Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

Title: Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

Patent · Tue Dec 09 00:00:00 EST 2014

OSTI ID:1165130

Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

View Patent

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-05CH11231

Assignee:: The Regents of the University of California (Oakland, CA)

Patent Number(s):: 8,906,610

Application Number:: 13/023,538

OSTI ID:: 1165130

Resource Relation:: Patent File Date: 2011 Feb 08

Country of Publication:: United States

Language:: English

References (138)

Surface plasmon resonance systems and methods having a variable charge density layer Franzen, Stefan; Brewer, Scott https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/7015471 US Patent Document 7,015,471	patent	March 2006
Surface imprinting: integration of molecular recognition and transduction Levon, Kalle; Zhou, Yanxiu; Yu, Bin https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20040058380 US Patent Application 10/242590; 20040058380	patent-application	March 2004
Multi-array, multi-specific electrochemiluminescence testing Wohlstadter, Jacob N.; Wilbur, James; Signal, George https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20040086423 US Patent Application 10/693441; 20040086423	patent-application	May 2004
Photothermal detection of nucleic acid hybridization Franzen, Stefan; Feldheim, Daniel https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20040180369 US Patent Application 10/759496; 20040180369	patent-application	September 2004
Method to ameliorate osteolysis and metastasis Mundy, Gregory; Yoneda, Yoshiyuki; Guise, Theresa https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050244414 US Patent Application 11/109470; 20050244414	patent-application	November 2005
Primer array synthesis and validation Kuimelis, Robert G.; McGall, Glenn H. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20060147969 US Patent Application 11/323067; 20060147969	patent-application	July 2006
Method and device for separating molecular targets in a complex mixture Ugolin, Nicolas; Chevillard, Sylvie; Coutant, Alexandre https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20080182758 US Patent Application 11/892672; 20080182758	patent-application	July 2008
Method of Manufacturing a Microarray Hah, Jung-hwan; Chi, Sung-min; Kim, Kyoung-seon https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20080076128 US Patent Application 11/748175; 20080076128	patent-application	March 2008
Microarray, Substrate for Microarray and Methods of Fabricating the Same Jung, Sun-Ok; Choi, Song-Jun; Ryoo, Man Hyoung https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20090137426 US Patent Application 12/137608; 20090137426	patent-application	May 2009
Functionalized Platform For Arrays Configured For Optical Detection Of Targets And Related Arrays, Methods And Systems Hoeprich, Jr., Paul D. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20090203549 US Patent Application 12/366476; 20090203549	patent-application	August 2009
Array for detecting microbes Andersen, Gary; DeSantis, Todd https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20090291858 US Patent Application 12/474204; 20090291858	patent-application	November 2009
Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge Hesselsoe, Martin; Füreder, Stephanie; Schloter, Michael The ISME Journal, Vol. 3, Issue 12 https://doi.org/10.1038/ismej.2009.78	journal	July 2009
Simultaneous analysis of microbial identity and function using NanoSIMS Li, Tianlun; Wu, Ting-Di; Mazéas, Laurent Environmental Microbiology, Vol. 10, Issue 3 https://doi.org/10.1111/j.1462-2920.2007.01478.x	journal	March 2008
Simultaneous measurement of ¹³ C- and ¹⁵ N-isotopic enrichments of threonine by mass spectrometry Godin, Jean-Philippe; Mermoud, Anne-France; Rémond, Didier Rapid Communications in Mass Spectrometry, Vol. 23, Issue 8 https://doi.org/10.1002/rcm.3976	journal	April 2009
The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function Adamczyk, J.; Hesselsoe, M.; Iversen, N. Applied and Environmental Microbiology, Vol. 69, Issue 11 https://doi.org/10.1128/AEM.69.11.6875-6887.2003	journal	November 2003
Stable isotope probing: Technical considerations when resolving ¹⁵N-labeled RNA in gradients Addison, S. L.; McDonald, I. R.; Lloyd-Jones, G. Journal of Microbiological Methods, Vol. 80, Issue 1, p. 70-75 https://doi.org/10.1016/j.mimet.2009.11.002	journal	January 2010
Bacterial 5-Nucleotidase in Aquatic Ecosystems: A Novel Mechanism of Phosphorus Regeneration Ammerman, J. W.; Azam, F. Science, Vol. 227, Issue 4692 https://doi.org/10.1126/science.227.4692.1338	journal	March 1985
Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS Behrens, S.; Losekann, T.; Pett-Ridge, J. Applied and Environmental Microbiology, Vol. 74, Issue 10 https://doi.org/10.1128/AEM.00191-08	journal	March 2008
Direct linking of microbial populations to specific biogeochemical processes by ¹³C-labelling of biomarkers Boschker, H. T. S.; Nold, S. C.; Wellsbury, P. Nature, Vol. 392, p. 801-805 https://doi.org/10.1038/33900	journal	April 1998
Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation Brodie, E. L.; DeSantis, T. Z.; Joyner, D. C. Applied and Environmental Microbiology, Vol. 72, Issue 9 https://doi.org/10.1128/AEM.00246-06	journal	September 2006
Integration of biological networks and gene expression data using Cytoscape Cline, Melissa S.; Smoot, Michael; Cerami, Ethan Nature Protocols, Vol. 2, Issue 10 https://doi.org/10.1038/nprot.2007.324	journal	September 2007
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior DeLong, E. F. Science, Vol. 311, Issue 5760 https://doi.org/10.1126/science.1120250	journal	January 2006
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
On the origin of prokaryotic species Doolittle, W. F.; Zhaxybayeva, O. Genome Research, Vol. 19, Issue 5 https://doi.org/10.1101/gr.086645.108	journal	May 2009
The role of ammonium and nitrate in spring bloom development in San Francisco Bay Dugdale, Richard C.; Wilkerson, Frances P.; Hogue, Victoria E. Estuarine, Coastal and Shelf Science, Vol. 73, Issue 1-2, p. 17-29 https://doi.org/10.1016/j.ecss.2006.12.008	journal	June 2007
Stable isotope probing — linking microbial identity to function Dumont, Marc G.; Murrell, J. Colin Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1162	journal	May 2005
A seasonal comparison of the dissolved free amino acid levels in estuarine and English channel waters Evens, Roger; Braven, James; Ian Butler, E. Science of The Total Environment, Vol. 76, Issue 1, p. 69-78 https://doi.org/10.1016/0048-9697(88)90285-9	journal	September 1988
The Global Carbon Cycle: A Test of Our Knowledge of Earth as a System Falkowski, P. Science, Vol. 290, Issue 5490 https://doi.org/10.1126/science.290.5490.291	journal	October 2000
Biomass production and variation in the biochemical profile (total protein, carbohydrates, RNA, lipids and fatty acids) of seven species of marine microalgae Fernández-Reiriz, M. J.; Perez-Camacho, A.; Ferreiro, M. J. Aquaculture, Vol. 83, Issue 1-2, p. 17-37 https://doi.org/10.1016/0044-8486(89)90057-4	journal	December 1989
Molecular diversity and ecology of microbial plankton Giovannoni, Stephen J.; Stingl, Ulrich Nature, Vol. 437, Issue 7057 https://doi.org/10.1038/nature04158	journal	September 2005
Ammonium regeneration and carbon utilization by marine bacteria grown on mixed substrates Goldman, J. C.; Dennett, M. R. Marine Biology, Vol. 109, Issue 3 https://doi.org/10.1007/BF01313502	journal	October 1991
Glucose exchanges in a salt marsh-estuary: Biological activity and chemical measurements1: Glucose exchange in an estuary Hanson, Roger B.; Snyder, James Limnology and Oceanography, Vol. 25, Issue 4 https://doi.org/10.4319/lo.1980.25.4.0633	journal	July 1980
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton Hunt, D. E.; David, L. A.; Gevers, D. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1157890	journal	May 2008
The genomic basis of trophic strategy in marine bacteria Lauro, F. M.; McDougald, D.; Thomas, T. Proceedings of the National Academy of Sciences, Vol. 106, Issue 37, p. 15527-15533 https://doi.org/10.1073/pnas.0903507106	journal	September 2009
Diversity and Metabolism of Marine Bacteria Cultivated on Dissolved DNA Lennon, J. T. Applied and Environmental Microbiology, Vol. 73, Issue 9 https://doi.org/10.1128/AEM.02674-06	journal	March 2007
ARB: a software environment for sequence data Ludwig, W. Nucleic Acids Research, Vol. 32, Issue 4 https://doi.org/10.1093/nar/gkh293	journal	February 2004
RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny Manefield, M.; Whiteley, A. S.; Griffiths, R. I. Applied and Environmental Microbiology, Vol. 68, Issue 11 https://doi.org/10.1128/AEM.68.11.5367-5373.2002	journal	November 2002
Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea Martinez, J.; Smith, Dc; Steward, Gf Aquatic Microbial Ecology, Vol. 10 https://doi.org/10.3354/ame010223	journal	January 1996
Who eats what, where and when? Isotope-labelling experiments are coming of age Neufeld, Josh D.; Wagner, Michael; Murrell, J. Colin The ISME Journal, Vol. 1, Issue 2 https://doi.org/10.1038/ismej.2007.30	journal	May 2007
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon Poretsky, Rachel S.; Sun, Shulei; Mou, Xiaozhen Environmental Microbiology, Vol. 12, Issue 3 https://doi.org/10.1111/j.1462-2920.2009.02102.x	journal	March 2010
Stable-isotope probing as a tool in microbial ecology Radajewski, Stefan; Ineson, Philip; Parekh, Nisha R. Nature, Vol. 403, Issue 6770, p. 646-649 https://doi.org/10.1038/35001054	journal	February 2000
Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina Rappé, Michael S.; Kemp, Paul F.; Giovannoni, Stephen J. Limnology and Oceanography, Vol. 42, Issue 5 https://doi.org/10.4319/lo.1997.42.5.0811	journal	July 1997
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade Rappé, Michael S.; Connon, Stephanie A.; Vergin, Kevin L. Nature, Vol. 418, Issue 6898 https://doi.org/10.1038/nature00917	journal	August 2002
Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array Singh-Gasson, Sangeet; Green, Roland D.; Yue, Yongjian Nature Biotechnology, Vol. 17, Issue 10, p. 974-978 https://doi.org/10.1038/13664	journal	October 1999
Dissolved Fatty Acids in the James River Estuary, Virginia, and Adjacent Ocean Waters Stauffer, T. B.; MacIntyre, W. G. Chesapeake Science, Vol. 11, Issue 4 https://doi.org/10.2307/1351097	journal	December 1970
Rapid ammonium cycling and concentration-dependent partitioning of ammonium and phosphate: Implications for carbon transfer in planktonic communities Suttle, Curtis A.; Fuhrman, Jed A.; Capone, Douglas G. Limnology and Oceanography, Vol. 35, Issue 2 https://doi.org/10.4319/lo.1990.35.2.0424	journal	March 1990
DNA-based stable isotope probing: a link between community structure and function Uhlík, Ondrej; Jecná, Katerina; Leigh, Mary Beth Science of The Total Environment, Vol. 407, Issue 12, p. 3611-3619 https://doi.org/10.1016/j.scitotenv.2008.05.012	journal	June 2009
Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes Cole, K. Nucleic Acids Research, Vol. 32, Issue 11 https://doi.org/10.1093/nar/gnh085	journal	June 2004
Estimating prokaryotic diversity and its limits Curtis, T. P.; Sloan, W. T.; Scannell, J. W. Proceedings of the National Academy of Sciences, Vol. 99, Issue 16, p. 10494-10499 https://doi.org/10.1073/pnas.142680199	journal	July 2002
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA DeSantis, T. Z.; Dubosarskiy, I.; Murray, S. R. Bioinformatics, Vol. 19, Issue 12 https://doi.org/10.1093/bioinformatics/btg200	journal	August 2003
Supported Membrane Composition Analysis by Secondary Ion Mass Spectrometry with High Lateral Resolution Galli Marxer, Carine; Kraft, Mary L.; Weber, Peter K. Biophysical Journal, Vol. 88, Issue 4 https://doi.org/10.1529/biophysj.104.057257	journal	April 2005
Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil Gans, J. Science, Vol. 309, Issue 5739 https://doi.org/10.1126/science.1112665	journal	August 2005
In-Situ Imaging Mass Spectrometry Analysis of Melanin Granules in the Human Hair Shaft Hallégot, Philippe; Peteranderl, Ralph; Lechene, Claude Journal of Investigative Dermatology, Vol. 122, Issue 2 https://doi.org/10.1046/j.0022-202X.2004.22217.x	journal	February 2004
An ecological perspective on bacterial biodiversity Horner-Devine, M. Claire; Carney, Karen M.; Bohannan, Brendan J. M. Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 271, Issue 1535 https://doi.org/10.1098/rspb.2003.2549	journal	January 2004
Whole-Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus Hu, P.; Brodie, E. L.; Suzuki, Y. Journal of Bacteriology, Vol. 187, Issue 24 https://doi.org/10.1128/JB.187.24.8437-8449.2005	journal	November 2005
Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis Jeffries, Thomas W.; Grigoriev, Igor V.; Grimwood, Jane Nature Biotechnology, Vol. 25, Issue 3 https://doi.org/10.1038/nbt1290	journal	March 2007
Transport of ¹³C-oleate in adipocytes measured using multi imaging mass spectrometry Kleinfeld, Alan M.; Kampf, J. Patrick; Lechene, Claude Journal of the American Society for Mass Spectrometry, Vol. 15, Issue 11, p. 1572-1580 https://doi.org/10.1016/j.jasms.2004.07.010	journal	November 2004
Phase Separation of Lipid Membranes Analyzed with High-Resolution Secondary Ion Mass Spectrometry Kraft, M. L. Science, Vol. 313, Issue 5795 https://doi.org/10.1126/science.1130279	journal	September 2006
Quantitative analysis of supported membrane composition using the NanoSIMS Kraft, Mary L.; Fishel, Simon Foster; Marxer, Carine Galli Applied Surface Science, Vol. 252, Issue 19, p. 6950-6956 https://doi.org/10.1016/j.apsusc.2006.02.116	journal	July 2006
The future of single-cell environmental microbiology Kuypers, Marcel M. M.; Jørgensen, Bo Barker Environmental Microbiology, Vol. 9, Issue 1 https://doi.org/10.1111/j.1462-2920.2006.01222_5.x	journal	January 2007
Oligonucleotide microarray for identification of Enterococcus species Lehner, Angelika; Loy, Alexander; Behr, Thomas FEMS Microbiology Letters, Vol. 246, Issue 1, p. 133-142 https://doi.org/10.1016/j.femsle.2005.04.002	journal	May 2005
Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome Lin, L. -H.; Wang, P. -L.; Rumble, D. Science, Vol. 314, Issue 5798 https://doi.org/10.1126/science.1127376	journal	October 2006
16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order "Rhodocyclales" Loy, A.; Schulz, C.; Lucker, S. Applied and Environmental Microbiology, Vol. 71, Issue 3 https://doi.org/10.1128/AEM.71.3.1373-1386.2005	journal	March 2005
Isolation of small-subunit rRNA for stable isotopic characterization MacGregor, Barbara J.; Bruchert, Volker; Fleischer, Swantje Environmental Microbiology, Vol. 4, Issue 8 https://doi.org/10.1046/j.1462-2920.2002.00324.x	journal	August 2002
Quantitative imaging of cells with multi-isotope imaging mass spectrometry (MIMS)—Nanoautography with stable isotope tracers McMahon, Greg; Glassner, Brian J.; Lechene, Claude P. Applied Surface Science, Vol. 252, Issue 19, p. 6895-6906 https://doi.org/10.1016/j.apsusc.2006.02.170	journal	July 2006
Extracellular Proteins Limit the Dispersal of Biogenic Nanoparticles Moreau, J. W.; Weber, P. K.; Martin, M. C. Science, Vol. 316, Issue 5831 https://doi.org/10.1126/science.1141064	journal	June 2007
Submicron-scale isotopic variations within biogenic ZnS record the mechanism and kinetics of extracellular metal-sulfide biomineralization Moreau, John; Weber, Peter; Martin, Michael Geochimica et Cosmochimica Acta, Vol. 70, Issue 18, A428 https://doi.org/10.1016/j.gca.2006.06.861	journal	August 2006
Microbial diversity and soil functions Nannipieri, P.; Ascher, J.; Ceccherini, M. T. European Journal of Soil Science, Vol. 54, Issue 4 https://doi.org/10.1046/j.1351-0754.2003.0556.x	journal	December 2003
Communities of microbes that inhabit the changing hindgut landscape of a subsocial beetle Nardi, James B.; Bee, Charles Mark; Miller, Lou Ann Arthropod Structure & Development, Vol. 35, Issue 1, p. 57-68 https://doi.org/10.1016/j.asd.2005.06.003	journal	March 2006
Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidarum sp. nov., isolated from green lacewings and beetles Nguyen, Nhu H.; Suh, Sung-Oui; Erbil, Cennet K. Mycological Research, Vol. 110, Issue 3, p. 346-356 https://doi.org/10.1016/j.mycres.2005.11.010	journal	March 2006
Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis Orphan, V. J. Science, Vol. 293, Issue 5529 https://doi.org/10.1126/science.1061338	journal	July 2001
Measure of carbon and nitrogen stable isotope ratios in cultured cells Peteranderl, R.; Lechene, C. Journal of the American Society for Mass Spectrometry, Vol. 15, Issue 4, p. 478-485 https://doi.org/10.1016/j.jasms.2003.11.019	journal	April 2004
Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil Pett-Ridge, J.; Firestone, M. K. Applied and Environmental Microbiology, Vol. 71, Issue 11 https://doi.org/10.1128/AEM.71.11.6998-7007.2005	journal	November 2005
Comparison between geochemical and biological estimates of subsurface microbial activities Phelps, T. J.; Murphy, E. M.; Pfiffner, S. M. Microbial Ecology, Vol. 28, Issue 3 https://doi.org/10.1007/BF00662027	journal	January 1994
Carbon and nitrogen fixation and metabolite exchange in and between individual cells of Anabaena oscillarioides Popa, Radu; Weber, Peter K.; Pett-Ridge, Jennifer The ISME Journal, Vol. 1, Issue 4 https://doi.org/10.1038/ismej.2007.44	journal	July 2007
Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing c Radajewski, Stefan; Prosser, James I.; Nedwell, David B. Microbiology, Vol. 148, Issue 8 https://doi.org/10.1099/00221287-148-8-2331	journal	August 2002
Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms Radajewski, Stefan; McDonald, Ian R.; Murrell, J. Colin Current Opinion in Biotechnology, Vol. 14, Issue 3, p. 296-302 https://doi.org/10.1016/S0958-1669(03)00064-8	journal	June 2003
Sub-cellular localisation of a ¹⁵N-labelled peptide vector using NanoSIMS imaging Römer, Winfried; Wu, Ting-Di; Duchambon, Patricia Applied Surface Science, Vol. 252, Issue 19, p. 6925-6930 https://doi.org/10.1016/j.apsusc.2006.02.183	journal	July 2006
The species concept for prokaryotes Rosselló-Mora, Ramon; Amann, Rudolf FEMS Microbiology Reviews, Vol. 25, Issue 1 https://doi.org/10.1111/j.1574-6976.2001.tb00571.x	journal	January 2001
Can biofuels finally take center stage? Schubert, Charlotte Nature Biotechnology, Vol. 24, Issue 7 https://doi.org/10.1038/nbt0706-777	journal	July 2006
Auto-associative Multivariate Regression Trees for Cluster Analysis Smyth, Christine; Coomans, Danny; Everingham, Yvette Chemometrics and Intelligent Laboratory Systems, Vol. 80, Issue 1, p. 120-129 https://doi.org/10.1016/j.chemolab.2005.09.001	journal	January 2006
Wood ingestion by passalid beetles in the presence of xylose-fermenting gut yeasts: GUT YEASTS OF PASSALID BEETLES Suh, Sung-Oui; Marshall, Christopher J.; Mchugh, Joseph V. Molecular Ecology, Vol. 12, Issue 11 https://doi.org/10.1046/j.1365-294X.2003.01973.x	journal	October 2003
Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles Suh, S. -O. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 6 https://doi.org/10.1099/ijs.0.63246-0	journal	November 2004
Microbial diversity and function in soil: from genes to ecosystems Torsvik, Vigdis; Øvreås, Lise Current Opinion in Microbiology, Vol. 5, Issue 3, p. 240-245 https://doi.org/10.1016/S1369-5274(02)00324-7	journal	June 2002
A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap J. van der Laan, Mark; Pollard, Katherine S. Journal of Statistical Planning and Inference, Vol. 117, Issue 2, p. 275-303 https://doi.org/10.1016/S0378-3758(02)00388-9	journal	December 2003
Studies on bacteria-like particles sampled from the stratosphere Wainwright, M.; Weber, P. K.; Smith, J. B. Aerobiologia, Vol. 20, Issue 3-4 https://doi.org/10.1007/s10453-004-1188-x	journal	September 2004
Reoxidation of Bioreduced Uranium under Reducing Conditions Wan, Jiamin; Tokunaga, Tetsu K.; Brodie, Eoin Environmental Science & Technology, Vol. 39, Issue 16 https://doi.org/10.1021/es048236g	journal	August 2005
Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing Wellington, Elizabeth MH; Berry, Andrew; Krsek, Martin Current Opinion in Microbiology, Vol. 6, Issue 3 https://doi.org/10.1016/S1369-5274(03)00066-3	journal	June 2003
The Difficult Road from Sequence to Function White, R. H. Journal of Bacteriology, Vol. 188, Issue 10 https://doi.org/10.1128/JB.188.10.3431-3432.2006	journal	May 2006
Prokaryotes: The unseen majority Whitman, William B.; Coleman, David C.; Wiebe, William J. PNAS https://doi.org/10.1073/pnas.95.12.6578	journal	June 1998
Microorganisms in the gut of beetles: evidence from molecular cloning Zhang, N. Journal of Invertebrate Pathology, Vol. 84, Issue 3 https://doi.org/10.1016/j.jip.2003.10.002	journal	November 2003
DNA buoyant density shifts during ¹⁵N-DNA stable isotope probing Cupples, Alison M.; Shaffer, Elizabeth A.; Chee-Sanford, Joanne C. Microbiological Research, Vol. 162, Issue 4, p. 328-334 https://doi.org/10.1016/j.micres.2006.01.016	journal	September 2007
probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007 Loy, A.; Maixner, F.; Wagner, M. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl856	journal	January 2007
Detection of DNA hybridization on indium tin oxide surfaces Moses, Selina; Brewer, Scott H.; Kraemer, Stephan Sensors and Actuators B: Chemical, Vol. 125, Issue 2, p. 574-580 https://doi.org/10.1016/j.snb.2007.03.009	journal	August 2007
High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering Bao, Paul; Frutos, Anthony G.; Greef, Charles Analytical Chemistry, Vol. 74, Issue 8 https://doi.org/10.1021/ac0111964	journal	April 2002
Exploring the new world of the genome with DNA microarrays Brown, Patrick O.; Botstein, David Nature Genetics, Vol. 21, Issue S1 https://doi.org/10.1038/4462	journal	January 1999
Formation of Thiolate and Phosphonate Adlayers on Indium−Tin Oxide: Optical and Electronic Characterization Brewer, Scott H.; Brown, Derek A.; Franzen, Stefan Langmuir, Vol. 18, Issue 18 https://doi.org/10.1021/la015720d	journal	September 2002
Pourable Artificial Diet for Rearing <I>Anoplophora glabripennis</I> (Coleoptera: Cerambycidae) and Methods to Optimize Larval Survival and Synchronize Development Keena, M. A. Annals of the Entomological Society of America, Vol. 98, Issue 4 https://doi.org/10.1603/0013-8746(2005)098[0536:PADFRA]2.0.CO;2	journal	July 2005
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments Orphan, V. J.; House, C. H.; Hinrichs, K.-U. Proceedings of the National Academy of Sciences, Vol. 99, Issue 11, p. 7663-7668 https://doi.org/10.1073/pnas.072210299	journal	May 2002
The human body as microbial observatory Relman, David A. Nature Genetics, Vol. 30, Issue 2 https://doi.org/10.1038/ng0202-131	journal	February 2002
Prevalence of Bacteria of Division TM7 in Human Subgingival Plaque and Their Association with Disease Brinig, M. M.; Lepp, P. W.; Ouverney, C. C. Applied and Environmental Microbiology, Vol. 69, Issue 3 https://doi.org/10.1128/AEM.69.3.1687-1694.2003	journal	March 2003
High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use Mayali, Xavier; Weber, Peter K.; Brodie, Eoin L. The ISME Journal, Vol. 6, Issue 6 https://doi.org/10.1038/ismej.2011.175	journal	December 2011
Urban aerosols harbor diverse and dynamic bacterial populations Brodie, E. L.; DeSantis, T. Z.; Parker, J. P. M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 1, p. 299-304 https://doi.org/10.1073/pnas.0608255104	journal	December 2006
High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment DeSantis, Todd Z.; Brodie, Eoin L.; Moberg, Jordan P. Microbial Ecology, Vol. 53, Issue 3 https://doi.org/10.1007/s00248-006-9134-9	journal	March 2007
Systems for orthogonal self-assembly of electroactive monolayers on Au and ITO: an approach to molecular electronics Gardner, Timothy J.; Frisbie, C. Daniel; Wrighton, Mark S. Journal of the American Chemical Society, Vol. 117, Issue 26, p. 6927-6933 https://doi.org/10.1021/ja00131a015	journal	July 1995
The Efficiency of Light-Directed Synthesis of DNA Arrays on Glass Substrates McGall, Glenn H.; Barone, Anthony D.; Diggelmann, Martin Journal of the American Chemical Society, Vol. 119, Issue 22, p. 5081-5090 https://doi.org/10.1021/ja964427a	journal	June 1997
Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray Schena, M.; Shalon, D.; Davis, R. W. Science, Vol. 270, Issue 5235 https://doi.org/10.1126/science.270.5235.467	journal	October 1995
Selective Functionalization of In ₂ O ₃ Nanowire Mat Devices for Biosensing Applications Curreli, Marco; Li, Chao; Sun, Yinghua Journal of the American Chemical Society, Vol. 127, Issue 19 https://doi.org/10.1021/ja0503478	journal	May 2005
Phenylphosphonic Acid Functionalization of Indium Tin Oxide: Surface Chemistry and Work Functions Koh, Sharon E.; McDonald, Krystal D.; Holt, David H. Langmuir, Vol. 22, Issue 14 https://doi.org/10.1021/la052379e	journal	July 2006
Surface characterisation of indium-tin oxide thin electrode films for use as a conducting substrate in DNA sensor development Moore, E.; O'Connell, D.; Galvin, P. Thin Solid Films, Vol. 515, Issue 4, p. 2612-2617 https://doi.org/10.1016/j.tsf.2006.03.025	journal	December 2006
Potentiometric Sensing of Chemical Warfare Agents: Surface Imprinted Polymer Integrated with an Indium Tin Oxide Electrode Zhou, Yanxiu; Yu, Bin; Shiu, Eric Analytical Chemistry, Vol. 76, Issue 10 https://doi.org/10.1021/ac035072y	journal	May 2004
A spatially resolved nucleic acid biochip based on a gradient of density of immobilized probe oligonucleotide Park, Sung Han; Krull, Ulrich Analytica Chimica Acta, Vol. 564, Issue 2, p. 133-140 https://doi.org/10.1016/j.aca.2006.01.107	journal	April 2006
Electrochemical sensor for detection of unmodified nucleic acids Popovich, N. Talanta, Vol. 56, Issue 5 https://doi.org/10.1016/S0039-9140(01)00651-8	journal	April 2002
An orientation analysis method for protein immobilized on quantum dot particles Aoyagi, Satoka; Inoue, Masae Applied Surface Science, Vol. 256, Issue 4, p. 995-997 https://doi.org/10.1016/j.apsusc.2009.05.065	journal	November 2009
An investigation of cobalt oxide based nanocrystalline thin films by secondary ion mass spectrometry Barison, Simona; Barreca, Davide; Daolio, Sergio Rapid Communications in Mass Spectrometry, Vol. 15, Issue 17 https://doi.org/10.1002/rcm.397	journal	January 2001
Improved Optical Transmittance and Crystal Characteristics of ZnS:TbOF Thin Film on Bi ₄ Ti ₃ O ₁₂ /Indium Tin Oxide/Glass Substrate by Using a SiO ₂ Buffer Layer Chia, Wei-Kuo; Yokoyama, Meiso; Yang, Cheng-Fu Japanese Journal of Applied Physics, Vol. 45, Issue 7 https://doi.org/10.1143/JJAP.45.5847	journal	July 2006
Novel Surface Modification of Indium-Tin-Oxide Films Using Ion Implantation for Organic Light-Emitting Diodes Choi, Nack-Bong; Lee, Kwang-Yeon; Yang, Myong-Su Japanese Journal of Applied Physics, Vol. 43, Issue 8A https://doi.org/10.1143/JJAP.43.5516	journal	August 2004
Analysis of thin layers and interfaces in ITO/a-Si:H/c-Si heterojunction solar cell structures by secondary ion mass spectrometry Christensen, J. S.; Ulyashin, A. G.; Maknys, K. Thin Solid Films, Vol. 511-512, p. 93-97 https://doi.org/10.1016/j.tsf.2005.12.007	journal	July 2006
Li+ distribution into V2O5 films resulting from electrochemical intercalation reactions Decker, Franco; Donsanti, Frederique; Salvi, Anna MAria Journal of the Brazilian Chemical Society, Vol. 19, Issue 4 https://doi.org/10.1590/S0103-50532008000400009	journal	January 2008
Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations Lee, Hye Jin; Wark, Alastair W.; Corn, Robert M. Langmuir, Vol. 22, Issue 12 https://doi.org/10.1021/la060223o	journal	June 2006
Surface Enzyme Kinetics for Biopolymer Microarrays: a Combination of Langmuir and Michaelis−Menten Concepts Lee, Hye Jin; Wark, Alastair W.; Goodrich, Terry T. Langmuir, Vol. 21, Issue 9 https://doi.org/10.1021/la046822h	journal	April 2005
The effect of buffer layer on the structural and electrical properties of (BaSr)TiO ₃ thin films deposited on indium tin oxide‐coated glass substrate by using a rf magnetron sputtering method Kim, Tae Song; Kim, Chong Hee; Oh, Myung Hwan Journal of Applied Physics, Vol. 76, Issue 7 https://doi.org/10.1063/1.357317	journal	October 1994
Influences of Indium Tin Oxide Layer on the Properties of RF Magnetron-Sputtered (BaSr)TiO ₃ Thin Films on Indium Tin Oxide-Coated Glass Substrate Kim, Tae Song; Oh, Myung Hwan; Kim, Chong Hee Japanese Journal of Applied Physics, Vol. 32, Issue Part 1, No. 6A https://doi.org/10.1143/JJAP.32.2837	journal	June 1993
Effect of barrier layers on the properties of indium tin oxide thin films on soda lime glass substrates Lee, Jung-Min; Choi, Byung-Hyun; Ji, Mi-Jung Thin Solid Films, Vol. 517, Issue 14, p. 4074-4077 https://doi.org/10.1016/j.tsf.2009.01.149	journal	May 2009
Characterization of polymeric light emitting diodes by SIMS depth profiling analysis Sauer, G.; Kilo, M.; Hund, M. Fresenius' Journal of Analytical Chemistry, Vol. 353, Issue 5-8 https://doi.org/10.1007/BF00321341	journal	January 1995
Micropatterning of Proteins and Mammalian Cells on Indium Tin Oxide Shah, Sunny S.; Howland, Michael C.; Chen, Li-Jung ACS Applied Materials & Interfaces, Vol. 1, Issue 11 https://doi.org/10.1021/am900508m	journal	October 2009
Exercising Spatiotemporal Control of Cell Attachment with Optically Transparent Microelectrodes S. Shah, Sunny; Lee, Ji Youn; Verkhoturov, Stanislav Langmuir, Vol. 24, Issue 13 https://doi.org/10.1021/la800231e	journal	July 2008
Label-free detection of biomolecules on microarrays using surface–colloid interaction Sun, Ye; Jacobson, K. Bruce; Golovlev, Val Analytical Biochemistry, Vol. 361, Issue 2, p. 244-252 https://doi.org/10.1016/j.ab.2006.11.002	journal	February 2007
Adsorption and electrically stimulated desorption of the triblock copolymer poly(propylene sulfide–bl-ethylene glycol) (PPS–PEG) from indium tin oxide (ITO) surfaces Tang, C.; Feller, L.; Rossbach, P. Surface Science, Vol. 600, Issue 7 https://doi.org/10.1016/j.susc.2006.02.004	journal	April 2006
DNA Attachment Chemistry at the Flexible Silicone Elastomer Surface: Toward Disposable Microarrays Vaidya, Ashish A.; Norton, Michael L. Langmuir, Vol. 20, Issue 25 https://doi.org/10.1021/la048509l	journal	December 2004
Effects of ITO thin films on microstructural and photocatalytic properties of layered TiO₂/ITO films prepared via an extended deposition period Wu, Kee-Rong; Hung, Chung-Hsuang; Tsai, Meng-Hsiu Applied Catalysis B: Environmental, Vol. 92, Issue 3-4, p. 357-366 https://doi.org/10.1016/j.apcatb.2009.08.023	journal	November 2009
Indium tin oxide films prepared by radio frequency magnetron sputtering method at a low processing temperature Zhang, Keran; Zhu, Furong; Huan, C. H. A. Thin Solid Films, Vol. 376, Issue 1-2, p. 255-263 https://doi.org/10.1016/S0040-6090(00)01418-8	journal	November 2000
Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays Wagner, Michael; Nielsen, Per H.; Loy, Alexander Current Opinion in Biotechnology, Vol. 17, Issue 1, p. 83-91 https://doi.org/10.1016/j.copbio.2005.12.006	journal	February 2006
The contribution of macrophyte-derived organic matter to microbial biomass in salt-marsh sediments: Stable carbon isotope analysis of microbial biomarkers Boschker, H. T. S.; de Brouwer, J. F. C.; Cappenberg, T. E. Limnology and Oceanography, Vol. 44, Issue 2 https://doi.org/10.4319/lo.1999.44.2.0309	journal	March 1999
Bacterial Community Dynamics across a Floristic Gradient in a Temperate Upland Grassland Ecosystem Brodie, E.; Edwards, S.; Clipson, N. Microbial Ecology, Vol. 44, Issue 3 https://doi.org/10.1007/s00248-002-2012-1	journal	October 2002
Role of Microorganisms in the Digestion of Lignocellulose by Termites Breznak, J. A.; Brune, A. Annual Review of Entomology, Vol. 39, Issue 1 https://doi.org/10.1146/annurev.en.39.010194.002321	journal	January 1994
Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.02609-06	journal	March 2007
Stable Isotope Probing with 15N2 Reveals Novel Noncultivated Diazotrophs in Soil Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.02610-06	journal	March 2007

Similar Records

Phylogenetically conserved resource partitioning in the coastal microbial loop

Journal Article · Fri Aug 11 00:00:00 EDT 2017 · The ISME Journal · OSTI ID:1165130

Bryson, Samuel; Li, Zhou; Chavez, Francisco; +6 more

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

Journal Article · Fri Apr 29 00:00:00 EDT 2016 · Frontiers in Microbiology · OSTI ID:1165130

Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou; +4 more

Stable Isotope Probing: Linking Functional Activity to Specific Members of Microbial Communities

Journal Article · Mon Mar 12 00:00:00 EDT 2007 · Soil Science Society of America Journal, 71(2):611-619 · OSTI ID:1165130

Kreuzer-Martin, Helen W

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
54 ENVIRONMENTAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Title: Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

Citation Formats

References (138)

Similar Records

Related Subjects