Archive for June, 2009

The scientists behind the Meselson-Stahl experiment

Tuesday, June 30th, 2009

The other day we talked about the historical moment when Matt Meselson and Frank Stahl elucidated the semi-conservative mechanism of DNA replication.

We briefly discussed the challenges that they faced at that time as a graduate student and a postdoc, which I think would give us insights to face our own challenges. I am still reading the longer book about the history behind this experiment. I think it is a very entertaining read but it is also very thick. A shorter historical account published in the PNAS would be easier for many of us to get an overall impression of the story.

References:

Hanawalt PC. Density matters: the semiconservative replication of DNA. Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):17889-94. [PubMed][pdf]
Holmes FL. Meselson, Stahl, and the Replication of DNA: A History of ‘The Most Beautiful Experiment in Biology’ [Amazon]

A good review paper on the architecture of retina

Friday, June 26th, 2009

I read several classic papers when I am planning projects with some of you. This is a very good review paper on the fundamental architecture of retina. There are a lot useful histological facts and observations. It has great discussions on how the retinal architecture has evolved and in turn provides the necessary visual functions to the animal. I believe you will also find this review paper useful.

Reference

Masland RH. The fundamental plan of the retina. Nat Neurosci. 2001 Sep;4(9):877-86.[PubMed][Nat Neurosci]

In the Light of Evolution III: Two Centuries of Darwin – Sackler Colloquium

Monday, June 22nd, 2009

This is a series of papers from a recent Sackler colloquium of the National Academy of Sciences entitled “In the Light of Evolution III: Two Centuries of Darwin“. You can watch most of the presentations online here. The conference papers are published in a supplemental issue of the PNAS.

I read Daniel Dennett’s paper because of my personal interest. He is a philosopher in science. In his paper, he provides a simple overview on why it is not necessary to have an intelligent designer to make complicated biological machines.

Reference

Dennett D. Darwin’s “strange inversion of reasoning”. Proc Natl Acad Sci U S A. 2009 Jun 15. [PubMed][pdf]

Journal club on 7/2

Saturday, June 20th, 2009

Please suggest your favorite paper by making a comment here. Once everyone has made a suggestion, we will vote for it. Let’s decide by this Thursday 6/25.

Thanks!

The origin of laughter

Monday, June 8th, 2009

Why do we laugh? Is there any evolutionary significance? Well, instead of pondering about these questions… why not tickle a primate to find it out?

Humans aren’t the only ones who like it in the armpit. Our fellow great apes — orangutans, chimps, bonobos and gorillas — also squeal in response to tickling, and new research shows this behavior may be the evolutionary root of human laughter.

….

Laughter is a key component of social interaction in humans. Humans are 30 times more likely to laugh when in the company of other humans than not, and tickling is inherently social — no animal is capable of tickling itself. Understanding the origins of laughter can also lend insight to the evolution of language, as both behaviors involve breath control and vocal cord vibrations.

References

Human Laughter Echoes Chimp Chuckles [Wired]

Ross MD, Owren MJ, Zimmermann E. Reconstructing the Evolution of Laughter in Great Apes and Humans. 2009 June [Current Biology]

Shark Fining Truth

Friday, June 5th, 2009

I know that we all take a lite attitude when talking about shark fin soup in the lab, but it really is a serious issue. After watching the documentary “Sharkwater” on youtube.com, which is about shark fining, I was shocked. I am definitely changing my tone about being open minded to trying any new food and will now have shark fin soup as my exception. I personally was unaware that the fin industry was so corrupt, dishonest, and dangerous. I think this movie is completely worth the 1 hour and 16 minutes to watch. You can go to youtube.com and search “Sharkwater” and the movie comes up in 9 segments about 10 minutes each. Hope you all take the time to watch it and see the truth behind this dish.

I do want to clarify that I don’t think that the shark fin soup dish should be done away with all together. However, I do think there needs to be a world wide push controlling the number of sharks harvested and also the methods of capture used in harvesting these animals. The ocean is a vast area and it will take all countries working together to protect the sea and it’s sharks.

The differentiation circuit of dopamine-secreting neurons

Tuesday, June 2nd, 2009

There are so many different kinds of neurons in the brain and they control all sorts of mechanisms. In C.elegans, several dopamine(a neurotransmitter) -secreting neurons are differentiated from different lineage, but they are all producing dopamine. This has raised an interesting question: are the genes controlling the dopamine synthesis regulated differently or the same way in different dopamine-secreting neurons?

A recent study by Nuria Flames & Oliver Hobert from Columbia University has revealed the latter is true. They made extensive promoter constructs of all the genes involved in dopamine production (which is a good example for those of us who are going to do similar promoter analyses). Their results showed all five genes were regulated by the same regulatory element, presumably by the same transcription factor(s). Therefore, these dopamine synthesis genes are regulated the same way in different dopaminergic neurons. More importantly, they have also found that this regulatory mechanism is conserved in mice!

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This is the terminal differentiation we have just discussed. The study has demonstrated that this differentiation circuit is modular and has been incorporated in different types of dopaminergic neurons to carry out the same final function. In other words, the final output function of the gene network is the same while the upstream specification architecture can be quite different.

Reference

Flames N, Hobert O. Gene regulatory logic of dopamine neuron differentiation. Nature. 2009 Apr 16;458(7240):885-9. [PubMed][Nature][Commentary in Nature]

Randy Pausch Last Lecture: Achieving Your Childhood Dreams

Tuesday, June 2nd, 2009

If you haven’t watched it, it’s worth an hour of your life.

Wikipedia entry of Randy Pausch.