POC Conf. Call 11-18-13 - Revision history

Cooperl at 21:32, 2 December 2013

2013-12-02T21:32:34Z

Cooperl: moved POC Conf. Call 12-3-13 to POC Conf. Call 11-18-13 over redirect

2013-12-02T21:31:40Z

moved POC Conf. Call 12-3-13 to POC Conf. Call 11-18-13 over redirect

Cooperl: moved POC Conf. Call 11-18-13 to POC Conf. Call 12-3-13

2013-11-20T23:15:06Z

moved POC Conf. Call 11-18-13 to POC Conf. Call 12-3-13

Cooperl: /* Next meeting scheduled for Monday, Dec 3rd, 2013 */

2013-11-20T23:14:39Z

Next meeting scheduled for Monday, Dec 3rd, 2013

Cooperl at 23:14, 20 November 2013

2013-11-20T23:14:20Z

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

2013-11-18T18:20:04Z

vascular leaf senescent stage (PO:0001054)

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

2013-11-18T18:19:52Z

vascular leaf senescence stage (PO:0001054)

Cooperl at 18:10, 18 November 2013

2013-11-18T18:10:10Z

Cooperl at 18:09, 18 November 2013

2013-11-18T18:09:35Z

Cooperl: Created page with '- please see the Items_for_future_meetings page, will be moved here before the meeting'

2013-11-06T17:35:55Z

Created page with '- please see the Items_for_future_meetings page, will be moved here before the meeting'

New page

- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting

← Older revision		Revision as of 21:32, 2 December 2013
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−	POC meeting, Skype Conference Call; Date: Tuesday ~~Dec 3rd~~, 2013 10:30am PST/1:30pm EST	+	POC meeting, Skype Conference Call; Date: Tuesday Nov 18th, 2013 10:30am PST/1:30pm EST

	In attendance:		In attendance:

← Older revision		Revision as of 23:14, 20 November 2013
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	* Laurel Cooper, Oregon State University		* Laurel Cooper, Oregon State University

−	=Next meeting scheduled for Monday, Dec ~~3rd~~, 2013=	+	=Next meeting scheduled for Monday, Dec 10th, 2013=

← Older revision		Revision as of 23:14, 20 November 2013
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−	POC meeting, Skype Conference Call; Date: ~~Monday Nov 18th~~, 2013 10:30am PST/1:30pm EST	+	POC meeting, Skype Conference Call; Date: Tuesday Dec 3rd, 2013 10:30am PST/1:30pm EST

	In attendance:		In attendance:

@@ Line 53: / Line 53: @@
 ==vascular leaf senescent stage (PO:0001054)==
-*  [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.
+*  [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/559/ vascular leaf senescent 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.  Need to add the references to the GO terms.''

@@ Line 52: / Line 52: @@
 from 9-10-13: ''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 Mahogany plants, but they are the exceptions.  Could add as a comment (get names from DWS). ''
-==vascular leaf senescence stage (PO:0001054)==
+==vascular leaf senescent stage (PO:0001054)==
 *  [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.
@@ Line 73: / Line 73: @@
 ** [http://www.nature.com/nature/journal/v434/n7032/abs/nature03410.html Independent recruitment of a conserved developmental mechanism during leaf evolution]
 ** [http://www.sciencedirect.com/science/article/pii/S1360138512000313 Gonzalez et al, Trends in Plant Science 2012]
 =Upcoming meetings and Presentations 2013-2014:=

← Older revision	Revision as of 21:31, 2 December 2013
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← Older revision	Revision as of 23:15, 20 November 2013
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← Older revision		Revision as of 18:10, 18 November 2013
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−	~~- please see the [[Items_for_future_meetings]] page~~, ~~will be moved here before the meeting~~	+	POC meeting, Skype Conference Call; Date: Monday Nov 18th, 2013 10:30am PST/1:30pm EST
		+
		+	In attendance:
		+
		+	Absent:
		+
		+
	=Wrapping up the vascular leaf development stages:=		=Wrapping up the vascular leaf development stages:=

← Older revision		Revision as of 18:09, 18 November 2013
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	- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting		- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting
		+	=Wrapping up the vascular leaf development stages:=
		+
		+
		+	==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/572/ vascular leaf differentiation stage (new PO:0025574)]==
		+
		+	*Revised def'n: '''vascular leaf differentiation stage (new PO:0025574)''': A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
		+
		+	''Last week we discussed utilizing the meristem layers L1, L2, and L3 in the definition, but these are really part of the shoot apical meristem at an earlier stage. Are these layers also part of the leaf primordium???''
		+
		+	==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/557/ vascular leaf expansion stage PO:0001052]==
		+
		+	old name and def'n: '''2 leaf expansion stage (PO:0001052)''': Stage of leaf development which begins when cell differentiation and cell expansion occurs and finishes when the leaf reaches its full size.
		+
		+	Proposed revised name and def'n '''vascular leaf expansion stage (PO:0001052)''': A vascular leaf development stage (PO:0025570) during which vascular leaf size increases primarily through cell expansion.
		+
		+	Proposed comment: During this stage leaf shaping (GO:0010358) occurs which is defined as the developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.
		+
		+	* Note: The majority of cell division occurs early in leaf development and cell expansion is the major agent of leaf expansion [http://www.plantcell.org/site/teachingtools/TTPB3.xhtml link] or see above image.
		+
		+	''Refer to the GO term: [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0016049&session_id=3608amigo1381856059 cell growth GO:0016049]: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.''
		+
		+	''Revised comment: During this stage, the process of cell growth (GO:0016049) occurs, defined as the process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.
		+
		+	===Children of vascular leaf expansion stage:===
		+	See [https://docs.google.com/spreadsheet/ccc?key=0AuKRnUE1LrAgdFlpaU5lZ0xvRkNfVG8xV1pSRFlWSVE&usp=drive_web#gid=0 Leaf Development Stages gDoc]
		+
		+	* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/566/ rapid elongation of leaf sheath stage (PO:0001024)]: Stage of leaf development during which a rapid elongation of the leaf sheath occurs, as in Poaceae.
		+
		+	* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/565/ rapid elongation of vascular leaf lamina stage (PO:0001023)]: A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf lamina (PO:0020039) occurs.
		+
		+	These are stages of development of the '''parts of the leaf'''; currently is_a children of leaf expansion stage:
		+
		+	* [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.
		+
		+	* [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).
		+
		+	* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/562/ hood-shaped primordium stage (PO:0001020)]: Stage of leaf development when a hood-shaped primordium is formed, partially enclosing P1 and SAM, as in Poaceae.
		+
		+	==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/558/ vascular leaf post-expansion stage (PO:0001053)]:==
		+
		+	old name and def'n: 3 leaf fully expanded stage (PO:0001053): Stage of leaf development when leaf is fully expanded.
		+
		+	Proposed new Name and def'n: vascular leaf post-expansion stage: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and ends with the onset of the vascular leaf senescence stage (PO:0001054).
		+
		+	from 9-10-13: ''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 Mahogany plants, but they are the exceptions. Could add as a comment (get names from DWS). ''
		+
		+	==vascular leaf senescence stage (PO:0001054)==
		+	* [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. Need to add the references to the GO terms.''
		+
		+	''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] ''
		+
		+
		+
		+	===Links to Relevant References- vascular leaf development===
		+	** [http://www.plantcell.org/site/teachingtools/TTPB3.xhtml Genetic Control of Leaf Development- Plant Cell teaching tools]
		+	** [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? Tsiantis & Hay, 2003 Nature Reviews Genetics]
		+	** [http://www.nature.com/ng/journal/v42/n12/abs/ng.703.html Li, Brutnell et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060–1067]
		+	** [http://pcp.oxfordjournals.org/content/53/7/1180.abstract Leaf adaxial–abaxial polarity specification and lamina outgrowth: evolution and development, Plant and Cell Physiology, 2012]
		+	** [http://www.ohio.edu/people/gleissbe/images/dgpe_2002.pdf Gleissberg 2002]
		+	** FERNS Barbara A. Ambrose: [http://www.frontiersin.org/Plant_Evolution_and_Development/10.3389/fpls.2013.00345/abstract The evolution, morphology, and development of fern leaves, Vasco et al 2013]
		+	** [http://www.nature.com/nature/journal/v434/n7032/abs/nature03410.html Independent recruitment of a conserved developmental mechanism during leaf evolution]
		+	** [http://www.sciencedirect.com/science/article/pii/S1360138512000313 Gonzalez et al, Trends in Plant Science 2012]
		+
		+
		+	=Upcoming meetings and Presentations 2013-2014:=
		+	* '''[http://www.intlpag.org/2014/80-front-page/24-welcome PAG 2014] January 11-15, 2014 - San Diego, CA, USA'''
		+
		+	** Registration is now open: [http://www.intlpag.org/2014/attend/registration-and-fees?utm_source=PAG+XXII+-+Newsletter+-+Attendee+%231&utm_campaign=PAG+XXII+Attendee+Newsletter+%231&utm_medium=email PAG 2014].
		+
		+	The deadline for Early Pre-Registration was November 1, 2013. Poster abstract submission date is Nov. 12
		+
		+	[https://pag.confex.com/pag/xxii/webprogram/Session2103.html Systems Biology and Ontologies Workshop]
		+
		+	Link to: [https://docs.google.com/document/d/13Jgbcqt7AOvU0r8gGVUZh590cYWLOh5GUhUhNtn2-Cc/edit?usp=sharing Googledoc]
		+
		+	Confirmed speakers:
		+	* Barbara Ambrose, NYBG
		+	* Stefan Rensing, Marlburg Germany
		+	* Trey Ideker, UCSD School of Medicine, San Diego, CA
		+	* Jim Beynon, Warwick University, Coventry, United Kingdom
		+	* Sushma Naithani, Oregon State University
		+	* Laurel Cooper, Oregon State University
		+
		+	=Next meeting scheduled for Monday, Dec 3rd, 2013=