This team manipulates genes to create LIFE from SCRATCH!? | BP2B: Student Edition! Ep.02

1. 0:00 – 0:40

   Intro

   1. SPSpeaker0:00

      When we have a colony on Mars, we want to make the medicines we need at Mars. Uh, so basically we try to produce paracetamol, uh, using some algae, uh, in the Martian environment.

   2. SPSpeaker0:10

      We are one of the few institutes in India that actually has an iGEM team.

   3. SPSpeaker0:14

      We were, uh, lucky enough to bag a, a title sponsor, uh, AstraZeneca.

   4. SPSpeaker0:19

      Wow.

   5. SPSpeaker0:19

      Uh, most of our lab work and our competition, uh, fees, uh, comes from our corporate sponsorship.

   6. SPSpeaker0:25

      Hi, guys. Welcome to Best Place to Build, Student Edition. I'm Vidhi, a fifth-year student in IIT Madras. Have you ever been curious about the term synthetic biology or genetic engineering? We're here today with Team iGEM of IIT Madras. Their team leads are

2. 0:40 – 1:00

   Welcome to the Best Place to Build: Student Edition!

   1. SPSpeaker0:40

      here with us minutes before the orientation to explain us more about this. [upbeat music]

3. 1:00 – 9:10

   Introducing team iGEM, IIT Madras

   1. SPSpeaker1:08

      I'm here with the team lead from iGEM, Aldes, and we're here minutes before the in- orientation to know more. So first of all, what is iGEM?

   2. SPSpeaker1:17

      So iGEM is a competition that happens every year in Paris, so it stands for International Genetically Engineered Machine. So it's basically a synthetic biology competition where, uh, undergraduate and postgraduate teams from across the world come and solve real-world problems every year.

   3. SPSpeaker1:32

      Okay, wow, that's a lot to take in at one time. So, uh, first, what is synthetic biology?

   4. SPSpeaker1:37

      All right. Uh, so yeah, synthetic biology is not that different from genetic engineering. So what we do is we apply genetic engineering principles, um, from an engineer's mindset. So we consider a bacteria as a system, and we want to make it produce something that we want, basically. So to, to, uh, do that, we introduce, uh, new genes and genetic circuits to make it do what we want it to do.

   5. SPSpeaker1:59

      Okay, could you give me some example of this being used in the real world?

   6. SPSpeaker2:03

      So be- one, I think very, um, widespread example would be insulin. So insulin is something that is normally produced in our own cells, and, uh, diabetes happens when you're not able to do it yourself. So what happens is, uh, scientists introduce the insulin, the gene that produces insulin, into E. coli, and then, uh, the cells then produce the insulin that we are able to then use, basically.

   7. SPSpeaker2:24

      Just by introducing that, now your body is able to make use of that E. coli bac-

   8. SPSpeaker2:28

      No, no, no.

   9. SPSpeaker2:29

      No?

   10. SPSpeaker2:29

       No, the bacteria is grown in a lab, uh, the insulin is extracted, and then it's post-processed, and then we get it as medicine.

   11. SPSpeaker2:36

       Oh, okay, so you're using a bacteria as like a manufacturing hub now-

   12. SPSpeaker2:39

       Yeah, yeah, yeah

   13. SPSpeaker2:39

       ... I understand. That's really cool. And have you guys done any such projects like this in the past?

   14. SPSpeaker2:44

       Uh, yeah, actually, uh, last year our project was based on space biomanufacturing. So what we did is, uh, like basically, uh, transporting material in space is expensive. So when we have a colony on Mars, we want to make the medicines we need at Mars. Uh, so basically we try to produce paracetamol, uh, using some algae, uh, in the Martian environment.

   15. SPSpeaker3:03

       Wow, that is really cool. So how do you guys even come up with... Was this part of the iGEM problem prompt, or was this something that you guys were trying to innovate yourself?

   16. SPSpeaker3:13

       Uh, no. So iGEM gives us complete freedom in terms of our problem statement, uh, design. Uh, so we take a new problem statement every year, so we do literature research, we reach out to, uh, different stakeholders in different, uh, uh, domains of life, and we, uh, basically find some problem that is worthwhile, and then we figure out a way to solve it using synthetic biology.

   17. SPSpeaker3:34

       Sounds really fascinating, and, uh, knowing your track record across the past years, I think you've won, like, three or four gold medals-

   18. SPSpeaker3:42

       Uh

   19. SPSpeaker3:42

       ... collectively?

   20. SPSpeaker3:43

       Yeah, yeah.

   21. SPSpeaker3:43

       I expect this year to, like, go the same or even better.

   22. SPSpeaker3:47

       Thank you. Thank you.

   23. SPSpeaker3:48

       So I guess we're running out of time for your orientation, only about five minutes left. So can I know a bit more about the orientation itself? What's it for?

   24. SPSpeaker3:54

       All right.

   25. SPSpeaker3:54

       What's happening today?

   26. SPSpeaker3:55

       So my co-lead Karthik is right here, and he's the best guy to ask about this.

   27. SPSpeaker3:59

       Sure, okay. Hi, Karthik.

   28. SPSpeaker4:01

       Hello, Vidhi.

   29. SPSpeaker4:02

       Hi, thank you for taking the time. I know we're running short.

   30. SPSpeaker4:04

       Yeah.
4. 9:10 – 15:26

   Inside the synthetic biology lab used by team iGEM

   1. SPSpeaker9:10

      here where it actually happens-

   2. SPSpeaker9:11

      Yeah

   3. SPSpeaker9:11

      ... and where you guys are in action. So what project are you guys working on this year?

   4. SPSpeaker9:16

      Right, so 2025, um, our project revolves around what's known as gene regulations. Have you heard of our gene regulations by any chance?

   5. SPSpeaker9:24

      No. I had bio till 10th.

   6. SPSpeaker9:26

      Okay. [chuckles]

   7. SPSpeaker9:27

      [chuckles] Then I haven't seen it.

   8. SPSpeaker9:28

      Right. So essentially, you have DNA that converts to RNA, and gets converts to protein. Um, what researchers is looking for is trying to overexpress these particular protein targets, so that way we can produce desired compounds or desired enzymes and things like that. So one way of doing that is by gene regulation, so you overexpress those gene targets. And this year, this is a very interesting field, if you think about it. We have come up with a novel system using what's known as epigenetics. Have you heard about epigenetics before?

   9. SPSpeaker9:56

      I've heard of genetics.

   10. SPSpeaker9:58

       Genetics.

   11. SPSpeaker9:59

       EP is out of it, but yeah.

   12. SPSpeaker10:00

       Yeah, but very similar. So in genetics, you're sort of manipulating with the DNA strand, right? In epigenetics, what you're doing is, is adding methylation sites. So what... A methyl group is a standard CH3. You, you would have studied it in ninth and tenth, right? So you add these methyl groups, or nature adds it, at different sites on the genome, and that way it sort of controls gene expression.

   13. SPSpeaker10:22

       So instead of... Like, you're not manipulating the DNA itself, but rather the [tsk] outer part or-

   14. SPSpeaker10:28

       Exactly. So that's, that's a good question that you ask, because, um, normally, gene regulation is controlled by, say, modifying the gene sequence itself. So you introduce what's known as different promoters. That way, the entire mechanisms happens much quicker, and so you have more protein being produced. What we're doing this year is we're designing a novel system that involves what's known as a CRISPR-dCas system. So a dCas, uh, I mean, it got the Nobel Prize, actually. So it targets specific sequences in the genome, and what we are attaching to it is a DMT, which is a way for the cell to recognize, "Okay, these are the sites I want to mark for methylation." And so now you're able to methylate certain sequences, certain parts of the sequence, and so that way we are now, um, allowing the natural process, that's the transcription factors, to produce more protein. So this is, I would say, our novel system that we are, um, doing this year.

   15. SPSpeaker11:24

       Sounds really cool, but I'm not able to connect, how does adding methyl groups on a DNA backbone affect how protein-

   16. SPSpeaker11:31

       Right. So one way it does it, uh, is by, like, modifying the secondary structure of the DNA. Uh, what you can think of is methyl groups acts as potential markers for transcription factors to go and bind. So the transcription factors, when they bind to the DNA sequence, they sort of produce more copies of the RNA, and then you have more copies of copies of the protein. Now, it has multiple applications. So say now you are able to mass produce an enzyme that produces an essential compound, that's involved in a reaction that produces a metabolite of your interest. What that allows is you have engineered cells, which in itself is amazing. You have engineered cells that can now produce a compound that normally is found in very less abundance in now mass.... and so that, you could use that in various biomanufacturing plants and other, uh-

   17. SPSpeaker12:22

       So you can have other drugs or like components or chemicals-

   18. SPSpeaker12:25

       Yes-

   19. SPSpeaker12:25

       Therapeutic

   20. SPSpeaker12:26

       ... because this is a system, now you can sort of engineer bacteria and add more genes, produce compounds, and then start overexpressing those genes, and now producing more enzymes, producing more metabolites. So that's essentially what we are, uh, sort of doing here.

   21. SPSpeaker12:41

       Wow! And how far along are you in this process?

   22. SPSpeaker12:45

       Uh, so we are done making the system in the prokaryotes. Um, so we've engineered E. coli to, you know, produce this. Now we're just trying to see if we can show these results, and show if we've successfully, you know, modified the organism to produce what we intended to do. Yeah.

   23. SPSpeaker13:02

       And so far it seems like it's doing that.

   24. SPSpeaker13:05

       It seems like, it seems like a-

   25. SPSpeaker13:05

       That is incredible.

   26. SPSpeaker13:07

       Yeah.

   27. SPSpeaker13:07

       Wow.

   28. SPSpeaker13:07

       Yeah. Um, so we hope to present this during the actual competition, the iGEM competition. We hope to get, like, a nomination, you know, even win the best track prize for biomanufacturing and, like, therapeutics and things.

   29. SPSpeaker13:17

       So Kartik, I've been hearing all this fancy stuff that you guys do, like, uh, editing genes or putting DNA into bacteria. But how do you actually do this?

   30. SPSpeaker13:27

       I mean, that's the big question, isn't it? We're doing all of this crazy stuff, and then... So why don't I just call one of my experimental members over here, Skanda. So he's been working on the project for over a year. He'll give you guys a better overview of how exactly we do this particular transformations.
5. 15:26 – 19:45

   How do you create life from scratch?

   1. SPSpeaker15:26

      in ice, and then, uh, uh, forty-two degrees for some time, and then back in ice. By this time, the bacterial cells would have, uh, taken up the, uh, circular DNA.

   2. SPSpeaker15:38

      Okay, so basically this is a sterile hood wherein you're doing whatever manipulation with the bacteria-

   3. SPSpeaker15:42

      Yeah

   4. SPSpeaker15:43

      ... and the DNA.

   5. SPSpeaker15:43

      Right.

   6. SPSpeaker15:44

      You make the bacteria healthy enough, or like-

   7. SPSpeaker15:46

      Yeah

   8. SPSpeaker15:46

      ... ready enough.

   9. SPSpeaker15:47

      Ready, yeah.

   10. SPSpeaker15:47

       Take up the DNA. You have the DNA ready, you mix it up.

   11. SPSpeaker15:50

       Yeah.

   12. SPSpeaker15:50

       After that, what?

   13. SPSpeaker15:51

       And now the bacteria, actually at this stage, are under a lot of stress, because this is not how they normally are, right? So we basically, after some time, we give, we give them food. So food for bacteria is basically, uh, the, the broth. So this is-

   14. SPSpeaker16:06

       Oh

   15. SPSpeaker16:07

       ... this is called a, uh, this is called a LB broth. This is basically, uh, a media in which bacteria thrive. So this has, this is food and very conducive for their growth. So we add some of this, uh, LB broth into this tube. So bacteria, bacteria, kind of, like, they recoup and they revive. And we incubate this, we incubate this bacteria in, uh, in something called an incubator. This incubator is an instrument which makes... Which gives the perfect environment for the bacteria to grow. So it, it looks like this. It has, uh, temperature and pressure probes, which-

   16. SPSpeaker16:45

       Okay

   17. SPSpeaker16:45

       ... uh, continuously monitor, uh, all the conditions required for bacteria.

   18. SPSpeaker16:50

       So there's some airflow conditions also which-

   19. SPSpeaker16:52

       Yeah, there are airflow conditions, which also, which are also maintained. Yeah, and, uh, after the bacteria have revived, that is-

   20. SPSpeaker16:59

       How long do you usually keep them in there?

   21. SPSpeaker17:01

       It is usually around an hour.

   22. SPSpeaker17:02

       Oh, okay.

   23. SPSpeaker17:03

       Yeah, and, uh, once the bacteria are revived, you can actually see them grow. You can see the density, the optical density change. And once they are grown, we plate them, we, we spread the, we spread this liquid culture on plates. So I'll just show you where the agar plates are kept. Yeah. So these are called agar plates. So these, this is basically a solid media for bacteria to grow on. Just like how the LB broth was a liquid media, this is a solid, uh, substrate on which, uh, bacteria grow. And, uh, so we spread this liquid culture on these plates, and we again incubate them in the incubator overnight, and, uh, uh, after around twenty, twenty-four hours, they grow into something like this. So these are actually-

   24. SPSpeaker17:57

       Oh

   25. SPSpeaker17:57

       ... bacterial streaks, so-

   26. SPSpeaker17:58

       So what are those red, those red streaky kind of things I'm seeing?

   27. SPSpeaker18:02

       Yeah, this is how... So that is the pattern, uh, in which, uh, we spread the bacteria after-

   28. SPSpeaker18:08

       Oh

   29. SPSpeaker18:08

       ... after they are revived. So they grow in something like this, and you can see single dots. They are, they are called colonies. So all the bacteria in each colony are actually identical, because each colony comes from a single bacterial cell.... so, yeah, each colony, we treat each colony as a single bacterial, a presentation of a single bacterial cell. Yeah. Yeah, so now we have bacteria growing on agar plates, which are, which actually have the plasmid, uh, taken up. So they, they have that circular piece of DNA inside them.

   30. SPSpeaker18:46

       That was really cool, okay.
6. 19:45 – 23:16

   What’s the structure of the team iGEM?

   1. SPSpeaker19:45

      basis. What is their structure to execute and be at such a good stage already? So we have Aldous for that. Uh, so Aldous, yeah, as I mentioned, how do you guys have the team structured? Like, I remember you mentioning that you're more of a computational guy, not in the wet lab much, so-

   2. SPSpeaker20:01

      Yeah. Um, yeah, so the form of a team, uh, really follows the function. So we, um, as you saw, we have the wet lab people who do the experimental work. Uh, we also have the computational team that works on, uh, modeling and the software, uh, development part of a project. Uh, so modeling is where we sort of computationally simulate the systems that we want to produce, like in experimentally, and see whether they'll work out or stuff like that. And in addition to that, we also have a WebOps team, so they help us, uh, put out our work in a way that it's, uh, accessible to the public and who wants to see the work.

   3. SPSpeaker20:33

      Oh, okay. Yeah, I've seen your website and how it's, like, always updated, and you can go through the different sections. That's really cool. And what about, like, other comp teams have sponsorship and-

   4. SPSpeaker20:43

      Yeah

   5. SPSpeaker20:43

      ... stuff like that. So is it funded through the professor itself, or how does it work with you?

   6. SPSpeaker20:47

      Okay. Um, I think similar to most competition teams, uh, most of our funding comes from corporate sponsorship. So, um, all, all the members pitch in, and we do outreach to multiple corporates. And, uh, this year actually, we were, uh, lucky enough to bag a, a title sponsor, uh, AstraZeneca.

   7. SPSpeaker21:03

      Wow!

   8. SPSpeaker21:03

      Uh, most of our lab work and our competition, uh, fees, uh, comes from our corporate sponsorship.

   9. SPSpeaker21:08

      Wow! And, um, how big would your team be, per se, in each of these divisions?

   10. SPSpeaker21:14

       Um, total, we have around 30 members in the team. So we have, like, 10 to 15 in each of wet lab and dry lab, and a small five-member WebOps team. Um, and, uh, sponsorship and human practices also, uh, all the members pitch in.

   11. SPSpeaker21:28

       So you get to learn a lot in that way. Like, you have the tech aspect and a bit of the management exposure, if you would like to have it. That's great. And since this is very research-heavy and you guys are working out of labs, I'm guessing you'll have some profs or PhD students helping you out, or?

   12. SPSpeaker21:42

       Yeah. Uh, so we have a couple of professors who guide us. Uh, so this year, for our lab work, we are working with two cell- cell lines. So one is a eukaryote, uh, which is a mammalian cell line, and one prokaryote, as Kanta showed you. So for each of them, we are consulting with different profs, who help us with the protocols and what to do. And of course, their PhD students al- also support us in the lab with the learning... uh, helping us learn the skills that we need to.

   13. SPSpeaker22:07

       iGEM doesn't seem like the typical competition team in the way it's structured and how it works. What do you think about that? Where does it sit-

   14. SPSpeaker22:15

       Mm

   15. SPSpeaker22:15

       ... in the whole spectrum of, like, tech teams in, in the com- competition teams or prof projects?

   16. SPSpeaker22:21

       iGEM as a competition in itself, um, is very open form, and it really, uh, encourages research and, uh, the mentality where you find a problem on your own, and you devise a solution to it on your own, and we, uh, implement it to fruition. So in that, uh, manner, it's a bit separated from, [lips smack] uh, other competition teams and clubs, and it's more close to a research project that one would take up in a lab.

   17. SPSpeaker22:45

       So you have the research aspect while also having the whole competition drive-

   18. SPSpeaker22:49

       Yeah

   19. SPSpeaker22:49

       ... and you get to go there as well.

   20. SPSpeaker22:51

       Yeah.

   21. SPSpeaker22:51

       It's like the best of both worlds, isn't it?

   22. SPSpeaker22:52

       Yeah, exactly.

   23. SPSpeaker22:53

       Yeah.

   24. SPSpeaker22:53

       So, um, uh, this sort of exposure with the research work, as well as the sort of, um, management sponsorship and, uh, the outreach work, is something that gives our members a very, um, well-rounded, uh, exposure and makes them really valuable in whatever they want to do next.

   25. SPSpeaker23:09

       So it sounds like a great experience. Are there any members in your team who are, like, thinking of continuing down in this field,

7. 23:16 – 24:50

   Future career paths pursued by students in iGEM

   1. SPSpeaker23:16

      given their experience in iGEM?

   2. SPSpeaker23:18

      Oh, uh, a large majority of our team, of course, wants to go into, um, uh, biotech research and stuff like that. Uh, there are people who go into consult and, uh, stuff like that, and, uh, software development. So these are the major things. So I myself am a mechanical engineer, so where I look at myself going forward is, uh, there are, um, uh, research fields where, um, really mechanical engineering and, uh, molecular biology come in together. So it's called an organ-on-a-chip. So yeah, so, uh, for, uh, medical testing, basically. So you are able to replicate those, uh, conditions in a chip, basically.

   3. SPSpeaker23:52

      Yeah, sounds fascinating. Organ-on-a-chip has captivated many people's attention right now.

   4. SPSpeaker23:57

      Definitely.

   5. SPSpeaker23:58

      Yeah.

   6. SPSpeaker23:58

      Yeah.

   7. SPSpeaker23:59

      And is there any, like, next big technology that you're just waiting for, or you think is gonna shake the world?

   8. SPSpeaker24:05

      Okay, um, I think, uh, the recent one was CRISPR, right? So that gives us this very selective way to change things however you want it to. And now, of course, um, uh, I'd say the, uh, next steps in where the biggest frontier is in, is in the computational side. So, uh, bringing in AI and, uh... Because as you saw, each and every experiment is really difficult to do, right? So if you're able to, uh, take the burden off from that and onto computers, we can really speed up the research process, and the discoveries can be, uh, made so many more.

   9. SPSpeaker24:35

      ... yeah, like having like digital twins of everything, like a bacteria, even the circular DNA, how that mechanism would work out. So you can just simulate it-

   10. SPSpeaker24:43

       Yeah, yeah

   11. SPSpeaker24:44

       ... and then work it out. That would be really cool. Yeah. And how do you feel about, like, ethics

8. 24:50 – 27:02

   Closing thoughts on the ethics of synthetic biology

   1. SPSpeaker24:50

      in synthetic biology? I feel like there's such a fine line between innovating and even, like, just, like, you're manipulating life, literally.

   2. SPSpeaker24:58

      Yeah, yeah.

   3. SPSpeaker24:58

      So there's a lot of responsibility in your hands.

   4. SPSpeaker25:00

      Correct. So yeah, that's what- So when I said anything can happen, really anything can happen, right? So, um, so that's why, uh, large part of what we do is also responsibility and managing our impact and the ethics of whatever we do. So, uh, the most basic bioethics question is biosafety and contamination. So right now, whatever we do are contained in labs. So, uh, like, I think Santa might have told you about the antibiotic resistance. So if anything were to get outside the lab, it wouldn't be able to survive. Uh, so that basically ensures that we don't have an impact on the environment that we don't want, want it to. Uh, so that, I think, is the main ethics question. Um, and then, so actually in all the jamborees that we present in, uh, there's always a presence from, uh, intelligence agencies like the CIA and the, uh, FBI. [chuckles]

   5. SPSpeaker25:44

      [chuckles] Okay.

   6. SPSpeaker25:45

      Yeah. So, uh, they, uh, do awareness about bioterrorism threats and how we have to be responsible, uh, in the way that we conduct our work.

   7. SPSpeaker25:53

      So what would you say is the main philosophy between, like, crossing the line with tech versus going towards a constructive path? 'Cause I feel like, you know, technology's always just been a tool, like it's a knife. It depends on the hands in who goes-

   8. SPSpeaker26:09

      Yeah, yeah, true. So that's actually a very good, uh, analogy. So, uh, whenever you're working on something, you always have to consider how someone might use it nefariously. So if there's a possibility of what I'm working on, being very, very... Because it's just a sequence of DNA, right? You publish it, someone else can take it, modify it a bit, and say, "Instead of helping save someone," it can just as easily be used to, uh, to a detriment to someone else. So that's something that we have to take responsibility of and make sure that, so if our work is going in such a direction, you stop there, and then you just don't publish that work.

   9. SPSpeaker26:45

      That was really nice chatting with all of you. Got to know a lot about iGEM, and synthetic biology is such a fascinating field.

   10. SPSpeaker26:52

       Oh, definitely. It was really a pleasure to talk to you and, uh, you know, explain all this stuff and get some new perspectives in as well.

   11. SPSpeaker26:59

       Yeah.

Episode duration: 27:07