On 13 Jul 2011, at Wed13 Jul  16:29 , Mary Beckerle wrote:
Hi Steven et al:
Thanks for your messages and thoughtful analysis of the nomenclature situation.
I am comfortable with either Zyx102 or simply Zyx. I agree that Zyx102EF is too cumbersome.   I think for the non-fly folks it is useful to use the full name, zyxin, for clarity.
The founding member of the zyxin family is zyxin, itself.  I think it would be helpful, as Ken points out, if flybase annotation could include a note that Zyx or Zyx102 refers to the single Drosophila gene, which likely represents the orthologue of vertebrate genes encoding  Zyxin, LPP, and TRIP-6 as outlined in the Renfranz paper (2003).
Thanks. Mary
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On 30 Jun 2011, at Thu30 Jun  15:40 , Julien Colombelli wrote:
Dear Steven
Thanks for your email and enquiry,
I have forwarded your email to Emmanuel Caussinus (university of Basel, CH) who was the person in charge of generating the flies we have used in our paper.
From my point of view, I am neither drosophilist nor biologist, therefore I would give little importance to my own opinion as I don't have much experience with Flybase,
having mainly worked on the forms of zyxin which we expressed in mammalian cells.
Thanks for your efforts to harmonize everything though, I do appreciate it.
with my best wishes,
Julien
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On 29 Jun 2011, at Wed29 Jun  17:16 , Ken Irvine wrote:
Dear Steven,
Thanks for looking into this. We thought about this before our recent paper, so I can elaborate on our thinking.
We went with Zyx102 as the gene name because of the issues you noted in points i), ii), & iV) below. The original publications on the gene are from Mary Beckerle's lab, and they used Zyx102.
We proposed Zyx as a symbol because as Drosophila geneticists we find it very convenient to have a short symbol rather than writing out a longer name each time.
A potential problem with using Zyxin as the Drosophila gene name is that there are 3 related genes in vertebrates: Zyxin, LPP, and TRIP6. If you refer to the Drosophila gene as Zyxin it might give the false impression that its the orthologue of Zyxin rather than of LPP and TRIP6. If you do a simple blast search the fly gene is actually closest to LPP, but probably the fly gene should be considered the orthologue of all three vertebrate genes. Complicating the issue is that these 3 genes together are sometimes collectively referred to as the Zyxin family. I would vote for just leaving the name as Zyx102, both for historical consistency and to avoid implying that its specifically related to Zyxin rather than the other family members. But Mary is the real Zyxin expert and if she wants to change the name I would be willing to go along with it.
Ken Irvine
Howard Hughes Medical Institute
Waksman Institute
Rutgers, The State University of New Jersey
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On Jun 29, 2011, at  11:37  AM, Steven Marygold wrote:
Dear Mary, Ken, and Julien,
I'd like, if possible, to tidy up the nomenclature for the gene currently known as "Zyx102EF " in FlyBase.
From digging in our records, it looks like this gene was originally given this symbol based on an email exchange with Beth Stronach (formerly of the Beckerle lab?) in 1996 (see /reports/FBrf0086253.html ).
However, there are a few problems with using "Zyx102EF" as the FlyBase symbol:
i) Nobody has ever referred to the gene with symbol 'Zyx102EF' in the published literature as far as I can tell.
ii) The Beckerle lab subsequently published on this gene using a slightly different symbol, "zyx102" (Renfranz, 2003, PMID:12594038; Renfranz 2010, PMID:20648572 )
iii) The only other papers that focus on this gene (of which I'm aware) use the symbol/name "Zyx" (Rauskkolb, 2011, PMID:21666802) or "zyxin" (Colombelli, 2009, PMID:19401336).
iv) Giving a symbol based on cytology (which is what the '102EF' or '102' refers to) isn't great because the cytological mapping can be revised, and this type of nomenclature isn't transferable to other Drosophilids or very accessible to non-fly researchers.
v) There's no real need to use a distinguishing suffix as there appears to be only one zyxin gene in the melanogaster genome.
Based on the above, I'd like to FlyBase to use the symbol 'Zyx' and the fullname 'Zyxin' for this gene.
But I wanted to get feedback from interested parties before making this change.
If my suggestion is unpopular, then I will at least change the symbol to "Zyx102" to be consistent with the first peer-reviewed publication to characterize the gene (Renfranz, 2003).
Can you let me know your views on this?  And let me know of any other parties I should be speaking to?
Thanks,
Steven Marygold.
FlyBase