Pierce, Jonathan

Jonathan Pierce

Associate Professor, Program Coordinator for IDD Classes
Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research

The genetic mechanisms that govern behaviors and contribute to neurological disorders.


Phone: 512-232-4137

Office Location
NMS 5.116

Postal Address
The University of Texas at Austin
Department of Neuroscience, College of Natural Sciences
1 University Station C7000
Austin, TX 78712

During my graduate career at the University of Oregon, Eugene, I studied the mechanisms for chemotaxis and taste discrimination in the nematode C. elegans with Dr. Shawn Lockery. I then switched to a more medically relevant topic — studying the molecular basis for intoxication by alcohol at University of California at San Francisco medical school. During this time, my elder son was born with Down syndrome. Back then, I was discouraged to find that very little research was being conducted on Down syndrome. My son inspired me to study the genetic basis for Down syndrome in my own lab at The University of Texas at Austin in 2008. Here, a vibrant collection of researchers are dedicated to discovering the causes and potential cures for genetic disorders through innovative research.

My laboratory studies genetic mechanisms that govern behaviors and contribute to neurological disorders. We approach this complex subject by studying how conserved genes contribute to behaviors in the simple but powerful model nematode C. elegans.

How does our nervous system switch between different patterns of movement?

We take for granted that we can switch seamlessly between walking and running gaits, and rapidly shift between different movements. For people with Parkinson’s disease, however, shifting between gaits and simply getting out of a chair become arduous tasks. We have recently found that the fundamental genetic mechanisms for switching between gaits can be studied in C. elegans. Parkinsonian worms fail to transition between swim and crawl gaits. New results in our lab suggest novel strategies to overcome gait dysfunction even in the absence of dopamine production.

How does alcohol affect our nervous system?

The mechanisms by which alcohol causes intoxication and addiction remain unclear at the molecular level. By using C. elegans as a minimal system, we can rapidly identify conserved molecular mechanisms responsible for behavioral responses to alcohol. For instance, we are intensely studying how alcohol activates a conserved BK potassium channel and developing novel drugs to interfere with this response.

Which genes cause problems in Down syndrome?

I initiated research on Down syndrome (DS) because my son has this condition. People with DS inherit an extra copy of the 21st chromosome which carries about 200 genes. It remains unknown which of these genes contribute to the difficulties in learning, memory and fine motor control in DS. We are using powerful genetic techniques specific to C. elegans to systematically study each one of these genes. Through our research we aim to identify the key genes that contribute to dysfunction of the nervous system when overexpressed in DS.

Can we stop neurodegeneration in Alzheimer’s disease?

Alzheimer’s disease (AD) is inevitable in DS due to an extra copy of the Amyloid Precusor Protein (APP). We have engineered C. elegans to mimic the key features of neurodegeneration observed in human AD by overexpressing a single copy of APP. With this new model, we can test with unprecedented speed whether novel drugs can prevent degeneration of neurons by simply counting them through their transparent body. While mouse studies of AD typically take two years, the compact lifespan of C. elegans affords studies as short as 1 week. We are also using our powerful new model of AD to study the basic science behind how specific types of neurons are vulnerable in AD.

What are the cellular-molecular bases for sensing humidity and magnetic fields?

Although molecules used to detect touch, temperature, taste, olfaction and vision have been discovered, it was unknown how animals detect two additional modalities: humidity and the Earth’s magnetic field. Our lab has recently exploited the simple nervous system and genetics of C. elegans to identify the first neurons and molecules that detect these mysterious sensory modalities in any animal.

2014 Davis, S. & Pierce-Shimomura, J. “Ca2+-sensing domains of the BK channel are dispensable for intoxication in Caenorhabditis elegans.” Accepted pending minor revisions at Genes, Brain & Behavior.

2014 Russell, J., & Pierce-Shimomura, J. “Apparatus for investigating the reactions of soft-bodied invertebrates to controlled humidity gradients.”  J Neurosci Methods in press.

2014 Davis, S., Scott, L., Hu, K., Pierce-Shimomura, J. "Conserved single residue on the BK potassium channel required for activation by alcohol and intoxication in C. elegans." J Neuroscience 34(29):9562-73.

2014 Russell, J., Vidal-Gadea, A.G., Makay, A., Lanam, C. & Pierce-Shimomura, J. “Humidity sensation requires dual mechanosensory and thermosensory pathways in C. elegans.Proc Nat Acad Sci 111(22): 8269-74.

2014 Topper, S., Aquilar, S.C., Topper, V., Ebel, E. & Pierce-Shimomura, J. “Alcohol disinhibition of behaviors in C. elegans.PLoS ONE 9(3):e92965.

2013 Zlotkowski, K., Pierce-Shimomura, J. & Siegel, D. “Small-molecule-mediated axonal branching in Caenorhabditis elegansChem Bio Chem 14(3):307-10.

2013 Iyer, S. & Pierce-Shimomura, J. “Worming our way to Alzheimer’s disease drug discovery.” Biological Psychiatry 1;73(5):396-8.

2012 Vidal-Gadea, A. & Pierce-Shimomura, J. “Conserved role of dopamine in the modulation of behavior.” Commun Integr Biol 5(5):440-7.

2012 Vidal-Gadea, A., Davis, S., Becker ,L. & Pierce-Shimomura, J. “Coordination of behavioral hierarchies during environmental transitions in Caenorhabditis elegans.” Worm 1(1):4-10. Cover article.

2012 Alaimo, J., Davis, S., Song, S., Burnette, C., Shelton, K. & Pierce-Shimomura, J., Davies, A. & Bettinger, J. “Ethanol metabolism and osmolarity modify behavioral responses to ethanol in C. elegans.” Alcoholism: Clinical and Experimental Research 36(11):1840-50.

2011 Vidal-Gadea AG, Topper S, Young L, Crisp A, Kressin L, Elbel E, Maples T, Brauner M, Erbguth K, Axelrod A, Gottschalk A, Siegel D, Pierce-Shimomura JT, Caenorhabditis elegans selects distinct crawling and swimming gaits via dopamine and serotonin, PNAS 108(42):17504-9.

2010 Speca, D.J., Chihara, D., Ashique, A.M., Bowers, M.S, Pierce-Shimomura, J.T., Lee, J., Rabbee, N. Speed, T.P., Gularte, R.J., Chitwood, J., Medrano, J.F., Liao, M., Sonner, J.M., Eger, E.I., Peterson, A.S. & McIntire, S.L. “Conserved Role of unc-79 in ethanol responses in Lightweight mutant mice” PLoS Genetics 6(8). pii: e1001057.

2010 Schreiber, M.A., Pierce-Shimomura, J.T., Chan, S., Parry, D. & McIntire, S.L. "Manipulation of behavioral decline in Caenorhabditis elegans with the Rag GTPase raga-1PLoS Genetics 6: e1000972.

2009 Kim, H., Pierce-Shimomura, J.T, Oh, H.J., Johnson, B.E., Goodman, M.B. & McIntire, S.L. "The dystrophin complex controls BK channel localization and muscle activity in C. elegansPLoS Genetics 5(12):e1000780.

2008 Pierce-Shimomura, J.T., Chen, B.L., Mun, J., Ho, R., Sarkis, R. & McIntire, S.L. "A genetic approach to locomotory pattern generation: Crawl and swim behaviors of C. elegans." Proc Nat Acad Sci 105: 20982-20987.

2006 Dunn N. A., Pierce-Shimomura, J. T., Conery, J. S., Lockery, S. R, Clustered Neural Dynamics identify motifs for chemotaxis in Caenorhabditis elegans, IEEE World Congress on Computational Intelligence. 2011:

2005 Pierce-Shimomura, J. T., Dores, M., Lockery, S. R., Analysis of turning bias on chemotaxis in C. elegans, J Experimental Biology 208: 4727-4733

2006 Dunn N.A., Pierce-Shimomura, J.T., Conery, J.S., Lockery, S.R. "Clustered Neural Dynamics identify motifs for chemotaxis in Caenorhabditis elegans." IEEE World Congress on Computational Intelligence. Paper number 2011.

2003 Davies, A.G., Pierce-Shimomura, J.T., Kim, H., VanHoven, M.K., Thiele, T.R., Bonci, A., Bargmann, C.I. & McIntire, S.L. "A central role of the BK potassium channel in behavioral responses to ethanol in C. elegans." Cell 115(6): 655-666.

2005 Pierce-Shimomura, J.T., Dores, M. & Lockery, S.R. "Analysis of turning bias on chemotaxis in C. elegans." Journal of Experimental Biology 208: 4727-4733.

2004 Dunn N.A., Lockery, S.R., Pierce-Shimomura, J.T. & Conery, J. S. "A neural model of chemotaxis predicts the function of synaptic connections in Caenorhabditis elegans." Journal of Computational Neuroscience 17(2): 137-147.

2001 Pierce-Shimomura, J.T., Faumont, S., Gaston, M.R., Pearson, B.J. & Lockery, S.R. "The homeobox gene lim-6 is required for distinct chemosensory representations in C. elegans." Nature 410 (6829): 694-698.

1999 Pierce-Shimomura, J.T., Morse, T.M. & Lockery, S.R. "The fundamental role of pirouettes in C. elegans chemotaxis." Journal of Neuroscience 19: 9557-9569.

1997 Streichert L.C., Pierce, J.T., Nelson, J.A. & Weeks, J.C. "Steroid hormones act directly to trigger segment-specific programmed cell death of identified motoneurons in vitro." Developmental Biology 183: 95-107.

1997 Weeks, J.C., Jacobs, G.A., Pierce, J.T., Sandstrom, D.J., Streichert, L.C., Trimmer, B.A., Wiel, D.E. & Wood, E.R. "Neural mechanisms of behavioral plasticity: metamorphosis and learning in Manduca sexta." Brain Behavior and Evolution 50 Suppl 1:69-80.


  • 1991    Rosefski Scholarship to study abroad at Kansai University in Japan

  • 1994    Phi Beta Kappa, Binghamton University

  • 1994    Graduated cum laude in Biological Sciences from Binghamton University

  • 1996    National Institutes of Health Predoctoral Fellow, Grant # GM07257

  • 2009    Summer Research Award, UT Austin, TX

  • 2009    Faculty of 1000 Biology “Must read” evaluation by Dr. Calabrese for our SFN presentation, “Neural Mechanisms for Switching Locomotory Patterns in C. elegans

  • 2010    New Investigator Grant from Alzheimer’s Association

  • 2011    NIH Director’s Transformative Research Project Award

  • 2012    Best poster at International Society for Neuroethology conference, Univ Maryland

  • 2012    “Upside of Down” ($3k) award for initiatives in hiring adults with Down syndrome

  • 2012    “Enterprise Rentals” ($3k) award for hiring adults with Down syndrome

  • 2013    National Down Syndrome Society ($10k) award for initiatives in adult education

  • 2013    Natural Sciences Council Student-Selected Exemplary Teaching Award at

                            University of Texas at Austin

  • 2013    “Enterprise Rentals” ($3k) award for hiring adults with Down syndrome

  • 2014    Faculty of 1000 recommendation on our humidity sensation paper in PNAS