Monkey Embryos Grow to 25 Days — No Womb Required

Research Roundup // Plus: Yeast evolve in the lab.

It’s easy to feel like other people are watching and judging your every move. Forget to send that draft? The boss must be furious! Made a mistake in public (as I often do)? Everyone surely thinks you’re an idiot!

This is called the “spotlight effect.” And the reality is this: Everyone has their own life and worries about their own things. Few have time to pay attention to you. Just keep doing what you love.

Now back to the newsletter.

In this week’s update, monkey embryos grow in the lab for 25 days, a suite of papers push prime-editing forward, and a small peptide kills microbes better than most antibiotics.

Let’s dive in!

🔥 Week in Review

Biotech research highlights in under 5 minutes.

1/ Watch Yeast Evolve

I’ve been moderately obsessed with yeast ever since I visited White Labs in San Diego, during a PhD interview at Scripps. White Labs has a little tasting room, and they make some nice beer, but I was there to see something else: Their massive collection of brewing yeast strains, each with a unique fermentation temperature and alcohol tolerance.

Yeast live just about everywhere, and they are remarkably adaptable. Saccharomyces cerevisiae are used to brew beer and are the workhorse for most biologists. But if you make just one change to their genome — a mutation in a gene that encodes a transcription factor, called ACE2 — cells that bud off during division adhere to their mothers. They don’t break off. Over time, chains of yeast begin to form; they resemble snowflakes. A biologist, William C. Ratcliff, figured this out back in 2015.

Now, in a drawn-out experiment that lasted nearly two years, Ratcliff’s group at the Georgia Institute of Technology has shown that these “snowflake yeast” can evolve to become 10,000 times tougher than their ancestors.

A comparison of ancestral yeast (left) with yeast that evolved over thousands of generations (right), and which form dense clusters that are visible to the naked eye. From Bozdag G.O. et al. in Nature.

How? The experiment is remarkably simple. Every day, for 600 days, a graduate student named Ozan Bozdag went into the lab, took some yeast out of a shaker, and transferred 1.5 milliliters into a tube. After waiting for 3 minutes, they sucked out the top 1.45 milliliters of liquid and left the remaining 50 microliters in the tube. This remaining liquid was used to “seed” the next day’s batch of cells.

By repeating this procedure again and again, the scientists gradually selected yeast that settle fastest to the bottom of a tube. After 200 days, some of the yeast became physically elongated. They became entangled with other cells, much like interwoven threads in fabric — but only when grown in the absence of oxygen!

From The New York Times:

Dr. Bozdag gave oxygen to some yeast in the experiment and grew others that had a mutation that kept them from using it. He found that over the course of 600 transfers, the yeast that lacked oxygen exploded in size. Their snowflakes grew and grew, eventually becoming visible to the naked eye…

…For yeast that could use oxygen, getting large had significant downsides. As long as snowflakes stayed small, the cells generally had equal access to oxygen. But large, dense wads meant that cells within each clump were cut off from oxygen.

Yeast that couldn’t use oxygen, in contrast, had nothing to lose, and so they went big. The finding suggests that feeding all the cells in a cluster is a crucial part of the trade-offs an organism faces as it goes multicellular.

The yeast that “went big” had key mutations across their genomes, including changes in genes linked to the cell cycle and budding. Out of 123 total mutations, 29 were associated with the cell cycle, 11 with cellular budding, and 7 with filamentous growth, or the thread-like extrusions of these cells.

So what? Every science journalist under the sun has covered this paper (though I recommend Ed Yong’s). The paper is also nearly two years old at this point; the preprint was published in August 2021. Hell, the paper isn’t even about biotechnology.

But I’m covering this paper, regardless, because it shows that simple changes at the cellular level can lead to remarkable, biophysical innovation. And it demonstrates — in vivid, visual terms — the remarkable plasticity of life. It proves that even simple experiments — grow some yeast, let them clump, repeat 600 times — can make it into Nature.

There is plenty of room to make discoveries, even with the simplest of tools.

Read more in Nature. See the Twitter thread from Will Ratcliff.

2/ Monkey Embryos Grow to 25 Days

Two Chinese groups published papers in Cell, back-to-back, that show how cultured monkey embryos can be grown in the laboratory, for up to 25 days, in 3-D gels. This is an impressive length of time to develop embryos outside the womb.

The embryos gastrulated, formed a neural plate (the start of a nervous system), and even kicked off the earliest stages of organ formation. There were also “signs that blood cells and their components were beginning to take shape in the yolk sac, which supplies embryos with nutrients,” according to reporting in Nature.

About two years ago, another study in Cell showed that monkey embryos injected with human stem cells — monkey-human chimeras — could develop for at least 19 days after fertilization in the lab.

How? For one of the studies, researchers collected blastocysts from cynomolgus monkeys, the long-tailed macaques native to southeast Asia. The blastocysts were carefully sandwiched between layers of matrigel and Geltrex (a goopy liquid filled with growth factors). Each blastocyst was washed with a TH3, a liquid containing glutamine and pyruvate. On day 9, the cells were fed sugar.

Both of these groups have previously cultured monkey blastocysts for up to 20 days, but then the cells died off. In those earlier papers, it was too early to see organs develop. The cells were also cultured on flat plates, rather than a three-dimensional gel, which restricted their growth.

So What? These experiments could be precursors to studying human development, in the lab, during its earliest stages. But this technique is still a bit unreliable; in one paper, the researchers tested 91 total embryos, just 33 percent of which survived to 20 days.

Read more in Cell. (#1, #2)

(Video credit: Gong Y. et al. in Cell.)

3/ Prime Editing Spree

Prime editors can change DNA in ways that Cas9 — and even base editors — cannot. Known as a "search-and-replace" gene-editing tool, prime editors can delete or replace DNA up to 10,000 bases in length, or substitute one base for another.

Made from a Cas9 nickase (the histidine at amino acid position 840 is swapped for an alanine) fused to a reverse transcriptase enzyme (which makes DNA from RNA; transcription in reverse), prime editing clinical trials are expected to begin by 2025. Early targets may include sickle-cell disease, Friedrich’s ataxia, and cystic fibrosis.

But prime editors also have a couple of issues: They cause some off-target changes in the genome, and they are physically big. It can be hard to get them into cells.

Three studies, from last week, have made the tool better.

PE-tag is a new method that detects off-target DNA changes during a gene-editing experiment. It can do this across the entire genome, using DNA extracted from mice or humans. This tool will be an important tool to ensure prime editors are safe in the clinic, and don’t change random parts of the genome all willy-nilly.

For another study, researchers made mouse models with prime editors encoded in the germline of various tissues. This means that there’s no need to deliver the proteins at all; they are already lurking in the genome. And a third study shows that prime editors can be split up and delivered into cells via two separate viruses. When the proteins are made inside the cells, they click together and edit DNA just like a normal prime editor. This “split” approach was tested in the brain, liver, and hearts of living mice. 🔻

The split prime editors (light blue) perform just as well as prime editors encoded by a single, continuous DNA sequence (gray). The prime editors were tested in liver, heart, and muscle. The y-axis shows how many DNA sequences, out of all those analyzed in a next-generation sequencer, carried the desired edit. From Davis J.R. et al. in Nature Biotechnology.

🧪 From the Lab

Other wet-lab papers worth checking out.
* = Recommended.
  • *Genomes from 47 ethnically diverse people were sequenced and compiled into a human “pangenome.” Nature. (link)

  • *A cell-penetrating peptide, derived from an enzyme that unwinds DNA, cured various bacterial infections in mice. It also outperformed state-of-the-art antibiotics, like ciprofloxacin. EMBO Reports. (link)

  • *New base editors can engineer both mitochondrial and nuclear DNA. Molecular Cell. (link)

  • *Hypoimmune pluripotent cells were engineered and then used for rejection-free transplantation in primates. This paper paves the way for off-the-shelf cell therapies that don’t require immunosuppressive drugs. Nature Biotechnology. (link)

  • A new method releases “trapped” DNA from ancient bones and teeth. Researchers used it to sequence a 20,000-year-old deer tooth pendant. Nature. (link)

  • Zebrafish injected with a conductive polymer were controlled with electricity. Preprint. (link)

  • A new type of organelle was discovered in fruit flies. It stores phosphate. Nature. (link)

  • Genetic circuits that contain interconnected ‘nodes’ are robust against mutations. Nature Communications. (link)

  • Engineered Pseudomonas microbes — which eat plant biomass — make isoprenol, a precursor to aviation fuels, with a 3.5 grams per liter titer. Preprint. (link)

  • In mice, eight different types of phage (viruses that kill bacteria) were used to clear out E. coli infections and eradicate biofilms. Nature Biotechnology. (link)

  • Add long genes to cells with >90% efficiency. Nature Biotechnology. (link)

  • A new method compares base editors head-to-head and benchmarks their performances. Cell Systems. (link)

  • Machine learning and high-resolution spatial transcriptomics mapped the cells that make up a tumor. Cell Systems. (link)

  • INSPECTR is a diagnostic tool to detect tiny amounts of viral RNA at room temperature. From the team at Sherlock Biosciences. Nature Biomedical Engineering. (link)

  • An ECoG device was implanted into a pig’s brain through a tiny, centimeter-wide bore hole. Science Robotics. (link)

  • A new toolkit uses the Cas3 gene-editing protein to manipulate Streptomyces bacteria. bioRxiv. (link)

  • CReATiNG is a technique to build synthetic chromosomes in yeast. bioRxiv. (link)

  • An E. coli universal chassis with reprogrammed metabolic flux suppresses overflow metabolism, enhancing the production and yield of chemicals and proteins, paving the way for efficient bioproduction strain design. bioRxiv. (link)

  • Administering multiple doses of lentiviral vectors (used for gene therapy) into mouse lungs is better for long-term gene expression than a single dose. Gene Therapy. (link)

  • The first-in-human study for RO7122290, a protein designed to stimulate T-cells to attack tumors. Science Translational Medicine. (link)

  • Just two enzymes are needed to convert formate, derived from CO2, into formaldehyde in E. coli. This is a key step toward a carbon-neutral bioeconomy. Nature Communications. (link)

  • A modified form of two-photon microscopy enables 3D imaging of subcellular dynamics at a millisecond scale, with minimal photobleaching. Cell. (link)

  • A phase I trial of a personalized neoantigen vaccine showed that they could boost T-cells and help fight off pancreatic tumors. Nature. (link) (Commentary)

💾 Computers x Bio

Papers from the worlds of AI & software.
  • *Foldseek can quickly search through protein structure databases to find what you’re looking for. It is between ten and one-hundred thousand times faster than other leading tools. Nature Biotechnology. (link)

  • *Anti-aging compounds were discovered by training a graph neural network to predict which molecules, out of 800,000+, would selectively kill off aged cells. Nature Aging. (link)

  • A diffusion model “learned” the distribution of protein structures and then generated novel protein backbone structures with high efficiency. Preprint. (link)

  • A deep-learning method predicts which pathogen is likely responsible for a person’s antibiotic-resistant infection before test results are returned. bioRxiv. (link)

  • VirPipe is a Python tool to detect viruses from sequencing data. Bioinformatics. (link)

  • AOminer is an open Python tool to discover proteins that inhibit CRISPR-Cas gene-editing systems. Bioinformatics. (link)

  • TransCRISPR is an online tool to design guide RNAs that target sequence motifs in 30+ genomes. Nucleic Acids Research. (link)

  • An open-source R tool visualizes and plots data from microbial genomes. Nucleic Acids Research. (link)

  • αCharges calculates partial atomic charges for over 200 million protein structures in AlphaFoldDB, which may help decode their functions. Nucleic Acids Research. (link)

  • OnTarget is a webserver to design MiniPromoters, specific DNA sequences that control where a gene is expressed. Nucleic Acids Research. (link)

  • MicrobiomeAnalyst 2.0 is a tool to analyze data from microbiome studies. It includes statistical analysis and visualization tools. Nucleic Acids Research. (link)

  • EVcouplings is an evolutionary model that can design highly divergent protein variants that have high thermostability and broad substrate availability. bioRxiv. (link)

  • scDesign3 is a statistical simulator that generates realistic single-cell and spatial omics data. Nature Biotechnology. (link)

  • ProteinGenerator is a diffusion model, based on RoseTTAfold, that can generate both protein sequences and structures. It’s a key step toward optimizing protein functions. bioRxiv. (link)

⚒️ In the Community

Education, resources, and events.
  • Have some free time? Like to play around with biology? Join the Homebrew Biology Club Grand Prix. Participants will develop a project over the next few months (whatever you’d like) and can win up to $10,000 at a year-end showcase. Email me if you want feedback or help with your ideas.

  • The Underground Garden Club released a DIY biology curriculum that covers everything from building a smartphone-based fluorescence microscope to making jet fuel with microbes.

  • Have you tried Mojo Lang (apparently up to 35,000 times faster than Python) in your research? I’d love to hear about it. Drop me a line!

📺 Meme of the Week

Please laugh.”

“It's not Nature Nature but it's from the Nature publishing group" (@OdedRechavi)


See you next week! In the meantime, find me on Twitter or LinkedIn.

— Niko McCarty

Disclosure: The views expressed in this blog are entirely my own and do not represent the views of any company or university with which I am affiliated.

All articles and posts that were published in Codon, the Substack newsletter that gave rise to Asimov Press.
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