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Biological Sciences Staff information

Susan Varnum

Biochemistry & Structural Biology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352
509/371-7299

Biography

Dr. Varnum has a Ph.D in Biology and ten years of experience in the analysis of proteins using MS-based proteomics and ELISA protein microarrays. She is currently a scientist in the Biological Sciences Division, Cell Biology and Biochemistry group at the Pacific Northwest National Laboratory. Her research interests focus on the identification of protein biomarkers for use in diagnostic assays. Areas of special interest include human disease (cancer, pre-diabetes), radiation exposure responses and host responses to pathogens. Recent work has focused on the detection of bacterial toxins in clinical fluids. This work is largely done within an interdisciplinary team of scientists, including biochemists, chemists, biostatisticans and epidemiologists.

Research Interests

  • The identification of protein biomarkers specific for human disease states (diabetes, cancer), radiation exposure responses, and host responses to pathogens
  • Protein microarray development
  • Diagnostic assays for the detection of bacterial toxins

Education and Credentials

  • Post-doctoral fellow, PNNL, 1996-2000
  • Post-doctoral fellow, University of Oregon, 1991-1996
  • Ph.D., Brandeis University, 1990
  • B.S., Iowa State University, 1980

Affiliations and Professional Service

  • Ad hoc member of multiple NIH special emphasis panels

PNNL Publications

2013

  • Varnum SM, MB Sowa, GJ Kim, and WF Morgan. 2013. "Radiation-induced Genomic Instability and Radiation Sensitivity." In Encyclopedia of Radiation Oncology, ed. LW Brady and TE Yaeger.  Springer, New York, NY. 
  • Zhang Y, A Gardberg, TE Edwards, B Sankaran, H Robinson, SM Varnum, and GW Buchko. 2013. "Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D." Biochimie 95(7):1379-1385.  doi:10.1016/j.biochi.2013.03.006

2012

  • Zhang Y, and SM Varnum. 2012. "The Receptor Binding Domain of Botulinum Neurotoxin Stereotype C Binds Phosphoinositides." Biochimie 94(3):920-923.  doi:10.1016/j.biochi.2011.11.004
  • Zhang Y, J Lou, KL Jenko, JD Marks, and SM Varnum. 2012. "Simultaneous and sensitive detection of six serotypes of botulinum neurotoxin using enzyme-linked immunosorbent assay-based protein antibody microarrays." Analytical Biochemistry 430(2):185-192.  doi:10.1016/j.ab.2012.08.021
  • Jin H, Y Zhang, GW Buchko, SM Varnum, H Robinson, TC Squier, and PE Long. 2012. "Structure Determination and Functional Analysis of a Chromate Reductase from Gluconacetobacter hansenii." PLoS One 7(8):Article No. e42432.  doi:10.1371/journal.pone.0042432
  • Varnum SM, BJM Webb-Robertson, JG Pounds, RJ Moore, RD Smith, C Frevert, SJ Skerret, and DS Wunschel. 2012. "Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida." Journal of Proteome Research 11(7):3690-3703. 
  • Varnum SM, DL Springer, ME Chaffee, KA Lien, BJM Webb-Robertson, KM Waters, and CA Sacksteder. 2012. "The Effects of Low Dose Irradiation on Inflammatory Response Proteins in a 3D Reconstituted Human Skin Tissue Model." Radiation Research 178(6):591-599.  doi:10.1667/RR2976.1

2011

  • Zhang Y, GW Buchko, L Qin, H Robinson, and SM Varnum. 2011. "Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions." Biochemical and Biophysical Research Communications 404(1):407-412.  doi:10.1016/j.bbrc.2010.11.134
  • Teeguarden JG, BJM Webb-Robertson, KM Waters, A Murray, E Kisin, SM Varnum, JM Jacobs, JG Pounds, RC Zangar, and A Shvedova. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120(1):123-135.  doi:10.1093/toxsci/kfq363
  • Varnum SM, BJM Webb-Robertson, N Hessol, RD Smith, and RC Zangar. 2011. "Plasma Biomarkers for Detecting Hodgkin's Lymphoma in HIV Patients." PLoS One 6(12):Article No. e29263.  doi:10.1371/journal.pone.0029263

2010

  • Zhang Y, GW Buchko, L Qin, H Robinson, and SM Varnum. 2010. "Structural analysis of the receptor binding domain of botulinum neurotoxin serotype D." Biochemical and Biophysical Research Communications 401:498-503.  doi:10.1016/j.bbrc.2010.09.063
  • Zhang Y, X Gao, L Qin, GW Buchko, H Robinson, and SM Varnum. 2010. "High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D." Acta Crystallographica. Section F 66(12):1610-1613.  doi:10.1107/S1744309110039874
  • Vomaske J, SM Varnum, R Melnychuk, P Smith, L Pasa-Tolic, JI Shutthanandan, and DN Streblow. 2010. "HCMV pUS28 initiates pro-migratory signaling via activation of Pyk2 kinase." Herpesviridae 1(1):Article No.: 2.  doi:10.1186/2042-4280-1-2
  • Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9(11):5748-5756. 

2009

  • Gonzalez RM, SM Varnum, and RC Zangar. 2009. "Sandwich ELISA Microarrays: Generating Reliable and Reproducible Assays for High-Throughput Screens ." Chapter 13 in Biomarker Methods in Drug Discovery and Development, ed. F Weng, pp. 273-290.  Humana Press, Totowa, NJ. 
  • Servoss S, RM Gonzalez, SM Varnum, and RC Zangar. 2009. "High-Throughput Analysis of Serum Antigens Using Sandwich ELISAs on Microarrays." Chapter 10 in Tumor Biomarker Discovery, Methods in Molecular Biology, vol. 520, pp. 143-150.  Humana Press, Totowa, NJ. 
  • Webb-Robertson BJM, LA McCue, N Beagley, JE McDermott, DS Wunschel, SM Varnum, JZ Hu, NG Isern, GW Buchko, K Mcateer, JG Pounds, SJ Skerret, D Liggitt, and CW Frevert. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, vol. 14, pp. 451-463.  World Scientific Publishing Co., Singapore, Singapore. 

2008

  • Daly DS, KK Anderson, AM White, RM Gonzalez, SM Varnum, and RC Zangar. 2008. "Predicting protein concentrations with ELISA microarray assays, monotonic splines and Monte Carlo simulation." Statistical Applications in Genetics and Molecular Biology 7(1):Article 21. 
  • Prichard MN, E Sztul, SL Daily, AL Perry, SL Frederick, RB Gill, CB Hartline, DN Streblow, SM Varnum, RD Smith, and ER Kern. 2008. "Human Cytomegalovirus UL97 Kinase Activity Is Required for the Hyperphosphorylation of Retinoblastoma Protein and Inhibits the Formation of Nuclear Aggresomes." Journal of Virology 82(10):5054-5067. 
  • Qian W, DT Kaleta, BA Ogata, H Jiang, T Liu, X Zhang, HM Mottaz, SM Varnum, DG Camp, II, huang, X Fang, W Zhang, and RD Smith. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7(10):1963-1973.  doi:10.1074/mcp.M800008-MCP200
  • Wu H, Q Huo, SM Varnum, G Liu, J Wang, Z Nie, J Liu, and Y Lin. 2008. "Dye-Doped Silica Nanoparticle Labels/Protein Microarray for Detection of Protein Biomarkers." The Analyst 133:1550 - 1555.  doi:10.1039/b719810h

2007

  • Varnum SM. 2007. "A Protein Microarray ELISA for the Detection of Botulinum neurotoxin A." Chapter 23 in Biodetection Technologies: Technological Responses to Biological Threats, 4th ed.  Knowledge Press, Brookline, MA. 

2006

  • White AM, DS Daly, SM Varnum, KK Anderson, N Bollinger, and RC Zangar. 2006. "ProMAT: protein microarray analysis tool ." Bioinformatics 22(10):1278-1279.  doi:10.1093/bioinformatics/btl093
  • Liu T, W Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, ME Monroe, SM Varnum, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome ." Molecular & Cellular Proteomics. MCP 5(10):1899-1913.  doi:10.1074/mcp.M600068-MCP200
  • Streblow DN, SM Varnum, RD Smith, and J Nelson. 2006. "A Proteomics Analysis of Human Cytomegalovirus Particles." Chapter 5 in Cytomegaloviruses: Molecular Biology and Immunology, ed. Matthias J. Reddehase, pp. 91-110.  Caister Academic Press, Hethersett, United Kingdom. 
  • Varnum SM, MG Warner, BP Dockendorff, NC Anheier, Jr, J Lou, JD Marks, LA Smith, MJ Feldhaus, JW Grate, and CJ Bruckner-Lea. 2006. "Enzyme-amplified protein micorarray and a fluidic renewable surface fluorescence immunoassay for botulinum neurotoxin detection using high-affinity recombinant antibodies." Analytica Chimica Acta 570(2):137-143. 

2005

  • Daly DS, AM White, SM Varnum, KK Anderson, and RC Zangar. 2005. "Evaluating concentration estimation errors in ELISA microarray experiments." BMC Bioinformatics 6:17.  doi:10.1186/1471-2105-6-17.
  • Zangar RC, SM Varnum, and N Bollinger. 2005. "Studying cellular processes and detecting disease with protein microarrays." Drug Metabolism Reviews 37(3):473-87. 

2004

  • Varnum SM, RL Woodbury, and RC Zangar. 2004. "A Protein Microarray ELISA for Screening Biological Fluids." Chapter 14 in Protein arrays : methods and protocols (Methods in Molecular Biology), vol. 264, ed. Eric Fung, pp. 161-172.  Humana Press, Totowa, NJ. 
  • Varnum SM, DN Streblow, ME Monroe, P Smith, KJ Auberry, L Pasa-Tolic, D Wang, DG Camp, II, KD Rodland, HS Wiley, W Britt, T Shenk, RD Smith, and J Nelson. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome ." Journal of Virology 78(20):10960-10966. 
  • Zangar RC, SM Varnum, CY Covington, and RD Smith. 2004. "A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays." Disease Markers 20(3):135-148. 

2003

  • Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer ." Breast Cancer Research and Treatment 80(1):87-97. 
  • Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer." Breast Cancer Research and Treatment 80(1):87-97. 
  • Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic characterization of nipple aspirate fluid: Identification of potential biomarkers of breast cancer." Breast Cancer Research and Treatment 80(1):87-97.  doi:10.1023/A:1024479106887

2002

  • Adkins JN, SM Varnum, KJ Auberry, RJ Moore, N Angell, RD Smith, DL Springer, and JG Pounds. 2002. "Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Molecular & Cellular Proteomics. MCP 1(12):947-955. 
  • Woodbury RL, SM Varnum, and RC Zangar. 2002. "Elevated HGF Levels in Sera from Breast Cancer Patients Detected Using a Protein Microarray ELISA." Journal of Proteome Research 2002(1):233-237. 

1999

  • Markillie LM, SM Varnum, PB Hradecky, and KK Wong. 1999. "Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants." Journal of Bacteriology 181(2):666-669. 

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