On the evolution of microRNAs and their targets

A couple of recent papers from the world of plant science.  As always, enjoy.

My ballot

I haven’t voted early, but I’ve pretty much made up my mind.  I’ll be voting for Obama/Biden on Tuesday.

Why, you may ask?  First, let me say it’s not because of the ads that have flooded the airways.  My rule of thumb when it comes to political ads is simple – when one candidate says something about his/her opponent(s), it’s a misrepresentation or outright lie.  That’s politics, they all do it, and I ignore it.

So, what is the difference maker?  How do the two candidates distinguish themselves?  For me, it’s simple.  From the get-go, I’ve felt that the war in Iraq was wrong.  It’s been an unpardonable drain on our economy, it’s done immeasurable damage to relations with our allies, it’s hurt the true war on terror, it’s brought on very frightening collateral damage (a stronger and emboldened Iran, a crumbling Pakistan, an irate Russia, a betrayed Turkey, to name a few), it has been probably the single worst adventure any president has ever embarked upon. One candidate stands up and says the war in Iraq was wrong, the other avoids the question studiously.

Now, I am not saying that I would be against any of the (majority of) politicians who supported the war in 2003.  But I expect that a presidential candidate today who supported the war in 2003 would have the intelligence and courage to admit the error, and pledge to learn from the mistake and avoid similar debacles.  Indeed, before the unfortunate choice of Palin, McCain could have earned my vote by doing just this.  (Don’t get me started on Palin – she’s a disastrous choice for VP, for too many reasons.)

But that’s water under the bridge.  We have a clear choice, and for me there can be only one correct one on Tuesday.

The Truth

That would be Paul Pierce.  When you care that much, you’re a Celtic for Life.

Bring on #18.

Target recognition by microRNAs

Recently, I broached the subject of small RNAs, and mentioned that there were two general classes of these regulatory RNA – microRNAs (miRNAs) and short interfering RNAs (siRNAs). These two classes of small RNAs recognize their targets by standard (Watson-Crick) base pairing. However, there are interesting differences regarding target recognition. siRNAs form duplexes that extend the length of the siRNA; this is not unexpected, as the siRNA is derived from a perfectly base-paired precursor that is usually derived from the target itself. miRNAs are a rather different beast; this is the subject of this essay.

The Small RNA World – a brief introduction

The first reflex when coming across the title of this blog is, most likely, that it is a blog that mentions microRNAs and small RNAs. Up until now, I suppose that I’ve been a disappointment, as the scientific focus has been on the subject matter of my lab – polyadenylation. But this changes with this essay, an overview of the field of small RNAs. My goal with this overview is to lay a foundation to which I can refer in other contexts. As always, enjoy (and feel free to ask questions or correct any mistakes you find).

Transgenesis vs breeding – one case study

One mantra that is repeated by anti-GMO advocates is that genetic engineering – the process of introducing foreign genes into a plant genome – has the potential to dramatically alter gene expression in the transgenic plant, and thus may lead to unanticipated and harmful changes in the plant.  The response from the scientist is that traditional breeding is logically expected to lead to much larger genome-wide changes, and that we actually will have less control over these.  With the advent of genome-wide transcription assays, it is now possible to test this directly (as opposed to trying to reason through the matter.  An example of such a study is that recently published by Baudo et al.  The bottom line of this study – gene expression is much less affected by the insertion of a transgene than by the process of traditional crop breeding.  The abstract of the study is after the fold.  As always, enjoy.

Structure? Who needs structure?

One of the more interesting aspects of the polyadenylation complex is the nature of the protein-protein interactions that help shape the machinery. A recent study has revealed a fascinating side of this story. It involves the interaction between a subunit known as Fip1 (Fip = Factor Interacting with Poly(A) polymerase) and poly(A) polymerase (affectionately abbreviated as PAP). This study is remarkable for two reasons. For one, it dispels some previously-held notions about the functional significance of this interaction. In addition, it reveals that Fip1 is a member of a large class of proteins that share a common feature – namely, they do not have a rigidly-specified 3-dimensional structure in and of themselves.

About that VP debate …

For present and future students who may have indulged in the Biden-Palin debate last week, a few bits of advice:

On exams, when I ask a question, do not expect anything other than a zero for an answer that takes the form “I don’t like the question, let me answer a different one”.  (Well, negative credit is possible, if you go ahead and give me an incorrect answer to the question you foisted on me.)

On qualifying exams, a similar tactic will be penalized most severely (it is not advisable to try and school your committee, and especially to try and distract your committee from the obvious fact that you haven’t a clue).  If you don’t know the answer, “I don’t know” is the best response.  Short, sweet, and mercifully to the point.

If you have passed these hurdles, again, at the time of your thesis defense, “let me answer a different question” is a perilous route to try.  You may be able to pull off an interesting change-of-pace and come across as provocative and informed.  More likely, you’ll seem like someone who is trying to bluff his/her way around a difficult question.  Bad move.

I’m just sayin’ ….

If I could only remember ….

A recent essay described the process of cytoplasmic polyadenylation, and the functioning of the process in animal oocyte maturation and early development.  Cytoplasmic control of translation is important, not only in the oocyte, but in other settings as well.  One of these is in the neuron, where gene expression in repsonse to synaptic stimulation can be controlled by the activation of stored mRNAs in the cytoplasm.  While details of this control have remained poorly understood, a suggestive requirement (well, it’s suggestive when it comes to the general subject of this blog) of CPEB for memory in Drosophila lends itself to the hypothesis that the activation of stored mRNAs in the neuron involves cytoplamsic polyadenylation.

It is thus of interest to see that Drosophila homologue of Gld2 (the cytoplasmic poly(A) polymerase mentioned here) is required for long-term memory.  The abstract of the recent report follows.  As always, enjoy.

Science stumbles on!

The AP press release regarding the 2008 Ig Nobel Prizes is here.

A snippet:

CHEMISTRY: Sheree Umpierre, Joseph Hill and Deborah Anderson for discovering that Coca-Cola is an effective spermicide, and C.Y. Hong, C.C. Shieh, P. Wu and B.N. Chiang for proving it is not.

Teach the controversy, I say!

UPDATE – Oct 13

A link to the Ig Nobel web site that has the listing of the prizes.