Tracking and Archiving PDFs; Clasp that Cover Slip; Electrifying Gene Therapy

Front Page Tracking and Archiving PDFs; Clasp that Cover Slip; Electrifying Gene Therapy SOFTWARE WATCH | Tracking and Archiving PDFs When Martin Kucej, a molecular biology postdoctoral fellow at Comenius University in Bratislava, Slovakia, couldn't find a journal article on his shelf of documents, he decided to digitize all the documents pertaining to his research project. But he could not find a program that would allow him to do that and share the library with his laboratory colleagues,

Sep 8, 2003
Sam Jaffe

Front Page

Tracking and Archiving PDFs; Clasp that Cover Slip; Electrifying Gene Therapy

SOFTWARE WATCH | Tracking and Archiving PDFs

When Martin Kucej, a molecular biology postdoctoral fellow at Comenius University in Bratislava, Slovakia, couldn't find a journal article on his shelf of documents, he decided to digitize all the documents pertaining to his research project. But he could not find a program that would allow him to do that and share the library with his laboratory colleagues, so he set out to write one himself. Three weeks later, he emerged with Librarian (bioinformatics.org/librarian/features.php), which organizes and automatically annotates all his PDF files.

Once a PDF file is put into the program, Librarian links up with the PubMed database and automatically annotates keywords from the abstract and citation references. "That way you don't have to waste time cutting and pasting," says Kucej.

But the real power of Librarian is in its intranet capabilities. It allows a user to establish a network quickly, and then the home PC acts as a server available to any member of the laboratory. Even if you're working on an international collaboration project, you can share all the journal articles related to the research with every member in every country. A free, open-source application, Librarian works on any Windows, Macintosh, or Unix-based computer.

--Sam Jaffe

 

GADGET WATCH | Clasp that Cover Slip

Courtesy of Starna

Measuring the fluorescence of bulk cultured cells can be awkward, particularly when a scientist wants to recheck the measurement, or compare one substance to another. The trick is to hold the quartz coverslip in the same position with each new measurement. "It could be helpful if you could put [the cover slip] back in the same spot," says Christine J. Watson, senior lecturer, Department of Pathology, University of Cambridge.

Now a manufacturer that specializes in fluor-escence, C&L Instruments of Hummelstown, Pa., has designed a system the company maintains will help scientists leave less to chance. The coverslip (11 x 22 mm) slides into the groove of a polyethylene cap that fits into a cuvette (10 x 10 mm), and a small screw holds both coverslip and retaining plate at a 45° angle to the excitation beam, according to a news release. The coverslip is positioned above the bottom of the cuvette, leaving room for a magnetic stir bar. Two models are offered; both provide a syringe access port, and one enables fluid exchange.

C&L markets the holders for $250 and $300; Optiglass, a UK-based distributor, and its sister company, Starna Cells of Astascadero, Calif., market packages of cuvettes, slides, and coverslip holders, starting at $500, depending on the number of items purchased, says John Webster, US marketing manager for Starna.

--Paula Park

 

PATENT WATCH | Electrifying Gene Therapy

Courtesy of Luyi Sen

Luyi Sen, a cardiologist at UCLA, trained as an electrical engineer before medical school, making her uniquely qualified to figure out how to apply electroporation techniques for gene therapy or protein or drug delivery to whole organs. According to Sen, the literature says that although electroporation is an efficient method of gene transfer, popular for 20 years because it is virus-free, it's impossible to do in large-organ or in vivo studies because of the high voltages theoretically required--200 volts, for example, for the heart. But when a student in her lab inadvertently transfected a large pellet of cells, instead of a cell suspension, Sen realized that the literature might be wrong.

So Sen designed a device that arranges a basket of electrodes on the epicardium and on the endocardium, and applies an electrical impulse to the heart while a gene, protein, or drug is extruded through a coronary artery. The device, which was awarded US patent 6,593,130 on July 15, 2003, and European patent EP1210144 on June 5, requires as little as 10 volts per square centimeter. Sen is now using the device to deliver cytokines that cause immunosuppression in hearts about to be transplanted, but says the method can be applied to any solid organs, including the prostate, breast, and liver, or to hollow organs such as blood vessels. "I'm personally making these catheters," Sen says. "I'd like to find a company to make them."

--Ivan Oransky


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