the ice bath. While this no-frills tool has its advantages (namely, low cost), it's not always the best choice. If the ice starts to melt, tubes may fall over and become contaminated, or worse: Caps can open, releasing the contents of the tube and destroying the experiment. Hamburg, Germany-based Eppendorf has an answer to this problem: the Eppendorf^® PCR-Cooler, a compact device that holds tubes upright and maintains a constant sample temperature of 0°C for more than one hour at room temperature.

Although other devices that maintain sample temperature exist, Andy Aguirre, product manager for centrifugation for Westbury, NY-based Brinkmann Instruments (Eppendorf's US division), notes that only the PCR-Cooler has a built-in temperature indicator. The color of the PCR-Cooler changes from purple to pink or dark blue to light blue if the temperature of the sample rises to 7°C. "So you're virtually assured the sample is at 0°C," says Aguirre. Starter kits containing one pink and one blue PCR-Cooler can be purchased for about $100 (US), or less with contract pricing, says Aguirre.

--Aileen Constans

PATENT WATCH | Proteomics Gets Sticky

	Courtesy of Ciphergen Biosystems

Feeding off of a steady stream of technological improvements, geno-mics' rise was meteoric. But with a relative paucity of tools, proteomics has lagged by comparison, says John Storella, vice president for intellectual property at Fremont, Calif.-based Ciphergen Biosystems. Ciphergen is hoping to change that with its Surface-Enhanced Laser Desorption Ionization (SELDI) system, which was awarded US patent 6,579,719 on June 17, 2003, for protein expression profiling capabilities, and European patent EP 0700521 B1 on June 4, 2003, for core aspects of the technology.

SELDI employs a chemically sticky target plate that selectively captures certain classes of proteins, allowing others to be washed away. The remaining proteins are then analyzed by mass spectrometry. The surfaces vary, employing metal ions or anionic exchange, for example. Storella says that in a second-generation version of SELDI, the inventors discovered that "if you took different combinations of these surfaces, you could capture many more proteins."

The method is already in use. David Ho's team at the Aaron Diamond AIDS Research Center in New York used the technology to identify the alpha-defensins, three proteins thought to be important in nonprogressors with HIV, Storella says. At the July meeting of the American Association for Cancer Research, 45 of the published abstracts used the technology. "Protein profiling is probably the most powerful utility that this technology has," says Storella, "but it's also useful for protein-interaction studies." Citing the example of the controversial prostate cancer marker, prostate-specific antigen, Storella says looking at patterns of proteins, rather than at a single biomarker, could significantly increase sensitivity and specificity.

--Ivan Oransky

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