Tuesday, November 16, 2004

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What happens if Conan the Bacterium infects Aquaman?

John J. Fialka has a front-pager in today's Wall Street Journal (this link should be good for non-subscribers as well) that spurs a "Wow, this is cool" reaction in me. It's about research into microorganisms that can not only survive in nuclear waste dumps -- they thrive there:

Eight years ago, scientists using a metal rod here to probe the radioactive depths of a nuclear-waste tank saw something that shocked them: a slimy, transparent substance growing on the end of the rod.

They took the specimen into a concrete-lined vault where technicians peered through a 3-foot-thick window and, using robot arms, smeared a bit of the specimen into a petri dish. Inside the dish they later found a colony of strange orange bacteria swimming around. The bacteria had adapted to 15 times the dose of radiation that it takes to kill a human being. They lived in what one scientific paper calls a "witches' brew" of toxic chemicals.

It was a step forward for the U.S. Department of Energy, which has been looking for a few good bugs -- in particular, members of an emerging family of microbes that scientists call "extremophiles." These microbes can survive in some of Earth's most inhospitable environments, withstanding enormous doses of radiation, thriving at temperatures above boiling, and mingling with toxic chemicals that would kill almost anything else.

That makes them a potentially valuable tool in the Energy Department's effort to clean up vast amounts of nuclear waste, including the Savannah River Site near Augusta, Ga., and the Hanford Site near Richland, Wash. The department says it could cost as much as $260 billion to clean up its messes with conventional methods, which rely heavily on chemical treatment and robots. Using extremophiles could slash that bill....

Scientists know of at least a dozen extremophiles. The first was discovered in 1956 in Corvallis, Ore. Scientists were zapping cans of horse meat with high radiation, trying to establish the preservative value of food irradiation. One can developed an ominous bulge. Inside, the scientists isolated pink bacteria they had never seen before.

They gave it the scientific name Deinococcus radiodurans. But researchers were so amazed by the bug's resilience that some years later, they nicknamed it "Conan the Bacterium," spawning a folklore and debate among scientists that continues today. Because the microbes endure radiation at levels higher than any natural source, some scientists have argued that they must have ridden in on comets. Others speculate that they were the Earth's first residents after the planet was born in a radioactive explosion.

The original Conan proved to be a wimp among extremophiles. It could handle radiation, but not the solvent toluene and other chemicals normally found in bomb makers' wastes. So, in 1997, the Energy Department started work on a genetically manipulated bug that researchers called Super Conan.

Super Conan now lives in a petri dish at the Uniformed Services University of the Health Sciences, a U.S. military research facility in Bethesda, Md. It can handle nasty chemicals as well as radiation, but the researcher who developed it, Michael J. Daly, says the government is afraid to let it out.

"We're at a point where we could do some field trials," he says, adding that his sponsors at the Energy Department doubt the public is ready for the release of this laboratory-engineered bug into the environment. It might eat nuclear wastes, but they worry about what else might it do, he says.

Rather than confront such touchy matters, the department is confident it can find Super Conan's equivalent in nature, says Ari Patrinos, the department's director of biological and environmental research. He estimates that fewer than 1% of the Earth's bacteria forms have been identified: "There are plenty out there for our needs. We just have to pick and choose." (emphasis added)

I will confess that the bolded section was my second reaction when reading the headline. I immediately flashed back to when I would watch Superfriends on Saturday mornings. Inevitably Aquaman would experience some "freak genetic mutation" and turn into some giant pissed-off fish that wreaked havoc on the high seas until Superman finally gave him the antidote. It was always a nuisance. [Er, but these extremophiles would prevent this from happening -- so why did you think of Aquaman?--ed. I didn't say I was following a rational chain of logic here. I was describing gut instinct.]

posted by Dan on 11.16.04 at 06:31 PM


Jokes aside, this is a serious issues. If we have an engineered bacterium that can eat radiation and chemicals for breakfast, and doesn't need a host, then we need to be darn sure we can stop it in some way.

Also, maybe I'm missing something here. It doesn't matter if you eat radiation, that just spreads it wherever the bacterium goes. The bacterium may be able to break down chemical wastes, but it can't remove the radiation in a radiation leak unless its from Krypton. So the radiation remains anyway.

posted by: erg on 11.16.04 at 06:31 PM [permalink]

There is much to worry about. I've seen quite a few movies (from the 50s and 60s) that show what can happen when tiny little critters get zapped with nuclear radiation.

posted by: Mike on 11.16.04 at 06:31 PM [permalink]

The human race is going to destroy itself eventually, whether it's by Conan or some other means. But I thought with Bush's reelection all the nuclear, I mean nucular, stuff was going to Yucca Mountain, so who needs Conan?

Anyway, the next ice age will wipe out most of us, and the sun's going supernova in about 5 billion years, so who cares.

posted by: Andrew Steele on 11.16.04 at 06:31 PM [permalink]

Aquaman would start sneezing, and then his head would explode. Then Black Manta would come in, hit on his wife, steal his kid, and Superman would fly underwater and totally flip out and kill everything. And then Batman would come up to Superman and he'd be all like "You suck, boy scout" and stab him with a Kryptonite sword. Because Batman's badass.

posted by: Jim Dandy on 11.16.04 at 06:31 PM [permalink]

Leaving aside the comic book perils, D. radiodurans is, like the vast majority of microbes, very unlikely to ever become harmful to humans (less than 3% of cultured bacteria are harmful, and far less than 1% of all bacteria have been cultured; since we tend to be interested in those closest to us, the things we don't know about probably can't hurt us). Extremophiles in general are not likely to deal well with the human body, which to them is an extreme environment. As an example, the bacterium that produces the enzyme used in PCR, the most revolutionary technology in biotech in the last 20 years, is called Thermus aquaticus, and comes from a hot spring. This organism doesn't grow at the temperature of the human body, because 37 degrees (Celsius) is just too cold for it. From the microbes perspective, it's environment is just fine, and not extreme at all, thank you very much.

In case you couldn't tell, I am a microbiologist, and I lurk all over the blogosphere just waiting for the rare moment when my knowledge is useful.

These bugs are fascinating, for all kinds of reasons, including their potential usefulness to clean up toxic waste in radioactive sites, as well as helping biologists understand the mechanisms for protecting a cell against radiation.

As to the fears of super Conan, the DOE people are being good and cautious, and they are right that it is probably out there already. However, lots of genetic engineering for bugs to eat nasty chemicals has already been done, so they should be able to figure out how to do it safely.

posted by: Paul Orwin on 11.16.04 at 06:31 PM [permalink]

One more thing. I'm not sure where the author got his info about riding in on a comet or some such, but my understanding is that the consensus is that radiation resistance is a subset of desiccation tolerance (drying), in terms of the molecular mechanisms.
The link below should take you to a review paper from 2001, if interested
Deinococcus review

If not, here is the citation and abstract. The story is a bit more complicated than I said above, but there is no scientific reason to impute extraordinary origins for this bacterium

Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79. Related Articles, Links   Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799,USA. The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.
The article is freely available from the publisher's website for anyone interested. Have fun!
posted by: Paul Orwin on 11.16.04 at 06:31 PM [permalink]

Okay, here's the thing:

1. Superfriends was ruined by the Super Twins (you know, "form of an ice sledge hammer"; "form of a gorilla").

2. The Plague came down from a comet. Wiped out a load of Europeans. So why couldn't the Conan thing have come down from a comet?

posted by: Andrew Steele on 11.16.04 at 06:31 PM [permalink]

Paul -- Thanks for the info, but could you explain one thing ?

'clean up toxic waste in radioactive site's

You mean, clean up chemical waste, right ? It should be impossible for bacteria outside of comic books to clean up actual radiation.

posted by: erg on 11.16.04 at 06:31 PM [permalink]

"Wonder Twins," not "Super Twins." But SF was ruined from the get-go by the Twins' predecessors, Wendy, Marvin, and Wonder Dog. Only after they *and* the twins were gone, in the Challenge of the Super-Friends (Legion of Doom) season, did everything come together.

posted by: Jacob T. Levy on 11.16.04 at 06:31 PM [permalink]

Thank you Jacob, I stand corrected.

Actually, let's face it, Superman could've kicked anyone's butt. It's not like Kryptonite is available at Wal-Mart.

posted by: Andrew Steele on 11.16.04 at 06:31 PM [permalink]

Yes, erg (if that is your real name!), that is exactly what I meant. Sorry if it wasn't quite clear. As you rightly point out, the organism can't increase the rate of radioactive decay, or stop it.

posted by: Paul Orwin on 11.16.04 at 06:31 PM [permalink]

Apparently, Andrew, kryptonite might as well be available at Wal-Mart. In addition to Luthor and Batman having shards, Ra's al Ghul has some red kryptonite lying around, and every other story in the comics has someone finding a shard. Not to mention god-awful Smallville.

::puts comic geek away::

posted by: Jim Dandy on 11.16.04 at 06:31 PM [permalink]

Re: erg

While the bacteria does not remove the underlining toxicity of the radioactive waste, the article does mentioned that they convert the waste into a form less likely to leak, thus easier to handle.

posted by: BigFire on 11.16.04 at 06:31 PM [permalink]

You know, I remember a Justice League comic from the mid-90s in which Zan and Jayna actually returned in dark, grim forms.

posted by: erg on 11.16.04 at 06:31 PM [permalink]

When kryptonite is outlawed, only outlaws will have kryptonite. And you can take my kryptonite when you pry it from my cold, dead hands.

posted by: Lex on 11.16.04 at 06:31 PM [permalink]

I remember a Justice League comic from the mid-90s in which Zan and Jayna actually returned in dark, grim forms.

"Justice League Task Force," written by Christopher Priest, who's almost-always terrific and almost never does something really, really wrong.

That was really, really wrong.

posted by: Jacob T. Levy on 11.16.04 at 06:31 PM [permalink]

They're able to contain it in the lab, so all we need to do if this Super Conan runs ramapant is scoop it up into petri dishes.

posted by: Boronx on 11.16.04 at 06:31 PM [permalink]

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