Two ways to use imaging: Focusing directly on mechanism, or indirectly via behaviour?

Current Opinion in Genetics and Development

Volumn 21, Issue 5, 2011, Pages 523-529

  Sharpe, James ^a  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

CAENORHABDITIS ELEGANS; DEVELOPMENTAL BIOLOGY; DROSOPHILA; EMBRYO DEVELOPMENT; IMAGE PROCESSING; IMAGING; MATHEMATICAL MODEL; MESOSCOPIC IMAGING; MORPHOGENESIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; DEVELOPMENTAL BIOLOGY; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MODELS, BIOLOGICAL;

EID: 82455192643     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2011.08.012     Document Type: Review

References (42)

1. Csikász-Nagy A., Novák B., Tyson J.J. Reverse engineering models of cell cycle regulation. Adv Exp Med Biol 2008, 641:88-97.
2. Sheetz M.P., Felsenfeld D., Galbraith C.G., Choquet D. Cell migration as a five-step cycle. Biochem Soc Symp 1999, 65:233-243.
3. Vallotton P., Small J.V. Shifting views on the leading role of the lamellipodium in cell migration: speckle tracking revisited. J Cell Sci 2009, 122:1955-1958.
4. Huisken J., Swoger J., Del Bene F., Wittbrodt J., Stelzer E.H.K. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 2004, 1007-1009.
5. Reynaud E.G., Krzic U., Greger K., Stelzer E.H. Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage. HFSP J 2008, 2:266-275.
6. Dodt H.U., Leischner U., Schierloh A., Jährling N., Mauch C.P., Deininger K., Deussing J.M., Eder M., Zieglgänsberger W., Becker K. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat Methods 2007, 4:331-336.
7. Keller P.J., Schmidt A.D., Santella A., Khairy K., Bao Z., Wittbrodt J., Stelzer E.H.K. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat Methods 2011, 7(8):637-642.
8. Keller P.J., Schmidt A.D., Wittbrodt J., Stelzer E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 2008, 1065-1069.
9. Swoger J., Muzzopappa M., López-Schier H., Sharpe J. 4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies. J Biophoton 2011, 4:122-134.
10. Sharpe J., Ahlgren U., Perry P., Hill B., Ross A., Hecksher-Sørensen J., Baldock R., Davidson D. Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 2002, 296:541.
11. Boot M.J., Westerberg C.H., Sanz-Ezquerro J., Cotterell J., Schweitzer R., Torres M., Sharpe J. In vitro whole-organ imaging: 4D quantification of growing mouse limb buds. Nat Methods 2008, 5:609-612.
12. Colas J.F., Sharpe J. Live optical projection tomography. Organogenesis 2009, 5:129-134.
13. Megason S.G., Fraser S.E. Imaging in systems biology. Cell 2007, 130:784-795.
14. Neumann B., Walter T., Hériché J.-K., Bulkescher J., Erfle H., Conrad C., Rogers P., Poser I., Held M., Liebel U., et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 2010, 464:721-727.
15. Held M., Schmitz M.H.A., Fischer B., Walter T., Neumann B., Olma M.H., Peter M., Ellenberg J., Gerlich D.W. CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nat Methods 2010, 7(9):747-754.
16. Bao Z., Murray J.I., Boyle T., Ooi S.L., Sandel M.J., Waterston R.H. Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2006, 103:2707-2712.
17. Boyle T.J., Bao Z., Murray J.I., Araya C.L., Waterston R.H. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. BMC Bioinform 2006, 7:275.
18. Murray J.I., Bao Z., Boyle T.J., Boeck M.E., Mericle B.L., Nicholas T.J., Zhao Z., Sandel M.J., Waterston R.H. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods 2008, 5:703-709.
19. Short K.M., Hodson M.J., Smyth I.M. Tomographic quantification of branching morphogenesis and renal development. Kidney Int 2010, 77:1132-1139.
20. Lemos M.C., Harding B., Reed A.A., Jeyabalan J., Walls G.V., Bowl M.R., Sharpe J., Wedden S., Moss J.E., Ross A., Davidson D., Thakker R.V. Genetic background influences embryonic lethality and the occurrence of neural tube defects in Men1 null mice: relevance to genetic modifiers. J Endocrinol 2009, 203(1):211-216.
21. Zamyadi M., Baghdadi L., Lerch J.P., Bhattacharya S., Schneider J.E., Henkelman R.M., Sled J.G. Mouse embryonic phenotyping by morphometric analysis of MR images. Physiol Genomics 2010, 42A:89-95.
22. Johnson J.T., Hansen M.S., Wu I., Healy L.J., Johnson C.R., Jones G.M., Capecchi M.R., Keller C. Virtual histology of transgenic mouse embryos for high-throughput phenotyping. PLoS Genet 2006, 2:e61.
23. Metscher B.D. MicroCT for developmental biology: a versatile tool for high-contrast 3D imaging at histological resolutions. Dev Dyn 2009, 238:632-640.
24. Dunlevy L., Bennett M., Slender A., Lana-Elola E., Tybulewicz V.L., Fisher E.M., Mohun T. Down's syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse. Cardiovasc Res 2010, 88:287-295.
25. Reinitz J., Sharp D.H. Mechanism of eve stripe formation. Mech Dev 1995, 49:133-158.
26. Sharp D.H., Reinitz J. Prediction of mutant expression patterns using gene circuits. Biosystems 1998, 47:79-90.
27. Perkins T.J., Jaeger J., Reinitz J., Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol 2006, 2:e51.
28. Houchmandzadeh B., Wieschaus E., Leibler S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 2002, 415:798-802.
29. Gregor T., Tank D.W., Wieschaus E.F., Bialek W. Probing the limits to positional information. Cell 2007, 130:153-164.
30. Gregor T., Wieschaus E.F., McGregor A.P., Bialek W., Tank D.W. Stability and nuclear dynamics of the bicoid morphogen gradient. Cell 2007, 130:141-152.
31. Spirov A., Fahmy K., Schneider M., Frei E., Noll M., Baumgartner S. Formation of the Bicoid morphogen gradient: an mRNA gradient dictates the protein gradient. Development 2009, 136:605-614.
32. Little S.C., Tkačik G., Kneeland T.B., Wieschaus E.F., Gregor T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol 2011, 9:e1000596.
33. Kicheva A., Pantazis P., Bollenbach T., Kalaidzidis Y., Bittig T., Jülicher F., González-Gaitán M. Kinetics of morphogen gradient formation. Science 2007, 315:521-525.
34. Rogulja D., Irvine K.D. Regulation of cell proliferation by a morphogen gradient. Cell 2005, 123:449-461.
35. Wartlick O., Mumcu P., Kicheva A., Bittig T., Seum C., Jülicher F., González-Gaitán M. Dynamics of Dpp signaling and proliferation control. Science 2011, 331:1154-1159.
36. Chung K., Kim Y., Kanodia J.S., Gong E., Shvartsman S.Y., Lu H. A microfluidic array for large-scale ordering and orientation of embryos. Nat Methods 2011, 8:171-176.
37. Welten M., Pavlovska G., Chen Y., Teruoka Y., Fisher M., Bangs F., Towers M., Tickle C. 3D expression patterns of cell cycle genes in the developing chick wing and comparison with expression patterns of genes implicated in digit specification. Dev Dyn 2011, 240:1278-1288.
38. Fisher M., Downie H., Welten M.C., Delgado I., Bain A., Planzer T., Sherman A., Sang H., Tickle C. Comparative analysis of 3D expression patterns of transcription factor genes and digit fate maps in the developing chick wing. PLoS ONE 2011, 6:e18661.
39. Ede D.A., Law J.T. Computer simulation of vertebrate limb morphogenesis. Nature 1969, 221:244-248.
40. Niswander L., Martin G.R. FGF-4 regulates expression of Evx-1 in the developing mouse limb. Development 1993, 119:287-294.
41. Boehm B., Westerberg H., Lesnicar-Pucko G., Raja S., Rautschka M., Cotterell J., Swoger J., Sharpe J. The role of spatially controlled cell proliferation in limb bud morphogenesis. PLoS Biol 2010, 8:e1000420.
42. Marcon L., Arqués C.G., Torres M.S., Sharpe J. A computational clonal analysis of the developing mouse limb bud. PLoS Comput Biol 2011, 7:e1001071.