POC Conf. Call 9-10-13 - Revision history

Cooperl at 17:54, 23 October 2013

2013-10-23T17:54:52Z

Atkinsob: /* leaf development stage (PO:0001050) */

2013-09-16T21:55:42Z

leaf development stage (PO:0001050)

Cooperl: /* vascular leaf development stage and child terms */

2013-09-16T19:13:39Z

vascular leaf development stage and child terms

Cooperl: /* vascular leaf development stage and child terms */

2013-09-16T19:13:24Z

vascular leaf development stage and child terms

Cooperl: /* vascular leaf senescence stage (PO:0001054) */

2013-09-14T21:36:51Z

vascular leaf senescence stage (PO:0001054)

Cooperl: /* vascular leaf senescence stage (PO:0001054) */

2013-09-14T21:36:33Z

vascular leaf senescence stage (PO:0001054)

Cooperl: /* vascular leaf post-expansion stage (PO:0001053) */

2013-09-14T21:26:14Z

vascular leaf post-expansion stage (PO:0001053)

Cooperl: /* vascular leaf expansion stage (PO:0001052) */

2013-09-14T21:15:30Z

vascular leaf expansion stage (PO:0001052)

Cooperl: /* vascular leaf initiation stage (PO:0007040) */

2013-09-14T21:10:01Z

vascular leaf initiation stage (PO:0007040)

Cooperl: /* vascular leaf initiation stage (PO:0007040) */

2013-09-13T23:35:31Z

vascular leaf initiation stage (PO:0007040)

← Older revision		Revision as of 17:54, 23 October 2013
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−	POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am ~~PST~~/1pm ~~EST~~	+	POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PDT/1pm EDT

	In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)''		In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)''

@@ Line 26: / Line 26: @@
 ** [http://www.nature.com/ng/journal/v42/n12/full/ng.703.html The developmental dynamics of the maize leaf transcriptome]
 ** [http://link.springer.com/article/10.1007%2Fs10265-009-0248-2 Uchida et al (2010) Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research 123: 7–14]
-* [http://www.nature.com/nrg/journal/v4/n3/full/nrg1002.html Comparative plant development: the time of the leaf?]
+** [http://www.nature.com/nrg/journal/v4/n3/full/nrg1002.html Comparative plant development: the time of the leaf?]
+** [http://www.nature.com/nature/journal/v434/n7032/abs/nature03410.html Independent recruitment of a conserved developmental mechanism during leaf evolution]
 ==vascular leaf development stage and child terms==
 Proposed new term and definition:

← Older revision		Revision as of 19:13, 16 September 2013
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	see also: [http://palaeos.com/plants/bryophyta/bryophyta.html#Leaves moss phyllides], [http://plantphys.info/plant_biology/copyright/moss.html moss info] and [[Background_info_on_Physco_biology_and_culture]].		see also: [http://palaeos.com/plants/bryophyta/bryophyta.html#Leaves moss phyllides], [http://plantphys.info/plant_biology/copyright/moss.html moss info] and [[Background_info_on_Physco_biology_and_culture]].

−	''PJ: We should have a parallel "generic" branch of leaf ~~developemnt~~ to group the stages such as leaf expansion across both non-vascular or vascular leaves.''	+	''PJ: We should have a parallel "generic" branch of leaf development to group the stages such as leaf expansion across both non-vascular or vascular leaves.''

← Older revision		Revision as of 19:13, 16 September 2013
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	* Need to do more research on the development of the [http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025075&session_id=5645b1377543007 non-vascular leaf]		* Need to do more research on the development of the [http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025075&session_id=5645b1377543007 non-vascular leaf]
	see also: [http://palaeos.com/plants/bryophyta/bryophyta.html#Leaves moss phyllides], [http://plantphys.info/plant_biology/copyright/moss.html moss info] and [[Background_info_on_Physco_biology_and_culture]].		see also: [http://palaeos.com/plants/bryophyta/bryophyta.html#Leaves moss phyllides], [http://plantphys.info/plant_biology/copyright/moss.html moss info] and [[Background_info_on_Physco_biology_and_culture]].
		+
		+	''PJ: We should have a parallel "generic" branch of leaf developemnt to group the stages such as leaf expansion across both non-vascular or vascular leaves.''

@@ Line 137: / Line 137: @@
 ''Need to look at this more-  abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf ''
-''Need to review leaf senescence- see [ http://www.plantcell.org/site/teachingtools/TTPB20.xhtml plant cell resource] ''
+''Need to review leaf senescence- see [http://www.plantcell.org/site/teachingtools/TTPB20.xhtml plant cell resource] ''
 =OBO Foundry Review of Plant Ontology=

@@ Line 133: / Line 133: @@
 *  [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/559/ vascular leaf senescence stage (PO:0001054)]: A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.
-''Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf.''
+''Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf.  Need to add the references to the GO terms.''
 =OBO Foundry Review of Plant Ontology=

@@ Line 128: / Line 128: @@
 * [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/558/ vascular leaf post-expansion stage (PO:0001053)]: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and cell expansion has ceased and ends with the onset of the vascular leaf senescence stage (PO:0001054).
-''Perhaps change term to vascular leaf mature stage''
+''Use the "begins with.... and ends with..." template.  Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage".  Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahongany plants, but they are the exceptions.  Could add as a comment (get names from DWS). ''
 == vascular leaf senescence stage (PO:0001054)==

@@ Line 103: / Line 103: @@
 **new comment: The majority of leaf expansion is due to cell enlargement. The leaves of some plants may not have a conspicuous midrib or rachis.
-''During vascular leaf expansion stage the vasculature is forming as well''
+''May be due to cell division or cell enlargement. During vascular leaf expansion stage the vasculature is forming as well- need to encompass that as well.''
 ===Children of vascular leaf expansion stage (PO:0001052)- revised names and definitions:===
@@ Line 112: / Line 112: @@
 * [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/562/ formation of vascular leaflet primordia stage (PO:0004500)]: A vascular leaf expansion stage (PO:0001052) at which a leaflet primordium (PO:0025481) is initiated on the leaf rachis (PO:0020055) of a compound leaf (PO:0020043).
-'' need to review this in terms of leaflet discussion''
+'' need to review this in terms of leaflet discussion, should move up to VL initiation stage as well, most likely''
 * [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/563/ formation of ligule primordium stage (PO:0001021)]: A vascular leaf expansion stage (PO:0001052) when conical P3 leaf completely encloses SAM, and the ligule (PO:0020105) primordium is visible.
 ''check "ligule (PO:0020105) primordium"- PO:id should be after the term, need to create a term ligule primordium''
+'' ligule PO:0020105 is not a leaf- it is a cardinal organ part, formation of ligule primordium stage would be part of leaf development, not is_a''
 '''''Discussion on these terms were tabled for the next meeting:'''''

@@ Line 77: / Line 77: @@
 ''DWS: Need to look at the organization of the SAM in ferns- Do they have the equivalent of a peripheral zone?: cup-shaped zone, runs from protoderm to protoderm, under the apical cell.  DWS will look into it.''
-''DWS: Need to look at the developement of phyllode leaves (PO:0025335).. This might go under the new 'vascular leaf surface polarity determination stage'
+''DWS: Need to look at the development of phyllode leaves (PO:0025335), such as those in Acacia and other desert plants. They expand perpendicularly to the pattern of normal leave, have strong adaxial meristems, rather than marginal meristem. Flattened in a proximal -
 Def'n: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane, throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in development. [source: PMID:18978364, PO_REF:00006, PO_REF:00007]
@@ Line 83: / Line 85: @@
 Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:0025336, transition phyllode leaf). Phyllodes are generally xeromorphic.
+''DWS will send us a diagram; need to think about how to encompass them.  Also in some moss plants''
 [[File:Leaf dev new.png]]

@@ Line 62: / Line 62: @@
 '''''revised Def'n: vascular leaf initiation stage:''' A vascular leaf development stage (PO:0025570) which begins with the onset of localized periclinal division in the peripheral zone (PO:0000225) and ends with the beginning of the vascular leaf primordium formation stage (PO:0001019).''
 ''can we leave out "in the SAM"?
@@ Line 73: / Line 77: @@
 ''DWS: Need to look at the organization of the SAM in ferns- Do they have the equivalent of a peripheral zone?: cup-shaped zone, runs from protoderm to protoderm, under the apical cell.  DWS will look into it.''
-''PJ- we should add a note that the concentration of auxin is highest under the spot where the primordium will form- the vascular leaf anlagen (PO:0025431).
+''DWS: Need to look at the developement of phyllode leaves (PO:0025335).. This might go under the new 'vascular leaf surface polarity determination stage'