Synthetic life is here? Deal with it.

via ted.com

That was the big story of the week in biology: the creation, in the lab, of a synthetic organism - a radically transgenic (transgenomic?) bacterium that had all its DNA replaced by a chromosome sequenced on a computer! So - not entirely synthetic, but enough where it counts, in its DNA. With a website url embedded within its code, no less! Heck, for all I know, the code for the above video might be embedded in there too! Or, at least, Dr. Venter's own face.

I know this has caused much stir in the media and for a number of people who were apparently not expecting anything like this to happen so soon (and Venter's hubris sure helps fan the flames as you can see in the comments thread responding to the TED video). Well, I think that most people familiar with modern molecular biology knew this was coming. Too soon? I don't know. Hardly surprising though, especially given Venter's record and stated ambitions in this area. I don't know enough about the molecular biology involved to say whether this is as big a breakthrough as is being suggested, but the feat sure seems pretty impressive.

As for what it means - I'll let the moralists on various sides (from the POTUS on down to your corner church and/or eco-anarchist co-op) sort that one out! We know (and have known for some time) that the technology is here, more or less, and now we have this semi-synthetic creature in our midst. Life just gets more exciting, doesn't it?

Venter was also interviewed on Science Friday earlier today, about this work. They don't have the audio up on the archive page for the interview yet, but I suspect they will soon enough, so keep an ear there if you want to hear more about this. And, for the gory details, you probably want to read the actual Science paper as well, right?

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Ooze like an amoeba, float like a bird - wish we could still do that when stressed!

Here's another fun weird science story from NPR, about a creature that might be in the dirt in your own backyard:

20100305 Me 03 by Npr
Download now or listen on posterous

Naegleria-NPR.mp3 (1426 KB)

Courtesy of Lillian Fritz-Laylan
Naegleria gruberi grows a pair of flagella when under stress. But unlike a sperm tail, it puts these appendages out front, and swims by breast stroke. The organism is stained to emphasize its anatomy.

If you prefer to read the story rather than listen to it aloud, here's the transcript via npr.org.

While that behavioral and morphological flexibility is remarkable enough in something we might, from our lofty hominid perch, consider rather "primitive" and "simple", what graduate student Lillian Fritz-Laylan and colleagues found in its genome is perhaps even more surprising. Whle the NPR story focuses on the physical transformation of the organism, cool as that is, the full story is much richer and has far more significance for our own origins from a common eukaryotic ancestor. As they describe in their paper in the current issue of Cell, Naegleria gruberi turns out to have almost 16000 protein-coding genes, which is over two-thirds of what you and I have! A single celled organism with that many genes - no wonder it can transform itself so radically.

Here's an image from the paper illustrating that transformation, which takes a mere 90 minutes or so (far cooler special effects at half the duration of Avatar, if you ask me!):

Figure 1: Schematic of Naegleria Amoeba and Flagellate Forms. Naegleria amoebae move along a surface with a large blunt pseudopod. Changing direction (arrows) follows the eruption of a new, usually anterior, pseudopod. Naegleria maintains fluid balance using a contractile vacuole. The nucleus contains a large nucleolus. The cytoplasm has many mitochondria and food vacuoles that are excluded from pseudopods. Flagellates also contain canonical basal bodies and flagella (insets). Basal bodies are connected to the nuclear envelope via a single striated rootlet. 

Is it just me, or does that upper image, of the amoeboid form, remind you of someone? And... I just realized... that someone also has two apparent flagellae at the top of his head, which unfurl during times of stress!! What better proof do you want of our shared ancestry with Naegleria, eh? No? Oh, what - you mean citing widely published and viewed cartoons is not good enough evidence for you (even though that is a standard of evidence good enough for a third of the good people of Texas)? You want all the boring science-y stuff instead? Well, go read the paper then, which the journal Cell has graciously made freely available!

The paper (luckily for you) turns out to be far from boring. It is indeed quite fascinating because, apart from presenting the complete genome sequence of this remarkable free-living protist, Fritz-Laylan et al also describe several genetic modules for aerobic and anaerobic metabolism (for these guys can do both), amoeboid motility, and a number of other structural and functional necessities of the ecologically diverse lifestyles common to their clade. Further, comparisons with genomes of other protists allow them to predict which genes might have been present in the genome of the common ancestor to all eukaryotes. As the first representative of a fifth (out of 6) major clade of eukaryotes whose genomes have been sequenced thus far, Naegleria holds great promise of generating fresh insights into the early evolution and diversificatiion of eukaryotes. While their lineage diverged from the one we hail from about, oh, a billion or so years ago, understanding their genome brings us closer to understanding and reconstructing the genome of our shared ancestors, those early free-living eukaryotes that gave rise to us both. For it turns out that they contain over 4000 protein families that are similar to ones we have, and therefore were likely found in that common ancestor! That ancestor was presumably also quite versatile and equipped with a set of flexible modules to deal with the diverse environments of that time. And that remarkable flexibility probably underlies the extraordinary diversity of organisms that subsequently evolved from that ancestor. How fascinating and wonderful is that! (Even if some of us later lost the ability to transform ourselves and float away when under stress!)

Let me end with a video where the lead authors talk about what Nargleria's genome can tell us about our own ancestry:

Reference:

Fritz-Laylin, L., Prochnik, S., Ginger, M., Dacks, J., Carpenter, M., Field, M., Kuo, A., Paredez, A., Chapman, J., & Pham, J. (2010). The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility Cell, 140 (5), 631-642 DOI: 10.1016/j.cell.2010.01.032

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