In the past, diploid Daphnia have been bred in the lab to cut down on extraneous genetic material that, in the wild, is necessary for their mainly mateless reproductive strategy. But this artificial inbreeding is less than desirable for researchers who are looking to study gene-environment interactions. So members of the research project launched a transcontinental search to find a specimen that was naturally inbred. What they found in The Chosen One was just that—a Daphnia in which "nature has gotten rid of all the bad alleles," simplifying the genome without losing its ecologically attuned adaptations, Colbourne says.
This little arthropod and her progeny received such a grand nickname as another Slimy Log Pond candidate line—now known as The Rejected One—was being sidelined. In preliminary analyses The Rejected One was found to have a genome that is quite heterozygous (with more differentiated alleles), Colbourne recalls. Its radical differences, however, did allow for some useful comparison with The Chosen One. "There was actually some great science that was done because of the Rejected One, although it created quite a heart attack in the community," he says.
Although D. pulex is the most common species, others, such as D. magna and Ceriodaphnia dubia are usually called on in standardized water quality tests. The D. magna genome sequence is currently in the pipeline, says Vulpe, who uses that species in his research and is part of the larger consortium. For his research, the D. pulex genome "has been an incredible boon to be able to compare and help us understand what's happening" in the D. magna genetics.
Beyond death
With its substantial genome now decoded, Daphnia might soon play an even more integral role in environmental assessment—beyond simple tests for dissolved oxygen or excessive chlorine.
Only a small fraction of tens of thousands of man-made chemicals have been tested for safety, and then they are usually only tested as isolated compounds—rather than in more realistic amalgamations as they often crop up in the environment. "We have so many damn chemicals," Vulpe says. "We're concerned about their effect on humans and on ecosystems."
But with so much analysis that remains to be done, "there's no way that our current methods of screening for the danger of these chemicals can catch up," Colbourne says. If Daphnia prove to be a solid model organism to study the effects of chemicals and environment on genes, they could enable a more efficient high-throughput process for assessing chemicals.
The relatively new field of "ecotoxicogenomics"—which Vulpe admits "doesn't really roll off the tongue very well"—is working to catch up to more biologically based genetics. But with the genome sequence of Daphnia, he hopes that it will allow the field to catch up. "We have the sequence of the mouse and human—and we can use genomics in a very powerful way—but unfortunately this has lagged behind in these eco-indicator species."
Bringing a genomic approach to studying toxicology promises to create a more "mechanistic understanding" of the field, Colbourne says. Vulpe explains that toxicology has relied on the "kill 'em and count 'em" approach, in which death was the primary endpoint in a chemical's dosage assessment: "We previously asked the question: Did they die?" he says. As researchers are now starting to be able to suss out particular genetic pathways, "it might help us consider endpoints that we hadn't considered," Vulpe adds, such as how chemicals are having more nuanced effects on reproductive or immune systems.
Daphnia are of course not a perfect foil for studying chemicals' potential effects on human biology, and their use as screening organisms will have to be validated by further research. "But it's certainly exciting that there is a similarity," Vulpe says. "Who would have thought that a little crab would have been similar to people?"
Subscription Center
Rights & Permissions
See what we're tweeting about
5 Comments
Add CommentWith earnest and devoted effort, scientists will be able to determine the effect of some toxins on Daphnia, and will be able to propose these findings to humans. That would be good science, but it does not directly address the problem. There is no, and that is no, reason to use or distribute toxins in the atmosphere or the waters. We can have wind, sun, nuclear,and tide produced electricity. We can grow enough food for our people, without using herbicides or pesticides. We can reforest on a massive scale. We can make paper, fabric, and even building materials out of the stalks of commercial hemp. If we art determined to live healthfully, to preserve life on earth, we can do it. It will require control of chemical companies, especially the biggest of them. These death organization have no role in a healthy world.
Reply | Report Abuse | Link to thisJacobSilver:
Reply | Report Abuse | Link to thisWhile your sentiments are admirable, your statements are not. I challenge you to present verifiable and tested ways to feed even the current population, not to mention the much larger one that will result absent a world-wide plague, without the use of herbicides or pesticides WHILE ALSO taking 'massive' amounts of arable land out of food production and putting it back into forest. And of course one also has to ask where all of the hemp you advocate using is going to be grown if arable land is removed from agriculture. And finally it would be good if you provided some actual data on how wind, solar, tidal and nuclear power can address the need for a high density, easily portable, and most likely liquid, transportation fuel without all of those nasty chemicals you are so against.
Sentiments are good. Opinions are good. But data trumps both of them every time.
macgrant,
Reply | Report Abuse | Link to thisI like data too. But what you're asking for is far too much to post here, these are incredibly complicated issues.
As for providing food - perhaps read up on Vertical Farming: http://www.verticalfarm.com/more
Also JacobSilver said "we can reforest on a massive scale" - he didn't say that NO arable land will be used for agriculture.
All he's trying to say is that we can do things so much more efficiently and dramatically reduce the toxins in our air and water - what's wrong with that? It's true. We already have the technology, we're just being slow about implementing it.
I don't know if it's possible to have NO toxins though, that claim is a bit 'out there' for my liking. Maybe in the future, but not with current technology, as far as I know.
"The majority of the genome is a reflection of how the animal has evolved to cope with environmental stress."
Reply | Report Abuse | Link to thisSo, if we continue to produce and dump toxins, apparently our genome will add the components necessary to allow humans to develop a chitinous shell, and other elements required for us to cope with environmental stress.
Data may trump sentiment when those with no sentiment are the producers. Unfortunately for the majority of us, there's this thing called Congress that allows the producers of those toxins to buy the laws that allow them to destroy our land - and us along with it. Personally, I think all emissions should filter through Congress before they're released into the environment.
Cathstuff, jacobsilver et al.
Reply | Report Abuse | Link to thisThanks for your comments. However I stand by my statements. There is no currently even theoretical way to feed the current world's population, not to mention the almost 2E9 more people who will need food in the next few decades, AND "reforest on a massive scale" AND eliminate pesticide and herbicide use AND grow very large amounts of hemp for all of our fiber and non-mineral construction needs. Vertical farming, at least as currently proposed, is neither economically or energetically viable - do the math. And I also challenge anyone to present an economically viable and SCALABLE way to use "wind, sun, nuclear,and tide produced electricity" to produce the truly enormous amounts of high density and portable fuels needed for transportation.
I'm not anti-green or anti-anything else. What I am is a professional scientist and a realist. I most assuredly want to find a path forward that accomplishes the goals you have described. I just don't think any of the ideas put forward so far will actually accomplish them - they are far too expensive or they don't scale well from the lab to the real world or they take far too long to implement or one of any number of other complications.
It's all well and good to rail about evil chemical companies or venal politicians. But until you can propose concrete, viable and proven alternatives all this accomplishes is to make you feel virtuous without actually solving anthing.