Chapter 12: Biotechnology and Synthetic Biology

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All right, diving in today, folks.

We're going deep, really deep into biotech and synthetic bio, you know, like manipulating life at the DNA level, crazy stuff and the things they're doing with it now,

mind blowing, honestly.

Absolutely.

It's amazing what's happening.

So for our listeners, think of this as our mission, right?

We're taking this whole chapter you gave us, breaking it down piece by piece, all the core concepts, tools and applications so that by the time we're done, you'll get it.

You'll understand the nuts and bolts of how these things work and the impact, the real impact they're having out in the world.

Definitely.

We want to equip our listeners with a solid grasp of the field.

And we know you folks are a smart bunch.

Some of you are deep in the science already and others are just super curious, which we love.

So we'll try to keep it clear, avoid the jargon overload where we can, but, you know, we won't shy away from the details either.

Right.

The details are what make it all come together.

Exactly.

And looking at this chapter, it's really well organized.

It breaks down into like three key areas.

We've got the tools of the genetic engineer, those are the core techniques, the essentials.

Then we move into making products from genetically engineered microbes,

biotechnology, which is where things get really interesting.

And then finally, the cutting edge, synthetic biology and genome editing, which honestly, it's like science fiction becoming reality.

It really is pushing the boundaries of what we thought was possible.

So let's start with those tools of the genetic engineer, specifically DNA manipulation in vitro, meaning outside a living organism.

What's the big deal about doing this outside a cell?

Well, working with DNA inside a living cell can be incredibly complex.

There are so many factors at play.

These in vitro techniques, though, they give scientists much more control, much more precision.

Makes sense.

So the first tool in this kit, and it's a big one, is PCR, polymerase chain reaction.

I always picture it as a molecular photocopier, right?

Start with a little DNA, end up with tons of it.

That's a great analogy.

That's essentially what PCR does.

It's all about replicating a specific DNA segment over and over, exponentially, all in a test tube.

And it works through a series of cycles, each with three steps, denaturation, annealing, and extension.

It's like a dance.

A DNA dance, huh?

I like it.

So first, you heat things up really hot.

That's denaturation.

The heat breaks the hydrogen bonds, holding the two DNA strands together so they separate, become single -stranded.

Got it.

Separate the strands.

What's next?

Next comes annealing.

You lower the temperature, and that lets these short pieces of DNA called primers bind to specific matching regions on the separated strands.

These primers are like the starting blocks for the next step.

So they attach at specific spots.

And then extension, raise the temperature a bit, and the special enzyme, DNA polymerase, comes into play.

It grabs onto the primer and starts building a new strand of DNA, using the original strand as a template.

So you're building new DNA strands based on the original.

And this happens over and over, exponentially increasing the amount of DNA, right?

You got it.

And a key player here is Taq polymerase, a heat -resistant enzyme from the bacterium thermus aquaticus.

Remember those high temperatures for denaturation?

Well, regular DNA polymerase would just fall apart, but Taq, it's a champ, thrives in the heat.

So it can keep working through all those cycles, even with those temperature swings.

Yeah.

Makes sense.

And the applications of PCR, I mean, wow, this is where things start to get really cool, right?

Absolutely.

PCR is used everywhere.

Cloning genes, figuring out the order of DNA bases in sequencing, phylogenetic studies, which is basically tracing the evolutionary relationships between different organisms.

Like building the family tree of life using DNA, pretty wild.

Precisely.

And then think about surveying microbial communities, understanding the diversity of microbes in different environments.

So we can look at, like, the microbes in soil, the ocean, even our own gut.

Exactly.

And don't forget the practical stuff, medical diagnostics.

Think about rapidly identifying a virus from a tiny patient sample.

Huge in healthcare, for sure.

And forensics.

Imagine solving a crime with a single hair.

PCR can make millions of copies of the DNA from that tiny sample, making analysis so much easier.

It's like a magnifying glass for DNA.

It's incredible how much information we can extract from such tiny amounts of DNA now.

It really is.

And there are even variations like qPCR, which not only amplifies the DNA but also tells you how much you started with, and RTPCR, which is super important for working with RNA.

Right.

RTPCR, you start with RNA, convert it to DNA using reverse transcriptase, and then amplify that DNA.

So it's a way to study gene expression to see which genes are actively being transcribed into RNA.

Plus, it lets you get rid of the introns, those non -coding sequences, and eukaryotic genes.

That's crucial if you want to express a eukaryotic gene in bacteria, because bacteria don't have the machinery to deal with introns.

Absolutely spot on.

And speaking of visualizing and separating DNA, that's where gel electrophoresis comes in.

It's like a sorting machine for DNA fragments.

Ah, yes.

Gel electrophoresis.

Back in my college days, I remember those agarose gels.

They're like firm jello.

You load your DNA samples into little wells, apply an electric current, and then magic.

Not magic, science.

But it's pretty cool.

DNA is negatively charged thanks to those phosphate groups, so when you apply an electric current, it moves towards a positive electrode.

The gel acts like a sieve, with the smaller DNA fragments zipping through the pores faster than the bigger ones.

So you end up with these bands of DNA separated by size, but you can't actually see the DNA itself, right?

Nope.

You need to stain it.

Ethidium bromide is a common dye.

It slips in between the DNA bases, and when you shine UV light on it, it fluoresces, making the DNA bands glow.

Ah, that's why we wear those funk -in -ringe goggles in the lab.

Safety first.

But yeah, gel electrophoresis is super useful.

You can check if your PCR worked, make sure you got the right size DNA fragment, and you can even purify specific fragments from the gel for further experiments.

Okay, so we can make copies of DNA separated by size.

The next tool, nucleic acid hybridization.

This one always felt a bit more abstract to me.

It's based on a really simple and elegant principle, though.

Complementary base pairing.

Remember, A always pairs with T, and C with G in DNA.

So a single -stranded DNA or RNA molecule will naturally seek out and bind to another single strand if their sequences match up, forming a double helix, like two halves of a zipper coming together.

So it's all about finding the perfect match.

Exactly.

And that's where nucleic acid probes come in.

These are short, single -stranded DNA or RNA sequences that we know the exact sequence of, and they're labeled either with a radioactive tag or a fluorescent molecule.

We can use these probes to specifically detect whether a particular DNA or RNA sequence is present in a sample.

So you introduce your probe into a mix of DNA or RNA, and if it's complementary sequences there they'll bind, and you can detect that binding because of the label, right?

Exactly.

And you can control how stringent this binding has to be.

Higher stringency means only a perfect match will do, which is really important for distinguishing between very similar sequences.

So it's like adjusting the sensitivity of your detector.

Precisely.

And the material mentions these techniques, southern blotting and northern blotting, which might sound a bit old school, but they're still widely used.

Southern blotting, that's for DNA, right?

You got it.

You separate DNA fragments on a gel, transfer them to a membrane, and then use your labeled probe to see if your target sequence is present on that membrane.

If it is, the probe binds, you see the signal, boom, you found your DNA fragment.

And northern blotting, that's the same idea, but for RNA instead of DNA.

You're on a roll.

It's the same basic principle.

But you start with RNA and use a probe to find a specific RNA molecule.

Really useful for studying gene expression, seeing which genes are being transcribed and how much of their RNA is present.

So you can actually see which genes are active in a cell or tissue.

Exactly.

And then there's IshIA fluorescence in -situ hybridization.

This one is about visualizing specific sequences directly within cells.

So instead of extracting the DNA or RNA, you're looking at it right where it lives inside the cell.

Precisely.

You use fluorescently labeled probes to target those sequences, and you can actually see where they are physically within the cell, often while they're still in the chromosomes.

Really helpful for identifying pathogens,

looking at environmental samples, and figuring out which organisms are present and what genes they have.

Amazing.

So from amplifying DNA to separating it and even visualizing specific sequences, it's an impressive toolkit.

But now, how do we actually move genes around, create these Frankenstein -like combinations of DNA?

That's molecular cloning, right?

It is.

It's the heart of genetic engineering.

It's all about taking a specific gene or DNA fragment, inserting it into a vector, which is like a little DNA carrier, creating this recombinant DNA molecule, and then getting that vector into a host cell where it can be replicated.

So the vector is like a delivery truck for our gene of interest.

A very efficient delivery truck.

And the DNA you want to clone, it can come from PCR, from reverse transcription of RNA, or even be chemically synthesized from scratch.

And there are different types of vectors, plasmids, viruses, cosmets, artificial chromosomes, each with its own strengths and limitations.

So like different types of delivery trucks for different cargo sizes and destinations?

Exactly.

And a key thing is that these vectors can replicate on their own inside the host cell.

They've got a special sequence called an origin of replication that tells the host cell to make copies of the vector.

Now to actually insert the DNA into the vector, we often use restriction enzymes and DNA liggies.

Ah, restriction enzymes, the molecular scissors.

I remember those.

They recognize specific DNA sequences, right?

Often palindromes, those sequences that read the same backward and forward.

You're spot on.

And when they cut the DNA, they can create these sticky ends, which are these single stranded overhangs.

Imagine cutting a piece of paper so that it has little flaps sticking out.

You cut another piece of paper with the same scissors, those flaps can match up and temporarily stick together.

It's the same with DNA.

So the sticky ends from the vector and the DNA fragment you want to insert, they can bringing the two pieces together, but it's not a permanent bond yet, right?

Right.

That's where DNA legus comes in, the molecular glue.

It seals the nicks in the DNA backbone, creating a continuous, stable DNA molecule.

And the material also mentions this newer technique, recombineering.

How does that work?

It's a more targeted approach.

It uses the cell's own homologous recombination machinery.

You basically provide short DNA fragments that match the target site in the bacterial chromosome or plasmid where you want to insert your DNA.

And then you introduce special enzymes, recombinases that facilitate the exchange of DNA at those matching regions.

So it's a way to insert DNA without needing those specific restriction enzyme sites.

Makes sense.

But once you've got your recombinant plasmid, how do you know which bacteria have actually taken it up?

That's where those selectable markers in the plasmid come in handy.

For example, the plasmid PUC19 has a gene for ampicillin resistance.

So you grow your bacteria on media -containing ampicillin, and only the bacteria that have taken up the plasmid will survive.

So it's like a test.

Only the bacteria with the plasmid pass.

Precisely.

And PUC19 also has this clever blue -white screening system.

The multiple cloning site, the MCS, where you insert your DNA, is located within the lacZ gene.

Wait, lacZ, isn't that the gene for ecolactosidase, the enzyme that cleaves X -gal and makes things turn blue?

You got it.

So if your DNA inserts correctly into the MCS, it disrupts the lacZ gene.

The bacteria can't make lactosidase, so the colonies stay white.

But if the plasmid doesn't have your DNA insert, the lacZ gene is intact, the enzyme is made, and the colonies turn blue when you add X -gal.

So white colonies mean success, blue colonies mean no insert.

It's like a built -in visual indicator.

That's clever.

It is.

Very clever.

The material also mentions some other specialized vectors, like PCR vectors, shuttle vectors, and YACs, which are specifically designed for different purposes.

PCR vectors, those are for efficiently cloning PCR products.

Shuttle vectors, those are cool because they can replicate in two different host organisms, like bacteria and yeast.

So you can do some manipulations in bacteria, then transfer your gene to yeast for expression or further studies.

And YACs, those are the heavy lifters, right?

They can carry really big pieces of DNA, like those found in complex organisms with large genomes.

You're absolutely right.

And the common host organisms used for cloning, those are the workhorses of molecular biology, E.

coli, Bacillus subtellus, and Saccharomyces cerevisiae, the baker's yeast.

And why are these particular microbes so popular?

Well, they're well studied, we know their genetics inside and out, and they're relatively easy to grow in the lab, which makes them ideal for a wide range of experiments.

E.

coli is like the lab rat of microbiology, used for all sorts of things.

Bacillus subtellus is really good at secreting proteins into the surrounding media, which can make purification easier.

And yeast, being a eukaryote, it's often preferred when you need some of the protein modification machinery that bacteria lack.

So different microbes for different needs.

Makes sense.

Okay, so now we have this powerful toolkit to manipulate DNA and get it into host cells.

But getting a foreign gene into a bacterium is only the first step.

The next challenge is getting it to actually express to produce the protein you want.

And there are some potential roadblocks here, right?

You bet.

Just because a gene is there doesn't mean it's going to be expressed properly.

It's like having the blueprint for a house, but not the builders or the right materials.

First off, you have to think about the promoter.

That's the DNA sequence that tells the RNA polymerase where to start transcribing the gene.

A bacterial promoter might not work for a eukaryotic gene, just like a builder might not understand the blueprints for a Martian house.

So you need to make sure the builder, the RNA polymerase, can actually read the blueprints, the promoter.

Yeah, exactly.

And then there are those pesky introns in eukaryotic genes.

Bacteria don't have the machinery to remove them, so you have to either use cDNA, which is DNA made from mRNA that's already had the introns removed, or you can synthesize the gene from scratch, leaving out the introns.

It's like editing the blueprints to make them easier for the bacterial builders to follow.

Precisely.

And even the way bacteria read the genetic code can be different.

They have their own preferred codons, which are the three -letter words in the DNA sequence that specify which amino acid to add to a protein.

If a eukaryotic gene uses a lot of codons that are rare in bacteria, it can slow down protein production or even introduce errors.

So you have to translate the blueprints, so to speak, making sure they use the bacterial language.

Exactly.

That's often done through codon optimization.

And finally, some proteins, especially eukaryotic ones, need modifications after they're made.

Things like glycosylation, where sugars are added.

Bacteria often can't do these modifications, which can mess up the propene's function.

It's like adding the finishing touches to the house, the paint, the landscaping.

If those are missing, it might not be quite right.

So how do we overcome these challenges?

We use special expression vectors.

These are vectors specifically designed to ensure efficient and accurate transcription and translation of the gene in the host cell.

So they're like deluxe delivery trucks that come with all the tools and materials needed for construction.

Exactly.

They often have strong bacterial promoters, sequences that really kickstart transcription, like having a super motivated construction crew.

And you can even include sequences that ensure the ribosomes, the protein -making machines, bind efficiently to the mRNA, and you can optimize the codon usage to make sure the bacteria can read the instructions smoothly.

And for eukaryotic genes, you can use cDNA or even synthetic genes that have been designed from scratch to include all the necessary elements for proper expression in bacteria.

Absolutely.

It's all about giving the bacteria the best possible blueprints and tools for the job.

And another neat trick is to use fusion proteins.

Here you fuse your gene of interest to another gene, often for a protein that's easy to purify.

So it's like attaching a handle to the protein, making it easier to grab and pull out of the mix.

Exactly.

And you can even engineer these handles so that they can be cleaved off after purification, leaving you with your pure protein of interest.

Very clever.

Now, let's talk about actually modifying genes themselves.

The material mentions molecular methods for mutagenesis.

That sounds like something out of a superhero movie.

It's not quite superhero powers, but it does allow us to make very precise changes to DNA sequences.

Site -directed mutagenesis is a key technique here.

It lets you change single DNA bases, add short sequences, or even delete parts of a gene.

So you can edit the blueprints at a very fine level, changing individual letters or even whole words.

Precisely.

And it's often done using synthetic oligonucleotides, these short, custom -designed DNA sequences that carry the desired mutation.

It's like having a tiny DNA editor.

And you can use these oligonucleotides as primers in PCR or incorporate them using recombineering.

So you trick the cell into copying the mutated DNA sequence during replication.

Exactly.

This is hugely important for studying how proteins work, like figuring out which amino acids are essential for an enzyme's activity.

And it's also used to engineer better proteins, ones that are more stable, more efficient, or have new functions.

So from understanding basic biology to engineering new and improved proteins, it's a powerful tool.

Absolutely.

And then there's cassette mutagenesis.

Here, you replace a bigger chunk of a gene with a synthetic DNA fragment, a cassette.

It's like swapping out an entire section of the blueprints.

Really useful for introducing multiple mutations at once.

Or for swapping out whole functional domains within a protein.

So more like a major renovation than just tweaking a few letters.

Precisely.

And finally, there's gene disruption, or gene knockout.

Here, the goal is to inactivate a gene, essentially turning it off.

You usually do this by inserting a piece of DNA into the gene, disrupting its coding sequence so it no longer produces a functional protein.

Like cutting the wires to a specific machine in the factory, seeing what happens when that machine stops working.

Exactly.

It helps us figure out what that gene normally does.

Now let's move on to reporter genes and gene fusions, which are like spies in the world of molecular biology.

Spies.

That sounds intriguing.

They're used to track gene expression.

To see when and where a gene is turned on or off.

Reporter genes code for proteins that are easy to detect, like galactosidase, which turns things blue.

Or green fluorescent protein, GFP, which glows green under UV light.

So you attach the reporter gene to the gene you're interested in, and then you can literally see when that gene is being expressed.

You create a reporter gene fusion.

You fuse the regulatory region of your gene of interest, the part that controls when it's turned on or off, to the coding sequence of the reporter gene.

If your gene is turned on, the reporter gene will also be expressed, and you'll see the blue color or the green fluorescence.

It's like having a light bulb that turns on whenever the gene is active.

So it's a visual readout of gene expression.

Very cool.

And the material mentions two types of fusions.

Operon fusions and protein fusions.

What's the difference?

In an operon fusion, you're essentially putting the reporter gene under the control of the regulatory elements of your gene of interest.

It's like wiring the light bulb directly to the switch that controls your gene.

In a protein fusion, you're actually fusing the coding sequences of the two genes together, so they're transcribed and translated as a single unit.

This creates a hybrid protein with your protein of interest attached to the reporter protein.

So operon fusion is like watching the switch, while protein fusion is like tagging the protein itself with a tracker.

Exactly.

Now, with all these tools at our disposal, we can really start using microbes as miniature factories to produce all sorts of valuable products.

That's biotechnology in action.

It's incredible to think that these tiny organisms can be engineered to make medicines, fuels, and all sorts of other useful stuff.

It really is.

One of the early successes of biotechnology was producing therapeutic human proteins in bacteria.

This has been a game changer for medicine, making many essential medicines much more affordable and accessible.

Absolutely.

Think about human growth hormone, for example.

It used to be extracted from cadavers, which was expensive, and carried risks.

Now we can produce it in bacteria thanks to recombinant DNA technology.

Precisely.

And the list goes on.

Erythropoietin for treating anemia, blood clotting factors for hemophilia, TPA for dissolving blood clots, even enzymes like DnaZi for cystic fibrosis.

All of these are now routinely produced in bacteria or other microbial systems.

It's truly remarkable.

And then there are transgenic organisms, GMOs, which have been engineered to carry genes from other organisms.

The most common application is in agriculture, right?

Exactly.

Using techniques like the T -plasmid from agrobacterium tumifatians, which can naturally transfer DNA into plant cells, we can now create crops that are resistant to herbicides, pests, or even diseases.

It's like giving them genetic armor.

But this is also an area that sparks a lot of debate, with concerns about potential environmental and health impact.

It's true.

The use of GMOs is a complex issue with ethical, social, and ecological dimensions that need to be carefully considered.

Absolutely.

Now let's talk about vaccines.

Recombinant DNA technology has also revolutionized how we make vaccines.

Indeed.

Instead of using weakened or inactivated pathogens, which can sometimes be risky, we can now use recombinant methods to create safer and more effective vaccines.

So what are some of the approaches here?

We have live, attenuated vaccines, where the pathogen is genetically modified to remove its virulence genes, making it harmless but still capable of triggering an immune response.

Then there are vector vaccines, where harmless viruses are used to deliver genes from a pathogen, essentially turning them into harmless mimics.

And subunit vaccines, which use only specific, highly immunogenic proteins from a pathogen, often produced in yeast or other systems.

So instead of using the whole pathogen, we're using just the parts that trigger the immune response, making the vaccines much safer.

Exactly.

And recombinant technology also allows us to create polyvalent vaccines, which can protect against multiple diseases at once.

That's amazing.

And then there's this really cool idea of using our own microbiome, the bacteria that live in and on us, as a drug delivery system.

That's a cutting edge area of research.

We can engineer commensal bacteria to produce therapeutic proteins right where they're needed in the body.

For example, bacteria can be engineered to release anti -cancer drugs directly at a tumor or to produce hormones like GLP -1 for diabetes treatment.

It's like having a personalized, targeted drug factory right inside our bodies.

And the material also mentions using engineered bacteria to deliver antibodies as anti -cancer therapies, especially for those tricky intracellular targets.

Yes.

Antibodies are great for targeting things on the cell surface, but getting them inside cells to target intracellular proteins is more challenging.

One approach is to use a modified version of the anthrax toxins protective antigen, which can naturally deliver proteins into cells.

We can engineer this system to carry therapeutic antibodies that target specific proteins inside cancer cells.

It's like sneaking past the cell's defenses with a Trojan horse.

Precisely.

Now, moving beyond individual products, we're also seeing exciting advances in metagenomics and pathway engineering.

Metagenomics, that's about exploring the vast genetic diversity of microbial communities, right?

Like looking for new and useful genes and enzymes in soil, water, or even our own gut.

Exactly.

It's like a treasure hunt for genetic gold.

And pathway engineering takes it a step further by assembling new or improved metabolic pathways in microbes, often by combining genes from different organisms.

This allows us to engineer microbes to produce valuable compounds like indigo dye, artemisinic acid, and even precursors to opiate drugs.

So we're not just using microbes to make copies of existing molecules, we're designing them to produce entirely new ones.

You got it.

And then there's biofuels, the quest for sustainable alternatives to fossil fuels.

We can use genetic engineering to improve the production of biofuels from sources like switchgrass and microalgae.

So we can engineer microbes to break down plant material more efficiently, or we can tweak algae to produce more lipids that can be turned into biodiesel.

Precisely.

However, scaling up these processes to make them commercially viable remains a challenge.

Okay, so we've covered the fundamental tools and the amazing applications of biotechnology using genetically engineered microbes.

Now let's dive into the really cutting edge stuff, synthetic biology and genome editing.

Synthetic biology is all about designing and building biological systems from the ground up.

It's like having a Lego set of biological parts promoters, ribosome binding sites, protein coding sequences that you can assemble into more complex modules.

So instead of just tweaking existing organisms, we're building entirely new biological systems with specific functions.

That's wild.

It is.

We can engineer microbes to produce valuable compounds like vanillin, ortomycinic acid, and even precursors to morphine.

And we can create complex genetic circuits, like those that control drug delivery based on cell density or even bacterial photography, where bacteria create images based on light patterns.

It's like programming living cells to do our bidding.

In a way it is.

And then there's the even more ambitious goal of creating synthetic genomes, essentially building entire cells from scratch.

The creation of JCVI SYN 1 .0, a cell with a fully synthetic genome, was a huge milestone.

It's incredible to think that we can now synthesize entire genomes and even create minimal cells with only the essential genes needed for life.

It really pushes the boundaries of what we thought was possible in biology.

And then of course we have genome editing, with CRISPR -Cas9 being the rock star of the field.

CRISPR -Cas9, that's the system that allows us to make incredibly precise edits to DNA, right?

Precisely.

It's like having a molecular scalpel.

The Cas9 protein is an enzyme that can cut DNA,

and it's guided to a specific target sequence by a guide RNA.

You can design the guide RNA to target virtually any sequence in the genome.

So you can target specific genes and make very precise changes, like correcting mutations or inserting new genes.

Exactly.

And the applications are vast.

Editing the genomes of plants and animals for agricultural improvements, correcting genetic defects in human cells for potential therapies, even engineering gene drives to control disease vectors like mosquitoes.

Gene drives are fascinating and a bit scary, too.

The idea that you can engineer a genetic trait to spread through an entire population is both powerful and potentially risky.

It's true.

There are significant ecological and ethical considerations that need to be carefully addressed before such technologies are deployed in the real world.

Absolutely.

And finally, we have the issue of biocontainment for GMOs.

How do we make sure these engineered organisms don't escape and cause unintended consequences?

That's a critical question.

Traditional methods like making GMOs dependent on specific nutrients or engineering them to be self -destructive have limitations.

Newer approaches like genome recoding, where you essentially rewire the genetic code of an organism, making it dependent on synthetic amino acids that don't exist in nature, offer a more robust way to contain GMOs.

So you create a biological firewall preventing the engineered organisms from surviving outside a controlled environment.

That's brilliant.

It is.

And CRISPR technology is also being explored as a tool to enhance biocontainment strategies.

Wow.

We've covered a lot of ground today.

From the basic tools of genetic engineering to the incredible applications of biotechnology, synthetic biology, and genome editing, it's mind -blowing to see how far this field has come.

It really is.

And it's just the beginning.

We're only scratching the surface of what's possible with these powerful technologies.

And with that power comes responsibility.

We need to have open and honest conversations about the ethical, social, and ecological implications of these technologies.

Absolutely.

It's crucial that we engage in thoughtful dialogue about the future we want to create with these tools.

Well said.

That brings us to the end of our deep dive.

Thank you so much for joining us on this incredible journey into the world of biotechnology and synthetic biology.

Until next time.