Agenda for Kidney Content Meeting

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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, The Wellcome Trust Genome Campus, Room C202/203 - shared facilities. 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 (Defn: The process whereby a relatively unspecialized cell acquires specialized features of a nephrogenic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells).


* Commitment of multipotent stem cells to the nephrogenic lineage (Defn: The initial commitment of cells whereby the developmental fate of a cell becomes restricted such that it will develop into some type of cell in the nephron).
* Mesenchymal cell condensation involved in nephron development (Defn: the cell adhesion process by which nephron precursor mesenchyme cells adhere to one another to form the pretubular aggregate in the initial stages of nephron development).
* 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)
* Sensing a quorum of cells / control of the number of cells in a cell group
* (Mesonephric/metanephric) mesenchyme-epithelial transition
* proximal/distal nephron patterning specification of proximal tubule identity; specification of intermediate tubule identity;
* Formation of tight junctions,
* Formation of adherens junctions,
* Formation of basement membrane,
* Epithelial patterning of the nephron epithelium {Syn: segmentation of the nephron epithelium},
* specification of distal tubule identity; pronephros proximal/distal patterning; pronephros development; pronephros proximal/distal patterning,
*SF -SF 2859892: specification of kidney anlage

,
11am Coffee break
11:45am Kidney morphogenesis - Kidney structure formation
* new children of GO:0002070 epithelial cell maturation,
*Podocyte differentiation,
*Proximal tubule cell differentiation,
* Loop of Henle cell differentiation,
* Distal tubule cell differentiation,
* Connecting tubule cell differentiation,
*. ....Differentiation of all other nephron cell types.
* ureteric bud specification/differentiation/development,
*mesenchymal cap epithelium,
* SF -SF 2860000: proximodistal kidney segmentation
12:30pm Lunch
2pm Anatomical structure development
*Formation of renal vesicle,
*Formation of comma-shaped body,
* Formation of s-shaped body,
* Formation/development/differentiation of glomerulus,
*Formation of mesangium,
*...Formation of each anatomical structure.
* Morphogenesis of epithelial tubules
*mesonephric tubule (anterior and posterior in mouse)
*Macula densa development
*nephric duct/ tubule specification, differentiation, morphogenesis
* morphogenic and migratory changes to those cell populations as they move towards formation of the nephric tube
*Collecting duct system development
Connecting tubule development
*Loop of Henle formation/development/differentiation (thin descending limb development, thin ascending limb development, Thick ascending limb,
* SF -SF 2902547: various kidney development terms
* SF -SF 2860000: proximodistal kidney segmentation
2:45pm kidney proximal tubule development;
*Morphogenesis of epithelial tubules (this is not GO:0001838 embryonic epithelial tube formation or GO:0060562 epithelial tube morphogenesis because it is not the formation of the tube but the morphogenesis of its form from a spherical vesicle to a comma shape and thence to an S shape). What is the difference between GO:0001838 embryonic epithelial tube formation and GO:0060562 epithelial tube morphogenesis? The definitions are very similar. Pretty similar also to GO:0035239 Tube morphogenesis. We need something that does not denote the generation and organization of tubes, but their subsequent changes in shape. One possibility would be 'comma-shaped body morphogenesis, but it would be good to have a more general ancestor term so that one could link basic processes that occur in the morphogenesis of different forms of epithelial tube.
* Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter)
* Oriented mitosis (could not find such a term in GO - not GO:0008356 asymmetric cell division)
* Cell morphogenesis
* SF -SF 2902547: various kidney development terms
* SF -SF 2860000: proximodistal kidney segmentation
3:30pm Coffee break
4pm * Signalling to blood vessel-forming cells (need to ask Jamie about this - is it GO:0060684 epithelial-mesenchymal cell signaling?)
* Connection of nephron tubule to collecting duct
* proximal convoluted tubule development;
*specification of proximal tubule identity
*kidney intermediate tubule development;
*thin descending limb development;
*thin ascending limb development;
*specification of intermediate tubule identity
*kidney distal tubule developmentCollecting duct formation/development/differentiation; thick ascending limb development;
*distal convoluted tubule development; specification of distal tubule identity
* SF -SF 2902547: various kidney development terms
* SF -SF 2860000: proximodistal kidney segmentation
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

Mouse Anatomy Browser - [2]

FMA human anatomy browser- [3]

GUDMAP browser - [4]; Metanephros [5]; renal vesicle [6]


Other reviews

Notes