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Microbiological and Chemical Exposure Assessment

Publications on qPCR Rapid Methods

  • Santo Domingo, J.W., S.C. Siefring and R.A. Haugland. 2003. Real-time PCR method to detect Enterococcus faecalis in water. Biotechnol. Lett. 25:261-265.
  • Haugland, R.A., Siefring, S.C.,. Wymer, L.J., Brenner, K.P. and Dufour, A.P. 2005. Comparison of Enterococcus density measurements by quantitative polymerase chain reaction and membrane filter culture analysis at two freshwater recreational beaches. Water Research. 39:559-568.
  • Siefring, S., M. Varma, E. Atikovic, L. Wymer and R.A. Haugland. 2008. Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems. J. Water and Health. 6:225-237.
  • Wade, T.J., R.J. Calderon, K.P. Brenner, E. Sams, M. Beach, R. Haugland, L. Wymer and A. Dufour. 2008. A rapid method of measuring recreational water quality demonstrates an enhanced sensitivity of children to swimming-associated gastrointestinal illness. Epidemiology. 19:375-383.
  • Shanks, O.C., E. Atikovic, A.D. Blackwood, J. Lu, R.T. Noble, J. Santo Domingo, S. Siefring, M. Sivaganesan, and R.A. Haugland. 2008. Quantitative PCR for genetic markers of bovine fecal pollution. Applied and Environmental Microbiology. 74:745-752.
  • Sivaganesan, M., Seifring, S., Varma, M., Haugland, R.A., and O.C. Shanks. 2008. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BCM Bioinformatics 9:120
  • Haugland, R.A. and S. J. Vesper. 2007. Genetic based analytical methods for bacteria and fungi in the indoor environment. In C. Yang and P. Heinsohn (ed.), Sampling and Analysis of Indoor Microorganisms. John Wiley & Sons, Hoboken, NJ.
  • Shanks, O.C., C. Kelty, M. Sivaganesan, M. Varma, and R.A. Haugland. 2009. Quantitative PCR for genetic markers of human fecal pollution. Applied and Environmental Microbiology, 75:5507-5513.
  • Varma, M., R. Field, M. Stinson, B. Rukovets, L. Wymer and R. Haugland. 2009. Quantitative real-time PCR analysis of total and propidium monoazide-resistant fecal indicator bacteria in wastewater. Water Research, 43: 4790-4801.
  • Chern, E.C., K.P. Brenner, L. Wymer and R.A. Haugland. 2009. Comparison of Fecal Indicator Bacteria Densities in Marine Recreational Waters by QPCR. Water Quality, Exposure and Health 1: 203-214.
  • Shanks, O.C., White, K., Kelty, C.A., Hayes, S., Sivaganesan, M., Jenkins, M., Varma, M., Haugland, R.A. 2010. Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution. Appl Environ Microbiol. 76:1359-66.
  • Whitman, R.L., Ge, Z., Nevers, M.B., Boehm, A.B., Chern, E.C., Haugland, R.A., Lukasik, A.M., Molina, M., Przybyla-Kelly, K., Shively, D.A., White, E., Zepp, R.G., Byappanahalli, M.N. 2010. Relationship and variation of qPCR and culturable enterococci estimates in ambient surface waters are predictable. Environ. Sci. Technol 44: 5049–54.
  • Shanks, O.C., White, K., Kelty, C.A., Sivaganesan, M., Blannon, J., Meckes, M., Varma, M., Haugland, R.A. 2010. Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples. Environ Sci Technol. 44:6281-88.
  • Haugland, R.A., Varma, M., Sivaganesan, M., Kelty, C., Peed, L., and Shanks, O.C. 2010. 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 real time PCR. Syst. Appl. Microbiol. 33: 348–357.
  • Sivaganesan, M., Haugland, R.A., Chern, E.C., Shanks O.C. 2010. Improved strategies and optimization of calibration models for real-time PCR absolute quantification. Water Research, 44: 4726-35
  • Wade, T.J., Sams, E., Brenner, K., Haugland, R., Chern, E., Beach, M., Wymer, L., Rankin, C.C., Love, D., Li, Q., Noble, R., Dufour, A.P. 2010. Rapidly measured indicators of recreational water quality and swimming-associated illness at marine beaches: A prospective cohort study. Environmental Health. 9:66. http://www.ehjournal.net/content/9/1/66
  • Chern, E.C., Siefring, S.C., Paar, J., Doolittle, M., and Haugland, R.A. 2011. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes. Lett. Appl. Microbiol. 52: 298-306.
  • Green, H.C., Shanks, O.C., Sivaganesan, M., Haugland, R.A. and Field, K.G. 2011. Differential decay of human faecal Bacteroides in marine and freshwater. Env. Microbiol. Doi:10.111/j.1462-2920.2011.02549.x.
  • Sivaganesan, M., Siefring, S., Varma, M., Haugland, R.A. 2011. MPN estimation of qPCR target sequence recoveries from whole cell calibrator samples. J. Microbiol. Meth. 87:343-349.
  • Heaney, C.D., Sams, E., Dufour, A.P., Brenner, K.P., Haugland, R.A., Chern, E., Wing, S., Marshall, S., Love, D.C., Serre, M.J., Seed. R., Beach, M., Noble, R., Wade, T.J. 2012. Fecal indicators in sand, sand contact, and risk of enteric illness among beach-goers. Epidemiology. 23:95-106.
  • Shanks, O., Sivaganesan, M., Peed, L., Kelty, C., Blackwood, A., Greene, M., Noble, R., Bushon, R., Stelzer, E., Kinzelman, J., Anna'eva, T., Sinigalliano, C., Wanless, D. Griffith, J., Cao, Y.,Weisberg, S., Harwood, V.J., Staley, C., Oshima, K., Varma, M., Haugland, R. 2012. Inter-laboratory comparison of real-time PCR methods for quantification of general fecal indicator bacteria. Env. Sci Technol. 46:945−953.
  • Converse, R.R., Griffith J.F., Noble R.T., Haugland R.A., Schiff, K.C., Weisberg S.B., 2011. Correlation between quantitative polymerase chain reaction and culture-based methods for measuring Enterococcus over various temporal scales and three California marine beaches. Appl. Environ. Microbiol 78:1237-1242.
  • Colford, J.M. Jr., Schiff, K.C., Griffith, J.F. , Yau, V., Arnold, B.F., Wright, C.C. Gruber, J.S., Wade, T.J., Burns, S., Hayes, J., McGee, C., Gold, M., Cao, Y., Noble, R.T., Haugland, R., Weisberg, S.B. 2012. Rapid Indicators for Enterococcus and the Risk of Illness after Exposure to Urban Runoff Contaminated Marine Water: A "Natural Experiment". Water Research. In Press.

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