Tag Archives: environmental DNA

Genetic Surveillance based on Stray DNA

Everywhere they go, humans leave stray DNA. Police have used genetic sequences retrieved from cigarette butts and coffee cups to identify suspects; archaeologists have sifted DNA from cave dirt to identify ancient humans. But for scientists aiming to capture genetic information not about people, but about animals, plants, and microbes, the ubiquity of human DNA and the ability of even partial sequences to reveal information most people would want to keep private is a growing problem, researchers from two disparate fields warn this week. Both groups are calling for safeguards to prevent misuse of such human genomic “bycatch.”

Genetic sequences recovered from water, soil, and even air can reveal plant and animal diversity, identify pathogens, and trace past environments, sparking a boom in studies of this environmental DNA (eDNA). But the samples can also contain significant amounts of human genes, researchers report today in Nature Ecology & Evolution. In some cases, the DNA traces were enough to determine the sex and likely ancestry of the people who shed them, raising ethical alarms…Similarly, scientists have for decades analyzed the genetic information in fecal matter to reveal the microbes in people’s intestines—the gut microbiome, which plays dramatic roles in human health and development.

The power to extract personal data from eDNA and microbiome samples will continue to increase, both groups of authors warn. That raises concerns about misuse by police or other government agencies, collection by commercial companies, or even mass genetic surveillance, says Natalie Ram, a law and bioethics scholar at the University of Maryland Francis King Carey School of Law. In the United States, she says, researchers and funding agencies should make greater use of federal Certificates of Confidentiality. They prohibit the disclosure of “identifiable, sensitive research information” to anyone not connected with a study, such as law enforcement, without the subject’s consent….

“Which companies and governments are going to pay and license to have poop-based surveillance technology?” he asks. “Imputing people’s identity based on their poop is compelling and interesting, for a number of reasons, and most of them are all the wrong reasons.”

Excerpts from Gretchen Vogel, Privacy concerns sparked by human DNA accidentally collected in studies of other Species, Science, May 15, 2023

New Drugs: Animals Stuck to the Seabed

Biologists are working with engineers to develop new tools to accelerate the development of medicines derived from marine animals, focusing on ocean-going robots with onboard DNA-sequencing gear. They foresee fleets of autonomous submersible robots trolling the ocean like electronic bloodhounds to sniff out snippets of the animals’ DNA in seawater—and then gathering and analyzing this so-called environmental DNA, or eDNA.

“The ultimate goal is an underwater vehicle that collects environmental DNA samples, sequences them and then sends the data back to the lab,” says Kobun Truelove, senior research technician at the Monterey Bay Aquarium Research Institute in California. “We would like to set up a network where you would have these autonomous vehicles out there sampling and then basically be getting the data back in real time.”

More than 1,000 marine-organism-derived compounds have shown anticancer, antiviral, antifungal or anti-inflammatory activity in medical assays, according to a database compiled by the Midwestern University Department of Marine Pharmacology. The U.S. Food and Drug Administration has approved 15 drugs derived from marine organisms, including ones for chronic pain and high cholesterol. Another 29 marine animal-derived compounds are now in clinical trials, according to the database.

Marine invertebrates are a key target of biomedical research because the animals—mostly attached to the seabed and unable to move—have evolved sophisticated chemical defenses to fend off fish, turtles and other predators in their environment. Research has shown that the natural toxins that comprise these defenses can be toxic to cancer cells and human pathogens. These sea creatures “make a broad range of different chemistries, things that synthetic chemists never thought of making,” says Barry O’Keefe, who have also identified compounds produced by bacteria living symbiotically with marine invertebrates. Once scientists have a suitable sample of eDNA and it’s been sequenced, they say, they can identify compounds the organisms are capable of producing. Then researchers can synthesize the compounds and test them to see if they have medicinal properties…

Collection of eDNA promises to be faster and less costly than the complex method commonly used   collect marine specimens—one that Amy Wright, director of the natural products group at Florida Atlantic University’s Harbor Branch Oceanographic Institution, likens to a treasure hunt. Currently, research vessels on weekslong expeditions launch submersible vehicles equipped with clawlike grabbers and suction tubes for gathering specimens. Once the vehicles and their payload are back on the ships, researchers preserve them and deliver them to labs, where their genomes are sequenced. The entire process can take weeks and is expensive. Just paying the crew to operate a research vessel for a single day can cost $35,000, according to the National Science Foundation.

Excerpts from  Eric Niile, Finding New Drugs From the Deep Sea via ‘eDNA’, WSJ, Sept. 3, 2022