I am fascinated by how beautiful and complex patterns form during development. The patterning process generally requires that one cell adopts a different identity from its neighbor. Patterns are generally formed while the cells are growing and dividing, yet the coordination of cell division and growth with the process of patterning is only beginning to be understood. In plants, regulation of cell division is crucial for proper development because plant cells cannot move or even slip relative to one another. I am interested in how growth and cell division themselves contribute to the both the development and patterning of specialized cell types in plants - a process which requires analysis of development in space and time. My laboratory uses a new, three pronged computational morphyodynamics approach that helps biologists understand how development occurs in space and time. First, we use a confocal microscope to image the living plant so that we can observe how cells grow and divide, as well as how gene expression patterns change in time during development. Every 6 hours we take the plant out of the growth room, put it on the microscope, take an image, and return the plant to the growth room. Second, we collaborate with image processing experts, who develop software that automatically detects features in the images such as nuclei and plasma membranes. For example, we can determine the number and size distribution of a population of cells. Finally, we use computational modeling to examine the consequences of our hypotheses in time. We compare our model to the live imaging data to see whether the model recreates the development of the plant. The models help us to refined hypotheses and design new experiments to test them.
The Arabidopsis sepal is a useful model system for examining the role of growth and cell division in patterning of the organ because it is accessible for imaging and manipulation. The outer epidermis of the sepal contains a characteristic pattern of giant cells, which stretch a fifth the length of the sepal, interspersed between smaller cells. This pattern of different cell sizes is tightly intertwined with cell division and growth: it arises from variation in the times when cells stop dividing and enter a specialized endoreduplication cell cycle (Roeder et al., 2010). We investigated the molecular networks underlying giant cell and small cell patterning. We found that the cell cycle inhibitor LGO (pronounced "lego ", because the lgo mutant loses giant cells and is made of small blocks) promotes giant cell formation by causing cells to exit division and enter endoreduplication early. The pattern is also regulated by intercellular signaling and transcriptional regulation via genes of the epidermal specification pathway, which control the identity of giant cells. Conversely, small cell identity appears to be linked to cell cycle regulation because altering the cell cycle is sufficient to change small cell identity. In my laboratory here at Cornell, we are using genomics combined with imaging to examine in more detail the coordination of regulation of the cell cycle with giant and small cell identity. First, we are characterizing these cells identities by asking how different are the gene expression patterns of giant and small cells. Second, we are using imaging and modeling to examine how the growth of cells within the sepal is coordinated to produce the pattern. Third, we continue to investigate the molecular networks controlling giant and small cell patterning with genetics and are currently focusing on a mutant that produces ectopic large cells. Finally, we are looking at how our findings in sepals apply to other cell types and organs in Arabidopsis and other plants. The close interrelationship between patterning, growth and division means that we must understand how manipulating one affects the other two in order to engineer better crop plants or biofuels.
Outreach and Extension Focus
My outreach activities primarily focus on interesting middle school girls in science. Through the Expanding Your Horizons program, I have taught hands on workshops in which girls isolate DNA from the vegetable cauliflower using kitchen ingredients. The girls learn that all living things, including our food, contain DNA. I also show the girls how to translate DNA sequences into the amino acids of the protein. They discover that a natural mutation in the cauliflower gene causes a truncation in the Cauliflower protein, which produces the big vegetable head that we like to eat.
In the cell biology and developmental biology sections of BIOPL 4841 Plant Form and Function: Anatomy, Cell Biology and Development, I introduce the students to plant cell biology, plant development and the techniques used to study these fields. In interactive lectures, I discuss microscopy, fluorescent proteins and construct design, subcellular localization and trafficking, the cytoskeleton and cell wall, organelles, plant cell division, specification of cell identity, transcription factors, pattern formation, intercellular signaling, morphogenesis, auxin and phyllotaxy, plant hormones, and environmental regulation of development. To solidify their understanding, the students discuss in great detail five recent research papers that illustrate these techniques and topics. For one of these papers I ask the student to practice their skills in evaluating papers by pretending they are referees for the journal. In additions I lead the students through a hands on image processing workshop in which they use open access software to visualize and analyze sample microscopy images. Homework problem sets and exams include experiment proposal and data interpretation problems so that students learn to apply their knowledge.
- Robinson, D. O., Coate, J. E., Singh, A., Hong, L., Bush, M., Doyle, J. J., & Roeder, A. (2018). Ploidy and Size at Multiple Scales in the Arabidopsis Sepal. The Plant Cell. 30:2308-2329.
- Whitewoods, C. D., Cammarata, J., Venza, Z. N., Sang, S., Crook, A. D., Aoyama, T., Wang, X. Y., Waller, M., Kamisugi, Y., Cuming, A. C., Szovenyi, P., Nimchuk, Z. L., Roeder, A., Scanlon, M. J., & Harrison, C. J. (2018). CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Current Biology. 28:2365-2376.
- Sapala, A., Runions, A., Routier-Kierzkowska, A., Das Gupta, Mainak,, Hong, L., Hofhuis, H., Verger, S., Mosca, G., Li, C., Hay, A., Hamant, O., Roeder, A., Tsiantis, M., Prusinkiewicz, P., & Smith, R. S. (2018). Why plants make puzzle cells, and how their shape emerges. eLIFE. 7:e32794.
- Tsugawa, S., Hervieux, N., Kierzkowski, D., Routier-Kierzkowska, A. L., Sapala, A., Hamant, O., Smith, R. S., Roeder, A., Boudaoud, A., & Li, C. B. (2017). Clones of cells switch from reduction to enhancement of size variability in Arabidopsis sepals. Development: For advances in developmental biology and stem cells. 144:4398-4405.
- Hong, L., Brown, J., Segerson, N. A., Rose, J., & Roeder, A. (2017). CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals. Molecular Plant. 10:560-574.
- Meyer, H. M., Teles, J., Formosa-Jordan, P., Refahi, Y., San-Bento, R., Ingram, G., Jönsson, H., Locke, J. C., & Roeder, A. (2017). Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. eLIFE. 6:e19131.
- Hong, L., & Roeder, A. (2017). Plant Development: Differential Growth Rates in Distinct Zones Shape an Ancient Plant Form. Current Biology. 27:R19-R21.
- Gillmor, C. S., Roeder, A., Sieber, P., Somerville, C., & Lukowitz, W. (2016). A Genetic Screen for Mutations Affecting Cell Division in the Arabidopsis thaliana Embryo Identifies Seven Loci Required for Cytokinesis. PLOS One. 11:e0146492.
- Hervieux, N., Dumond, M., Sapala, A., Routier-Kierzkowska, A., Roeder, A., Smith, R. S., Boudaoud, A., & Hamant, O. (2016). A mechanical feedback restricts sepal growth and shape in Arabidopsis. Current Biology. 26:1019–1028.
- Hong, L., Dumond, M., Tsugawa, S., Sapala, A., Routier-Kierzkowska, A., Zhou, Y., Chen, C., Kiss, A., Zhu, M., Hamant, O., Smith, R. S., Komatsuzaki, T., Li, C., Boudaoud, A., & Roeder, A. (2016). Variable Cell Growth Yields Reproducible Organ Development through Spatiotemporal Averaging. Developmental Cell. 38:15-32.