A random hot chick approached me and started talking to me on the street, real aggressive like. I was pretty taken aback until I realized she was a Jehovah’s Witness, though I didn’t comprehend that until I looked at the literature she gave me. I don’t really know what she said, and I left the literature in the coffee shop where I got my morning fix, but this is certainly the first time that I’ve been approached by a smokin’ JW. But I don’t know if it’s good for the spread of the faith since I doubt this individual induces moral rectitude in most males who she approaches with a bright smile. Of course she could take it to the next step, in the late 4th century though the emperor was Christian the Senate in Rome was the redoubt of pagan males. Nonetheless, many of their wives were Christian, and they raised their children in that faith.

Via Free Association comes a profile of Craig Venter, the so-called “maverick biologist”.

1. Apparently Venter is going to be publishing his own genome sequence shortly and making it publicly available, which is pretty cool. If technically trivial, would you do the same? I’ll go ahead and say I would–Venter makes the good point that we don’t know what most of it does anyways, so GATTACA-like scenarios are far from being reality. And data is hard enough to come by as it is; I’d be happy to let other people play around with my genome sequence and see what they find.

2. The article makes some mention of the “race” to sequence the genome, and how it ended in a tie. I’ve explained before why that’s BS: Venter and Celera published eventually published an independent genome sequence, but they didn’t do it until 2004.

When I’m writin’ I’m trapped in between the lines. I escape when I finish the rhyme. – Rakim

I wanted to go a little deeper into one of the new papers in the recent Cell. It is a set of findings in miRNA research that can be tangentially related to synaptic plasticity. For the field of miRNA research, this paper is important because it is one of the clearest examples of miRNA derepression. To date, in most examples of miRNA-mediated gene silencing the target RNA is moved to P bodies where it is eventually degraded. Why make all this RNA just to destroy it? Not to mention that the system would be a lot more flexible if new RNAs didn’t have to be transcribed each time new proteins were needed. A couple papers have come out recently that show RNAs being released from repression in response to environmental signals, but this one proposes a distinct mechanism and examines the relationship with P bodies. Interestingly, the other two papers were both concerned with synaptic plasticity.

The authors were able to find modular elements in the 3′ UTR (untranslated region, a common area for regulatory elements in mRNA) of the cationic amino acid transporter 1 (CAT-1) mRNA that confer susceptibility to repression by a specific miRNA (miR-122) and derepression by interaction with a protein called HuR. These elements can act independently of the rest of the CAT-1 message. For instance, certain chunks of the 3′ UTR can be attached to a glowy protein stolen from fireflies (luciferase) to make it a target for miR-122. They do a decent job mimicking the behavior of CAT-1 in a human hepatoma cell line in ideal growth conditions.

Under less than ideal growth conditions, such as amino acid starvation, CAT-1 protein is upregulated within an hour while CAT-1 mRNA comes up in a range around 4 hours. So CAT-1 protein is regulated independently of the mRNA levels. The luciferase reporter constructs that only contain miR-122 binding sites are not affected in the starvation condition. Translation remains low. A further 1-kb of the CAT-1 3′ UTR is needed for a protein increase in response to cellular stress. This chunk of UTR contains three adenine (A) and uracil (U) rich regions. These, like other AU-rich elements (AREs), interact with an RNA-binding protein called HuR. People have generally thought that Hu binding to AREs stabilized the RNA by blocking exonucleolytic degradation. The authors carried out binding assays and also measured the effect of each of these AREs independent of the others. They found that the strength of HuR binding to a particular ARE predicts the amount of stress-inducibility of a reporter with that ARE.

Thus, the story so far is that miR-122 represses CAT-1 constitutively, but in response to certain environmental conditions, HuR becomes active and binds to elements downstream from the miRNA sites and derepresses CAT-1. Now, often when a miRNA binds its target they will both localize to cytoplasmic processing bodies (PBs). This is the case for CAT-1 and miR-122. Under normal conditions CAT-1 is found in PBs, but in response to starvation CAT-1 moves out of PBs and associates with polysomes (protein synthesis machinery). HuR binding to the AREs is necessary for this relocalization. The authors mention a preliminary finding that Ago2 (of Slicer fame) remains associated with CAT-1 when it relocalizes, but they show data that miR-122 abundance in PBs doesn’t change. I find it a little difficult to square these two, as one would expect that the interaction of Ago2 and CAT-1 RNA would be mediated by the miRNA, but perhaps miR-122 is just so abundant that some of it can wander off with CAT-1 without making a dent.

So HuR is little like a molecular Lee Marvin rescuing CAT from certain destruction (yes, I went there). The ability of HuR to do this even when the AREs are on a different RNA being repressed by a different miRNA makes the mechanism seem more general. HuR is part of a family of proteins called ELAV-like RNA-binding or Hu proteins, some of which (HuB, HuC, and HuD) are neuron-specific. Research into regulation of neuronal proteins by these Hu proteins goes back several years now and has focused on regulation of a protein called GAP-43.

GAP-43 is associated with axonal growth during development and is phosphorylated by protein kinase C (PKC) in response to LTP induction. It is not entirely clear what GAP-43 does at a mechanistic level yet, but the vague impression is that when GAP-43 is involved axons are growing and establishing new connections. I find it interesting that PKC may be regulating GAP-43 at more than one level. PKC can directly phosphorylate GAP-43 which leads to a number of changes in intracellular and membrane signaling. PKC activation also leads to upregulation of all three neuron-specific Hu family proteins. These proteins in turn stabilize GAP-43 mRNA and lead to GAP-43 protein increase.

Hu proteins and GAP-43 are regulated in response to hippocampus-dependent learning tasks too.

Abstract:

Increase of the RNA-binding protein HuD and posttranscriptional up-regulation of the GAP-43 gene during spatial memory

Alessia Pascale, Pavel A. Gusev, Marialaura Amadio, Tania Dottorini, Stefano Govoni, Daniel L. Alkon, and Alessandro Quattrone

Neuronal ELAV-like proteins (HuB, HuC, and HuD) are highly conserved RNA-binding proteins able to selectively associate with the 3′ UTR of a subset of target mRNAs and increase their cytoplasmic stability and rate of translation. We previously demonstrated the involvement of these proteins in learning, reporting that they undergo a sustained up-regulation in the hippocampus of mice trained in a spatial discrimination task. Here, we extend this finding, showing that a similar up-regulation occurs in the hippocampus of rats trained in another spatial learning paradigm, the Morris water maze. HuD, a strictly neuron-specific ELAV-like protein, is shown to increase after learning, with a preferential binding to the cytoskeletal fraction. HuD up-regulation is associated with an enhancement of GAP-43 mRNA and protein levels, with an apparently increased HuD colocalization with the GAP-43 mRNA and an increased association of neuronal ELAV-like proteins with the GAP-43 mRNA. These learning-dependent biochemical events appear to be spatiotemporally controlled, because they do not occur in another brain region involved in learning, the retrosplenial cortex, and at the level of protein expression they show extinction 1 month after training despite memory retention. By contrast, HuD mRNA levels still remain increased after 1 month in the CA1 region. This persistence may have implications for long-term memory recall.

The Morris water maze is one of the most common behavioral tasks used to assess hippocampal function in rodents. It is assumed that the animals are learning to navigate in a two-dimensional space using distal cues to create a cognitive map. All of this should make synaptic changes in the hippocampus. Others have shown directly using zinc staining that over-training on the water maze task can actually lead to axonal growth into new layers of the hippocampus, which is a major structural change that may well contribute to permanent memory storage.

I guess what I’m saying is that GAP-43 is probably a good candidate for a memory-related molecule that is regulated by miRNAs. If I had the bioinformatics kn
ow-how I would go look up the potential miRNA binding sites in GAP-43’s 3′ UTR. Then I would look to see if they had similar distance from the AREs in GAP-43’s 3′ UTR as they do in CAT-1. Then I would stretch and see if other proteins that have similar function to GAP-43 and share conserved sequences such as MARCKS and Neurogranin also have these sorts of motifs. These guys are also regulated in response to synaptic plasticity, and I think it would be really cool if they were regulated in coordination by Hu proteins derepressing the same miRNA. MARCKS has a CU-rich element that is recognized by HuD and HuR. I’m really thinking that miRNAs, since they don’t have to be specific, could regulate protein modules, so GAP-43 and MARCKS could share the same miRNA.

Here are a couple other interesting things that I haven’t really integrated. Recently, a SNP in a human neuron-specific Hu protein (ELAVL4) was associated with age-at-onset of Parkinson’s disease. Also, HuD and HuR appear to regulate acetylcholinesterase through an ARE in its 3′ UTR. 1 in 20 human genes have AU-rich elements, so just tying things together with AREs isn’t going to be enough, but if things had AREs and similar miRNA-binding sites I could see room for coordination.

Manish points me to this bizarre article about a successful young American who happens to be gay, and, is seeking a “marriage of convenience” with a suitably inclined lesbian. Oh, and guess what, he is a practicing Muslim to boot! A few months ago rik asked me if I thought science and religion were fundamentally compatible. My somewhat lame answer was that they must be, as there are individuals who are great scientists who seem sincerely religious. Now, is a homosexual orientation which is active and unabashed compatible with Islam? Most of the scholars and clerics interviewed in the article disavow any hint of such a possibility, and yet people live this ideal. Is it possible to be a vegan for ethical reasons all the while being a promiscuous zoophile?¹ Hell if I know. The illusion of an integrated and rational mind is really getting to be a problem for me. The power of ideas is overrated, the persuasiveness of preference is neglected.
1 – I do not believe animals can give consent, so zoophilia is rape in my eyes.

Well, pretty soon Craig Newmark’s cherubic visage is going to be on Time. Craig’s List is expanding and taking over the world.

So, the numbers of “personals” posted in Sweden’s Craig’s List: 131. Finland? 34. As for the debate about which is the “gay capital of Europe” between partisans of Stockholm & Helsinki:

Men seeking men in Stockholm: 13
Men seeking men in Helsinki: 1 (and I think this is a bisexual individual?)

Are Finns even terrified of the internet? It seems that they are proto-Solarians.

(note, Finland’s total fertility rate is a bit higher than Sweden’s).

If you’re a pseudo-intellectual such as myself who gets tired of reading all the time but still wants to be able to pretend to be familiar with the great thinkers and major political figures of our time, you may be interested to find that many episodes of Charlie Rose are available for free on Google Video right now.

I have thus far been entertained and educated watching Milton Friedman, Bashar Al-Assad (President of Syria), Salman Rushdie and Deepa Mehta, and Shirin Neshat.

Half Sigma has piqued my interest of late. He makes really bold claims, above and beyond what a cautious reading of data might imply, but, at least he consults the data. That’s more than can be said for most political blogging, which seems to draw from the bullshit of the heart. Inductivist is worth a go too (seem’s that he’s Half Sigma‘s GSS dealer that started him on the habit). Some of the sample sizes are way too small for my taste, but at least they deal in samples which have an N you can criticize. Read them like you’d read Peter Gammons (I never liked Gammons actually, I was always a Dick Schaap Sport’s Reporters kind of guy, but Schaap is dead and I don’t have a TV).

Before you read this, check out Razib’s excellent 10 questions with Jim Crow, which I am unfortunately knocking off the top of the blog.

So a little while back, I wrote about a paper describing the evolution of a bacteria over the course of an infection (Aetiology also had a post–a better one, truth be told– on the same paper). I speculated that different individuals might present different environments for the bacteria, thus presenting slightly different selective pressures.

Moving up one level, one could imagine two populations being different genetically, so a pathogen could in theory adapt differently to life being passed around in the two. But does this happen?

A new paper suggests that the answer is yes. The authors analyse HIV sequences from a couple genes isolated from individuals in two different African populations. From the sequences, they determine which codons are under selection in the different populations, and come up with seven amino acid sites under differential selection. They link this to the different genetics (especially genetics of the immune response) of the two groups.

I certainly find that plausible, but I think there’s certainly another possibility here: essentially, there’s more than one way to skin a cat. We’re talking about differential selection at the level of a single codon and assuming that the differential selection reflects differential selective pressures in the populations. But maybe the different virus populations just came across different, yet equivalent, ways to adapt to the same selective pressures. That is, maybe we’re just seeing an example of the stochasticity of evolution.

My 10 questions for James F. Crow are up. It isn’t often that a nobody gets to interview the greatest living thinker in a field (theoretical population genetics), so you should check it out.

OK, people, check out the leader board. I suck, but that’s cool, we’ve raised thousands & thousands of dollars. But, I would like to stand a little taller and say that I did my part, so lift me up on your shoulders!