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Zyomyx, DuPont, Yale University, Illumina, Corixa


Zyomyx, of Hayward, Calif., has been awarded US Patent Number 6,329,209, “Arrays of protein-capture agents and methods of use thereof.” The patent covers arrays in which antibodies or other protein-capture agents are used for the detection of proteins that are expressed in a cell or cell populations. The array technology is designed to theoretically be capable of detecting the entire complement of proteins in a cell. It can include a substrate, an organic film that covers it, and patches of protein capture agents that bind to specific target proteins.


DuPont has received a patent describing methods for identification of differentially expressed genes in microbes, US Patent Number 6,329,151, “High density sampling of differentially expressed prokaryotic mRNA.” The method involves the arbitrary priming of PCR reactions. This method is particularly effective at finding metabolic genes because these genes, when expressed, are present in high numbers. It has been used to identify genes implicated in the degradation of picric acid from Rhodococcus erythropolis strain HL PM-1, and those involved in cyclohexanol degradation in various organisms.


Yale University has received a patent for another of rolling circle amplification creator Paul Lizardi’s inventions. The patent, US Patent Number 6,329,150, is entitled “Unimolecular segment amplification and sequencing.” It refers to a method used in the universal microarrays being developed by Agilix, of which Lizardi is a cofounder. The method can involve an association step when probe molecules are tagged to target molecules, and next, an amplification operation that uses rolling circle amplification, in which the probe molecules are part of the probes or are hybridized to them. Finally, multicolor probes are used to detect the presence of tagged target molecules. This method of analyte detection, according to the patent, offers the advantages of being able to provide simultaneous detection of a large number of molecules at once, and to quantify the relative amounts of different molecules. Signals can be quantitated because rolling circle amplification is linear.


Illumina, of San Diego, Calif., has licensed the patent “Target analyte sensors utilizing microspheres,” US Patent Number 6,327,410, from Tufts University. This patent covers an invention by Tufts professor David Walt, scientific co-founder of Illumina, which is the foundation for Illumina’s BeadArray technology. The technology consists of DNA strands attached to microspheres, which then fit into the hemispherical craters at the ends of these fiber optic bundles. Up to 2,000 different genes, with thousands of beads per gene, can fit into the end of a single bundle. The company then arrays these bundles into hairbrush like matrices on a cassette that can fit into the wells of a 96-well plate. Given that each bead includes hundreds of thousands of molecules, the technology can provide a sensitive platform for analyte detection.


Corixa, of Seattle, Wash., has received US Patent Number 6,329,505, “Compositions and methods for therapy and diagnosis of prostate cancer.” The patent covers polynucleotides that encode prostate-specific proteins, as well as the proteins themselves or portions of them. It also provides for microarray- and similar nucleic acid-based diagnostic methods for detection of these biomarkers.

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.