Curriculum Vitae

CURRICULUM VITAE

 

Deborah R. Yoder-Himes, Ph.D.

Associate Professor

Department of Biology

354 Shumaker Research Building

139 Life Sciences Building

University of Louisville

Louisville, KY 40292

Phone: 502-852-0991

Email:  deborah.yoder-himes@louisville.edu

 INTERESTS

Bacterial pathogen interactions and host-pathogen interactions in respiratory infections; transmission of opportunistic pathogens from the environment to humans; the role of bacterial pathogens in natural, non-human environments; the evolution of pathogenesis; microbial ecology of temperate soils, rhizospheres, waters, and air

 

EDUCATION

2000 – 2005    Ph.D.               Microbiology and Molecular Genetics, Michigan State University (MSU)

1996 – 2000    B.S.                  Biology, Purdue University

 

PROFESSIONAL APPOINTMENTS, RESEARCH AND WORK EXPERIENCE

2019 - Present      University of Louisville, Department of Biology (PRIMARY)

                           Associate Professor, Graduate Faculty member

2013- 2018           University of Louisville, Department of Biology

                           Assistant Professor, Graduate Faculty member

2017-Present        Center for Predictive Medicine, University of Louisville - Associate Member

2015- Present       University of Louisville Dental School, Department of Oral Immunology and Infectious Diseases - Associate

                           Member, Graduate Faculty member

2013- Present       University of Louisville Medical School, Department of Microbiology and Immunology - Associate Member

2009 – 2012         Carol Basbaum Memorial Research Fellow at Harvard Medical School/Children’s Hospital Boston

                           Postdoctoral Fellow with Dr. Stephen Lory and Dr. Craig Gerard

2005 – 2008         MSU Center for Microbial Ecology

                           Postdoctoral Researcher with Dr. James M. Tiedje

2000 – 2005         MSU Department of Microbiology and Molecular Genetics

                           Graduate Assistant with Dr. Lee R. Kroos

                           Ph.D. Dissertation Title: Transcriptional Regulation of the C signal-dependent gene Omega4400 in Myxococcus 

                                 xanthus: the cis elements and trans-acting factors          

1998, 1999           City of Elkhart Wastewater Treatment Facility – Microbiology Lab

1997 - 2000           Purdue University Department of Biology

                            Undergraduate Researcher with Dr. Mark Levinthal

                            Undergraduate Thesis Title:  Global Regulation of the Methionine Biosynthetic Pathway of Escherichia coli by the Lrp Protein.

TEACHING ACTIVITY (50% OF EFFORT)

Coming to the University of Louisville, I had little formal training in teaching pedagogy.  Because of this, I started my courses in a traditional lecture-based format.  I took advantage of many of the programs offered by the Delphi Center for Teaching and Learning and am now including in my courses specific means to teach students about critical thinking through metacognition assignments, reviewing primary scientific literature, group-based activities, and higher-ordered thinking questions in my assessments.  I have also adapted modules for the course conducted in our new active learning classroom (TILL) and have developed preliminary units to engage students in non-lecture-based techniques.  In doing so, I hope to expose my upper-division biology majors to a broad range of teaching techniques and types of questions to further enhance their performance in my class, in other undergraduate course, and in their professional schools of choice.   

COURSES TAUGHT

University of Louisville

2017-2018    BIOL 601 – Graduate Seminar; Course Co-Instructor

This course is used to educate new graduate students in the Biology department on professional activities related to being a Ph.D. Students are introduced to networking skills, grant writing, scientific article writing, ethics, and finding funding opportunities.

2013-Present    BIOL 357 – General Microbiology (11 semesters); Course Instructor

This course is geared toward upper-division biology majors.  While the general purpose is to introduce students to fundamental concepts in bacteria, archaea, viruses, and eukaryotes, critical topics also include ethical quandaries facing the medical world (e.g. antibiotic resistance, the anti-vaccination movements).  Students are trained in critical thinking, metacognition, the critical analysis of scientific literature, and group-based learning strategies depending on the semester.  Examples of topics covered include cell division, how the central dogma works in bacteria, microbial genomics, ecology, symbioses, epidemiology, and controlling microbial growth.  Evaluation scores from students: ~4.5 out of 5.0 (range 4.19 – 4.59 with improvements almost every semester; in general >4.5 is considered very good in our upper division electives).

2013-Present    BIOL 358 – General Microbiology Lab (9 semesters); Course Instructor

This laboratory course is designed to complement the BIOL 357 lecture course by instructing students on the proper techniques to work with microbes, how to differentiate microbes, how abiotic factors influence microbial growth, and surveying the microbial world surrounding the students.  The culminating project is the identifications of multiple bacteria from a consortium associated in individual case reports.  This exercise gives students a taste of clinical microbiology as well. Student evaluations are for the teaching assistant, not the instructor.

2013-Present    BIOL 404, 405, 406 – Independent Research for Undergraduates; Course                                         Instructor

2013-Present    BIOL 691, 692 – Independent Research for Graduate Students; Course Instructor

These courses are designed to allow students to explore independent projects in my research lab.  Example projects include exploring the cytokine response of human and mouse cells to Burkholderia dolosa, examining the interaction between two bacterial species in biofilms, investigating the transcriptome of microbes grown in mono-culture vs co-cultures, and assessing the cytotoxicity potential and antibiotic resistance profiles of environmental isolates.  No evaluations are taken for these courses.

2018-Present    BIOL 258 – Introductory Microbiology Lab for Non-Majors

2016                BIOL 571/671 – Virology; Course Instructor

This graduate/undergraduate course was designed to introduce students to the world of viruses through short lectures and critical analyses of scientific literature.  Example topics covered include viral structures, viral genomes and replication, viral evolution, and students voted for their favorite viruses to learn about: HIV, Rabies, and MERS.  Students led the discussion of the scientific literature and were trained on critical analysis of scientific experiments.  Evaluation scores from students: 4.67 out of 5.0 (in general >4.5 is considered very good in our upper division electives).

 2016                BIOL 501 – Microbial Ecology of Antibiotic Resistance; Course Co-Instructor

Independent research opportunities are sometimes limited based on the availability of funds.  To engage students in medically-relevant bacteriology, Dr. Paul Himes and I secured a SUN Teaching and Innovation Grant from the UofL Delphi Center to conduct a course in which we trained students on experimental design, hypothesis generation, data interpretation, and ecological statistics.  Students worked in small teams to design the experiments, collect bacterial samples from local water sources, isolate the bacteria, and identify the organisms.  Ten students then joined either my lab or Dr. Himes’ lab to continue their work.  Six of these conducted bioinformatic analysis of 16S metagenomes in my lab which was amazing because we currently offer no courses in bioinformatics to undergraduates. Evaluation scores from students: ~4.5 out of 5.0.

Michigan State University

2002–2008      HM 525 and 526 – Microbiology Lab for 2nd Year Medical Students

                        Teaching Assistant for Dr. Martha Mulks

2001–2008      MMG 522 – Microbiology Lab for 1st Year Medical Students

                        Teaching Assistant for Dr. Cindy Grove Arvidson.

2005 – 2006    MMG 522 – Microbiology Lab for 1st Year Medical Students

                        Instructor for Dr. Cindy Grove Arvidson.                   

2001                MMG 408 -Advanced Microbiology Lab

                        Teaching Assistant for Dr. Loren Snyder

Purdue University

1999                BIOL 132 – Biology II: Development, Structure, and Function

                        Teaching Assistant for Dr. Laurie Iten

GUEST LECTURES

2014-Present            MBIO 687 – Microbial Pathogenesis; Guest Lecturer

2013- Present           BIOL 388 – Honors Seminar; Guest Lecturer

TEACHING AWARDS

2016-2017                Faculty Favorite Nominee, University of Louisville

2017-2018                Faculty Favorite Nominee, University of Louisville

 

TEACHING AND FACULTY DEVELOPMENT WORKSHOPS

February 2019              Celebration of Teaching and Learning, UofL; panelist

January 2019               Faculty Working Group - Teaching Transformation Spring 2019

May 2018                    Course Redesign Institute; Delphi Center,

February 2018              Celebration of Teaching and Learning, UofL; panelist

May 2017                    Course Redesign Institute; Delphi Center

March 2017                 Make Your Teaching Transform Lives; Delphi Center

January 2017               A Work in Process: Research Assignment Design; Delphi Center

September 2016          Using Community-Engaged Work in Support of Promotion and Tenure; Delphi Center

May 2016                    Ideas to Action (i2a) workshop; UofL

November 2015            How Fundamental and Powerful Concepts Foster Deep          Learning; Delphi Center

November 2015            Teaching Naked, Delphi Center Reading Circle

October 2015               Challenging Assumptions and Faulty Mental Sets; Delphi Center

October 2015               Teaching Students to Write and Communicate Effectively in Ways that Make Sense; Delphi Center

October 2015               Teaching for Critical Thinking: Tools and Techniques to Help Students Question Their Assumptions; Delphi Center Reading Circle

September 2015           How Can I Collect Meaningful Data to Inform What – and How- I Teach?; Delphi Center

May 2015                    Ideas to Action (i2a) workshop; UofL

March 2015                 Creating Self-Regulated Learners; Delphi Center Reading Circle

March 2015                 Strategies for Enhancing Your Teaching Effectiveness; Delphi Center

November 2013           Four Critical Ingredients for Stimulating Your Growth as a Teacher; New Faculty Workshop; UofL

 

GRADUATE STUDENTS MENTORED (4 thus far)

Co-author on publications in the Yoder-Himes lab

Co-author on manuscripts in preparation

David Jensen, M.S. (graduated 04/15)

Danielle Gosney, M.S.-intended (left program 2014)

Bradley Clark (Ph.D. anticipated 1/20) ††∂

Tiffany Brandt (M.S. anticipated 7/19)

Krittika Nandy, Ph.D.-intended (left program 2018)

Rhiannon Cecil (Ph.D., anticipated 07/22)

 

GRADUATE COMMITTEES SERVED (7 thus far)

Adarsh Gopinath (Ph.D., Biology) - current

Aubrey Mojewsky (Ph.D., Biology) - current

Katie Humrick (Ph.D., Biology) - current

Nicholas Short (Ph.D., Biology) - current

Margaret Wallen (Ph.D., Biology) –graduated 2017

Hima Gogegeni (Ph.D., UofL Dental School) –graduated 2017

Sarah Spaulding (Ph.D., Biology) – stepped down when project changed

 

POST-BACCALAUREATE STUDENTS MENTORED (8 thus far)

* indicates co-mentoring with Dr. Paul Himes, UofL Biology department

Co-author on manuscripts in preparation

 Morgan Robinson (2016-Present)

Laura Davis (2016-2017)

David Breedlove (2016*)

John Dickens (2016*)

Andrea Howes (2016*)

Shelly Holland (2016*)

Eric Curtsinger (2015-2016)

Danielle Gosney (2013-2014)

 

UNDERGRADUATE STUDENTS MENTORED (48 thus far)

* indicates co-mentoring with Dr. Paul Himes, UofL Biology department

Co-author on publications in the Yoder-Himes lab

Co-author on manuscripts in preparation

Completed an undergraduate thesis in the Yoder-Himes lab

Bridget Wall (2019-Present)

Shelby Rauck (2018-Present)

Lloyd Bartley (2018)

Josh Stewart (2018-Present)

Matthew Hill (2017-Present)

Kelsey Thomas (2017-2018)

Amy Priest (2016-2018)

Easton Ford (2016-Present)

Rachel Mahbubani (2016-2018)

Steve Tran (2014-2018) ‡∂

Marcus Rommelman (2017)

Grant Berry (2017)

Rachel Thompson (2016-2017)‡∂

Tiffany Brandt (2016-2017)

Akhila Ankem (2015-2017)

Kryshawna Beard (2015-2017)

Lauren Barrett (2014-2017)

Annie Koenig (2016-2017*)

Douglas Krauth (2016-2017*)

Phillip Larkin (2016*)

George Kushner (2016*)

Jacob Karem (2016*)

Taylor Mann (2016*)

Aamina Qadir (2016*)

Cara Schwartz (2016*)

Carter Simmons (2016*)

James Thomas (2016*)

James Zechella (2016*)

Hallie Lyninger (2015-2016)

Kat King (2015)

Adrienne Michael (2015)

Ruth McIntyre (2015)

Mia Starcevcic (2015)

Jimmy Mey (2014*)

Willow Dietsch (2014*)

Jae Seo (2014*)

Lindsey Duffy (2014*)

Ethan Shelton (2014*)

Jake Trimble (2014*)

Abi Zhang (2014*)

Mariam Ahmed (2014*)

Devin McBride (2014*)

Trevor Loomis (2014*)

Charlie Keown (2014*)

Molly Weatherholt (2013-2016) ††‡

Bradley Clark (2013-2015)

Trusha Mehta (2013-2014)

Emily Ostrowski (2013-2014)

Mitchell Jacobs (2013-2014*)

Christine Invergo (2013-2014*)

Nicholas Seibold (2013-2014*)

Harold Ghooray (2013-2014*)

Chris Ulmer (2013)

 

 

PROFESSIONAL ACTIVITIES (44% OF EFFORT)

The research in my lab has focused on three aspect surrounding microbes: the interactions between microbes and between microbes and hosts; antibiotic resistance reservoirs in natural niches, and the discovery of genes essential from niche survival.  Our first studies eludicated the molecular mechanisms by which Burkholderia dolosa causes virulence and interacts with the host immune response.  As a postdoc, I obtained funding to initiate this work and have continued it since coming to UofL.  This work was independent of my postdoctoral mentor’s research programs.

I have recently focused our lab’s research primarily upon three groups of bacteria: the Burkholderia cepacia complex, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia – all of which are naturally found in waters and soils, have genome similarities, are human opportunistic pathogens, can be plant-associated symbionts, and are naturally resistant to a broad set of antibiotics.  We are currently exploring fundamental biological questions related to how these organisms interact in biofilms (naturally occurring mats of cells relevant to plants and humans).

 PEER-REVIEWED PUBLICATIONS PUBLISHED OR SUBMITTED

Since coming to UofL (12 entries)

  1. Phillips-Houlbracq M, Ricard J-D, Foucrier A, Yoder-Himes D, Gaudry S, Bex J, Messika J, Margetis D, Chatel J, Dobrindt U, Denamur E, Roux D. Pathophysiology of Escherichia coli pneumonia: respective contribution of pathogenicity islands to virulence. International Journal of Medical Microbiology. In press.
  2. Yoder-Himes DR,  Roux D, Schaefers MM,  Clark BS,  Weatherholt M, Thomas K, Renaud D,   Priebe GP,  Scott D,  LiPuma JL, Gerard C. 2017. A Putative Lateral Flagella of the Cystic Fibrosis Pathogen Burkholderia dolosa Regulates Swimming Motility and Host Cytokine Production.  PLoSONE. In press. This work was initiated by me independently of my postdoctoral mentors while I was still at Harvard.  I completed most of the work either at the University of Louisvillein my own lab or with my collaborator Damien Roux in France.
  3. Miller DP, Hutcherson JA, Wang Y, Nowakowska ZM, Potempa J, Yoder-Himes DR, Scott DA, Whiteley M, Lamont RJ. 2017. Genes Contributing to Porphyromonas gingivalis Fitness in Abscess and Epithelial Cell Colonization Environments. Frontiers in Cellular and Infection Microbiology. 28 Aug. https://doi.org/10.3389/fcimb.2017.00378.
  4. Roux D, Weatherholt M, Clark B, Gadjeva M, Renaud D, Scott D, Skurnik D, Priebe GP, Pier G, Gerard C, Yoder-Himes DR. 2017. Host Immune Recognition of the Epidemic Cystic Fibrosis Pathogen Burkholderia dolosa. Infection and Immunity. March 27. doi: 10.1128/IAI.00765-16.  This work was initiated by me independently of my postdoctoral mentors while I was still at Harvard.  I completed most of the work either at the University of Louisvillein my own lab or with my collaborator Damien Roux in France.
  5. Schaefers MM, Liao TL, Boisvert NM, Roux D, Yoder-Himes D, Priebe GP. 2016. An Oxygen-Sensing Two-Component System in the Burkholderia cepacia complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity. PLoS Pathogens. Jan 3;13(1). doi: 10.1371/journal.ppat.1006116.
  6. Hutcherson JA, Gogeneni H, Yoder-Himes D, Hendrickson EL, Hackett M, Whiteley M, Lamont RJ, Scott DA. 2015. Comparison of inherently essential genes of Porphyromonas gingivalis identified in two transposon sequencing libraries. Molecular Oral Microbiology. Sep 11. doi: 10.1111/omi.12135.
  7. Lawrenz M, Biller A, Cramer D, Kranzle J, Sotsky J, Vanover C, Yoder-Himes D, Pollard A, Warawa J. 2015. Development of a lung-specific disease model for therapeutic efficacy testing targeting multidrug resistant Pseudomonas aeruginosa. Pathogens and Disease. 73(5). doi: 10.1093/femspd/ftv025.
  8. Gutierrez M, Yoder-Himes DR, Warawa J. 2015.Comprehensive identification of virulence factors required for respiratory melioidosis using Tn-seq mutagenesis. Frontiers in Cellular and Infection Microbiology. Nov 4; 5:78. doi: 10.3389/fcimb.2015.00078. (Cited > 12 times as of 1/4/18)
  9. Siddiqui H, Yoder-Himes D, Mizgalska D, Nguyen K, Potempa J, and Olsen I. 2014. Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984). Genome Announcements.  Sept-Oct 2(5). doi: 10.1128/genomeA.00947-14. (Cited > 16 times as of 1/4/18)
  10.  
  11. Skurnik DS, Roux D, Cattoir V, Danilchanka O, Lu X, Yoder-Himes DR, Han K, Guillard T, Jiang D, Gaultier C, Guerin F, Aschard H, Leclercq R, Mekalanos JJ, Lory S, and Pier GB. 2013. Enhanced in vivo fitness of carbapenem-resistant oprD mutants of Pseudomonas aeruginosa revealed through high-throughput sequencing. Proceedings of the National Academy of Sciences USA. Dec 17; 110(51):20747-52. doi: 10.1073/pnas.1221552110.  My work on this article was conducted in my position at the University of Louisville. (Cited >  61 times as of 1/4/18)
  12. Skurnik DS, Roux DR, Haschard, Cattoir V, Yoder-Himes DR, Lory S, Pier GB. 2013. A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries. PLoS Pathogens. 9(9):e1003582. doi: 10.1371/journal.ppat.1003582. Recommended by Faculty of 1000 (Oct 2013). My work on this article was conducted in my position at the University of Louisville. (Cited > 60 times as of 1/4/18)
  13. Dong TG, Ho BT, Yoder-Himes DR, Mekalanos JJ. 2013. Identification of T6SS-dependent effector and immunity proteins by Tn-Seq in Vibrio cholerae. Proceedings of the National Academy of Sciences USA. Feb 12; 110(7):2623-8. doi: 10.1073/pnas.1222783110. Cited > 141 times (as of 1/4/2018)

Prior to UofL (10 entries)

  1. Wurtzel O*, Yoder-Himes DR*, Han K*, Dandekar AA, Edelheit S, Greenberg EP, Sorek R, Lory S. 2012. The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature.  PLoS Pathogens.  8(9):e1002945. [September 2012]. * authors contributed equally. doi: 10.1371/journal.ppat.1002945. (Cited > 118 times as of 1/4/18)
  2. Oh S-D, Buddenborg S, Yoder-Himes DR, Tiedje JM, Konstantinidis KT .2012. Genomic Diversity of Escherichia Isolates from Diverse Habitats.  PLoSONE. 7(10):e47005. doi: 10.1371/journal.pone.0047005. (Cited >23 times as of 1/4/18)
  3. Kimelman A, Levy A, Sberro H, Kidron S, Leavitt A, Amitai G, Yoder-Himes DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R. 2012. A vast collection of microbial genes that are toxic to bacteria. Genome Research. Apr; 22(4):802-9. doi: 10.1101/gr.133850. (Cited > 43 times as of 1/4/18)
  4. Yang X, Medvin D, Yoder-Himes DR, Lory S, Narasimhan G. 2011. CloG: A pipeline for closing gaps in a draft assembly using short reads. Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 202-207.  (Cited > 10 times as of 1/4/18)
  5. Oh S-D*, Yoder-Himes DR*, Tiedje JM, Konstantinidis KT. 2010. Evaluating the performance of oligonucleotide microarrays for strains of increasing genetic divergence to the reference strain. Applied and Environmental Microbiology. May; 76(9): 2980–2988. * authors contributed equally. doi: 10.1128/AEM.02826-09. (Cited > 17 times as of 1/4/18)
  6. Yoder-Himes DR, Konstantinidis KT, Tiedje JM. 2010. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics.  PLoS ONE 5(1): e8724. doi: 10.1371/journal.pone.0008724. (Cited > 28 times as of 1/4/18)
  7. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R.  2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proceedings of the National Academy of Sciences USA. 2009 Mar 10;106(10):3976-81.  doi: 10.1073/pnas.0813403106. Recommended by Faculty of 1000 (Mar 2009).  Cited > 245 times (as of 1/4/2018)
  8. Yoder DR, Kroos L. 2006. Regulation of the Myxococcus xanthus C-Signal-Dependent W4400 Promoter by the Essential Developmental Protein FruA. Journal of Bacteriology. July 188(14):5167-5176. doi: 10.1128/JB.00318-06. doi:    10.1128/JB.186.12.3766-3776.2004. (Cited > 21 times as of 1/4/18)
  9. Yoder DR, Kroos L. 2004. Mutational Analysis of the Myxococcus xanthus W4499 Promoter Region Reveals Shared and Unique Properties in Comparison with Other C-signal-dependent Promoters. Journal of Bacteriology. Jun; 186(12):3766-76. (Cited > 15 times as of 1/4/18)
  10. Yoder DR, Kroos L. 2004. Mutational analysis of the Myxococcus xanthus W4400 promoter region provides insight into developmental gene regulation by C signaling. Journal of Bacteriology. Feb; 186(3):661-71. (Cited > 16 times as of 1/4/18)

 Complete List of Published Work in MyBibliography:   http://www.ncbi.nlm.nih.gov/sites/myncbi/deborah.yoder-himes.1/bibliography/42730214/public/?sort=date&direction=descending or find links to most of these articles on the Selected Publicationspage

MANUSCRIPTS IN PREPARATION

  1. TranS, Clark BS, Soucy T, Himes P, Yoder-Himes DR. Surveying bacteria resistant to colistin and tobramycin in natural environments. To be submitted to Applied and Environmental Microbiology.
  2. Hundley T, Brandt TJ, Nandy K, Rommelman M Yoder-Himes DR. Imaging and Quantifying Polymicrobial Biofilms. To be submitted to Frontiers in Microbiology.
  3. Robinson M, Ford E, Priest A, Mahbubani R, Himes P, Yoder-Himes DR. Microbial populations resistant to vancomycin and colistin from freshwater sources. Submitted to Frontiers in Microbiology.
  4. Clark BS, Soucy T, Yoder-Himes DR. The role of the TolQRAB-Pal complex in Burkholderia dolosa. To be submitted to the Journal of Bacteriology.

 

GRANTS AND FELLOWSHIPS

Funded or in Review (22 entries, 18 since joining UofL)

2018    In Vitro Assessments of Antimicrobial Activity. National Institutes of Health RFP.  Collaborative Grant to use CPM facilities to evaluate new antibiotics.  Role: Key Personnel with Bill Severson, Center for Predictive Medicine (PI).  In review.

2018    University of Louisville Emerging and Re-emerging Infection Diseases (ERID) Research Education Program. National Institutes of Health R25. Role: Mentor with Lawrenz (PI). In review.

2017    Predicting Bacterial Interactions in Multispecies Biofilms. National Science Foundation. MCB division. $1.2 million/4 years. Four year grant to study how environment, community, time, and genotypes influence the structure and function of multi-species communities of bacteria in biofilms. Role: PI. In review.

2017    Prenatal ETS: Impact of bacterial community composition on Neonatal Colon Development. National Institutes of Health R15. $300,000/3 years. Three year grant to study the effects of cigarette smoke on fetal and maternal microbiomes. Role: Co-investigator with Michele Pisano (UofL Dental School) and Rachel Neal (UofL School of Public Health). In review.

2017    Kentucky Center of Epitranscriptomics Research. National Science Foundation EPSCoR grant. $6,800,000/5 years.  Five year study to elucidate the role of mRNA-modifications in bacteria and insects and to develop the nation’s first center dedicated to studying epitranscriptomics. Role: co-PI with Xiang Zhang. In review.

2017    Bridge to Undergraduate Success (BUS).  National Institutes of Health R25. Collaborative grant to develop resources and opportunities for underrepresented groups in biology. Role: Mentor (one of ~20 potential UofL mentors, PIs – Irving Joshua and Sham Kakar, UofL Department of Physiology). In review.

2017    Identifying Risks Associated with Antibiotic Resistant Bacteria in Louisville Environments. Kentucky Bioinformatics Research Infrastructure Network.  Pilot grant to study genomic diversity of antibiotic resistant isolates from Kentucky. Role: co-PI. Funded.

2017    Burkholderia cenocepacia inhibition of Staphylococcus aureus biofilms. Cystic Fibrosis Foundation. $106,000. Two year grant to elucidate the mechanism by which a bacteria pathogen inhibits biofilm formation and maintenance of another. Role: PI. Funded.  Start date moved to April 2018 due to lack of tuition remission at UofL.

2017    Endogenous and exogenous innate suppression in bacterial-driven periodontal diseases. NIH R01. To study the role of cigarette smoke on oral microbiota and pathogen virulence. Role: Co-investigator with David Scott and Rich Lamont (UofL Dental School). Funded R01DE026963-01.

2017    Microbial Ecology of Antibiotic Resistance. University of Louisville Undergraduate Research Scholar’s Grant. $500. One year grant to support bioinformatics and genomic sequencing of naturally occurring antibiotic resistant bacteria isolated from natural waterways of Louisville, KY by undergraduate Easton Ford. Funded.

2017    Antibiotic Resistance in Naturally Occurring Areas. Undergraduate Research Scholar’s Grant. University of Louisville. $500. One year grant to support bioinformatics and genomic sequencing of naturally occurring antibiotic resistant bacteria isolated from natural waterways of Louisville, KY by undergraduate Doug Krauth. Funded.

2016    Architecture of Biofilms of Cystic Fibrosis Pathogens. University of Louisville Research Initiation Grant. $10,000. To conduct microscopy and RNA-seq experiments on CF pathogens co-cultures.  Role: PI. Funded.

2016    Microbial Ecology of Antibiotic Resistance in Louisville Environments. Kentucky Biomedical Research Infrastructure Network. To fund meta-community sequencing for antibiotic resistance project – sequencing costs. Role: Co-PI with Paul Himes. Funded.

2016    Co-culture biofilm dynamics between S. aureus and B. cenocepacia. University of Louisville Undergraduate Research Scholar’s Grant. $500. One year grant to support undergraduate thesis of Rachel Thompson. Funded.

2016    Thinking critically about antibiotic resistance in the environment. University of Louisville Supporting Undergraduate Innovation Grant. $4000. This is an educational grant from the University of Louisville Delphi Center for Teaching and Learning was to run a large scale undergraduate microbiology project for independent research credit. Role: Co-PI with Paul Himes. Funded.

2016    The influence of co-living species on colonization of the human pathogen Stenotrophomonas maltophilia in host tissues. University of Louisville Research Initiation Grant. $7,000.  To conduct preliminary experiments examining the role of pathogens and commensal bacteria on murine lung colonization of the cystic fibrosis pathogen Stenotrophomonas maltophilia. Role: PI. Funded.

2014    The response of human cells to Burkholderia dolosa and its flagellin. University of Louisville Undergraduate Research Grant. $3000. One year grant to encourage the development of an undergraduate research project. Role: PI. Funded.

2013    Small Animal Model of Lung Infection For Testing Therapeutics For Multiple Drug Resistant Pseudomonas aeruginosa. National Institutes of Health. Role: Key personnel. Collaboration with Jonathan Warawa and Matthew Lawrenz (University of Louisville Medical School). Funded.

2013    Interspecies communication in mixed bacterial populations. University of Louisville Research Initiation Grant. $4500.  One year grant to provide seed money for new projects.  Role: PI. Funded.

2013    The TolQRAB-Pal complex of Burkholderia dolosa and its role in bacterial pathogenesis. University of Louisville Undergraduate Research Grant. $2700. One year grant to encourage the development of an undergraduate research project. Role: PI. Funded.

2010    Cystic Fibrosis Foundation Postdoctoral Fellowship.  Two year competitive award for salary and some research and travel support.  Granted the Carol Basbaum Memorial Research Award for highest scoring fellowship of the year. Role: PI. Funded.

2007    Genes associated with epidemic Burkholderia cenocepacia. NIH competitive R21. $429,620 (total costs). Co-author status with 4 other researchers led by John J. LiPuma (University of Michigan School of Public Health). Funded.

2007    Identifying Burkholderia cenocepacia genes expressed under conditions that mimic the CF lung. Cystic Fibrosis Foundation Therapeutics. $8,100.  Role: Co- I with James M. Tiedje (Michigan State University). Equipment costs for microarray experiments. Funded.

 

Unfunded (16 entries since coming to UofL)

2017    Stopping a killer: determining the mechanism by which B. cenocepacia inhibits Staphylococcus aureus biofilms. National Institutes of Health. $450,000. Three year grant to explore co-culture inhibition by CF pathogens. Role: PI. Unfunded.

2016    Endogenous and exogenous innate suppression in bacterial-driven periodontal diseases. NIH R35. Role: Co-investigator with David Scott and Rich Lamont (UofL Dental School).

2016    Evolution of Tradeoff. NIH R15. Role: Co-PI with Susi Remold and Jeff Bara (UofL, Biology Department).

2016    Exploring the Genetic Response of Human Respiratory Pathogens to Co-Culture Conditions. Kentucky Biomedical Research Infrastructure Network. Role: PI

2016    Zinc homeostasis in Yersinia pestis. NIH R01. Role: Co-investigator with Matt Lawrenz (UofL Microbiology and Immunology).

2015   Escaping constraint: is tradeoff between response to competition and abiotic stress labile in Pseudomonas aeruginosa? National Institutes of Health. Role: Co-PI with Susanna Remold (UofL Biology Department).

2015    Tobacco-induced alternations to P. gingivalis-host interactions. National Institutes of Health. Role: Co-investigator with David Scott (UofL Dental School).

2015    Coordinate Regulation by the b mating locus and ammonium sensors of Ustilago maydis Genes Involved in Dimorphism, Mating and Pathogenicity. NSF (IOS). Role: Co-PI with Mike Perlin (UofL Biology Department).

2015    Towards Therapeutic Target Development For Burkholderia Species. Cystic Fibrosis Foundation. Role: PI.

2015    The Response of Pseudomonas aeruginosa and MRSA to Co-Culture Infections. Cystic Fibrosis Foundation. Role: PI.

2014    Identifying Potential Therapeutic Targets in Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus. Gilead Sciences. Role: PI.

2014    Identifying new therapeutic targets and vaccine antigens for bacterial pathogens. National Institutes of Health. Role: PI.

2014    Identifying Potential Therapeutic Targets in Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus. Searle Scholars Program. Role: PI. 

2014    Importance of intracellular lifestyle for Klebsiella pneumoniae disease. Burroughs Wellcome Fund.  Role: Co-investigator (with Jon Warawa, UofL Department of Microbiology and Immunology). 

2014    Urban Stream Revitalization. Surdna Foundation. Letter of Intent.  Role: co-PI with Mark French (Stream Institute, Dept of Civil and Environmental Engineering, UofL).

2013    Identification of novel and host targets impacting disease. Defense Threat Reduction Agency. Role: additional personnel with Jon Warawa (UofL School of Medicine).

 

MEETINGS, TALKS, AND POSTERS

* indicates undergraduate, post-baccalaurate, or graduate students in the Yoder-Himes lab

Since coming to UofL (25 entries)

March 2018     Invited Speaker (Yoder-Himes DR), Vaccines: a big reason you didn’t die as a kid. Univeristy of Louisville REDtalks. Louisville, KY, USA

Nov 2017        Poster, The Prevalence of Bacteria Resistant to Vancomycin and Colistin in Waters Around Louisville.  Mahbubani R*, Priest A*, Koenig A*, Ford E*, Krauth D*, Himes P, Yoder-Himes DR. Kentucky Academy of Sciences, Bowling Green KY, USA.  Awarded 1st place in Microbiology. 

Nov 2017        Poster, Survey of Vancomycin- and Colistin-Resistant Bacteria in Environmental Water Samples Across Louisville.  Ford EE*, Robinson M*, Priest A*, Mahbubani R*, Davis L*, Krauth D*, Himes P, Yoder-Himes DR. Kentucky Academy of Sciences, Bowling Green KY, USA.  Awarded 3rd place in Microbiology. 

Sept 2017        Invited Speaker (Yoder-Himes DR), Mixed community biofilms in the cystic fibrosis lung: friends and foes. University of Louisville School of Dentistry Department of Oral and Infectious Diseases. Louisville, KY, USA

Sept 2017        Poster, Survey of Vancomycin- and Colistin-Resistant Bacteria in Environmental Water Samples Across Louisville. Ford EE*, Robinson M*, Priest A*, Mahbubani R*, Davis L*, Krauth D*, Himes P, Yoder-Himes DR. Research! Louisville, Louisville, KY, USA

June 2017        Invited Speaker (Yoder-Himes DR), Understanding Polymicrobial Interactions in the Cystic Fibrosis Lung. University of Louisville Center for Predictive Medicine, Louisville, KY, USA

May 2017        Poster, Tn-seq analysis identifies genes required for Burkholderia cenocepacia survival in a mouse model of chronic granulomatous disease. Varga JJ, Fankhauser SC, Yoder-Himes DR, Goldberg J.B. American Society of Microbiology. New Orleans, LA , USA

April 2017       Poster, The Prevalence of Bacteria Resistant to Vancomycin and Colistin in Wastewaters in Louisville, KY. Priest A*, Koenig A*, Himes P, Yoder-Himes DR. Undergraduate Research and Community Engaged Symposium, Louisville, KY, USA

April 2017       Poster, Burkholderia cenocepacia-mediated destruction of Staphylococcus aureus biofilms. Thompson R*, Brandt TJ*, Yoder-Himes DR. Undergraduate Research and Community Engaged Symposium, Louisville, KY, USA

April 2017       Poster, Antibiotic Resistance in Louisville Natural Waters. Ford EE*, Krauth DM*, Yoder-Himes DR, Himes P. Undergraduate Research and Community Engaged Symposium, Louisville, KY, USA

October 2016   Poster, Antibiotic Resistant Bacteria in Natural Environmental Within Kentucky. Tran S*, Himes P, Yoder-Himes DR. Research! Louisville, Louisville, KY, USA

October 2016   Poster, The Effects of Mutations in the TolQRAB Complex of Burkholderia dolosa.  Clark BS* and Yoder-Himes DR. Research! Louisville, Louisville, KY, USA

June 2016        Poster, Identification of Porphyromonas gingivalis genes essential for surviving cigarette smoke exposure. Hutcherson J, Gogeneni H, Yoder-Himes DR, Want H, Lamont R, Scott DA. International Association of Dental Research Conference. Seoul, South Korea

April 2016       Speaker (Yoder-Himes DR), The Host Immune Response to Burkholderia dolosa.  International Burkholderia cepacia Working Group Annual Meeting, Columbus, OH USA

April 2016       Invited Speaker (Yoder-Himes DR), Pathogenomics and Host Immune Response of Burkholderia dolosa. Indiana University Department of Biology. Bloomington, IN, USA

March 2016     Invited Speaker (Yoder-Himes DR), Pathogenomics of the Opportunistic Respiratory Pathogens: The Burkholderia cepacia Complex. Western Kentucky University Department of Biology, Bowling Green, KY USA

March 2016     Poster, The Vast and the Dangerous: Antibiotic Resistant Bacteria. Tran S* (presentation on thesis work from Yoder-Himes lab).  SRHC Orlando Conference, Orlando, FL USA

Sept 2015        Poster, Comparison of inherently essential genes of Porphyromonas gingivalis identified in two transposon sequencing libraries. Himabindu G, Hutcherson  J, Yoder-Himes DR, Hendrickson E, Hackett M, Lamont R, Scott D. Research! Louisville, Louisville KY, USA

April 2015       Poster, Diversity of Plant Associated Antibiotic Resistant Bacteria in Louisville. Tran S*(presentation on thesis work from Yoder-Himes lab).  Kentucky Honors Roundtable Conference, Bowling Green, KY, USA

Jan 2015          Speaker (Yoder-Himes DR), Pseudomonads. Department of Microbiology and Immunology Guest Lecturer, University of Louisville, Louisville, KY, USA

Nov 2014        Poster, Diversity of Antibiotic Resistant Bacteria within Distinct Ecological Niches in Kentucky.  Clark BS*, Loomis T*, McBride D*, Tran S*, Yoder-Himes DR, Himes P. Kentucky Academy of Science Annual Meeting.  Lexington, KY, USA

Sept 2014        Poster, Diversity of Antibiotic Resistant Bacteria within Distinct Ecological Niches in Kentucky.  Tran S*, Mey J*, Ostrowski E*, Seo J*, Yoder-Himes DR, Himes P. Research! Louisville, Louisville, KY USA

May 2014        Poster, Interactions of Cystic Fibrosis Pathogens When Grown in Polymicrobial Conditions. Jensen D* and Yoder-Himes DR. American Society of Microbiology Annual Meeting. Boston, MA, USA

May 2013        Invited Speaker (Yoder-Himes DR), Pathogenomics of the opportunistic respiratory bacteria Burkholderia and Pseudomonas. School of Public Health, University of Louisville, Louisville, KY, USA

April 2013       Speaker (Yoder-Himes DR), The Role of Burkholderia dolosa Flagella in Host Colonization.International Burkholderia cepacia Working Group 16th Annual Meeting, Ann Arbor, MI, USA

March 2013     Invited Speaker (Yoder-Himes DR), Pathogenomics of the opportunistic respiratory bacteria Burkholderia and Pseudomonas.  School of Dentistry, University of Louisville, Louisville, KY, USA

Prior to the University of Louisville (13 entries)

April 2012       Speaker, International Burkholderia cepacia Working Group 15th Annual Meeting, Montreal, Canada

April 2010       Speaker, International Burkholderia cepacia Working Group 13th Annual Meeting, Seattle, Washington, USA

April 2009       Speaker, International Burkholderia cepacia Working Group 13th Annual Meeting, Toronto, Ontario, Canada

May 2007        Poster, 107th General Meeting, American Society for Microbiology, Toronto, Ontario, Canada

April 2007       Speaker, International Burkholderia cepacia Working Group 11th Annual Meeting, Ann Arbor, MI, USA

August 2006    Speaker, 11th International Symposium on Microbial Ecology, Vienna, Austria

January 2006   Genomics of Closely Related Organisms Conference, Tucson, AZ, USA

July 2004         Speaker, 31st International Conference on the Biology of Myxobacteria. Helsingør, Denmark

July 2003         Speaker, 30th International Conference on the Biology of Myxobacteria. Long Beach, CA, USA

July 2002         Speaker and Poster, 29th International Conference on the Biology of Myxobacteria.  Quebec, Canada

July 2002         Poster, American Society of Microbiology - Prokaryotic Development Conference.  Quebec City, Canada

May 2002        Poster, Gene Expression in Development and Disease Focus Group and Genetics Program – Transcription in Development Symposium.  East Lansing, MI, USA

May 2000        Poster, Indiana Branch of the American Society of Microbiology.  Turkey Run State Park, IN, USA

 

AWARDS IN PROFESSIONAL ACTIVITY

2010                Carol Basbaum Memorial Research Award (top scoring fellowship; Cystic Fibrosis Foundation)

2005                Doctoral Dissertation Completion Fellowship-Michigan State University

2005                DuVall Doctoral Scholarship (awarded to two outstanding PhD candidates in the Microbiology and Molecular Genetics department) - Michigan State University

2004                Hsiung-Kimball Award (for graduate students in the Microbiology and Molecular Genetics department) - Michigan State University

2003                Travel Awards - Michigan State University College of Natural Science, Michigan State University Graduate School, Michigan State University Department of Microbiology and Molecular Genetics

2002                Travel Grant - American Society for Microbiology

 

SERVICE (6% OF EFFORT)

As a tenure-track faculty member, my service to my university, college, and department is relatively low to allow for more time to establish my research lab and teaching repertoire.  However, I have performed service in my profession, in my local community, and for my department, including several high-effort committees.

 

PROFESSIONAL COMMITMENTS

2013 –Present  Ad hoc reviewer for BMC Microbiology

2013 –Present  Ad hoc reviewer for Molecular Ecology

2013 –Present  Ad hoc grant reviewer for the National Medical Research Council (UK)

2013 –Present  Review Editor for Frontiers in Cellular and Infection Microbiology

2013 –Present  Review Editor for Frontiers in Systems Microbiology

2010 –Present  Peer reviewer for Journal of Medical Microbiology

2008 –Present  Ad-hoc grant reviewer for the National Science Foundation

 

PROFESSIONAL SOCIETIES

1997- Present               American Society for Microbiology

2011- 2016                  American Association for the Advancement of Science (AAAS)

2005 – 2008                International Society for Microbial Ecology

 

COMMUNITY ENGAGEMENT

2017                UofL Today with Mark Hebert. Interview broadcast on local radio and TV show.  Discussed our studies on antibiotic resistant bacteria in local water sources.  Link: https://louisville.edu/artsandsciences/news/podcasts/antibiotic-resistance

2016                Boonanza at the Kentucky Science Center – Microbiology of Forensics – our group demonstrated how microbes could be used to identify a thief.

2016                Youth Science Summit Youth Science Summit at the Kentucky Science Museum – Murder Mystery Microbiology Lab in which students discovered who killed Col. Sanders using bacteria in a Clue-like experience. Asked to return as it was the most popular event.

2016                Research! Louisville poster judge

2015                Youth Science Summit at the Kentucky Science Museum – Murder Mystery Microbiology Lab in which students discovered who killed Col. Sanders using a bacteria in a Clue-like experience.

2015                Science Proofs – “Antibiotic Resistance” – discussing the emergence and mechanisms of antibiotic resistance to the general public at the BBC Taproom, Louisville, KY

2014                “LIFE: Everywhere Here…Anywhere Out There?”, UofL Planetarium Show script editor and science advisor

2013-2016       Kentucky Junior Science and Humanities Symposium (KY-JSHS) – paper reviewer

2014                DNA Day at the Kentucky Science Center – took lab members to the Science Center and demonstrated how we purify, examine, and use DNA to benefit human health to the general public

2014                STEM camp for Girl Scouts of Louisville – worked with 9th and 10th girls interested in the STEM fields and performed DNA extractions, gel electrophoresis, discussed our bacterial research, field trip to my lab.

 

COMMITTEES AND DEPARTMENTAL SERVICE

2018-Present   Director of Undergraduate Studies, Biology Department, UofL

2016-2018       University of Louisville Biology Department Graduate Committee

2016-2017       University of Louisville Biology Department Faculty Search Committee

2014-2015       University of Louisville Biology Department Personnel Committee

2003 - 2004     MSU Department of Microbiology and Molecular Genetics Graduate Committee

2002 - 2003     MSU Department of Microbiology and Molecular Genetics Planning Committee