Abstracting the principles of development using imaging and modeling

Integrative Biology (United Kingdom)

Volumn 7, Issue 6, 2015, Pages 633-642

  Xiong, Fengzhu ^a   Megason, Sean G ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MORPHOGEN;

ARTICLE; DEVELOPMENTAL BIOLOGY; IMAGE ANALYSIS; MATHEMATICAL MODEL; MORPHOGENESIS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SYSTEMS BIOLOGY; ZEBRA FISH; ANIMAL; BIOLOGICAL MODEL; EMBRYOLOGY; FLUORESCENCE IMAGING; PROCEDURES; TRENDS;

DANIO RERIO;

ANIMALS; BODY PATTERNING; DEVELOPMENTAL BIOLOGY; MODELS, BIOLOGICAL; OPTICAL IMAGING; SYSTEMS BIOLOGY; ZEBRAFISH;

EID: 84930887947     PISSN: 17579694     EISSN: 17579708     Source Type: Journal    
DOI: 10.1039/c5ib00025d     Document Type: Article

References (43)

1. M. W. Kirschner The meaning of systems biology Cell 2005 121 503 504
2. S. G. Megason S. E. Fraser Imaging in systems biology Cell 2007 130 784 795
3. S. G. Megason S. Srinivas M. E. Dickinson A. K. Hadjantonakis Microscopy to mechanism across the scales of development Curr. Opin. Genet. Dev. 2011 21 519 522
4. S. F. Gilbert, Mathematical Modeling of Development, Developmental Biology, Sinauer Associates, Sunderland, MA, 6th edn, 2000, (http://www.ncbi.nlm.nih.gov/books/NBK10126/)
5. L. A. Davidson B. Baum Making waves: the rise and fall and rise of quantitative developmental biology Development 2012 139 3065 3069
6. P. Pantazis W. Supatto Advances in whole-embryo imaging: a quantitative transition is underway Nat. Rev. Mol. Cell Biol. 2014 15 327 339
7. J. Sharpe Two ways to use imaging: focusing directly on mechanism, or indirectly via behaviour? Curr. Opin. Genet. Dev. 2011 21 523 529
8. D. W. Thompson, On Growth and Form, Cambridge University Press, Cambridge, 1942
9. G. Odell G. Oster P. Alberch B. Burnside The mechanical basis of morphogenesis. I. Epithelial folding and invagination Dev. Biol. 1981 85 446 462
10. M. Barkoulas J. S. van Zon J. Milloz A. van Oudenaarden M. A. Félix Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation Dev. Cell 2013 24 64 75
11. W. Ma A. Trusina H. El-Samad W. A. Lim C. Tang Defining network topologies that can achieve biochemical adaptation Cell 2009 138 760 773
12. A. L. Hodgkin A. F. Huxley A quantitative description of membrane current and its application to conduction and excitation in nerve J. Physiol. 1952 117 500 544
13. E. Neher B. Sakmann Single-channel currents recorded from membrane of denervated frog muscle fibres Nature 1976 260 799 802
14. I. Imayoshi A. Isomura Y. Harima K. Kawaguchi H. Kori H. Miyachi T. Fujiwara F. Ishidate R. Kageyama Oscillatory control of factors determining multipotency and fate in mouse neural progenitors Science 2013 342 1203 1208
15. F. Xiong W. Ma T. W. Hiscock K. R. Mosaliganti A. R. Tentner K. A. Brakke N. Rannou A. Gelas L. Souhait I. A. Swinburne N. D. Obholzer S. G. Megason Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis of Developing Epithelia Cell 2014 159 415 427
16. S. G. Megason S. E. Fraser Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development Mech. Dev. 2003 120 1407 1420
17. M. Westerfield E. Doerry A. E. Kirkpatrick S. A. Douglas Zebrafish informatics and the ZFIN database Methods Cell Biol. 1999 60 339 355
18. J. Sulston E. Schierenberg J. White J. Thomson The embryonic cell lineage of the nematode Caenorhabditis elegans Dev. Biol. 1983 100 64 119
19. J. P. Junker E. S. Noël V. Guryev K. A. Peterson G. Shah J. Huisken A. P. McMahon E. Berezikov J. Bakkers A. van Oudenaarden Genome-wide RNA Tomography in the zebrafish embryo Cell 2014 159 662 675
20. C. B. Kimmel W. W. Ballard S. R. Kimmel B. Ullmann T. F. Schilling Stages of embryonic development of the zebrafish Dev. Dyn. 1995 203 253 310
21. C. B. Kimmel R. D. Law Cell lineage of zebrafish blastomeres. III. Clonal analyses of the blastula and gastrula stages Dev. Biol. 1985 108 94 101
22. D. Strehlow G. Heinrich W. Gilbert The fates of the blastomeres of the 16-cell zebrafish embryo Development 1994 120 1791 1798
23. D. Kane M. Hammerschmidt M. Mullins H. Maischein M. Brand F. van Eeden M. Furutani-Seiki M. Granato P. Haffter C. Heisenberg Y. J. Jiang R. N. Kelsh J. Odenthal R. M. Warga C. Nüsslein-Volhard The zebrafish epiboly mutants Development 1996 123 47 55
24. P. J. Keller A. D. Schmidt J. Wittbrodt E. H. Stelzer Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy Science 2008 322 1065 1069
25. N. Olivier M. A. Luengo-Oroz L. Duloquin E. Faure T. Savy I. Veilleux X. Solinas D. Debarre P. Bourgine A. Santos N. Peyrieras E. Beaurepaire Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy Science 2010 329 967 971
26. D. A. Kane K. N. McFarland R. M. Warga Mutations in half baked/E-cadherin block cell behaviors that are necessary for teleost epiboly Development 2000 132 1105 1116
27. M. Köppen B. G. Fernández L. Carvalho A. Jacinto C. P. Heisenberg Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila Development 2006 133 2671 2681
28. M. Behrndt G. Salbreux P. Campinho R. Hauschild F. Oswald J. Roensch S. W. Grill C. P. Heisenberg Forces driving epithelial spreading in zebrafish gastrulation Science 2012 338 257 260
29. A. Turing The chemical basis of morphogenesis Bull. Math. Biol. 1953 52 153 197
30. L. Wolpert Positional information and the spatial pattern of cellular differentiation J. Theor. Biol. 1969 25 1 47
31. P. Muller K. W. Rogers B. M. Jordan J. S. Lee D. Robson S. Ramanathan A. F. Schier Differential diffusivity of nodal and lefty underlies a reaction-diffusion patterning system Science 2012 336 721 724
32. F. Xiong A. R. Tentner P. Huang A. Gelas K. R. Mosaliganti L. Souhait N. Rannou I. A. Swinburne N. D. Obholzer P. D. Cowgill A. F. Schier S. G. Megason Specified neural progenitors sort to form sharp domains after noisy shh signaling Cell 2013 153 550 561
33. S. Ahn A. L. Joyner Dynamic changes in the response of cells to positive hedgehog signaling during mouse limb patterning Cell 2004 118 505 516
34. E. Dessaud L. L. Yang K. Hill B. Cox F. Ulloa A. Ribeiro A. Mynett B. G. Novitch J. Briscoe Interpretation of the sonic hedgehog morphogen gradient by a temporal adaptation mechanism Nature 2007 450 717 720
35. P. J. Keller Imaging morphogenesis: technological advances and biological insights Science 2013 340 1234168
36. K. Chung J. Wallace S. Y. Kim S. Kalyanasundaram A. S. Andalman T. J. Davidson J. J. Mirzabekov K. A. Zalocusky J. Mattis A. K. Denisin S. Pak H. Bernstein C. Ramakrishnan L. Grosenick V. Gradinaru K. Deisseroth Structural and molecular interrogation of intact biological systems Nature 2013 497 332 337
37. N. Renier Z. Wu D. J. Simon J. Yang P. Ariel M. Tessier-Lavigne iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging Cell 2014 159 896 910
38. K. Tainaka S. I. Kubota T. Q. Suyama E. A. Susaki D. Perrin M. Ukai-Tadenuma H. Ukai H. R. Ueda Whole-body imaging with single-cell resolution by tissue decolorization Cell 2014 159 911 924
39. K. M. Dean A. E. Palmer Advances in fluorescence labeling strategies for dynamic cellular imaging Nat. Chem. Biol. 2014 10 512 523
40. M. Eiraku N. Takata H. Ishibashi M. Kawada E. Sakakura S. Okuda K. Sekiguchi T. Adachi Y. Sasai Self-organizing optic-cup morphogenesis in three-dimensional culture Nature 2011 472 51 56
41. H. J. Kim D. E. Ingber Gut-on-a-chip microenvironment induces human intestinal cells to undergo villus differentiation Integr. Biol. 2013 5 1130 1140
42. K. R. Mosaliganti R. R. Noche F. Xiong I. A. Swinburne S. G. Megason ACME: automated cell morphology extractor for comprehensive reconstruction of cell membranes PLoS Comput. Biol. 2012 8 e1002780
43. F. Amat W. Lemon D. P. Mossing K. McDole Y. Wan K. Branson E. W. Myers P. J. Keller Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data Nat. Methods 2014 11 951 958