Biology Reference
In-Depth Information
14. The macro output fi le, Phenotype Results, is a .txt fi le that
contains a table of all the data gathered by the ImageJ macro.
Within this table are several columns that read Area, Circularity,
Solidity, Threshold, Perimeter, Convexity, CHArea, and
CHPerim. The area column represents the area occupied by
the thresholded plant. The circularity column computes a unit-
less number ranging from zero to one that describes how well
the plant can be defi ned by a circle with a value of one indicat-
ing a perfect circle. Circularity is computed by the following
equation: circularity = 4
^2). Solidity is the
ratio between an object's area and the area of the object's con-
vex hull. Solidity is computed by the following equation: solid-
ity = area/convex hull area. The threshold column indicates
what intensity was used to threshold each plant. Perimeter is
the true perimeter of each plant. Convex hull area is the mini-
mum area needed to encase the entire plant by line segments.
Convex hull perimeter is the sum of the length of all the line
segments that encase the plant. Convexity = convex hull perim-
eter/perimeter. We recommend doing statistics on solidity,
which is normally distributed, when trying to resolve the dif-
ference between stunted and branched plants.
π
(area/
perimeter
15. An alternative approach to verify gene silencing is to generate
a GFP fusion of the gene of interest and quantify the reduction
in its level of expression by the reduction in fl uorescence.
Acknowledgments
This work was supported by NSF (IOS 1002837 and MCB
1253444 to L.V.). We thank Erin Agar, Jennifer Garbarino, and
Graham Burkart for comments on this manuscript and to Luisanna
Paulino for sample images. We also thank other members of the
Vidali and Bezanilla laboratories for their support.
References
1. Cove D, Bezanilla M, Harries P et al (2006)
Mosses as model systems for the study of
metabolism and development. Annu Rev Plant
Biol 57:497-520
2. Vidali L, Bezanilla M (2012)
Physcomitrella
patens
: a model for tip cell growth and
differentiation. Curr Opin Plant Biol. 15:
625-631
3. Augustine RC, Vidali L, Kleinman KP et al
(2008) Actin depolymerizing factor is essential
for viability in plants, and its phosphoregula-
tion is important for tip growth. Plant J
54:863-875
4. van Gisbergen PA, Li M, Wu SZ et al (2012)
Class II formin targeting to the cell cortex by
binding PI(3,5)P(2) is essential for polarized
growth. J Cell Biol 198:235-250
5. Vidali L, Augustine RC, Kleinman KP et al
(2007) Profi lin is essential for tip growth in the
moss
Physcomitrella patens
. Plant Cell
19:3705-3722
6. Vidali L, Burkart GM, Augustine RC et al
(2010) Myosin XI is essential for tip growth in
Physcomitrella patens
. Plant Cell 22:1868-1882
7. Vidali L, van Gisbergen PAC, Guerin C et al
(2009) Rapid formin-mediated actin-fi lament
Search WWH ::
Custom Search