KDM: FlyRenalDefUpdate_Skaerlab

[gocentral]

Hi David, Here are the corrections suggested by the fly experts (Dr Stephanie Bunt; Prof. Helen Skaer and Dr Barry Denholm) , mainly relating to the definitions of the fly-related kidney development terms that were recently created:

GO:0061318 renal filtration cell differentiation FROM: def: "The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features of a renal filtration cell. Renal filtration cells are specialized cells of the renal system that filter fluids by charge or size. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." TO: def: "The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features of a renal filtration cell. Renal filtration cells are specialized cells of the renal system that filter fluids by charge and/or size. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state."

GO:0061320 pericardial nephrocyte differentiation FROM: def: "The process whereby a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is a renal cell that filters hemolymph and is found near the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." TO:
def: "The process whereby a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is a renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state."

GO:0061326 renal tubule development FROM: def: "The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, reabsorbs and secretes substances to rid an organism of waste and help maintain fluid homeostasis." TO: def: "The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, reabsorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis."

GO:0061327 anterior Malpighian tubule development FROM: def: "The process whose specific outcome is the progression of the anterior Malpighian tubule over time, from its formation to the mature structure. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which leads into the posterior part of the gut." TO: def: "The process whose specific outcome is the progression of the anterior Malpighian tubule over time, from its formation to the mature structure. The pair of anterior tubules arise from a dorsal region of the embryonic hindgut, project forwards through the body cavity, and each mature tubule contains an average of 146 principal cells and 33 stellate cells. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which connects with the posterior part of the gut."

GO:0061328 posterior Malpighian tubule development FROM: def: "The process whose specific outcome is the progression of the posterior Malpighian tubule over time, from its formation to the mature structure. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which leads into the posterior part of the gut." TO: def: "The process whose specific outcome is the progression of the posterior Malpighian tubule over time, from its formation to the mature structure. The pair of posterior tubules arise from a ventrolateral region of the embryonic hindgut, project backwards through the body cavity, and each mature tubule contains 105 principal cells and 22 stellate cells. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which connects with the posterior part of the gut."

GO:0061329 Malpighian tubule principle cell differentiation FROM: def: "The process whereby a relatively unspecialized cell acquires specialized features of a Malpighian tubule principle cell. A Malpighian tubule principle cell is an epithelial secretory cell that transports cations into the lumen of the tubule." TO: def: "The process whereby a relatively unspecialized cell acquires specialized features of a Malpighian tubule principal cell. A Malpighian tubule principal cell is an epithelial secretory cell that transports cations into the lumen of the tubule."

Require new term id: GO:0061XXX name: Malpighian tubule tip cell differentiation def:The process whereby a relatively unspecialized cell acquires specialized features of a Malpighian tubule tip cell. A Malpighian tubule tip cell is a mitogenic signaling cell that secretes the EGF ligand Spitz. (I found this possible definition at http://www.zoo.cam.ac.uk/zoostaff/skaer/projects.htm - Yasmin)

GO:0061331 cell proliferation involved in Malpighian tubule morphogenesis FROM: def: " The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population and contributing to the shaping of a Malpighian tubule." TO: def: " The division of epithelial cells, resulting in the expansion of a cell population and contributing to the shaping of a Malpighian tubule."

GO:0061332 Malpighian tubule bud morphogenesis FROM: def: "The morphogenetic process by which a bud forms from a the hidgut epithelial sheet to form the Malpighian tubule. A bud is a protrusion that forms from the sheet by localized folding." TO: def: "The morphogenetic process by which a bud forms from the embryonic hindgut tube to form the Malpighian tubule. A bud is a protrusion that forms from the tube by localized changes in cell shape and position."

GO:0061333 renal tubule morphogenesis FROM: def: " The process by which the renal tubule is generated and organized. Morphogenesis pertains to the creation of form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and help maintain fluid homeostasis." TO: def: " The process by which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. Morphogenesis pertains to the creation of form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and help maintain fluid homeostasis."

FROM: GO:0061334 cell migration involved in Malpighian tubule morphogenesis def: "The orderly movement of an epithelial cell from one site to another that contributes to the shaping of the Malpighian tubule." COMMENT: We do not like this term because the mechanism is cell rearrangement not cell migration.

GO:0061335 cell growth involved in Malpighian tubule morphogenesis FROM: def: "The growth of an epithelial cell, where growth contributes to the shaping of the Malpighian tubule." TO: def: "The growth of an epithelial cell dependent on cycles of endoreplication, where growth contributes to the shaping of the Malpighian tubule."

GO:0061336 cell morphogenesis involved in Malpighian tubule morphogenesis FROM: def: " The shape change of an epithelial cell that contributes to the shaping of the Malpighian tubule TO: def: " The shape change of an epithelial cell from a columnar to squamous cell morphology that contributes to the shaping of the Malpighian tubule."

GO:0061352 cell chemotaxis involved in Malpighian tubule morphogenesis FROM: def: "The directed movement of a motile Malpighian tubule cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis) that contributes to the shaping of the tubule TO: def: "The directed movement of the outgrowing Malpighian tubule guided by specific chemical cues/signals. Movement may be towards a guidance cue (positive chemotaxis) or away from it (negative chemotaxis). Guidance contributes to the final positioning of the tubule."

GO:0061353 FROM name: transforming growth factor beta receptor signaling pathway involved in Malpighian tubule cell chemotaxis def: "The series of molecular signals generated as a consequence of a transforming growth factor beta receptor binding to one of its physiological ligands and contributing to the directed movement of a Malpighian tubule cell in a chemical gradient." TO: name: Bone morphogenetic factor receptor signaling pathway involved in Malpighian tubule cell chemotaxis def: "Activation of the BMP signaling pathway in the Malpighian tubule cells The series of molecular signals generated as a consequence of a BMP transforming growth factor beta receptor binding to one of its physiological ligands leading to the directed movement of a Malpighian."

Cheers, Yasmin

Reported by: yafaruque

Original Ticket: geneontology/ontology-requests/7962

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: yafaruque

[gocentral]

extension to definition of new term: Require new term id: GO:0061XXX name: Malpighian tubule tip cell differentiation def:The process whereby a relatively unspecialized cell acquires specialized features of a Malpighian tubule tip cell. A Malpighian tubule tip cell is a mitogenic signaling cell that secretes the EGF ligand Spitz to adjacent cells in the distal proliferation zone thereby controlling the proliferation of its neighboring cells. (I found this possible definition at http://www.zoo.cam.ac.uk/zoostaff/skaer/projects.htm - Yasmin)

Original comment by: yafaruque

[gocentral]

done!

Original comment by: ukemi

[gocentral]

• status: open --> closed-accepted

Original comment by: ukemi