Kidney - Agenda for Kidney Development Ontology Content Meeting: Difference between revisions

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== '''Minutes''' ==
== '''Minutes''' ==
[[Minutes]]
[[Minutes]]
== '''KDM Minutes''' ==
[[KDM Minutes]]


== '''Current Kidney Development Ontology Terms''' ==
== '''Current Kidney Development Ontology Terms''' ==

Revision as of 05:30, 25 January 2010

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/EBI)
Dr Emily Dimmer (GOA/EBI)
Dr Rachael Huntley (GOA/EBI)
Dr Rebecca Foulger (UniProt/Xenopus/EBI)
Dr Susan Tweedie (Flybase/EBI)
Dr Doug Howe (ZFIN/USA) (via Skype)
Dr David Hill (Jax/USA)
Dr Midori Harris (EBI)
Dr Jane Lomax (EBI)
Professor Adrian Woolf (ICH)
Dr Duncan Davidson (GUDMAP)
Professor Randall Thomas (IBISC CNRS)
Professor Jamie Davies (GUDMAP) (available pm via phone/email)

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

  • Travel instructions to the EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD [1]
  • Further information about the on-site accommodation [2]

Programme

9:15am Tea/ Coffee and Cookies
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
* Formation of tight junctions/ adherens junctions/ basement membrane,
* formation of pronephric-, mesonephric-, metanephric-specific terms?
* SF 2859892: specification of kidney anlage *PMID 18715948
* SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF 2916204: mesenchymal cell differentiation involved in kidney development *PMID 12399320 and SF 2929915 mesenchymal cell differentiation involved in urinary tract development *PMID 17442697
* SF 2926832: metanephric + nephrogenic mesenchyme morphogenesis PMID 15342483
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,
* Macula densa formation/ development
* Oriented mitosis
* SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF 2903833: kidney glomus development *PMID 10572058
* SF 2905937: Glomerular mesangium PMID 8910451 and PMID 10077614
* SF 2928268: specification of renal capsule PMID 15634693
12:30pm Lunch @ on-site campus restaurant
1:30pm Anatomical structure development/ formation
* Epithelial patterning of the nephron epithelium: proximal/distal nephron tubule patterning/ specification/ identity/ 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)
* 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)
* nephric duct/ tubule specification/ differentiation/ morphogenesis
* Collecting duct system development/ formation/ differentiation
* Connection of nephron tubule to collecting duct
* Connecting tubule development;
* SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF 2907403 Podocyte development/ differentiation PMID 19050011
3pm Coffee break
3:20pm Continue with Anatomical structure development/ formation
* kidney proximal tubule development/ specification; proximal convoluted tubule;
* kidney intermediate tubule development/ identity/ specification:- thin descending limb; thin ascending limb; thick ascending limb;
* kidney distal tubule development/ specification; distal convoluted tubule
* Signalling to blood vessel-forming cells/ renal vasculature development (GO:0060684 epithelial-mesenchymal cell signaling?)
* renal smooth muscle cell differentiation
* SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF 2903833: kidney glomus development *PMID 10572058
* SF 2929817 Ureter development *PMID 17442697
* SF 2930545 Glomerular capillary formation *PMID 18272846
5pm Close

Minutes

Minutes

KDM Minutes

KDM Minutes

Current Kidney Development Ontology Terms

The currently available kidney development process ontology (November 2009) [[3]]
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:
    • Mammalian reviews:
  • PMID 19906853 Advances in early kidney specification, development and patterning. Dressler M 2009. Talks about the essential roles of intrinsic nuclear factors and secreted signaling molecules in specifying renal epithelial stem cells and their self-renewal, in driving the complex dynamics of epithelial cell branching morphogenesis, and in nephron patterning.
  • 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).


    • Other resources:


  • Kidney Development Websites:
    • Mouse Anatomy Browser - [5]
    • FMA human anatomy browser- [6]
    • GUDMAP browser - [7]; Metanephros [8]; renal vesicle [9]
  • Kidney Development GO wiki [10]
  • Loop of Henle GO Cocuration wiki [11]

Notes

  • Added KDM acronym to any NTR via SF relating to kidney development
  • All KDM requests currently in SF [12]
  • GO:0060677 ureteric bud elongation (Def: The process by which the ureteric bud grows along its axis) - does this term cover ureteric bud invasion? (the initial key step of metanephros devpt, the ureteric bud invades the mesenchyme and induces epithelialization and differentiation of the mesenchyme into the glomeruli, the Loop of Henle and the proximal and distal tubules - see PMID 18470945|PMID 11688560). If so, need to improve definition.
  • Keep an eye on definition compatability across species/taxa