• Molecular mechanism of the Synechococcus elongatus prokaryotic circadian clock

• Photic entrainment of the Synechococcus elongatus circadian clock

• Efficacy of novel antimicrobial compounds

• Chemotaxis toward aromatic hydrocarbons in Pseudomonads

Names in bold denote student research collaborators.

• Wammer, K.M., Slattery, M.T., Stemig, A.M., and Ditty, J.L. (2011). Analysis of the antibacterial activity of tetracycline’s photoproducts. In review: Chemosphere.
• 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, vol. 74. Elsevier
• 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 Biol 8(8): e1000448. doi:10.1371/journal.pbio.1000448
• R.E. Parales and Ditty, J.L. (2010) Chemotaxis. In K.N. Timmis (Ed.), Handbook of hydrocarbon and lipid microbiology. Berlin: Springer-Verlag.
• R.E. Parales and Ditty, J.L. (2010) Substrate transport. In K.N. Timmis (Ed.), Handbook of hydrocarbon and lipid microbiology. 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.
• 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, J.L., Mackey, S.R., and Johnson, C.H. (Eds.) (2009). Bacterial Circadian Programs. 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.
• Ebner, D., Culhane, J., Winkelman, T., Haustein, M.D., Ditty, J.L., and Ippoliti, J.T. (2008). Synthesis of a novel oxazolidinone antimicrobial agent. Bioorg. Med. Chem. 16:2651-2656.
• Parales R.E., Parales J.V., Pelletier D.A., and Ditty J.L. (2008). Diversity of microbial toluene degradation pathways. Adv. Appl. Microbiol. 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.
• 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.
• 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.
• 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., 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.
• Canales, S.R., J.L. Ditty, E.M. Clerico, and S.S. Golden. (2005) Detection of rhythmic bioluminescence from luciferase reporters in cyanobacteria. Methods in Molecular Biology (in press)
• Ditty, J.L., S.R. Canales, B.E. Anderson, S.B. Williams, and S.S. Golden. (2005) Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes. Microbiology 151: 2605-2613.
• Ditty, J.L., S.B. Williams, and S.S. Golden. (2003) A cyanobacterial circadian timing mechanism. Annual Review Genetics 37: 513-43.
• Nair, U., J.L. Ditty, Y. Xu, H. Min, and S.S. Golden. (2002) Roles for sigma factors in global circadian regulation of the cyanobacterial genome. Journal of Bacteriology 184:3530-3538.
• Ditty, J.L., and C.S. Harwoood. (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., J.L. Ditty, and C.S. Harwood. (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 C.S. Harwood. (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., A.C. Grimm, and C.S. Harwood. (1988) Identification of a chemotaxis gene region from Pseudomonas putida. FEMS Microbiology Letters 159: 267-273.
• Harwood, C.S., N.N. Nichols, M.-K. Kim, J.L. Ditty, and R.E. Parales. (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.

• LI-COR Genomics Education Matching Fund 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)
• Starter Grant, National Science Foundation MCB-0329366.  Project title: Circadian Rhythms in Cyanobacteria.
• Research Assistance Grant, University of St. Thomas Faculty Development program.  Project title: How do bacteria tell time? Characterizing Regulatory Elements in Circadian Clock Genes in Cyanobacteria.