Ricki Lewis

As autumn looms, we're enjoying the last bites of sweet, juicy watermelon.

Conventional agriculture has molded our fruits and veggies to suit our palates, gradually crafting domesticated Citrullus lanatus from three ancestral melon species. But the process may have also removed valuable traits.

Researchers at the Boyce Thompson Institute in Ithaca, New York, have analyzed genomes of watermelon and its ancestors, revealing traits that early breeders may have inadvertently removed in their quest to maximize the red, sweet, watery flesh of the fruit. Their report appears in Plant Biotechnology Journal.

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

The history of genetics begins, not with Gregor Mendel's pea experiments, but with people long ago noticing family resemblances and vulnerabilities so distinctive that shared environment alone can't explain them.

In the new literary fiction masterpiece The Covenant of Water, author-physician Abraham Verghese traces an unusual trait through three generations of a Christian family in India, against the historical backdrop of the coalescence of three states into Kerala, on the Malabar Coast, spanning 1900 to 1977. "The family … suffers a peculiar affliction: in every generation, at least one person dies by drowning – and in Kerala, water is everywhere," reads the jacket cover.

Through time, the drownings have been ascribed to bad luck and a familial recklessness, rather than to anything as cut in stone as an inherited condition. Frequent drownings seem more coincidence, harder to explain biologically than bleeding from missing a clotting factor or impaired breathing from cystic fibrosis. But the 700+ page tale is indeed about a rare manifestation of a rare condition.

The narrative captures the dread of an autosomal dominantly inherited disease, striking every generation, males and females. Dr. Verghese names all of the characters except the patriarch, who passed down the mutation behind the illness that isn't revealed until well into the saga. Perhaps keeping him nameless is a metaphor for the mysterious origin of what the family calls "the Condition."

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

Determining the sequence of building blocks of entire genomes – aka genomics – first came to public attention in the 1990s, with the race to decode the first human genomes. Today, smartphones can carry our personal genome sequences.

Genomics applies to all species, revealing evolution in action, because we all use the same genetic code – that is, the correspondence between DNA sequences and the amino acid sequences of proteins. Many popular uses of "genetic code" actually mean "genome sequence."

Analysis of environmental DNA (eDNA) catalogs the DNA in specific places, from microorganisms inhabiting a human armpit to vast ecosystems. Several recent DNA Science posts describe eDNA:

A Glimpse of The Ocean's "Twilight Zone" Through Environmental DNA
A 2-million-year-old Ecosystem in the Throes of Climate Change Revealed in Environmental DNA
DNA in Strange Places: Hippo Poop, Zoo Air and Cave Dirt
Microbiome Analysis of Ancient Feces

Genome sequencing was critical from the start of COVID, as the first SARS-CoV-2 sequences were posted for researchers just days after initial case reports. That information led, thanks to vaccine shelved from the first SARS circa 2003, to the rapid development and deployment of mRNA vaccines against the new infectious disease.

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

Humans aren't very good at regeneration — we can do it for skin, bone, and liver, but that's about it.

Flatworms, zebrafish, cockroaches, and salamanders can regenerate entire limbs. Yet even these abilities are unimpressive compared to those of Hydractinia symbiolongicarpus, aka a "squishy sea creature."

Only Simpler Animals Regenerate

Hydractinia, along with jellyfish, sea anemones, hydra, and  corals, are among 11,000 or so species in phylum Cnidaria, from the Greek cnidos for "stinging nettle." The tiny animals have soft bodies, circular symmetry, and sting. The hydractinia are among the most ancient of the Cnidaria. We last shared an ancestor with these animals more than 600 million years ago. They live in saltwater and are small and tube-shaped, clinging to hermit crabs.

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

Several recent reports are filling in the gaps of what we know about the earliest days and weeks of human prenatal development. Rather than attempting to image human embryos, researchers are tracking gene expression – that is, which genes a particular cell turns on or off at a particular time, providing a view of overall function.

The early embryos that are being investigated are donated by women undergoing assisted reproductive technologies, or are nurtured from induced pluripotent stem cells, which are created by culturing skin cells (fibroblasts) in a brew of growth factors. The stem cells divide and differentiate into early embryos, but with only partial supportive structures, like the amnion and placenta, so development ceases before the fetal period begins at 8 weeks after fertilization. The stem cells provide a Goldilocks solution, glimpsing early embryos, but not sustaining their development past a few weeks.

Three New Reports

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

"If you're an adult with newly diagnosed non-small cell lung cancer that's spread and tests positive for PDL1 without an abnormal EGFR your first option could be …" announces a TV ad for a pair of targeted cancer drugs, flying by so fast that I doubt many patients can grasp anything.

According to the FDA, the wording of the ads comes from a "research team of social psychologists." Science journalists might better communicate drug mechanisms to consumers.

Another way to fathom the info in cancer drug ads is to go back to high school biology and consider the cell cycle – the molecular choreography that tells a cell whether, when, and how often to divide. The cycle has offshoots, called checkpoints, which enable a cell to die by apoptosis (aka programmed cell death) or pause for a time-out. Many targeted cancer drugs interrogate cell cycle enzymes and proteins that oversee checkpoints, stopping runaway cell division.

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

What I love most about science in general, and genetics in particular, is when new findings upend everything we thought we knew about something. That was so in 1977, when "intervening DNA sequences" – aka "introns" – were discovered to interrupt protein-encoding genes.

Sometimes, we discover new ways that organisms do things. Changing gene expression – the set of genes that are transcribed into mRNA and then translated into proteins under a particular circumstance – is how organisms rapidly respond to a challenge. For an octopus, that might be a sudden plunge in water temperature, which slows enzyme activity.

But some species control genetic responses another way – via RNA editing. Changes in one of the four types of nitrogenous bases of an mRNA alter the encoded protein in ways that alter the protein's function.

In a new report in Cell, Joshua Rosenthal of the Marine Biological Laboratory at Woods' Hole and Eli Eisenberg at Tel Aviv University describe how the cephalopods – octopi, squid, and cuttlefish – change mRNAs in ways that alter enzymes. Because the edits are in RNA, and not DNA, they are fleeting. "We're used to thinking all living things are preprogrammed from birth with a certain set of instructions. The idea the environment can influence that genetic information, as we've shown in cephalopods, is a new concept," said Rosenthal.

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

The newest FDA-approved gene therapy treats the severe, skin-peeling condition dystrophic epidermolysis bullosa (DEB). The gene treatment has been a long time coming, but it differs from the handful of other approved gene therapies: it isn't a one-and-done.

My now decade-old book The Forever Fix: Gene Therapy and the Boy who Saved It, told the stories of children who had received one-time deliveries of working copies of genes, to compensate for their mutations. The initial gene therapies helped people with a form of inherited retinal blindness to see and children with profound immune deficiencies to survive. Today, several single-gene blood, brain, muscle, and metabolic disorders are responding to one-time infusions of a gene therapy.

The biology behind a single-gene condition suggests how a particular gene therapy would be delivered, targeted, and the effect maintained. Compared to slash-and-burn technologies like standard chemo and radiation that impact cells beyond the targeted ones, a gene therapy is both rational and tailored.

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

Myotonic dystrophy type 1 (DM1), an inherited disease affecting muscles, was one of the first described "expanding repeat" disorders. In these 50 or so conditions, symptoms may appear earlier and worsen from generation to generation, as the mutant gene grows, adding copies of a 3- or 4-base DNA sequence. For many expanding repeat disorders, forty copies seems to be a threshold, causing symptoms when crossed.

In a family with myotonic dystrophy type 1, a grandfather might experience mild weakness in his forearms, while his daughter may have more noticeable arm and leg weakness, slurred speech, and a flat facial expression. Her children have even weaker muscles that contract for too long, creating limitations like being unable to unclench a fist or release a grip.

In MD1, skeletal muscle fibers that contract for too long impair balance and coordination, called ataxia. The condition also causes cataracts, small gonads, frontal balding, fatigue, sleepiness, digestion problems, and cognitive and behavioral impairment. Life may be shortened. MD1 affects about one in 7,500 people, or more than 40,000 people in the US.

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

When a dear friend recommended The Love Songs of W. E. B. Du Bois, I thought the book was a tribute to the famous Black historian, sociologist, scholar, and civil rights activist. Although excerpts of his writings open chapters, the book is sweeping historical fiction – perhaps the best I've ever read.

The Love Songs of W. E. B. Du Bois, the first novel by award-winning poet Honoree Fanonne Jeffers, traces an American Black family back eight generations, through the eyes of Ailey Pearl Garfield, who untangles her own origins while doing research for a doctorate in American history. I expected something similar to Alex Haley's Roots: The Saga of an American Family from 1976, but the added dimension of a contemporary Black female perspective transcends even that classic.

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