Cane Toads, Gene Drives & Engineered Kombucha - 2021.01.15

Plus: Other biotech news stories that you may have missed this week.

☀️ Good morning

This newsletter surpassed 1,000 subscribers on Monday. That’s great! Thanks for reading. Feel free to comment on this post, or send me an email, if you’d like to talk about your work.

Share Cell Crunch

CRISPR & Cane Toads Take Center Stage in New Yorker

In the January 18 issue of The New Yorker, Elizabeth Kolbert (Pulitzer Prize-winning author of ‘The Sixth Extinction’) discusses how CRISPR and gene drives can be used to eradicate invasive species, or bring species back from extinction (CRISPR and the Splice to Survive). The highlight of the story, at least for me, was its discussion of an ongoing Australian effort to mitigate the looming threats caused by an invasive amphibian.

Towards the start of the article, Kolbert recounts a trip to the BSL-4 Australian Animal Health Laboratory, outside Melbourne. Inside, Mark Tizard and Caitlin Cooper are devising new strategies to rid Australia of Rhinella marina, or cane toads.

Cane toads arrived in Australia from Hawai’i in 1935, and have a splotchy brown color. Some, writes Kolbert, resemble a boulder; the largest cane toad spotted on the continent “was fifteen inches long and weighed six pounds.” Though they spend much of their day stewing in puddles, cane toads are not innocuous. Since landing in Australia, they have decimated native species; the toads are venomous.

To rid their neighborhoods of these toads, some Australians have resorted to extreme measures. People kill them with golf clubs, or poison them, or crunch them with their cars (if you’re looking for more…scientific ways to rid yourself of cane toads, consult this review on the topic). When hit with force (via golf club, for instance), the toads secrete and spray a toxic poison. When eaten, they can kill dogs and other critters.

To get rid of the cane toads for good, Tizard and Cooper are genetically-editing them with properties that will make them less viable in the Australian wild. To do that, they wash fertilized cane toad eggs, puncture them with a microneedle, and inject the eggs with the proteins and RNA molecules needed to edit their DNA.

At first, the researchers just changed the color of the cane toads. Then, they started to level up their experiments. In one case, writes Kolbert, Cooper used CRISPR to delete a section of the gene responsible for their potent venom, resulting in “a batch of less toxic toadlets.” In future experiments, Tizard and Cooper plan to edit genes in a way that could prevent the toad eggs from being fertilized at all.

The piece also touches, briefly, on the American effort to revive the Chestnut tree, nearly all of which (about four billion) were wiped out by a fungal blight that was introduced from Japan around 1900. She also mentions an effort to implement a suppression drive in mice, which I admittedly have not heard of before.

Later in the article, Kolbert revives a repetitive and ever-present theme of popular science articles about synthetic biology; namely, is bioengineering akin to donning the costume of some omniscient creator? To broach the question, Kolbert invokes Stewart Brand, who wrote in 1969 that “We are as gods and might as well get good at it.”

While I agree that synthetic biologists have a moral obligation to think critically about their work, I must say that I have never—in my meager 7 years working in research labs—felt as if I had the power over life akin to that of an omniscient creator.

One evening, at the end of what felt like a ten-meal course of experiments, I placed some bacterial cells in an incubator to grow overnight. When I came back in the morning, I realized that I had placed them in the cold room instead.


📰 More News

Feature stories, then industry news.

The first time I made kombucha at home, I stared alarmingly at the dense, semi-solid film that formed on top my opaque liquid concoction. Nose pressed to glass, I weighed whether it was a fungal infection, or perhaps newly revealed evidence for spontaneous generation. But no—it was just a pellet of cellulose, a material amenable, it turns out, to engineering feats of wonder. A study published this week in Nature Materials—a joint effort by Timothy Lu and Tom Ellis’ groups—shows how “kombucha-inspired living materials” (e.g. cellulose) can be made from S. cerevisiae yeast and K. rhaeticus bacteria. The yeast—embedded in the cellulose biomaterials—live for a long while, and can be engineered to sense and remove pollutants, for example. Study author Tzu-Chieh (Zijay) Tang explained the experiments behind the paper. Bioengineering Community. Link

Kathryn Hamilton wrote an in-depth piece on lab-cultured meat, proteins, and the ever-pressing struggle to feed a growing population. Bioeconomy.XYZ. Link

A new article offers an intriguing glance into the world of Artificial Life—computer programs made to simulate reproduction, and life, and death, and entropy, in the vein of John Conway’s legendary Game of Life. Written by Claire Evans, it recounts the history of Tierra (simulation software made in the 1990s) and its creator, Tom Ray. Grow by Ginkgo. Link

For a study this week in Nature Chemical Biology, researchers at Columbia University took bacterial cells, engineered them with a modified CRISPR system that can sense and respond to redox reactions, and then pulsed them with electricity, pushing the CRISPR system to encode data (in 3-bit units) into CRISPR arrays in the bacterial genomes. Using this method, they could store up to 72 bits of information. Ars Technica and Science covered this article.

Artificial intelligence could increase the success rate of in-vitro fertilization, and “help patients get pregnant faster by scanning images of their embryos and picking out the ones that have the best chance of resulting in a pregnancy.” Future Human. Link

This newsletter, on Monday, highlighted a new study from David Liu’s lab, at Harvard, to treat progeria (a rapid aging disease) in mice. That article was covered, in much greater and more rigorous depth, by Emily Mullin. Future Human. Link

A great explainer piece explains how chemists can measure trace amounts of thiols in beer, potentially helping brewers create better aromas. Ars Technica. Link

The journal Nature Methods unveiled their “top technologies” last week. In the number one spot: spatially-resolved transcriptomics. In de-jargonized terms, this technique measures how many RNA transcripts are made from each gene, and also where those transcripts came from within the genome. Nature Methods. Link

  • Prime editors, which can introduce small mutations into genomes, also made the list as a “technology to watch”.

This article briefly highlights 21 promising European biotechnology companies (a lot of gene-editing and DNA synthesis, it seems). Labiotech.eu. Link

Oxford Nanopore announced a partnership with NVIDIA to make some beefed-up genetic sequencers. A press release states that the partnership “aims to deliver the world’s most powerful sequencer that supports real-time analyses at scale, and can also analyse any length fragment of DNA/RNA.” Nanoporetech.com. Link

Eligo Bioscience—a “microbiome gene therapy company”—recently announced a partnership with GlaxoSmithKline to develop therapies for diseases related to the microbiome, including a CRISPR-related treatment for acne. Forbes. Link

Vedanta Biosciences received $25 million from the Pfizer Breakthrough Growth Initiative (a $500 million dollar biotechnology investment fund). Vedanta—a company that develops clinical therapies via engineered bacterial consortia—plans to use those funds for a phase II clinical trial of their “living medicine” for inflammatory bowel disease. Business Wire. Link

This is cool—Conagen is scaling up their production of musk fragrance compounds using some nifty biotech tricks. SynBioBeta. Link

A venture capital firm, called OMX Ventures, announced a $150 million fund for synthetic biology investments. Forbes. Link

The FDA gave Editas Medicine the green light to begin “the safety phase of the Company’s EDIT-301 clinical trial,” according to a press release. EDIT-301 is a CRISPR/Cas12a-based therapy for sickle cell disease. SynBioBeta. Link

Until Monday,

Niko


Thanks for reading Cell Crunch, part of Bioeconomy.XYZ. If you enjoy this newsletter, please share it with a friend or colleague.

A version of these newsletters is also posted on Medium. Reach me with tips and feedback on Twitter @NikoMcCarty or via email.