OHSU

Holly Simon

Holly Simon

Email: 
Phone:  503 748-1873
Fax:  503 748-1273
Lab Phone:  503 748-1126
Website: Simon Research Group

 

Current Appointments

Associate Professor, Division of Environmental and Biomolecular Systems
Affiliate Scientist, Center for Coastal Margin Observation and Prediction

 

Education

B.S., (magna cum laude) Biology/Chemistry, Metropolitan State College of Denver, Colorado
Ph.D., Bacteriology, University of Wisconsin-Madison, 1996

 

Biography

  • University of Wisconsin-Madison, Department of Plant pathology; Research Associate 1996-2000, Assistant Scientist, 2000-2004
  • OHSU/OGI School of Science & Technology, Visiting Assistant Professor, Department of Environmental and Biolecular Systems, 2004

 

Research Interests

Projects in the lab cover a range of topics in microbial ecology, including the study of bacteria and archaea involved in carbon and nitrogen biogeochemical cycles, identification/monitoring of sentinels for environmental change, and remediation of environmental contaminants.

 

Selected Publications

Smith, MW, Maier, M, Suciu, D, Peterson, T.D., Bradstreet, T, Nakayama, J, Simon H.M. (2012). High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae 19: 169–180. (DOI: 10.1016/j.hal.2012.07.003)

Xu, M.; Schnorr, J.; Keibler, B.; Simon, H. M. (2012) Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture. Appl. Environ. Microbiol., 78, 2137-2146. (DOI: 10.1128/aem.06845-11)

Ghindilis, A. L.; Smith, M. W.; Messing, D. S.; Haynes, V. N.; Middleton, G. B.; Schwarzkopf, K. R.; Campbell, C. E.; Zhan, C.; Ulrich, B.; Frasier, M. J.; Schuele, P. J.; Evans, D. R.; Sezan, I.; Hartzell, J. W.; Simon, H. M. (2012) Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: Optimization and data analysis. Biosens. Bioelectron., 35, 87-93. (DOI: 10.1016/j.bios.2012.02.021)

Pinto-Tomas, A. A.; Sittenfeld, A.; Uribe-Lorio, L.; Chavarria, F.; Mora, M.; Janzen, D. H.; Goodman, R. M.; Simon, H. M. (2011) Comparison of midgut bacterial diversity in tropical caterpillars (Lepidoptera: Saturniidae) fed on different diets. Environ. Entomol., 40, 1111-1122.

Brauer, S. L.; Adams, C.; Kranzler, K.; Murphy, D.; Xu, M.; Zuber, P.; Simon, H. M.; Baptista, A. M.; Tebo, B. M. (2011) Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environ. Microbiol., 13, 589-603.

Smith, M. W.; Herfort, L.; Tyrol, K.; Suciu, D.; Campbell, V.; Crump, B. C.; Peterson, T. D.; Zuber, P.; Baptista, A. M.; Simon, H. M. (2010) Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. PLoS One, 5. (DOI: 10.1371/journal.pone.0013312)

Ghindilis, A. L.; Schwarzkopf, K. R.; Messing, D. S.; Sezan, I.; Schuele, P.; Zhan, C.; Smith, M. W.; Simon, H. M.; Evans, D. R. (2010) Real-time biosensor platform: fully integrated device for impedimetric assays. ECS Trans., 33, 59-68. (DOI: 10.1149/1.3484107)

Brow, C. N.; Johnson, R. O. B.; Xu, M.; Johnson, R. L.; Simon, H. M. (2010) Effects of cryogenic preservation and storage on the molecular characteristics of microorganisms in sediments. Environ. Sci. Technol., 44, 8243-8247. (DOI: 10.1021/es101641y)

Ghindilis, A. L.; Smith, M. W.; Schwarzkopf, K. R.; Zhan, C.; Evans, D. R.; Baptista, A. M.; Simon, H. M. (2009) Sensor array: impedimetric label-free sensing of DNA hybridization in real time for rapid, PCR-based detection of microorganisms. Electroanalysis, 21, 1459-1468. (DOI: 10.1002/elan.200904549)

Simon, H. M.; Jahn, C. E.; Bergerud, L. T.; Sliwinski, M. K.; Weimer, P. J.; Willis, D. K.; Goodman, R. M. (2005) Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl. Environ. Microbiol., 71, 4751-4760. (DOI: 10.1128/aem.71.8.4751-4760.2005)

Simon, H. M.; Smith, K. P.; Dodsworth, J. A.; Guenthner, B.; Handelsman, J.; Goodman, R. M. (2001) Influence of tomato genotype on growth of inoculated and indigenous bacteria in the spermosphere. Appl. Environ. Microbiol., 67, 514-520. (DOI: 10.1128/aem.67.2.514-520.2001)