Comments for Byte Size Biology

Comment on The Inside Poop by Iddo

Iddo — Sat, 05 May 2012 18:13:49 +0000

Another possibility is that the pathogenic genes identified are not (or not all) T3SS proteins, but homologous proteins that construct the flagella. Thus, these babies do not have low number of pathogens, but gram negative non-pathogens which have flagella (locomotory complexes). Flagella and T3SS are constructed from homologous proteins, and it is likely that MG-RAST may have identified some flagella genes as the T3SS. Flagellin (a major component in flagelle) is a well-known activator of innate immune system, specifically of a receptor called TLR-5 (toll-like receptor 5).

Comment on The Inside Poop by Dave

Dave — Sat, 05 May 2012 13:25:07 +0000

> Taken together, this tells us that the following scenario may apply:
> mother’s milk tends to enrich certain types of gram negative bacteria,
> and those, in turn, stimulate the babies’ immune system. It’s as if the
> mother’s milk is setting up an immunity boot camp for the breastfed
> babies

Hmm, to me that seems somewhat biased towards an assumption that the process you’re observing is good.
I agree, from what you say (I’m not a biologist) it sounds like the babys immune system is being used in the BM case – but is that good? Does it have any good end effect (or should I say is that the cause of the beleived good effect of BM) – or is it just the baby having to fight off some bugs?

Dave

Comment on It’s a smORF world, after all? by gasstationwithoutpumps

gasstationwithoutpumps — Sat, 28 Apr 2012 07:14:31 +0000

Check out the paper by my former student:
Identification of prokaryotic small proteins using a comparative genomic approach
J Samayoa, FH Yildiz, K Karplus
Bioinformatics 27 (13), 1765-1771 2011

Comment on It’s a smORF world, after all? by Habib Maroon

Habib Maroon — Sat, 28 Apr 2012 06:11:26 +0000

Thanks a lot for this. It’s an important and controversial subject; especially in relation to the extent of lincRNAs. I especially liked the finding that tarsel-less encodes multiple 9aa polypeptides in a polycistron. I do wonder just how prevalent this type of protein is, as you would’ve thought they’d be found more commonly by classical genetic screens. Anyway could say the same about ncRNAs.

Comment on Biocuration 2012 by Paul

Paul — Mon, 09 Apr 2012 02:06:24 +0000

Thanks for the post. I always picture the Biocuration meeting as a bunch of people sitting around arguing about how to define protein-coding gene boundaries. After reading your post it does sound moderately more interesting than that. The Wikipedia annotation model is most definitely alive and well. You may be confusing it with the closed-wiki model which seems to have limited success. I've summarised some of the successes Rfam has had with this approach in a recent editorial I wrote. And I believe Pfam is generating even more impressive results with their trial.

Comment on Biocuration 2012 by Iddo

Iddo — Fri, 06 Apr 2012 16:06:29 +0000

Where I’m sitting both URLS lead to the page featuring GenESP and Dizeez. Check your routing tables, if you are at TSRI now.

Comment on Biocuration 2012 by Ben

Ben — Fri, 06 Apr 2012 16:03:10 +0000

Hi Iddo, Great to meet you at biocuration and thanks for summing things up here. For some reason genegames.org is heading straight to the dizeez game right now – should be going to what you see at genegames.com which includes the somewhat more advanced and more fun GenESP.

Comment on You. Want. This. Job. by Sean

Sean — Tue, 03 Apr 2012 06:29:52 +0000

Congrats on the grant and all the best bringing on the next Jedi!

Comment on Does Open Access benefit small universities? by Dan Scott

Dan Scott — Wed, 14 Mar 2012 10:06:09 +0000

Dear all

I’m very interested to read all of your comments, and as somebody who has left a subscription publisher to set up as an open access publisher (http://www.socialsciencesdirectory.com), I have strong views on it. The argument about Quality is a misnomer and has been refuted repeatedly by highlighting the flaws in the peer review process, the poor quality of some subscription journals and the citation levels of open access journals.

Open access is unquestionably the right way to go and there is a general acceptance that there is a cost inherent in publishing, regardless of the model. I disagree that granting agencies are the answer because these funds will always be at risk of cuts and therefore unreliable.

The fundamental problem and the answer to Mark’s inital question, is that most APCs have simply been set too high. Even if publishers can justify them in terms of their overheads, they look expensive. Four figure fees are out of reach of the individual and there are not many libraries or departments currently that have money kicking around to be used up.

Comment on The Origin of Gender Symbols in Biology by Symbolseeker

Symbolseeker — Mon, 12 Mar 2012 18:45:08 +0000

The names of the planets can be traced back to at least 4000 BC, as the names of the days were derived from the names of the planets at that time. Sun = Sunday, Moon = Monday etc. The Vanir culture of that time kept records in picture form to accompany their oral tradition. The names of the days are ordered to reflect the speed of the planets’ movement in orbit. At the time, Saturday was the first day of the week. The symbols used have roots in the notations of the Vanir culture; these not only emerged as symbols for the planets, but their picture language survives in many areas today, such as the Rx symbol we use for drugstores and medicine appears 12,500 BC in the Magdalenian inscriptions, translating to “medicine lady and medicine.” See iceagelanguage.com, and Once Upon a Time: world of symbols blog.