Ditty Lab: Microbiology Research

August 23, 2017 / By: Jayna L. Ditty Ph.D
Researcher: Jayna Ditty, Ph.D.

 

PROFESSIONAL INTERESTS

◦ Chemotaxis toward aromatic hydrocarbons in Pseudomonas species

◦ Use of Bioinformatic tools in the undergraduate curriculum

◦ Photic entrainment of the Synechococcus elongates circadian clock

◦ Efficacy of novel antimicrobial compounds

 P putida ditty research

PUBLICATIONS

Primary Articles  (Names in bold indicate student collaborators.)

Ditty, J.L and Parales, R.E. (2017). Protocols for the measurement of bacterial chemotaxis to hydrocarbons. In: Hydrocarbon and Lipid Microbiology Protocols. T.J. McGenity, K.N. Timmis, B.N. Fernandez (eds.), Springer-Verlag, Berlin.

Ditty, J.L., Nichols, N.N., and Parales, R.E. (2017). Protocol for the measurement of hydrocarbon transport in bacteria. In: Hydrocarbon and Lipid Microbiology Protocols. T.J. McGenity, K.N. Timmis, B.N. Fernandez (eds.), Springer-Verlag, Berlin

Parales, R.E. and Ditty, J.L. (2017). Substrate transport. In: Handbook of Hydrocarbon and Lipid Microbiology (Cellular Ecophysiology of Microbes). T. Krell (ed.), Springer-Verlag, Berlin.

Parales, R.E. and Ditty, J.L. (2017). Chemotaxis. In Handbook of Hydrocarbon and Lipid Microbiology (Cellular Ecophysiology of Microbes). T. Krell (ed.), Springer-Verlag, Berlin.

Mahatmya, D., Morrison, J., Jones, R., Garner, P, Davis, S., Manske, J., Berner, N., Johnson, A., and Ditty. J.L. (2017) Pathways to Undergraduate Research Experiences: A Multi-institutional Study. Innovative Higher Education. doi:10.1007/s10755-017-9401-3.

Ditty, J.L. and R.E. Parales. (2015). Protocols for the measurement of bacterial chemotaxis to hydrocarbons. In T.J. McGenity, K.N. Timmis, B. Nogales (Eds.), Hydrocarbon and Lipid Microbiology Protocols. Berlin: Springer-Verlag. 

Luu, R.A., Koostra, J.D., Nesteryuk, V., Brunton, C.N., Parales, J.V., Ditty, J.L., and Parales, R.E. (2015). Integration of chemotaxis, transport, and catabolism in Pseudomonas putida and identification of the aromatic acid chemoreceptor PcaY. Molecular Microbiology 96:134-147. 

Parales, R.E, Nesteryuk, V., Hughes, J.G., Luu, R.A., and Ditty, J.L. (2014). Chemotaxis to nicotinic acid and identification of the methyl-accepting chemotaxis protein in Pseudomonas putida F1. Microbiology 160:2661-2669.

Parales, R.E, Luu, R.A., Chen, G.Y., Liu, X., Wu, V., Lin. P., Hughes, J.G., Nesteryuk, V., Parales, J.V., and Ditty, J.L. (2013). Pseudomonas putida F1 has multiple chemoreceptors with overlapping specificity for organic acids. Microbiology 159:1086-1096.

Luu, R.A., Schneider, B.J., Ho, C.C., Nesteryuk, V., Ngwesse, S.E., Liu, X., Parales, J.V., Ditty, J.L., and Parales, R.E. (2013). Taxis to phenylacetic acid by Pseudomonas putida F1 is mediated by the energy taxis receptor Aer2. Applied and Environmental Microbiology 79:2416-2423.

Nichols, N.N, Lunde, T.A., Graden, K.C., Hallock, K.A., Kowalchyk, C.K., Southern, R.M., Soskin, E.J., and Ditty, J.L. (2012). Chemotaxis to furan compounds by furan-degrading Pseudomonas strains. Applied and Environmental Microbiology 78:6365-6368.

Wammer, K.M., Slattery, M.T., Stemig, A.M., and Ditty, J.L. (2011). Analysis of the antibacterial activity of tetracycline’s photoproducts. Chemosphere 85:1505-1510.

Ebner, D., Culhane, J., Winkelman, T., Haustein, M.D., Ditty, J.L., and Ippoliti, J.T. (2008). Synthesis of a novel oxazolidinone antimicrobial agent. Bioorganic and Medicinal Chemistry 16:2651-2656.

Ditty, J.L., Canales, S.R., Anderson, B.E.,Williams, S.B., and Golden, S.S. (2005). Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes. Microbiology 151:2605-2613.

Nair, U., Ditty, J.L., Xu, Y., Min, H., and Golden, S.S. (2002). Roles for sigma factors in global circadian regulation of the cyanobacterial genome. Journal of Bacteriology 184:3530-3538.

Ditty, J.L., and Harwood, C.S. (2002). Charged amino acids conserved in the aromatic acid/H(+) symporter family of permeases are required for 4-hydroxybenzoate transport by PcaK from Pseudomonas putida. Journal of Bacteriology 184:1444-1448.

Parales, R.E., Ditty, J.L., and Harwood, C.S. (2000). Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene.  Applied and Environmental Microbiology 66:4098-4104.

Ditty, J.L., and Harwood, C.S. (1999). Conserved cytoplasmic loops are important for both the transport and chemotaxis functions of PcaK, a 12 membrane-spanning protein from Pseudomonas putida. Journal of Bacteriology 181:5068-5074.

Ditty, J.L., Grimm, A.C., and Harwood, C.S. (1998). Identification of a chemotaxis gene region from Pseudomonas putida. FEMS Microbiology Letters 159:267-273.

Harwood, C.S., Nichols, N.N., Kim, M.-K., Ditty, J.L., and Parales, R.E. (1994). Identification of the pcaRKF gene cluster from Pseudomonas putida: Involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. Journal of Bacteriology 176:6470-6488.

 

    Edited Book

Ditty, J.L., Mackey, S.R., and Johnson, C.H. (Eds.) (2009). Bacterial Circadian Programs. Berlin: Springer-Verlag.

 

    Book Chapters and Reviews

Parales, R.E., Luu, R.A., Hughes, J.G., and Ditty, J.L. (2015). Bacterial chemotaxis to xenobiotic chemicals and naturally-occurring analogs. Current Opinion in Biotechnology 33:318-326.

Mackey, S.R., Golden, S.S., and Ditty, J.L. (2011). The itty-bitty time machine: Genetics of the cyanobacterial circadian clock. In S. Brody (Ed.) Advances in Genetics 74:13-53.

Parales, R.E. and Ditty, J.L. (2010). Chemotaxis. In K.N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology. Berlin: Springer-Verlag.

Parales, R.E. and Ditty, J.L. (2010). Substrate transport. In K.N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology. Berlin: Springer-Verlag.

Ditty, J.L. and Mackey, S.R. (2009). Classic circadian characteristics: historical perspective and properties relative to the Synechococcus elongatus PCC 7942 model. In J.L. Ditty, S.R. Mackey, & C.H. Johnson (Eds.) Bacterial Circadian Programs. Berlin: Springer-Verlag.

Mackey, S.R., Ditty, J.L., Zeidner, G., Chen, Y., and Golden, S.S. (2009). Mechanisms for entraining the cyanobacterial circadian clock system with the environment. In J.L. Ditty, S.R. Mackey, & C.H. Johnson (Eds.) Bacterial Circadian Programs. Berlin: Springer-Verlag.

Parales R.E., Parales J.V., Pelletier D.A., and Ditty J.L. (2008). Diversity of microbial toluene degradation pathways. Advanced and Applied Microbiology. 64:1-73.

Parales, R.E., Ju, K.-S., Rollefson, J.B., and Ditty, J.L. (2008). Bioavailability, transport, and chemotaxis towards organic pollutants. In E. Diaz (Ed.), Microbial Biodegradation: Genomics and Molecular Biology. Norfolk, UK: Caister Academic Press.

Parales, R.E., and Ditty, J.L. (2005). Laboratory evolution of catabolic enzymes and pathways. Current Opinion in Biotechnology 16:315-325.

Ditty, J.L., Williams, S.B., and Golden, S.S. (2003). A cyanobacterial circadian timing mechanism. Annual Review Genetics 37:513-43.

 

    Methods Book Chapters

Ditty, J.L., Nichols, N.N., and Parales, R.E. (2014). Protocol for the measurement of hydrocarbon transport in bacteria. In K.N. Timmis (Ed.), Hydrocarbon and Lipid Microbiology Protocols. Berlin: Springer-Verlag.

Ditty, J.L., Nichols, N.N., and Parales, R.E. (2010). Measurement of hydrocarbon transport in bacteria. In K.N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology. Berlin: Springer-Verlag.

Mackey, S.R., Ditty, J.L., Clerico, E.M., and Golden, S.S. (2007). Detection of rhythmic bioluminescence from luciferase reporters in cyanobacteria. In E. Rosato (Ed.), Circadian Rhythms: Methods and Protocols. In J.M. Walker (Series Ed.) Methods in Molecular Biology. Totowa, New Jersey: Humana Press.

Clerico, E.M., Ditty, J.L., and Golden, S.S. (2007). Specialized techniques for site-directed mutagenesis in cyanobacteria. In E. Rosato (Ed.), Circadian Rhythms: Methods and Protocols. In J.M. Walker (Series Ed.) Methods in Molecular Biology. Totowa, New Jersey: Humana Press.

 

    Pedagogical Publications

Ditty, J.L., Williams, K.M., Keller, M.M., Chen, G.Y., Liu, X., and Parales, R.E. (2013). Integrating Grant-funded Research into the Undergraduate Biology Curriculum Using IMG-ACT. Biochemical and Molecular Biology Education 41:16-23.

Ditty, J.L. et al. (2010). Faculty Incorporating Genomics and Bioinformatics Across the Life Sciences Curriculum: Development and Implementation of the Integrated Microbial Genomes Annotation Collaboration Toolkit. PLoS Biology 8(8): e1000448. doi:10.1371/journal.pbio.1000448

Ditty, J.L., Kelley, D., Lorah, P., Steyermark, A., Werner, R., and Zimmer, K. (2007). Cross-departmental implementation of GIS at a mid-sized undergraduate University. CUR Quarterly 27:120-123.

 

    Other Publications

Ditty, J.L., and Rolnick, P.A. (2010). Keeping faith: Evolution and Theology. Logos: A Journal of Catholic Thought and Culture. St. Paul: University of St. Thomas

 

 

ditty research

 

GRANTS and AWARDS

Applied and Environmental MicrobiologyEditorial board member (2014-2016)

Microbial Genome Annotation Network (MGAN):   Governing board member (2012 to present)

LI-COR Genomics Education Matching Instrumentation Grant:   LI-COR Model 4300 Analysis System (2010)

DOE-JGI Undergraduate Research Program in Microbial Genome Annotation:  Pilot faculty collaborator (2008)

Merck/AAAS Undergraduate Science Research Program:   Project 3: Synthesis and testing of novel antimicrobial compounds (2007-2009)

National Science Foundation MCB-0919930:   Bacterial chemotaxis to Aromatic Hydrocarbons and Related Pollutants. (2009-2012)

National Science Foundation Starter Grant MCB-0329366:   Circadian rhythms in cyanobacteria. (2003)

National Science Foundation Post-Doctoral Fellowship in Microbial Biology DBI-0074386:   Characterization of a second circadian oscillator in Synechococcus sp. PCC 7942. (2000-2002)