Field of Science

MolBiol Carnival #04

Welcome to the fourth edition the MolBiol Carnival!

With a GRE to write this Thursday, don't have much time or energy for creativity, so I'll just run the submitted posts on a gel this time. The submitted posts were measured for word count* and run on a gel in Excel (didn't know you could do that, did you?) – aside from a contaminant (and mysterious primer dimers despite not using any primers), the gel seems to have worked and is displayed below:
(Sorry, was too lazy to make a fake ladder too...)
*Ideally, one would use character count instead, but that requires extra clicking and I'm lazy energetically-challenged.

Now I'll do some gel extractions and run the resulting sketchy solution through a sequencer (ie dumped them off at the sequencing unit, to be glared at by the personnel as usual). Ooooh, it came back like this: nnnnnnynnnnnrmnnnnhrnnnnnnrannnnnn. That's right, I have a single base pair recognised! And that was my longest read! nnnn's are so easy to assemble into contigs. Am I doing it right? Nothing wrong with sequencing single posts without amplification, you see?

And this is why wise ones keep hardcore molecular biology preferrably in an entirely separate building from cell biologists like me. Preferably with security. For the greater good of Science.

So I have up on 'sequencing' the posts from scratch and went directly to 'GenBank' (reads, The Internet) where these posts were strangely already deposited. As they say, "Two months in the lab can save two hours in the library." – source unknown.

Saving the best for last, or going straight for the best first, we start with our friendly and not-so-friendly prokaryotes. First off we have an explanation of the effect of ATP on bacterial biofilms in the medical context by Michael Scott Long at Phased. Next we have another biofilm-forming bacterium, beautifully-named Golden Staph, with a really nice SEM, seen at the right. It has a close relative which may actually be quite helpful to us medially, explained at James Byrne's Disease of the Week!. Another post from his blog features Pseudomonas aeruginosa and amazing antiseptic honey action. Apparently, biofilms don't fell so well after being smothered with honey. Last item from Disease of the Week this issue comes just in time for flu season – an explanation of how vaccines work, in two parts.

Next up we hear about bacteria being 'floxed'. To find out what the Cre-lox system and Streptomyces have to do with each other, head over and read LabRat's post for your daily flox. She also has a nice post on bacterial division.

Taking a break from small things, we have a post on thoroughbred horses: turns out, while the pedigree of the stallions was well-maintained, it did not dawn upon the ancients that the mares contribute half of the phenotype. Thus, while the males were imported from various exotic locations, any local female was considered to suffice...find out more at GrrlScientist's Punctuated Equilibrium.

Next we have Lucas Brouwers on tinkering and the evolution of novelty at Thoughtomics, tracing the story of the metazoan nuclear receptor. Of course, this receptor could be misfolded upon formation, like any other protein. How are defect proteins removed before they wreck havoc upon the cell? Enter E3 ubiquitin ligases and their role in removing proteins originating from mRNAs devoid of stop codons, in a post by David Weinberg at You'd Prefer an Argonaute (a title that makes me feel oddly...silenced *groan*).

And last but not least, all the proteins must fit somewhere. Well, the genes that code for them anyway. Often, these genes have a very spacious home in a massive genome(amid piles of junk), as discussed in Iddo Friedberg's Byte Sized Biology. Here I must shamelessly add a plug for 'my' kingdom: the coolest genomic gymnastics happen among the protists, aka "the other 99% of eukaryotic diversity, that you don't hear about". We have the smallest eukaryotic genomes, called nucleomorphs, as relict algal nuclei remaining after secondary endosymbiosis (in cryptomonads and chlorarachniophytes). We also have [arguably] the largest eukaryotic genomes: Amoeba proteus and Amoeba dubia, the latter around 670GBp, as well as dinoflagellates with their unusual low-histone nuclei. And size is not all that matters – some nuclei, eg. of euglenozoans, have polycistronic messages consisting of many eukaryotic genes riding off a single promoter. They rely upon splice leader trans-splicing to work, and that is only the beginning of awesome... feel free to stick around here for more! ;)

That's it for this month's edition of The MolBio Carnival. You can check future hosts and past editions on the Carnival's home page. Be sure to subscribe to the RSS feed to receive notifications and summaries when new editions of the Carnival are posted. Also, you are welcomed to submit your best molbio blog articles to the next edition of The MolBio Carnival which will be hosted by LabRat. More info here. The previous edition was hosted by Alexander Knoll at Alles was lebt.

My favourite thing about carnivals is the exposure you get to various topics and writers as a reader, and the forced exposure to various topics as a host. Thus, submit, submit, submit – feel responsible for enlightening the next host as well as the readership about the existence of topics they never come across! Molecular biology is everywhere – let's see more of that!

PS: Carnival of Evolution #19 came out yesterday at Byte Sized Biology.
Also, if hungry and poor, Sci at Neurotic Physiology has an awesome compilation of recipes at her The Grad Student Eating in Style Carnival.

PPS: Apologies for slight delay. Reason – my life looks roughly like this comic. INTERNET! FOREVER...

Some cited references:
[Will add as soon as I wake up + get to a computer tomorrow. Don't want to be walked in on still being in the lab at 6am...]


  1. LOL Awesome. Well done for getting it out (almost) on time, sounds hectic at the moment. It looks like we've got a nice number of submissions as well, looking forward to hosting it next month. :)

  2. I love the gel! Scary that I'm in the top 3 of 'heaviest' post though, I always thought I kept my posts concise :P . Good luck with the GRE!

  3. That gel is awesome! Nice to see I have the 'heaviest' and 'lightest' posts above contamination lol. Thanks for the links!


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