Question for Geneticists & Biologists about DNA sequence nomenclature?

[Mr. Lobo]

Hey Henry,

First an intro - I have a Ph.D. in microbiology and immunology and specialize in bacterial genetics and pathogenesis.

Many genes are also named for their function using a three letter code maybe followed by another letter or some numbers. For example the hemolysin gene of E. coli (a bacterium) is named hly followed by another letter designation such as A, B, or C. All hly genes are involved in the expression of hemolysin from the bacterium but may have different functions that are involved in the process. (Hence hlyA, hlyB,..etc. for making and secretion of the hemolysin from the bacterium). A mutation in any of these genes would result in a bacterium that has its hemolysin expression altered. As stated before many times genes are discovered by "breaking" (mutating) the organism and then trying to find out what it was you broke.

Many functions in bacteria and more complex organisms are the result of multiple gene interactions. In a gaming situation this would mean that the ability for a mutant creature to be born that suddenly has a pair of wings, where its parents did not, would most likely not occur by a single gene defect. However over years of selection a mutant could be selected by the geneticist in your game as a step by step evolutionary approach. Alternatively a mutant creature and its parents could have genes present for a particular trait but the "on" (regulator gene) button is not active except for in the mutant. When the "on" gene is flipped (by mutation) a whole cascade of other genes could be turned on and the mutant trait (phenotype) expressed in the offspring.

As a player trying to to determine the genetics of mutant organisms perhaps some spells could be devised to look at a creatures genome and verify that certain regions have different coding from others.

Also "Genes" by Lewin or a Bio 101 textebook should have a lot of good introductory material that goes into the nomenclature and rationale for mutation and selection.

Hope this helps some,

Mr. Lobo

 

[Henry]

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.

And thanks to Conaill for that link to Pseudo-Babble Heaven. That looks like the kind of info I really need to dig into if I pursue this.

 

[diaglo]

I think (Psi)SeveredHead is hitting closer to the mark of what I'm looking for; basically, if I were spouting off some pseudobabble in-game about "X gene sequence" causing a mutation that causes him to see in the dark, or "DNA sequence X through Y causing those claws growing out of his arms", then what I was looking for was specific nomenclature where someone could find a specific DNA sequence, as if someone were referring to it in a madical paper.

Or is our understanding of genetic sequencing nowhere near that precise yet?

we are a diverse group. many scientists in the field of biogenetics have particular emphasis in one organism. i work in fingerprinting of Mycobacteria.

genes i deal a lot with involve sig A-... (sigma factors). they are involved with other bacteria but act differently and thus much research is done in trying to understand the differences and similarities. and also to understand the effects.

we are mostly curious to turn off or turn on various effects as possible vaccines or mechanisms to prevent disease in hosts...like humans.

 

[Conaill]

3) With more modern sequencing of whole genomes, we have whole genomes that are named by the sequencing results. Thus every potential gene is named in the genome in some formulaic manner. ex: every gene that is on this chromosome will begin with ylr, the direction of the reading frame is indicated with a w or c (for watson and crick) and then the genes are number 1,2,3... , so you can end up with the really memorable gene names such as ylr219w.

That example is very specific to Yeast genetics though. YLR219W stands for Yeast chromosome 12 (A=1, B=2... L=12), Right arm of the chromosome, 219th potential gene, on the "Watson" strand of the DNA.

For human genes, the situation isn't nearly as pretty as in yeast. Probably the most stable identifiers are what's called "accession numbers", which is just some identifier in a database. But each database uses a different identifier scheme, and some of them even keep changing over time.

There is a similar naming scheme to the "Y-names" in yeast for human DNA fragments, which may or may not correspond to actual genes (see Appendix 1.1). For example, DXS9879E stands for DNA, X chromosome, unique DNA segment (S), number 9879, Expressed (i.e. this one actually seems to be part of a real gene).

I would encourage *anyone* to play around a bit with the Human Genome Browser at ensembl.org: pick a chromosome, zoom in on a random piece of it, and start clicking around... hours of fun for the whole family!

 

[(Psi)SeveredHead]

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.

And thanks to Conaill for that link to Pseudo-Babble Heaven. That looks like the kind of info I really need to dig into if I pursue this.

The lack of standardized language is one of biology's greatest (hidden) weaknesses. It's the reason why a biologist can't fix a radio.

I'll have to check that site too.

 

[Fenris]

Hey Henry,

First an intro - I have a Ph.D. in microbiology and immunology and specialize in bacterial genetics and pathogenesis.

Many genes are also named for their function using a three letter code maybe followed by another letter or some numbers. For example the hemolysin gene of E. coli (a bacterium) is named hly followed by another letter designation such as A, B, or C. All hly genes are involved in the expression of hemolysin from the bacterium but may have different functions that are involved in the process. (Hence hlyA, hlyB,..etc. for making and secretion of the hemolysin from the bacterium). A mutation in any of these genes would result in a bacterium that has its hemolysin expression altered. As stated before many times genes are discovered by "breaking" (mutating) the organism and then trying to find out what it was you broke.

Many functions in bacteria and more complex organisms are the result of multiple gene interactions. In a gaming situation this would mean that the ability for a mutant creature to be born that suddenly has a pair of wings, where its parents did not, would most likely not occur by a single gene defect. However over years of selection a mutant could be selected by the geneticist in your game as a step by step evolutionary approach. Alternatively a mutant creature and its parents could have genes present for a particular trait but the "on" (regulator gene) button is not active except for in the mutant. When the "on" gene is flipped (by mutation) a whole cascade of other genes could be turned on and the mutant trait (phenotype) expressed in the offspring.

As a player trying to to determine the genetics of mutant organisms perhaps some spells could be devised to look at a creatures genome and verify that certain regions have different coding from others.

Also "Genes" by Lewin or a Bio 101 textebook should have a lot of good introductory material that goes into the nomenclature and rationale for mutation and selection.

Hope this helps some,

Mr. Lobo

Got to give love to the plants here with my soon to be complete Ph.D. in Plant Genetics.
In some systems though you would capitalize the first letter to designate the gene others and put the mutation in all lower case, in others you put the gene in all lower case and the mutation in italics and then there are proteins!
But really one thing people have overlooked are species appelations. In the day to day functioning of science we don't refer to genes by their accession numbers (although we keep them handy), rather the gene names people have been giving are useful within one's own field. However, when looking across species you need to keep clear where the gene comes from. For instance the gene Leukotriene A4 Hydrolase is abbreviated as LTA4H (or soemtimes as LKH depending on who you ask). The human gene would then be HsLTA4H and say the chimp gene (similar but not exact) would be PtLTA4H. This convention would be helpful (and simple) for use in a game where you want to introduce a gene into another organism.

And in reference to the gorilla myosin gene given above, and for Henry, remember it isn't always about the gene, but how active the gene is and where (the regulation of the gene). Many of my superheros had transgenes that had tweaks to their promoter regions

 

[hong]

The lack of standardized language is one of biology's greatest (hidden) weaknesses. It's the reason why a biologist can't fix a radio.

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

 

[Shemeska]

Q: Why can't a biologist fix a radio?

A: Because of the lack of a standardised language.

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. There's a standard for what a gene is named as compared to what protein it might produce to distinguise if you're referring to gene or protein in a paper. However there's proteins named anything from SonicHedgehog (SHH), to FoxC1, to BZLF1, to BRLF1 (the latter two being my neck of the woods for work). You can name them whatever you want to an extent, and this leads to problems later on when people are working with other genes/proteins that have interactions with those. It can be hard to remember them all when oftentimes the name has little relation to function.

*shrugs* This is what's fun about Enworld, as opposed to the WotC boards. A question gets asked like in this thread here and you've got PhD's springing out of the woodwork to answer it here (or those of us working on PhD's but not there yet). On WotC you just have an overabundance of 11 year olds who love Pokemon and have algebra homework.

*smile*

 

[Tinker Gnome]

Gattaca

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.

 

[Mista Collins]

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