Orin C Shanks

Summary

Affiliation: U.S. Environmental Protection Agency
Country: USA

Publications

  1. doi request reprint Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, United States
    Environ Sci Technol 46:945-53. 2012
  2. pmc Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces
    Catherine A Kelty
    US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 78:4225-32. 2012
  3. pmc Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
    Appl Environ Microbiol 82:2773-82. 2016
  4. pmc Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 74:745-52. 2008
  5. pmc Community structures of fecal bacteria in cattle from different animal feeding operations
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Dr, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 77:2992-3001. 2011
  6. pmc Quantitative PCR for genetic markers of human fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 75:5507-13. 2009
  7. pmc Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA
    Appl Environ Microbiol 76:1359-66. 2010
  8. doi request reprint Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA
    Environ Sci Technol 44:6281-8. 2010
  9. doi request reprint Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR
    Richard A Haugland
    US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
    Syst Appl Microbiol 33:348-57. 2010
  10. pmc Identification of bacterial DNA markers for the detection of human fecal pollution in water
    Orin C Shanks
    US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 73:2416-22. 2007

Detail Information

Publications29

  1. doi request reprint Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, United States
    Environ Sci Technol 46:945-53. 2012
    ..No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol...
  2. pmc Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces
    Catherine A Kelty
    US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 78:4225-32. 2012
    ....
  3. pmc Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
    Appl Environ Microbiol 82:2773-82. 2016
    ..The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark. ..
  4. pmc Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 74:745-52. 2008
    ....
  5. pmc Community structures of fecal bacteria in cattle from different animal feeding operations
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Dr, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 77:2992-3001. 2011
    ....
  6. pmc Quantitative PCR for genetic markers of human fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 75:5507-13. 2009
    ....
  7. pmc Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA
    Appl Environ Microbiol 76:1359-66. 2010
    ..Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest...
  8. doi request reprint Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA
    Environ Sci Technol 44:6281-8. 2010
    ....
  9. doi request reprint Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR
    Richard A Haugland
    US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
    Syst Appl Microbiol 33:348-57. 2010
    ..These results suggest that analyses for multiple individual Bacteroidales species may be useful in identifying human fecal pollution in environmental waters...
  10. pmc Identification of bacterial DNA markers for the detection of human fecal pollution in water
    Orin C Shanks
    US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
    Appl Environ Microbiol 73:2416-22. 2007
    ..We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds...
  11. pmc Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, MS 387, Cincinnati, OH 45268
    Appl Environ Microbiol 72:4054-60. 2006
    ....
  12. doi request reprint Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution
    Lindsay A Peed
    US Environmental Protection Agency, Cincinnati, OH, USA
    Environ Sci Technol 45:5652-9. 2011
    ....
  13. pmc Temporal assessment of the impact of exposure to cow feces in two watersheds by multiple host-specific PCR assays
    Yong Jin Lee
    National Research Council Research Associateship Programs, U S Environmental Protection Agency, Athens, Georgia 306051, USA
    Appl Environ Microbiol 74:6839-47. 2008
    ..This study also provided practical insights for implementation of microbial source-tracking practices to determine sources of fecal pollution and the influence of environmental variables on the occurrence of source-specific markers...
  14. ncbi request reprint Identification of chicken-specific fecal microbial sequences using a metagenomic approach
    Jingrang Lu
    US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, MS 387, Cincinnati, OH, USA
    Water Res 41:3561-74. 2007
    ..The competitive DNA hybridization approach used in this study can rapidly select for numerous chicken fecal metagenomic regions that can be used as potential genetic markers for fecal source tracking...
  15. doi request reprint Improved strategies and optimization of calibration models for real-time PCR absolute quantification
    Mano Sivaganesan
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
    Water Res 44:4726-35. 2010
    ..In addition, the 'mixed' model achieved uncertainty estimates similar to the 'single' model while increasing the number of available reaction wells per instrument run...
  16. pmc A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards
    Mano Sivaganesan
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
    BMC Bioinformatics 9:120. 2008
    ..Here we report the use of a Bayesian approach to generate calibration curves for the enumeration of target DNA from genomic DNA samples using absolute plasmid DNA standards...
  17. pmc Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon
    Orin C Shanks
    National Risk Management Research Laboratory, U S Enviromental Protection Agency Office of Research and Development, Cincinnati, Ohio, USA
    Appl Environ Microbiol 72:5537-46. 2006
    ..This may be important if fecal indicator counts are used as a criterion for source loading potential in receiving waters...
  18. pmc Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river
    Asja Korajkic
    National Exposure Research Laboratory, Office of Research and Development, U S Environmental Protection Agency, Cincinnati, Ohio, USA
    Appl Environ Microbiol 80:3952-61. 2014
    ..e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence. ..
  19. pmc Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 80:1588-94. 2014
    ....
  20. pmc Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources
    Asja Korajkic
    National Exposure Research Laboratory, Office of Research and Development, United States Environmental Protection Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 79:2488-92. 2013
    ..In this study, sunlight exposure and indigenous aquatic microbiota were also important contributors, whose effects on FIB also differed between water types...
  21. pmc Comparison of the microbial community structures of untreated wastewaters from different geographic locales
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 79:2906-13. 2013
    ....
  22. doi request reprint Differential decomposition of bacterial and viral fecal indicators in common human pollution types
    Pauline Wanjugi
    U S Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
    Water Res 105:591-601. 2016
    ..This study offers new insights on the decomposition of common human fecal pollution types in a subtropical marine environment with important implications for water quality management applications...
  23. doi request reprint Human fecal source identification with real-time quantitative PCR
    Orin C Shanks
    National Risk Management Research Laboratory, Office of Research and Development, U S Environmental Protection Agency, Cincinnati, OH, USA
    Methods Mol Biol 1096:85-99. 2014
    ..The following protocol includes water sample collection, filtration, DNA isolation with a sample processing control, qPCR amplification with an internal amplification control, and quality control data analysis. ..
  24. pmc Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples
    Hyatt C Green
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management and Research Laboratory, Cincinnati, Ohio, USA
    Appl Environ Microbiol 80:3086-94. 2014
    ....
  25. doi request reprint Differential decay of human faecal Bacteroides in marine and freshwater
    Hyatt C Green
    Dept of Microbiology, Oregon State University, Corvallis, OR 97331, USA
    Environ Microbiol 13:3235-49. 2011
    ....
  26. doi request reprint Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water
    Asja Korajkic
    National Exposure Research Laboratory, U S Environmental Protection Agency, Cincinnati, USA
    Water Res 69:30-9. 2015
    ....
  27. doi request reprint Development of rapid canine fecal source identification PCR-based assays
    Hyatt C Green
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268, United States
    Environ Sci Technol 48:11453-61. 2014
    ..As a proof-of-concept, these markers were detected in urban stormwater samples, suggesting a future application of newly developed methods for water quality monitoring. ..
  28. doi request reprint Dramatic improvements in beach water quality following gull removal
    Reagan R Converse
    US Environmental Protection Agency, Chapel Hill, North Carolina 27514, United States
    Environ Sci Technol 46:10206-13. 2012
    ..005). This study demonstrates that gull removal can be a highly successful beach remedial action to improve microbial water quality...
  29. ncbi request reprint Use of competitive DNA hybridization to identify differences in the genomes of bacteria
    Orin C Shanks
    U S Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
    J Microbiol Methods 66:321-30. 2006
    ..The GFE strategy we describe efficiently identified genomic differences between two enterococcal genomes, and will be widely applicable for studying genetic variation among closely related bacterial species...