Julie Dunning Hotopp

 http://www.tigr.org/~jdunning

Microbial Genomics

Telephone: (301)795-7812

The Institute for Genomic Research

Fax: (301)838-0208
9712 Medical Center Dr.

E-mail: jdunning@tigr.org
Rockville, MD 20850

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Education and Research Experience
2005-present
 Staff Scientist

Microbial Genomics, The Institute for Genomic Research, Rockville, MD

Mentor: Dr. Hervé Tettelin

  • Microarray-based expression studies of Wolbachia sp.
  • Comparative genome hybridization studies of Neisseria meningitidis and Wolbachia sp.
  • Sequence-based evolution analysis of Wolbachia species
  • Streptococcus, Neisseria, and Wolbachia genomics
  • Mentor research associates and undergraduate interns

2002-2005

Postdoctoral Researcher

Microbial Genomics, The Institute for Genomic Research, Rockville, MD

Mentor: Dr. Hervé Tettelin
  • Comparative genome hybridization studies of Neisseria meningitidis, Ehrlichia spp., Anaplasma spp., Neorickettsia spp., Streptococcus pneumoniae, and Wolbachia spp.
  • Microarray-based expression studies of Streptococcus agalactiae, Wolbachia sp.
  • Sequence-based evolution analysis of Wolbachia species
  • Microarray method development for obligate intracellular bacteria
  • Software development for mCGH data analysis and whole genome degenerate primer design
  • Mentor research associates and summer interns

1997-2002

Ph.D.

Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI
Mentor: Dr. Robert P. Hausinger

  • Substrate specificity, substrate-based inhibition and structural modeling of the enzyme TfdA (2,4-D/alpha-ketoglutarate dioxygenase)

1993-1997

B.S., magna cum laude, degree with distinction in research

Microbiology and Immunology, University of Rochester, Rochester, NY
Mentor: Dr. Robert E. Marquis

  • Effects of oxidative damage from inorganic and organic peroxides and/or reduced transitional metals on cell death and acid production in Streptococcus mutans GS-5

Professional Service

1998-2001

Graduate Student Workshop Coordinator 
Department of Microbiology, Michigan State University

2000-2001

Seminar Committee 
Department of Microbiology, Michigan State University

1999-2001

Biology Coordinator,
Science Theatre, Michigan State University

Teaching Experience
2006
 Guest Lecturer, Comparative Microbial Genomics: From Sequence to Significance, Johns Hopkins University, Montgomery County Campus

2000

Teaching Assistant, Biological Sciences Lab, Michigan State University

1998

Teaching Assistant, Medical Microbiology Lab, Michigan State University

1998

Teaching Assistant, Introductory Microbiology Lab, Michigan State University

1996-1997

Teaching Assistant, Introductory Chemistry Labs, University of Rochester

1995

Teaching Assistant, Introductory Biology Lecture, University of Rochester
Fellowships and Awards

2001

Rudolph Hugh Fellowship, Department of Microbiology and Molecular Genetics, Michigan State University

2001

Dr. Marvin Hensley Endowed Fellowship, College of Natural Science, Michigan State UniversityState University

2000-2001

Distinguished Fellowship, Michigan State University

1997-1998

College of Natural Science Recruiting Fellowship, College of Natural Science, Michigan State University

1997

Distinction in Research, “Oxidative and Transition Metal Ion Damage to Streptococcus mutans GS-5”, Department of Microbiology and Immunology, University of Rochester

Publications

  1. Dunning Hotopp, J. C., M. E. Clark, D. C. S. G. Oliveira, J. M. Foster, P. Fischer, M. C. Muñoz Torres, J. D. Giebel, N. Kumar, N. Ishmael, S. Wang, J. Ingram, R. V. Nene, J. Shepard, J. Tomkins, S. Richards, D. J. Spiro, E. Ghedin, B. E. Slatko, H. Tettelin, and  J. H. Werren. (2007) “Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.” Science, Epub ahead of print on ScienceExpress Aug 30, 2007. [Abstract] [Reprint]
  2. Ioannidis, P., J. C. Dunning Hotopp, P. Sapountzis, S. Siozios, G. Tasiamis, S. R. Bordenstein, L. Baldo, J. H. Werren, and K. Bourtzis. (2007) “On the Origin of DNA Replication of Wolbachia and Closely Related Bacteria.” BMC Genomics 8:182.
  3. Dunning Hotopp, J. C., R. Grifantini, N. Kumar, Y. L. Tzeng, D. Fouts, E. Frigimelica, M. Draghi, M. M. Giuliani, R. Rappuoli, D. S. Stephens, G. Grandi, and H. Tettelin. (2006) “Comparative Genomics of Neisseria meningitidis: Core Genome, Islands of Horizontal Transfer and Pathogen Specific Genes.” Microbiology 152:3691-3700. [PubMed] [Featured in Microbiology Today]
  4. Baldo, L., J. C. Dunning Hotopp, K. A. Jolley, S. R. Bordenstein, S. A. Biber, R. R. Choudhury, C. Hayashi, M. C. J. Maiden, H. Tettelin, and J. H. Werren. (2006) “A Multilocus Sequence Typing System for the endosymbiont Wolbachia.” Appl. Environ. Microbiol. 72(11):7098-7110. [PubMed]
  5. Dunning Hotopp, J. C., M. Lin, R. Madupu, J. Crabtree, S. V. Angiuoli1, J. Eisen, R. Seshadri, Q. Ren, M. Wu, T. R. Utterback, S. Smith, M. Lewis, H. Khouri, C. Zhang, N. Hua, Q. Lin, N. Ohashi, N. Zhi, W. Nelson, L. M. Brinkac, R. J. Dodson, M. J. Rosovitz, J. Sundaram, S. C. Daugherty, T. Davidsen1, A. Durkin, M. Gwinn1, D. H. Haft1, J. D. Selengut, S. A. Sullivan, N. Zafar1, L. Zhou, F. Benahmed, H. Forberger, R. Halpin, S. Mulligan, J. Robinson, Y. Rikihisa, and H. Tettelin. (2006) “Comparative Genomics of Emerging Human Ehrlichiosis Agents.” PLoS Genet 2(2):e21. [PubMed] [Featured in Nature Reviews Microbiology]
  6. Dunning Hotopp, J. C., Nelson, W. C., and S. L. Salzberg. (2005) A response to “New names for old strains? Wolbachia wSim is actually wRi.” Genome Biology 6:401. [PubMed]
  7. Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop M., Smith, D. R., Eisen, M. B. and W. C. Nelson. (2005) “Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.” Genome Biology 6:R23. [PubMed]
  8. Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop M., Smith, D. R., Eisen, M. B. and W. C. Nelson. (2005) “Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology 6:R23. [PubMed]
  9. Dunning Hotopp, J. C., Auchtung, T. A., Hogan, D. A., and R. P. Hausinger.” (2003) “Intrinsic tryptophan fluorescence as a probe of metal and alpha-ketoglutarate binding to TfdA, a mononuclear non-heme iron dioxygenase.” J. Inorg. Biochem. 93(1-2):66-70. [PubMed]
  10. Dunning Hotopp, J. C., and R. P. Hausinger. (2002) “Probing the 2,4-dichlorophenoxyacetate/-ketoglutarate dioxygenase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation.” Biochemistry 41(31):9787-94. [PubMed]
  11. Elkins, J. M., Ryle, M. J., Clifton I. J., Dunning Hotopp, J. C., Lloyd , J. S., Burzlaff, N. I., Baldwin, J. E., Hausinger, R. P., Roach, P. L. (2002) “X-ray Crystal Structure of Escherichia coli Taurine/-Ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates”  Biochemistry 41(16):5185-92. [PubMed]
  12. Dunning Hotopp, J. C., and R. P. Hausinger. (2001) “Alternative substrates of 2,4-dichlorophenoxyacetate/-ketoglutarate dioxygenase.” J. Molec. Catalysis B: Enzymatic 15(4-6):155-162.
  13. Dunning, J. C., Y. Ma, and R. E. Marquis. (1998) “Anaerobic killing of oral streptococci by reduced, transitional metal cations.” Appl. Environ. Microbiol. 64(1): 27-33. [PubMed]

Oral Presentations

  1. Dunning Hotopp, J. C. (2007) “Lateral Gene Transfer from Bacteria to Eukaryotes.” Ecology and Evolutionary Biology Seminar, University of Arizona, Tucson, AZ, USA.
  2. Dunning Hotopp, J. C. (2007) “The Impact of Lateral Gene Transfer on Prokaryotic and Eukaryotic Genomes.” Microbial Population Genomics Conference, Novartis Vaccines Research Center, Siena, Italy.
  3. Dunning Hotopp, J. C. (2006) “Emerging Ehrlichiosis Agents and Their Feminist Sibling.” TIGR/VI Seminar Series, Rockville, MD, USA.
  4. Dunning Hotopp, J. C., M. Clark, M. C. Muñoz Torres, J. Tomkins, J. Werren, and H. Tettelin. (2006) “WolbachiaGene Transfer to Insect Chromosomes.” 4th International Wolbachia Conference, Paradisius, Puerto Rico, USA.
  5. Dunning Hotopp, J. C. (2005) “Wolbachia functional genomics.” Wolbachia FIBR Meeting, Southwest Biological Research Station, AZ, USA.
  6. Dunning Hotopp, J. C., M. Ermolaeva, S. Peterson and H. Tettelin. (2004) Oral presentation entitled “Comparative analysis of sequencing and comparative genomic hybridization data.” International Conference on Analysis of Genomic Data, Boston, MA, USA.
  7. Dunning Hotopp, J. C. and H. Tettelin. (2004) “Wolbachia functional genomics.” Wolbachia FIBR Meeting, Southwest Biological Research Station, AZ, USA.

Poster Presentations

  1. Dupraw, D. L., K. Trzciński, N. Kumar, J. C. Dunning Hotopp, M. Lipsitch, H. Tettelin, S. K. Hollingshead. (2007) “Co-transformation of unselected variation during transformation in Streptococcus pneumoniae.” 107th American Society for Microbiology General Meeting, Toronto, Ontario, Canada.
  2. Dupraw, D. L., K. Trzciński, N. Kumar, J. C. Dunning Hotopp, P. Coan, M. Lipsitch, H. Tettelin, S. K. Hollingshead. (2006) “Unselected Variation During Natural Transformation in Streptococcus pneumoniae: A View from Comparative Genome Hybridization.” 1st Annual Conference on Gram-Positive Pathogens, Omaha, Nebraska, USA.
  3. Hobb, R., M. Schmidt, S. Zimmer, J. C. Dunning Hotopp, and D. Stephens. (2006)“ Integrated Bacteriophage and Invasive and Carriage Isolates of Neisseria meningitidis in the United States.” International Pathogenic Neisseria Conference 2006, Queensland, Australia.
  4. Ishmael, N., J. C. Dunning Hotopp, S. Bordenstein, S. Biber, J. Werren, and H. Tettelin. (2006) “Wolbachia Microarray-based Functional Genomics.” 4th International WolbachiaConference, Paradisius, Puerto Rico, USA.
  5. Ioannidis, P., J. C. Dunning Hotopp, P. Sapountzis, S. Siozios, G. Tsiamis, S. Bordenstein, L. Baldo, J. H. Werren, and K. Bourtzis. (2006) “On the Origin of DNA Replication of Wolbachia and Closely Related Bacteria.” 4th International Wolbachia Conference, Paradisius, Puerto Rico, USA.
  6. Lin, M., J. C. Dunning Hotopp, C. Zhang, H. Niu, H. Tettelin, and Y. Rikihisa. (2005) “Analysis of biotin biosynthesis pathways in genomes of Ehrlichia chaffeensis, Anaplasma phagocytophilum, and Neorickettsia sennetsu.” 105th American Society for Microbiology General Meeting, Atlanta, GA, USA.
  7. Kumar, N., J. C. Dunning Hotopp, S. K. Hollingshead, and H. Tettelin. (2005) “Comparative genome hybridization analysis of Serotype 4 and Serotype 6B strains of Streptococcus pneumoniae.” International Conference on Microbial Genomes, Halifax, Canada.
  8. Dunning Hotopp, J. C., R. Madupu, M. Lin, J. Crabtree, S. Angiuoli, S. Peterson, C. Zhang, Q. Lin, N. Ohashi, Y. Rikihisa, and H. Tettelin. (2004) “Comparative and functional genomics of three intracellular pathogens.” 16th International Genome Sequencing and Analysis Conference, Washington, DC, USA.
  9. Dunning Hotopp, J. C., et al. (2003) “Comparative genomics of Neisseriaspecies.” 103rd American Society for Microbiology General Meeting, Washington, DC, USA.
  10. Dunning Hotopp, J. C., P. Raghavakaimal, and R. P. Hausinger. (1999) “Characterization of alternative substrate utilization by TfdA.” 99th American Society for Microbiology General Meeting, Chicago, IL, USA.
  11. Curran, T. M., J. C. Dunning, and R. E. Marquis. (1996) Poster on the effects of oxidative stress on Streptococcus mutans GS-5. 96th American Society for Microbiology General Meeting, New Orleans, LA, USA.



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