Charles Konsitzke: using eDNA to find missing people
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Another lead on the Missing in Action Recovery and Identification Project and one of Kirstin’s collaborators is Charles Konsitzke, Associate Director at the Biotechnology Centre at University of Wisconsin-Madison. Before we ‘dive’ back into to the details of how it’s possible to extract and sequence human eDNA from the sediment cores and water samples, I first wanted to know about the uses for human eDNA more generally…
Sally: How has eDNA been used for human DNA already? Because we've heard a lot about it being used for bats and zoos, and I've come across it being used in conservation, all of these kind of ecological sides, but in the back of my brain I'm like, "Oh my God. We now have this technology that can find which humans have been passing through a room."
Sally: The thought of what forensics and police could do with that is kind of scary, I'm not gonna lie. So what is the reality of how it's actually been used for human DNA?
Charles: It's now come to the forefront. So it's very new, and I think you're seeing a lot more use of this. As you stated, it can be used in a forensic sense as well. I mean, you can take a sample of air and extract the DNA from what is within that to determine who was in that environment, you know, just recently.
Sally: Who walked through the crime scene if you were there soon enough.
Charles: Yes, and we have an idea of a type of micro vacuum that we've created that would have plates inside it that would grab the material. So if an investigator would walk in first with this vacuum, they could get the material in the air in real time.
Sally: And has that been used? What is science fact and what is science fiction?
Charles: Right. Going in the forensic focus, the idea is if somebody were to - talking about a crime scene - if somebody were to bury somebody and then they removed the remains but then transported them somewhere else, the goal is you could test the soil where that initial site was, extract the human DNA, compare it to a reference family member and say, yes, the remains were here.
Charles: So that is the hopes in developing this further.
Sally: And I mean that is, from a technological, methodological point of view, kind of similar to what you are doing, right? In that you are looking for remaining DNA in sediments. It just so happens that yours is tens of metres under the sea and a few decades old.
Charles: Yes, yes.
Charles: So we actually have been working with the University of Nebraska, Lincoln, where they have a swine field and we have samples of the soil before they put a swine down in the field. And then we will then also go back there and test to see how the DNA plumes from the site, but then other contaminants as well.
Sally: Wait, you're saying "swine field". I remember a story back in the day where a lab buried bodies in order to see how bodies decompose for forensic purposes. Is that what we're talking about when you say "swine field"?
Charles: Exactly. That is it exactly, yes.
Sally: So it's a field with dead pigs presumably, to monitor what the process - the biological process of decomposition is like?
Charles: For eDNA, yes. And sediment DNA, yes. So we're looking to see how it plumes out, if it plumes away, down. What the activity is. And then also the micro-environment; how does the micro-environment change too? So we're looking at the bacterias within that environment too to help, because we're hoping that has a similar relation to the micro-environment where humans are buried as well.
Charles: We're hoping we can tell by that micro environment that there is this change. Yes. So it shows that a human was buried in the site at some period of time.
Sally: And are you gonna be chucking pigs in the Great Lakes then to see if that affects the sediment? Because this is gonna be on land, presumably, if you're chucking it in a field. A lot of your research is gonna be looking for bodies underwater; are there plans to drop pigs under the sea?
Charles: Uh, no, not at this time, but we have an aquatic and a terrestrial focus, so we have both focuses that we're working on. Great idea though. I don't know who would accept it.
Sally: So one of the big questions I have for your project is there's a lot of human DNA in the ocean.
Charles: Yes.
Sally: There are now 8 billion people on the planet. Most of them live near the sea. How on Earth, from a biotechnology point of view, are you going to be able to separate out all of that background human DNA from the DNA that you're interested in?
Charles: That's the work that we have ahead of us, the heavy work ahead of us because yes, there's human DNA everywhere. But a lot of that will be statistically and bioinformatically, a lot of that will need to be figured out. And that's one of the things that we've been working with.
Sally: When you say bioinformatics, what do you mean?
Charles: We've got a lab that is focused specifically on working with the data and extracting and identifying what we have within that.
Charles: So we extract all of the DNA and then we sequence everything, a deep sequence. And then our informatics team does the analysis and sorts that out for us.
Sally: And once you've got the DNA out of the sediment, which is a lot easier to say than do I imagine, is there ever gonna be the chance that you can then reconstruct the fragments to a high enough fraction of the genome that then you can identify not only have we found a person in this plane wreck, ship wreck, but we know who it was?
Charles: So our hope is; we have three phases. Phase one is that we can extract human DNA and we can see human DNA, which we have done that and that has been successful.
Charles: Our second phase is can we determine the ethnicity with the material that we have? So that will help in regions where, like a country that doesn't allow one to extract or do a recovery mission if there are native burials nearby. We could actually test the soil to determine if they're native or not native by the ethnicity of the DNA.
Charles: And then the third phase is identification. Can we obtain enough material to give a probability that this individual, to the reference sample, is 65%. There's much to be done. But the three aims are our current focus at this moment.
Sally: And I imagine that middle one, especially because you're looking at World War I, World War II sites, if you've got European American ethnicity outside of Japan, for example, or vice versa, chances are it's gonna be an enemy fighter for that region.
Charles: Exactly. You're right on.
Sally: What would the success of this project mean for this kind of repatriation of bodies and finding missing service people more generally?
Charles: Well, it's not just focused on missing service people. The current project is, but in hopes with other projects where there are mass burials of individuals from past conflicts that need to be investigated. So forensically, this can be a new era for seeking the missing out. And that's our hopes here, is that we can help move this along to help with that recovery mission and possible missing individuals in general.
Charles: If a container that you knew individuals were housed in in transport - you could swab the whole container and then sequence it and use it as a reference to missing family members.
Charles: You know, biology is impressive. It is absolutely fascinating and many things can be done with it. We haven't even touched the forefront of it.
That was Charles Konsitzke from the University of Wisconsin-Madison
