Workshop Readings (Year 1)

Header of Progam for Workshop
  • Friday (April 24) – Invited Experts

(I) Lance Davidson

  • Essential Reading
  1. von Dassow, M. and L.A. Davidson. 2011. Physics and the canalization of morphogenesis: a grand challenge in organismal biology. Physical Biology 8:045002.
  2. Zhou, J., S. Pal, S. Maiti, and L.A. Davidson. 2015. Force production and mechanical accommodation during convergent extension. Development 142:692–701.
  •  Background Papers
  1. Blanchard, G.B., A.J. Kabla, N.L. Schultz, L.C. Butler, B. Sanson, N. Gorfinkiel, L. Mahadevan, and R.J. Adams. 2009. Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation. Nature Methods 6:458–464.
  2. Keller, R., L.A. Davidson, A. Edlund, T. Elul, M. Ezin, D. Shook, and P. Skoglund. 2000. Mechanisms of convergence and extension by cell intercalation. Philosophical Transactions of the Royal Society B: Biological Sciences 355:897–922.
  3. Miller, C.J., and L.A. Davidson. 2013. The interplay between cell signalling and mechanics in developmntal processes. Nature Reviews Genetics 14:733–744.

(II) Eric Wieschaus

  • Essential Reading
  1. Dubuis, J.O., G. Tkačik, E.F. Wieschaus, T. Gregor, and W. Bialek. 2013. Positional information, in bits. Proceedings of the National Academy of Sciences USA 110:16301–16308.
  2. Gergen, J.P., D. Coulter, and E.F. Wieschaus. 1986. Segmental pattern and blastoderm cell identities. In: Gametogenesis and the Early Embryo, ed. J.G. Gall, 195–220. New York: Alan R. Liss, Inc.
  • Background Papers
  1. Ephrussi, A., and D. St Johnston. 2004. Seeing is believing: the Bicoid morphogen gradient matures. Cell 116:143–152.
  2. Gregor, T., A.P. McGregor, and E.F. Wieschaus. 2008. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Developmental Biology 316:350–358.
  3. Gregor, T., D.W. Tank, E.F. Wieschaus, and W. Bialek. 2007. Probing the limits to positional information. Cell 130:153–164.

(III) Claudio Stern

  • Essential Reading
  1. Dias, A.S., I. de Almeida, J.M. Belmonte, J.A. Glazier, and C.D. Stern. 2014. Somites without a clock. Science 343:791–795.
  • Background Papers
  1. Cooke, J., and E.C. Zeeman. 1976. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. Journal of Theoretical Biology 58:455–476.
  2. Palmeirim, I., D. Henrique, D. Ish-Horowicz, and O. Pourquié. 1997. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91:639–648.
  3. Primmett, D. R., W.E. Norris, G.J. Carlson, R.J. Keynes, and C.D. Stern. 1989. Periodic segmental anomalies induced by heat shock in the chick embryo are associated with the cell cycle. Development 105:119–130.

(IV) Michael Levin

  • Essential Reading
  1. Levin, M. 2014. Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration. The Journal of Physiology 592:2295–2305.
  2. Pezzulo, G., and M. Levin. 2015. Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs. Annual Review of Biomedical Engineering.
  • Background Papers
  1. Levin, M. 2012. Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning. Biosystems 109:243–261.
  2. Levin, M. 2014. Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo. Molecular Biology of the Cell 25:3835–3850.
  3. Tseng, A., and M. Levin. 2013. Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation. Communicative & Integrative Biology 6:e22595.
  • Saturday (April 25) – Topical Discussions

(I) False Starts and Historical Perspective

  • Background Papers
  1. Akam, M. 1989. Making stripes inelegantly. Nature 341:282–283.
  2. Goodwin, B.C., and M.H. Cohen. 1969. A phase-shift model for the spatial and temporal organization of developing systems. Journal of Theoretical Biology 25:49–107.
  3. Harris, A.K., P. Warner, and D. Stopak. 1984. Generation of spatially periodic patterns by a mechanical instability: a mechanical alternative to the Turing model. Journal of Embryology and Experimental Morphology 80:1–20.
  4. Lu, K., T. Cao, and R. Gordon. 2012. A cell state splitter and differentiation wave working-model for embryonic stem cell development and somatic cell epigenetic reprogramming. Biosystems 109:390–396.

(II) Working Models

  • Background Papers
  1. Davidson, L.A. 2012. Epithelial machines that shape the embryo. Trends in Cell Biology 22:82–87.
  2. Gonzalez-Rodriguez, D., K. Guevorkian, S. Douezan, and F. Brochard-Wyart. 2012. Soft matter models of developing tissues and tumors. Science 338:910–917.
  3. Sampathkumar, A., A. Yan, P. Krupinski, and E.M. Meyerowitz. 2014. Physical forces regulate plant development and morphogenesis. Current Biology 24:R475–R483.

(III) Experimental Challenges & Opportunities

  • Background Papers
  1. Arends, F., C. Nowald, K. Pflieger, K. Boettcher, S. Zahler, and O. Lieleg. 2015. The biophysical properties of basal lamina gels depend on the biochemical composition of the gel. PLoS ONE 10:e0118090.
  2. Bambardekar, K., R. Clément, O. Blanc, C. Chardès, and P.-F. Lenne. 2015. Direct laser manipulation reveals the mechanics of cell contacts in vivo. Proceedings of the National Academy of Sciences USA 112:1416–1421.
  3. Haack, T., D.T. Bergstralh, and D. St Johnston. 2013. Damage to the Drosophila follicle cell epithelium produces “false clones” with apparent polarity phenotypes. Biology Open 2:1313–1320.
  4. Shestopalov, I.A., C.L.W. Pitt, and J.K. Chen. 2012. Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nature Chemical Biology 8:270–276.

(IV) Computational Approaches

  • Background Papers
  1. Moore, S.R., G.M. Saidel, U. Knothe, and M.L. Knothe Tate. 2014. Mechanistic, mathematical model to predict the dynamics of tissue genesis in bone defects via mechanical feedback and mediation of biochemical factors. PLoS Computational Biology 10:e1003604.
  2. Morelli, L.G., K. Uriu, S. Ares, and A.C. Oates. 2012. Computational approaches to developmental patterning. Science 336:187–191.
  3. Shyer, A.E., T. Tallinen, N.L. Nerurkar, Z. Wei, E. Seok Gil, D.L. Kaplan, C.J. Tabin, and L. Mahadevan. 2013. Villification: how the gut gets its villi. Science 342:212–218.

(V) Different Developmental Problems

  • Background Papers
  1. Fagotto, F. 2014. The cellular basis of tissue separation. Development 141:3303–3318.
  2. Perathoner, S., J.M. Daane, U. Henrion, G. Seebohm, C.W. Higdon, S.L. Johnson, C. Nüsslein-Volhard, and M.P. Harris. 2014. Bioelectric signaling regulates size in zebrafish fins. PLoS Genetics 10:e1004080.
  3. Raspopovic, J., L. Marcon, L. Russo, and J. Sharpe. 2014. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients. Science 345:566–570.
  4. Varner, V.D., and C.M. Nelson. 2014. Cellular and physical mechanisms of branching morphogenesis. Development 141:2750–2759.

(VI) Different Explanatory Factors

  • Background Papers
  1. Freund, J.B., J.G. Goetz, K.L. Hill, and J. Vermot. 2012. Fluid flows and forces in development: functions, features and biophysical principles. Development 139:1229–1245.
  2. Milinkovitch, M.C., L. Manukyan, A. Debry, N. Di-Poï, S. Martin, D. Singh, D. Lambert, and M. Zwicker. 2013. Crocodile head scales are not developmental units but emerge from physical cracking. Science 339:78–81.
  3. Ríos-Barrera, L.D., I. Gutiérrez-Pérez, M. Domínguez, and J.R. Riesgo-Escovar. 2015. acal is a long non-coding RNA in JNK signaling in epithelial shape changes during Drosophila dorsal closure. PLoS Genetics 11:e1004927.

General Background Readings

  1. Howard, J., S.W. Grill, and J.S. Bois. 2011. Turing's next steps: the mechanochemical basis of morphogenesis. Nature Reviews Molecular Cell Biology 12:392–398.
  2. Kicheva, A., M. Cohen, and J. Briscoe. 2012. Developmental pattern formation: insights from physics and biology. Science 338:210–212.
  3. Mammoto, T., and D.E. Ingber. 2010. Mechanical control of tissue and organ development. Development 137:1407–1420.
  4. Newman, S.A. 2014. Physico-genetics of morphogenesis: the hybrid nature of developmental mechanisms. In: Towards a Theory of Development, eds. A. Minelli, and T. Pradeu. Oxford: Oxford University Press.