Cell Biology & Molecular Genetics
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Todd J. Cooke


Ph.D. - Cornell University, 1979
Telephone: (301) 405-1628
Fax: (301) 314-9082

Research Interests:
Plant biology; developmental mechanisms responsible for the origin and diversification of land plants; generation of biological form; biology education research

Because the goal of our lab is to train independent and creative scientists, each student is strongly encouraged to design his/her own research project to address an important question in one of the above research areas. Plant biology projects are carried out on a wide range of green plants by using appropriate techniques from developmental biology, biophysics, genetics, analytical biochemistry, and other disciplines.  Biology education research is primarily devoted to studying how biology students learn physics and mathematics in biology classes.

1) Novel developmental mechanisms in the origin and diversification of land plants - The successful invasion of the terrestrial environment by certain charophycean green algae represented in a pivotal event in the evolution of life. We are very interested in how evolutionary contingency (i.e., the genetic, developmental, and physiological toolkits already present in those ancestral algae) and subsequent innovation resulted in novel developmental mechanisms that operated in the evolution of early land plants. We are devoting particular emphasis to the small bryophytes (hornworts, liverworts, mosses), which represent the most basal lineages of living land plants. For example, DorothyBelle Poli studied g how these bryophytes generate post-embryonic axes, which is the key process for constructing plant bodies. In contemporary vascular plants (e.g., ferns, gymnosperms, flowering plants), axis formation is regulated by polar transport of the hormone auxin (indole-3-acetic acid) via specific transmembrane proteins; therefore, DB investigated the mechanism of auxin movement in bryophyte axes. She discovered different mechanisms of auxin movement mechanisms operating in bryophyte lineages: simple diffusion in hornworts, facilitated apolar diffusion in liverworts, and genuine polar transport in mosses. One plausible interpretation is that the earliest land plants evolved various mechanisms for regulating axis formation, with the common ancestor of the moss-vascular plant lineage evolving a transport mechanism that is preadapted for constructing the long axes of vascular plants.

    Poli, DB, Jacobs, M, and Cooke, TJ. 2003. Auxin regulation of axial growth in bryophyte sporophytes: Its potential significance for the evolution of early land plants. American Journal of Botany 90: 1405-1415. (article 3)

    Cooke, TJ, Poli, DB, and Cohen, JD. 2003. Did auxin play a crucial role in the evolution of novel body plans during the late Silurian-early Devonian radiation of land plants? In: AM Hemsly and I Poole, eds. The Evolution of Plant Physiology, pp. 85-107. Academic Press: London. (article 4)

2) Generation of biological form (morphogenesis) - Research problems in plant morphogenesis are especially challenging because morphogenetic processes appear to depend not only on specific gene expression being regulated in time and space but also on physicochemical mechanisms capable of operating on all living and non-living structures. For example, Wanda Kelly investigated leaf arrangement (also are quite unique because they have the unique potential to arrange their leaves in either Fibonacci spirals or non-Fibonacci whorls. In essence, in spiral phyllotaxis, if the leaves are assigned a number in the order of their origin, then the intervals in the numbers between successive leaves in each spiral can be related to the enigmatic Fibonacci series (1, 1, 2, 3, 5, 8, 13, etc.). By contrast, the leaves in whorled phyllotaxis are arranged in stacked rings encircling the axis. Wanda’s research has led her to discover elusive geometrical principles underlying the phyllotactic patterning of all plants.

    Kelly, W.J, and Cooke, T.J. 2003. Geometrical principles governing the phyllotaxis of aquatic plants. American Journal of Botany 90: 1131-1143. (article 1)

    Cooke, T.J. 2006. Do Fibonacci numbers reveal the involvement of geometrical imperatives or biological interactions in phyllotaxis? Botanical Journal of Linnean Society. 150: 3-24. (article 7)

3) Undergraduate Biology Education – Since 2005, I have devoted considerable effort toward transforming undergraduate biology curriculum at UM. For example, the portion of introductory biology sequence devoted to organisms and their functions is traditionally taught as a series of separate lectures on each major group, which is often called “the forced march through the phyla”. My biology colleague Jeff Jensen and I created a new course named BSCI 207 Principles of Biology III: Organismal Biology, which focuses on the mathematical, physical, chemical, genomic, and evolutionary principles operating in all organisms. However, the BSCI 207 lectures by themselves were relatively ineffective at conveying fundamental principles so that we have recently devised a set of small group, active-engagement (GAE) exercises for helping students in a large classroom to learn and apply these principles. In conjunction with the Physics Education Research Group at UM, Jess Watkins and Kristi Hall are studying the effectiveness of these GAE’s as the first stage in a larger research effort on how biology students learn fundamental scientific principles and how our current teaching strategies might be changed to foster more effective learning in biology classrooms.

    Watkins J.E., Hall, K.L., Redish, E.F., and Cooke T.J. (In press). Understanding how students use physical ideas in introductory biology courses. Physics Education Research Conference Proceedings.

    Hall, K.L., Watkins, J.E., Coffey, J.E., Cooke, T.J., and Redish, E.F. (In press). Examining the impact of student expectations on college-level curricular reform. 2011 American Educational Research Association Symposium Proceedings.

Ph.D. students (degree year, dissertation topic, and present position)

  • Carol Auer (1990) - cytokinin metabolism in Petunia (Associate Professor, University of Connecticut)

  • M. Stephen Ailstock (1996) - structure-function relationships in aquatic angiosperms (Chair of Biology and Director of Environmental Center, Anne Arundel Community College)

  • Roxanne H. Fisher (1996) - genetic basis of morphogenetic processes in Arabidopsis (Associate Professor, Chatham College)

  • David M. Ribnicky (1996) - auxin regulation of carrot embryogenesis (Research Associate, Rutgers University)

  • Ester Sztein (1999) - auxin metabolism in land plants (Assistant Director, International Scientific Organizations Board, National Academies)

  • DorothyBelle Poli (2005) - aauxin transport mechanisms in basal land plants (Assistant Professor, Roanoke College)

  • Kristi Hall (current Ph.D. candidate) - biology education research


I am currently teaching an introductory course in organismal biology called BSCI 207 Principles of Biology III: Organismal Biology and its honors version HLSC 207. I am also serving as the Director of Integrated Life Sciences, which is a new Living-Learning Program in the Honors College. On an ad hoc basis, I participate in graduate seminars focusing on recent advances in plant biology and in biology education research.


  • NSF Graduate Fellowship, 1974-1977
  • Jeanette Siron Pelton Award for Outstanding Research in Experimental Plant Morphology (Botanical Society of America), 1983
  • John Simon Guggenheim Memorial Fellowship, 1995-1996
  • Outstanding Contributions to Seniors Award (Office of Vice President for Student Affairs, UM), 1996
  • Lilly Foundation Excellence and Innovation in Undergraduate Teaching Awards (Center for Teaching Excellence, UM), 1997, 2008, 2009 (each award for a different course shared with several colleagues)
  • Faculty Service Excellence Award (College of Chemical and Life Sciences, UM), 2002
  • Fellow, Academy for Excellence in Teaching and Learning (UM), 2005-present
  • Lilly Fellowship (Center for Teaching Excellence, UM), 2007-2008
  • Teaching and Curriculum Development Excellence Award (College of Chemical and Life Sciences, UM), 2008
  • Education Fellow in the Life Sciences (National Academies), 2009-2010



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