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Allele symbols/acronyms?

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Allele symbols/acronyms?

Postby BioGradStudent » Mon Sep 08, 2008 7:07 pm

I am currently reading a research paper where I get the general idea of what they are trying to say, but I don't understand what exactly their symbols mean. When they list the alleles for a certain protein (Rb) they have fl/fl or delta/delta (actual delta symbol). I have figured out that fl/fl animals have the Rb protein and delta/delta animals do not.

What exactly does fl and delta stand for?

Thanks for your help!
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Re: Allele symbols/acronyms?

Postby blcr11 » Tue Sep 09, 2008 4:02 pm

Hard to say without knowing what the paper is about. Rb could stand for Retinoblastoma or ruby—both of which, it turns out, are X-linked; ruby is an eye color marker. fl is probably fluted: a phenotypic marker of wing morphology located on chromosome 3, which isn’t quite consistent with a study of something on the X-chromosome. I suppose fl could be part of a Balancer? or a transposition used soley as a marker to follow the real gene of interest, or something like that. So a designation of fl/fl means that the fly is homozygous for fluted, though whether that makes any sense in the context of the paper, I can’t say. Delta usually stands for a deletion, though for well-defined cases they are now designated as Df—something-or-other—where Df stands for “deficiency.” A “delta/dela” fly should have the same deleted chromosome for each chromosome of the pair--a homozygous deletion is the simplest way I can think of to say it. If the deleted region would normally contain “Rb” then it makes sense that delta/delta flies don’t have “Rb” but what, if anything, that has to do with fluted, I couldn’t say.
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Postby BioGradStudent » Tue Sep 09, 2008 6:20 pm

Thanks for your reply! In this case, Rb is retinoblastoma. The paper is talking about how Rb influnces the regulation of hematopoietic stem cells. Sorry, I should have said that in the first place! I guess it is silly of me to assume that "fl" would always stand for the same thing?

From what I can understand, after hours of research on the internet, is that the fl/fl animals has Rb and delta/delta does not. I'm not clear on what fl actually stands for in this case though..
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Postby alextemplet » Wed Sep 10, 2008 12:04 am

It might stand for a gene. Can you post a link to the paper in question?
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Re: Allele symbols/acronyms?

Postby blcr11 » Wed Sep 10, 2008 1:25 am

Sorry, wrong system. For some reason—and now that I look again at the original question, I don’t know why—I thought this was about Drosophila genetics. I see this must be the mouse system. The fl/fl designates a specially constructed allele of Rb; one that is flanked on either side by Cre-recombination sites. This is being done to create what amounts to an Rb knockout cell. You can’t create homozygous Rb-knockout mice under normal conditions; Rb-/- is lethal. To get around this, you have to create what are called conditional-lethal mutations of some sort—under permissive conditions, the gene in question expresses normally, while under non-permissive conditions you may see the effect of the absence of the gene’s expression. For the fl/fl cells, in the absence of Cre recombinase, Rb is present, just as if it were a normal cell. When you transfect with something that carries the recombinase, Rb is excised from both chromosomes simultaneously by the action of the recombinase and you are left with what amounts to cells which are Rb-/- which you can use to study the effect the absence of Rb on induced hematopoiesis. I’m taking it on faith it is possible to isolate fl/fl precursor cells and that they can be induced to differentiate in vitro. I think the delta/delta cells will be the fl/fl cells after the action of Cre recombinase. This will be a very specific deletion directed by the flanking Cre recombination sequences.
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Re: Allele symbols/acronyms?

Postby blcr11 » Wed Sep 10, 2008 10:19 am

Just to be clear: the allele designation is fl. I dunno, but I guess in this case fl stands for flanked or something like that. The mouse or cell is homozygous for the fl allele of Rb. That condition is indicated by the name Rb fl/fl. A mouse or cell that is heterozygous for the fl allele of Rb would be called Rb fl/+ or Rb fl/w. The slash notation is used to indicate the status of both alleles of a diploid cell.
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Re: Allele symbols/acronyms?

Postby blcr11 » Wed Sep 10, 2008 4:20 pm

Mystery solved. Any gene can have an "fl" allele. It stands for "floxed" which itself stands for "flanked by loxP sites" the loxP sequence being the recognition site for Cre recombinase. See Kuhn, et. al. (1995) Science 269, 1427-1429. You put Cre recombinase under the control of a promoter (Mx1) which is sensitive to stimulation by interferons or polyinosinic-polycytidylic acid, a dsRNA sometimes abbreviated pIpC. That makes the recombinase inducible in whole animals. When induced, the recombinase eliminates any "floxed" gene and there you have it. I suppose you can call your deleted chromosomes anything you want. Delta/delta is a natural choice it seems to me.
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Postby BioGradStudent » Wed Sep 10, 2008 4:23 pm

Hey, thanks so much!! That is very helpful! I actually had come across that and was wondering if that's what it meant. The explaination I had found for it wasn't very clear though.

THANK YOU!!
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