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Genetic Linkage

COVID-19 Vaccine Will Close in on the Spikes

As epidemiologists try to stay ahead of the spread of new coronavirus COVID-19, vaccine developers, like Sanofi and Johnson & Johnson, are focusing on the "spike" proteins that festoon viral surfaces. Following clues in genomes is critical to disrupting the tango of infectivity as viruses meet and merge with our cells.

 

Vaccine developers look specifically to the molecular landscapes where viruses impinge upon our respiratory and immune system cells. Targeting COVID-19 is especially challenging, because efforts to develop a vaccine against its relative, the SARS coronavirus (SARS-CoV), elicit only partial responses. But those steps are now serving as jumping off points for pharma.

 

The relationship between viruses and humans can seem like a science fiction plot. The viruses that make us sick may be little more than snippets of genetic material borrowed, long ago, from human genomes. Packaged with their own proteins, viruses return to our bodies, taking over to make more of themselves.

 

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

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Will scientists ever get ahead of fast-mutating deadly health viruses? Exploring the coronavirus and the genetics of other viral outbreaks

While COVID-19, the novel coronavirus, dominates health news headlines, less exotic viral foes are still around: influenza, the rhinovirus, adenovirus, and respiratory syncytial virus behind the common cold, norovirus outbreaks aboard cruise ships, and always hepatitis and HIV.

 

What these viruses share is RNA as their genetic material, a nucleic acid less familiar than DNA. Among the RNA viruses are also West Nile, chikungunya, and those behind Ebola and Marburg hemorrhagic fevers, dengue, rabies, and yellow fever.

 

When science writer David Quammen made the media rounds recently to discuss COVID-19, he skipped the RNA part – "don't worry about that right now." But his excellent book Spillover: Animal Infections and the Next Human Pandemic, which charts the predictions of the current situation starting nearly a decade ago, details the significance of RNA viruses.

 

RNA is a nucleic acid like its cousin DNA, but has uracil in place of thymine as one of the four nitrogen-containing bases that carry each molecule's encrypted information. RNA's sugar – ribose – has an oxygen atom in a place that DNA's deoxyribose doesn't. DNA is the same in every cell of an individual, whereas shorter and shorter-lived RNA molecules carry out the specific DNA instructions that sculpt different cell types and functions.

 

The inability of RNA to repair itself, as DNA can, allows mutations to accrue in RNA viruses, enabling them to replicate wantonly and spread explosively. And our bodies help them. New viral particles spew from coughs and sneezes, are propelled in vomit, and ooze from blood and diarrhea, often before our immune systems begin to respond.

 

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

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A Fruit Fly Love Story: The Making of a Mutant 2020

For Valentine's Day, I offer a fly's eye view of my PhD research on the mutation Antennapedia, which replaces fruit flies' antennae with legs. 

 

"The Making of a Mutant" initially appeared in this millennium at Scientific American blogs in 2012. But I wrote it in 1978, sneaking it into a manuscript bound for the journal Genetics to see if my mentor, Thom Kaufman, was paying attention. He was. My story was referenced at his retirement party, generations of genetics grad students at Indiana University having read it.

 

The story started as a joke, "fly porn." But over the years it has morphed into a metaphor for our times. It's a little like this year's Academy Award winning film Parasite being much more than the crazy narrative it at first seems, instead a simmering statement on classism.

 

Today, Anton O. Pedia's tale of being different is more timely than ever, as the increasing mixing of people of different ancestries hurtles forward against a frightening new backdrop of hatred, division, marginalization, and dehumanization. As the flies find out, the perception of being different is transient. Life is all about context.

 

The events and facts reported here are all accurate, to the best of my knowledge.

 

CHAPTER 1

 

She knew she was different long before her mother had told her the truth. A sensitive youngster, she could tell from the sneering glances of her neighbors that she was, somehow, not quite like them.

 

To continue reading, go to DNA Science.

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The Giant Squid Genome Holds Surprises

I've been thinking about invertebrates often lately, and so was delighted to learn that the genome of the giant squid has been sequenced. I'll never tire of reading new genome papers.

 

One of the largest animals known, the giant squid is also one of the most elusive, appearing to us mainly as body parts sporting telltale suckers that have washed ashore. A full grown giant squid can't be comfortably stuffed into an aquarium tank. So most of us know about it from fiction.

 

Giant Squid in Culture

 

The giant sea monster of Scandinavian folklore, the Kraken, terrified sailors in vessels along the coastal waters of Norway and Greenland. It was likely a giant squid, as was Homer's tentacled Scylla in The Odyssey. Jules Verne's 20,000 Leagues Under the Sea, written in 1869, famously featured the animal.

 

More recently, the 2005 film The Squid and the Whale evokes the image of a giant squid battling a sperm whale depicted in a mesmerizing diorama at the American Museum of Natural History. Director Noah Baumbach borrowed the image as a metaphor for the battling parents of his young protagonists.

 

True squid stories are intriguing too.

 

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

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New View of the Brink of Cancer May Validate Preventive Mastectomy

Women who have prophylactic mastectomies to stay ahead of a BRCA2 mutation may have made a wise choice, according to findings of a study just published in Science Advances.

 

Inheriting a BRCA2 mutation brings a 50 to 80 percent lifetime risk of developing breast cancer. But how does that population statistic shake out at a personal level? Is an individual among the 20 to 50 percent who won't develop the cancer? If not, how long can she safely delay surgery until just before the first inklings of cancer arise?

 

There's no crystal ball that can predict when cancer will begin, but Leif W. Ellisen and colleagues at the Massachusetts General Hospital Cancer Center are coming close. Their clever study detects genetic changes that happen before the effects of the underlying BRCA2 mutation kick in.

 

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

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What’s your ‘ageotype’? Classification system explains why some of us are older—or younger—than we look

We hardly need another way to classify people, and especially not another metric of the biological fallout from the passage of time. The mirror does a pretty good job of doing that, highlighting spreading wrinkles and graying or disappearing hair.

 

Medical tests track various ups and downs as the years go by. Triglycerides, cholesterol, and blood pressure rise, while vision, hearing, taste and smell, joint flexibility, muscle mass and bone density fall. Deep within our cells, chromosome tips whittle down as DNA errors accrue.

 

The "ageotypes" described in a new study from researchers at Stanford University may help health care providers add a dose of precision medicine to the one-size-fits-all approach that still pervades many a clinical encounter. The findings of the new study appear in Nature Medicine.

 

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

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The Wuhan Coronavirus Inspires a Look Back at the Discovery of Viruses

I'm astonished at the speed with which geneticists and epidemiologists are zeroing in on the Wuhan coronavirus.

 

Nomenclature is still up in the air. The first name, "2019-nCoV" for "novel coronavirus first seen in 2019," is descriptive but not easy to remember. "Wu Flu" isn't correct – it's not a flu virus, nor is "Wuhan SARS" quite right because the new pathogen's genome isn't exactly like that of SARS.

 

I'll call it the Wuhan coronavirus until the World Health Organization decides on a name. WHO avoids places in disease names to avoid stigma, although I don't see the Rocky  Mountains suffering from lack of visitors due to the spotted fever that takes it's name (which isn't viral, but still).

 

Two Weeks to a Genome Sequence

 

Awareness of the new infectious disease began as 2019 drew to a close.

 

"On December 30th, China reported an outbreak of respiratory disease in Wuhan City, a major transportation hub about 700 miles south of Beijing with a population of more than 11 million people," Nancy Messonnier, director of CDC's National Center for Immunization and Respiratory Diseases, said at a press briefing January 17. A chart from the Wuhan Municipal Health Commission that shows the rapid uptick in cases means that you don't have to have seen the final scene in Rise of the Planet of the Apes, showing a virus ricocheting around the globe, to know where things are headed.

 

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

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How fertile are you? ‘Ovarian reserve’ DTC tests that count your eggs offer mixture of control and misinformation

The direct to consumer testing market comes in many flavors these days, with companies like 23andMe dominating headlines with their genetic/ancestry tests targeting folks eager to learn more about themselves. Also joining the fray are tests designed to help women — in theory, at least — assess fertility by counting the number of eggs left in their ovaries.

 

Sounds like a great idea. Just one problem: egg counts may not be such a great indicator of fertility, according to the American College of Obstetricians and Gynecologists.

 

Still, that doesn't mean these tests have no value. A new study suggests they can empower women. And that's especially true for those who do not fit into the binary gender categories that health insurers may require for covering clinical versions of the test that cost ten times as much.

 

 

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

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Will 2020 see the debut of promising gene therapy for hemophilia A? It’s up to the FDA.

The clotting disorder hemophilia A may become the third gene therapy that the US Food and Drug Administration approves, joining treatments for a form of retinal blindness in 2017, and spinal muscular atrophy in 2019.

 

Biomarin Pharmaceutical Inc. has submitted a biologics license application to FDA and documentation of clinical trial results to the European Medicines Agency, with reviews slated to begin early this year at both organizations.

 

An article in the January 2 New England Journal of Medicine from a UK research team presents the findings of a phase 3 analysis of continuing success of a phase 1/2 trial (instead of a new phase 3 trial). The hemophilia gene therapy – called valoctocogene roxaparvovec for now – can mean a one-time infusion that replaces the more than 100-150 infusions of clotting factor a patient takes each year, and can also alleviate the painful joint bleeding that is the hallmark of the disease.

 

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

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Novels ‘All About Evie’ and ‘The Family Upstairs’ illustrate how DNA tests can reveal ‘dark secrets’, from rape to unknown siblings

I recently read two works of fiction, "All About Evie" and "The Family Upstairs," that touch on the issue of defining family. The plots inadvertently echo current concerns over the possible fallout from unexpected consumer DNA ancestry testing results.

 

Each book is a multi-generational saga blooming with secrets and surprises. But one novel uses DNA testing to reveal relationships and the other doesn't.

 

My unplanned reading of one after the other served as a metaphor of sorts for the fallout from receiving a DNA surprise. The ending of the book based on the DNA test was abrupt and seemed contrived, much as discovering an insta-family can be. The ending of the book that slowly uncovered secrets as relatives recognized each other and connected was satisfying and rang true.

 

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

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