Technology Front Page

Front Page
Sam Jaffe | Dec 1, 2003 | 4 min read
Front Page Bibliographies for the Penguin Faithful; Legible Lab Labels; High-Power Proteomic Fractionation SOFTWARE WATCH | Bibliographies for the Penguin Faithful Courtesy of Larry Ewing EndNote, the commercial bibliographic management program, has been a godsend to scientists, provided they work on PCs or Macs. Those who depend on Linux are out of luck--or at least, they were. Now Pybliographer (, from French programmer Frederic Gobry, is trying to fill the void. Th
Front Page
Sam Jaffe | Nov 16, 2003 | 4 min read
SOFTWARE WATCH | Green Tea, Anyone? Scientists who have unlimited hardware budgets, a dedicated IT staff versed in the arcana of networks, and lots of time on their hands probably find setting up a computer cluster a breeze. Everyone else knows it's difficult and expensive. A new Java software program called GreenTea ( offers an alternative. Instead of a cluster, GreenTea works as a peer-to-peer client, chopping large computing tasks into smaller, more workable fragmen
Front Page
June Holloway | Nov 2, 2003 | 4 min read
GADGET WATCH | Object Inspector in Your Pocket Protector Courtesy of Chris Chou Chris Chou wants you to put your microscope where no microscope has gone before: in your pocket. Chou is the inventor of the microscope pen, a portable, lightweight, but durable microscope that fits easily into a shirt or pants pocket and comes with a convenient pen clip to keep it there. Measuring 0.75 x 5.5 inches and weighing in at a mere two ounces, the microscope pen provides all-glass optics, 100x magnifi
Front Page
Paula Park | Oct 19, 2003 | 4 min read
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
I Spy ... Something Green!; Soldering Issue; Putting a Pretty Face on Multiple Sequence Alignment
Paula Park | Oct 5, 2003 | 4 min read
FASHION WATCH | I Spy ... Something Green! To most eyes, a mouse is a mouse is a mouse. It's the underlying genetics, of course, that matter, and those are usually hard to see. But scientists working with green fluorescent protein (GFP)-expressing transgenic mice have a new gadget that will help them spot their mice with ease. Constructed like goggles with a miner's headlight, the GFsP-5, manufactured by Biological Laboratory Equipment, Maintenance, and Service (BLS) in Budapest, Hungary,
One-Stop Genome Shop; A Safer Squeeze Bottle; Watching -- and Manipulating -- Stem Cell Growth
Sam Jaffe | Sep 21, 2003 | 4 min read
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
Tracking and Archiving PDFs; Clasp that Cover Slip; Electrifying Gene Therapy
Sam Jaffe | Sep 7, 2003 | 4 min read
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,
Map Protein Interactions; A Cooler Cooler; Proteomics Gets Sticky
Sam Jaffe | Aug 24, 2003 | 4 min read
SOFTWARE WATCH | Map Protein Interactions Click to view enlarged map (26K) 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 minute
Fluorophore Fingerprinting; Gene Therapy Hybrid; Low-Level Annotation
Ivan Oransky | Jul 27, 2003 | 4 min read
PATENT WATCH | Fluorophore Fingerprinting The Molecular Sciences Institute in Berkeley, Calif., has been awarded a patent for a protein fingerprint system (US patent 6,569,685, issued May 27, 2003). The patent covers a method that, in the simplest case, consists of covalently modifying reactive residues using orthogonal chemistries, by attaching one fluorophore to lysine residues under appropriate chemical conditions, and a different fluorophore to cysteine residues. "The general idea is to
RNA Interference without the Interferon; Simplifying Dialysis and Electroelution; Microarray Analysis, TIGR-Style
Ivan Oransky | Jul 13, 2003 | 4 min read
PATENT WATCH | RNA Interference without the Interferon The red-hot field of RNA interference (RNAi) could benefit from patents issued jointly to Queensland, Australia-based Benitec, and the State of Queensland (US patent 6,573,099, issued June 3, 2003, and UK patent 2353282, granted May 3, 2003). The patents describe a method Benitec calls "DNA-directed RNA interference" (ddRNAi) to differentiate it from typical double-stranded small interfering RNA (siRNA). Using this method, a DNA constru
Sequencing on Compact Disc?; Microgenomics of Breast Cancer; Better Binding Site Prediction
Ivan Oransky | Jun 29, 2003 | 4 min read
PATENT WATCH | Sequencing on Compact Disc? Burstein Technologies of Irvine, Calif., has entered the alternative sequencing strategy arena (see related article, Beyond Sanger: Toward the $1,000 Genome), winning patent protection for its hybridization-based sequencing approach, which employs the company's BioCompact Disc (BCDT) technology. (US patent 6,566,069, issued May 30, 2003) "Oligonucleotide arrays hold great promise in gene sequencing," inventor Jorma Virtanen writes in the applicati
Fighting the Membrane Protein-Extraction Blues; Cell-Free Apoptosis System; Database Searching on Your Schedule
Jeffrey Perkel | Jun 15, 2003 | 4 min read
GADGET WATCH | Fighting the Membrane Protein-Extraction Blues Courtesy of Geno Technology Efficient extraction of membrane proteins can be a dicey business: Add too little detergent, and you fail to extract the protein; add too much, and purification procedures and downstream applications may be compromised. Geno Technology ( of St. Louis offers one solution: Optimizer-blueBALLS™, which are glass beads coated with a hydrophobic blue dye that behaves like membrane-bound
/i> Optimization; Microarray Analysis: It's a GAAS!
Jeffrey Perkel | Jun 1, 2003 | 4 min read
GADGET WATCH | Ultrafast Gel Loading Courtesy of Andre Marziali Technicians at the British Columbia Genome Sequence Centre in Vancouver spend hours loading agarose gels for high-throughput, bacterial artificial chromosome fingerprinting. Such repetition cries out for automation, and Andre Marziali, platform director for technology development at GenomeBC, was asked to design a fix. His solution--a "capillary comb loader"--can apply an entire microplate-worth of samples in one shot, reducing
Smaller, Better, Faster Transfection Assays; Really Ready Redivue; Visualizing RNA with RnaViz 2
Ivan Oransky | May 18, 2003 | 4 min read
PATENT WATCH | Smaller, Better, Faster Transfection Assays Courtesy of Akceli Cambridge, Mass.-based Akceli has been awarded a US patent for a reverse-transfection assay method (US patent 6,544,790, issued April 8, 2003). Akceli says the method condenses more than 6,000 data points on a single microtiter plate, which can be imaged in about 20 minutes. "Our technology allows us to do very rapid compound profiling and target ID and validation," says David Chao, president and cofounder of Akc
Capillary Electrophoresis, Meet Lab-on-a-Chip; Virtual NMR; Researchers Map Worm ORFeome
Jeffrey Perkel | May 4, 2003 | 4 min read
TECH BRIEF | Researchers Map Worm ORFeome Courtesy of Marc Vidal Citing the need to verify genome annotations and to provide a resource for functional genomics, Marc Vidal of the Dana-Farber Cancer Institute and an international team of researchers have tackled what they call the "ORFeome," the complete set of protein-encoding open-reading frames (ORFs) in the Caenorhabditis elegans genome (Nat Genet, advance online publication, DOI:10.1038/ng1140, April 7, 2003). Using annotation data, the
Au Revoir, Ponceau S; Solving Proteins from Scratch; From the Office of Oligo Defense
Jeffrey Perkel | Apr 20, 2003 | 3 min read
GADGET WATCH | Au Revoir, Ponceau S Courtesy of Pierce Biotechnology Western blotting is a standard facet of gene expression analysis: Separate protein extracts electrophoretically, blot the proteins to a nitrocellulose or nylon membrane, and probe for the presence of a particular protein. Traditionally, verifying the efficiency of protein transfer to the membrane is accomplished by staining with Ponceau S or Coomassie® Blue. Ponceau is a relatively insensitive red dye (250 ng detection
Good Vibrations; Annotation Illustration; Speedy Sequencing
Jeffrey Perkel | Apr 6, 2003 | 3 min read
Gadget Watch | Good Vibrations Courtesy of Bel-Art Products Who hasn't experienced this frustration: When measuring out a minute quantity of a precious reagent in the microgram balance, your hand slips, and whoops! You've just dumped--and possibly lost--way more powder than you need. The Quaver® nonmotorized vibrating spatula and its nimbler sibling, the Quaverette®, could make such problems things of the past. Manufactured by Bel-Art Products ( of Pequannock, NJ, t
DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck
Brendan Maher | Mar 23, 2003 | 3 min read
Front Page | DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck Courtesy of AcaClone Software SOFTWARE WATCH | Sequence-Analysis Beerware DNA sequence analysis software needn't be expensive. For a decade, molecular biologist Kjeld Olesen has spent much of his spare time developing pDRAW32, a free sequence-analysis software package for Windows PCs. Researchers can perform restriction enzyme analyses, edit sequences, create plasmid maps, cut and ligate "in silico
An Eternal Fluorescent Protein?; Model Behavior; Compacting DNA Shrinks Gene Therapy Barriers
Brendan Maher | Mar 9, 2003 | 3 min read
Front Page | An Eternal Fluorescent Protein; Model Behavior; Compacting DNA Shrinks Gene Therapy Barriers Reprinted with permission J Biol Chem, 275:25879-82, 2000. GADGET WATCH | An Eternal Fluorescent Protein? Researchers at Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry in Moscow who developed the fluorescent protein DsRed are tinkering with a new chromoprotein with some unique properties.1 Discovered in the sea anemone, Anemonia sulcata (at left), this GFP-like protein, ca
Golden Electroporation; Reduce, Reuse, Recycle; Rad! Volocity Goes Modular
Jeffrey Perkel | Feb 23, 2003 | 3 min read
Front Page | Golden Electroporation; Recyclable Microarrays?; Rad! Volocity Goes Modular Courtesy of BTX GADGET WATCH | Golden Electroporation Scientists in high-throughput labs are no longer limited to chemical transfection technologies; thanks to BTX, they can opt to electroporate, instead. The San Diego-based company ( recently released a 96-well, gold-plated, disposable electroporation microplate--a high-throughput alternative to single-use cuvettes. Now, rather than