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Genetic Linkage

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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Menkes Disease Treatment on the Horizon, After Nearly Three Decades

Lucas DeFabio

Headlines often trumpet the latest in gene editing, RNA drugs, or gene therapy. The less buzzy, but more classic strategy of providing a nutrient that a genetic glitch blocks, has been quietly making strides against Menkes disease, which impairs copper absorption. November is Menkes disease awareness month.


Copper Deficiency


Menkes disease results from a mutation in a gene (ATP7A) on the X chromosome, so its affects boys. About 70% inherit the mutation from their mothers, who are carriers. The rest have a new mutation that arises in egg or sperm.


The healthy version of the gene encodes a protein that controls enzymes that shuttle copper from food through the lining of the small intestine into the bloodstream, and into the brain, where copper is vital for neural connectivity. The mineral is also essential for hair growth and pigmentation, which is why Menkes is also called kinky hair disease. Boys have sparse, pale, and twisty hairs.


Aside from the unusual hair, the child seems healthy until about 3 months. Then symptoms become increasingly noticeable: poor growth, developmental delay, seizures, weak muscles, and low body temperature. Many boys die before their third birthdays.


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

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A lucky segment of the population is genetically immune to the COVID virus. What can we learn from them?

In March 2020, Eleanor A. had been sick for several days. Thinking it might be the new respiratory illness going around, she called her internist, who sent her for a COVID-19 test. She was positive. "Results didn't come back for six days, and Jesse and I shared a bed and bathroom during that wait time," she recalled. Both are in their 80s. 


Eleanor's case was harrowing, but fortunately she didn't need to be hospitalized. "I experienced overwhelming fatigue for much of the next ten days. I slept a lot. One night I got up and felt disoriented, hot and cold at the same time, and very unstable. I thought I wouldn't make it to the bathroom or back to bed. I kept calling for Jesse, but he was sound asleep and never heard me."


Fatigue and shortness of breath persisted. Scans revealed lung scarring, but Eleanor slowly recovered.


Through it all, Jesse never had a sniffle, cough, throat scratch or fatigue. Although he'd been beside his wife as the virus invaded her body for days, he never got sick. Later, his blood showed no antibodies against SARS-CoV-2, the virus that causes COVID. That meant that unlike people who are infected but then shake off the virus without getting sick, Jesse wasn't infected in the first place.


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

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A Glimpse of the Ocean’s Twilight Zone Through Environmental DNA

Environmental DNA, or eDNA, gives researchers clues about which species are in that water–and their relative abundance. A WHOI-led study finds that changes in eDNA concentration reveal details of a creature's movement to and from the ocean twilight zone. Natalie Renier © Woods Hole Oceanographic Institution

To most people the Twilight Zone evokes memories of Rod Serling's iconic TV series of the 1950s and 1960s, or the less tantalizing recent reboot. But the Twilight Zone project at the Woods Hole Oceanographic Institution isn't a peek at William Shatner seeing a monster on an airplane's wing or Billy Mumy turning an annoying adult into a jack-in-the-box.


The twilight zone is a layer of the ocean that encircles the planet, from about 200 to 1,000 meters (650 to 3,300 feet) deep. It's also called the mesopelagic or midwater region. The zone is cold and dark, with flashes from bioluminescent organisms that shield them from predators. Pressure reaches 1,500 pounds per square inch. The biomass of fish in the twilight zone may exceed that of the rest of the ocean – but we know little about their distribution.


Residents of the twilight zone range from tiny bacteria and plankton, to fish, crustaceans, squid, and all sorts of gooey variations on the animal theme, like jellyfish and comb jellies. Quadrillions of bristlemouth fish, named for their spiny teeth, live in the zone. And we don't even know how many species have yet to be described. The animals in the twilight zone support the vast food web, moving carbon from the surface to the depths, regulating climate.


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

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