Ricki Lewis

"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.

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.

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.

 

 

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

Last week DNA Science covered a setback in a clinical trial of a gene therapy for Duchenne muscular dystrophy (DMD). Also recently, FDA's Cellular, Tissue, and Gene Therapies Advisory Committe turned down a stem cell treatment for amyotrophic lateral sclerosis, aka ALS, Lou Gehrig's disease, or motor neuron disease.

 

The two conditions and the therapeutic approaches differ, but their clinical trials illustrate the importance of selecting patients whose characteristics suggest that they are the most likely to respond.

DMD affects 1 in 3,500 male births, compared to approximately 1 in 400 people who develop ALS during their lifetime.

 

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

In the final chapter of my 2012 book The Forever Fix: Gene Therapy and the Boy Who Saved It, I predicted that the technology would soon expand well beyond the rare disease world.

 

I was overoptimistic. Gene therapy clearly hasn't had a major impact on health care, offering extremely expensive treatments for a few individuals with rare diseases. We're still learning possible outcomes of sending millions of altered viruses into a human body. Can they deliver healing genes without triggering an overactive immune response?

 

A report in the September 28, 2023 The New England Journal of Medicine describes a young man with Duchenne Muscular Dystrophy (DMD) who died just days after receiving gene therapy. The details are disturbingly reminiscent of the famous case of Jesse Gelsinger, who died from a ferocious immune response to experimental gene therapy in September 1999.

 

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

When it comes to estimating risk of a disease that is either genetic or has a genetic component, ancestry of an individual plays an important role. That's because increased risk of a particular health condition may be associated with a gene variant (aka mutation) in one population, but not another. Someone from a group not represented in the data on which a clinical test is based could receive an incorrect risk assessment, or even prescribed a drug unlikely to work.

 

A team from the Johns Hopkins Bloomberg School of Public Health and the National Cancer Institute has developed a new algorithm for genetic risk-scoring for major diseases across diverse ancestral populations. Their findings are published in Nature Genetics.

 

Although the algorithm is a start, and takes a logical approach to address health care disparities, it doesn't go far enough. Considering large groups – like Latinos or Africans – doesn't parse humanity sufficiently to hold much predictive power for genetic diseases, or conditions with large genetic components.

 

Tools to Track Disease: Biobanks to AI

 

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

One of the most anticipated returns to normalcy following the pandemic is the in-person conference. Like the mythical Phoenix bird arising from the ashes, live get-togethers are finally replacing zoom life, bringing back the sharing of ideas and spontaneity that catalyzes insights and inspiration – especially in science and technology.

 

The Festival of Genomics and Biodata comes to the Boston Convention & Exhibition Center October 4-5. More than 150 speakers presenting in 7 "theaters" will cover a diversity of topics, plus round table discussions, "speed networking," and poster, career, and start-up "zones." Researchers, clinicians, and those working in drug discovery and development are welcome.

 

Front Line Genomics (FLG) is organizing the meeting. The best part? For 90 percent of participants, the conference is free! More than 2,000 attendees have already signed up. Register here.

 

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

I just used ChatGPT for the first time. Initially, I was concerned about my future as the chatbot near-instantaneously answered my queries on increasingly obscure terms from my field, genetics. Stumping the AI tool, however, took only about 10 minutes.

 

ChatGPT was released November 30, 2022, from OpenAI/Microsoft. "Chat Generative Pre-trained Transformer" is a little like Google on steroids. But after my brief encounter, I can't help but wonder whether it can handle the nuance, context, humor, and creativity of a human mind. Could it replace me as a textbook author?

 

My Career

 

I've been writing life science tomes for a long time. My favorite has always been Human Genetics: Concepts and Applications, the first edition published in 1994, at the dawn of the human genome sequencing era. The 14th edition published this week, from McGraw-Hill. A revision takes two years, one for updating and addressing reviewers' suggestions, another for "production," from copyediting through final pages. Then, a year off.

 

As genetics morphed into genomics, artificial intelligence stepped in, layering the combinatorial information of comparative genomics onto DNA sequences. Training on data sets and then searching for patterns could be used to deduce evolutionary trees depicting species relationships, in ancestry testing and forensics, and in identifying sequences of mutations that appear as a cancer spreads.

 

ChatGPT is too recent for me to have used it in revising the new edition, but I'm curious now. I could imagine it spitting out definitions, but a textbook is much more than "content." A human author adds perspective, experience, and perhaps knowledge beyond what ChatGPT can extract from the Internet.

 

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

The Maui firestorm was so vast and fast that most identification of human remains will come from bits of persisting DNA from mitochondria.

 

The "Powerhouse of the Cell"

Most people likely last encountered mitochondria in high school biology class. The footprint-shaped "powerhouse of the cell" releases energy from breaking the chemical bonds that hold together nutrient molecules. The energy released in digesting food is held, fleetingly, in molecules of ATP, which serves as an energy debit card of sorts.

 

Each mitochondrion harbors its own tiny genome, a mere 36 genes compared to the 20,000 or so in a human cell's nucleus. And mitochondrial genes aren't just copies of nuclear ones – they're unique. Most encode enzymes that extract energy from ATP.

 

Mitochondria likely came from bacteria that single-celled organisms in ancient seas engulfed about 1.5 billion years ago. The idea is famous in biology as the endosymbiont theory. The bacteria in their new cellular homes, over time, retained some genes while surrendering others to the nucleus. And, gradually, the ancient bacteria evolved into mitochondria. Two recent reports in ScienceAdvances describe a contemporary contender for a descendant of the original stowaway bacterial genome that birthed mitochondria.

 

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