Ricki Lewis

Dense living communities of hundreds of bacterial species form biofilms on our teeth. Without careful brushing and flossing of this dental plaque, minerals seep in, hardening it into tartar. When proteins in saliva adhere tartar to tooth surfaces, a trip to the dentist is required to hack the stuff off.

Over time, the mineralized microbes of tooth tartar come to comprise a mouthful of tiny fossils, including snippets of degraded bacterial DNA. Because many antibiotic drugs come from or are based on modern bacteria, tooth tartar – aka dental calculus – from ancient people may hold genetic recipes for novel antibiotics from the past.

A team of researchers from the Leibniz Institute for Natural Product Research and Infection Biology, the Max Planck Institute for Evolutionary Anthropology, and Harvard University has reconstructed "paleogenomes" of previously unknown bacteria from the dental tartar of ancient and modern people. The work appears in Science.

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

I just finished revising the fourteenth edition of my college textbook, Human Genetics: Concepts and Applications. The first was published at the dawn of the human genome sequencing era, 1994. I'm accustomed to incorporating feedback from professors and updating content every 2 or 3 years, but this revision threw something new at me: the publisher asking all textbook authors to strive for DEI:

DIVERSITY: depicting various identities and differences
EQUITY: providing fair and equitable access and opportunity
INCLUSION: respecting and welcoming all individuals

Ironically, just as I finished the new edition, the American College of Medical Genetics and Genomics (ACMG) published a "points to consider" statement in Genetics in Medicine, "Clinical, technical, and environmental biases influencing equitable access to clinical genetics/genomics testing."

The subtext: Textbooks shouldn't use only or mostly photos of white people, and interpreting DNA test results shouldn't be based on research done mostly on white people.

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

On April 25, 1953, "MOLECULAR STRUCTURE OF NUCLEIC ACIDS: A Structure for Deoxyribose Nucleic Acid" was published in Nature. J. D. Watson and F. H. C. Crick's work was a brilliant deduction based on the experimental findings of many others.

DNA is a sleek double helix, with "rungs" consisting of a purine base paired with a smaller pyrimidine base: adenine (A) with thymine (T) and guanine (G) with cytosine (C). Hydrogen bonds link the pairs, individually weak but in large numbers powerfully strong, like a zipper.

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material," Watson and Crick wrote near the end of the one-page article, planting the seeds for modern biotechnologies like recombinant DNA, transgenic organisms, gene silencing and therapy, and CRISPR gene editing.

The April 1953 paper was groundbreaking yet a bit of a tease, a "save-the-date" of sorts to announce the discovery and briefly describe the structure, for much confirming work needed to be done. Six months later, Francis Crick eloquently laid out the clues in "Structure of the Hereditary Material," in a Scientific American volume, "Genetics": "A genetic material must carry out two jobs: duplicate itself and control the development of the rest of the cell in a specific way." DNA encodes amino acid sequences comprising proteins, which impart traits.

On this anniversary of the famous paper, DNA Science revisits the discoveries that catalyzed Watson and Crick's deduction of how a molecule could carry and transmit genetic information.

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

Drug addiction is prevalent and deadly. In the US in 2021, more than 46 million people aged 12 or older had addiction to at least one substance, yet only 6.3% received treatment, according to the National Institute on Drug Abuse (NIDA).

A complex mix of gene variants and environmental factors lies behind the compulsion to repeatedly take a drug and increase the dose, despite knowing the dangers. Environmental influences are well known. Now a report in Nature Mental Health from an international team led by researchers at Washington University in St. Louis fills in the genetics side of the picture. They have identified shared points of variability among more than a million human genomes that track with substance use disorders.

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

A urine test for DNA pieces bearing 10 key mutations can indicate early inklings of bladder cancer, according to a report at the European Association of Urology meeting in Milan last month. Urothelial carcinoma is the most common type of bladder cancer, according to the National Cancer Institute.

The technique is called urinary comprehensive genomic profiling (uCGP). It copies telltale DNA sequences in urine, using a tool called "UroAmp," developed at Convergent Genomics. Like other cancers tests, it is being pioneered on people who already have the cancer to detect recurrence or response to treatment. If validated on many patients, the test might then be used for screening – that is, as part of the initial diagnostic process.

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

In "The Last of Us," a video game and recently-wrapped HBO series, giant mutant fungi turn much of humanity into zombies. In real life, another fungus, the yeast Candida auris, is spreading, just as COVID finally fades.

Candida auris is the first multi-drug resistant fungus identified. It is deadlier than familiar relative Candida albicans, which lies behind common vaginal and throat infections. Candida yeasts are normal inhabitants of our skin and other superficial body parts, but are dangerous when they enter the bloodstream or reach solid organs, like the heart or kidneys.

"What is different and particularly scary about Candida auris is that it can survive on skin and healthcare surfaces up to two weeks, allowing the spread from person-to-person in healthcare settings and nursing homes. This fungus is not usually killed by clinically used antifungal drugs, which makes infection difficult to treat and can often result in death. It is also difficult to identify with standard laboratory methods," summed up Mahmoud Ghannoum, director of the Center for Medical Mycology at University Hospitals Cleveland Medical Center.

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

Startling images in the journal Neurology made the media rounds last week. CT scans show a partial fetus wedged within a space (ventricle) in the brain of its one-year-old sister. In photos, the removed potential sibling resembles a pink tadpole.

The report, called a Teaching NeuroImage, is from four researchers at Beijing Tiantan Hospital, and entitled "Intraventricular Fetus-in-Fetu, With Extensive De Novo Gain in Genetic Copy Number." That means the genome of the doomed fetus-within-a-fetus had lots of copies of certain short DNA sequences that aren't in the parents' genomes ("de novo" means new).

With only two short paragraphs, the report doesn't explore the significance of the discovery of the repeat-riddled genome. But I thought immediately of young children with combinations of developmental delay, intellectual disability, autism, learning disabilities, and behavioral conditions that turn out to have microduplications or microdeletions – that is, bits of DNA copied too many times, or missing. Might the partial fetus have had an extreme version of the DNA repeats that are associated with these syndromes, halting development well before birth?

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

In the original Planet of the Apes, the Forbidden Zone is a future radiation-devastated landscape from which hardy new mutants arise, shifting the evolutionary course of humanity.

The "nuclear exclusion zone" sounds similar, but is real, referring to the 3,004-square-kilometer (about 1,160-square-mile) environs of the Chernobyl nuclear power plant that exploded on April 26, 1986, at 1:23:58 am. The Chernobyl Dog Research Initiative has published their analysis of genetic changes among the dogs who live today in what researchers call the aftermath of "an ecological catastrophe of massive proportions." Gabriella Spatola and Elaine Ostrander of the National Human Genome Research Institute and colleagues report their findings in Science Advances.

Soon after the explosion, as humans fled, workers remained to clean up and to cull the canine population. But some dogs survived, and the workers as well as tourists have cared for them since. Yes, Chernobyl was and remains a tourist destination, by jeep or jet.

An Unnatural Experiment

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

The road to naming an unusual collection of unfolding symptoms is called the "diagnostic odyssey" for good reason: the journey takes, on average, nearly 5 years.

Worldwide, about 400 million people have one of the 10,000 or so recognized rare diseases, or one in ten people, according to Global Genes. About half are children, and 95 percent of the conditions do not have FDA-approved treatments.

In the US, 25 to 30 million people have a rare disease. Ten-year-old Isla Richman is one of them. She has NGLY1 deficiency. Her family shared their story with me in recognition of Rare Disease Day 2023, the last day of February.

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

Monoclonal antibody drugs to fight COVID are being taken off the market while new COVID vaccines are arriving, even as the old ones are standing up quite well against new viral variants. How can two interventions that tweak an immune response have such different outlooks? It stems from the biology.

Understanding what antibodies are, how our bodies make them, and how vaccine and monoclonal antibody technologies work and differ, explains the distinction.

The Antibody Response is Naturally Polyclonal

The immune system is a vast army of cells and their secretions that recognize and respond to the presence of "non-self" cells and molecules, like the spike proteins that fringe SARS-CoV-2, the virus behind COVID. One of the first things I learned in college is that "biology is really chemistry," and that's certainly true for the immune response. It's all about recognizing molecules.

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