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

Assistant 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

Simon, H. M., C. E. Jahn, L. T. Bergerud, M. K. Sliwinski, P. J. Weimer, D. K. Willis, and R. M. Goodman. (2005). Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Applied and Environmental Microbiology 71: 4751-4760.

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.

Smith, MW, Herfort, L, Tyrol, K, Suciu, D, Campbell, V, Crump, BC, Peterson, TD, Zuber, P, Baptista, AM, Simon, HM (2010). Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients of the Columbia River coastal margin. PLoS ONE 5(10): e13312.

Ghindilis, AL, Schwarzkopf, KR, Messing, DS, Sezan, I, Zhan, C, Smith MW, Simon, HM, Evans, DR (2010). Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions, Volume 33, Chemical Sensors 9: Chemical and Biological Sensors and Analytical Systems, Las Vegas, NV.

Brow, C, Johnson, RO’B, Xu, M, Johnson, RL, Simon HM (2010). Effects of cryogenic preservation and storage on the molecular characteristics of microorganisms in sediments. Environmental Science & Technology 44(21): 8243-8247.

Bräuer SL, Adams C, Kranzler K, Murphy D, Xu M, Zuber P, Simon HM, Baptista AM and BM Tebo (2011). Culturable Rhodobacter spp. and Shewanella sp. are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology 13: 589-603; doi:10.1111/j.1462-2920.2010.02360.x

Pinto-Tomás, AA, Sittenfeld, A, Uribe, L, Chavarría, F, Mora, M, Janzen, DH, Goodman, RM and HM Simon (2011). Comparison of midgut bacterial diversity in tropical saturnid caterpillars fed on different diets. Environmental Entomology 40(5): 1111-1122; DOI: http://dx.doi.org/10.1603/EN11083.

Xu, M, Schnorr, J, Keibler, B, and HM Simon (2011). Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture. Applied and Environmental Microbiology, in revision.

Ghindilis, AL, Smith, MW, Messing, DS, Haynes, VN, Middleton, GB, Schwarzkopf, KR, Campbell, CE, Zhan, C, Ulrich, B, Frasier, MJ, Schuele, PJ, Evans, DR, Sezan, I, Hartzell, JW, and HM Simon (2011). Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: optimization and data analysis. Submitted.

Smith, MW, Maier, M, Suciu, D, Peterson, TD, Bradstreet, T, Nakayama, J, and HM Simon (2011). High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Submitted.

Smith, MW, Maier, M, Suciu, D, Peterson, TD, Bradstreet, T, Nakayama, J, and HM Simon. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Submitted.