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The art of getting DNA out of decades-old pickled snakes – Phys.org

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The art of getting DNA out of decades-old pickled snakes
Part of the Field Museum’s underground “bunker” of reptile specimens. Credit: Field Museum

Two levels underground, Chicago’s Field Museum has a secret bunker. The sub-basement Collections Resource Center houses millions of biological specimens for scientists around the world to use in their research, including countless bottles and jars containing pickled fish, lizards, and snakes, arranged like a library. Many of these specimens are decades or even centuries old, near-perfectly preserved by a combination of formalin and alcohol. But the process that preserves tissues often destroys or at least makes acquiring DNA for modern studies very difficult, which is bad news for scientists who study genetic relationships between organisms. A new study in Frontiers in Ecology and Evolution, however, reveals new approaches for getting and maximizing usable DNA from decades-old pickled specimens, and uses these techniques to solve a long-standing mystery about a small snake from the island of Borneo.

“As a true crime aficionado, it reminds me of how people didn’t take DNA samples when a crime was committed in the 1960s, because nobody could have predicted that one day DNA samples would let you pinpoint who committed a crime,” says Sara Ruane, assistant curator of herpetology at the Field Museum and the study’s senior author. “These older museum specimens are sometimes the only available examples of a species, but they weren’t preserved with DNA in mind— this paper is about how we can squeeze every bit of information possible out of them.”

The project was born of the dissertation research of Justin Bernstein when he was Ruane’s student at Rutgers University-Newark. “My primary study is on a group of snakes, called homalopsids or mud snakes, that live in South and Southeast Asia, New Guinea, and Australia,” says Bernstein, the paper’s lead author. “They’re really fascinating; they live in muddy, aquatic environments, and there are 56 species of them. We use DNA to study their , to try to describe new species, and to learn what happened to these groups over tens of millions of years that led to the diversity we see today.”

Alcohol-preserved specimens of Hydrablabes periops in the Field Museum’s collections. Credit: Josh Mata, Field Museum

For this paper, there was one animal in particular that Bernstein and Ruane were trying to place into a family group, a two-foot-long greenish-brown snake called Hydrablabes periops, aka the olive small-eyed snake. It’s found on Borneo, a large island east of mainland Malaysia and northwest from Australia that contains parts of Malaysia and Indonesia and the entire nation of Brunei. Based on its appearance, scientists had suggested two different families that it might be a part of. Analyzing its DNA could reveal its closest relatives and thus, its family, but that was easier said than done. “About half of mud snake diversity and all Hydrablabes vouchers are known from older specimens that were chemically treated, and this chemical treatment breaks down the DNA,” says Bernstein.

Part of the process of preserving an animal in alcohol is “fixing” it with a substance called formalin, a solution of formaldehyde gas and water, that makes its tissues rubbery and rigid. Unfortunately, the DNA in its cells gets altered as well. “It does something called crosslinking, which binds up the DNA,” says Ruane. “If you want to study its DNA, you need to undo or try to force the DNA out from those crosslinks.”

Studying the olive small-eyed snake meant taking small samples of liver tissue from some of the few specimens in the United States, both from the Field Museum’s collections. One from 1964, and the other from a 1993 collecting trip by the Field’s then-curator Robert Inger and his wife Tan Fui Lian.

Lead author Justin Bernstein visiting the Field Museum’s reptile collections. Credit: Sara Ruane, Field Museum

Such old specimens required new lab techniques. Normally, getting DNA out of a tissue sample involves adding digestive enzymes that break apart the tissue, leaving the DNA behind, and heating it to 130 ℉ for several hours. “We had to modify the way we got the DNA out by making it hotter for longer and using more of these digestive enzymes,” says Ruane. These more extreme preparation methods have been effective for other snakes in previous studies, but the resulting genetic analysis still contained lots of gaps for Borneo’s Hydrablabes snake specimen.

Lead author Justin Bernstein working with snake specimens at University of Kansas Biodiversity Institute & Natural History Museum, taking morphological data to examine homalopsid snake diversity. Credit: Justin Bernstein

“The chemicals used to preserve the snakes sheared their DNA into shorter pieces of code, which made them hard to compare with longer, more complete genes from other specimens,” says Bernstein. “The first software that I used made it hard to understand how much fragmented DNA there was across the study specimens, but switching to a different software that visualized the pieces of genetic code made it easier to see where there were problems.” And even the smaller, more fragmented pieces of code could be added to larger, published datasets to help build an evolutionary tree.

An important aspect of this paper for Bernstein was being transparent about the difficulties of using older specimens and the troubleshooting required to study them. “I wanted to show scientists that you can still do work with these specimens, it just requires a bit of finagling,” he says. “On a broader level, the study is really showing how to leverage the data you do obtain and how you can combine it with previously published datasets to investigate some really cool hypotheses.”

One of the decades-old snake specimens from the Field Museum used in this study. Credit: Sara Ruane, Field Museum

As for the Bornean at the heart of the study, the researchers were able to determine that it’s a member of the family Natricidae, which contains distant relatives such as the North American garter snakes. Which might not seem like a big deal, but “knowing that a particular species is part of a certain group can tell us a lot about biogeography and about how life on Earth has changed over time,” says Ruane.

And beyond the study of snakes, she notes that overall, “this project underscores the importance of museum collections, because you never know what you’ll be able to learn from specimens in the future.”


Explore further

Scientists discover a way to sequence DNA of rare animals


More information:
Maximizing molecular data from low-quality fluid-preserved specimens in natural history collections, Frontiers in Ecology and Evolution (2022). DOI: 10.3389/fevo.2022.893088.
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Calvin Lucyshyn: Vancouver Island Art Dealer Faces Fraud Charges After Police Seize Millions in Artwork

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In a case that has sent shockwaves through the Vancouver Island art community, a local art dealer has been charged with one count of fraud over $5,000. Calvin Lucyshyn, the former operator of the now-closed Winchester Galleries in Oak Bay, faces the charge after police seized hundreds of artworks, valued in the tens of millions of dollars, from various storage sites in the Greater Victoria area.

Alleged Fraud Scheme

Police allege that Lucyshyn had been taking valuable art from members of the public under the guise of appraising or consigning the pieces for sale, only to cut off all communication with the owners. This investigation began in April 2022, when police received a complaint from an individual who had provided four paintings to Lucyshyn, including three works by renowned British Columbia artist Emily Carr, and had not received any updates on their sale.

Further investigation by the Saanich Police Department revealed that this was not an isolated incident. Detectives found other alleged victims who had similar experiences with Winchester Galleries, leading police to execute search warrants at three separate storage locations across Greater Victoria.

Massive Seizure of Artworks

In what has become one of the largest art fraud investigations in recent Canadian history, authorities seized approximately 1,100 pieces of art, including more than 600 pieces from a storage site in Saanich, over 300 in Langford, and more than 100 in Oak Bay. Some of the more valuable pieces, according to police, were estimated to be worth $85,000 each.

Lucyshyn was arrested on April 21, 2022, but was later released from custody. In May 2024, a fraud charge was formally laid against him.

Artwork Returned, but Some Remain Unclaimed

In a statement released on Monday, the Saanich Police Department confirmed that 1,050 of the seized artworks have been returned to their rightful owners. However, several pieces remain unclaimed, and police continue their efforts to track down the owners of these works.

Court Proceedings Ongoing

The criminal charge against Lucyshyn has not yet been tested in court, and he has publicly stated his intention to defend himself against any pending allegations. His next court appearance is scheduled for September 10, 2024.

Impact on the Local Art Community

The news of Lucyshyn’s alleged fraud has deeply affected Vancouver Island’s art community, particularly collectors, galleries, and artists who may have been impacted by the gallery’s operations. With high-value pieces from artists like Emily Carr involved, the case underscores the vulnerabilities that can exist in art transactions.

For many art collectors, the investigation has raised concerns about the potential for fraud in the art world, particularly when it comes to dealing with private galleries and dealers. The seizure of such a vast collection of artworks has also led to questions about the management and oversight of valuable art pieces, as well as the importance of transparency and trust in the industry.

As the case continues to unfold in court, it will likely serve as a cautionary tale for collectors and galleries alike, highlighting the need for due diligence in the sale and appraisal of high-value artworks.

While much of the seized artwork has been returned, the full scale of the alleged fraud is still being unraveled. Lucyshyn’s upcoming court appearances will be closely watched, not only by the legal community but also by the wider art world, as it navigates the fallout from one of Canada’s most significant art fraud cases in recent memory.

Art collectors and individuals who believe they may have been affected by this case are encouraged to contact the Saanich Police Department to inquire about any unclaimed pieces. Additionally, the case serves as a reminder for anyone involved in high-value art transactions to work with reputable dealers and to keep thorough documentation of all transactions.

As with any investment, whether in art or other ventures, it is crucial to be cautious and informed. Art fraud can devastate personal collections and finances, but by taking steps to verify authenticity, provenance, and the reputation of dealers, collectors can help safeguard their valuable pieces.

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Ukrainian sells art in Essex while stuck in a warzone – BBC.com

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Somerset House Fire: Courtauld Gallery Reopens, Rest of Landmark Closed

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The Courtauld Gallery at Somerset House has reopened its doors to the public after a fire swept through the historic building in central London. While the gallery has resumed operations, the rest of the iconic site remains closed “until further notice.”

On Saturday, approximately 125 firefighters were called to the scene to battle the blaze, which sent smoke billowing across the city. Fortunately, the fire occurred in a part of the building not housing valuable artworks, and no injuries were reported. Authorities are still investigating the cause of the fire.

Despite the disruption, art lovers queued outside the gallery before it reopened at 10:00 BST on Sunday. One visitor expressed his relief, saying, “I was sad to see the fire, but I’m relieved the art is safe.”

The Clark family, visiting London from Washington state, USA, had a unique perspective on the incident. While sightseeing on the London Eye, they watched as firefighters tackled the flames. Paul Clark, accompanied by his wife Jiorgia and their four children, shared their concern for the safety of the artwork inside Somerset House. “It was sad to see,” Mr. Clark told the BBC. As a fan of Vincent Van Gogh, he was particularly relieved to learn that the painter’s famous Self-Portrait with Bandaged Ear had not been affected by the fire.

Blaze in the West Wing

The fire broke out around midday on Saturday in the west wing of Somerset House, a section of the building primarily used for offices and storage. Jonathan Reekie, director of Somerset House Trust, assured the public that “no valuable artefacts or artworks” were located in that part of the building. By Sunday, fire engines were still stationed outside as investigations into the fire’s origin continued.

About Somerset House

Located on the Strand in central London, Somerset House is a prominent arts venue with a rich history dating back to the Georgian era. Built on the site of a former Tudor palace, the complex is known for its iconic courtyard and is home to the Courtauld Gallery. The gallery houses a prestigious collection from the Samuel Courtauld Trust, showcasing masterpieces from the Middle Ages to the 20th century. Among the notable works are pieces by impressionist legends such as Edouard Manet, Claude Monet, Paul Cézanne, and Vincent Van Gogh.

Somerset House regularly hosts cultural exhibitions and public events, including its popular winter ice skating sessions in the courtyard. However, for now, the venue remains partially closed as authorities ensure the safety of the site following the fire.

Art lovers and the Somerset House community can take solace in knowing that the invaluable collection remains unharmed, and the Courtauld Gallery continues to welcome visitors, offering a reprieve amid the disruption.

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