Agenda for Kidney Content Meeting: Difference between revisions

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[[Category:Reference Genome]]
Please suggest agenda items, relevant papers and other information relating to kidney development GO terms that you would like discussed at this workshop, to enable us to form an agenda.
Please suggest agenda items, relevant papers and other information relating to kidney development GO terms that you would like discussed at this workshop, to enable us to form an agenda.


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== Participants ==
== Participants ==
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== Location ==
== Location ==


EMBL-EBI, The Wellcome Trust Genome Campus, Room C202/203 - shared facilities.
EMBL-EBI, Room C202/203 - shared facilities, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD.
Date: Monday 25th January 2010, 9:30am to 5pm
Date: Monday 25th January 2010, 9:30am to 5pm


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|'''9:45am'''
|'''9:45am'''
| Kidney precursor cells and tissues (segmentation)<br/>* Development of kidney field <br/>* Nephrogenic stem cell differentiation.<br/>* Commitment of multipotent stem cells to the nephrogenic lineage. <br/>* Mesenchymal cell condensation involved in nephron development. <br/>* ureteric bud specification/differentiation/development, <br/>*mesenchymal cap epithelium, <br/>* chemoattraction of in mesenchymal cells involved in nephron development (Defn: not sure if there is sufficient evidence for the involvement of chemotaxis in the formation of the pretubular aggregate) <br/>* Sensing a quorum of cells / control of the number of cells in a cell group <br/>* (Mesonephric/metanephric) mesenchyme-epithelial transition <br/>* proximal/distal nephron patterning specification of proximal tubule identity; specification of intermediate tubule identity; <br/>* Formation of tight junctions, <br/>* Formation of adherens junctions, <br/>* Formation of basement membrane, <br/>* Epithelial patterning of the nephron epithelium {Syn: segmentation of the nephron epithelium},<br/>* specification of distal tubule identity; pronephros proximal/distal patterning; pronephros development; pronephros proximal/distal patterning, <br/>*SF -[https://sourceforge.net/tracker/?func=detail&aid=2859892&group_id=36855&atid=440764 SF 2859892: specification of kidney anlage] *PMID 17875669 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 12925600''  
| Kidney precursor cells and tissues (segmentation)<br/>* Development of kidney field <br/>* Nephrogenic stem cell differentiation.<br/>* Sensing a quorum of cells / control of the number of cells in a cell group <br/>* (Mesonephric/metanephric) mesenchyme-epithelial transition <br/>* Epithelial patterning of the nephron epithelium <br/>* proximal/distal nephron tubule patterning/ specification/ identity; <br/>* Formation of tight junctions/ adherens junctions/ basement membrane, <br/>* specification of distal tubule identity; pronephros proximal/distal patterning and development <br/>*SF -[https://sourceforge.net/tracker/?func=detail&aid=2859892&group_id=36855&atid=440764 SF 2859892: specification of kidney anlage] *PMID 18715948 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 17875669 *PMID 18715948 *PMID 12925600''  
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|'''11:45am'''
|'''11:20am'''
|Kidney morphogenesis - Kidney structure formation <br/>*Formation of renal vesicle, <br/>*Formation of comma-shaped body, <br/>* Formation of s-shaped body, <br/>* Formation/development/differentiation of glomerulus, <br/>*Formation of mesangium, <br/>* Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter) <br/>* Oriented mitosis (could not find such a term in GO - not GO:0008356 asymmetric cell division) <br/>* Cell morphogenesis  <br/>* new children of GO:0002070 epithelial cell maturation, <br/>*Podocyte differentiation, <br/>*Proximal tubule cell differentiation, <br/>* Loop of Henle formation/development/differentiation (Loop of Henle cell differentiation)(thin descending limb development, thin ascending limb development, Thick ascending limb, <br/>* Distal tubule cell differentiation, <br/>* Connecting tubule cell differentiation, <br/>*. ....Differentiation of all other nephron cell types. <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 12925600''
|Kidney morphogenesis - Kidney structure formation <br/>*Cell morphogenesis <br/>*Formation of renal vesicle, <br/>*Formation of comma-shaped body/ S-shaped body/ glomerulus <br/>*Formation of mesangium, <br/>* Oriented mitosis <br/>* new children of GO:0002070 epithelial cell maturation: Podocyte/ Proximal tubule/ Loop of Henle/ Distal tubule/ Connecting tubule cell differentiation (and other nephron cell types) <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2903833&group_id=36855&atid=440764 SF 2903833: kidney glomus development] *PMID 10572058 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 17875669 *PMID 18715948 *PMID 12925600''
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|'''2pm'''
|'''1:30pm'''
|Anatomical structure development/ Formation <br/>* Morphogenesis of epithelial tubules <br/>*mesonephric tubule (anterior and posterior in mouse) <br/>*Macula densa development <br/>*nephric duct/ tubule specification, differentiationmorphogenesis<br/>* morphogenic and migratory changes to those cell populations as they move towards formation of the nephric tube<br/>*Collecting duct system development <br/>*Connecting tubule development <br/>*kidney proximal tubule development; <br/>*Morphogenesis of epithelial tubules <br/>* SF -[https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2902547&group_id=36855 SF 2902547: various kidney development terms] <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 16790474 *PMID 18835385''
|Anatomical structure development/ Formation <br/>*Macula densa development <br/>* Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter) <br/>* Morphogenesis of epithelial tubules <br/>*mesonephric tubule (anterior and posterior in mouse) <br/>*nephric duct/ tubule specification/differentiation/morphogenesis <br/>*Collecting duct system development/formation/differentiation <br/>*Connecting tubule development <br/>*kidney proximal tubule development; <br/>* SF -[https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2902547&group_id=36855 SF 2902547: various kidney development terms] *PMID 16790474 *PMID 18835385 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 17875669 *PMID 18715948 *PMID 12925600 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2903833&group_id=36855&atid=440764 SF 2903833: kidney glomus development] *PMID 10572058''
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|'''3:30pm'''
|'''3pm'''
|Coffee break
|Coffee break
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|'''4pm'''
|'''3:20pm'''
|* Signalling to blood vessel-forming cells (is it GO:0060684 epithelial-mesenchymal cell signaling?) <br/>* Connection of nephron tubule to collecting duct  <br/>* proximal convoluted tubule development; <br/>*specification of proximal tubule identity<br/>*kidney intermediate tubule development; <br/>*thin descending limb development; <br/>*thin ascending limb development; <br/>*specification of intermediate tubule identity <br/>*kidney distal tubule developmentCollecting duct formation/development/differentiation; thick ascending limb development; <br/>*distal convoluted tubule development; specification of distal tubule identity <br/>* SF -[https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2902547&group_id=36855 SF 2902547: various kidney development terms]<br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 16790474 *PMID 18835385''
|Continue with Anatomical structure development/ Formation <br/>* Connection of nephron tubule to collecting duct  <br/>* proximal convoluted tubule development/ specification; <br/>*kidney intermediate tubule development/ identity specification:- thin descending limb development; thin ascending limb development; thick ascending limb development; <br/>*kidney distal tubule development:- distal convoluted tubule development/ specification <br/>*Signalling to blood vessel-forming cells (GO:0060684 epithelial-mesenchymal cell signaling?) <br/>*renal smooth muscle cell differentiation <br/>* SF -[https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2902547&group_id=36855 SF 2902547: various kidney development terms] *PMID 16790474 *PMID 18835385<br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2860000&group_id=36855&atid=440764 SF 2860000: proximodistal kidney segmentation] *PMID 17875669 *PMID 18715948 *PMID 12925600 <br/>* SF -[https://sourceforge.net/tracker/?func=detail&aid=2903833&group_id=36855&atid=440764 SF 2903833: kidney glomus development] *PMID 10572058''
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[[http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0001822&session_id=5603amigo1258994462]]
[[http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0001822&session_id=5603amigo1258994462]]
<br/>*GO:0001656 GO:0001657 GO:0001658 GO:0001822 GO:0001823 GO:0032835 GO:0032836 GO:0034671 GO:0034672 GO:0048793 GO:0060675 GO:0060676 GO:0060677 GO:0060678 GO:0060679 GO:0060680 GO:0060681 GO:0060682
<br/>*GO:0001656 GO:0001657 GO:0001658 GO:0001822 GO:0001823 GO:0032835 GO:0032836 GO:0034671 GO:0034672 GO:0048793 GO:0060675 GO:0060676 GO:0060677 GO:0060678 GO:0060679 GO:0060680 GO:0060681 GO:0060682
*chart [http://upload.wikimedia.org/wikipedia/commons/1/12/Kidneydevtermschart.png]


== Relevant papers and other resources ==
== Relevant papers and other resources ==

Latest revision as of 14:23, 9 April 2014

Please suggest agenda items, relevant papers and other information relating to kidney development GO terms that you would like discussed at this workshop, to enable us to form an agenda.


Participants

GO annotators GO Editors Kidney Development Experts
Dr Yasmin Alam-Faruque (GOA)
Dr Emily Dimmer (GOA)
Dr Rebecca Foulger (UniProt/Xenopus)
Dr Susan Tweedie (Flybase)
Dr Rachael Huntley (GOA)
Dr Midori Harris
Dr David Hill
Professor Adrian Woolf
Professor Jamie Davies
Dr Duncan Davidson


Location

EMBL-EBI, Room C202/203 - shared facilities, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD. Date: Monday 25th January 2010, 9:30am to 5pm

Programme

9:15am Tea/ Coffee and biscuits
9:30am Welcome and introduction Yasmin
9:35am Introduction to GO David Hill
9:45am Kidney precursor cells and tissues (segmentation)
* Development of kidney field
* Nephrogenic stem cell differentiation.
* Sensing a quorum of cells / control of the number of cells in a cell group
* (Mesonephric/metanephric) mesenchyme-epithelial transition
* Epithelial patterning of the nephron epithelium
* proximal/distal nephron tubule patterning/ specification/ identity;
* Formation of tight junctions/ adherens junctions/ basement membrane,
* specification of distal tubule identity; pronephros proximal/distal patterning and development
*SF -SF 2859892: specification of kidney anlage *PMID 18715948
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
11am Coffee break
11:20am Kidney morphogenesis - Kidney structure formation
*Cell morphogenesis
*Formation of renal vesicle,
*Formation of comma-shaped body/ S-shaped body/ glomerulus
*Formation of mesangium,
* Oriented mitosis
* new children of GO:0002070 epithelial cell maturation: Podocyte/ Proximal tubule/ Loop of Henle/ Distal tubule/ Connecting tubule cell differentiation (and other nephron cell types)
* SF -SF 2903833: kidney glomus development *PMID 10572058
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
12:30pm Lunch
1:30pm Anatomical structure development/ Formation
*Macula densa development
* Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter)
* Morphogenesis of epithelial tubules
*mesonephric tubule (anterior and posterior in mouse)
*nephric duct/ tubule specification/differentiation/morphogenesis
*Collecting duct system development/formation/differentiation
*Connecting tubule development
*kidney proximal tubule development;
* SF -SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF -SF 2903833: kidney glomus development *PMID 10572058
3pm Coffee break
3:20pm Continue with Anatomical structure development/ Formation
* Connection of nephron tubule to collecting duct
* proximal convoluted tubule development/ specification;
*kidney intermediate tubule development/ identity specification:- thin descending limb development; thin ascending limb development; thick ascending limb development;
*kidney distal tubule development:- distal convoluted tubule development/ specification
*Signalling to blood vessel-forming cells (GO:0060684 epithelial-mesenchymal cell signaling?)
*renal smooth muscle cell differentiation
* SF -SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF -SF 2903833: kidney glomus development *PMID 10572058
5pm Close

Minutes

Current Kidney Development Ontology Terms

The currently available kidney development process ontology (November 2009) [[1]]
*GO:0001656 GO:0001657 GO:0001658 GO:0001822 GO:0001823 GO:0032835 GO:0032836 GO:0034671 GO:0034672 GO:0048793 GO:0060675 GO:0060676 GO:0060677 GO:0060678 GO:0060679 GO:0060680 GO:0060681 GO:0060682

Relevant papers and other resources

  • Kidney Development Review Papers:
  • PMID 15554941 Transcriptional control of kidney development. Bouchard M. 2004. Talks about genes involved in nephric lineage specification (Pax2/Pax8/Lim1/Bmp4/Wt1/GDNF1/Eya1/Foxc1); metanephros development - UB positioning, induction, nephron induction, ureter branching, Stromal cell differentiation(Gdnf1/Eya1/Foxc1/2/Slit2/Robo2/Bmp4/Pax2/Hox11(HoxA11/C11/D11)/ Sall1/Wt1/Six1/Wnt4/Emx2/Gata3/BF2/Pod1/Pbx21.
  • PMID 15380247 Recent genetic studies of mouse kidney development. Yu J, McMahon AP, Valerius MT. 2004. Has a nice diagram of the stages of nephron formation on p.551. Also lists genes investigated with particular molecular regulation of outgrowth of the uteric bud and regulation of tubulogenesis (Table 1; p552 - Gdf1, Six1, Slit2/Robo2, Wnt1, Fras1+Grip1, Pod1, Pbx1, Brn1, Psen1/2).
  • PMID 16760375 Role of transcriptional networks in coordinating early events during kidney development. Boyle S, de Caestecker Mark. 2006. Has nice diagrams of stages of early mammalian kidney development. Reviews transcription factors in mesenephric mesenchyme: Eya1/ Foxc1/2/ Hoxa/c/d11/ Pax2/ Pbx1/ Rar-alpha/beta2/ Sall1/ Six1/ Wt1.
  • PMID 12094231 Coordinating early kidney development: lessons from gene targeting. Vainio S, Lin Y. 2002. Nice diagrams of kidney development. List of genes essential for early kidney development (Transcription Factors: Emx2/Eya1/Foxc1/Foxd1/Pax2/Rara,Rarb/Sall1/Wt1; Growth factors: Bmp4/Bmp7/Fgf7/Gdnf/Wnt4; Growth factors/receptors: Gfra1/Notch2/Ret; Proteoglycans and their biosynthetic enzymes: Hs2st/Gpc3.
  • Kidney Development Websites:
  • Mouse Anatomy Browser - [3]
  • FMA human anatomy browser- [4]
  • GUDMAP browser - [5]; Metanephros [6]; renal vesicle [7]


Other reviews

Notes