Tag: biotech

Plant synthetic biology

Historically, synthetic biology has heavily focused on using well understood microbes such as E. coli as the “chassis” for engineering new biological processes—which at times has been criticized as a shortcoming of the field. Plants grow to an astounding number of different sizes and shapes, feed us, clothe us, provide the majority of our materials, and are estimated to constitute ~80% of the total biomass on Earth. Despite their central role in our existence, plants have been largely ignored in synthetic biology because of the difficulty associated with engineering them.

A central goal of synthetic biology has been to improve our ability to design new genetic circuits capable of carrying out complex processes. This type of computation is not a metaphor. An active area of research has been to establish a hardware description language for cells, where engineers can describe their intended process, and compile it into a DNA sequence with the appropriate circuits. They were specifically interested in lateral root density, which quantifies the number of outgrowths branching to the side from the main descending root. A higher lateral root density enables plants to better sample their environment for water and nutrients. Being able to precisely engineer this type of trait has global implications—this type of technology may be essential for sustaining agriculture in the future, and could be used as a tool to mitigate challenges plants will face in a warming climate.

Small Molecule Medicine

Unless you are old or chronically sick, it’s likely that the only drug you’ve ever taken that hasn’t been a small molecule is a vaccine. Indeed, drugs that aren’t small molecules are so strange and rare we usually don’t think of them as “drugs” but as a separate entity: vaccines, monoclonal antibodies, anabolic steroids.

But, like, the vast majority of molecules found in our body, and in all of organic life, are not classified as “small”. And the vast majority of the things doing something interesting are not really molecules, but more so fuzzy complexes of molecules (ribosomes, lysosomes, lipoproteins, membranes).

So why are virtually all drugs small molecules? Prima facie we’d expect most of them to be complexes made up of 10s to 1000s of very large molecules.

The answer lies in several things:

  • Easy to mass-produce
  • Simple to administer
  • Cheap to store
  • Homogenous in effect
  • Quick to act

Medicine is slowly undergoing the process of learning how to work with complex molecules. In parallel with normal medicine, I’d like to think that biohackers with the ability to custom order whatever they can dream of, will lead the way with self-experimentation. Figuring out the limits and benefits from individualized design and continuous monitoring. For now, this is mainly click-bait, people injecting a bioluminescence gene with CRISPR kinda stuff, but some of it isn’t. As an example, the guy from ThoughtEmporium self-designed a therapy to get rid of lactose intolerance (though the solution is not permanent, it lasts for a few months). 100s of other such people are engaging in similar experiments, and the more people do it, the more resources become available, the easier it will get, and the better the ROI. As this happens, social acceptance will follow and pharmaceutical companies will get more on the deal.

Casein Fermentation

Vegan cheese has been quite disgusting to date. But not the mozzarella that I tasted. The missing ingredient has been the casein protein of milk (and until now, it could only be had from milk). Melding innovative microbial fermentation science and traditional cheesemaking, New Culture’s mozzarella is the first animal-free cheese to melt and stretch. When I tasted it, it tasted, smelled, and stretched like milk cheese. The cheese is healthier (cholesterol and lactose-free) and better for the environment: of all food products, cheese requires the most water and is 3rd in greenhouse gas emissions and land use. Producing cheese from casein fermentation rather than animal milk reduces greenhouse gas emissions, and land and water usage by orders of magnitude, making the New Culture approach radically more climate-friendly than animal farming.

2023-03-13: A bit more progress

28 companies have sprouted up to develop milk proteins made by yeasts or fungi. The companies’ products are already on store shelves in the form of yogurt, cheese and ice cream, often labeled “animal-free.” The burgeoning industry, which calls itself “precision fermentation,” has its own trade organization, and big-name food manufacturers such as Nestlé, Starbucks and General Mills have already signed on as customers.
The dairy industry, with its clout and hefty lobbying budget, may not agree there is room for everyone: In 2022, US cow dairy had ceded 16% of all retail milk sales to plant-based milk. Plant-based milk companies also may not welcome the competition, especially if cultivated dairy products are positioned as more sustainable and less resource-intensive. A glass of almond milk takes 90 liters of water to produce.

50% more Food

Humans have an enzyme called FTO that demethylates N6-methyladenosine through oxidation. It’s part of a large family of enzymes that do this sort of thing using an iron atom in their active sites, along with molecular oxygen. Plants, though, don’t have an FTO homolog – they have some other enzymes that can demethylate this substrate, but not like FTO itself. So the team behind this paper wanted to see what would happen if you engineered the FTO enzyme into plants. In rice and potatoes, the crop yields went up by 50%. Grain size in the rice plants didn’t change, nor did the height of the plants – they just produced a lot more rice grains in general. How does this happen? The plants’ root systems were deeper and more extensive, and photosynthetic efficiency went up by a startling 36%. Transpiration from the leaves was up 78%, but at the same time, the plants of both species showed significantly higher drought tolerance. These are highly desirable traits, and it’s worth noting that a lot of this extra biomass is coming from increased usage of carbon dioxide from the air.

Now we just need to crush the GMO luddites to roll this out.

Put Silk in it

Researchers kept searching for the path to engineered silk. Yet, year after year, they failed. Each ran into scaling issues, production costs, and regulatory due diligence. After all this time, silk-based tech is weaving its way into health care, the food industry, and clothing.

SilkVoice is a gluey mix of hyaluronic acid and microscopic particles of regenerated silkworm silk meant to treat vocal fold disorders. SilkVoice is authorized for human use. The majority of the 40 people who have received the injections have retained their improvements.

Mori has commercialized silk as a way of protecting food. Unlike wax, Mori’s coating can cling to both water-repellent and porous surfaces, like the outside and inside of a zucchini. Mori already has pilots running at farms and food companies around the US, and larger-scale manufacturing is supposed to start later this year.

Kraig Labs claims to have produced the first “nearly pure” spider silk fabricated by silkworms and has scaled up production. It has partnered with a company in Singapore to make luxury street wear and is working with Polartec on performance outerwear. The company is also considering biomedical uses and bullet-resistant protective apparel.

Purdue University engineers have developed a method to transform existing cloth items into battery-free wearables resistant to laundry. These smart clothes are powered wirelessly through a flexible, silk-based coil sewn on the textile. “By spray-coating smart clothes with highly hydrophobic molecules, we are able to render them repellent to water, oil and mud. These clothes are almost impossible to stain and can be used underwater and washed in conventional washing machines without damaging the electronic components sewn on their surface.”

Retron Library Recombineering

RLR generates up to millions of mutations simultaneously, and “barcodes” mutant cells so that the entire pool can be screened at once, enabling massive amounts of data to be easily generated and analyzed. “RLR enabled us to do something that’s impossible to do with CRISPR: we randomly chopped up a bacterial genome, turned those genetic fragments into single-stranded DNA in situ, and used them to screen millions of sequences simultaneously. RLR is a simpler, more flexible gene editing tool that can be used for highly multiplexed experiments, which eliminates the toxicity often observed with CRISPR and improves researchers’ ability to explore mutations at the genome level.”

Human Glycome Project

The glycoletters in the data set could have formed nearly 1.2 trillion different glycowords. Yet, surprisingly, the researchers’ results indicated that only 19866 distinct glycowords were present across all the available sequences. The evidence suggested that all organisms follow very similar rules in assembling them and use essentially the same biomolecular language to define their structure.

Engram

Almost all neuroscientists base their search—for the physical basis of memory (the engram)—on the assumption that temporal-pairing causes learning. They are dedicated to this assumption—even though, as Rescorla pointed out 50 years ago, experimental attempts to define temporal-pairing have always failed. This failure is as striking now as it was 50 years ago. Anything that gets neuroscientists to abandon the idea that temporal-pairing is a useful scientific concept is a step toward discovering the physical basis of memory. Each neuron contains billions of (almost) incomprehensibly-tiny molecular machines. Molecular biologists have developed an astonishing array of techniques for visualizing/manipulating the actions of these little machines. These techniques will allow molecular biologists to follow the machines inside this huge neuron to the engram—to the tiny machine that encodes the experience-gleaned facts so that these learned/remembered facts can inform later behavior.

2021-11-19: This feels like a really big deal:

Biology feels different right now. New broadly enabling technologies and tools are driving forward progress in nearly every specific field at a rapid pace. The large scale adoption and application of a powerful set of common tools has created a virtuous cycle of further technology refinement and engineering. The rate of iteration is increasing, and previously intractable problems are now within reach. While RNA-seq and MPRAs are both valuable approaches, they come with some limitations. Fundamentally, each measurement represents a single static slice of a dynamic process which is only inferred by attempting to piece together the slices. The quality of the reconstruction is limited by sampling density. What if we could measure these systems continually as they occurred in a way that didn’t require destructive sampling? Here, the fundamental idea is that “DNA is the natural medium for biological information storage, and is easily ‘read’ through sequencing.” This forms the basis for this new technology: ENGRAM (ENhancer-driven Genomic Recording of transcriptional Activity in Multiplex). The workflow of this technique is very similar to that of the MPRA introduced above, but with an important twist. Instead of destroying the cell and sequencing a ratio of barcodes, the transcription event is recorded by the insertion of a barcode into a locus of DNA in the cell via prime editing. They went further and showed that they could effectively multiplex this technique by reading out all 3 signals in response to stimulants in a single population of cells. Even more, they showed a proof-of-concept for reading out the order in which events occurred.

Kati Kariko

Kati is a leading candidate for a Nobel. Amazing work.

1 fateful day, the 2 scientists hovered over a dot-matrix printer in a narrow room at the end of a long hall. A gamma counter, needed to track the radioactive molecule, was attached to a printer. It began to spew data.

Their detector had found new proteins produced by cells that were never supposed to make them — suggesting that mRNA could be used to direct any cell to make any protein, at will.

“I felt like a god,” Dr. Kariko recalled. [..] On Nov. 8, the first results of the Pfizer-BioNTech study came in, showing that the mRNA vaccine offered powerful immunity to the new virus. Dr. Kariko turned to her husband. “Oh, it works. I thought so.” To celebrate, she ate an entire box of Goobers chocolate-covered peanuts. By herself. Dr. Weissman celebrated with his family, ordering takeout dinner from an Italian restaurant, “with wine”. Deep down, he was awed.

“My dream was always that we develop something in the lab that helps people”. I’ve satisfied my life’s dream.” Dr. Kariko and Dr. Weissman were vaccinated on Dec. 18 at the University of Pennsylvania. Their inoculations turned into a press event, and as the cameras flashed, she began to feel uncharacteristically overwhelmed.

A senior administrator told the doctors and nurses rolling up their sleeves for shots that the scientists whose research made the vaccine possible were present, and they all clapped. Dr. Kariko wept.

Xenobots

The researchers let the cell clusters assemble in the right proportions and then used micro-manipulation tools to move or eliminate cells — essentially poking and carving them into shapes like those recommended by the algorithm. The resulting cell clusters showed the predicted ability to move over a surface in a nonrandom way.

The team dubbed these structures xenobots. While the prefix was derived from the Latin name of the African clawed frogs (Xenopus laevis) that supplied the cells, it also seemed fitting because of its relation to xenos, the ancient Greek for “strange.” These were indeed strange living robots: tiny masterpieces of cell craft fashioned by human design. And they hinted at how cells might be persuaded to develop new collective goals and assume shapes totally unlike those that normally develop from an embryo.

2021-11-29: And now they reproduce

The same team that built the first living robots (“Xenobots,” assembled from frog cells — reported in 2020) has discovered that these computer-designed and hand-assembled organisms can swim out into their tiny dish, find single cells, gather 100s of them together, and assemble “baby” Xenobots inside their Pac-Man-shaped “mouth” — that, a few days later, become new Xenobots that look and move just like themselves. And then these new Xenobots can go out, find cells, and build copies of themselves. Again and again. “These are frog cells replicating in a way that is very different from how frogs do it. No animal or plant known to science replicates in this way. We’ve found Xenobots that kinematically replicate. What else is out there?”

2023-07-04: Interview with Michael Levin about the amazing latent abilities of cells. This seems to be true recursively.

A big theme of your work has been that organisms have latent abilities—that the behavior we see in nature is contextual and that, by altering the circumstances, you coax them to do totally different things. What are some examples?

We are lulled into thinking that frog eggs always make frogs, and acorns always make oak trees. But the reality is that once you start messing around with their bioelectrical software, we can make tadpoles that look like other species of frogs. We can make planaria that look like other species of flatworms across 150 million years of evolutionary distance—no genetic change needed, same exact hardware. The same hardware can have multiple different software modes.

You can look at frog skin cells and say, “All they know how to do is how to be this protective layer around the outside. What else would they know how to do?” But it turns out that if you just remove the other cells that are forcing them to do that, you find out what they really want to do—which is to make a xenobot and have this really exciting life zipping around and doing kinematic self-replication. They have all these capacities that you don’t normally see. There’s so much there that we haven’t even begun to scratch the surface of.

Some object to speaking of what the cells “know” or “want” to do. Do you think that a concern about being anthropomorphic or anthropocentric has hindered research in this?

Incredibly so. I love to make up the words for this stuff because I think they need to exist—“teleophobia.’’ People go screaming when you say, “Well, it wants to do this.” People are very binary because they’re still carrying this pre-scientific holdover. Back in before-science times, you could be smart like humans and angels, or you could be dumb like everything else. That was fair enough for our first pass in 1700, but now we can do better. You don’t need to be at either of these endpoints. You could be somewhere in the middle. When I say this thing “wants to do XYZ,” I’m not saying it can write poetry about its dreams. It doesn’t necessarily have that kind of second-order metacognition; it doesn’t know what it wants. But it still wants.

Are the cells of our body continually measuring the payoff of cooperating vs. defecting, too?

Yes, but if you are a cell that’s connected strongly to its neighbors, you are not able to have these kinds of computations. “Well, what if I go off on my own? I could just leave this tissue. I could go somewhere else where life is better. I could set up my own little tumor.” You can’t have those thoughts because you are so tightly wired into the rest of the network. You can’t say, “Well, I’m going to ….” There is no I; there’s we. You can only have those thoughts, “What am I going to get?” when you’re not part of the group.

But as soon as there’s carcinogen exposure or maybe an oncogene that gets expressed, the electrical connection starts to weaken. It’s a feedback loop, because the more you have those thoughts, the more you’re like, “Well, maybe let me just turn that connection down a little bit. Now I’m really coming into my own. Now I’m out of here. I’m metastasizing.”

So a carcinogen would work in this case by disrupting the bioelectrical connections.

Exactly. What we’ve done in the frog system, and we’re now moving into human cells, is to show that [electrical weakening] happens, and that you can prevent it and prevent normalized tumors by artificially forcing the electrical connection. We can shoot up a frog with strong human oncogenes and then show that, even though those are blazingly strongly expressed, there’s no tumor because you’ve intervened. You’ve forced the cells to be in electrical communication despite what the oncogene is trying to get it to do.

2024-01-22: Basal cognition

Regular cells—not just highly specialized brain cells such as neurons—have the ability to store information and act on it. Now Levin has shown that the cells do so by using subtle changes in electric fields as a type of memory. These revelations have put the biologist at the vanguard of a new field called basal cognition. Researchers in this burgeoning area have spotted hallmarks of intelligence—learning, memory, problem-solving—outside brains as well as within them. Basal cognition offers an escape from the trap of assuming that future intelligences must mimic the brain-centric human model. For medical specialists, there are tantalizing hints of ways to awaken cells’ innate powers of healing and regeneration. “What we are is intelligent machines made of intelligent machines made of intelligent machines all the way down.”