Allan D. Shapiro

I'M MOVING TO FLORIDA GULF COAST UNIVERSITY!

Yes, as of the end of December 2004, I will no longer be with the U. of Delaware. I am joining the faculty of the Biotechnology Program at FGCU as of January 1, 2005. FGCU is located in Fort Myers in South Florida. It is the newest campus of the University of Florida system; it opened its doors in the late 90s. I will be on campus for the first two years. After that point, I will move to the new Plant Research Center that will be constructed on the grounds of the Naples Botanical Garden (~20 minutes away). FGCU is a primarily undergraduate institution; however, M.S. and Ph.D. programs in Biotechnology are planned. I will be continuing my current line of research, with an increasing focus on the systems biology aspects of the work. However, I will also be starting work on new areas for which the university already has substantial funding from various sources.

TEMPORARY CONTACT INFORMATION:

I do not yet have an email address at FGCU; however, my alternate email address

will be functional at least through Spring. I will last check my current primary email address on December 29 or 30. The phone number for the secretary for the Biotechnology Program is (239) 590-7205. She'll be able to tell you my phone number when I have one. My new mailing address is as follows:

Florida Gulf Coast University
Biotechnology Program
10501 FGCU Blvd. South
Ft. Myers, FL 33965

If you are reading this in 2005, I apologize for not updating it. I no longer have access to the system, and this page will likely be deleted at some point.

RESEARCH INTERESTS:

The focus of my program has been signal transduction in plant disease resistance. Research used principally bacterial pathogens and Arabidopsis as a model system. Specific focus was in two areas: 1. Control of programmed cell death in Arabidopsis disease resistance; 2. Genetic circuitry, feedback regulation, pathway cross-talk and control of informational flux in disease resistance signaling and development of quantitative assays and mathematical modeling techniques to underlie these studies. Close collaboration with colleagues in the Dept. of Chemical Engineering underlied our "Systems biology" approaches. We have recently developed a website that highlights these approaches and includes all of our published data and code in multiple forms that we thought would be useful to other systems biologists. Knowledge of disease resistance signaling gained from this model system should guide future transgenic approaches to disease control in crop plants.

At FGCU, focus on computational systems biology approaches will increase. In addition to getting a paper out the door we are currently preparing (in which we extended our computational models to address cell-to-cell signaling in the Arabidopsis hypersensitive response and came to some very interesting conclusions about how the HR contributes to disease resistance), in 2005 my engineering collaborators and I will be writing an undergraduate systems biology textbook and beginning to develop new ways of modeling qualitative biological data. As all models must be tested, I expect to continue the experimental biology also, as guided by the modeling. The only experimental work from my U. of Delaware days that has not yet been published (or is not at least in press), aside from a few experiments that were necessary to support the modeling work that will be included in our "in preparation" paper on cell-to-cell signaling, are the results of our genetic screen for mutants affecting the HR. I'm hoping to bring that work to the point of the first publication within my first year at FGCU.

PUBLICATIONS FROM THE DELAWARE YEARS (1997 - 2004):

Agrawal, V., Ogunnaike, B., Czymmek, K.J., Dhurjati, P.S. and Shapiro, A.D. (2005) Computational Modeling of Cell-to-Cell Signaling in Arabidopsis Defense Responses. Manuscript in preparation.

Shapiro, A.D. (2005) Nitric Oxide Signaling in Plants. Vitamins and Hormones, In press (Invited review article). Publication expected August 2005 as part of Special issue on Plant Hormones.

Zhang, C., Gutsche, A.T. and Shapiro, A.D. (2004) Feedback Control of the Arabidopsis Hypersensitive Response. Molecular Plant-Microbe Interactions 17: 357-365.

Agrawal, V., Zhang, C., Shapiro, A.D. and Dhurjati, P.S. (2004) A Dynamic Mathematical Model to Clarify Signaling Circuitry Underlying Programmed Cell Death Control in Arabidopsis Disease Resistance. Biotechnology Progress 20: 426-442.

Zhang, C., Czymmek, K.J. and Shapiro, A.D. (2003) Nitric Oxide Does Not Trigger Early Programed Cell Death Events but May Contribute to Cell-to-Cell Signaling Governing Progression of the Arabidopsis Hypersensitive Response. Molecular Plant-Microbe Interactions 16: 962-972.

Shapiro, A.D. and Gutsche, A.T. (2003) Capillary Electrophoresis-based Profiling and Quantitation of Total Salicylic Acid and Related Phenolics for Analysis of Early Signaling in Arabidopsis Disease Resistance. Analytical Biochemistry 320: 223-233.

Zhang, C. and Shapiro, A.D. (2002) Two Pathways Act in an Additive Rather than Obligatorily Synergistic Fashion to Induce Systemic Acquired Resistance and PR Gene Expression. BioMedCentral Plant Biology 2:9.

Shapiro, A.D. and Zhang, C. (2001) The Role of NDR1 in Avirulence Gene-Directed Signaling and Control of Programmed Cell Death in Arabidopsis. Plant Physiology 127: 1089-1101.

Shapiro, A. D. (2000) Using Arabidopsis Mutants to Delineate Disease Resistance Signaling Pathways. Canadian Journal of Plant Pathology 22: 199-216.

Century, K. S., Shapiro, A. D., Repetti, P. P., Dahlbeck, D., Holub, E. and Staskawicz, B. J. (1997) NDR1: A Pathogen-Induced Component Required for Arabidopsis Disease Resistance. Science 278: 1963-1965.

WHAT HAPPENED TO MY LAB PERSONNEL?

My first Ph.D. student, Chu Zhang, started in the lab September 1998 and defended her thesis in September 2003. She is now a postdoc with Dr. Cindy Carson in the Biological Sciences Dept. of the University of Delaware, working to understand the molecular basis of metastatic prostate cancer. My second Ph.D. student, Vikas Agrawal, started with us in August 2001. He defended his Ph.D. in August 2004 and moved on to a postdoctoral appointment with Dr. Elliot Meyerowitz (Cal Tech). He is continuing to do computational biology, with current efforts directed towards understanding plant meristem function. My postdoctoral fellow Dr. Cathy Worley (January 1999 - June 2001), who played the leading role in the genetic screens we did, went on to become a research manager with Dade-Berhing Corporation in Glasgow, Delaware, working with medical diagnostics. My postdoctoral fellow Raghavan Ramanathan (August 2000 - August 2001), who worked on early aspects of our computational modeling, returned to his orginal field of computational fluid dynamics in a second postdoc at U. Penn and then returned to India. Former visiting scholar Dr. Anita Brinker (February 2000 - October 2000) left to take a permanent position working with Dr. Ilya Raskin at Rutgers. Former visiting scholar Yang Hong-yu (January 2001 - September 2001) returned to her Associate Professor position at Kunming University in China. My technician Barb Farnworth (August 2000 - September 2002) moved upstairs to work for Dr. Blake Meyers. My original technician Cindy Boettger (November 1997 - June 2000) now works for John Doms in the Animal Sciences Department. Two other graduate students initiated degree programs but left for personal reasons. Both of them (Thaya Ganzke and Revital Herrmann) are currently working at DuPont.

We also had 14 undergraduate research interns, most of whom are now in graduate/professional school: Christina Williams (1998-1999) and Katie Guhl (1999) are now both Ph.D. students in Janine Sherrier's lab at U. of Delaware. Matt Sincock went on to medical school at Thomas Jefferson University. Candy Tong (1999) went on to the Ph.D. program in the Dept. of Chemistry at Cal Tech. Josh Hubner (2000-2001) went on to law school at the U. of Florida. Ojay Okefore was a summer student in 2000 from Del State--current whereabouts unknown. Laura Sorrentino was a summer student in 2001 from Rowan University who went on to graduate school in Chemical Engineering at Rowan. Laura Maliszewski (1999-2001) went on to a Ph.D. program in the Dept. of Virology at Harvard University. Kyle Dorkoski (2001) went on to a position as a technician at Dade-Behring Corporation in Glasgow, Delaware for two years and is now studying to be a physician's assistant at Arcadia College. Marla Tocker (2001) went on to graduate school in the Biotechnology program at Johns Hopkins University. Chiara Ciotoli (2001-2002) went on to the Ph.D. program in Plant Biology at U. Mass, Amherst. Carrie Jacobus (2001-2002) went on to the Ph.D. program in Genetics at North Carolina State University. Bevan Kirley (2001-2003) went initially on to the Ph.D. program in Biochemistry and Molecular Biology in the School of Public Health at Johns Hopkins, but then transferred to the U. of Maryland, Baltimore, into a program with a more explicit focus on public health. Alleen Yu (2002-2003) has worked at Christina Hospital in preparation for applying to medical school.

PARTING MESSAGES:

To the spectacular scientific colleagues I had at the U. of Delaware, I offer my sincere thanks. I wish you all the best of luck. Thanks also to all of the scientists and managers at DuPont with whom I've had wonderful interactions; much of what I accomplished here would not have been possible without you.

To all the students I've advised or taught, I leave the following advice: Don't sell out and compromise the quality of your science to make things trendy. Keep pursuing even what appears borderline impossible. Keep dancing to the rock-and-roll, and don't let the bastards get you down (paraphrased from Lou Reed and Kris Kristofferson lyrics for the .mp3 generation).

Created November 1997
Last updated December 20, 2004