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.

‘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