Ricki Lewis's Blog, page 3

A Genetic Crystal Ball: When Newborn Genome Sequencing Findings Explain Illnesses in Relatives

In 2019, I wrote about how sequencing the genomes of newborns might compromise their privacy if genetic information was not adequately protected as they grew up. Now five years later, researchers are recognizing a perhaps unexpected benefit of newborn DNA analysis – explaining seemingly unrelated symptoms in relatives.

 

Newborn Screening for Metabolites, not DNA

 

Screening newborns for telltale molecules other than DNA has been around for decades. Blood from a heel prick shortly after birth is tested for various molecules (metabolites) that serve as biomarkers of specific conditions.

 

The Recommended Uniform Screening Panel (RUSP) tests for 61 disorders. The list varies by state (see Baby's First Test). Illinois tests for 57 conditions, for example, and California for 80. Separate programs have expanded the RUSP over the years.

 

The goal of newborn screening is to identify "actionable" conditions early enough to prevent or treat symptoms. But some people see newborn screening as creating "patients-in-waiting," causing anxiety among new parents.

 

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

Anthony Fauci’s Memoir “On Call” Journeys through a Half Century of Plagues Amid the Politics of Public Health

On Call, Dr. Anthony Fauci's memoir, is a riveting read that ricochets through infectious disease challenges since the early 1980s. It concludes with the most insidious of afflictions – the ignorance of how science works that led to threats to his life and the safety of his family during COVID.

 

Dr. Fauci has saved many millions of lives, as a physician-scientist for decades as well as through the legions of medical workers he's trained. And what a joy to read a memoir that the author clearly wrote! I loathe the politico tell-alls that are magically written, edited, and published in mere months, thanks to ghostwriters.

 

On Call was a trip back in time for me. It opens at the dawn of HIV/AIDS, just after I got my PhD in genetics and started my writing career. I've included links to some of my articles, where relevant.

 

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

An “Unsilencer” Drug May Treat Angelman Syndrome – Someday

Angelman and Prader-Willi syndromes are intriguing related conditions. Each arises from missing the same small section of chromosome 15, but one develops if the gap comes from the female parent, the other if it comes from the male.

 

A Peculiar Pair of Disorders

Prader-Willi syndrome is the more distinctive, and therefore more likely to make headlines.

 

A newborn with Prader-Willi is small and struggles to put on weight. A toddler becomes obsessed with eating as metabolism slows precipitously. Frantic parents lock kitchen cabinets, garbage cans, and refrigerators to keep their children from eating until their digestive organs burst.

 

The brain's hypothalamus malfunctions and can't regulate appetite, and so children can't sense when they are full. Plus, their stomachs do not empty quickly enough. The unremitting hunger becomes life-threatening.

 

In contrast, a child with Angelman syndrome has autism spectrum disorder and intellectual disability, an extended tongue, large jaw, poor coordination, and convulsions that make the arms flap. The distinctive facial features led Harry Angelman, when he described the condition in 1962, to call affected individuals "puppet children." In 1982 "Angelman syndrome" replaced the derogatory puppet comparison.

 

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

Michael Crichton and James Patterson’s “Eruption” is Riveting, but with a Shaky Genetic Foundation

I eagerly awaited publication of the novel Eruption, the brainchild of the late, great Michael Crichton and James Patterson, a master storyteller whose trademark staccato sentences and short chapters propel his thrillers. Crichton authored 28 novels, Patterson more than 200.

 

The Associated Press deemed Eruption "a seismic publishing event." Proclaimed BookBub, "an "instant #1 New York Times bestseller was in the cards the moment James Patterson agreed to complete Michael Crichton's partial manuscript!"

 

I can't wait for the film. But the book has a glitch in a genetic explanation. It might seem minor, just a few pages, but the entire subplot of a nefarious government cover-up of a biotech disaster unfurls from it.

 

A Spectacular Hybrid

 

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

Will Coffee Plants Survive Climate Change? Genomes Reveal Clues from the Past

I gaze at the ever-changing Starbucks menu, flummoxed.

 

Should I get a skinny caramel macchiato? A java chip frappucino? Or a plain flat white?

 

The many variations on the coffee theme might suggest a great diversity among the plants behind the drinks, but actually, about 60 percent of coffee is of the Arabica variety. Starbucks uses these beans exclusively, which are grown in only a few places in the world, where pathogens are scarce and climate favorable. Arabica plants are highly vulnerable to many pests and pathogens due to its low genetic diversity, reflecting a long history of inbreeding in small populations.

 

Now re-sequencing the Arabica genome reveals that nature gave us the much beloved plant – not selective breeding by ancient farmers. A research team from the University at Buffalo relate the refined family history of Coffea arabica in Nature Genetics. "With an estimated production of 10 million metric tons per year, coffee is one of the most traded commodities in the world," they write. Nestlé Research funded the project.

 

A Sensor for Climate Change?

 

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

Cave Coronavirus in Wuhan Lab Seeded COVID – The Truth Has Always Been Out There, in the Genetics

When former Director of the National Institute of Allergy and Infectious Diseases, Anthony Fauci testified before a House Select Subcommittee on the coronavirus pandemic on June 3 to share his thoughts about the possible origin of SARS-CoV-2, the idea that sampling from nature and alteration at the Wuhan Institute of Virology returned to the headlines.

 

For those of us who consider viral genome sequences instead of tea leaves, rumors, and politically expedient explanations, the cave origin-lab leak hypothesis is hardly a surprise – the genetic puzzle pieces have fit for quite some time.

 

Ruling Out Alternate Explanations Requires Logic and Science

 

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

Can Engineered Tobacco Plants that Make Human Sugars Improve Infant Formula and Plant-Based Milks?

In an eclectic application of transgenic technology, researchers at the University of California at Berkeley and Davis describe retooling cells of a tobacco relative to produce enzymes required to synthesize the short sugars (oligosaccharides) found in human milk. The work appears in Nature Food.

 

Transgenic Technology

 

Plants have been genetically modified since the 1980s, programmed to produce molecules of use to us. In contrast to the controlled breeding of conventional agriculture, genetic modification inserts or removes specific genes, crafting a plant variant with some use for us.

 

Plants aren't only genetically modified to create or enhance fruits and veggies, or make them easier to cultivate or protect from pests and pathogens, but also to manufacture the enzymes required to catalyze biochemical reactions behind the synthesis of such ingredients as corn syrup, cornstarch, corn oil, soybean oil, canola oil, and even sugars.

 

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

Can Global Genomic Surveillance Forecast the Next Pandemic?

COVID took the world by stunned surprise – but, to quote an old Who song, we won't be fooled again.

 

That's thanks to accelerated genome sequencing technologies, expanded laboratory capabilities, and interacting infrastructure on a global level. These factors are converging to enable both identification of novel infectious diseases as well as microbial resistance, before these threats can impact public health, write a team from the European Society for Clinical Microbiology and Infectious Diseases in Frontiers in Science.

 

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

CRISPR to Reveal How “Water Bears” (Tardigrades) Survive Extreme Environments

Tardigrades are among the weirdest of animals.

 

Also known as "water bears" or "moss piglets," the 1,300 recognized species are the only members of phylum Tardigrada, a term that means "slow stepper" for their somewhat waddling gait. German zoologist Johann August Ephraim Goeze first described the tardigrades in 1773. They live in seas, in fresh water, and on land.

 

Tardigrades are famous for hiding when environmental conditions turn treacherous, only to emerge years or even decades later unscathed. They survive extremes of dehydration, radiation, and great ranges of temperature and pressure. For example, tardigrades live under almost 6,000 times the pressure of the Earth's atmosphere at sea level. They're called "extremotolerant."

 

They live pretty much everywhere, from mountain peaks to beneath glaciers and oceans and lakes, under the leaf carpet of forests, along logs and stones. To see them, collect a bit of lichen or moss and soak it overnight, then squeeze it onto a light microscope slide.

 

We could learn a lot about how tardigrades survive in the extremes. Now a report in PLoS Genetics from researchers at the University of Tokyo describes use of the gene-editing tool CRISPR to better understand the unusual traits of the just-barely-visible tardigrades.

 

Unusual Anatomy and Physiology Enables Survival

 

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

“Extinction” echoes Jurassic Park, with a Pleistocene epoch backdrop

Multiple spoiler alert! 

 

In the classic film Jurassic Park (JP), disasters unfurl at a theme park populated with dinosaurs cloned from reptile DNA in mosquitoes fossilized in amber, with modern frog DNA filling in gaps. 

 

Douglas Preston's new novel Extinction – really De-extinction — riffs on the 1993 Steven Speilberg epic, substituting in genetic material from a half dozen mammals from the Pleistocene, circa 2.58 million to 11,700 years ago. The animals were cloned from DNA in tiny, preserved ear bones, and doctored a bit. 

 

The resulting animals roam a resort nestled into the remote Colorado Rockies, thanks to biotech company Erebus. At sundown, guests gather at a panoramic window in the lodge's lobby to watch the behemoth herbivores wander to a stream, the mammoths especially beloved. 

 

But unlike Jurassic Park's out-of-control carnivores, the Ice Age bestiary boasts only mellow vegetarians: Irish elk, giant beavers and ground sloths, glyptodonts (armadillos), and woolly rhinoceri and mammoths. The rhino is about the size of a Trader Joe's! 

 

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