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Genetic Linkage

Yellow Mealworm Genome Sequence May Ease Farming Insects for Food

I have a special fondness for the yellow mealworm, Tenebrio molitor.

 

As a child, I fed the mealworm stage of this beetle to my pet chameleon.

 

As a teen, I babysat for a family that owned a pet shop. The house was filled with animals, and I was thrilled to be there. That is, until right before bedtime.

 

As I was trying to get the kids upstairs, a monkey grabbed a can, leaped atop a curtain rod, whipped the top off, and happily sprayed dozens, perhaps hundreds, of writhing, fat, pale mealworms all about the living room. It was great fun collecting them.

 

Then a few days ago I got a news release from Paris-based Ynsect. The company's goal: to farm massive numbers of yellow mealworms as food for humans. And I instantly remembered the creatures festooned around that long-ago living room.

 

Ynsect's good news was that the yellow mealworm's genome had finally been sequenced. Thank goodness! It was a tough one to crack.

 

Eating Mealworms

 

Farming yellow mealworms for food makes sense.

 

To continue reading go to my blog DNA Science.

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Omicron Evolves and the Covidization of Scientific Publishing

Just as we thought Omicron was rolling across the US and into oblivion, a new "subvariant" has arrived and is, again, taking over. At the same time Moderna is announcing dosing of the first participant in its phase 2 study of an Omicron-specific booster. But Omicron's evolution wasn't unexpected – the World Health Organization's recent update cites four lineages of Omicron, dubbed BA.1 through BA.4.

 

"So it goes," to quote Kurt Vonnegut in Slaughterhouse Five. But that statement was in response to death among the Tralfamadorians – not the robust activity of a tiny virus.

 

It seems to me that the continual categorization of SARS-CoV-2 reflects the human urge to group, categorize, and name things to help us understand them. I think the situation is eventually going to dissolve into a continuum of genetic flux as the tango of mutation and selection continues. That's what nucleic acids do.

 

Since it still new days for Omicron 2.0, here's a snapshot:

 

WHAT WE KNOW 

 

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

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Will parental vaccine hesitancy retard the embrace of life-saving newborn genetic screening and emerging gene therapy revolution?

In these days of the never-ending pandemic, other health problems continue to take a backseat. That's especially true for the 7,000 or so rare diseases that collectively affect only one in ten people, while the number of COVID fatalities in the US nears the million mark. 

 

Although some clinical trials for rare disease treatments have stalled, they'll resume once COVID settles into some version of endemicity. More than 60 cell and gene therapy FDA approvals are expected by 2030, according to the Massachusetts Institute of Technology's New Drug Delivery Paradigms Initiative. They range from RNA-based drugs to gene therapies to CRISPR fixes.

 

Rare diseases tend to strike the youngest. Clinicaltrials.gov hints at what's to come.

 

CRISPR is tackling sickle cell disease and thalassemia, while antisense technology is being tried for Duchenne muscular dystrophy. Searching for "gene therapy" brings up 5000 hits for this older approach, many targeting childhood diseases.

 

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

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DNA in Strange Places: Hippo Poop, Zoo Air, and Cave Dirt

Many years ago, a dear friend took me to the Detroit zoo to see the Hippoquarium. Much to my delight, the resident hippo positioned her rear to the glass of the enclosure and let loose, her whirring tail distributing the intestinal contents like blowing on an open milkweed pod.

 

A few years later I saw the same demonstration at the Tampa zoo, a hippo's whirligig-of-a-tail in action.

 

Hippo Microbiomes

 

Recently, researchers from the US and Kenya described in Scientific Reports their investigation of the ejection of hippo feces into the pools of the Serengeti's Mara River. A more natural environs than a zoo, the river is home to more than 4,000 hippos wallowing in some 170 hippo pools in the Kenyan part of the territory.

 

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

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Pandemic Predictions Take a Turn Towards the Positive – Finally

An end may be in sight. For the first time since the pandemic began, I listened to a press briefing from medical experts that did not give me nightmares.

 

It was December 11, 2022, the weekly zoom from the Massachusetts Consortium on Pathogen Readiness (MassCPR). The group of eloquent experts formed at the dawn of the pandemic. They've held sporadic briefings for journalists over these many months, ramping up to weekly as Omicron loomed in early December.

 

From JAMA to MassCPR

 

At the beginning, I was a fan of the online Conversations with Howard Bauchner, who was then editor-in-chief of the Journal of the American Medical Association. Dr. Bauchner's laid-back manner got the superstars of the pandemic – from Anthony Fauci to Rochelle Walensky to Paul Offit – to relax, in an environment far from Clorox-pitching presidents and the like. Those were the days when the experts talked of the goal of herd immunity. I suspect none of them imagined that so many people would shun life-saving vaccines and even make the decision political, endangering us all and providing fertile ground for Omicron and the other variants to evolve, emerge, and threaten us in new ways. I know it blindsided me.

 

 

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

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Please Help My Liberian “Son” Achieve his Dream as an Infectious Disease Physician

For many years I've ended editions of my human genetics textbook with a request for students to email me to share their thoughts on what they'd learned. Only one student has ever contacted me.

 

Emmanuel Zoboi Gokpolu was in high school in Monrovia, Liberia, when he emailed me at the end of his genetics course, in 2007.

 

My husband Larry and I quickly developed a friendship with Eman; he calls us Mom and Dad. We sent him a package of Obama tee shirts, which he distributed to his family. Free people of color from the US founded an independent Liberia in 1847, so there was a connection.

 

I recognized something special in Emmanuel right away, a love of biology and a compelling interest in health care and helping people. Larry and I supported him through college and then we encouraged him to go to medical school – fulfilling a dream of mine (bad chemistry grades kept me from applying).

 

Med school in Liberia was going well, until Ebola struck in 2014. With half the instructors dying and classes halted, Eman led medical students in carrying out public health measures. He organized a group called "Determined Youth for Progress" to sensitize rural communities to Ebola awareness and prevention measures, sent text alerts, and did contact tracing.

 

He told his story during the Ebola crisis here at DNA Science, in Eman's Emails from Liberia: Through September and then Eman Reports from Ebola Ground Zero. During that time, instead of paying his tuition, we sent support for gloves, detergent, bleach, and long sleeve shirts to keep him and his family as safe as possible.

 

Reading over that first post about Eman now gives me chills, in the context of COVID. Eman wrote on August 6, 2014:

 

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

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Sandy From the Mountains Dies, Leaving a Message to the Unvaxxed

Five days ago, Sandy's husband allowed the staff in the ICU to turn off her life support, and COVID claimed yet another.

 

Sandy and her husband lived in a cabin nestled into a mountainside in a small town in the Rockies, next door to my daughter Sarah. I met Sandy last March, when Larry and I and our daughter Carly visited.

 

I'd heard about Sandy, how she helped Sarah deal with encroaching wildfires right after she moved in. But she wasn't what I expected.

 

Sandy looked younger than her 70+ years and remarkably like Stevie Nicks, pretty and vibrant and warm, with glimmering white-blond hair and beautiful permanent makeup that accentuated her eyes. She was owl-like. Her husband reminded me a little of a rumpled, flannel-shirted Eddie Vedder, or James Taylor with much better hair, an aging yet striking rock star couple.

 

We all clicked. Two friends dropped by, and we held an impromptu seder on that first night of Passover. We sang the traditional songs to our new Christian friends – Dayenu, Let My People Go – then inexplicably listened to Led Zeppelin's "Ramble On" playing on repeat.

 

It was exciting to gather after months of lockdown. Vaccination had just begun, and so my husband and I, our ages a risk factor, were the only ones who were fully protected. The neighbors weren't, tragically believing their isolation would keep them safe, although Sandy's husband went into town for work.

 

We all tried to warn them.

 

Sandy knew I was a biologist and wanted to know more about the vaccines, so I explained how they work. I told her that I couldn't imagine how a vaccine could be more harmful than the threat of what the virus could do. She asked insightful questions, many of them, but still looked skeptical.

 

And that triggered my younger daughter.

 

Carly tried to hold it in, but couldn't. And so she tearfully poured out what she had seen from her sixth-story window in Astoria, Queens during those horrid months as winter turned to spring in 2020, as the white-shrouded bodies were stacked up at the ambulance bay of the hospital right next door, like bleachers of death. It's an image she nor the rest of our family can never unsee.

 

But to Sandy, in her cabin in the woods, an inner city hospital must have seemed a million miles away. In March 2020, the mantra "it can't happen here" was still playing in many parts of the country.

 

Sandy remained unconvinced. Unvaxxed. I can only imagine where she got her information. Sarah persisted in offering to take her to get vaccinated, through the summer. But then Sandy cut her off completely over the issue, silencing Sarah's good intentions. Until that time, Sandy and I had talked and texted. We liked the same books, bands, and TV shows. We bonded. I considered her a friend.

 

Two weeks ago, Sandy got COVID. Her husband had brought it home.

 

I knew that Sandy wasn't stupid and that she knew biology – during the conversation on Passover she'd mentioned mitosis, cell structure, DNA. I see now that when it came to vaccination, she was simply scared. And her fear and denial cost her her life.

 

Statistics on the never-ending pandemic become obsolete almost as soon as they are compiled these days. It is undeniable that most COVID deaths are among the unvaxxed. There's no more hiding in the woods, especially now with omicron and its off-the-charts transmissibility.

Still, an astounding fifteen percent of the overall US population refuses vaccination, the percentages distributed unevenly among the states.

 

It is unfathomable to me that anyone could compare the graphs of hospitalizations for the protected versus the unprotected, the vaxxed a line hugging the X axis at the bottom and the unvaxxed a hockey stick of frightening exponential growth, and remain unconvinced.

 

I'll admit that I never saw this coming, the vaccine hesitancy that has catalyzed COVID, not only enabling a deadly virus but giving it room to evolve. The pandemic wasn't a surprise, as I suspect it wasn't to many other biologists. And I've always thought herd immunity – not a new idea – was more a theoretical ideal than an achievable goal in the real world. But I never imagined the politicization of a national public health crisis stemming from an infectious disease, nor the fear that spawns willful ignorance.

 

I'm trying now to understand why Sandy died, why she thought the government was trying to take away a "right" by offering, at no cost, something that could prevent her death. It's too late for Sandy, but perhaps someone will read this post and go roll up a sleeve. I can't wrap my head around the glaring fact that thousands have made the same stubborn choice as Sandy.

 

But Sarah found some closure the day after Sandy died, last Sunday. She and a friend were hiking in the spectacular mountains that are the backdrop to the log homes, some built onto cabins going back a century. She texted us images of a tree with a small, perfect, owl sitting on a lower branch.

 

"Last night! It was so beautiful, little, white, we got really close to her and she just stared right back for awhile. I know this sounds crazy but it felt like Sandy coming to see me! I really felt that and cried and said everything I wanted to say to Sandy, that I was sorry she was misled, sorry she suffered. And when I finished, she flew off."

 

So RIP Sandy from the Mountains who looked like Stevie Nicks.

 

"And I saw my reflection in the snow-covered hills
'Til the landslide brought me down."

 

May your story save lives. We have the tools to hold off the landslide.

 

 

Originally posted at my blog DNA Science at Public Library of Science.

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Pandemic Too Fast to Follow as Three Waves of Infection Wash Over the US: Delta, Omicron, and Flu

Next Tuesday, December 21, marks two years since the China CDC Weekly acknowledged the first "cluster of pneumonia cases with an unknown cause … in Wuhan."

 

On the Origin of COVID

 

Half of the two-page report from China is an illustration of seven colored ovals, each enclosing symbols for closely-related viruses. Within one oval, 3 of the 7 viral lineages bear asterisks. The trio includes what was then called 2019-nCoV.

 

In that initial report, China claims that the origin of the novel coronavirus "is still being investigated … all current evidence points to wild animals sold illegally in the Huanan Seafood Wholesale Market."

 

That's a little like saying the Beatles came from Hamburg because they played there often in their early days – rather than from Liverpool.

 

An alternate hypothesis of the possible origin, based on genome sequence evidence, unfolds in a report on bats from Cambodian caves collected in 2010, published recently in Nature. Predecessors of SARS-CoV-2 might have arisen in many places, such as southeast Asia, where investigators weren't looking. (I covered the bats in April when the study appeared in preprint form – the pandemic has instilled a never-ending sense of déjà vu to science journalists.)

 

The Cambodian bats are the closest known relatives to the enemy, yet they are curiously missing the precise part of the genome that encodes the region of the spike protein that the virus uses to grab onto and slip into our cells. Coincidence? Perhaps. Genetic material is well known to flit from genome to genome, crossing what we humans call species boundaries. But there are other hypotheses.

 

As Fox Mulder said often in The X Files era, the truth is out there. But we may never know it.

 

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

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Learning about early human development from an aborted embryo

wo weeks after sperm fertilizes egg is a critical time in human prenatal development. Intricate waves of signals stamp cells with their eventual fates as part of a particular organ. But studying such early-stage human embryos is both technically and bioethically complex. 

 

Now a report in Nature from researchers in the UK and Germany provides an unprecedented view into the early human embryo – thanks to a woman who donated one after having an abortion. She donated through the Human Developmental Biology Resource, which provides automatic bioethical approval from the Institute of Human Genetics, Newcastle and the Institute of Child Health, London.

 

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

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How Watson and Crick Predicted the Origin of Omicron and Laid the Groundwork for COVID-19 Vaccines

The tantalizing final sentence to James Watson and Francis Crick's landmark 1953 paper in Nature introducing the genetic material, DNA, is almost as famous as the report itself:

 

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

 

That copying mechanism gone awry spawns the mutations that create new viral variants.

 

Mutation, Natural Selection, and Recombination, Oh My!

 

Like Dorothy of Wizard of Oz fame exclaiming "lions and tigers and bears, oh my!" three major forces of nature set the stage for genome evolution: mutation, natural selection, and recombination.

 

The virus we're battling has a single strand of RNA for its genetic material, and not the more familiar double-stranded DNA. But an RNA genome must also replicate – copy itself – when one virus becomes two. And mistakes, mutations, can happen when they do so, like perpetuating a typo when copying a document.

 

"Every chance a virus has to replicate it can come up with a new strategy to evade the immune system," said Bruce Walker, MD, Director of the Ragon Institute of MGH, MIT and Harvard, at a recent press briefing of the Massachusetts Consortium on Pathogen Readiness (MassCPR). That's too teleological an explanation for me – a virus doesn't intentionally change itself into a fitter form. Instead, mutations tend to arise at genome locations where the sequence is repetitive, like CGCGCGCG compared to ACGCCUCGAU. It's easier to mistype when "the" is next to "they" in a document, compared to "hippopotamus" next to "diarrhea."

 

 

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

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