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Introduction to Developmental Biology

Instructors: Anna Kicheva, Carl-Philipp Heisenberg, Eva Benková, Jiri Friml

Teaching Assistants: Martina Greunz, Karla Huljev


Credits: 6


Tuesdays, 10:15-11:30 (Mondi 2) 

Thursday, 11:20-12:35 (Mondi 3)


Introduction and start of the experiments: 10:15 - 12:35 in Eva's, CP's or Ani's lab;

Final presentations:

A list of papers will be provided on the course website. Each student will choose one paper from the list and present it at the end of the course. Presentation + discussion should be approximately 25 min per paper.

Schedule (subject to change)

Tue 11 Part 1 CP
Thu 13 Part 1 Ani
Tue 18 Part 1 Jiri
Thu 20 Part 1 Eva
Tue 25 Practicum (plants)
Thu 27 recitation
Thu 3 Part 2 Eva
Tue 8 Part 2 Jiri
Thu 10 Part 2 Ani
Tue 15 Part 2 CP
Thu 17 recitation
Tue 22 Practicum (fish)
Thu 24 Part 3 Jiri
Tue 29 Part 3 Jiri
Thu 1 Part 3 CP
Tue 6 Part 3 Ani
Tue 13 Practicum (mouse)
Thu 15 recitation
Tue 20 Part 4 Eva
Thu 22 Part 4 Eva
Tue 10 Part 4 CP
Thu 12 Part 4 Ani
Tue 17 Discussion
Thu 19 presentations
Tue 24 presentations
Thu 26 presentations

Material covered in the course and further reading

October 11, 2016 CP

Early oocyte polarization events in zebrafish

Patterning of the early zebrafish embryo

Forces driving early zebrafish morphogenetic events 


Langdon YG, Mullins MC Maternal and zygotic control of zebrafish dorsoventral axial patterning. Annu Rev Genet. 2011

Elkouby YM, Jamieson-Lucy A, Mullins MC Oocyte Polarization Is Coupled to the Chromosomal Bouquet, a Conserved Polarized Nuclear Configuration in Meiosis. PLoS Biol. 2016

Schier AF, Talbot WS Molecular genetics of axis formation in zebrafish. Annu Rev Genet. 2005

Sako K et al. Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation. Cell Rep. 2016

Bensch R, Song S, Ronneberger O, Driever W Non-directional radial intercalation dominates deep cell behavior during zebrafish epiboly. Biol Open. 2013


October 13, 2016  Ani

Mouse gastrulation

Early gut formation in mouse

Neural lineage

Neural crest



Philos Trans R Soc Lond B Biol Sci. 2014 Dec 5;369(1657). pii: 20130547.Gutsy moves in mice: cellular and molecular dynamics of endoderm morphogenesis. Viotti MFoley ACHadjantonakis AK.

Development. 2015 Sep 1;142(17):2864-75. Neuromesodermal progenitors and the making of the spinal cord. Henrique D1, Abranches E1, Verrier L2, Storey KG3. 

PLoS Biol. 2014 Aug 26;12(8):e1001937. In vitro generation of neuromesodermal progenitors reveals distinct roles for wnt signalling in the specification of spinal cord and paraxial mesoderm identity. Gouti MTsakiridis AWymeersch FJ2, Huang Y2, Kleinjung J1, Wilson VBriscoe J.

Nat Rev Genet. 2016 Sep 12. doi: 10.1038/nrg.2016.98. Transition states and cell fate decisions in epigenetic landscapes. Moris N1, Pina C2, Arias AM1. 

Developmental Biology. Scott F Gilbert. ISBN: 978-1-60535-470-5

Cell. 2016 Feb 11;164(4):656-67. Self-Organization of Embryonic Genetic Oscill ators into Spatiotemporal Wave Patterns.Tsiairis CDAulehla A.

Elife. 2016 Feb 13;5. pii: e08438. Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock. Webb ABLengyel IMJörg DJValentin GJülicher FMorelli LGOates AC. 

Development. 2012 Feb;139(4):625-39. Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock. Oates ACMorelli LGAres S.


November 10, 2016 Ani

Reaction-diffusion systems

Positional information

Morphogen gradient formation at the cellular and tissue level


Tickle C, Summerbell D, Wolpert L. (1975) Positional signalling and specification of digits in chicklimb morphogenesis. Nature.  20;254(5497):199-202.

Ephrussi and St Johnston (2004) Seeing is believing: the bicoid morphogen gradient matures. Cell 23;116(2):143-52. 

Wartlick O, Kicheva A, González-Gaitán M. (2009) Morphogen gradient formation. Cold Spring Harb Perspect Biol. 1(3):a001255.

Müller P, Rogers KW, Jordan BM, Lee JS, Robson D, Ramanathan S, Schier AF. (2012) Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science 336(6082):721-4.

Briscoe J, Vincent JP.(2013) Hedgehog threads to spread. Nat Cell Biol. 15(11):1265-7.

Green JB, Sharpe J. (2015) Positional information and reaction-diffusion: two big ideas in developmental biology combine. Development.  142(7):1203-11.


November 15, 2016 CP

 Gradients in morphogenesis 

I. Biochemical gradients in morphogenesis 

Somite formation and segmentation in vertebrates

Pourquié O. Segmentation of the paraxial mesoderm and vertebrate somitogenesis. Curr Top Dev Biol. 

Bertrand S, Aldea D, Oulion S, Subirana L, de Lera AR, Somorjai I, Escriva H. Evolution of the Role of RA and FGF Signals in the Control of Somitogenesis in Chordates. PLoS One. 2015 

Yabe T, Takada S. Molecular mechanism for cyclic generation of somites: Lessons from mice and zebrafish. Dev Growth Differ. 2016 


II. Mechanical gradients in morphogenesis 

Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill SW, Heisenberg CP. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012 

Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg CP. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nat Cell Biol. 2013 

Campinho P, Heisenberg CP. The force and effect of cell proliferation. EMBO J. 2013 


December 6, 2016 Ani

Models of tissue morphogenesis

Aigouy BFarhadifar RStaple DBSagner ARöper JCJülicher FEaton S. (2010) Cell flow reorients the axis of planar polarity in the wing epithelium of Drosophila. Cell 142(5):773-86. doi: 10.1016/j.cell.2010.07.042.

Farhadifar R, Röper JC, Aigouy B, Eaton S, Jülicher F. (2007) The influence of cell mechanics, cell-cell interactions, and proliferation on epithelial packing. Curr Biol. 17(24):2095-104.

Etournay R, Merkel M, Popović M, Brandl H, Dye NA, Aigouy B, Salbreux G, Eaton S, Jülicher F. (2016) TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics. Elife 5. pii: e14334. doi: 10.7554/eLife.14334.

Fletcher, A. G., Osterfield, M., Baker, R. E., & Shvartsman, S. Y. (2014). Vertex Models of Epithelial Morphogenesis. Biophysical Journal, 106(11), 2291–2304.


Boehm, B., Westerberg, H., Lesnicar-Pucko, G., Raja, S., Rautschka, M., Cotterell, J., Swoger, J. and Sharpe, J. (2010). The role of spatially controlled cell proliferation in limb bud morphogenesis. PLoS Biol. 8, e1000420.


Jan. 12, 2017 Ani

Regulation of organ growth in Drosophila and mammals

Intrinsic vs extrinsic growth control in Drosophila


Mirth, C. K. and Shingleton, A. W. (2012). Integrating body and organ size in Drosophila: Recent advances and outstanding problems. Front. Endocrinol. (Lausanne). 3, 1–13.

Edgar, B. a (2006). How flies get their size: genetics meets physiology. Nat. Rev. Genet. 7, 907–16.

Day, S. J. and Lawrence, P. A. (2000). Measuring dimensions: the regulation of size and shape. Development 127, 2977–87.

Neufeld, T. P., Flor, A., Cruz, A. De, Johnston, L. A. and Edgar, B. A. (1998). Coordination of Growth and Cell Division in the Drosophila Wing. 93, 1183–1193.

Wartlick, O., Mumcu, P., Kicheva, A., Bittig, T., Seum, C., Jülicher, F. and González-Gaitán, M. (2011). Dynamics of Dpp Signaling and Proliferation Control. Science 331, 1154–9.

Lewis, N. E. and Rossant, J. (1982). Mechanism of size regulation in mouse embryo aggregates. J. Embryol. Exp. Morphol. 72, 169–181.

Clavería, C., Giovinazzo, G., Sierra, R. and Torres, M. (2013). Myc-driven endogenous cell competition in the early mammalian embryo. Nature 500, 39–44.

Sancho, M., Di-Gregorio, A., George, N., Pozzi, S., Sánchez, J. M., Pernaute, B. and Rodríguez, T. a (2013). Competitive interactions eliminate unfit embryonic stem cells at the onset of differentiation. Dev. Cell 26, 19–30.

Papers for final presentations