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Recent Patents of Interest in Proteomics : Nov 1, 2007

US Patent 7,288,382. Methods for structural analysis of proteins. Inventors: Pehr Harbury; Joshua Silverman; Warham Lance Martin. Assignee: The Board of Trustees of Stanford University
Methods include analysis of substrate binding sites, sites of protein-protein interaction, 3D structure analysis, and stability, all with single amino acid resolution. Generally, methods involve the introduction of cysteine residues into a protein by translational misincorporation in vivo.

US Patent. 7,288,372. Methods for the preparation of chemically misaminoacylated tRNA via protective groups. Inventors: Jerzy Olejnik; Edyta Krzymanska-Olejnik; Sergey Mamaev; Kenneth Rothschild. Assignee: Ambergen
Methods are described for the preparation of chemically aminoacylated tRNAs to introduce markers into nascent proteins. The invention also relates to methods for non-radioactive labeling, detection, quantitation, and isolation of nascent proteins translated in a cellular or cell-free translation system using chemically aminoacylated tRNAs.

US Patent 7,286,940. Method of predicting functions of protein using ligand database. Inventors: Akiko Itai; Masazumi Imamura. Assignee: Akiko Itai
Invention pertains to a method for prediction of the biological function of one or more query proteins having predetermined or predictable steric structures using a 3D structure database. The method comprises selecting at least one bioactive compound that can bind to the query protein as ligand candidates from the database based on the capability of complex formation between the query protein and the bioactive compound. It also predicts “that a biological function of the query protein are identical or similar to the biological functions of proteins with predetermined biological functions to which the ligand candidates bind, wherein the database comprises the structure of at least one bioactive compound which binds to proteins with predetermined biological functions,” according to the abstract.

US Patent 7,285,422. Systems and methods for preparing and analyzing low volume analyte array elements. Inventors: Daniel Little; Maryanne O’ Donnell-Maloney; Charles Cantor; Huber Koster. Assignee: Sequenom
Described are methods for dispensing tools that can be used to create multi-element arrays of sample material on a substrate surface. The surface of the substrate can be geometrically altered to include wells of receiving materials. The tool can form an array of sample material while moving the pin above the substrate surface. The invention then moves the prepared sample arrays to a plate assembly that disposes the sample arrays for analysis by mass spectrometry. “To this end, a mass spectrometer is provided that generates a set of spectra signal which can be understood as indicative of the composition of the sample material under analysis,” according to the abstract.

US Patent 7,283,937. Method, apparatus, and program product for distinguishing valid data from noise data in a data set. Inventor: David Goldberg. Assignee: Palo Alto Research Center
Invention relates to a system for processing data values in a dataset for the creation of data value representation having a signal side. “The system determines a statistically significant portion of the signal side and fits a curve to the statistically significant portion which extends beyond the statistically significant portion of the signal side” according to the abstract. When the curve is determined, the system can be used to determine a data-validity confidence value for one of the data values responsive to the curve.

US Patent 7,282,572. Method and device for improving protein stability and solubility. Inventor: Mitchell Sanders. Assignee: ECI Biotech
Inventors proposed a method for expressing proteins as a fusion chimera with a domain of p26 or alpha crystalline-type proteins to improve the protein stability and solubility when over-expressed in bacteria. Genes that are of interest are cloned into the multiple cloning site of the vectors system downstream of the p26 or alpha crystalline type-protein and a thrombin cleavage site. A strong bacterial promoter drives protein expression, which is induced by the addition of 1 millimolar isopropyl beta-D-1-thiogalactopyranoside. The soluble recombinant protein is purified by a fusion tag.

US Patent 7,282,194. Nanoparticles for protein drug delivery. Inventors: Hsing-Wen Sung; Yu-Hsin Lin; Hsiang-Fa Liang; Hosheng Tu. Assignees: GP Medical, National Tsing Hua University
Invention pertains to nanoparticles made up of chitosan, poly-gamma-glutamic acid and at least one bioactive agent “characterized with a positive surface charge and their enhanced permeability for paracellular drug delivery,” according to the abstract.

US Patent 7,282,129. Traveling wave algorithms to focus and concentrate proteins in gel electrophoresis. Inventors: Meng Lean; Huangpin Ben Hsieh; John Fitch; Armin Volkel; Bryan Preas; Scott Elrod; Richard Bruce; Eric Peeters; Frank Torres; Michael Chabinyc. Assignee: Palo Alto Research Center
Invention pertains to an electrophoretic cell configuration and method employing oppositely directed traveling electrical waves. The waves travel across the cell and samples undergoing separation. Different strategies are used to direct the movement and arrangement of the samples and resulting sample patterns.

US Patent 7,280,921. Method for visualizing large-scale protein interaction data. Inventors: Kyungsook Han; Byong-Hyon Ju. Assignee: Inha University Foundation
Described is a method for visualizing large-scale protein interaction data comprising steps to produce an initial layout by placing all nodes of protein interaction data on the surface of a sphere by increasing horizontal and vertical angles of polar coordinates. A graph is also created by iterating a process “moving each node of the initial layout to an equilibrium position considering global spring forces between non-adjacent nodes as well as local spring forces between adjacent nodes on a predetermined number of times,” according to the abstract. Large-scale protein interaction data is effectively visualized in 3D space.

US Patent 7,279,679. Methods and systems for peak detection and quantitation. Inventors: William Old; Dean Thompson. Assignee: Agilent Technologies

Invention pertains to methods, systems, and computer-readable media for the identification of peaks in a 3D MS/elution time dataset. The dataset is represented as a matrix of intensity values with column and row positions “corresponding to a specific elution time and m/z value,” according to the abstract. Methods, systems, and recordable media are also provided to create a mask matrix to be overlaid on a 3D dataset represented as an image matrix, to identify a much smaller portion of the 3D dataset of interest, and to reduce the amount of processing for data of interest.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.