F
Fibrosis......................................................... 23, 27, 29, 55
Fluorescence recovery after photobleaching
(FRAP)............................ 145–157, 417, 419, 422
Fluorescent in situ hybridization (FISH) ....... 5, 353–382
Fo ¨rster resonance energy transfer (FRET) .................276,
289–292, 295, 296, 298
G
Gal4....................................................... 84, 104, 117–120,
123, 125, 130, 162, 163
Gastrulation .............................................. 7, 8, 11, 13, 35,
45, 48, 52, 65–68, 71, 76, 80, 135–144, 199, 200,
257, 271, 341
Genome .........................26, 47, 309, 328, 354, 358, 370
Glycolysis ..................................................... 328, 329, 331
H
Heterogeneity
non-genetic..................................................... 391, 392
I
Image
analysis ............................................90, 109, 137, 140,
163, 169, 178, 206, 210, 247, 251, 278, 282,
290, 295, 296, 375
processing ......................................... 92–97, 111, 113,
177, 193, 194
Imaginal disc ........................................................ 115–132
Immunofluorescence ........................................... 345–347
Invasion .................................3, 7, 11, 24–26, 36, 37, 50,
161, 162, 199, 200, 228, 243–255, 304, 316,
329, 354, 385
In vitro ................................ 17, 36, 45, 52, 55, 108, 228,
231, 232, 239, 276, 289, 316, 342, 386, 391, 409
In vivo ................................. 8, 17, 36, 79–105, 107, 118,
120, 124, 126, 131, 145–157, 173, 183–195,
199–221, 228, 231, 258, 259, 268, 276,
303–312, 316, 386, 391, 409, 415
M
Mechanotransduction ..................................................... 55
Mesenchymal cells (MCs).................................14, 30, 35,
43, 44, 46, 47, 65, 80, 135, 145, 174, 185, 186,
257, 276, 277, 316, 317, 320, 321, 341, 347,
401–403, 405, 407
Mesenchymal-epithelial transition (MET) .............29–32,
35–37, 43–46, 65, 183–195, 275–285, 328,
341–350, 354, 376, 385, 393, 398, 401, 405, 409
Mesoderm............................................... 7, 46, 53, 65–77,
115, 135, 136, 148, 174–177, 185, 257,
262–264, 268–271, 279, 303, 304
Metabolism.............................................. 24, 36, 328–338
Metastasis......................................... 3, 11, 13, 14, 25, 26,
31, 36, 37, 44, 48, 55, 65, 115, 161–169, 244,
258, 316, 328, 329, 342, 354
Micropatterns .................................................55, 227–240
Mitochondria.............................................. 328–331, 333,
334, 337, 338
Modeling
computational ....................................... 389, 392, 399
mathematical ..................................... 5, 155, 385–409
Morphogenesis .......................................3, 11, 35, 47, 50,
52, 66, 107, 173, 174, 228, 239, 342
Mosaicism ...................................................................... 139
Multi-photon microscopy........................... 175, 179, 180
Multistability ................................................................. 409
Myosin ........................................... 10, 17, 67, 69, 70, 76,
120, 121, 200, 218, 415
N
Neural crest
chicken ............................................................ 107–114
Xenopus ...................................................... 4, 257–270
zebrafish.............................................................79–105
Neural tube (NT).................................................... 24, 49,
107, 109–112, 174–177, 183, 189, 191, 262,
263, 270
O
Optogenetics ........................................................ 415–423
Oxidative phosphorylation (OXPHOS) .....................328,
329, 331, 334
Oxygen ......................................111, 147, 329, 330, 332,
334, 336–338, 378
P
Photoconversion ............................................90, 101, 105
Plasticity........................................... 4, 14, 22, 24, 25, 32,
37, 43, 48, 258, 315, 328–334, 385–409
Polarity
apico-basal .................................. 4, 35, 257, 258, 415
front-rear .......................................................... 35, 258
Post-transcriptional regulation ......................................... 5
Protrusions ................................... 15, 116, 200, 220, 423
R
Respiration...........................................329, 334, 336, 338
Rho GTPases .........................................17, 415, 416, 420
RNAi ...................................................115, 116, 118–120,
123, 124, 130, 131
S
Secondary neurulation (SN)................................ 183–195
428
THE EPITHELIAL-TO MESENCHYMAL TRANSITION: METHODS AND PROTOCOLS
Index
Fibrosis......................................................... 23, 27, 29, 55
Fluorescence recovery after photobleaching
(FRAP)............................ 145–157, 417, 419, 422
Fluorescent in situ hybridization (FISH) ....... 5, 353–382
Fo ¨rster resonance energy transfer (FRET) .................276,
289–292, 295, 296, 298
G
Gal4....................................................... 84, 104, 117–120,
123, 125, 130, 162, 163
Gastrulation .............................................. 7, 8, 11, 13, 35,
45, 48, 52, 65–68, 71, 76, 80, 135–144, 199, 200,
257, 271, 341
Genome .........................26, 47, 309, 328, 354, 358, 370
Glycolysis ..................................................... 328, 329, 331
H
Heterogeneity
non-genetic..................................................... 391, 392
I
Image
analysis ............................................90, 109, 137, 140,
163, 169, 178, 206, 210, 247, 251, 278, 282,
290, 295, 296, 375
processing ......................................... 92–97, 111, 113,
177, 193, 194
Imaginal disc ........................................................ 115–132
Immunofluorescence ........................................... 345–347
Invasion .................................3, 7, 11, 24–26, 36, 37, 50,
161, 162, 199, 200, 228, 243–255, 304, 316,
329, 354, 385
In vitro ................................ 17, 36, 45, 52, 55, 108, 228,
231, 232, 239, 276, 289, 316, 342, 386, 391, 409
In vivo ................................. 8, 17, 36, 79–105, 107, 118,
120, 124, 126, 131, 145–157, 173, 183–195,
199–221, 228, 231, 258, 259, 268, 276,
303–312, 316, 386, 391, 409, 415
M
Mechanotransduction ..................................................... 55
Mesenchymal cells (MCs).................................14, 30, 35,
43, 44, 46, 47, 65, 80, 135, 145, 174, 185, 186,
257, 276, 277, 316, 317, 320, 321, 341, 347,
401–403, 405, 407
Mesenchymal-epithelial transition (MET) .............29–32,
35–37, 43–46, 65, 183–195, 275–285, 328,
341–350, 354, 376, 385, 393, 398, 401, 405, 409
Mesoderm............................................... 7, 46, 53, 65–77,
115, 135, 136, 148, 174–177, 185, 257,
262–264, 268–271, 279, 303, 304
Metabolism.............................................. 24, 36, 328–338
Metastasis......................................... 3, 11, 13, 14, 25, 26,
31, 36, 37, 44, 48, 55, 65, 115, 161–169, 244,
258, 316, 328, 329, 342, 354
Micropatterns .................................................55, 227–240
Mitochondria.............................................. 328–331, 333,
334, 337, 338
Modeling
computational ....................................... 389, 392, 399
mathematical ..................................... 5, 155, 385–409
Morphogenesis .......................................3, 11, 35, 47, 50,
52, 66, 107, 173, 174, 228, 239, 342
Mosaicism ...................................................................... 139
Multi-photon microscopy........................... 175, 179, 180
Multistability ................................................................. 409
Myosin ........................................... 10, 17, 67, 69, 70, 76,
120, 121, 200, 218, 415
N
Neural crest
chicken ............................................................ 107–114
Xenopus ...................................................... 4, 257–270
zebrafish.............................................................79–105
Neural tube (NT).................................................... 24, 49,
107, 109–112, 174–177, 183, 189, 191, 262,
263, 270
O
Optogenetics ........................................................ 415–423
Oxidative phosphorylation (OXPHOS) .....................328,
329, 331, 334
Oxygen ......................................111, 147, 329, 330, 332,
334, 336–338, 378
P
Photoconversion ............................................90, 101, 105
Plasticity........................................... 4, 14, 22, 24, 25, 32,
37, 43, 48, 258, 315, 328–334, 385–409
Polarity
apico-basal .................................. 4, 35, 257, 258, 415
front-rear .......................................................... 35, 258
Post-transcriptional regulation ......................................... 5
Protrusions ................................... 15, 116, 200, 220, 423
R
Respiration...........................................329, 334, 336, 338
Rho GTPases .........................................17, 415, 416, 420
RNAi ...................................................115, 116, 118–120,
123, 124, 130, 131
S
Secondary neurulation (SN)................................ 183–195
428
THE EPITHELIAL-TO MESENCHYMAL TRANSITION: METHODS AND PROTOCOLS
Index