 Terry so I like most of that but murderous replicant as someone who self-identifies as replicant I find that to be an offensive stereotype So my name is Terry Johnson my background is in chemical engineering because when I started There was no synthetic biology. It's a relatively new field And I work with a lot of synthetic biologists at UC Berkeley and I want to talk about partially what we do But why So in each of you, there's approximately 10 trillion human cells. They look like this and There's also approximately a hundred trillion microbes mostly in the guts about three percent of your body weight. It's extremely significant In that gut, there's about a thousand different species and the species are different from person to person There's interesting correlations between your genotype and the kind of bacteria that sort of hang around in your guts Now why are they so important because they're incredibly versatile? They can survive the following They can survive temperatures from minus 17 to 266 degrees Fahrenheit to give you an idea that ice and that's boiling water They can survive pH is from minus 0.06 to 11.5. That's your stomach and that's milk of magnesium They can survive pressures from 0 to 30,000 pounds per square inch We're currently experiencing about 14 pounds per square inch. That is space and that is the bottom of the ocean the deepest part of the ocean and They're fine with this not everyone is fine with all of those things But you'll be able to find a strain of microbe that can deal with all of those So I'm sure you've heard if you took a Monkey and you gave that monkey a typewriter and then you had a million of those monkeys with typewriters And you gave them infinite time to bang on the typewriters. You would eventually get the complete works of William Shakespeare That's already happened on earth We've got the oceans which is where a lot of bacteria have happened And there it's been estimated that on earth There's about 10 to the 30 microbial cells 10 to the 30 is 10 follow up one followed by 30 zeros It is approximately equivalent to the number of water molecules in this room, which is tremendous It's one of those numbers where I double-checked it and triple-checked it and looked up other papers that said that because it seemed too damn ridiculous And if you take those and you give them four billion years You end up with a lot of really interesting solutions to difficult problems Okay So beating the cell at its own game from our point of view is synthetic biologists microbes are very good at what they do They don't always do what we want them to do. So we should build new microbes. It's a very simple statement Okay, so how do you get a new biological system? Well, you can do genetic selection and we've been doing genetic selection for a long time This is a 10,000 year old cave painting and you can see the hunter has dogs With this is 10,000 years of corn by selecting the corn that is increased in deliciousness effectively and also, you know Gives you more bang for your ear For 50,000 years of sweet sweet loving we've been deciding on which mate we are going to have sex with and Have been undergoing selection throughout that entire time So we've been doing genetic selection for a long time The differences that we're going to use a different technique instead of breeding and selecting We're now going to do some sort of genetic engineering genetic engineering started in 1973 with Antibiotic resistance in E. Coli found that if you took a little tiny piece of DNA and you did some things with it Very particularly and you moved it over to a new E. Coli. It would have the resistance of the old E. Coli Now that's 73 in 78. We were producing human insulin in E. Coli Five years Because there was a tremendous demand for insulin there still is a tremendous demand for insulin today We produce over six tons of insulin per year six tons of medical grade insulin most of that using biotechnological methods You know not You're in from animals or a lot of other sources that have some pretty serious problems attached to it okay, so Really quick background from like your biology. You've got the cell you have DNA DNA is transcribed into RNA which is translated into protein and Effectively the protein is usually the interesting part. It's the stuff that does things right If you need an analogy you have a computer You have an installed program on the computer's hard drive you open a program to get a program window that's like the RNA and The program window is all set up to deliver what you actually want the output to the screen which would be cute animal gifts I'm told that there's other things on the internet that some of you might want to look at I'm gonna stick with that for this talk So let's say I want to build bacteria that make red fluorescent protein And this is a protein that if you shine a UV light at it. It's gonna glow red Well, I would install our red fluorescent protein DNA and that would make red fluorescent protein RNA Which would make the red fluorescent protein and if you do that you see cells that look like this under a black light Normally these colonies would look white, but because we've made them to make this new protein. They will glow red Okay, so it seems like what do we need synthetic biology for is this synthetic biology? Is that all we do? Well, let's go step back and look at what DNA is and here's Something I stole from Wikipedia because I'm an academic. That's what we do and this is a rotating DNA and it's made up of a bunch of nucleotides for and these nucleotides are in one chain and in another chain and they're Compatible in such a way that they bind to one another and then they twist because of the way that the molecule is is Because of the chemistry of the molecule, but we already abstract these things We never really think of DNA as a molecule. We typically think of it as strings of letters and those letters are associated with actual chemicals on That strand so the first thing that I want to note is we already Abstract what DNA is DNA is actually a molecule that looks something like that, but we think of it as strings of letters So keep that in mind for later This is a small part of the DNA for making bacteria that glow red It'll be a quiz later. Just memorize this so pause for a second If I wanted to sort of focus in on what different parts of the DNA do That's a promoter up there That's a terminator in green and the red part is actually the code that says this is what the red fluorescent protein would look like Okay, so that's sort of useful All right, so if I've got a bacteria, it doesn't make any red fluorescent protein I add a small little loop of new DNA. It's that little little O of blue in the center of that it Will start making stuff and it'll turn red But let's say I want to make another bacteria that turns a very deep red. It makes tons of red fluorescent protein Or I want another bacteria that doesn't Change color unless I were to add a small molecule like a pollutant and when it senses the pollutant I would want it to turn red, but only under those conditions Okay, so Different function requires different DNA Which means that I have to do more design work. I have to go back to the drawing board Which is like this. Oh, okay, so this is the thing I need this but with different letters And whenever we have to do design in this It's actually quite painful because we need to it's not as if we have a DNA editor it's not as simple as just typing new letters We add this is a giant molecule and what we have to do is we have to break it apart in very particular places and insert Things and delete things. It's extremely time-consuming. It's just a pain So my question that I want to explore is this really the way that we should be thinking about DNA to solve problems And I'll give you an example of a more complex problem So this is artemisinin. It's a fairly complex molecule and This is a treatment potentially for cancer, but definitely for malaria alright Artemisinin comes from plants so what you have to do is you have to destroy some forest and you have to Get a bunch of sweet warm wood and you have to grow it up And you have to hope that there's no hurricane because then there's no malaria medicine And then you have to take that stuff and you have to pound it up So you have to have some pretty significant industry You have to add some very harsh solvents to get the drug out of the plant You have to hope that not too much of that stuff escapes into the air and you've got a bunch of your artemisinin What we would like to do is Put it into bacteria or yeast right put it into some kind of microbe So how difficult could this be right? I'm just editing DNA Well, that is the chemistry behind artemisinin And you'll notice that there's a bunch of Tiny arrows up here, which means that this is part of the chemistry to make artemisinin Okay, so you might be able to take some enzymes from the plants and Somehow start making them in the yeast and in this case they used yeast But the problem is is that it's not as simple as just putting really complicated things into bacteria or yeast And then saying hey bacteria and yeast figure it out bacteria and yeast are highly tuned Machines and effectively you're installing something and saying yeah do whatever you're currently doing and also make a ton of the shit The bacteria and yeast typically freaks out because now all of a sudden you're saying yeah all that carbon You're using to like survive Use it to make this but also survive and grow really fast. We make lots So what it ends up being is I need to figure out ways to get that plant enzyme DNA into the yeast I need to tune the yeast because now I've made some very significant changes to it and that process if you're working on it Is something like this? So imagine having to go through that and tune and fail and tune and fail and tune and fail and every time you're doing this You're going back to these giant strings of DNA All right, this is not the way that we want to think about DNA or I'm going to argue at least this isn't the way We want to think about DNA, but if I'm going to do that I should probably offer up something better So my question would be who can teach us a better way to think about DNA now. Why all right, so building a Bjorken I Went online. This is a Bjorken. It's a medicine cabinet. So I chose it for two reasons one It's appropriate for a bioengineer, right? It's a medicine cabinet two. I like saying Bjorken If I mispronouncing it, please do not tell me So if you were to buy one of these you would see the little I have no idea. It's it's a human of some kind And there would be instructions that many of us are familiar with how many have been put together an IKEA furniture before All right. Thank you. So the instructions look something like this now what I want to note Is that if you abstract this you have a device? Which is what you want to build and that's the Bjorken and you have a list of parts Which is what I want to build it with which looks something like this What I want you to focus on for a second is to consider what is left out of the Bjorken instructions This is one of the parts. This is a screw The instructions do not say this is a screw The length of the screw is 17 millimeters the screw turns Seven times with an angle of 22 degrees. It is made out of number three stainless steel It was made in Switzerland unless you bought this in July meaning it was made in Germany There's a ton of information that is left out of this and for good reason. I don't care Nobody cares When you think about parts the maker of a part needs to know how the part was built But the user of the part needs to know how the part interacts with other parts That's the critical concept So instead of thinking about DNA. Let's think about DNA as parts and let's see where that takes us so Instead of looking at this I'm going to say that this is a combination of a promoter part a protein part making RFP and a terminator part Now where does that abstraction take us? Well first off? I know this is the connection between the two parts So I know there are certain places that connect the parts But it also means that I can use parts in different contexts. So for example, that's what we built to make Selgar red This would be a new promoter and this is a promoter. That's not as active So it would just say make a little bit of red fluorescent protein This would make lots of red fluorescent protein. This would say only make the red fluorescent protein in response to heat This would say make the red fluorescent protein in response to pollutant The promoter part is responsible for saying when I turn on and how hard I turn it on Now I could also have a green fluorescent protein or a yellow fluorescent protein So I can mix and match these parts. It's a modular approach to considering how to build things with DNA Okay, so things that synthetic biology isn't apologies It is not giant insects It is not super intelligent cats It is not lizards with laser eyes That's down the hall What synthetic biology really is is Instead of thinking about nucleotides, let's think about these collections of nucleotides as parts Take those parts put them together to make devices And this is a device that came out of a Berkeley lab Which effectively delivers a payload to a particular other kind of cell and to do that It actually needs a significant number of parts This is by by the way, not nearly the largest sort of device that people have built But just gives you an idea if I were to try to build different versions of this in a research lab I would drive myself mad if I'm always thinking of it only in terms of a giant string of letters usually thousands upon thousands of letters Eventually to be able to think in terms of building entire genomes and this is the Venture Institute sort of minimal Microbe effectively what they did was they completely synthesized a Genome that was just what you needed to survive and no bigger Now the reason why they do this partially is to raise funding because it sounds really impressive But it's also important because this way you can build specialized microbes For building things in I mean one of the things that we have to worry about in synthetic biology Is you build this big device and then you're throwing it into a strain maybe a V. Coli, right? But you're limited. There are only so many strains of E. Coli that are out there and it's not like they evolved Well, I knew a synthetic biology was gonna start in like, you know the late 90s early 2000s So I just minimize my genomes to be easy to throw stuff into me. There are no bacteria out there like that So we're interested in also building genomes So that we can make larger and larger and more and more complex devices inside of them Okay, I want to give you an idea of some of the things that I have done working with UC Berkeley Undergraduates in terms of synthetic biology. So how have we applied this sort of general tech set of technologies? This is a self-licous device and I admit not doesn't look all of that fancy It's you know two tubes one of which is cloudy and one of which isn't but effectively what we've done is we built Bacteria that break themselves apart They do so only under a particular command and the reason why you'd want to do that It's actually a number of reasons why but one of the ones that I find most interesting as a chemical engineer is if you take a Bacteria and it makes drugs and the drugs are stuck inside the cell you have to break the cell apart to get at your product It would be much easier instead of having to add harsh chemicals To actually tell the bacteria no no we're ready break yourself apart release the drugs so then we can harvest it from the broth This is cellulose degradation device and honestly it was not incredibly successful But we did get some activity. This would be something that you could use to sort of break down biomass for biofuels and you as you can see the Blue indicates that there has been some breakdown of cellulose We're also interested in using this for basic science. We're gonna look at Coano flagellate gene delivery Coano flagellates look like this They're actually an animal. They're Very very primitive animal and if you are a evolutionary biologist and you'd like to object to my use of the word primitive write your own talk They are primitive I would say because they're right on the edge of single cellularity and multi-cellularity So in an evolutionary sense they're really interesting because oh, okay. Well, they're the right on the edge What are those changes that sort of moved them from single cells to building up these colonies? Well, it turns out it's hard to study them because it's hard to manipulate them in any way So we looked at them and said they do one interesting thing they eat bacteria So what if we genetically modify bacteria that get eaten by them and then break apart their Stomics and release things on to the inside and what we did was we released green fluorescent protein and That is the inside of a Coano flagellate We were also interested in biosensors and this is a work ongoing work in progress what we did was we took a look at The toxar system and this is an existing biological system The two blue toxars just kind of hang around Unless the green toxas is there and if it is then the tox ars come together around the toxas and That brings their inner bits the parts inside of the cell close together and that actually causes a signal it turns genes on So what we were interested in is in building something that has the bottom that looks like Toxar and the top that will recognize a small molecule in the video. It's estrogen So you could use this if we get it working to actually detect say estrogen in groundwater Which is an environmental contaminant that a number of people are worried about as an aside the Student on the IGM team who worked on that is currently working at Pixar And she's gonna have a credit on something. I probably can't tell you about but it's awesome The last project from last year these are fluorescent barcodes we took yeast cells and We took various fluorescent molecules and we targeted them to various organelles in yeast And the idea is that if you have a number of fluorescent molecules and a number of organelles You can give every cell a particular set of colors in particular regions It's a barcode if you look at the cell I can go that cell is this genotype that cell is this genotype That cell is this genotype and that means that looking in a microscope I can take a picture and I can screen all of the genotypes very very quickly I don't have to do a lot of expensive monitoring of the actual genetics if I know that This one has this genetic this one has these genetics this one has these genetics So these are a couple of examples of the things that we've done Synthetic biologists work on tons of different things and I want to emphasize these are actually projects for Undergraduates that are accomplished in a semester and a half If you tried to do this 20 years ago, this would be an entire lab working for 10 years So this abstraction this new way of thinking about DNA Allows us to do things that were very very difficult very shortly or a very short period of time ago Okay, so what next well if I were designing an engine I would probably build that engine in solid works or CAD or something like that If I were building a chemical plant, I would probably design that chemical plant in aspen And if I were building a circuit, I would probably use H spice These are all computer aided design programs that effectively say if I put all these things together What's going to happen, but that means that all of these things really say how do the parks work parts work together with one another now? In an electronic circuit those parts are capacitors or resistors in a chemical plant those parts are Reactors and heat exchangers in an engine. There are pistons right and other stuff in engines Not a mechanical engineer What we're working on at UC Berkeley among many other things is a bio CAD design tool for building DNA Effectively this would be something that would help you figure out how to combine different pieces of DNA and also do things like Automatically search. Are you using any virulence factors? What is the the risk group of the? Organisms that you're working from are there any sort of combinations of parts that you should be worried about So the idea would be that this would aid not only in building very quickly and building very well, but also building safely But really the main goal is this We want to use microbes as tools There's a tremendous amount of genetic information out there these bacteria Yeasts all of these microbes have been on the planet for billions of years Figuring out ways to survive and do things figuring out ways to get energy from this figuring out ways to survive under these conditions Which means that out there is a tremendous amount of interesting information that could be applied to problems that we actually have So our goal basically is to use microbes to solve problems Thank you very much for listening. I'm happy to take questions and I'll be in two which is also in this building Evidently after the talk