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Front Page A Better Bottle; Turning to Yeast for Human Antibodies; An Open-Source Alternative to SMD GADGET WATCH | A Better Bottle? Courtesy of USA Scientific Glass reagent bottles may be standard fixtures in the lab, but they are not without problems. Their height can make them awkward to use, especially in a hood, and their narrow openings do not easily accommodate micropipettes. USA Scientific's new reagent bottles address these concerns. The Ocala, Fla.-based company's durable polypr

Oct 20, 2003
Paula Park

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A Better Bottle; Turning to Yeast for Human Antibodies; An Open-Source Alternative to SMD

GADGET WATCH | A Better Bottle?

Courtesy of USA Scientific

Glass reagent bottles may be standard fixtures in the lab, but they are not without problems. Their height can make them awkward to use, especially in a hood, and their narrow openings do not easily accommodate micropipettes. USA Scientific's new reagent bottles address these concerns.

The Ocala, Fla.-based company's durable polypropylene Smart Bottle™ "combines the convenience of a pipetting reservoir with the higher volume and secure closure of a bottle," according to product literature. The bottle is shaped like a skewed rhomboid, which allows the user to angle it so that the entry is either at the side or at the top. Rock it forward to create a side entry for disposable micropipette tips, or rock it back to create an opening on top for serological pipettes.

Either way, the bottle holds as much as 100 ml and stands only 2.5 inches, which is 35% to 40% less than many 100-ml bottles. At that height, standard 1000-µl pipette tips can reach the bottle's base without contaminating the solution or the pipette shaft. The bottle's flat bottom accommodates magnetic stir bars.

Polypropylene can withstand autoclaving, freezing, and some solvents, but "if you use aggressive organic solvents," cautions product manager Woody Moser, "it will, over time, degrade." It won't eat away at your grant money, though: A pack of 12 sterilized Smart Bottles costs just $11.50 (US).

--Paula Park

 

PATENT WATCH | Turning to Yeast for Human Antibodies

Though therapeutic antibodies have garnered considerable interest lately--witness Herceptin--their development is bedeviled by bottlenecks, says Li Zhu, president and CEO of Genetastix, San Jose, Calif. The company recently received a patent, the fourth in a series, for a two-hybrid yeast-based genetics system that generates such antibodies. Zhu says the system "can make these development processes faster, better, and more cost-effective."

The company's latest patent (US patent 6,610,472) is for a system involved in building antibody libraries directly in yeast, which are then screened by mating with altered yeast into which a particular antigen cDNA has been cloned; the process requires no purified proteins as starting antigens. After mating, yeast cells are spread on selection plates, from which millions of clones can be scored. The system also includes a process that can quickly generate antibodies with higher affinity, says Zhu.

Although the method has not yet been licensed to other companies or researchers, the company would consider such agreements. Genetastix has collabo-rated with a number of academic groups and with partners in China. During the SARS epidemic, the company built a SARS-specific antibody library using blood RNA from convalescent patients; it was able to isolate a "good number" of anti-SARS antibody candidate clones, says Zhu.

--Ivan Oransky

 

SOFTWARE WATCH | An Open-Source Alternative to SMD

Courtesy of Patrick Killion

The Stanford Microarray Database (http://genome-www.stanford.edu/microarray) is a hugely popular resource. Containing tools to store, visualize, and process microarray data, as of September 2003, it archived over 39,000 microarray experiments representing 900 million spots. Though the SMD source code is freely available, its reliance on a back-end Oracle database and Sun Solaris hardware makes it both expensive and difficult for a lab to set up locally.

A new software project at the University of Texas now offers a cheaper and simpler alternative. The Longhorn Array Database (www.longhornarraydatabase.org) does almost everything SMD can do, except it can do it all on a standard Intel-based PC using open-source software.

The Linux-based system uses the PostgreSQL database software instead of an Oracle relational database, so it provides the same functionality and power for thousands of dollars less. Data can be input in such traditional formats as Axon GenePix and ScanAlyze, while results can be downloaded into any spreadsheet. In addition, the database is fully MIAME (minimum information about a microarray experiment) compliant, allowing easier comparisons of results from different research groups. The program's modular architecture makes it easy to add functionality later as the microarray field continues to mature.

--Sam Jaffe


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