koeng

Recently got genomic DNA purification automated for yeast (plus have automated library prep for nanopore+ a promethion)! As part of the DNA purification task, I had to journey up to Healdsburg to buy some lysis enzyme (thank god for winemakers, 100x cheaper than the biotech grade stuff), and noticed catalogs of different yeast strains with all their flavor profiles and stuff characterized.

I'm thinking about buying all the strains and pushing them through my automated sequencing pipeline, and building a yeast genotype -> flavor converter. Then, I think it'd be neat if you could have someone try a bunch of wines to get their favorite, and then genetically engineer a yeast strain specifically for their favorite flavors. Think that could be neat.

I've worked in this field for many years. It's unfortunate that fears of AI have tarnished the field of synthetic cells so dramatically and yet so ignorantly. It's somewhat akin to believing we should ban charcoal because it is used to make (black) gunpowder, which is equally ridiculous

Another thing I’m working on: homemade linen.

Right now I just germinated a 4x8 bed with flax for fiber. The plan is to grow it for 100 days or so and then harvest, dry, ret, dry, and spin. I need a lot more to do anything serious, but I think it’d be awesome to have a scarf that I made with linen I grew and harvested myself

I’m smelting ore!

I got into creating my own rings, and I’d really like to create one with ore I harvest myself. Gold is too hard and silver can be kinda dangerous, but malachite is pretty safe and I can just drive to Copperopolis to pick some up.

Basically: smelt the malachite with flux and charcoal to get pure copper, flow that into an ingot mold, hammer it into shape. Then I’ll have my own ring, with metal I collected with my own hands

I met Craig about a year ago or so at a synthetic biology conference. Even though his institute was the one which created the first synthetic cell, he pretty much just talked about how disappointing it was that we couldn't engineer the ribosome more. Was a funny memory :) guess you always want more once you do something great.

I do some synthetic biology as a hobby - genetically engineered a baker’s yeast to produce grape aroma and then baked bread with it, and gave it to like 100 people at an event I was at.

Also do a few others - learned Esperanto (exclusively through listening and speaking with people), beekeeping, woodworking, etc.

if 10x the average amount of microplastics are showing changes that are approximately equivalent to hormonal or behavioral changes, it's not a significant factor to be worried about.

There are many times where unblinded experiments are still valid. And unfortunately, n=1 means that you can't have controls. The question: "did this intervention, in one person, cause a greater-than-normal increase in epigenetic changes, above baseline?"

eh, not that concerned

yes

Microplastics are bad. People are concerned that there are microplastics in your balls! And that this could epigenetically affect downstream generations. I want to test that theory with a real human, not an animal model.

My plan: collect my own sperm samples over time and do whole DNA preps + basic body metrics. Sperm regenerates approximately every 10w, so planning time series over 10w. Next, inject myself to ~10x the average amount of microplastics, directly into the bloodstream. Continue with the sperm collection, DNA preps, and basic body metrics. Nanopore sequence, and see if there actually ARE any epigenetic changes. Eventually I'll go back down to baseline - are there any lasting changes?

Of course, this is an N=1 experiment, but rather than a metastudy I'm directly changing one variable, so I think it is valuable. We should have more people doing controlled experiments on themselves for the sake of all of society - and as a biologist, I actually have the capacity to design the experiments and scientifically interpret the results. In a way, it's part of civic duty :)

I work in DNA assembly and synthesis. Here is my take:

They don't use oligo pools - "This capacity may be adapted to use large oligo pools to substantially reduce the cost per construct45 but requires further engineering to account for the formation of the unintended Sidewinder heteroduplexes before assembly and the higher truncation rate of pooled oligos"

This absolutely destroys any unit economics when it comes to DNA synthesis. Oligo pool synthesis isn't 10x cheaper, it's 100x to 1000x cheaper than individual oligo synthesis.

So what they really have is a good way to do DNA assembly from synthesized oligos; fair. But we have that: GoldenGate can do 40 part assemblies, hell it can do 52 part assemblies, and you CAN use oligo pools - https://pmc.ncbi.nlm.nih.gov/articles/PMC10949349/ (there are a couple enzymatic properties which allow this, mainly that you can use full doublestranded DNA, which you can make with a PCR. Can't make these overhang guys with a PCR).

We've even found that with some GoldenGate enzymes, the biology somehow breaks the current models of the physics of ligation by being so efficient - https://www.biorxiv.org/content/10.64898/2026.01.31.702778v1

Their gels do look really good, I'll admit. I can imagine circumstances (exception cases) where this would be better. But not only is this kind of thing for 99% of cases has already been available for many years while being orders of magnitude cheaper (plural).

I am also a fan of SQLite. One of the best parts during development is how easy it is to spin up and spin down databases for full integration tests without containers or anything. It also simplifies backups, and is probably good enough.

I don’t think it’s legal for me to sell it (it is a genetically modified organism used in food), but I’d like to figure out if I can just give it away

keonigandall.com

Very neat! How do you standardize the gluten free mixes?

I’ve been thinking about trying this since my mom is gluten free

Already answered there: I’m using bakers yeast, not lab yeast (store-bought S cerevisiae). It’s not haploid, often it’s tetraploid. HR doesn’t guarantee homozygous transformation.

Same answer for electroporation vs spheroplasty. I’ve found with wild yeasts or less tamed yeasts (pichia), sometimes just nuking the damn thing with kV will just work, whereas those chemical methods can be way more finicky. Time is money

I’d recommend buying an Odin kit and just trying it. Doesn’t take THAT much to get into genetic engineering.

The tough part is mostly the finesse in the simple things, like trying this in bakers yeast rather than lab yeast, or the genetic design.

Cost is quite high for mistakes, but LLMs are honestly quite good to help you out with the basics. You MUST at least try to read the papers though - it’s not like coding where you can mostly let it do its thing.

Eh, other than the electroporator I could probably do it for about $100-$200 bucks of equipment if I had a decent kitchen.

Reagents probably about $300, but you can use em in a bunch of reactions, in aggregate down to like $50.

The fundamentals of biology are really cheap, but the skills to actually do it are really expensive. It’s way more manual than you imagine - like how my thumb moves. The equipment is way more fundamentally basic than you imagine: the only thing you can’t 3d print and build from off-the-shelf stuff is the instant pot I use for media prep

I’ve only done grape so far. It’s on the verge of subtle vs unsubtle. If you’re real used to smelling yeast OR are a woman who has a strong sense of smell, you can smell it. Otherwise it’s just bread.

It’s kinda unfair how much better women were at smelling it (empirically)

I really need to do a write-up. I kinda just whip up the easiest path and do it.

For example for the grape, I needed to knock out some tryptophan synthesis genes so I could redirect the bioflux. Problem is that in bakers yeast they have a whole buncha copies of their chromosomes, so I had to knock out one of the genes and replace it with a different gene from grapes. Did that with a quick lil CRISPR switch.

Had to electroporate tho because the transformation rates on wild/bakers/non-lab yeast are so garbage

I’m genetically engineering yeasts to make subtly flavored breads. I’ve already done grape aroma, now working on wintergreen.

Also working on a red chamomile (using beat red biosynthesis). Just for fun. Red chamomile tea!

The idea is to have niche invite-only genetically engineered flavors that I can bring to parties around SF :) what’s more special than a genetically engineered organism that you can ONLY get if I’m there? Good calling card

Neat! Would this mainly be used for JavaScript servers running bun (ie, not end users)?

“The Panopticon is good”

I've been working on a sillier project lately. Green teeth!

Lumina has made a probiotic strain that is able to, theoretically, prevent cavities. I don't care that much about, but I do think it is a neat strain that can likely colonize your mouth. I'm genetically engineering it to express sfGFP, which would theoretically make my teeth fluorescent green under black light. Would be fun at raves! Also, if I make out with anyone, you could theoretically see changes in microbiome composition just from green-ness. I do wonder how much microbiomes are shared while kissing: this would be an example of a way to directly measure that, instead of just measuring on proxy like much microbiome research

I don’t think Java and Rust were so ok with completely removing features. For example, in Zig 0.15 they completely overhauled the io, meaning all libraries now have to rewrite up usage. Just to make sure they did it right

95% for humans. Who failed to get the butter?

Very chill :)

I do this at an industrial scale. It gets really annoying as you scale up to hundreds / thousands of different strains, all of which need pickable colonies.

A serial dilution 3 or 4 times seems to always do the trick. Typically on a robotic workstation you have to aspirate 6.5uL, then slowly dispense 5.5uL above the Petri dish (sbs format) and then stab into the agarose. Makes lovely perfectly-sized and separated wells, so 96 cell lines fit on only 3 or 4 plates.

With better plate reading you can get that down to 1 or 2 plates but it’s less reliable

We've known TALENs work for years. For example - https://pmc.ncbi.nlm.nih.gov/articles/PMC4817924/ - from 2015

I worked on a project many years ago to do RNA import into yeast mitochondria (and then hopefully reverse transcribe there). Didn't work, and a lot of the info on RNA import into the mitochondria is... suspect.

Mitochondria engineering is just actually tough. 30 years and no new protocols for getting DNA in there :(

I've thought a lot about this! My main goal is to create a cloud lab that doesn't suck - ie, a remote lab that is actually useful for people, and a lot of these are relevant things. Let me run down the ideas I have for each

1. You can purchase gel boxes that do 48 to 96 lanes at once. I'd ideally have it on a robot whose only purpose is to load and run these once or twice a day. All the samples coming through get batched together and run

2. Bioanalyzer seems nice for quantification of like PCRs to make sure you're getting the right size. But if I'll be honest I haven't though that much about it. But qPCRs actually become very cheap, if you can keep the machines full. You can also use something like a nanodrop and it is much much cheaper

3. Pichia pastoris expression ^

4. You can use a plate reader (another thing that goes bulk nicely), but the reagents you can't really get around (but cheaper in bulk from China)

5. If you aggregate, these become really cheap. The complicated bits are getting the proper cytomat parts for shaking, as they are limited on the used market

6. These can't be automated well, so I honestly haven't thought too much about it.

7. Reagents cheaper in bulk China

8. ehhhh, maybe? But not really. But if you think about a scaled centralized system, you can get away with not using oligos for a lot of things