John R. Erb-Downward, Ph.D.

Research Investigator

Division of Pulmonary and Critical Care Medicine

University of Michigan Health System

1150 W. Medical Center Drive, 6301 MSRB III

Ann Arbor, MI, 48109-5642

(734) 936-9368; fax (734) 764-2655

Title and Contents1

Education and Training

Research Interests

Honors and Awards

Memberships in Professional Societies

Teaching

Committee, Organizational, and Volunteer Services

Bibliography

John R. Erb-Downward, Ph.D.

Research Investigator

Division of Pulmonary and Critical Care Medicine

University of Michigan Health System

1150 W. Medical Center Drive, 6301 MSRB III

Ann Arbor, MI, 48109-5642

(734) 936-9368; fax (734) 764-2655

Education and Training

08/92-05/94Wheaton College, Norton, MA

08/94-12/96Cornell University, Ithaca, NY

B.S. (Biochemistry)

12/96-08/98IA. Inc., Ann Arbor, MI

Laboratory Technician

08/98-07/05Graduate student; University of Michigan Medical School, Ann Arbor, MI

Ph.D. (Microbiology and Immunology)

09/05-12/09Postdoctoral fellow; University of Michigan Medical School, Ann Arbor, MI; Dept. of Internal Medicine, Division of Pulmonary Medicine and Critical Care

12/09-present Research Investigator; University of Michigan Medical School, Ann Arbor, MI; Dept. of Internal Medicine, Division of Pulmonary Medicine and Critical Care

Research Interests

  1. Bioinformatics
  2. Microbial Ecology
  3. Immunology
  4. Small Molecule Mediators
  5. Biochemistry
  6. Prostaglandins
  7. Allergy
  8. Disease Mechanisms

Honors and Awards

09/05-09/08NIH-NHLBI T32 HL007749, Research Fellowship, Multidisciplinary Training Program in Lung Diseases

Memberships in Professional Societies

2011 - currentSigma Xi

2008 - currentAmerican Society for Microbiology

Teaching

Cornell University Department of Biological Chemistry

01/95-05/95Teaching Assistant, Biochemistry

01/96-12/96Senior Teaching Assistant, Biochemistry

The University of Michigan

Didactic:

1999 (Spring)Teaching Assistant, Introduction to Medical Microbiology

1999 (Fall)Teaching Assistant, Immunology 642

2007 (Fall)Guest Lecturer, Eukaryotic Microbial Symbiosis

2008 (Fall)Guest Lecturer, Eukaryotic Microbial Symbiosis

Student Mentoring:

2001-2003Rachael Noggle (Undergraduate)

2011-currentRyan Muraglia (post-undergraduate)

Committee, Organizational, and Volunteer Services

Medical School

2006-currentTraining in computational methods of microbial ecology

Department

2006-currentTraining in computational methods of microbial ecology

2001-currentVolunteer Apple IT support

BibliographyPeer-Reviewed Publications

  1. Smith RH, Lemon WJ, Erb JL, Erb-Downward JR, Downward JG, Ulrich OE, Wittliff JL. Development of kinetic ligand-binding assays using a fiber optic sensor. Clin Chem. 1999; 45(9): 1683-1685. PMID: 10471688
  1. Noverr MC, Erb-Downward JR, Huffnagle GB. Production of eicosanoids and other oxylipins by pathogenic eukaryotic microbes. Clin Microbiol Rev. 2003; 16(3): 517-33 Review. PMCID: PMC164223
  1. Hernandez Y, Arora S, Erb-Downward JR, McDonald RA, Toews GB, Huffnagle GB. Distinct roles for IL-4 and IL-10 in regulating T2 immunity during allergic bronchopulmonary mycosis. J Immunol. 2005; 174(2): 1027-36. PMID: 15634927
  1. Arora S, Hernandez Y, Erb-Downward JR, McDonald RA, Toews GB, Huffnagle GB. Role of IFN-gamma in regulating T2 immunity and the development of alternatively activated macrophages during allergic bronchopulmonary mycosis. J Immunol. 2005; 174(10): 6346-56. PMID: 15879135
  1. Erb-Downward JR, Huffnagle GB. Role of oxylipins and other lipid mediators in fungal pathogenesis. Future Microbiol. 2006; 1: 219-27 Review. PMID: 17661667
  1. Erb-Downward JR, Huffnagle GB. Cryptococcus neoformans produces authentic prostaglandin E2 without a cyclooxygenase. Eukaryot Cell. 2007; 6(2): 346-50. PMCID: PMC1797952
  1. Erb-Downward JR, Noverr MC. Characterization of prostaglandin E2 production by Candida albicans. Infect Immun. 2007; 75(7): 3498-505. PMCID: PMC1932954
  1. Erb-Downward JR, Noggle RM, Williamson PR, Huffnagle GB. The role of laccase in prostaglandin production by Cryptococcus neoformans. Mol Microbiol. 2008; 68(6): 1428-37. PMID: 18410494

9.Jain AV, Zhang Y, Fields WB, McNamara DA, Choe MY, Chen GH, Erb-Downward J, Osterholzer JJ, Toews GB, Huffnagle GB, Olszewski MA. Th2 but not Th1 immune bias results in altered lung functions in a murine model of pulmonary Cryptococcus neoformans infection. Infect Immun. 2009; 77(12):5389-99. PMCID: PMC2786439

10.Milam JE, Erb-Downward JR, Chen GH, Osuchowski MF, McDonald R, Chensue SW, Toews GB, Huffnagle GB, Olszewski MA. CD11c+ Cells Are Required to Prevent Progression from Local Acute Lung Injury to Multiple Organ Failure and Death. Am J Pathol. 2010; 176: 218-226. PMCID: PMC2797884

11.Erb-Downward, JR, Thompson, DL, Han MK, Freeman CM, McCloskey L, Young VB, Toews GB, Curtis JL, Sundaram B, Martinez FJ, Huffnagle GB. Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD. PLoS One. 2011 Feb 22;6(2):e16384.PMID: 21364979

12.Luther J, Owyang SY, Takeuchi T, Cole TS, Zhang M, Liu M, Erb-Downward J, Rubenstein JH, Chen CC, Pierzchala AV, Paul JA, Kao JY. Helicobacter pylori DNA decreases pro-inflammatory cytokine production by dendritic cells and attenuates dextran sodium sulphate-induced colitis. Gut. 2011 Nov;60(11):1479-86.PMID: 21471567

13.Mason KL, Erb Downward JR, Falkowski NR, Young VB, Kao JY, Huffnagle GB. The Interplay between the Gastric Bacterial Microbiota and Candida albicans during Post-antibiotic Recolonization and Gastritis. Infect Immun. 2011 Oct 10. [Epub ahead of print]. PMID: 21986629

14.Gillilland M., Erb Downward J.R., Shen M., Toews G.B., Young V.B., and Huffnagle G.B. Ecological Succession of Bacterial Communities During Conventionalization of Germ-Free Mice. Appl Environ Microbiol. 2012 Apr;78(7):2359-66. PMID:22286988

15.Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ. Significance of the microbiome in obstructive lung disease. Thorax. 2012 May;67(5):456-63. PMID: 22318161

16.Katie L. Mason, John R. Erb Downward, Kelly D. Mason, Nicole R. Falkowski, Kathryn A. Eaton, John Y. Kao, Vincent B. Young, and Gary B. Huffnagle. Candida albicans and bacterial microbiota interactions in the cecum during re-colonization following broad spectrum antibiotic therapy. Infect Immun. 2012 Jul 9

17.Erb-Downward JR, Sadighi Akha AA, Wang J, Shen N, He B, Martinez FJ, Gyetko MR, Curtis JL, Huffnagle GB.Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond. Sci Rep. 2012;2:774.

18.Osterholzer JJ, Olszewski MA, Murdock BJ, Chen GH, Erb-Downward JR, Subbotina N, Browning K, Lin Y, Morey RE, Dayrit JK, Horowitz JC, Simon RH, Sisson TH.Implicating Exudate Macrophages and Ly-6Chigh Monocytes in CCR2-Dependent Lung Fibrosis following Gene-Targeted Alveolar Injury.J Immunol. 2013 Apr 1;190(7):3447-57

19.Erb-Downward JR., Mason KL., Falkowski NR., McDonald R., and Huffnagle GB

Analysis of the Microbiome of Mice with Increased Allergic Responsiveness Resulting from a Distrubance of the Microbiota (in revision).

Patents

  1. Method and Apparatus for Measurement of the Binding between a Protein and a Nucleotide. Patent # 6,251,688 B1 (2001). Judith L. Erb, James G. Downward, John R. Erb-Downward, Otho Ulrich

2.Method and Apparatus for Measurement of the Effect of Test Compounds on Signal Transduction at the Level of Biological Receptors. Patent # 6,3000,082 B1 (2001). Judith L. Erb, James G. Downward, John R. Erb-Downward, James L. Wittliff

3.Method and Apparatus for Measurement of the Effect of Test Compounds on Signal Transduction at the Level of Biological Receptors. Patent # 6,962,808 B2 (2005). Judith L. Erb, James G. Downward, John R. Erb-Downward, James L. Wittliff

Selected Abstracts

  1. Erb-Downward JR, Noggle RM, Williamson PR, and Huffnagle GB. Cryptococcal Laccase is Required for Prostaglandin Synthesis. 6th International Conference on Cryptococcus & Cryptococcosis, 2005.
  1. Erb-Downward JR, Noggle RM, Williamson PR, and Huffnagle GB. The Role of Laccase in Prostaglandin Production by Cryptococcus neoformans. American Society for Microbiology General Meeting 2008
  1. Erb-Downward JR and Huffnagle GB. Introducing K9 – A User Fiendly Data Analysis and Visualization Tool for Microbiome Data. Department of Internal Medicine Research Symposium 2008, University of Michigan, Ann Arbor, MI.
  1. Erb-Downward JR, Falkowski NR, and Huffnagle GB. A Model of Allergic Inflammation Resulting from a Disruption of the Host Microbiota. Department of Internal Medicine Research Symposium 2008, University of Michigan, Ann Arbor, MI.
  1. Erb-Downward JR, Falkowski NR, Mason KL, McDonald RA, and Huffnagle GB. Toward Understanding the Effects of Microbiota Disruption on the Immune System. Department of Internal Medicine Research Symposium 2009, University of Michigan, Ann Arbor, MI.
  1. Erb-Downward JR, Thompson D, Han MLK, FreemanCM, Chensue SW, Arenberg DA, Meldrum C, Getty C, McCloskey L, Gillilland MG, Young VB, Toews GB, Curtis JL, Martinez FJ, Huffnagle GB. Analysis of the Microbiome of the Normal and COPD Lung. American Thoracic International Meeting, May, 2010, New Orleans, LA.

7. J.R. Erb-Downward, D.L. Thompson, M.K. Han, C.M. Freeman, L. McCloskey, V.B. Young, G.B. Toews, J.L. Curtis, B. Sundaram, F.J. Martinez, G.B. Huffnagle

Analysis of the Lung Microbiome in the Spectrum of Smoking Disease

Keystone Conference on Microbial Communities as Drivers of Ecosystem Complexity, March 2011

8 John R. Erb-Downward, Amir A. Sadighi Akha, Juan Wang, Ning Shen, Bei He, Fernando J. Martinez, Margaret R. Gyetko, Jeffrey L. Curtis and Gary B. Huffnagle

The Use of Direct Gradient Analysis to Uncover Biological Hypotheses in 16S Survey Data and Beyond, Internal Medicine Research Symposium 2012, University of Michigan, Ann Arbor, MI.

9John R. Erb-Downward, Robert P. Dickson, MeiLan K. Han, Christine M. Freeman, Zachary Britt, Natalie Walker, Vibha N. Lama, Jeffery L. Curtis, Fernando J. Martinez,

Gary B. Huffnagle. (Abstract selected for research talk.)

A Comparative Analysis of Bacterial Phylotypes of the Lung Microbiota of Healthy, IPF and Transplanted Lungs, European Respiratory Society Lung Science Conference 2013, Estoríl, Portugal.

Software

  1. K9, a computational tool for the processing, analysis, and visualization of T-RFLP and microbiome community data.
  2. PCR Array Processing, a program for formatting and analyzing the raw data output of the LightCycler 480 for qPCR arrays used in the lab.
  3. PyroProcessing, a program for rapidly pre-processing 16S pyrosequencing data and formatting for input into RDP-Classifier or Mothur.
  4. Card-to-Card Normaization a program for performing card-to-card normalization for PCR arrays using the method detailed in J Biol Chem. 2011 Sep 2;286(35):30344-51
  5. TaxonSorter and FormatClassifierFile, two R scripts for converting the hundreds of thousands of organisms identified during pryosequencing into usable Excel-style tables.
  6. ClassifierSorter an R script written with Ryan Muraglia for turning the results of the classify.seqs() function of mothur into Excel-style table.

John R. Erb-Downward, Ph.D.05/01/121