Fluorophore Fingerprinting; Gene Therapy Hybrid; Low-Level Annotation

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 differentiate between protein species in a sample by turning sequence information into physically measurable characteristics," says Rob Carlson, a research fellow emeritus at the Institute. Carlson, now at Glendale, Calif.-based Applied Minds, says he envisions the method being used in the field of proteomics to quantify protein content, and, "when used in conjunction with immunoprecipitation, [to do] mapping of protein networks." The method "utilizes simple chemistries and simple instruments, many of which are already present on lab benches worldwide," Carlson says. "It is relatively fast, is quantitative, and given recent progress in measuring signals from single molecules, can also be very sensitive." The method remains under development. --Ivan Oransky TECH WATCH | Gene Therapy Hybrid A group of Japanese researchers has developed a novel gene therapy approach that it says offers the tissue specificity and high efficiency of virus-mediated methods, without their harmful side effects. The team, led by Shun'ichi Kuroda, Osaka University, used yeast to produce "L particles," nanometer-scale fat droplets studded with envelope L protein from hepatitis B virus.1 They then loaded the particles with cargo using electroporation, and observed highly efficient, tissue-specific delivery of genes encoding green fluorescent protein or human clotting factor IX, both in vitro and in vivo. These particles can deliver pieces of DNA at least 40 kb long, which is far more than most viruses can. "That, to me, is really what is the improvement here," says gene therapy expert Eric Kmiec, department of biological sciences, Delaware Biotechnology Institute, Newark. Next, he says the team must show that it can infect other tissue types. They already have demonstrated that they could redirect the particles to nonhepatic cells; now they are developing L particles specific for various other tissues. Kuroda is currently developing a "stealth version" of the L particles to minimize their immunogenicity, and preparing the factor IX particles for clinical trials, which he anticipates within three years. --Jeffrey M. Perkel 1. T. Yamada et al., "Nanoparticles for the delivery of genes and drugs to human hepatocytes," Nat Biotechnol, e-pub ahead of print, doi:10.1038/nbt843, June 29, 2003. SOFTWARE WATCH | Low-Level Annotation Annotation pipelines coordinate the workflow of sequence-feature identification, keeping track of executed algorithms and their outputs and ensuring that all interesting features are found. Now, Genescript Annotation Pipeline, a new tool, is available to researchers working with human genomic DNA (tcag.bioinfo.sickkids.on.ca/genescript). Alexander Hudek, currently a computer science graduate student at the University of Waterloo, Canada, originally wrote Genescript to support research in the Centre for Applied Genomics at the Hospital for Sick Children, Toronto. "I created this software to speed up the process so people didn't have to do the whole thing manually, and it just grew from there," he says. Like other sequence annotation pipelines such as GeneMachine and Genotator, Genescript is used for gene prediction, EST (expressed sequence tag) similarity searching, and comparative homology searching, with added features such as dBEST searching, EST clustering, and automated gene model scoring. An open-source Perl application, Genescript supports GFF, FASTA, GenBank, and EMBL file formats. Third-party programs used by Genescript must be obtained separately, but are free to academic users. Hudek says Genescript's biggest advantage is that it is lightweight. "If somebody wants an annotation system but doesn't want to go through the trouble of setting up something like EnsEMBL locally ... this would be perhaps a solution for them," he explains. He emphasizes that the software is geared toward users looking at smaller sequences and specific regions, as the user interface is "low-level." --Aileen Constans function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (document.frm.score[2].checked) result = true; if (document.frm.score[3].checked) result = true; if (document.frm.score[4].checked) result = true; if (!result) alert("Please select") return result; } .myradio{background-color : #94bee5} Please indicate on a 1 - 5 scale how strongly you would recommend this article to your colleagues? Not recommended 1 2 3 4 5 Highly recommended Please register your vote

Fluorophore Fingerprinting; Gene Therapy Hybrid; Low-Level Annotation

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