Science/Technology blog

Soon it will be clear that this year old manuscript by Kazutoshi Takahashi and Shinya Yamanaka will be the basis of a future Nobel Prize.

The paper is how to transform any cell into a stem cell. In the paper the authors took an “I’m so smart” approach to the whole problem. These smart guess approaches rarely work, but it’s always worth trying. This paper demonstrates why.

So let’s get back to the problem. Reprogramming cells so that they can become totipotent. How to proceed? From the paper:

We selected 24 genes as candidates for factors that induce pluripotency in somatic cells, based on our hypothesis that such factors also play pivotal roles in the maintenance of [embryonic stem] cell identity.

So here is a list of 24 genes that when activated COULD promote the reprogramming of cells so that they can acquire stem cell like properties. Then what? The researchers inserted the genes into vectors and then threw the mix of all 24 DNA constructs onto fibroblasts (mouse embryonic fibroblasts) that had an drug resistance marker controlled by a stem cell specific promoter. The idea is that if the MEFs became stemcells, they will turn on stemcell specific promoters and thus acquire resistance to the drug G418. All you have to do to find these “stemcells” is grow the cells in the presence of the drug and see whether any cells survive.

Sure enough they could find such cells. Wow! And not only that but these resistant cells formed colonies and according to the authors each colony

exhibited morphology similar to ES cells, including a round shape, large nucleoli, and scant cytoplasm.

Wow!!

The next thing to do is cut down the number of genes, after all 24 is quite a huge number.

And so they did … to four genes, each of which encodes a transcription factor.

So what is the identity of these genes?

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Earlier, I was mildly perturbed that Canada was leading my country in the cheesy science “museum” race; this is, of course, a race to the bottom. Scott Hatfield has come to my rescue, though, and sent in some photos of Carl Baugh’s double-wide “Creation Evidence Museum” which is surely one of the tackiest examples of creationist silliness in the country—although, when you get right down to it, Ham’s opulent exhibit is just this same thing with buckets of money thrown at it.

You also might be able to find a picture of Scott in here if you’ve been wondering what he looks like. Hint: he’s not the guy in the purple robes in the last picture.

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I want to lay this at Julie’s feet, or maybe John Lynch’s, but I’m starting to think the LOLcats are taking over! My kids speak to each other in LOL dialect, and I’ve been mentally captioning … well, everything.

My internal dialogue from part of commencement transcribed below. If you know a good deprogrammer, please email me!

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National Geographic and New Scientist are both reporting on a new study, in the journal Science, that provides an interesting angle on the question. The study is the result of over 3,000 observations on orangutan behavior in Sumatra (from New Scientist):

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Over at National Geographic you can read all about Fish Trap! a great piece of equipment designed right here at MBARI.

If that is not enough for you then head over to NPR where you can catch an listen to NPR’s On Point discussing Deep Ocean Ecology with Katrin Linse (part of the recent expedition to survery deep Antarctic biodiversity), Lisa Levin (a deep-sea biologist from Scripps), Tim Shank (a deep-sea biologist from Woods Hole), and Claire Nouvian (author of the The Deep).

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Matt Stoller makes a very interesting observation about Senator Obama, although I think it could apply to most of the presidential candidates in both parties. Stoller writes:

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Late last week, my PCRs stopped working. One day I was able to amplify DNA from multiple different templates using different primers, and the next day I couldn’t. This is a major setback for me — a huge chunk of the remaining work I need to complete for my PhD involves doing PCR. If I can’t get my PCRs to work, I’m royally screwed.

As soon as I couldn’t get any PCR products, I went into troubleshooting mode. I had just made a new batch of dNTPs, so those were the first thing to get replaced. No dice. I thought there might be something wrong with my water, so I grabbed a new bottle and made another batch of dNTPs. Nothing. I replaced my buffer solution. No luck. I made a new dilution of each primer. Nope. I bought new Taq DNA polymerase and new stock solutions of each dNTP, and I remade my dNTP solution again. Nada. I prepped a new dilution of my template DNA (and I had been testing my PCRs using multiple templates that had worked in the past), but that didn’t help. I tried multiple other primers, two different thermal cyclers (I’m currently trying a third machine tonight), different containers of tubes and tips, but none of it helps. When I run my gels, I still get no bands in any of my lanes.

I can pretty much rule out the possibility that I’m getting amplification, but my gels are screwy for two reasons. First of all, my ladder runs perfectly fine in all the tests. Secondly, I reran some PCR products from a couple of weeks ago (back when I was able to perform a successful PCR), and they looked a-ok.

So I’m turning to you guys. Now that I have replaced every reagent, every solution, and my template, what can I do? Is there anything I haven’t thought of (tinkering with Mg²⁺ concentration, perhaps?) that will fix this problem? Keep in mind, I went from really nice PCR products to none at all, and my primers are designed to the genome sequence of the species and strain I’m amplifying. What’s a helpless grad student to do?

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Bush said something about climate change. Sounds like the usual nothing to me: My proposal is this: By the end of next year America and other nations will set a long-term global goal for making sure we don’t have to do anything in the near future. Sorry, that should read …for reducing greenhouse gases. Predictably enough, Blur hailed this as a Great Leap Forwards whilst Merkel was sensibly more cautious.

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tags: Homer Simpson, humor, politics, Tonight Show, streaming video

As everyone in the entire world knows, America is getting ready to elect a president for the first time in nearly 8 years. Of course, this means that we all are quite excited to have our votes counted this time — really counted, yaknowwhatImean? — and we are having fun debating the relative merits of the many candidates we have to choose from. It turns out that most of the candidates are also putting in their two-cents’ worth on the topic as well, including Homer Simpson [2:20]

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This photo was taken in the early 1900’s by Charles Lillybridge, during a flood that very likely threatened his own studio. I haven’t been able to pinpoint the year of this particular flood. Once upon a time, the river, meandering naturally through the plain, flooded quite frequently. The surrounding prairie wasn’t disturbed; rather, the local wildlife flourished after such an event. The nomadic people who originally lived along these banks were able to adapt to the changing waters of what they called the Moonshell River. By the late 19th century, when Lillybridge moved in, humans were adapting the river to their use, rather than adapting to the river.

As people built cities along the banks and canals along the tributaries, the shape of the river was eventually transformed. To satisfy the consumer-happy demands of a growing nation, new industries moved into the area. The once meandering path of the Platte was lined with rigid concrete, utilized by the factories, smelters, and power plants. By the 1960’s, the South Platte River was filled with debris, including discarded vehicles and industrial waste. They weren’t really expecting it to flood.

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