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.

‘Liquid biopsy’ blood test predicts cancer

A new blood test that can detect methylation of DNA can accurately predict whether a person has any one of 50 cancers and where the tumour is growing…

…In all, more than 15,000 volunteers from over 140 clinics in North America took part, and their samples revealed that this ‘liquid biopsy’ had a 0.7% false positive rate for cancer detection. The test was also able to predict the tissue that the cancer originated in with more than 90% accuracy. It performed best on 12 of the most common cancers, including ones that are most lethal and have no established screening paradigms such as pancreatic and ovarian cancers…

The test works because when a tumour cell dies its DNA enters the bloodstream. This genetic material still carries methylation patterns that differ from healthy cells, and this is what the liquid biopsy measures. ‘The test exploits the fact that cancers are abnormally methylated, and … that different cancers have different methylation patterns,’ explains study co-author Eric Klein from the Cleveland Clinic in Ohio.

Fortunately, solid scientific research finds a way to keep to task, direction mostly unaffected by the politics of ignorance.

Leeches may help prevent the next coronavirus outbreak

Using the latest biotechnology, a team led by Professor Douglas Yu of Britain’s University of East Anglia extracted DNA from digested blood in leeches’ stomachs, determined what animals they had fed on, and then produced a model of the distribution of wild animals in the Ailao Shan Nature Reserve in Yunnan province.

The same DNA analysis method could feasibly be used to examine drain water for evidence of illegal wildlife consumed or traded in markets, Yu says…

Wild animals are a reservoir of viruses that, due to their ability to rapidly change genetic make-up, regularly “jump” to other species, including humans…

Until recently, biotechnology couldn’t separate individual bits of DNA in the “soup” to identify which animals they came from. But the latest technology can process multiple DNA molecules at the same time, and it has become a powerful forensic tool.

Without seeing or touching the animals, their presence can be detected from a sample of soil, water – or the remnants of digested blood in a leech’s stomach.

Yu’s team extracted DNA from leeches’ stomachs, then applied sophisticated statistical software that could compare the different DNA sequences against animal DNA sequences in existing databases, similar to how facial recognition software matches an image of an individual face from a set of millions…

The results closely matched the biology of the animals. “The right species were found in the right places,” Yu says. It also gelled with previous records of animal sightings in Ailao Shan. The leeches could be trusted.

Scientific methods don’t really care what country, culture or economic system they operate in. Yes, everything from context to funding vary; but, real data produces a catalog of information that can provide new and revealing information, conclusions.

Good for you, Doctor Yu.

Pentagon says they’re worried about consumer DNA testing


Lisa Ferdinando/DOD

The Pentagon is advising troops that there are security risks, to include mass surveillance and potential tracking, associated with using consumer DNA kits. The products have become popular in recent years with people looking to discover potential medical issues or uncover information about ancestry and even find unknown relatives…

“These DTC [direct-to-consumer] genetic tests are largely unregulated and could expose personal and genetic information, and potentially create unintended security consequences and increased risk to the joint force and mission,” the memo reads.

“Moreover, there is increased concern in the scientific community that outside parties are exploiting the use of genetic data for questionable purposes, including mass surveillance and the ability to track individuals without their authorization or awareness,” the memo states.

Humbug! Yes, we all should be concerned about privacy and access to personal information. Automatic call for anyone spending any time on the Web. Anyone applaud the Pentagon for worrying about citizens becoming security risks from DNA testing? Drivel!

As much as geeks drive concern over privacy and corporate use of that info – it should take a century or two for non-government snoops to catch up to the files in possession of the FBI, NSA and the rest of the vegetable soup tracking ordinary citizens under the umbrella of security. Cripes, last time I was involved with challenges to federal snoops, the active file went back to my first sit-in over sixty years ago.

The life and appearance of a hunter-gatherer in Denmark about 6000 years ago

At the dawn of the Neolithic era, a young woman discarded a lump of ancient chewing gum made from birch tar into a shallow, brackish lagoon that drew fishers to the coast of southern Denmark.

Nearly 6,000 years later, researchers excavating the site spotted the gum amid pieces of wood and wild animal bone and from it have reassembled her complete DNA and so painted the broadest strokes of her portrait.

” The strands of DNA preserved in the gum point to a hunter-gatherer from continental Europe who had dark skin, dark hair and blue eyes. She lived near the lagoon, itself protected from the open sea by shifting sand barriers, about 5,600 years ago, according to carbon dating of the birch tar.

Alongside her DNA, the researchers found genetic material from duck and hazelnuts – presumed remnants of a recent meal – and at least 40 types of microbes.

Anders Götherström said the latest work was exciting. “As for human DNA, these mastics may present an alternative source for DNA from where there are limited amounts of preserved bones. But even more exciting is the ancient microbial DNA,” he said. “The mouth is an exposed area of the body. It is possible that this type of material will outcompete bones when looking for DNA from ancient pathogens.”

Thanks, Honeyman

When your DNA says you aren’t you, not from anywhere around here


Tiffany Brown Anderson/NY Times

” Three months after his bone marrow transplant, Chris Long of Reno, Nev., learned that the DNA in his blood had changed. It had all been replaced by the DNA of his donor, a German man he had exchanged just a handful of messages with…

But four years after his lifesaving procedure, it was not only Mr. Long’s blood that was affected. Swabs of his lips and cheeks contained his DNA — but also that of his donor. Even more surprising to Mr. Long and other colleagues at the crime lab, all of the DNA in his semen belonged to his donor. “I thought that it was pretty incredible that I can disappear and someone else can appear,” he said.

” Mr. Long had become a chimera, the technical term for the rare person with two sets of DNA. The word takes its name from a fire-breathing creature in Greek mythology composed of lion, goat and serpent parts. Doctors and forensic scientists have long known that certain medical procedures turn people into chimeras, but where exactly a donor’s DNA shows up — beyond blood — has rarely been studied with criminal applications in mind.

I can see a B-Movie already glazing over the eyes of someone in Hollywood.

Sewage measures global levels of antimicrobial resistance

❝ A comprehensive analysis of sewage collected in 74 cities in 60 countries has yielded the first, comparable global data, which show the levels and types of antimicrobial resistant bacteria that are present in mainly healthy people in these countries. The National Food Institute, Technical University of Denmark, headed the study, which was conducted by an international team of researchers.

❝ In a metagenomics study, the researchers have mapped out all the DNA material in the sewage samples and found that according to antimicrobial resistance the world’s countries fall within two groups. North America, Western Europe, Australia and New Zealand generally have the lowest levels of antimicrobial resistance, while Asia, Africa and South America have the highest levels.

Brazil, India and Vietnam have the greatest diversity in resistance genes, while Australia and New Zealand have the lowest…

❝ According to the researchers, the use of antimicrobials only explains a minor part of the occurrence of antimicrobial resistance in the various countries…Their work shows that most of the variables, which are associated with the occurrence of antimicrobial resistance in a country, are related to the sanitary conditions in the country and the population’s general state of health.

Nothing startling. Still, worth keeping your brain – and behavior – up to date on news about a growing problem.

DNA Reveals Intricate Connections Between The First People of The Americas

Comparisons between two extraordinary sets of ancient American remains have added rich detail to the spread of ancient human populations through the New World more than 13,000 years ago. And it shows a surprising and far-reaching connection between native North, South, and Central Americans.

What started as a simple story of migration is quickly turning into an intricate web of movement and cross-pollination, revealing connections that stretch not just deep into South America, but perhaps around the world.

None of these movements replaced existing populations, but rather show a melting pot of migrations that ebbed and flowed.

Interesting stuff. Information growing from DNA studies proceeds in so many directions as different database projects grow and interchange information. Studies on the formation and intermingling of so many ethnicities are fascinating – confirming or denying myth, legend and early science.