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Genetic Linkage

DNA Study Adds Branch to North American Mammoth Family Tree

An international team has assembled billions of DNA snippets from molars that three mammoths left in the permafrost of northeastern Siberia, at widely different times. The research reveals an unrecognized ancestor that contributed half of the genome of the mammoth species that came to North America some 1.5 million years ago. The report appears in Nature.

 

The timescale of the study paints a portrait of mammoth evolution, perhaps even capturing a glimmer of speciation. The finding also sets back the clock of ancient DNA analysis; a horse that lived 780,000 to 560,000 years ago holds the record.

 

The three mammoth specimens were excavated in the 1970s from different locations in Siberia, dating from half a million to roughly 1.2 million years ago. They reside at the Geological Institute, Russian Academy of Sciences, in Moscow. The permafrost helped to preserve the DNA.

 

The Land Bridge Where It Happened

 

To continue reading, go to DNA Science, where this post first appeared.

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How My “Fruit Fly Love Story” Presaged The Rise of COVID-19 Viral Variants

I wrote "The Making of a Mutant" in 1978. Then a PhD student in the lab of Thom Kaufman at Indiana University, I snuck the story into a draft of a manuscript we were submitting to the journal Genetics – just to see if the boss was paying attention. The tale was about our research on the mutation Antennapedia in the fruit fly Drosophila melanogaster, which reroutes development so that legs grow where antennae normally extend.

 

My story was passed down to generations of graduate students, and read aloud at Thom's 60th birthday party many years later. I published "The Making of a Mutant" at Scientific American blogs in 2012, and then here at DNA Science in 2013. It's a geneticist's love story for Valentine's Day.

 

But never in a million years could I have imagined that my vision of a mutation that takes over a population would echo in the form of a novel coronavirus that is continually reinventing itself as it tears through human bodies and populations.

 

My story chronicles how the abnormal becomes the normal, and the new normal eventually spawns a new abnormal. That's what evolution is, change at the molecular level that reverberates up through populations of organisms – and viruses. The mutations in my imagined world in a milk bottle, home to the flies, were induced – in contrast to the situation for SARS-CoV-2.

 

We can't stop evolution. Mutation is a fundamental characteristic of a genetic material, endowing it with the plasticity that underlies adaptation, which fuels evolutionary change.

 

Evolution of SARS-CoV-2 in a Single Patient

 

 

To continue reading, go to DNA Science, where this post first appeared. 

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Getting a COVID Vaccine is More Transparent Than Eating a Hot Dog: Countering Vaccine Hesitancy

"So, you've been eatin' hot dogs and chicken nuggets all your life and you don't want the vaccine 'cuz you don't know what's in it??" asks a befuddled chicken in a meme.

 

Actually, plenty of information is out there about "what's in it."

 

Upon entering a vaccination center, you're handed a multi-page fact sheet that, among many other things, lists the chemicals about to be plunged into your arm.

 

The first two COVID vaccines are roughly the same recipe, adjusted for proportions and tiny details: mRNA, 4 fats (including cholesterol), a pinch of sugar, and a few salts. No eggs, preservatives, ricin, or leechee nut extract. (See The First COVID-19 Vaccines: What's mRNA Got to do With it?) Ingredient lists for hot dogs and chicken nuggets are far longer and complex.

 

Yet the comparative transparency of vaccine ingredient lists isn't enough to dispel the fear of something new and unfamiliar being jabbed into your body. For many people that fear arises against a backdrop of the history of dishonesty in medicine that has misled and mistreated marginalized groups, as well as the record of unethical clinical trials for some vaccines, notably influenza.

 

To continue reading go to my DNA Science blog at Public Library of Science, where this post first appeared.

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Are We Hurtling or Hurdling Towards Herd Immunity for COVID-19?

Vaccines against COVID-19 were developed in record-smashing time, and now that the rollout has begun, attention is returning to herd immunity, in a real rather than hypothetical sense.

 

Herd immunity refers to the protection against an infectious disease that arises when a critical mass of individuals in a population becomes immune. The pathogen can't find welcoming bodies, and the epidemic dies out. Once herd immunity is attained, mitigation measures can be relaxed. But if society opens too soon, a second and even third wave of disease can ensue – as we've seen.

 

A vaccine, engineered to evoke a strong and diverse antibody response, is more likely to build herd immunity than is natural infection.

 

Establishing herd immunity against COVID-19 requires that a whole bunch of ducks align. The variables include:

 

To continue reading, go to my DNA Science blog, where this post first appeared.

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Marketers are beginning to use data mined from consumer DNA tests. Should we be worried?

(Angie Wang)

A woman lingers at a display of coffeemakers. Soon after, images of the very same contraptions festoon her Facebook feed, courtesy of her phone's GPS and store cameras.

 

A man diagnosed with a blood clot gets TV ads for a drug to prevent further episodes.

 

A person peruses ads for indoor herb gardens for a gift and is later bombarded with botanical options on social media.

 

People turn 65, and suddenly Joe Namath interrupts their favorite TV shows, with unending descriptions of Medicare Supplement plans.

 

Coincidences? Hardly. In this age of TMI, it can feel as if our very brains are being intrusively picked, constantly.

Even our DNA can be trolled for embedded preferences and habits, if we (sometimes unknowingly) provide permission.

 

How foreboding is the 'privacy crisis'?
Remi Daviet, Gideon Nave, and Jerry Wind, from the Wharton School of the University of Pennsylvania, dissect "Genetic Data: Potential Uses and Misuses in Marketing," in a report in a special issue of the Journal of Marketing.

 

To continue reading, go to Genetic Literacy Project, where this post first appeared.

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What Do Non-identical Identical Twins Have to do with COVID-19? Mutation!

Identical twins Stella and Desiree Vignes were born in 1938 in a Louisiana town so small that it wasn't on any maps. Light-skinned Blacks, the girls left town together at the age of 16 to head to New Orleans to work and escape a bleak future. Stella was mistaken for White at a job interview and continued the deception to get the position, eventually marrying her boss and leaving her sister behind. Stella experienced adulthood as White, Desiree as Black.

 

The Vignes sisters were born in the imagination of Brit Bennett, an extraordinary young writer. Her bestseller "The Vanishing Half" traces the experiences of the twins in a world where what happens to them depends upon how others perceive them – as Black or White. Of course, they go on to live starkly different lives, Stella in wealthy Brentwood, California, and Desiree back in her hometown waitressing in a diner. The drama intensifies when their grown daughters meet, one a pale blonde, the other "a dark girl" black as ebony.

 

Identical twins and higher multiples are, indeed, fascinating. The 2018 film Three Identical Strangers tells the tale of triplet brothers who met by chance at age 19 in 1980. It echoes the fictional film The Parent Trap, from 1961 with Hayley Mills and reborn in 1998 with Lindsay Lohan, each in dual roles.

 

Twin Studies

 

To continue reading, go to my DNA Science blog, where this post first appeared.

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A dangerous stage in the evolution of the novel coronavirus is upon us with the discovery of “escape mutations.” Artificial intelligence may be our best response

Real life with COVID-19 is now scarier than anything a sci-fi writer could envision. So-called "escape mutations" that can turn the virus into an out-of-control shape-shifter that hides from the immune system are now a frightening reality. And they can't be totally stopped with masks or social distancing, lockdowns or travel restrictions. Even if we could keep all viruses out, the ones already here are mutating in a direction that keeps them infectious and deadly. The battle between us and this often-lethal virus has just jumped to a new level. 

 

While it may take awhile to see whether these escape mutations will evade the vaccines approved or in the pipeline, Tyler Starr from the Fred Hutchinson Cancer Research Center and colleagues report in a new study in Science an effect on two already available treatments — monoclonal antibodies. They've identified an escape mutation with a single glitch that enables the virus to evade Regeneron's double-antibody REGN-COV2 "cocktail" (which Trump took) and a third antibody in Eli Lilly's LY-CoV016. The researchers found the escapee using a new lab mapping technique that displays viruses contorted with mutation, and then they found it in a patient who was still testing positive, 145 days after the first test.

 

What does this mean? The discovery of escape mutations derailing antibody treatments means that the companies' initial tests hadn't caught them all. And the escape mutations — the new mapping revealed three others — are already in circulation.

 

To continue writing, please go to Genetic Literacy Project, where this post first appeared.

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Mutants Come to Saratoga: COVID New Variants Explained

When a new variant of the COVID-19 virus appeared in the UK as 2020 drew to a close, I didn't think it would show up a half hour's drive from my home soon after. The first cases were near Denver and in San Diego, and then traced to a jewelry store on Broadway in Saratoga Springs. We've felt rather insulated and isolated here, hours from New York City.

 

The Legacy of Caffe Lena

This week began with an email from Sarah Craig, executive director of Caffe Lena, the oldest coffeehouse in the US. Don McLean debuted "American Pie" there, Arlo Guthrie first tried out "Alice's Restaurant," and Bob Dylan and many others have commanded the iconic tiny stage in the small, homey establishment that opened in 1960.

 

The café is now in "Safe Mode," with even the fabulous online events it has held throughout the pandemic too risky to record. The one-month shutdown follows the death January 12 from COVID of Matt McCabe, owner of Saratoga Guitar and frequent performer at the coffeehouse. The opening image captures his final show, in December.

 

To continue reading, please go to my DNA Science blog at Public Library of Science. 

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The First COVID-19 Vaccines: What’s mRNA Got To Do With It?

Most of us have an intuitive understanding of how a vaccine works: show the immune system a bit of a pathogen, or something mimicking it, and trick it into responding as if natural infection is happening. The COVID-19 pandemic ushered in a flood of vaccine options.

 

When I was writing "How the various COVID vaccines work," which ran here at DNA Science on September 10, I had to keep reviewing summary charts to remember who was doing what. Vaccine technology has gone beyond live, weakened, or killed virus, even past the once-groundbreaking subunit vaccines that present parts of a pathogen, like the hepatitis B surface antigen or pertussis toxin. Now we have DNA and RNA vaccines too, delivered in different ways.

 

The first two vaccines against COVID-19, Tozinameran (the Pfizer/BioNTech vaccine) and mRNA-1273, Moderna's still unchristened candidate on the brink of emergency use authorization, are mRNA. And that's confusing people, based, perhaps, on when they took high school biology (more on that coming). So here's a brief consideration of mRNA and how it can alert the immune system to fight SARS-CoV-2.

 

To continue reading, go to my blog DNA Science at Public Library of Science.

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Are Old Vaccines Helpful Against COVID-19?

The idea that old vaccines might have a role in the fight against COVID-19 has been floated since the early days of the pandemic. Vaccines stimulate the broad, innate immune response, which appears to play a key role in fighting COVID-19. Can the approach bridge the time until entire populations are vaccinated specifically against SARS-CoV-2?

 

Three vaccines dominate the discussion: bacillus Calmette-Guérin (BCG) against tuberculosis; measles, mumps, and rubella (MMR); and oral polio vaccine (OPV).

 

To continue reading, go to MedPage Today, where this article first appeared.

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