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Affymetrix, Emilio Barbera-Guillem, Stephanie Castro, Tomasz Heyduk, Picoliter, SomaLogic

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Affymetrix received US Patent No. 6,548,257, “Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid.” This patent covers a system for monitoring genetic expression levels by hybridizing nucleic acid samples to a high-density array of oligonucleotides, preferably as many as 1,000,000 different oligonucleotide probes, to quantify the relative abundance of the target sequences in a complex nucleic acid pool. The inventors say that, prior to this invention, it was unknown that hybridization to high density probe arrays would permit small variations in expression levels of a particular gene to be identified and quantified in a complex population of nucleic acids that outnumber the target nucleic acids by 1,000-fold to 1,000,000-fold or more. This invention provides a system of simultaneously monitoring the expression of a number of genes. The levels of transcription for virtually any number, most preferably at least 10,000 different genes, may be determined simultaneously.

Affymetrix received US Patent No. 6,546,340, “Computer-aided probability base calling for arrays of nucleic acid probes on chips.” The patent covers a computer system for analyzing nucleic acid sequences. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biolog-ical chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Emilio Barbera-Guillem of Powell, Ohio, and Stephanie Castro of Columbus, Ohio, of the company BioCrystal, received US Patent No. 6,548,171, “Fluorescent nanocrystal-embedded microspheres for fluorescence analyses.” The patent covers: a fluorescent micro-sphere made of fluorescent nanocrystals embedded in a polymer; a kit of microspheres; and a method for manufacturing them that includes a process for swelling the polymer so that the nanocrystals can enter pores, and then become entrapped. The system is used to analyze samples by physical contact and detection of the resultant fluorescent signal emitted by bound molecules.

Tomasz Heyduk of St. Louis University received US Patent No. 6,544,746, “Rapid and sensitive proximity-based assay for the detection and quantification of DNA binding proteins.” The patent covers a method to determine the level of activity of DNA binding factors, proteins, or fragments based on a change in luminescent or fluorescent signal. The system also provides for a microsphere bead attached as one part of a binding element, and a fluorochrome attached to a nucleic acid as another part. A binding event in this element affects a change in light given off and can be measured.

Picoliter of Sunnyvale, Calif., received US Patent No. 6,548,308, “Focused acoustic energy method and device for generating droplets of immiscible fluids.” The patent covers a method and device for generating extremely fine droplets, on the order of 1 picoliter, using focused acoustic energy to eject the droplets from a reservoir containing two or more fluids. Optionally, the droplets may be ejected onto discrete sites on a substrate surface to form an array.

SomaLogic of Boulder, Colo., received US Patent No. 6,544,776, “Nucleic acid ligand diagnostic biochip.” The patent covers a biochip with a solid support to which nucleic acid ligands are attached in a organized manner. The ligands bind specifically to target molecules in test mixtures such as bodily fluids.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.