Nucleic acid arrays to monitor water and other ecosystems

Details Nucleic acid arrays to monitor water and other ecosystems Nucleic acid arrays to monitor water and other ecosystems

2007-05-08

2007-05-08

Switzer, Juliet C. (Department: 1634)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S283100, C435S287200, C536S023100, C536S024300

Reexamination Certificate

active

11071849

ABSTRACT:
Disclosed are arrays for monitoring ecosystems, such as bodies of water, and methods and systems for making such arrays. In one embodiment, the array may include a plurality of oligonucleotides immobilized at known locations on a substrate, such that each location on the array is an oligonucleotide having a sequence derived from a single, predetermined operational taxonomic unit (OTU). The sequences immobilized on the array may be from known, or unknown organisms. Also disclosed are methods for identifying and isolating bioindicators diagnostic of specific ecosystems. The arrays and bioindicators of the invention may be used for rapid, and continual monitoring of ecosystems.

REFERENCES:
patent: 5429807 (1995-07-01), Matson et al.
patent: 5667667 (1997-09-01), Southern
patent: 5770367 (1998-06-01), Southern et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 6054270 (2000-04-01), Southern
patent: 6080585 (2000-06-01), Southern et al.
patent: 6150095 (2000-11-01), Southern et al.
patent: 6225067 (2001-05-01), Rogers
patent: 6228575 (2001-05-01), Gingeras et al.
patent: 6307039 (2001-10-01), Southern et al.
patent: 6309822 (2001-10-01), Fodor et al.
patent: 6355420 (2002-03-01), Chan
patent: 6537801 (2003-03-01), Ida et al.
patent: 6808879 (2004-10-01), Guillot et al.
patent: 1396270 (2003-02-01), None
patent: 0 950 720 (1999-10-01), None
patent: 2844522 (2004-03-01), None
patent: WO 96/41893 (1996-12-01), None
patent: WO 97/22720 (1997-06-01), None
patent: WO 01/61038 (2001-08-01), None
patent: WO 02/101094 (2002-12-01), None
patent: WO 04/104211 (2004-12-01), None
Campbell, Biology, 1993, Benjamin/Cummings, Redwood City, CA, 3rd ed., p. 1053.
Castiglioni, B. et al., “Development of a Universal Microarray Based on the Ligation Detection Reaction and 16SrRNA Gene Polymorphism to Target Diversity of Cyanobacteria,” Applied and Environment Microbiology, vol. 70, No. 12, pp. 7161-7172, 2004.
Adleman, L. M., “Molecular Computation of Solutions to Combinatorial Problems,” Science, vol. 266, pp. 1021-1024, 1994.
Anantharaman, V. et al., “TRAM, A Predicted RNA-Binding Domain, Common to tRNA Uracil Methylation and Adenine Thiolation Enzymes,” FEMS Microbiology Letters, vol. 197, pp. 215-221, 2001.
Anantharaman, V. et al., “Regulatory Potential, Phyletic Distribution and Evolution of Ancient, Intracellular Small-Molecule-binding Domains,” J. Mol. Biol., vol. 307, pp. 1271-1292, 2001.
Aravind, L. et al., “The α/β Fold Uracil DNA Glycosylases: A Common Origin with Diverse Fates,” Genome Biology, vol. 1, No. 4, pp. research0007.1-0007.8, 2000.
Bej, A. K. et al., “Multiplex PCR Amplification and Immobilized Capture Probes for Detection of Bacterial Pathogens and Indicators in Water,” Molecular and Cellular Probes, vol. 4, pp. 353-365, 1990.
Bassett Jr., D. E. et al., “Gene Expression Informatics—It's All in your Mine,” Nature Genetics Supplement, vol. 21, pp. 51-55, 1999.
Bowtell, D. D. L., “Options Available—From Start to Finish—for Obtaining Expression Data by Microarray,” Nature Genetics Supplement, vol. 21, pp. 25-32, 1999.
Cheung, V. G. et al., “Making and Reading Microarrays,” Nature Genetics Supplement, vol. 21, pp. 15-19, 1999.
Geourjon, C. et al., “Identification of Related Proteins with Weak Sequence Identity using Secondary Structure Information,” Protein Science, vol. 10, pp. 788-797, 2001.
Grech, A. et al., “Complete Structural Characterisation of the Mammalian andDrosophilaTRAF Genes: Implications for TRAF Evolution and the Role of RING Finger Splice Variants,” Molecular Immunology, vol. 37, pp. 721-734, 2000.
Guschin, D. Y. et al., “Oligonucleotide Microchips as Genosensors for Determinative and Environmental Studies in Microbiology,” Applied and Environmental Microbiology, vol. 63, No. 6, pp. 2397-2402, 1997.
Hacia, J. G. et al., “Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays,” Genome Research, vol. 8, pp. 1245-1258, 1998.
Kitazoe, Y. et al., “A New Theory of Phylogeny Inference through Construction of Multidimensional Vector Space,” Mol. Biol. Evol., vol. 18, No. 5, pp. 812-828, 2001.
Liberles, D. A. et al., “The Adaptive Evolution Database (TAED),” Genome Biology, vol. 2, No. 4, pp. preprint0003.1-0003.18, 2001.
Liu, Q. et al., “DNA Computing on Surfaces,” Nature, vol. 403, pp. 175-179, 2000.
Muller, S. et al., “Defining the Ancestral Karyotype of All Primates by Multidimensional Chromosome Painting between Tree Shrews, Lemurs and Humans,” Chromosoma, vol. 108, pp. 393-400, 1999.
Natale, D. A. et al., “Towards Understanding the First Genome Sequence of a Crenarchaeon by Genome Annotation using Clusters of Orthologous Groups of Proteins (COGs),” Genome Biology, vol. 1, No. 5, pp. research0009.1-0009.19, 2000.
Ramsay, G. et al., “DNA Chips: State-of-the-Art,” Nature Biotechnology, vol. 16, pp. 40-44, 1998.
Sayada, C. et al., “Genomic Fingerprinting ofYersinia enterocoliticaSpecies by Degenerate Oligonucleotide-Primed Polymerase Chain Reaction,” Electrophoresis, vol. 15, pp. 562-565, 1994.
Southern, E. et al., “Molecular Interactions on Microarrays,” Nature Genetics Supplement, vol. 21, pp. 5-9, 1999.
Woese, C. R., “Interpreting the Universal Phylogenetic Tree,” PNAS, vol. 97, No. 15, pp. 8392-8396, 2000.
Antolin, M. et al., “Genes, Description of,” Encyclopedia of Biodiversity, vol. 3, 2001.
Bavykin, S. et al., “Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis,” Applied and Environmental Microbiology, vol. 67 , p. 922-928, 2001.
Call, D. et al., “Detecting and GenotypingEscherichia coliO157:H7 using Multiplexed PCR and Nucleic Acid Microarrays,” International Journal of Food Microbiology, vol. 67, p. 71-80, 2001.
Chizhikov, V. et al., “Microarray Analysis of Microbial Virulence Factors,” Applied and Environmental Microbiology, vol. 67, No. 7, p. 3258-3263, 2001.
Friend, S. et al., “The Magic of Microarrays,” Scientific American, vol. 286, No. 2, p. 44-53, 2002.
Gibson, G. et al., “Microarrays in Ecology and Evolution: A Preview,” Molecular Ecology, vol. 11, p. 17-24, 2002.
Greer, C. et al., “Genomics Technologies for Environmental Science,” Environmental Science and Technology, vol. 35, Issue 17, p. 360A-366A, 2001.
Lucchini, S. et al., “Microarrays for Microbiologists,” Microbiology, vol. 147, p. 1403-1414, 2001.
Schonfelder, I. et al., “Relationships between Littoral Diatoms and their Chemical Environment in Northeastern German Lakes and Rivers,” J. Phycol., vol. 38, p. 66-82, 2002.
Small, J. et al., “Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays,” Applied and Environmental Microbiology, vol. 67, No. 10, p. 4708-4716, 2001.
Tatusov, R. et al., “A Genomic Perspective on Protein Families,” Science, vol. 278, p. 631-637, 1997.
Tatusov, R. et al., “The COG Database: A Tool for Genome-Scale Analysis of Protein Functions and Evolution,” Nucleic Acid Research, vol. 28, No. 1, p. 33-36, 2000.
Tatusov, R. et al., “The COG Database: New Developments in Phylogenetic Classification of Proteins from Complete Genomes,” Nucleic Acids Research, vol. 29, No. 1, p. 22-28, 2001.
Ye, R. et al., “Applications of DNA Microarrays in Microbial Systems,” Journal of Microbiological Methods, vol. 47, p. 257-272, 2001.
Yen-Lieberman, B. et al., “Nucleic Acid Amplification Techniques and Evaluation of RNA Quantitation Assays in HIV 1 Subtype B Virus,” 1998 Conference on the Laboratory Science of HIV.
Hiorns, W. et al., “Bacterial Diversity in Adirondack Mountain Lakes as Revealed by 16S rRNA Gene Sequence,”

Affiliated with

Also associated with

Rating

Nucleic acid arrays to monitor water and other ecosystems does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Nucleic acid arrays to monitor water and other ecosystems, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Nucleic acid arrays to monitor water and other ecosystems will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3810069