MolBiol Carnival #10: Assays, cyanobacteria and metabolism regulation

Welcome to the 10th edition of the MolBiol Carnival!

Apologies for the delay – am behind on pretty much everything and frantically trying to tie up loose ends of my degree, fun times. Also, it's kinda awkward to write up a carnival post with only THREE submissions – you guys really need to submit more and/or write more MolBiol posts!

It seems molecular biology doesn't get blogged about specifically as much as evolution and diversity – perhaps because molecular biologists are usually busy troubleshooting their PCRs and RNA work for weeks on end, and have little time left over to write. In fact, judging from recent woes experienced by some of my lab buddies, I'm beginning to doubt the existence of RNA and believe it may all be a giant elaborate hoax invented to enslave more grad students. Have any of you ever *seen* RNA? That's what I thought...

This month we have a very biochemical (post-translational, if you will) MolBiol Carnival featuring enzyme spec, cyanobacterial biofuel precursors and some sweet diastereomer metabolism regulation.

Enzyme Assay
Christopher Dieni at BitesizeBio has a nice write-up on measuring enzyme kinetics using UV spectrophotometry, complete with procedure, tips and troubleshooting – the kind of thing you wish accompanied every assay you've been assaulted by. Not being anything close to a biochemist, I had no idea you could actually observe enzyme action using something as simple as a spec, so this is quite cool!

Cyanobacteria and biofuel production
With growing concerns with using land plants for biofuels (for one thing, kind of odd to use food to power cars when not everyone has enough of it...), increasing attention has been turned towards algae eukaryotic and not. For one thing, algae are already quite good at photosynthesising and are vastly more abundant than plants, and arguably have the largest contribution to global photosynthesis – not surprising given the earth's surface is 70% ocean. Michael Scott Long at a NASW.org blog explains recent developments in genetic engineering and domestication of cyanobacteria for fatty acid production.

Diastereomers and regulation of metabolism
Stereoisomers are the beginning chemistry student's worst nightmare – they're so similar and easy to mix up, particularly if you're like me and can't tell left from right to begin with. However, a bacterium (rather, its enzymes) would have little trouble with the stereochemistry portion of a intro biochem class – to them, stereoisomers are day and night (and other things). Glucose and galactose are 'close enough' to each other for a biochem student, but a flipped arrangement at just a single stereocentre is enough to require a whole new set of enzymes and drastic changes in the pathway. E.coli prefers glucose, but can also process galactose (compromising its growth rate) by embellishing its metabolic pathways a little – the products of galactose digestion are sent to the tricarboxylic acid cycle via the glycoxylate shunt. Becky Ward at It Takes 30 discusses how sugar type availability affects the transcriptional regulation of this glycoxylate shunt, among other things, featuring a galactose-loving mutant.

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This was fun. Wish there were more submissions – having to write up random blog posts forces me to revisit forgotten subjects and explore new ones: I'd never brave a post on metabolic regulation on my own! By not submitting, y'all are having a deleterious effect on my education... ;-)

The next edition will be hosted by our resident microbiologist @labratting at Lab Rat, and she better get more than three submissions... come on, we do so much molecular biology in almost every field of biology! Write 'er up, dammit!

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...]

Call for submissions for MolBiol Carnival! (and CoE)

Have you written about fancy little molecules doing something biological lately? Have you written about biologists doings something molecular? Do you have pretty gels to show off, in a polite manner as to not offend those of us who chronically fail at PCR? Have you aligned some proteins into pretty super-neat colourful blocks screaming OCD! to the rest of the world? And written about it?

If so, you should submit your post to the high Impact Factor MolBiol Carnival. That way, not only will your wonderful exhibit be hosted amid members of the world's awesomest kingdom, but you'd reach a much wider readership than you would through Obscure Journal of Experimental Molecular Shit No-one Understands Anyway (Aka Journal of HAHAHA YOU'RE NOT IN CANCER RESEARCH SO WE DON'T CARE ABOUT YOU) And you thought that post was going to Nature, eh? What are you, an undergrad summer intern? ;-)
You can even cross-submit to the Carnival of Evolution, as evolution cannot be properly studied without molecular biology (Ha, suck on that, ecologists!*)

Was all of the above too much text for you? Too confusing? Lemme rephrase that:

CLICK HERE and SUBMIT YOUR POST to MolBiol Carnival NOW. Please ;) Scheduled for 01 Nov, 2010, here; please have the submissions in by 31 Oct. Make 'em spooky if you'd like.

Are you happy now, Alejandro?

*I'm perfectly cool with ecologists. I even have a friend who is one. It's kind of like the token 'gay friends' of flaming fundie Republicans. Except that I'm not actually an ecologist** myself. ;-)

** Please don't tell my cell biology peeps I'm applying to a graduate program with "ecology" in its title...I would get shunned by the entire field.

Speaking of evolution, Carnival of Evolution is alive and kicking too. You should submit. Next one is also 01 Nov at Byte Size Biology, and even though it won't be as cool as ours, it will still be totally awesome and the perfect place for you evolution posts.

Incidentally, I should probably write some real posts. Haven't done that in a while...

New carnival in molecular biology and CoE#25

Sorry for the delays in posting - was out of town and away from internet, and then frantically scrambling to get back into the writing zone and get work done. Only half a month ago, another edition of the Carnival of Evolution went out: #25 at Culturing Science. Go check it out, she even has drawings for each heading!


Coming up soon is the first edition of the new MolBio Carnival, headed by Alejandro at MolBiol Research Highlights, where the first edition will happen (posts on the first Monday of each month). We need submissions (form here), and after a couple months, hosts. From the the carnival's main page:

We encourage the submission of posts discussing peer-review articles, techniques, books and related topics. Specific areas of interest include, but are not limited to: structure and function of proteins, nucleic acids and other macromolecules, gene expression and its regulation, signal transduction, apoptosis, developmental biology, cell cycle and cell growth, microbiology, biochemistry, structural biology, membrane dynamics and many others. Systems and synthetic biology-related posts are also welcomed.

So go on and share anything molecular biology related, which is perhaps the bulk of modern biology anyway ;-) (except my stuff -- really need to crank up the molecular details here someday...) Feel free to double or triple post or whatever to multiple carnivals. The more linkage action going on, the better.

Ok, the carnival's gonna be waaay better than my miserable failure at advertising it. So go hit that shiny submit button *sparkle*. And please help spread the word!


Finally, I find many old illustrations to be quite beautiful. This one is from 1938 (Myers, PNAS) discussing the sex life of forams: