skip to main content
DOE Patents title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Array for detecting microbes

Abstract

The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.

Inventors:
;
Issue Date:
Research Org.:
University of California, Oakland, CA (USA).
Sponsoring Org.:
USDOE
OSTI Identifier:
1140129
Patent Number(s):
8,771,940
Application Number:
12/474,204
Assignee:
The Regents of the University of California (Oakland, CA)
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Andersen, Gary L., and DeSantis, Todd D. Array for detecting microbes. United States: N. p., 2014. Web.
Andersen, Gary L., & DeSantis, Todd D. Array for detecting microbes. United States.
Andersen, Gary L., and DeSantis, Todd D. Tue . "Array for detecting microbes". United States. https://www.osti.gov/servlets/purl/1140129.
@article{osti_1140129,
title = {Array for detecting microbes},
author = {Andersen, Gary L. and DeSantis, Todd D.},
abstractNote = {The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2014},
month = {7}
}

Patent:

Save / Share:

Works referenced in this record:

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis
journal, February 2001


Bacterial Species Determination from DNA-DNA Hybridization by Using Genome Fragments and DNA Microarrays
journal, August 2001


Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays
journal, May 1998

  • Gingeras, Thomas R.; Ghandour, Ghassan; Wang, Eugene
  • Genome Research, Vol. 8, Issue 5
  • DOI: 10.1101/gr.8.5.435

Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment
journal, October 2002


Label-free detection of 16S ribosomal RNA hybridization on reusable DNA arrays using surface plasmon resonance imaging: 16S rRNA hybridization using SPRi
journal, November 2002


Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays
journal, October 2001


Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors
journal, May 2002


Real time quantitative PCR.
journal, October 1996

  • Heid, C. A.; Stevens, J.; Livak, K. J.
  • Genome Research, Vol. 6, Issue 10, p. 986-994
  • DOI: 10.1101/gr.6.10.986

Group testing with DNA chips: generating designs and decoding experiments
conference, January 2003

  • Schliep, A.; Torney, D. C.; Rahmann, S.
  • Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003
  • DOI: 10.1109/CSB.2003.1227307

A fast and flexible approach to oligonucleotide probe design for genomes and gene families
journal, March 2007


Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays
conference, January 2003

  • Krause, A.; Krautner, M.; Meier, H.
  • International Parallel and Distributed Processing Symposium (IPDPS 2003), Proceedings International Parallel and Distributed Processing Symposium
  • DOI: 10.1109/IPDPS.2003.1213289

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities
journal, July 2006

  • Peplies, J.; Lachmund, C.; Glockner, F. O.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7
  • DOI: 10.1128/AEM.02949-05

Optimization Strategies for DNA Microarray-Based Detection of Bacteria with 16S rRNA-Targeting Oligonucleotide Probes
journal, March 2003


The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function
journal, November 2003


Microarray-Based Identification of a Novel Streptococcus pneumoniae Regulon Controlled by an Autoinduced Peptide
journal, September 2000


A(r)Ray of Hope in Analysis of the Function and Diversity of Microbial Communities
journal, April 2003

  • Polz, Martin F.; Bertilsson, Stefan; Acinas, Silvia G.
  • The Biological Bulletin, Vol. 204, Issue 2
  • DOI: 10.2307/1543558

Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation
journal, September 2006

  • Brodie, E. L.; DeSantis, T. Z.; Joyner, D. C.
  • Applied and Environmental Microbiology, Vol. 72, Issue 9
  • DOI: 10.1128/AEM.00246-06

Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA
journal, August 2003


Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray
journal, April 2005

  • DeSantis, Todd Z.; Stone, Carol E.; Murray, Sonya R.
  • FEMS Microbiology Letters, Vol. 245, Issue 2, p. 271-278
  • DOI: 10.1016/j.femsle.2005.03.016

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05

High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment
journal, March 2007


Sequence-specific identification of 18 pathogenic microorganisms using microarray technology
journal, April 2002

  • Wilson, W. J.; Strout, C. L.; DeSantis, T. Z.
  • Molecular and Cellular Probes, Vol. 16, Issue 2
  • DOI: 10.1006/mcpr.2001.0397

High-Density Microarray of Small-Subunit Ribosomal DNA Probes
journal, May 2002


Urban aerosols harbor diverse and dynamic bacterial populations
journal, December 2006

  • Brodie, E. L.; DeSantis, T. Z.; Parker, J. P. M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 1, p. 299-304
  • DOI: 10.1073/pnas.0608255104

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
journal, January 2007

  • Cole, J. R.; Chai, B.; Farris, R. J.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl889

Estimating prokaryotic diversity and its limits
journal, July 2002

  • Curtis, T. P.; Sloan, W. T.; Scannell, J. W.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 16, p. 10494-10499
  • DOI: 10.1073/pnas.142680199

Open source clustering software
journal, February 2004


Empirical and Theoretical Bacterial Diversity in Four Arizona Soils
journal, June 2002


Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa
journal, April 2007

  • Flanagan, J. L.; Brodie, E. L.; Weng, L.
  • Journal of Clinical Microbiology, Vol. 45, Issue 6
  • DOI: 10.1128/JCM.02187-06

Using ecological diversity measures with bacterial communities
journal, February 2003


Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome
journal, October 2006


Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing
journal, January 2009

  • Sagaram, U. S.; DeAngelis, K. M.; Trivedi, P.
  • Applied and Environmental Microbiology, Vol. 75, Issue 6
  • DOI: 10.1128/AEM.02404-08

Phylogenetic structure of the prokaryotic domain: The primary kingdoms
journal, November 1977

  • Woese, C. R.; Fox, G. E.
  • Proceedings of the National Academy of Sciences, Vol. 74, Issue 11
  • DOI: 10.1073/pnas.74.11.5088

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
journal, August 2007

  • Frank, D. N.; St. Amand, A. L.; Feldman, R. A.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 34, p. 13780-13785
  • DOI: 10.1073/pnas.0706625104

Microarray Applications in Microbial Ecology Research
journal, August 2006


Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria
journal, August 2010


Optimal robust non-unique probe selection using Integer Linear Programming
journal, July 2004


Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment
journal, October 2002


Probe selection for high-density oligonucleotide arrays
journal, September 2003

  • Mei, R.; Hubbell, E.; Bekiranov, S.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 20, p. 11237-11242
  • DOI: 10.1073/pnas.1534744100

Rapid quantitative profiling of complex microbial populations
journal, January 2006


Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions
journal, March 2007