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Posts Tagged ‘dna’

Photo: Natasha de Vere & Col Ford, Barcode Wales, Flickr, CC BY 2.0.
Samples of an organism’s genome are obtained in the field, before being brought back to the lab for the barcoding process.

Some years ago, I learned that students at High Tech High, which involves kids in real-world projects (click here), were helping rangers in Africa to identify poached meat with a DNA test they had developed. Turns out, using DNA that way was just the beginning of its possibilities for the environment.

According to the radio show Living on Earth, the 1.3 million species that have been identified and recorded on Planet Earth are just a small fraction of what exists. So host Steve Curwood decided to look at how DNA is helping to catalog many more.

“CURWOOD: To make it easier to identify species, the International Barcode of Life Consortium is using a technique known as DNA barcoding. It can give a quick readout that tells whether a sampled organism is known to modern science, and if not, provide a marker to register it as a newly discovered life form. Paul Hebert is the molecular biologist who developed DNA barcoding.

“Paul, welcome to Living on Earth. Take us through the process of DNA barcoding. You find an organism you want to identify, and then?

Photo: LarissaFruehe, Wikimedia Commons.

“HEBERT: [You] might just touch it … and pick up enough of its DNA. [But] in the case of smaller organisms, where we may be prepared to sacrifice them, and where we want to have a voucher specimen in a collection that we can look at and photograph and analyze in other ways, we might remove a tiny piece of tissue. If it were an insect, six legs, remove one of those legs and extract the DNA from that. That’s a fairly simple process. When you do that DNA extraction, of course, you get all of the DNA in the genome. … In the case of an insect, it might be 500 million base pairs. And we just want to read 500 of them. And you can think of the whole genome as sort of a book of life. And we want to read just one of those pages. So to do that, we use the polymerase chain reaction, which basically Xerox copies a selected page in that much larger book of life. And that prepares [for] sequencing the DNA. …

“CURWOOD: Where can that information go from there? And what can it do? …

“HEBERT: It was important to develop an informatics platform that’s now been adopted by the global community. It’s a platform called the Barcode of Life Data System, acronym ‘BOLD’. And basically, all of the data from each individual specimen go into that database, together with an image of the specimen and where it was collected, and by whom; all of the details. And so, let’s say you begin by sequencing an American Robin, next time you were to encounter a feather on your lawn that happened to derive from that bird species, you would get a connection to that reference sequence in the bar code library, in BOLD. …

The idea is to build up this reference library, so it has representative sequences for every species on our planet. And that’s what we’re in the process of doing now.

“CURWOOD: Now, of course, this is a very handy approach in academia with nice big laboratories. What about somebody who’s in the field? How useful is this? …

“HEBERT: In Kruger National Park, [the rangers who] normally are involved in suppressing poaching of rhinoceroses joined in a massive collection program that gathered up about a million specimens from that largest national park in South Africa … and we then translated those specimens into barcode records and built a DNA barcode reference library for Kruger National Park. … In the future, [you’re] going to be able to take a walk through the woods with your kids or your grandkids and see an organism and simply touch it and from its DNA barcode sequence, gain its identity. …

“CURWOOD: What’s your biggest surprise now, in this project? …

“HEBERT: For a very long time, it has been argued that beetles were the most diverse group of insects, the most diverse order of insects. … But it turns out that’s wrong. Barcoding revealed that flies are by far the most diverse group of insects. And [one] particular group of flies, gall midges, are hugely diverse, more diverse than all of the beetles on our planet. [And] one of the earliest studies that we did in Costa Rica involved a beautiful iridescent blue butterfly that for the last 200 years has been regarded as a single species. [When] we barcoded that species, we found that in fact, it was 10 species, not one. There’s a lot of hidden diversity, even within the large species that we share on this planet, when you move down to the small stuff, it’s massive discovery.

“CURWOOD: Now, the International Barcode of Life Consortium has this mission of identifying each and every species on Earth using barcoding. What is the ultimate goal of the project? …

“HEBERT: Creating that reference sequence library for all species on the planet is going to place us in a position where it’s going to be possible for us to set up global bio surveillance system. So we can track what humanity is doing to the other life forms. … I see detailed information on the shifts in biodiversity that are happening on our planet motivating humanity to take the action needed to do better. …

“CURWOOD: Paul Hebert is a molecular biologist at the University of Guelph in Canada, and science director of the International Barcode of Life Consortium. Thank you so much, Paul, for taking the time with us today.”

More at Living on Earth, here.

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Photo: Xinhua/Rex/Shutterstock.
This is a Bryde’s whale, related to the newly described whale species called Rice’s whales. Rice’s whales were previously believed to be a population of Bryde’s but were recently found to be a whole new species.

Lately, I’ve noticed how many mainstream publications reuse stories from other publications, which helps me feel less guilty sharing others’ work at Suzanne’s Mom’s Blog. As a former magazine editor myself, I am pretty scrupulous about providing links and credits and not using the whole original piece.

And if the use of a photo is blocked, I try to find a different photo elsewhere. But I must say that blocking your photo reduces the number of ways people online can find your article.

In an article from Hakai magazine (an online publication about science and society in coastal ecosystems), Joshua Rapp Learn reported on a unique whale. I learned about it from a reprint at the Guardian.

“Genetic analysis and a close examination of the skulls from a group of baleen whales in the north-eastern Gulf of Mexico have revealed that they are a new species.

“ ‘I was surprised that there could be an unrecognized species of whale out there, especially in our backyard,’ says Lynsey Wilcox, a geneticist with the US National Oceanic and Atmospheric Administration who helped uncover the new species. ‘I never imagined I would be describing a new species in my career, so it is a very exciting discovery.’

“The newly described whales weren’t exactly hiding in plain sight. With a population estimated at fewer than 100, the new whales – which researchers have dubbed Rice’s whales after American biologist Dale Rice – aren’t commonly seen even in the corner of the Gulf of Mexico they call home. It doesn’t help that the whales, previously believed to be a population of Bryde’s whales, have a feeding strategy that takes them deep under the water around DeSoto Canyon, about 100km south of Mobile, Alabama.

“Researchers have long known that this group of Bryde’s-like whales in the Gulf of Mexico was different. They seemed to mostly stay put in the north-eastern corner of the gulf, and didn’t mingle with Bryde’s whales, which … typically forage near the surface.

“But it’s difficult even for experts to tell large baleen whales apart in the field – so much so that Bryde’s whales sometimes get confused with fin whales, says John Hildebrand, a biological oceanographer at Scripps Institution of Oceanography at the University of California San Diego who was not involved in the recent study. …

“Wilcox’s colleagues first began collecting tissue samples from Rice’s whales in 2000, eventually collecting samples from 36 different individuals.

Comparing their genes with Bryde’s whales, Wilcox says she and her colleagues ‘noticed that they weren’t quite what was expected.’

“To compare their morphologies, the scientists inspected skeletons held in museums. Then, in January 2019, an 11-meter-long Rice’s whale washed up on a key in the Florida Everglades. Examining the whales’ skulls revealed some differences in the shape and size of the bone material around the blowhole. …

“Rice’s whales are already considered endangered by the United States. They were listed under the Endangered Species Act as a population of Bryde’s whales in April 2019, and the discovery that they are a distinct species is unlikely to change much – other than requiring an update of their name. Living in the Gulf of Mexico, the whales face threats from oil spills, ship strikes, ocean noise and entanglement in fishing gear.

“Hildebrand says the whales are particularly vulnerable to ship strikes because they have the ‘unfortunate habit’ of sleeping at night just under the sea’s surface. … Hildebrand speculates that the whales might once have been more widespread in areas with deeper water, but they are now holing up in an area that sees less ship traffic.

“ ‘They are the most endangered, or nearly the most endangered, baleen whales in US waters,’ Hildebrand says. ‘In terms of the responsibility for the health of the whale, it really does fall on us.’ ”

Read some really wonderful stories about sea life at hakaimagazine.com.

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Photo: University of York
A UK lab is learning what the DNA in old books has to tell us about the past. Even the beeswax used in seals is rich with data, including the flowers that grew in that region year to year.

Do you know what set you on your career? As an oldest child, I spent a certain amount of time explaining things, and I liked making a school for my dolls. Although I ended up as an editor for many years, I started my worklife as a teacher and am now back to volunteer work as a teacher.

The scientist in the following story got launched on his passion after watching the movie Jaws.

Sarah Zhang writes at the Atlantic, “It was in the archives of the Archbishop of York that Matthew Collins had an epiphany: He was surrounded by millions of animal skins.

“Another person might say they were surrounded by books and manuscripts written on parchment, which is made from skins, usually of cows and sheep. Collins, however, had been trying to make sense of animal-bone fragments from archaeological digs, and he began to think about the advantages of studying animal skins, already cut into rectangles and arranged neatly on a shelf. …

“In recent years, archaeologists and historians have awakened to the potential of ancient DNA extracted from human bones and teeth. DNA evidence has enriched — and complicated — stories of prehistoric human migrations. It has provided tantalizing clues to epidemics such as the black death. It has identified the remains of King Richard III, found under a parking lot. But Collins isn’t just interested in human remains. He’s interested in the things these humans made; the animals they bred, slaughtered, and ate; and the economies they created.

“That’s why he was studying DNA from the bones of livestock — and why his lab is now at the forefront of studying DNA from objects such as parchment, birch-bark tar, and beeswax. … With ample genetic data, you might reconstruct a more complete picture of life hundreds of years in the past.

“Collins splits his time between Cambridge and the University of Copenhagen, and it’s hard to nail down exactly what kind of -ologist he is. He has a knack for gathering experts as diverse as parchment specialists, veterinarians, geneticists, archivists, economic historians, and protein scientists (his own background). ‘All I do is connect people together,’ he said. …

“Collins began his scientific career studying marine biology, thanks to a formative teenage viewing of Jaws. He specialized first in marine fossils and, later, in the ancient proteins hidden inside them. This turned out to be a dead end. For the most part, the fossils were too old and the proteins no longer intact enough to study. He was forced to look at younger and younger material, until he crossed from paleontology into archaeology. He applied the techniques of protein analysis to pottery shards, in which he found milk proteins that hinted at the diet of the people who used those pots.

“Collins quickly realized that DNA held even more potential than ancient proteins, which can be ‘a blunt tool compared to DNA.’ The DNA of any single animal is, after all, a library coding for all the proteins their cells can make. …

“When Collins embarked on the parchment project, he gathered a team that included geneticists as well as archivists, bookmakers, and historians.

“It didn’t take long for the group to hit their first culture clash. In science and archaeology, destructive sampling is at least tolerated, if not encouraged. But book conservators were not going to let people in white coats come in and cut up their books. Instead of giving up or fighting through it, Sarah Fiddyment, a postdoctoral research fellow working with Collins, shadowed conservationists for several weeks. She saw that they used white Staedtler erasers to clean the manuscripts, and wondered whether that rubbed off enough DNA to do the trick. It did; the team found a way to extract DNA and proteins from eraser crumbs, a compromise that satisfied everyone.”

Read how the research evolved, here.

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It’s amazing what you can learn from DNA. Recently, scientists have been collecting insights from camel DNA about how camel ancestors were used on ancient trade routes.

Victoria Gill writes at the BBC, “Scientists examined DNA samples from more than 1,000 one-humped camels. Despite populations being hundreds of miles apart, they were genetically very similar. Scientists explained that centuries of cross-continental trade had led to this ‘blurring’ of genetics.

“The findings are published in the Proceedings of the National Academy of Sciences.

“One of the team, Prof Olivier Hanotte, from Nottingham University, explained that what made the dromedary so biologically fascinating was its close link to human history.

” ‘They have moved with people, through trading,’ he told BBC News. ‘So by analysing dromedaries, we can find a signature of our own past. … Our international collaboration meant we were able to get samples from West Africa, Pakistan, Oman and even Syria.’ …

” ‘People would travel hundreds of miles with their camels carrying all their precious goods. And when they reached the Mediterranean, the animals would be exhausted.

” ‘So they would leave those animals to recover and take new animals for their return journey.’

“This caused centuries of genetic ‘shuffling’, making dromedaries that are separated by entire continents remarkably similar.

“Crucially, this has also ensured that the animals maintained their genetic diversity — constantly mixing up the population. This means that dromedaries are likely to be much more adaptable in the face of a changing environment. …

” ‘The dromedary will be our better option for livestock production of meat and milk. It could replace cattle and even sheep and goats that are less well-adapted.’ ”

More at the BBC website, here.

Photo: Mark Payne/Gill/NPL
Ships of the desert: camels provide transport, milk and food in arid, hostile environments

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