Happy to announce a new preprint from my former academic lab, where we use PACE to evolve halogenase enzymes!
Congrats to Andre Pulschen and Justin Booth who led the study!
Continuous evolution of a halogenase enzyme with improved solubility and activity for sustainable bioproduction
biorxiv.org/content/10.1101/202…
What’s ‘halogenated’?
It’s anything with fluorine/chlorine etc from over on the right of the period table. Often halogenated compounds have a hydrogen swapped for, say, a fluorine. They all need one more electron, and so can stand in for one another.
Halogenated compounds aren’t well recognized by degradation machinery of the cell, making them more stable. As a result, a fourth of all drugs are halogenated! 💊
BUT
Halogenation is a pain to do with normal chemistry. It’s not stereoselective, and can require quite toxic or expensive chemicals.
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Also provided
🧬 Complete set of .gb plasmid maps. SI Table 1 describes which plasmids were used to create every subfigure, and which can be obtained from addgene
🖼️ Complete set of .ai figure files. Hopefully sharing these saves someone from re-making cartoons from scratch yet again. 🙏
🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford📣 Evolutionary Scale is supporting the 2025 Protein Engineering Tournament!
Teams get sponsored ESM inference through
@evolutionaryscale.bsky.social's API (Forge), bringing frontier protein AI models into the competition.
Level playing field, real experiments, open results. Register now 👇
By this time next year, either:
🏆 we'll have engineered PETase enzymes actually work industrially & recycle plastic
... or we'll know that AI-for-proteins is still a bit underbaked 😜
Excited to see what happens!!!! 😬
Spread the word ⬇️
1/4
🚀 Announcing the 2025 Protein Engineering Tournament.
This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️
#AIforBiology #ClimateTech #ProteinEngineering #OpenScience
Heads up: terraforming Mars isn’t just sci-fi, it’s a real possibility that’s possible with today’s technology.
Mars could be green in MY lifetime. 🚀 🌼
What’s stopping us? We need a lot more real research into how to do it right. Don’t nuke Mars!
👇
Today I and 11 other scientists describe in Nature Astronomy how recent breakthroughs in launch capabilities, climate, and synthetic biology demand a new assessment of the feasibility of terraforming Mars.
www.erikadebenedictis.com/s/The-case-f...Mars could be green in MY lifetime.
With new tech we could:
[Decades] Warm Mars enough to permit outdoor plant growth 🌞
[Decades] Cultivate a global biosphere 🌱
[Centuries] Allow plants to breathe oxygen into the atmosphere for human life. (Just like they did on Earth!) 🌳
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We’re lucky to be a nonprofit supported by the
@asterainstitute.bsky.social and get to do open science - rapidly sharing all our research and data. Follow along here:
pioneerlabs.substack.com
Pioneer Labs Reports | Substack
Science updates from the Mars microbe lab. Click to read Pioneer Labs Reports, a Substack publication with thousands of subscribers.
I went to the 2025 Symposium on Biomaterials, Fuels and Chemicals with an invitation from
@nils-averesch.bsky.social to speak about our work at
@pioneerlabs.bsky.social engineering organisms for sustainable biomanufacturing on Mars! I took 80 pages of notes.
docs.google.com/document/d/1...
Devon SBFC 2025 Notes
These are Devon’s conference notes for the 2025 Society for Industrial Microbiology and Biotechnology (SIMB) 47th Symposium on Biomaterials, Fuels, and Chemicals (SBFC). This version is intended for p...
Can we do BETTER than evolution with the help of AI? It starts with data. 🧬 🔢
Check out
@pioneerlabs.bsky.social's breakdown of how we get large-scale, high-fidelity data out of every engineering and evolution experiment!
This proposal is really interesting. Can you measure enzyme kinetics by adjusting substrate concentration *inside* the cell?
On one hand, cells are noisy. On the other, enzymes behave differently in vitro & in vivo. Best to measure in the conditions you care about!
Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇
Very excited by all the execution that's happening at Align! 💪
You know me, I just want to be drowning in data 😛
Q1 at Align =
✅ Team doubled
✅ 65k GROQ-seq datapoints
✅ Genotype-by-Phenotype platform
✅ Global conf. circuit
✅ Tournament prep underway
Get the full download →
hubs.la/Q03hT_V60
#ProteinEngineering #AIxBiology #SynBio #OpenScience
Time for a LOT of microbe data! 📊 🦠 🤖
@alignbio.bsky.social is aiming to gather a core dataset composed of phenotypes for 1000 diverse microbes cultivated in 1000 diverse conditions.
This labeled data has the potential to take our ability to predict how microbes will behave to the next level!
🚀 New proposal from Align! The experimental platform aims to standardize
#microbial #phenotyping & support predictive modeling. 🦠 Capturing data across 1k strains & 1k conditions; using BacterAI; generating high-quality datasets for ML @jensen_lab
Genotype to Phenotype: Design of an Extensible Experimental Platform for Characterizing Microbes
Government funding mechanisms for science need to evolve in the age of AI. 🤖 💰
How? Check out our Day One memo on how to repurpose 'Center' grants to fund large dataset acquisition.
🎄
@alignbio.bsky.social is hiring! Join The Align Foundation as the Chief of Staff or Open Science Admin and help make life science reproducible, scalable, shareable.
📍 Remote-friendly roles
🗓 Apply now, aiming to hire by Feb 2025
📧 Email cover letter + resume to contact@alignbio.org
•Switched gears to
@erika-alden.bsky.social and Align to Innovate!!
•she also switched gears from mathematical sims in astrophysics to biology and later on proteins ;)
•mission: “interface of biology, automation, and machine learning to rapidly convert the life sciences to a data-first discipline”
Had a lot of fun with this interview with
@agapakis.com. If you don’t know Christina, she is the one who resurrected an extinct flower scent during her time at Ginkgo. 🌸 Who better to talk about the big questions - like WHY we do science!
The first astronauts on Mars will use bacteria to make food, therapeutics & building materials.
What do you feed the 🦠? Here's the recipe:
- 40g of Mars dirt
- 1 liter of water
- Mix and strain
In our substack post, Pioneer Labs defines how to mimic this recipe on Earth. 🚀🌼
Check out 🏆A Biologist’s Guide to Mars Dirt, where we present a receipt for soluble Mars Regolith Media (sMRM) that best simulates what you’d get if you added water to Mars dirt.
Will anything grow in this media? Stay tuned!
💧+ 🪨 → 🌱 ?
open.substack.com/pub/pioneerl...
🏆 A Biologist’s Guide to Mars Dirt
Just add water
The next Alphafold2 will be a predictive model of protein expression. I think it's possible, and
@alignbio.bsky.social is going for it! 🧬
Every single protein engineering project I have ever worked on at one point or another ran into expression issues. 😠 It can't come soon enough! 🙏
🚀 News from Align! Today, we're sharing our proposal for building a predictive model of protein expression. Check it out here! ➡️
buff.ly/3OqtPZf ⬅️
🌍✨#ProteinExpression
#Bioengineering #Collaboration #MachineLearning #DataScience #AlignToInnovate
E11 Bio making *headway* on brain mapping... 🧠😜
🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains.
Read more:
e11.bio/news/roadmap
