An integrated pipeline for the multidimensional analysis of branching morphogenesis

Nature Protocols

Volumn 9, Issue 12, 2014, Pages 2859-2879

  Combes, Alexander N ^a   Short, Kieran M ^b   Lefevre, James ^a   Hamilton, Nicholas A ^a   Little, Melissa H ^a   Smyth, Ian M ^b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BRANCHING MORPHOGENESIS; CELL COUNT; CELL CYCLE S PHASE; CELL DIVISION; CELL GROWTH; CELL INTERACTION; CELL LABELING; CELL POPULATION; CELL PROLIFERATION; DEVELOPMENTAL STAGE; EPITHELIUM CELL; FEMALE; IMAGE ANALYSIS; KIDNEY DEVELOPMENT; KIDNEY STRUCTURE; MESENCHYMAL STEM CELL; MOUSE; NONHUMAN; ANALOGS AND DERIVATIVES; ANIMAL; C57BL MOUSE; COMPUTER PROGRAM; CONFOCAL MICROSCOPY; CYTOLOGY; EMBRYOLOGY; GROWTH, DEVELOPMENT AND AGING; KIDNEY; MORPHOGENESIS; OPTICAL TOMOGRAPHY; ORGAN CULTURE TECHNIQUE; ORGANOGENESIS; PROCEDURES; STEM CELL; THREE DIMENSIONAL IMAGING;

5-ETHYNYL-2'-DEOXYURIDINE; DEOXYURIDINE;

ANIMALS; CELL PROLIFERATION; DEOXYURIDINE; IMAGING, THREE-DIMENSIONAL; KIDNEY; MICE, INBRED C57BL; MICROSCOPY, CONFOCAL; MORPHOGENESIS; ORGAN CULTURE TECHNIQUES; ORGANOGENESIS; SOFTWARE; STEM CELLS; TOMOGRAPHY, OPTICAL;

EID: 84911462558     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.193     Document Type: Article

References (52)

1. Herriges, M. & Morrisey, E.E. Lung development: orchestrating the generation and regeneration of a complex organ. Development 141, 502-513 (2014).
2. Costantini, F. & Kopan, R. Patterning a complex organ: branching morphogenesis and nephron segmentation in kidney development. Dev. Cell 18, 698-712 (2010).
3. Huebner, R.J. & Ewald, A.J. Cellular foundations of mammary tubulogenesis. Semin. Cell Dev. Biol. 31, 24-31 (2014).
4. Patel, V.N. & Hoffman, M.P. Salivary gland development: a template for regeneration. Semin. Cell Dev. Biol. 25-26C, 52-60 (2014).
5. Grobstein, C. Inductive epithelio-mesenchymal interaction in cultured organ rudiments of the mouse. Science 118, 52-55 (1953).
6. Grobstein, C. Inductive interaction in the development of the mouse metanephros. J. Exp. Zool. 130, 319-339 (1955).
7. Short, K.M., Hodson, M.J. & Smyth, I.M. Tomographic quantification of branching morphogenesis and renal development. Kidney Int. 77, 1132-1139 (2010).
8. al-Awqati, Q. & Goldberg, M.R. Architectural patterns in branching morphogenesis in the kidney. Kidney Int. 54 1832-1842, 1998).
9. Cebrian, C., Borodo, K., Charles, N. & Herzlinger, D.A. Morphometric index of the developing murine kidney. Dev. Dyn. 231, 601-608 (2004).
10. Sims-Lucas, S. et al. Three-dimensional imaging reveals ureteric and mesenchymal defects in Fgfr2-mutant kidneys. J. Am. Soc. Nephrol. 20, 2525-2533 (2009).
11. Hoy, W.E. et al. Nephron number, glomerular volume, renal disease and hypertension. Curr. Opin. Nephrol. Hypertens. 17, 258-265 (2008).
12. Luyckx, V.A. et al. Effect of fetal and child health on kidney development and long-term risk of hypertension and kidney disease. Lancet 382, 273-283 (2013).
13. Boyle, S. et al. Fate mapping using Cited 1-CreERT2 mice demonstrates that the cap mesenchyme contains self-renewing progenitor cells and gives rise exclusively to nephronic epithelia. Dev. Biol. 313, 234-245 (2008).
14. Kobayashi, A. et al. Six2 def ines and regulates a multipotent self-renewing nephron progenitor population throughout mammalian kidney development. Cell Stem Cell 3, 169-181 (2008).
15. El Agha, E. et al. Fgf10-positive cells represent a progenitor cell population during lung development and postnatally. Development 141, 296-306 (2014).
16. Cunha, G.R. et al. Mammary phenotypic expression induced in epidermal cells by embryonic mammary mesenchyme. Acta Anat. (Basel) 152, 195-204 (1995).
17. Short, K., Hodson, M. & Smyth, I. Spatial mapping and quantification of developmental branching morphogenesis. Development 140, 471-478 (2013).
18. Short, K.M. & Smyth, I.M. Analysis of native kidney structures in three dimensions. Methods Mol. Biol. 886, 95-107 (2012).
19. Lefevre, J. et al. Modelling cell turnover in a complex tissue during development. J. Theor. Biol. 338, 66-79 (2013).
20. Packard , A. et al. Luminal mitosis drives epithelial cell dispersal within the branching ureteric bud. Dev. Cell 27, 319-330 (2013).
21. Rumballe, B.A. et al. Nephron formation adopts a novel spatial topology at cessation of nephrogenesis. Dev. Biol. 360, 110-122 (2011).
22. Combes, A.N. et al. Three-dimensional visualization of testis cord morphogenesis, a novel tubulogenic mechanism in development. Dev. Dyn. 238, 1033-1041 (2009).
23. Combes, A.N. et al. Endothelial cell migration directs testis cord formation. Dev. Biol. 326, 112-120 (2009).
24. Davies, J .A. et al. Access and use of the GUDMAP database of genitourinary development. Methods Mol. Biol. 886, 185-201 (2012).
25. Georgas, K.M., Chiu, H.S., Lesieur, E., Rumballe, B.A. & Little, M.H. Expression of metanephric nephron-patterning genes in differentiating mesonephric tubules. Dev. Dyn. 240, 1600-1612 (2011).
26. Harding, S.D. et al. The GUDMAP database-An online resource for genitourinary research. Development 138, 2845-2853 (2011).
27. Little, M.H. et al. A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expr. Patterns 7, 680-699 (2007).
28. McMahon, A.P. et al. GUDMAP: The genitourinary developmental molecular anatomy project. J. Am. Soc. Nephrol. 19, 667-671 (2008).
29. Short, K.M. et al. Global quantification of tissue dynamics in the developing mouse kidney. Dev. Cell 29, 188-202 (2014).
30. Sharpe, J. et al. Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 296, 541-545 (2002).
31. Schuchardt, A., D'Agati, V., Pachnis, V. & Costantini, F. Renal agenesis and hypodysplasia in ret-k-mutant mice result from defects in ureteric bud development. Development 122, 1919-1929 (1996).
32. Enomoto, H. et al. RET signaling is essential for migration, axonal growth and axon guidance of developing sympathetic neurons. Development 128, 3963-3974 (2001).
33. Schuchardt, A., D'Agati, V., Larsson-Blomberg, L., Costantini, F. & Pachnis, V. Defects in the kidney and enteric ner vous system of mice lacking the tyrosine kinase receptor Ret. Nature 367, 380-383 (1994).
34. Metzger, R.J., Klein, O.D., Martin, G.R. & Krasnow, M.A. The branching programme of mouse lung development. Nature 453, 745-750 (2008).
35. Hockendorf, B., Thumberger, T. & Wittbrodt, J. Quantitative analysis of embryogenesis: a perspective for light sheet microscopy. Dev. Cell 23, 1111-1120 (2012).
36. Francois, M. et al. Segmental territories along the cardinal veins generate lymph sacs via a ballooning mechanism during embryonic lymphangiogenesis in mice. Dev. Biol. 364, 89-98 (2012).
37. Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56-62 (2007).
38. Chung, K. & Deisseroth, K. CLARITY for mapping the nervous system. Nat. Methods 10, 508-513 (2013).
39. Becker, K., Jahrling, N., Saghafi, S., Weiler, R. & Dodt, H.U. Chemical clearing and dehydration of GFP expressing mouse brains. PLoS ONE 7, e33916 (2012).
40. Kuwajima, T. et al. ClearT: a detergent-And solvent-free clearing method for neuronal and non-neuronal tissue. Development 140, 1364-1368 (2013).
41. Hornblad, A., Cheddad, A. & Ahlgren, U. An improved protocol for optical projection tomography imaging reveals lobular heterogen eities in pancreatic islet and beta cell mass distribution. Islets 3, 204-208 (2011).
42. Theiler, K. The House Mouse: Atlas of Embryonic Development 2nd edn. (Springer-Verlag, 1989).
43. Wanek, N., Muneoka, K., Holler-Dinsmore, G., Burton, R. & Bryant, S.V. A staging system for mouse limb development. J. Exp. Zool. 249, 41-49 (1989).
44. Nagy, A., Gertsenstein, M., Vintersten, K. & Behringer, R. Alcian blue staining of the mouse fetal cartilaginous skeleton. Cold Spring Harbor Protoc. 2009 doi:10.1101/pdb.prot5169 (2009).
45. McDonald, J.H. Handbook of Biological Statistics 161-168 (Sparky House Publishing, 2009).
46. Welch, B.L. The generalization of 'Student's' problem when several different population variances are involved. Biometrika 34, 28-35 (1947).
47. Buck, S.B. et al. Detection of S-phase cell cycle progression using 5-ethynyl-2?-deoxyuridine incorporation with click chemistry, an alternative to using 5-bromo-2?-deoxyu ridine antibodies. BioTechniques 44, 927-929 (2008).
48. Salic, A. & Mitchison, T.J. A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc. Natl. Acad. Sci. USA 105, 2415-2420 (2008).
49. Zeng, C. et al. Evaluation of 5-ethynyl-2?-deoxyuridine staining as a sensitive and reliable method for studying cell proliferation in the adult nervous system. Brain Res. 1319, 21-32 (2010).
50. Farah, M.H. Cumulative labeling of embryonic mouse neural retina with bromodeoxyuridine supplied by an osmotic minipump. J. Neurosci. Methods 134, 169-178 (2004).
51. Alanentalo T.,et al High-resolution three-dimensional imaging of islet-infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas J. Biomed. Optics 13, 054070, 2008).
52. Walls, J.R., Coultas, L., Rossant, J. & Henkelman, R.M. Three-dimensional analysis of vascular development in the mouse embryo. PLoS ONE 3, e2853 (2008).