One-Stop Genome Shop; A Safer Squeeze Bottle; Watching -- and Manipulating -- Stem Cell Growth

Front Page One-Stop Genome Shop; A Safer Squeeze Bottle; Watching -- and Manipulating -- Stem Cell Growth SOFTWARE WATCH | One-Stop Genome Shop Sequenced genomes are no longer a rarity. Scientists have sequenced more than a hundred organisms and released the results on public databases. Many of those databases speak in different languages, however, making cross-referencing and comparative genomics difficult. Christos Ouzounis and his colleagues at the European Bioinformatics Institute in

Sep 22, 2003
Sam Jaffe

Front Page

One-Stop Genome Shop; A Safer Squeeze Bottle; Watching -- and Manipulating -- Stem Cell Growth

SOFTWARE WATCH | One-Stop Genome Shop

Sequenced genomes are no longer a rarity. Scientists have sequenced more than a hundred organisms and released the results on public databases. Many of those databases speak in different languages, however, making cross-referencing and comparative genomics difficult.

Christos Ouzounis and his colleagues at the European Bioinformatics Institute in Cambridge set out to fix that with COGENT, their Web-based Complete Genome Tracking database (http://maine.ebi.ac.uk:8000/services/cogent). "Compiling genomic information was becoming more and more difficult, given the variety of different formats and distribution mechanisms," explains Ouzounis. For instance, gene-naming standards can differ from database to database, making computer comparisons unwieldy, if not impossible.

Now, the complete sequences of 135 organisms, from Aeropyrum pernix strain K1, to Yersinia pestis strain KIM, and every sequenced archaeon, bacterium, and eukaryote in between, are available for download from Cogent as FASTA- formatted peptide data, using a single naming convention. The open-source database engine, based on MySQL, is also available, so users can incorporate their own sequencing data, no matter what species it's from.

--Sam Jaffe

 

GADGET WATCH | A Safer Squeeze Bottle

Courtesy of Nalgene Labware

It looks like a simple wash bottle, but a new Teflon bottle, created by Nalgene Labware of Rochester, NY, is both inert and chemically stable. Able to withstand temperatures of -105°C to 150°C, the bottle is even autoclavable.

The bottle's nozzle system features a closure device designed to reduce dripping, which is probably the most attractive feature for many lab workers. Turning the assembly in one direction closes it tightly; in the other direction it allows the user to adjust the force of the spray. Because the nozzle creates a steady stream, it reduces splashing. Meanwhile, a nonwettable O-ring releases internal pressure.

Herbert P. Schweizer, associate head for graduate education and research at Colorado State University in Fort Collins, says an adjustable nozzle could be useful, though he has not used the Nalgene bottle. "Solvents have a tendency to expand and leak," he observes. "It could be helpful to be able to close the bottle tight. If you have a squirt bottle, with just one nozzle, you have to squirt it just right. If it would be adjustable that would be nice."

This patented nozzle assembly is unique to the Nalgene bottle, says Dan Dwyer, product development technical specialist. "Some companies have dispensing-type systems," he says. "But no one has an O-ring dispensing model." The Nalgene bottle costs $75 (US).

--Paula Park

 

PATENT WATCH | Watching--and Manipulating--Stem Cell Growth

Courtesy of NIH technology transfer office

Typical cell culture bottles grant limited access to growing cells. But researchers at the National Institutes of Health have come up with a stem cell culture, monitoring, and storage system that allows observation of cells in culture under a microscope and the addition of gases or liquids by microcapillaries, according to Michael Shmilovich, a patent attorney and licensing specialist in the NIH's Office of Technology Transfer.

The system consists of a chamber with top- and bottom-mounted coverslips, an inlet tube and outlet tubes at two different vertical positions, and a ball-joint assembly that gives users the opportunity to manipulate a glass microcapillary or microelectrode to come into close contact with cells. "When you put it under the microscope, you can visualize growth of cells in real time," Shmilovich says.

"It's not just for stem cells," Shmilovich adds. "It's applicable to any cell type that you would grow in culture media." Anyone interested in licensing the chamber, developed by Rea Ravin, James Sullivan, and Ronald McKay, should contact Shmilovich at (301) 435-5019 or shmilovm@mail.nih.gov. US Patent Application serial number 10/334,565 was filed for the chamber on Dec. 30, 2002.

--Ivan Oransky


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