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Genetic Linkage

Designing a Better Probiotic. CRISPR Hubris?

Every morning I pop a Pearl probiotic. I try hard not to drop it, for the tiny, slippery yellow sphere bounces, is impossible to pick up, and cats love to bat them into unreachable domains.

 

A probiotic is, technically speaking, a population of live microorganisms that confers health benefits on the multicellular organism that they inhabit – such as a human. Probiotics alter the bacterial, viral, and fungal milieu within and on us – our microbiomes – in ways that ease digestion, counter inflammation, strengthen the gut lining, affect brain function, and even squelch tumors.

 

Each Pearl – or other variation on the probiotic theme – delivers billions of Lactobacilli to the twists and turns, nooks and crannies, of the human host's intestines, maintaining the microbial community within and keeping digestion flowing along smoothly. Other commonly used probiotics are Bifidobacterium and the yeasts Saccharomyces cerevisiae and boulardii.

 

Borrowed from Bacteria

 

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

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Transmissible Alzheimer’s Disease? Long-Ago Growth Hormone Treatment and a Legacy of Cannibalism and Mad Cows

A stylized slice through an Alzheimer's brain depicts amyloid-beta plaques in brown and tau tangles in blue.

Five people treated for pituitary dwarfism decades ago with human growth hormone (hGH) pooled from cadavers have shown cognitive decline reminiscent of early-onset Alzheimer's disease. Their dementia likely arose from transmission of the bits of amyloid-beta protein that lie behind Alzheimer's delivered along with the needed hormone, initiating a molecular chain reaction that led to brain effects decades later. Recombinant DNA technology has since provided a pure source of the hormone.

 

The cognition decline in these people is iatrogenic – caused by a medical procedure. The pooled hGH included infectious proteins, called prions (pronounced "pree-ons"), short for "proteinaceous infectious agent." The research appears in Nature Medicine from long-time prion researcher John Collinge, director of the University College London Institute of Prion Diseases, and colleagues.

 

The team followed 8 patients. Two of the five with clinical signs of Alzheimer's died during the investigation, and autopsy revealed the telltale brain changes. Two other patients had mild cognitive impairment, and the eighth had no symptoms. None had mutations that cause Alzheimer's disease, ruling out genetics as a cause.

 

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

 

 

 

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Chewing Gum Reveals Stone Age Diet and Disease

Did Barney Rubble and Fred Flinstone chew gum?

 

We can learn about life, past and present, anywhere we find DNA and determine its sequence. DNA Science has described intriguing sources of environmental DNA, aka eDNA: DNA in Strange Places: Hippo Poop, Zoo Air, and Cave Dirt and A Glimpse of the Ocean's Twilight Zone Through Environmental DNA.  

 

Human remains also harbor bits of DNA that can reveal how people lived long ago.

 

A recent report in PLOS ONE analyzes DNA from an adenovirus and a herpes virus discovered in preserved feces – coprolites – from 5,500 to 7,000 years ago at an archaeological site in Japan. The findings suggest that those people might have suffered from similar infections to humans today.

 

A second recent report uncovers clues in preserved chewing gum, reminding me of Flintstones gummy vitamins. (See A Brief History of Flintstones Vitamins). 

 

About 9,700 years ago, a group of teens were hunting, gathering, and fishing along the western coast of Scandinavia, north of what is today Göteborg. They chewed a concoction of hardened birch tar, the preserved lumps bearing bitemarks that suggest the stuff was used as a chewing gum of sorts, perhaps also as an adhesive in construction. An international research team published their findings on the Mesolithic gum in Scientific Reports.

 

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

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Multi-cancer Early Detection Blood Tests (MCED) Debut

A 52-year-old woman is at her annual physical exam. The physician assistant mentions he'll need two extra vials of blood for new cancer screening tests, one just FDA-approved, the other available as part of a clinical trial.

 

"But I already get mammograms and colonoscopies based on family history, and my husband gets his PSA screen for prostate cancer every year. So far, so good. Why do I need these new tests?" the patient asks.

 

"They can catch cancers much earlier, from DNA and proteins in your blood plasma, the liquid part. Including cancers much rarer than breast, colon, and prostate."

 

"Sure," says the patient, rolling up a sleeve. She'd be one of the first to have "multi-cancer early detection" – MCED – blood tests that zero in on clues that cancer cells shed into the bloodstream. A treatment begun early is more likely to work. An MCED blood test could be a gamechanger for people who haven't had cancer.

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CRISPR Tackles Diverse Single-Gene Conditions

The end-of-year FDA approval of the first CRISPR-based therapy, for sickle cell disease, came a mere dozen years after Jennifer Doudna and Emmanuelle Charpentier introduced the technology. They shared the Nobel Prize in Chemistry in 2020.

 

CRISPR is one of the better abbreviations in genetics. It's certainly more memorable than RFLPs, GWAS, and even SNPs, so euphonious that few reports – technical or otherwise – actually use the term "clustered regularly interspaced short palindromic repeats." CRISPRs are short DNA sequences, peppered with repeats, that latch onto DNA-cutting enzymes, commandeering and directing them to snip certain parts of a chromosome.

 

The genomes of certain bacteria naturally harbor CRISPR sequences. The microbes deploy them to dismantle the genetic material of infecting viruses, a little like an immune response.

 

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

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The 500th Blog Post at DNA Science: In Celebration of Vaccines

A few weeks ago, I noticed a surprising metric when posting my weekly DNA Science blog – at year's end, I'd hit #500!

 

That got me thinking. Looking back, which blog post was the most important? The answer came to me quickly – but it's not what I would have expected when I began more than a decade ago.

 

The Birth of DNA Science

 

When St. Martin's Press was about to publish my book about gene therapy in 2012, my agent urged me to start blogging. I needed to widen my audience beyond college students forced to buy my textbooks and readers of the articles I'd been cranking out since the 1980s.

 

The book that kickstarted DNA Science was The Forever Fix: Gene Therapy and the Boy Who Saved It. It's a history of gene therapy told through the voices of the patients, families, researchers, and clinicians behind the first FDA approvals, which didn't come until 2017.

 

I launched a website and blog, "Genetic Linkage," through the Author's Guild. Soon, an editor at Public Library of Science asked me to post Genetic Linkage at PLoS. We renamed it DNA Science.

 

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

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Perfume from Extinct Flowers, Thanks to Ancient DNA and Synthetic Biology

"Enchant your loved ones with nature's lost scents, revived through biotechnology and perfume artistry."

 

When that popped up on Facebook, I was intrigued. So I clicked.

 

"Meet Invisible Woods: a clean, refreshing scent revived from extinct flower DNA," beneath an image of "origin flower" Wendlandia angustifolia.

 

A quick search revealed that this plant had been presumed extinct, until one popped up in a 1998 survey of its natural habitat in Tamil Nadu, India. Invisible Woods is not really "revived," but "reimagined," using clues from ancient flowers and the tools of biotechnology.

 

Future Society offers six fragrances inspired by past plants, for $98 per 50 milliliters (a little under 2 ounces) or a $35 sampler ideal for a stocking stuffer. Boston-based Ginkgo Bioworks provides the expertise in genetics.

 

I don't use scented products other than Pine-Sol, so this was all new to me. DermNet defines "fragrance" as a combination of organic compounds that produces a distinct smell, whereas a perfume is a liquid mixture that emits a pleasant odor, and oilier than a fragrance. I don't exactly get the distinction, but apparently perfume is the oilier of the two and perfume, cologne, and aftershave are all fragrances.

 

Before I dig into the science, I'll relate taking a quiz on the Future Society website that would help me choose a product. I clicked on the "friend" option, my bestie, Wendy. 

 

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

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Why Cats Sniff Each Other's Butts

Anyone who lives with more than one member of Felis catus knows that our beloved felines love to smell each other's anal regions. Now a research team from the Department of Evolution and Ecology and Genome Center University of California, Davis, explains why, with their cataloging of the microbiomes of domestic cat anal glands. The bacterial members of the microbiome produce and release organic compounds that affect the behavior of another cat. The findings are published in Scientific Reports.

 

A microbiome is the collection of microbes that live in or on an organism. The microbiome accounts for 90 percent of a person's cells, packed in because bacterial cells are so much smaller than ours. These microscopic residents live under our arms, between our toes and butt cheeks, in our guts and noses and spleens and eyebrows and, well, everywhere.

 

The new cat study compared the DNA sequences of a gene commonly used in evolutionary investigations, to identify bacterial species residing in domestic feline anal glands. The investigators also identified the "volatile organic compounds" (VOCs) that the anal glands emit, thanks to those microbes. The study evaluated anal gland emissions of several other mammals, including dogs, hyenas, foxes, pandas, and of course humans.

 

An Explanation from Microbiology

 

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

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Breeding Better Butternut Squash – and a Recipe

After a long career as a science writer, textbook author, and genetic counselor, I've become an accidental authority on squashes.

 

I began volunteering at the largest food pantry in my small city in June 2020, where my husband Larry had been in charge of the plant and fungal kingdoms for years. It was the height of the pandemic. So gloved and masked, we shoved fruits and veggies into plastic bags, filled shopping carts with the bags, and wheeled them over to a window at which another masked, gloved volunteer quickly pushed the bags to the clients waiting outside.

 

Like most activities back then without human contact, it wasn't much fun.

 

Nowadays, Larry and I help the clients choose fruits and veggies, and I share cooking and storage tips as well as recipes. I love the challenge of figuring out how to prepare something unfamiliar – plantains, Jerusalem artichokes, broccoli rabe.  

 

My favorite client is a 95-year-old Ukrainian woman. I know which days she'll show up with her helper, so I assemble bags of bountiful beets so she can make borsht for her congregation. Schenectady has a large Guyanese community, and the ladies with whom I share tips and recipes call me "mommy." I tell our Black clients how to make stuffed cabbage; they share how to cook collards.

 

But I'm still a biologist at heart. Here at DNA Science a few years ago, I shared The Peaceable Genomes of Pumpkins.

 

For this year's Thanksgiving post, I came upon an article, Genomic Prediction and Selection for Fruit Traits in Winter Squash, published in G3: Genes, Genomes, and Genetics, from Michael R Mazourek of Cornell University and colleagues, from 2020.

 

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

 

 

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The Dawn of Molecular Genetics: A Glimpse of History in a Textbook from 1952

The email from my former neighbor Shaun Kuczek was unexpected.

 

"Hi Ricki! My Dad passed in July, and we're cleaning out his house. He was a biology teacher for 35 years and I have 40 or so old biology textbooks. I remember that you write biology textbooks, and maybe you have an idea of a way to pass them along? They're all old, 1950s, 1960s. If you think of anything, please let me know."

 

Bernie Kuczek had been 91. In addition to teaching high school biology and chemistry and coaching baseball, Bernie's claim to fame was being drafted by the Brooklyn Dodgers and sitting alongside Jackie Robinson in the dugout. Alas, a broken leg ended his baseball career. Bernie served in the Korean War and worked summers as a fisheries biologist.

 

Treasure from 1952, Just Before Watson and Crick's Paper

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