See, Larry Moran approves of my column in Seed — I’ll mention when it is available online, but you’d have it already if you subscribed…and this is also the perfect time to give a gift subscription.

(I know, I’m such a shameless pitchman.)

Here’s another interesting question from our most recent neurobiology exam. With some luck PZ won’t get irritated that I keep recycling my work. This paper was a bit of a brain thumper but also very interesting after deciphering what it’s talking about.

3) Summarize this paper and describe both the neural circuit and the genes underlying this particular rhythm.
Stoleru D, Peng Y, Agosta J, Rosbash M (2004). Coupled oscillators control morning
and evening locomotor behavior of Drosophila. Nature 431:862-868

The roughly one hundred bilaterally arranged circadian clock neurons in adult fly brains occur in six groups: dorsal neurons (DN1, DN2, DN3), dorsal lateral neurons (LNdS), and the PDF neuropeptide expressing small and large ventral lateral neurons (LNvS). Extirpation via proapoptotic genes was used to assess that D.melanogaster lacking LNvS in natural light/dark conditions displayed little change however in continuously dark environments yield arrhythmicity. Time intervals in the light/dark experiment were determined using Zeitgeber time in which lights on (sunrise) corresponds with ZT0 and lights off (sunset) corresponds with ZT12. Although the two LNvS cell groups have an imperative role in rhythmic gene expression, neurons expressing circadian photoreceptor cyrptochrome (cry) genes were also found to assist rhythmicity in natural light/dark conditions.

Green fluorescent protein reporter was used to stain the six clock neuron groups, determining that the cry-GAL4 driver, which facilitates cry gene expression, is present in all dorsal and ventral lateral neurons (LNdS and LNvS) and in two dorsal neurons (DN1). The proapoptotic gene hid was used to excise the cry gene in LNdS and LNvS generating cry-GAL4;UAS-hid flies that were arrhythmic in both natural light/dark and continuously dark environments. The dorsal neuron groups (DN1, DN2, DN3) are mostly unaffected by hid expression meaning that because cry-GAL4;UAS-hid flies are arrhythmic in both environments, these neuron groups are incapable of maintaining circadian rhythms independently.

Crossing D.melanogaster exhibiting the Pdf-GAL80 gene, which represses GAL4-mediated transcriptional activity, with flies exhibiting green fluorescent protein in circadian neuron groups via Pdf-GAL4 and cry-GAL4 drivers yielded flies without green fluorescent protein. This means that the cry and Pdf promotors, segments of DNA that control gene expression, coupled with GAL80 genes override and prevent their corresponding GAL4 drivers from transcribing. With the crossing of cry-GAL4 driver and Pdf-GAL80 repressor, and other mixed crosses, green fluorescent protein was observed only in some circadian neuron groups.

Crossing Pdf-GAL80 with cry-GAL4;UAS-hid allowed researchers to determine the effects of extirpating PDF+, CRY+PDF-, and CRY+ neurons on D.melonogaster circadian rhythm. They found that flies extirpated of CRY+ neurons were phenotypically arrhythmic and flies extirpated of PDF+ neurons had diminished morning lights-on anticipation with normal evening lights-off anticipation. Flies extirpated of CRY+PDF- had diminished evening lights-off anticipation and normal morning lights-on anticipation. These flies maintained a circadian rhythm in continuous darkness indistinguishable from wild type flies based unimodally on the morning oscillator. The phenotypes of these three strains of D.melonogaster are not affected by whether the environment is light and dark or continuously dark meaning that the oscillators are not driven by light. Using deductive logic, the researchers concluded that PDF+ neurons correspond to lights-on behavior and oscillate independently of CRY+PDF- neurons, which correspond to lights-off behavior.

Green fluorescent protein techniques for visualizing neurons confirm that the CRY+PDF- and PDF+ oscillators are coupled through PDF- axonal processes that protrude from the LNd neuron group into the LNv region. Immunostaining visualization techniques reveal that PDF neuropeptide travels in the opposite direction that the PDF- axons extend, that is, from the LNv to LNd neuron group. PDF neuropeptides function to coordinate the lights-on anticipation behaviors in the morning with the independently oscillating lights-off anticipation behaviors in the evening.

References:
Stoleru D, Peng Y, Agosta J, Rosbash M (2004). Coupled oscillators control morning
and evening locomotor behavior of Drosophila. Nature 431:862-868

The bad news: Terry Pratchett has been diagnosed with early onset Alzheimer’s disease. The good news: there’s no immediate danger, he’s still optimistic, and he’s got more work in progress.

We shouldn’t leave the Moslems hanging with all the blame for bad behavior — so here’s some more deplorable activities that have show up in my mailbox in the last few hours.

• The typographer who designed the popular font Gill Sans was a devout Catholic…who had sex with his sisters, his daughters, and his dog. Who could have seen that coming?

• More Christmas displays are in the news: in this case, the Christians are vandalizing a Wiccan symbol. Or who knows…maybe it’s some vicious atheist who is running over the pentacle and leaving the nativity scene alone.

• Running over Wiccan symbols is much milder than what they are doing in Nigeria: evangelical Christians there are organizing witch hunts. Literally. And the ‘witches’ are often children, who may be murdered for their imaginary crime.

• Look! Australian fundies blame their drought on sinners! I hate those sweeping generalizations. I say it’s all Wilkins’ fault.

WARNING. What follows is a a bit of a rant. Worse, it’s an undergraduate rant. If awkward phrases, fallacious arguments and poor grammar offends you, I would suggest skipping this post.

It could be that I’m seeing the world through cobalt-colored glasses– it is winter in MN and very cold and dark– and it is highly probable that the onslaught of medical school rejection letters biases me, but I think today was the most depressing day of school I’ve had in recent history.

It started with neurobiology (Ok…this one’s a bit of a stretch) when we learned about the development of nervous tissue and how progenitor cells literally compete via lateral inhibition with each other to see who will become what. Neuroectoderm cells that “lose” become dispensable support cells while the ones that “win” are lavished with ‘cytoplasmic gifts’ (PZ’s words) and differentiate into a neuroblasts. I couldn’t help but think, “Wow, our very cells viciously jockey to establish hierarchies!?” I mean… who wants to be the little peon cell? They lied to us in kindergarden…

Next came ecology. This was a killer. The professor even had a disclaimer before lecture warning us that what would ensue would be upleasant. Yep. It was the global warming lecture. I had seen the “hockey stick” graphs before and the receding glacier pictures and yes, they’re all very disturbing, but what really got me was a picture of the arctic circle in the summer. There appeared to be about half of the ice cover that usually persisted pre-industrial revolution.

Things got worse in ecology lab. We had to calculate our carbon footprint. Apparently I use about 24 acres to support my lifestyle. It would take 4 earths for everyone to live like me (and I didn’t even count this l’il methane producer):

…or these guys…

The final blow was a film screening for my class on human aggression. The movie? Natural Born Killers. It was a double whammy. Even if the self-destructing, unsavory, hopeless nature of the characters doesn’t get to you than the indictment of society’s commodification of violence certainly does.

Man. Days like today almost make me yearn for the good ol’ days when I had my class on” critical pedagogy” with excerpts from Paulo Freire on the necrophilic and dehumanizing nature of oppression.

I… think I need to go hold one of the bunnies…

We can all breathe a sigh of relief. The gunman who killed four people at evangelical churces in Colorado was not a buddhist atheist Jew evilutionist. He was a deranged disgruntled former member.

The gunman believed to have killed four people at a megachurch and a missionary training school had been thrown out of the school about three years ago and had been sending hate mail to the program, police said in court papers Monday.

The gunman was identified as Matthew Murray, 24, who was home-schooled by his family and raised in what a friend said was a deeply religious Christian household. Murray’s father is a neurologist and a prominent multiple-sclerosis researcher.

I suppose they could blame it all on the fact his father was a scientist, still.

Two serious shooting incidents this weekend — one at Ted Haggard’s old church in Colorado Springs, another in Arvada, Colorado — is awfully troubling. No word on motives yet, but I hope the crazies aren’t erupting into random violence against each other.

(I’m getting a lot of email about this, but really, I don’t know anything more than anyone else right now.)

Arthur C. Clarke turns 90 next week — so go leave him a birthday greeting.

My fish have (theoretically) been sleep deprived for three days. I can’t tell much of a difference. If anything they seem more active than the other fish, but they do have to constantly outswim a rotating ruler and their tank is pretty small. There is also a bright lamp on a timer that turns on and off every 30 minutes, so even if I can’t prevent sleep I know they’re regularly disturbed.

This is what the set up looks like:

I’m testing the sleepless group against control fish in a behavioral assay. I wanted to use a T-maze adopted from Mark Antimony’s experiment but the initial results were dismal. It took some fish over ten minutes to find the food reward (during which I once left to find a food reward of my own. Sweet sweet NutterButters…).

So… I modified the test. I’m a bit embarrassed to admit that now I’m prodding the fish with a pen and timing how long it takes them to “escape” (go to a protected side of the tank). The results are definitely cleaner than the ones from the maze, but I still don’t think I’ll be able to describe a difference between the groups. What is cool is to see the way fish learn. Individuals generally get faster each trail; I think that trend should be significant.

The holiday season is upon us, and our source of cocoa is going on strike. I hope the US Strategic Chocolate Reserve is well stocked, or Santa will go into withdrawal this Christmas eve.

(We ‘podmas celebrants have no worries, at least, unless the herring supplies are depleted.)