To: Gillian Millburn <gm119@XXXX>
Subject: Re: FlyBase Help Mail
Date: Tue, 27 Aug 2002  16:31:46  \+0200 (CEST)
From: 'Antonio J. Giraldez' <giraldez@XXXX>
Dear Gillian,
Please find the answer to your questions.
If I've missed something or you need more information, I'll be happy to answer
you.
Best regards and thanks for your interest in curating this information.
Antonio.
Quoting Gillian Millburn <gm119@XXXX>:
> Dear Antonio,
>
> I have finished curating your Dev. Cell paper on Notum (Dev. Cell 2(5):
> 667--676), and I have some questions about the various mutants and
> constructs you used.
>
..
>
> You state that 'Notum4' ( <up></up> = superscript) is l(3)72Da.
>
> We have a record of 4 l(3)72Da alleles in FlyBase \- which one did you
> use ?
>
> Did you get the l(3)72Da allele from the Bloomington Stock Center \- if
> you did what is the Stock number ?
>
Stock Number: 5051
Genotype: l(3)72Da1/TM6C, cu1 Sb1 ca1
All the alleles obtained from the stock center contained second side lethal
mutations. The stocks used in my paper were cleaned
this also applies for Notum5, which is viable in homozygosis.
Stock Number: 4117
Genotype: w1118?; l(3)72CDfI6 P{w+m*=*}71F/TM3, Sb1
..
Antonio J. Giraldez PhD.
Stephen Cohen's Lab
EMBL, Meyerhofstrasse 1
Heidelberg. Germany
Phone \+49 6221 387 290
Fax \+49 6221 387 166
Home \+49 6221 656 586
To: giraldez@XXXX
Subject: Re: FlyBase Help Mail
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Tue, 10 Sep 2002  10:32:27  \+0100
Dear Antonio,
sorry for the delay in replying. Thanks for your answers to my
questions about your Dev. Cell paper on Notum, they were very helpful.
..
1. You say in your reply that 'Notum4' (l(3)72Da1, stock 5051) has a
second site lethal. I need to know whether or not the cleaned
'Notum4' allele is lethal when homozygous or over a deficiency that
removes Notum \- i.e. is there lethality associated with the Notum
mutant in this allele or is the only lethality due to the separable
second site lethal. At the moment in FlyBase we have a separate gene
record for 'l(3)72Da' and I need to know whether or not to merge this
lethal complementation group in with Notum or keep it as a separate
lethal gene (which corresponds to the second site lethality).
2. Also you say that Notum5 is homozygous viable.
In the paper:
Gerlitz and Basler, 2002, Genes Dev. 16(9): 1055--1059
they say that Notum5 is a pupal lethal as a homozygote and also is
lethal over Df(3L)st-f13. So I am wondering:
Is Notum5 lethal over a deficiency that removes Notum ? i.e. is it a
hypomorph that is homozygous viable but is lethal over a deficiency for
Notum because less Notum product is present in the hemizygous case.
OR is it lethal over Df(3L)st-f13 because this Df removes the locus
responsible for the secondary lethal. Again, I need to know this to
establish whether there is any lethality associated with Notum in the
Notum5 chromosome, or whether all the lethality is due to a separate
second site lethal.
3. Finally, if the lethality in Notum4 and Notum5 is all due to
secondary lethals i.e. there is no lethality associated with the
mutation of the Notum gene in these alleles, do you know whether the
second site lethals in Notum4 and Notum5 are in the same
complementation group ?
sorry to ask such a complicated question, but it would really help sort
things out properly in the database if you could help with any of this,
thanks
Gillian
> >
> > You state that 'Notum4' ( <up></up> = superscript) is l(3)72Da.
> >
> > We have a record of 4 l(3)72Da alleles in FlyBase \- which one did you
> > use ?
> >
> > Did you get the l(3)72Da allele from the Bloomington Stock Center \- if
> > you did what is the Stock number ?
> >
>
> Stock Number: 5051
> Genotype: l(3)72Da1/TM6C, cu1 Sb1 ca1
>
> All the alleles obtained from the stock center contained second side lethal
> mutations. The stocks used in my paper were cleaned
>
> this also applies for Notum5, which is viable in homozygosis.
> Stock Number: 4117
> Genotype: w1118?; l(3)72CDfI6 P{w+m*=*}71F/TM3, Sb1
>
To: Gillian Millburn <gm119@XXXX>
Subject: Re: FlyBase Help Mail
Date: Fri, 13 Sep 2002  10:47:32  \+0200 (CEST)
From: 'Antonio J. Giraldez' <giraldez@XXXX>
Dear Gillian,
Thanks for your interest, please find the answer to your questions below.
Quoting Gillian Millburn <gm119@XXXX>:
> Dear Antonio,
>
> sorry for the delay in replying. Thanks for your answers to my
> questions about your Dev. Cell paper on Notum, they were very helpful.
>
> 1. You say in your reply that 'Notum4' (l(3)72Da1, stock 5051) has a
> second site lethal. I need to know whether or not the cleaned
> 'Notum4' allele is lethal when homozygous or over a deficiency that
> removes Notum \- i.e. is there lethality associated with the Notum
> mutant in this allele or is the only lethality due to the separable
> second site lethal. At the moment in FlyBase we have a separate gene
> record for 'l(3)72Da' and I need to know whether or not to merge this
> lethal complementation group in with Notum or keep it as a separate
> lethal gene (which corresponds to the second site lethality).
The stock 5051 has a second site lethal because over itself it is embryonic
lethal but over the deficiency Df(3L)st-f13 or Notum alleles is larval-early-
pupal lethal. also the Notum alleles that I isolated are, once cleaned, larval-
early-pupal lethal over the Df(3L)st-f13. I would say that they are one
complementation group.
Notum complements with stock 5052
l(3)72Db8/TM6C, cu1 Sb1 ca1
If you want to send me some of the other alleles l(3)72Da, I can do a
complementation test with Notum.
> 2. Also you say that Notum5 is homozygous viable.
After cleaning it, I have been able to generate a semi-lethal stock that shows a
strong phenotype in homozygosis. This stock can be kept in homozygosis. Many
pupae die.
>
> In the paper:
>
> Gerlitz and Basler, 2002, Genes Dev. 16(9): 1055--1059
>
> they say that Notum5 is a pupal lethal as a homozygote and also is
> lethal over Df(3L)st-f13. So I am wondering:
I can get viable flies Notum5 over Df(3L)st-f13 but very few. The phenotype is
stronger than Notum5 homozygous.
>
> Is Notum5 lethal over a deficiency that removes Notum ? i.e. is it a
> hypomorph that is homozygous viable but is lethal over a deficiency for
> Notum because less Notum product is present in the hemizygous case.
Yes I would say it is the case.
>
> OR is it lethal over Df(3L)st-f13 because this Df removes the locus
> responsible for the secondary lethal. Again, I need to know this to
> establish whether there is any lethality associated with Notum in the
> Notum5 chromosome, or whether all the lethality is due to a separate
> second site lethal.
In all the cases I've look at, Notum mutants are lethal from embryonic to
larval-
early pupae. Except when one of the alleles is Notum5 then I get some flies
and the number is under mendelian ratios.
>
> 3. Finally, if the lethality in Notum4 and Notum5 is all due to
> secondary lethals i.e. there is no lethality associated with the
> mutation of the Notum gene in these alleles, do you know whether the
> second site lethals in Notum4 and Notum5 are in the same
> complementation group ?
No, the second site lethals are different because in transheterozygosis they
show
a lethality that goes form the embryo to the pupae, getting some adults (
because
Notum5 from my point of view is a hypomorph. This contrasts with the sequence
data of Notum5 that appears as a stop codon at the beginning of the protein.
(there might be another starting codon after?)
>
> sorry to ask such a complicated question, but it would really help sort
> things out properly in the database if you could help with any of this,
>
> thanks
>
> Gillian
>
> > >
> > > You state that 'Notum4' ( <up></up> = superscript) is l(3)72Da.
> > >
> > > We have a record of 4 l(3)72Da alleles in FlyBase \- which one did
> you
> > > use ?
> > >
> > > Did you get the l(3)72Da allele from the Bloomington Stock Center \-
> if
> > > you did what is the Stock number ?
> > >
> >
> > Stock Number: 5051
> > Genotype: l(3)72Da1/TM6C, cu1 Sb1 ca1
> >
> > All the alleles obtained from the stock center contained second side
> lethal
> > mutations. The stocks used in my paper were cleaned
> >
> > this also applies for Notum5, which is viable in homozygosis.
> > Stock Number: 4117
> > Genotype: w1118?; l(3)72CDfI6 P{w+m*=*}71F/TM3, Sb1
> >
>
Antonio J. Giraldez PhD.
Stephen Cohen's Lab
EMBL, Meyerhofstrasse 1
Heidelberg. Germany
Phone \+49 6221 387 290
Fax \+49 6221 387 166
Home \+49 6221 656 586