Wednesday, April 22, 2009

WTH?

Who in their right mind, when submitting the 16S rDNA gene sequence for a type strain, submits a sequence riddled with N*'s? It's a type strain for crying out loud ... you can't make sure you've got a clean sequence? I mean, WTF folks ... combined, a new forward and reverse read would cost you $7. You lazy sons of motherless goats.

Idiots!

*According to IUPAC nomenclature, N stands for aNy nucleotide, which certainly doesn't narrow the field for that position.

6 comments:

Epicanis ( http://www.bigroom.org/wordpress ) said...

Making sure there is as little useful information in the sequence itself is only part of the job, though. Did they also remember to name the strain something like "[insert genus here] sp. ZXKUQYB27"?

(At least I can be 98% certain that being a "type strain" they didn't name it "Uncultured Isolate [some abstract code]")

microbiologist xx said...

If my laptop weren't in front of me, I would probably bang my head on my desk in frustration over this. Why can't people just take a little bit of pride in what they are doing? That crap shouldn't even be accepted. Ugh.
Idiots indeed!

Thomas Joseph said...

Epicanis, I'm not so much worried about the strain designation. Everyone has their own weird way of keeping track of their strains ... besides ... once they get sent to the ATCC or DSMZ or another countries major culture collection they'll get another designation (and people use each one interchangably). I'm actually fascinated by naming conventions. When I started up my own lab I gave very careful consideration to what I was going to name my lab strains and my plasmids.

What would be wicked though would be, upon identifying a unique genus and species, bestowing upon them the names Uncultured and isolate respectively.

I can see it now ...

Uncultured isolate gen. nov., sp. nov., a novel bacterium from some random environment.Brilliant!

MXX, you ain't kidding.

Mad Hatter said...

"You lazy sons of motherless goats."LMAO! I'm going to have to steal that phrase sometime!

Epicanis ( http://www.bigroom.org/wordpress ) said...

Since historically I've mainly used Genbank for 16s sequences for identification of cultured bacteria, the "completely meaningless to anyone else" naming conventions applied to 16s sequences drive me nuts. "Ah, yes, after all this work I can definitively state the my isolate is closely related to...'Uncultured Isolate QX97'. Uh, and...'Uncultured Isolate QX84'j. And, uh, 'Uncharacterized Bacterium 77318/B'..."

(Yes, I'm aware of the Ribosomal Database Project and its ability to filter by only characterized bacteria, too, I'm just saying....)

Personally, since the names are meaningless anyway, I just give as-yet-uncharacterized isolates actual "names", e.g. "Fred", "Lucy", "Helmut", etc...

Thomas Joseph said...

I think it's a forest for the trees issue here Epicanis, though I agree that some of those names get to be rather unwieldy and impractical for inclusion in other peoples work. Rather, what's important at the point that you start comparing uncultured isolates is ... where they were cultured from. At least that's what I start looking at.

Are they all cultured from marine environments and yours happens to be a landlocked lagoon? Soils with low pH? Soils with high salinity? If I find it in a soil with a low pH, and someone else finds it in a soil with high pH, then we can surmise that whatever genus this organism belongs to has a wide pH range of growth. Perhaps this may have importance further down the road, perhaps it's nothing more than a trivial observation. For me, I don't even include those naming conventions in my trees (maybe people will disagree with me on this, but frankly I don't care, they're my trees after all :P ) ... when I list those "uncultured isolates" in my trees (which I do only on occasion as I prefer to list only type isolates when feasible) I list them as follows: Uncultured isolate (GenBank Accession)

I suppose "Fred" and "Lucy" might fly as well. :)