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Genetic Linkage

The Age of the Pangenome Dawns

"Pan" has several meanings.

 

As a noun, it refers to "a round metal container that often has a long handle and a lid."

 

As a verb, it means criticism, like panning a film.

 

Peter Pan refers to an adult who doesn't want to behave like one, from Sir James Barrie's play about the boy who didn't want to grow up

 

As a prefix, "pan," from the Greek, means "all, every, whole, and all-inclusive."

 

Sigmund Freud reportedly used the term pan-sexualism in 1914, to mean "sex as a motivator of all things."

 

In genetics, the human pangenome is a complete reference of human genome diversity. It is envisioned as a new type of map that represents all of the ways that the sequence of 3,054,832 billion DNA base pairs – the building blocks of a genome – vary, plus or minus a few from short repeated sequences. The depiction is so densely packed that it resembles a map of the New York City subway system.

 

The Human Pangenome Reference Consortium is spearheading creation of a "genome reference representation that can capture all human genome variation and support research on the full diversity of populations."

 

 

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

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Nobel Prize to Paleogenetics Rockstar Svante Pääbo Evokes Memories of Being Drawn to Science

One of my favorite places as a child was the American Museum of Natural History. While most kids would rush to the towering dinosaur skeletons, I'd stand, transfixed, at a small glass-enclosed display of skulls and try to envision what their owners had looked like – australopithecines, Neanderthals, a few others. I remember that part of the museum as The Hall of Man; it's now the Hall of Human Origins.

 

Discovering My First Fossil

 

I loved the museum, but yearned to discover things myself. That happened when I was in the fourth grade, and my parents took my sister and me to the Baseball Hall of Fame in Cooperstown, NY. We couldn't have cared less about baseball. But behind the motel, we waded in a stream, where the angle of the sun on the wet rocks revealed striking patterns of stripes. I picked one up, and realized that it wasn't an ordinary rock.

 

It was a fossil. Edith and I spent the weekend collecting.

 

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

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Two Newly-Approved Gene Therapies Cost Millions

The FDA recently approved two gene therapies with hefty price tags, the first for an inherited anemia and the second for a degenerative brain condition. The two new treatments, from bluebirdbio, double the number of gene therapies on the market.

 

Most biotechnologies evolve over three decades or so, but the idea of gene therapy has been around since the late 1950s, blooming soon after Watson and Crick solved the structure of DNA. When my book The Forever Fix: Gene Therapy and the Boy Who Saved It was published a decade ago, it would still be 5 years before the first approval. That treatment, the subject of my book, enabled the blind to see, sometimes in just days.

 

Why has the pace of gene therapy been so slow? Cost is one barrier. Other concerns are the degree to which a gene therapy actually helps, how long the effect lasts, and what proportion of patients respond.

 

A Short List

 

FDA's gene therapy roster is here, but a caveat is necessary.

 

 

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

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Thoughts on a Return of Polio

When a case of polio showed up in Rockland county, just north of New York City, in July 2022, and then polioviruses with the same genetic sequence as from the paralyzed man were found in three samples of wastewater collected from near his home, public health officials were alarmed. The man, from an Orthodox Jewish community with low vaccination rates in general, had not been immunized against polio.

 

Definitions from the World Health Organization kicked in.

 

The viral RNA sequence from the patient was close to that of oral polio vaccine, which is "live" (weakened, aka attenuated). He was infected with vaccine-derived polioviruses (VDPV). Then finding the telltale RNA sequence in wastewater elevated the situation to circulating vaccine-derived polioviruses (cVDPV). The US now joins 30 other nations experiencing a return of this infectious disease that was once thought to be nearly gone.

 

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

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Mellow Yellow: A Biotech Way to Make Saffron

Biotechnology mass-produces valuable molecules from nature, from drugs to textiles to a jellyfish protein that lights up most anything a glowing green. Now add saffron to the list.

 

To cooks, saffron is a bright yellow spice derived from Crocus sativus flowers, aka "saffron crocus." The dried red threads at the blooms' centers are used to season and color foods. Popular for thousands of years, saffron comes today mostly from Iran. It's used to infuse meats, grains, salads, and even to color marshmallows molded into baby chick shapes for Easter.

 

Saffron has medicinal potential. The main pigment crocin may be useful as a neuroprotectant, an antidepressant, a sedative, and an antioxidant.

 

Inspiring a Song

To those of us of a certain age, the word "saffron" conjures up "mellow yellow," a 1966 song by Donovan:

 

I'm just mad about saffron
A-saffron's mad about me …
They call me mellow yellow …

 

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

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Can Curcumin, Black Pepper, and Ginger Treat Retinitis Pigmentosa? Steve Fialkoff’s Excellent Experiment

Steve Fialkoff and I weren't friends at James Madison High School in Brooklyn, NY. We were in the class of 1972; earlier alums include Chuck Schumer, Bernie Sanders, and Carole King. The near-thousand of us self-sorted into three cliques, based on neighborhood. Steve was from Mill Basin, me Kings Highway.

 

While super-popular Steve was everywhere with his massive blond 'fro, capturing our experiences with his camera and leading the class in drama productions, I was on the fast track to nerddom. I spent my time in the chem lab with the groovy new teacher in charge, a 24-year-old who showed my bestie Wendy and me how to make bongs and water pipes. But Steve now says he was a closet nerd, a "frizzy-haired, freckle-faced, big-nosed, crooked-smile, toothy guy."

 

It wasn't surprising that Steve became a film editor and now a playwright. What was surprising was learning at age 25 that he had retinitis pigmentosa, after he tripped over a seat in a darkened theater and had a few other stumbles.

 

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

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DNA Analysis Solves the Mystery of the Rabbit Invasion of Australia

COVID and monkeypox seem to have come out of nowhere and exploded across continents. But the phenomenon of natural selection acting on genetic variants – of viruses or organisms – that have an advantage in a certain place and time is ages old. The rabbits of Australia provide a powerful example of natural selection run amok, favoring a particularly robust mix of domestic and wild traits against an environmental backdrop of plenty of food and a paucity of predators.

 

The animals that have overrun the continent eat almost any plant, their appetites reverberating along food webs, costing an estimated $200 million a year. Over decades, interventions to control their numbers – from rabbit-proof fences to intentional infections with nasty viruses to shooting – have all failed. "In Australia, the rabbit has survived drought, fire, flood, diseases, predators, poisons and other stratagems devised by man and remains this country's most serious vertebrate pest," wrote Brian Coman in "Tooth and Nail: The Story of the Rabbit in Australia."

 

Now researchers from the University of Cambridge and CIBIO Institute in Portugal have wed genetics to history to illuminate the precise source of Australia's problem. Their report is in the Proceedings of the National Academy of Sciences.

 

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

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Revising my genetics textbook: A PC exercise or an appropriate evolution of science and sensitivity? Or both.

Beyoncé is facing a lot of criticism for using an ableist slur in her new co-written song Renaissance. She used the word "spaz" twice in a derogatory reference to a neurological disorder in Heated, which dropped in late July.

 

Just a few weeks before, while promoting her new song GRRLS, Lizzo used the same slur. The tweet went viral, prompting a sharp rebuke by Hannah Diviney, who has cerebral palsy. Her tweet also viral, landed on the front page of the BBC, New York Times and the Washington Post. 

 

Lizzo took notice and changed the lyrics. "I never want to promote derogatory language," she wrote.

 

I've lapsed too in word choices, but I'm not a pop star – I write college life science textbooks. I'm currently revising the 14th edition of my human genetics textbook. I've written or co-written four textbooks, totaling 38 editions: intro biology, human anatomy and physiology, and human genetics. Other authors have taken over all but human genetics: I update it every three years. 

 

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

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Where Will the Next Pandemic Come From? Highlights from CDC’s Emerging Infectious Diseases

When monkeypox came from out of nowhere in the spring, it sounded like a joke to our collective COVID-fatigued brains. I think we've all got CDC fatigue too. When revised recommendations recently told us it was okay to do or not do what we've been doing or not doing for months, I don't think many people paid attention. I'm glad the agency is finally re-evaluating things.

 

What may not be as well known is that CDC publishes an excellent, open-access, international, peer-reviewed monthly journal, Emerging Infectious Diseases. Since 1995, EID has provided a window into future health concerns, for us and other animals, with historical and cultural background as well as current epidemiology, covering all sorts of things.

 

Underlying the research reports on eclectic infectious diseases in the journal are a set of shared and converging factors:
• global climate change shifting habitats
• metagenomics technology comparing genome sequences in environmental samples
• perhaps we're looking harder
• a much more epidemiologically literate public than pre-pandemic

 

So I thought I'd investigate the August 2022 issue of EID. The focus is zoonoses – diseases that jump from non-human animals to us.

 

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

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OrganEx Revives Pigs an Hour After Death, Holding Promise for Transplants

Transplant medicine could take a giant leap forward if donor organs could soak up oxygen for longer and decay delayed. A technology called OrganEx, described in Nature from a team at Yale, promises to do just that. The researchers stopped the hearts of pigs and an hour later used OrganEx, then cataloged the return of bodily functions. The new approach far exceeded the ability of existing technology to prolong organ viability.

 

Popular Pigs

Pigs have long been a popular animal model of human disease because they are about our size and their hearts and blood vessels are quite similar. They have also had fictional roles in medicine.

 

 

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

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