Question for Geneticists & Biologists about DNA sequence nomenclature?

[tarchon]

Only thing I know about genes is that I can buy them in a store in many different types of styles.

*crowd throws tomatoes*

This is a very interesting thread

I think that's the (TTAGG)n right there.

 

[LazarusLong42]

Q: Why can't a biologist fix a radio?
A: Because of the lack of a standardised language.
I don't get it.
Hong "shouldn't the answer be: two in the front, and two in the back?" Ooi

There's an argument that reductionist biology--which is what most molecular biologists practice--could never do something as simple as fixing a radio. It goes a bit like this.

How does a biologist determine how a radio works? First, he gathers a group of ten thousand radios, places them in a pile on the backlot, and shoots a few dozen shotgun shells at them. Then, he takes the ones that are not working, and determines why they don't work.

This leads to an absurd situation in which one group of scientists might find a crucial part (CP1) that they say is required for the radio to function. Soon after, another group sayd that CP1 is in fact not necessary, but CP2 (a second crucial part is. THen a third gropu will note that there is a switch which, in one position, causes CP1 to be necessary, and in another position, causes CP2 to be necessary. In other words, neither one is truly crucial, it depends on the switch.

(The switch is the AM/FM switch; the two "crucial parts" are the interior connections to the AM and FM antennae, respectively.)

This may or may not be what PsiSeveredHead was alluding to, of course, and I'm paraphrasing the original article.

Thanks to everyone - this is some useful information! It's surprising to me, given my background in Organic and Physical Chemistry, that the previous nomenclature is not as formalized. In Chemistry there are OBSCENE levels of detail in describing molecules.

Chemical nomenclature is FUN! Teaching it to students is even more fun.

A mosquito cried out in vain:
"A chemist has poisoned my brain!"
The cause of his sorrow
Was 2,2-dichloro-
Diphenyltrichloroethane.

--Eric/LL (BS Chemistry, MS Neuroscience, and still don't know a DAMN thing.)

[Edit: like the meter for a limerick....]

 

[LazarusLong42]

Cuaaugu(Not sure if that is right).

Kinda funny, cause in my Biology class we just finished with DNA. And are doing Genetics right now.

Watch out Galeros; you need to switch it 5' to 3' as well.

 

[Fenris]

Well it's true that at least for naming genes there's no standard nomenclature. You discover a gene and you get to name it more or less what you want to name it.

Not in my field, or at least not with my PI We just discovered a new gene and we went through 5 names to get one that was acceptable (ran the lab ragged re-labeling everything).

 

[LightPhoenix]

A thread in d20 Systems got me thinking abut something, and I was hoping a poster familiar with the science of Genetics (either a professional or a student) would help point me in the right direction.

Woot, my biochem degree comes in handy!

I was wondering how certain Genes and DNA sequences in a Genome are properly named and described. I have absolutely no clue, but I know that there has to be a proper I.D. system for identifying a certain gene or DNA sequence in a genome, especially since so much work has now been done on identifying parts of the human genome.

Ho boy.

Nomenclature

Generally, a gene is named after one of two things - the phenotype (physical appearance) of the mutated gene, or the protein that it codes for. Now, a gene can take different forms - for instance, a fruit fly can have red eyes, or white eyes. These different forms of the gene are called alleles. Two alleles make up the genotype, which very simply causes you to have a certain phenotype.

With me so far?

Now, the most common allele in a population is called the wild type (basically). The wild type allele is commonly denoted with a +. So to continue my example above, the wild type fruit fly eye color could be expressed as eye+. Note that the plus sign should be a superscript. eye+ would indicate a red-eye allele, eye would indicate a white-eye allele. The eye part... well, basically it's up to whomever discovers the gene.

Alright, great for fruit flies, what about humans? Well, the same principles exist for nomenclature - it's pretty much up to the discoverer, and usually has to do with phenotype or the protein produced. For instance, the beta-hemoglobin chain is commonly annotated as the Greek beta. Alternatively, you can call it by its full name - beta-hemoglobin chain, fruit fly eye color, and so on.

Identification

This is going to be really tough to simplify, but I'm going to try.

If you know where a gene is, it's simple - say 3q15. This means, third chromosome, the shorter arm (p for the longer one), 15 units from the center.

If you know the genetic code, it's still pretty simple. DNA is double-stranded, and they are complementary strands - that is, if you know one strand, you know the other. What you can do to identify the gene is make something called a primer. A primer is a short sequence of genetic code complementary to the one you are look for - so it'll stick to it. You attach a phosphorescent or fluorescent molecule to the primer - you make it glow. You can then disrupt the DNA, put in the primer, and it will stick naturally. You then seperate and isolate the glowing bits . Like I said, very simple.

If you don't know the code, but you have the protein it produces, you can attempt to sequence the protein, reverse engineer from that the genetic code, and then make primers to try and find it in the DNA. It's a long and arduous process, and it's why it takes so long to find genes. This is the most common way of doing things. Of course, isolating a specific protein is pretty difficult, and there are some problems with this approach, but once it's isolated the hard part is essentially over.

A good shortcut is if you've identified the protein in another animal, you can use that as a base to start - chances are if the proteins have similar functions, they'll have similar code. This isn't always true, but it works enough to be a viable shortcut to investigate.

I'd really need a more specific question to make a more coherent answer.

Oh, btw, biochem people unite! Actually, if you people with Ph.D.s wouldn't mind, I'd like to ask you guys a few questions in e-mail or PM, if that's okay with you guys.

 

[Chaldfont]

I just got out of a meeting that ran over 40 minutes because of arguments over what to put in a "Gene Name" label in some data mining software we are writing.

If biologists had a more rigorous naming conventions for genes and their products (say, like the chemists do with IUPAC), my job as an informatics programmer/analyst would be a lot easier.

On the other hand, if this were the case, I probably wouldn't have a job.

 

[Henry]

A mosquito cried out in vain:
"A chemist has poisoned my brain!"
The cause of his sorrow
Was 2,2-dichloro-
Diphenyltrichloroethane.

AAAAAAAAAAAGGGGHHH!

I should sue you for emotional torture!

(My senior BS Chemistry project was "variants of DEET and their effect on Mosquitoes." How did it go? you ask? Well, I'm a Computer I.T. Admin... )

 

[LazarusLong42]

Heh heh Note that's not DEET (N,N-diethyl-3-toluamide), but DDT.

 

[LazarusLong42]

Just thought of something else--there IS at least a uniform cataloguing system for genes. Just as you can refer to chemicals by CAS number, you can refer to genes by their accession numbers in the Entrez/BLAST catalog.

The problem with these designations is that they carry, inherently, zero information.

 

[Chaldfont]

Anybody here a fan of Cowboy Bebop? One of the episodes is about a group of eco-terrorists who have engineered some kind of retro-evolution virus that turns people into pre-humans.

In one of the scenes, they show a Genbank record up on a big screen threat board.