Oldest Poop DNA contains Neanderthal microbiome

Biologist Marco Candela and his colleagues recently sequenced ancient microbial DNA from 50,000-year-old Neanderthal feces found at the El Salt archaeological site in Spain. The sequences included DNA from several of the microbes that still call our intestines home, as well as a few that have nearly vanished from today’s urban dwellers. According to Candela and his colleagues, their results suggest that the microscopic population of our guts may have been with us since at least 500,000 years ago, in the era of our species’ last common ancestor with Neanderthals.

Mixed in with the layer of sediment that once formed the floor of a Neanderthal rock shelter in eastern Spain, archaeologists found millimeter-sized coprolites (fossil poop) and chemical signatures of human feces. An earlier study, published in 2014, sifted through the tiny coprolites to look for traces of Neanderthal diets. “These samples therefore represent, to our knowledge, the oldest known positive identification of human fecal matter,” wrote Candela and his colleagues.

They recently returned to El Salt for new samples, which they scoured for fragments of ancient DNA from the bacteria and other microbes that once lived in the intestines of Neanderthals. To weed out possible contamination, Candela and his colleagues sorted out the old, obviously degraded ancient DNA from the more pristine modern sequences. Most of the ancient DNA in the sediments came from bacteria that lived in the soil and water—tiny relics of the Pleistocene environment. But the rest included some familiar companions.

“There are probably more differences between the gut microbiomes from modern traditional (rural, hunter gatherers) populations and the modern industrial urban populations than between Neanderthal and modern traditional populations,” Candela, a biologist at the University of Bologna, told Ars.

That’s reassuring. I think.

Famous Viking Warrior was a Woman


David Guttenfelder/NatGeo

More than a millennium ago in what’s now southeastern Sweden, a wealthy Viking warrior was laid to rest, in a resplendent grave filled with swords, arrowheads, and two sacrificed horses. The site reflected the ideal of Viking male warrior life, or so many archaeologists had thought.

New DNA analyses of the bones, however, confirm a revelatory find: the grave belonged to a woman

Viking lore had long hinted that not all warriors were men. One early tenth-century Irish text tells of Inghen Ruaidh (“Red Girl”), a female warrior who led a Viking fleet to Ireland. And Zori notes that numerous Viking sagas, such as the 13th-century Saga of the Volsungs, tell of “shield-maidens” fighting alongside male warriors.

But some archaeologists had considered these female warriors to be merely mythological embellishments—a belief colored by modern expectations of gender roles…

Since the late 1880s, archaeologists had viewed the “Birka warrior” through this lens; textbooks had listed the grave as belonging to a man, but not because the bones themselves said so. Since the remains were found alongside swords, arrowheads, a spear, and two sacrificed horses, archaeologists had considered it a warrior’s grave—and, thus, a man’s.

Sad; but, true. Even reputable scholars are sometimes trapped in the preconceptions of the culture that affords them speech and record. Hard to learn the truth, eh?

DNA sequenced from Woolly Mammoths — what’s next?

Teeth from mammoths buried in the Siberian permafrost for more than a million years have yielded the oldest DNA ever sequenced, according to a study published on Wednesday, shining a genetic spotlight into the deep past…

The genomes far exceed the oldest previously sequenced DNA – a horse dating to between 780,000 and 560,000 years ago…

Using a genome from an African elephant, a modern relative of the mammoth, as a blueprint for their algorithm, researchers were able to reconstruct parts of the mammoth genomes…

They found gene variants associated with life in the Arctic, like hairiness, thermoregulation, fat deposits and cold tolerance in the older specimen, suggesting mammoths were already hairy long before the woolly mammoth emerged…

As previously noted, this may, sooner or later, result in techniques which lead to reintroduction of a modern-day distant cousin of the Woolly Mammoth to the Arctic. Like most geeks (I’d bet), I’d be looking forward to such an event. Questions? Difficulties – scientific and ethical? You betcha. Comment if you feel one way or another.

Subway’s Tuna Sub Ain’t…so saith 19 out of 20 samples in SoCal

Pescatarians may want to avoid eating Subway’s tuna, if one is to believe the allegations in a revived lawsuit questioning the ingredients in the restaurant chain’s seafood.

Nineteen of 20 tuna samples from Subway outlets throughout Southern California contained animal protein including chicken, pork or cattle, but no discernible tuna DNA, according to the latest complaint filed on Monday in U.S. District Court in California…

The complaint filed on Monday includes findings based on DNA tests by the Barber Lab at UCLA’s Department of Ecology and Evolutionary Biology. Beyond finding “no detectable tuna DNA sequences whatsoever” in 19 of the samples, all 20 held “detectable sequences of chicken DNA,” according to the complaint. Eleven samples held pork DNA and seven cattle DNA, results that run counter to Subway’s marketing claims, it stated.

Maybe Subway is confident in the number of judges available to rule against scientific methodology. Preferring commercials…over proven commercial testing.

Coffee linked to DNA integrity

A controlled randomized study conducted on 100 healthy Europeans just vindicated you and your coffee obsession. As far as DNA integrity is concerned coffee is actually more beneficial than water

The coffee group exhibited much less DNA strand breakage than the control group by the end of the 4-week span…

As it stands – all coffee is rich with anti-oxidants, a compound that enables cells to better repair themselves in the wake of the damage done by free radicals. Free radicals, birthed by sunlight, oxygen, and pollution, deteriorate the collagen fibers in the skin. The microbial properties in coffee help ward off germs in the skin. Its caffeic acid boosts collagen levels which in turn reduces the aging process…The antioxidants found in coffee are also instrumental in fighting diseases, preventing cavities, diabetes, cirrhosis of the liver and various forms of cancer.

Take a minute to click through to the original – and you’ll discover even more great reasons to drink coffee. Good old dark roast used in most of this research. Delicioso!

mRNA technology promises to revolutionize future vaccines

More than 80 million Americans have been vaccinated against SARS-CoV-2 — the virus that causes COVID-19 — using the game-changing possibilities of mRNA technology. And while some people worry that the technology has been “rushed,” for more than 25 years university labs have been exploring the use of RNA, rather than viruses, to build the body’s immunity against diseases…

Messenger RNA (mRNA) — the basis of the first two vaccines cleared for public use by the Food and Drug Administration — induces cells to set off an immune response against the coronavirus that causes COVID-19. Vaccine researchers believe the success of these inoculations will usher in the most radical change to vaccine development since Jenner tapped a cow virus two centuries ago.

mRNA emerged as an alternative to traditional vaccine development in the early 1990s, building on research involving RNA injections into mice at the Waisman Center at the University of Wisconsin-Madison. mRNA is a molecule that essentially delivers instructions to cells to build specific proteins. Proteins are key to the success of a viral infection, because they enable a virus to replicate after it attaches to a cell. The coronavirus, for example, attaches to a cell with a so-called “spike” protein, which triggers the viral replication that turns the infection into COVID-19.

The theory behind the vaccines is that mRNA will tell a cell to make a protein that’s used by a certain virus, which would set off an immune response that builds the body’s ability to fend off the actual virus.

“It’s essentially biological software,”…says John Cooke, MD, PhD, medical director of the RNA Therapeutics Program at the Houston Methodist Research Institute.

Yes, it really is that simple to explain. That simplicity is part and parcel of time saved, costs lowered, for the design of production-ready vaccines.

20,000 Years Ago, a Coronavirus Epidemic Left Its Mark in Our DNA

A crown of spike-shaped proteins make coronaviruses recognizable when viewed under a microscope. But modern genetic analysis offers another way to find evidence of coronaviruses: detecting the marks the virus leaves behind in the populations it infects.

In a study published on June 24 in the journal Current Biology, researchers analyzed the DNA of thousands of people from around the world from 26 populations to look for signs of ancient coronavirus epidemics. The researchers found that people living in China, Japan and Vietnam faced a coronavirus for about 20,000 years in an epidemic that ended 5,000 years ago…

When coronaviruses infect humans, they rely on the microscopic machinery made by human genes in order to make more virus particles. So the research team focused on a few hundred human genes that interact with coronaviruses—but not other microbes—during an infection…

In five groups of people, 42 of those genes had enough mutations to suggest they had evolved because of an epidemic. The genes may have become better at fighting off the viral infection, or less hospitable for the virus to use to copy itself. People with those mutations would have been more likely to survive an outbreak of the disease, and later, have children with the same genetic mutations.

Science like this makes me wonder about price and availability of a nice secondhand electron microscope. Probably would mess up retirement as much as a regular job. :-]

Tracking history before DNA


F.Chen et al./Nature

Over the past two decades, DNA retrieved from ancient fossils has transformed scientists’ understanding of human evolution. Analysis of the similarities and differences in the DNA of different hominin groups has allowed researchers to map out the tangled family tree in a way that was previously not possible. And genetic material has led to some major finds, such as the discovery of Denisovans in the first place…

Ancient DNA has also left geographical blind spots. DNA degrades faster in warm environments, so although a 100,000-year-old specimen found in a cold Siberian cave might still harbour genetic material, a fossil that has spent that long in the heat of Africa or southeast Asia generally will not. As a result, little is known about the genetics of even relatively recent hominins from these regions, such as H. floresiensis…

Now researchers are hoping that protein analysis might begin to fill in some of those blanks. The idea is not new: as early as the 1950s, researchers had reported finding amino acids in fossils. But for a long time, the technology needed to sequence ancient proteins just didn’t exist … That changed in the 2000s, after researchers realized that mass spectrometry — a technique used to study modern proteins — could also be applied to ancient proteins. Mass spectrometry essentially involves breaking down proteins into their constituent peptides (short chains of amino acids) and analysing their masses to deduce their chemical make-up.

RTFA. Fascinating as paleontology can always be. Learning the where and when of how we got to here and now. True science never walks away from a problem because it’s difficult. Even when it takes generations to resolve.

Unaffected by Covid? Maybe thank your Neanderthal ancestors

People who survive a bout of Covid-19 with mild symptoms or even no symptoms may be able to thank their Neanderthal ancestors, a new study suggests.

Researchers found a genetic mutation that reduces the risk of severe Covid-19 infection by about 22%. It was found in all the samples they took of Neanderthal DNA, and in about 30% of samples from people of European and Asian origin.

The genetic region involved affects the body’s immune response to RNA viruses such as the coronavirus, as well as West Nile virus and hepatitis C virus, the researchers reported Tuesday in the Proceedings of the National Academy of Sciences…

The finding could help explain why Black patients are so much more likely to suffer severe coronavirus disease. Neanderthals, who went extinct about 40,000 years ago, lived alongside and sometimes interbred with modern humans in Europe and Asia but not in Africa, and people of purely African descent do not carry Neanderthal DNA. Studies estimate that about 2% of DNA in people of European and Asian descent can be traced back to Neanderthals.

RTFA. Details on the research. And it’s certainly interesting to our household. Genetic analysis shows my wife with about 2% Neanderthal DNA. I’m actually at about 3%.

A man was reinfected with coronavirus after recovering…!


May James/AFP/Getty

A 33-year old man was found to have a second SARS-CoV-2 infection some four-and-a-half months after he was diagnosed with his first, from which he recovered. The man, who showed no symptoms, was diagnosed when he returned to Hong Kong after a trip to Spain.

There is no published peer-review report on this man – only a press release from the University of Hong Kong – although reports say the work will be published in the journal Clinical Infectious Diseases.

The author, Megan Culler Freeman, asks and answers questions raised by the news reports.