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Researchers were able to detect DNA from elephants at the Copenhagen Zoo simply by sampling the air nearby. IDA MARIE ODGAARD/Ritzau Scanpix/AFP via Getty Ima hide caption

Researchers were able to detect DNA from elephants at the Copenhagen Zoo simply by sampling the air nearby.

A key part of protecting endangered species is figuring out where they're living. Now researchers say they have found a powerful new tool that could help: vacuuming DNA out of the air.

"This is a bit of a crazy idea," admits Elizabeth Clare, a molecular ecologist at York University in Toronto, Canada. "We are literally sucking DNA out of the sky."

But it works. Clare's group was one of two to publish papers in the journal Current Biology Thursday showing that dozens of animal species could be detected by simply sampling the air.

Using environmental DNA, or eDNA, to track species isn't new. For a few years now, researchers have been using DNA in water to track aquatic animals. They've also been able to pick up eDNA from plants floating in the air.

"One thing that we've discovered in eDNA research is really that any environmental medium (water, soil, snow, etc.) has the potential to harbor DNA that we can sample," Stephen F. Spear, a Research Biologist with the U.S. Geological Survey, wrote via e-mail. Spear has used eDNA to track a species of aquatic salamander known as the hellbender.

But the idea of using eDNA from air to track a large land animal like a rhinoceros or a giraffe still seemed "crazy" to Kristine Bohmann, a researcher at the GLOBE Institute at the University of Copenhagen in Denmark, and the lead author on the second paper in Current Biology.

Bohmann and her team thought up the idea independently from Clare's group a few years ago. She was trying to come up with a wacky research idea for a Danish foundation that funds far-out science.

"In the end I got so frustrated that I just blurted out, 'No! It has to be crazier! It has to be, like, vacuuming animal DNA out of air!'" she recalls.

The idea stuck, and she eventually got funding and hired a postdoc named Christina Lynggaard. Lynggaard's first job was to figure out what kind of device the team could use to vacuum eDNA from the air.

"We tried three different devices, and one of them was a vacuum cleaner, a commercial one," Lynggaard says.

It worked. They could sample DNA simply by using it, although it was "super noisy." Lynggaard also used some home-made samplers that used a small fan, like a computer blower fan, mounted in a 3-D printed housing. They worked just as well and were far quieter and more power efficient. Bohmann suspects they will be more useful in actual sampling in the wild.

To make the experiment successful the team also needed a good place to look for animal DNA.

"We realized we are based in Copenhagen... we had the Copenhagen Zoo," Bohmann recalls. It was almost like the zoo was custom-built for this experiment: Most of the animals are non-native, so they really stick out in a DNA analysis.

"If we detect a flamingo, well we're sure that it's not coming from anywhere else but that flamingo enclosure," she says.

The team took samples from around the zoo. And they were shocked. They picked up 49 animal species including rhinos, giraffes, and elephants.

"We even detected the guppy that was living in the pond in the rainforest house," Bohmann says. "It was just absolutely mind-blowing."

Meanwhile, Elizabeth Clare, who is also affiliated with Queen Mary University of London, was sampling at an outdoor zoo park in Cambridgeshire, UK.

Her team was able to detect 25 species, even some non-zoo animals: "Things like the Eurasian Hedgehog, which is critically endangered in the UK," Clare says. Zookeepers verified that hedgehogs have been seen wandering the area.

The two groups were nearing submission to a scientific journal when they learned of each other's work.

"I woke up to this flurry of text messages from my co-authors saying, 'There's another paper, have you seen this?'" Clare recalls.

Clare and Bohmann knew each other, and rather than compete to rush out a publication first, the two groups got in touch and decided to publish their findings as a pair.

"We are independently confirming this works to ourselves, and to everybody else," Clare says. "I think, we both thought, the papers are stronger together."

There are a lot of unanswered questions. For one thing, Clare says, researchers still aren't sure what the eDNA they're detecting actually is. It could be skin, saliva, or even urine or feces.

Also, "there were some species we simply never detected even though we know they were there," she notes. Her group missed maned wolves, even though she could smell them throughout the zoo park. Lynggaard says their team missed the Copenhagen Zoo's hippos.

"I see the current state of airborne eDNA as very similar to when the first papers on aquatic eDNA came out over a decade ago," says Stephen Spear, the USGS biologist who was not affiliated with either group.

He believes much more research will be needed to show just how air sampling of eDNA can be applied: "Will this technique work consistently for animals that are smaller or are more mobile? How does it compare to other methods such as camera traps? What's the best way to sample and collect eDNA from the air?"

For her part, Clare is eager to dive into answering these questions, and developing eDNA air sampling into a cornerstone technology for conservation.

"I have this vision of samplers that are deployed globally that can suck up the DNA from all these different sources, from soil and honey and rain and snow and air and water, sequence them on site, beam the data up to the servers," she says. The goal would be a global system of biomonitoring the world's animals. "We don't have a coordinated system for that."

Clare believes the answers to some of the toughest questions in conservation could literally be in front of our faces, hanging in the air.

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Zoo studies show vacuuming DNA from air could help track endangered species - NPR

Our gut microbiome helps us out every day by processing the fiber we cant digest. The bacteria ferment the fiber into key chemicals known as short-chain fatty acids, or SCFAs, that are essential for human health. SCFAs fight inflammation, help kill dangerous bacteria, protect the lining of the gut, and can even help prevent cancer.

In a new study, the John Denu lab at the University of WisconsinMadisons Wisconsin Institute for Discovery has learned that the fatty acids butyrate and propionate also activate p300, a crucial human enzyme that promotes the unspooling of DNA. This unwound DNA allows more genes to become active and expressed, which ultimately affects human health.

Previous research had suggested that SCFAs might instead contribute to this process by inhibiting a different set of enzymes.

John Denu

Sydney Thomas

This new understanding opens the possibility of activating p300 in a diet-dependent way or even independently of the microbiome. Knowing how to target p300 is vital because it is implicated in a wide variety of physiological processes and diseases, such as propionic acidemia, autism spectrum disorder, and Alzheimers disease.

Knowing that butyrate and propionate directly interact with this protein opens up a lot of new areas of research that we didnt even think to look at before, because we thought that it was happening the opposite way than it actually is, says Sydney Thomas, a Denu lab graduate student and co-author on the paper.

Thomas and Denu, a professor of biomolecular chemistry, published their findings Oct. 22 in the journal eLife.

Earlier work in mice had shown that SCFAs are a crucial link between the microbiome and epigenetic states the modifications to DNA that affect how active any given gene is. These epigenetic modifications allow different cells to use the same DNA instructions to perform different tasks and can affect health.

One key mechanism of control that cells use is to organize the DNA so only certain parts of it can be accessed for the work at hand. To do this, cells wrap DNA around histone proteins, which act like spools for the DNA thread. Modifying histones changes the accessibility of the DNA wrapped around them, and ultimately changes which part of DNA a cell uses.

Science is most thrilling when you discover something unexpected and when the results challenge long-held beliefs. This work checks both those boxes.

John Denu

The mouse model work had left it unclear precisely how cells sense SCFAs and react by altering their histones to control gene expression. To address these outstanding questions, Thomas and Denu treated several human cell lines directly with SCFAs, bypassing the more complex mouse experiments.

Adding propionate or butyrate to the cells led to rapid changes in the cells histones. When they looked at how the compounds accomplished these changes, the team discovered that the fatty acids released the brakes on p300, which went on to modify histones in a way that opened up DNA to be used by the cell.

These findings largely replicated the results from the prior mouse work, indicating that the cells were an effective and simpler system to test how SCFAs alter the epigenome of the host.

We are hoping that now that we have a better understanding of how SCFAs work (and) can use this knowledge to create better drugs and a deeper understanding of how the microbiome interacts with the host, says Thomas.

For decades, textbook dogma held that butyrate and propionate altered chromatin by inhibiting the enzyme histone deacetylase. But the new findings that the fatty acids instead work by activating p300 call this old model into question.

Science is most thrilling when you discover something unexpected and when the results challenge long-held beliefs. This work checks both those boxes, adds Denu.

The research was funded by the National Institutes of Health.

See the article here:
New way to alter DNA, affect health circumvents gut bacteria - University of Wisconsin-Madison

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Original post:
Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs - Nature.com

HASTINGS, Mich. (WOOD) Ashley Copelin was 2 months old when her mom left the family home in Barryton, a small village east of Big Rapids, for a gallon of milk. They were living with grandpa and grandma.

That was on May 17, 1987.

Nobody has seen her mom, Margie Ann Ranshaw, in the nearly 35 years since.

I just want people to know her name, Copelin said on Friday.

She said recent breakthroughs in missing persons cases in Kent and Ottawa counties are giving her renewed hope for her moms case which quickly went cold.

I dont believe that shes alive, she said. But I do believe that her body is out there somewhere, and I do believe that we deserve to know what happened to her, regardless if shes dead or not.

Her mom was 29 when she vanished. Shed be turning 64 this month.

In NAMUS, the National Missing and Unidentified Persons System, shes listed as Missing Person Case No. 14788.

She was sick. She had schizophrenia, Copelin said of her mom. She told my grandfather right before she left that the voices were telling her to leave, and my grandfather was telling her she had to fight through that and she had to ignore those voices.

Her mom, she said, had dreams of living out west.

She would often hitchhike and she would be gone for months at a time. She would always come back, Copelin said.

This time, police found her car abandoned two weeks later two hours away at a hotel in Howell. Most of her family believes she was the victim of foul play.

The investigation by the Mecosta County Sheriffs Department never turned up any answers.

An aunt and uncle adopted and raised the missing moms daughter.

I had a great life, and I had a great childhood, Copelin said.

She now is raising two kids of her own in Hastings.

There was a hole missing in my heart, and I had pain that stuck with me my whole entire life, she said.

She has tried finding her mom on her own background searches, Google searches with an outside hope that shes still alive.

No matter what kind of research I do, no matter what I do, it comes to a dead-end with her, she said. And I believe, I have come to the conclusion that its something that maybe God doesnt want to reveal.

She reached out to Target 8 after learning that genealogy researchers working with DNA had identified two bodies found decades ago in West Michigan: remains previously known as Ada Bones in Kent County and Matilda in Ottawa County.

It gives me a lot of hope, she said. Some families are getting their justice 40, 45 years later, and Im hoping for that chance ourselves.

Her mom is among 619 people listed by NAMUS as missing from Michigan. Anyone with information on this case is asked to call the Mecosta County Sheriffs Department at 231.592.0150.

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DNA breakthroughs give new hope to daughter of missing mom - WOODTV.com