This Week in Microbiology
With Vincent Racaniello, Ankur Dalia, Julia Van Kessel, and Xindan Wang
Episode 164: Indiana Quorum
Aired November 16, 2017
Vincent: This Week in Microbiology is brought to you by the American Society for Microbiology at asm.org/twim.
Vincent: Welcome to TWIM!
Vincent: That’s awesome, that may be the best one yet. (laughter) Hi everybody, I am Vincent Racaniello, and this is TWIM, This Week in Microbiology, this is episode 164 and today is November 3rd2017. You are listening to the podcast that explores unseen life on Earth. Today I am coming to you from Bloomington, Indiana.
Vincent: It’s my first visit here, never been here before, I’m at Indiana University and I am here to do this TWIM and I am also recording a TWIV later on. Kathy Spindler is here for that. In between, I am going to talk about communicating science. We have a great audience here today, as you heard, and if you have the chance, my seminar is at 2:30, I think, right. You should come because it’s not a data seminar, it’s something different. I want to talk about what we do, communication, why you need to do it, and so if you have time, please come and I think you’ll enjoy it. Anyway, I have a couple of guests that I’ve selected from the faculty here. Since this is This Week in Microbiology I’ve selected some people who work on bacteria. Who thinks that viruses are microbes, by the way? Kathy Spindler. Yeah, I think they are microbes. I’m in a microbiology department anyway, so they must be microbes. But for TWIM, we have 3 relatively new faculty members here. On my left, Xindan Wang, welcome to TWIM.
Xindan: Hi, everybody.
Vincent: And next to Xindan, Ankur Dalia.
Ankur: Hello, thanks.
Vincent: Welcome to the podcast.
Ankur: Thanks for having me.
Vincent: And all the way at the end, Julia Van Kessel, thanks for coming, Julia.
Julia: Hi, everybody.
Vincent: Welcome to the podcast. Do any of you know these individuals? (laughter) Is anyone in any of their labs?
Vincent: That’s good, there’s only a few and the rest just came. So this is really great (laughter) we have a great audience, I’m really happy to see you. We have an hour, which as you know, if you listen to any of our podcasts, who listens to any of our podcasts, by the way?
Vincent: A good number, almost half. So the others who don’t, you should try listening, as I always say, just subscribe, anyway, even if you don’t want to listen. Having downloads really helps us to do what we want to do. So I’m going to talk with these three faculty members today, a little bit about their histories, and a little bit about their science, and we are going to see if we can do that in about an hour, because that’s when we have to get out of here. So first I want to hear about where you are from and your training and so forth. So let’s start with you, Xindan, were are you from originally?
Xindan: So I was born and raised in China. I did my first degree in Shanghai, where I studied human genetics. I was studying the association of some genes with schizophrenia. Back then, I was doing a lot of PCR and sequencing and seeing if certain genes are associated with the disease.
Vincent: This was in high school?
Xindan: This was my first degree, bachelor’s degree. And then I found that this research was exciting but it was just too complex (laughter) If I wanted to tweak the system and make the mutations and study whether this gene is actually contributing to the disease, it is too hard in humans. So I decided to go to the extreme and study bacteria. So then I did my PhD at Oxford in England in studying chromosome dynamics in E. coli and from there, after graduating, I decided to stay with microbiology and stay with bacteria but do similar research on a different organism. So Bacillus subtilis, that’s where I did my post doc at Howard Medical School with David Rudnerr and there I was doing research on chromosome biology and I was there for almost 7 years and then I came here at Bloomington in this February and here I am.
Vincent: February of this year?
Xindan: Yeah. This year.
Vincent: Wow, I think this is the youngest person we’ve ever had on TWIM (laughter) or the youngest faculty member. That’s great. So what got you interested in science way back when, do you know?
Xindan: So I think I was sort of born, I wanted to do science when I was very little, right when I learned how to do addition and subtraction I just got into numbers so I was very fascinated by the math and how to do this sort of, you add something together, it gives you something, and then you subtract, so I was very interested in numbers when I was just very little. And then I discovered the logic of mathematics and later I found that mathematics is not only used for just doing number work, it is also used to do physics. And then chemistry, and then later, biology. So I just felt I was just very intrigued with solving problems, so I could sit there for hours and work on a problem and when I finished it I want to find different ways of solving it and find a better way to do that and I got inspired by my teacher in middle school and he gave me a book with all these interesting problems to solve, and then I got a book from my parents’ friends about “100,000 Whys”.
Vincent: 100,000 Whys! (laughter)
Xindan: Yes, it’s like an encyclopedia with many questions. So I just got into science very early on and I think how I get to where I am now is kind of to the basic research I do is kind of by chance. At certain points I met certain people and I got inspired and went to this particular path, but if I didn’t do this science I would end up doing something else, some other science. I am driven by my curiosity and I will always try to find out why.
Vincent: That’s funny, 100,00 Whys, we always say on TWIV, you can’t ask why questions in science (laughter) We don’t know why things happen. So we should sequence your genome and see what genes are associated with being born curious about science, that would be great. So why did you come to Indiana University?
Xindan: Well, there are several parts of this story. The first is the year when I was on the job market, IU was hiring, so I applied for the job and they gave me the offer so this is part of the story. If this didn’t happen I wouldn’t be here. So the second part of the story is I also applied to a handful of positions, I only applied to the positions I really wanted to go. The last part of the story is that in the end I also have to choose from this offer and a separate offer, so I had to decide which place I want to go, and so that other school actually has a better ranking, maybe this means a lot for undergraduate students, and it is also at a more attractive location and it has a nice department, it has all the equipment I needed, facilities, but in the end I decided to come here and the reason is the things they have here that they don’t have is the microbiologist community. So we have a large group of microbiologists doing exciting stuff and so I feel my expertise could be more useful, explored more, by the faculty around here and people are doing the work they do, I could also use in my research. So I feel I am a better fit in this position, so here I am.
Vincent: Was it the right decision?
Xindan: Yes. (laughter)
Vincent: Great. Ankur, where are you from?
Ankur: I’m originally from New Jersey.
Ankur: I’m from Bergenfield, up north, right next to Paramus.
Vincent: Oh, I know it well, I was born in New Jersey and I grew up in Bergen County.
Ankur: Oh wow.
Vincent: So I know Bergenfield.
Ankur: So Jersey boys, great. (laughter)
Vincent: Yeah, we are Jersey boys. That’s right, that’s right. I have a stronger accent than you.
Ankur: Yeah. (laughs) I guess so. That is the one thing I’m told by all my students that I talk too fast, I blame that on Jersey all the time. Yeah, so I grew up in Jersey and I went to undergrad at Cook College which is part of Rutgers University and that’s where I really started doing science work with Don Kobayashi there, working on Enterobacter cloacae and selenate reduction and from that experience basically the one thing I knew was I liked bacterial genetics, so I decided to kind of pursue that further, so I went to grad school at U Penn working for Jeff Wiser on Streptococcus pneumoniae, looking at the host-pathogen interaction, and while that was fun and kind of interesting I didn’t like the host side of things, I was more interested in the bacterial side.
So I decided I wanted to further push bacterial genetics and see if I could pursue that further. So I tried to find a lab that was doing cutting edge bacterial genetics and I found Andy Camilli who was looking for a post doc so it worked out perfectly. So I did my post doc with him for about 5 years until I made the switch to kind of go on the job market and luckily I ended up here.
Vincent: When did you come here, roughly?
Ankur: Two years ago. Yeah.
Vincent: So we had Andy Camilli on a TWIM some time ago and I was just at Tufts two weeks ago recording a TWIV, so there’s all sorts of coincidence. So for you, what catalyzed your interest in science?
Ankur: I mean, since I was a child I guess I was always interested in taking stuff apart and putting it back together. I wasn’t very good at the putting it back together part, I guess (laughter) but I slowly got better at that, and then what really gelled the idea of academia is kind of a science position or going in this field is when I was an undergrad working with Don Kobayashi, I remember thinking at one point, oh my God, he gets paid to do this? (laughter) And I was sold from that point on, so I kind of always wanted to end up doing what he was doing and luckily I have been able to but, you know, you never know at the time.
Vincent: He gets paid but not very much (laughter) as we all do. So why did you come to Indiana?
Ankur: It’s the environment, I’m going to mirror what Xindan said a little bit, but basically I had a couple of offers to look at, but in terms of the environment and the people here, the science that is being done here is truly cutting edge, and the collisions and kind of collegiality in the department is unparalleled, in my opinion. So I have already had opportunities to interact a number of faculty who have published papers together in the short time that I have been here. So it has paid off in spades.
Vincent: And you’re glad you came here?
Ankur: Oh absolutely.
Vincent: I can’t ask him, I really shouldn’t ask him that question (laughter) he’s not going to say no. But that’s right, that’s right. We’ll wait until after tenure and then say was it the right place to be. Julie, what’s your story, where are you from?
Julia: I am from New York.
Vincent: New York, what part?
Julia: It’s near Poughkeepsie, it’s a tiny little town called Millbrook.
Vincent: Oh, I know Poughkeepsie well, my son goes to Marist.
Julia: Oh, yeah, absolutely. Vaster is there as well.
Vincent: It’s a nice part of New York.
Julia: It is.
Vincent: So you grew up around there?
Julia: I did. And then I went to undergraduate at a small school called Utica College which is in central New York. I was really lucky, there was one microbiology lab in my very small college and the person who ran it, Laurence Aaronson, he was incredibly generous with his time. He was one of the best mentors I’ve ever known and I was really lucky to study with him. We looked at the microflora on redbacked salamanders and it was really fun. So I got really into bacteriology that way, then I went and did my graduate work at the University of Pittsburgh in the lab of Graham Hatfull, where I studied Mycobacterium tuberculosis and bacteriophages, and then I decided I did not want to work in a BSL3 facility for the rest of my career, so I was looking for a change. I went to an American Society for Microbiology conference, the general meeting, and I saw Bonnie Bassler talk and I was instantly starstruck which, if you’ve ever seen Bonnie talk, you would understand. So I wanted to study quorum sensing and I was lucky enough to get a position in her lab as a post-doc. So I was at Princeton for about 5 years and then I came here.
Vincent: When did you come here, how long ago?
Julia: About 4 years ago actually.
Vincent: Why did you come to Indiana?
Julia: So we looked at a lot of places like many people do, like Xindan and Ankur, so we had what we would call a two-body problem. So my husband is a biochemist in the biochemistry department here. It’s not easy to find two positions at the same time, but we did, and we are very thrilled and very lucky to be here. Again, same reasons as Xindan and Ankur. The community is fantastic, and just the kinds of science that we can do here, we have learned so much in just a short amount of time. New kinds of experiments and methodologies and collaborations. It’s not possible anywhere else.
Vincent: I always love to point out the connections. So I know Graham very well, we had him, so here’s a quick story, I was giving a talk in Edinboro many years ago about communicating science and he sat in the front row, and he raised his hand and he said, do you ever talk about phages? (laughter) And I knew who he was. I said, why don’t you come on and do it? So he did, and we talked about his Sea Phages program and so forth. So that was good. And then of course, Princeton, as I told you, when we work on our virology book, we go to Princeton to do it. I was just there last week, we are starting again to do it. So it’s a great place, I love Princeton.
Julia: It is.
Vincent: That’s great. So there you go. For you it has probably been the right decision also to come here, right?
Julia: Absolutely (laughter)
Vincent: Let’s talk a little bit of science and find out what you do. Xindan, let’s start with you. I know you have this wonderful website, if you haven’t seen it you should go. She’s got a .com of her, what is it, what’s the url? Tell us.
Xindan: It’s just my name, wangxindan.com.
Vincent: wangxindan.com. And so it takes you away from the university but it’s really well done and I’m told it is mobile friendly which is really important these days if you want to make a website. And what did you tell me?
Xindan: Thank you? (laughter) This is thanks to my husband, who is a web designer and developer.
Vincent: So if you want a website made, you should check out his work and I might use him, too, because I could use some web design, as well. It’s really well done. Why did you do that, why did you make your own little site off by itself, I’m wondering?
Xindan: I’ve had it since 2006, so back then I just wanted something unique, something that is not like any other website and I asked my husband to make it for me and I had it all that time. So it has changed a lot, so every couple of years I change it completely. This is a new face that I just redo, it’s like my personal little world, I can put anything there. (laughter)
Vincent: Well, almost anything (laughter) I think it is a great idea, for those of you who are just starting out or early on, it is a great idea to have a website where you can put things, you can write or talk about your experiences in science. And then people can find it and that’s one of the ways you can communicate what you’re doing. So as you said before, you are interested in chromosomes and how they move around in bacteria. Why don’t you tell us big picture what you’re interested in?
Xindan: My lab studies how the chromosome is organized inside living cells and how this organization is passed on through generations. So we study a set of protein factors that are important for this organization and we study how these factors structure the chromosome. So some of these proteins are conserved from bacteria to humans and they are found in many organisms and we hope that by studying these proteins using bacteria as a simple model organism, we could uncover some fundamental mechanisms of chromosome folding in other organisms. This is sort of the general theme of my lab’s work.
Vincent: So you use Bacillus subtilis as a model, right? Why not E. coli or some other bacteria?
Xindan: That’s a good question. I did my PhD studying chromosome organization in E. coli and in the end, I decided to switch for several reasons. The first one is that in most bacteria, chromosome segregation is driven by a conserved factor called the partitioning system, and this factor is present in about 70% of the genomes and E. coli is the outlier here. It doesn’t have the system. If there are a certain percent of bacteria that don’t have them, maybe they are not important, so why bother, but there are also the 70% that have them so they make this segregation process more efficient and I want to study how they do it. So this is the first reason, the partitioning system. The second reason is Bacillus, when they grow out of this exponential phase when they are in nutrient limiting state, they differentiate into different cell types and the one type is sporulating cells. They form a spore so then they can resist many environmental harshness.
Vincent: By the way, are spores alive? (laughter)
Xindan: Spores are sort of dormant but they are also constantly sensing the environment, and there are some triggers, when there is a good food around, they will germinate like a seed and try to make more of the cells. So they have the sporulation cells and also some cells designed to take genomic DNA and become competent and take new genes in their system to be better.
Vincent: That’s what Ankur works on, right?
Xindan: Yeah, putting cells in a competent state, and they can also, so they sense some surface so they can also move in a certain way so there is swarming motility. So bacillus just have all this different cell types and by microscope, you will see that the chromosome can adopt unique, special conformations that you don’t see in other cell types. So I like to study bacillus because I want to look into the chromosome and see how they are folded in these different states and what are the factors that make them fold like this. So this is the second reason I got into bacillus. The third one, I only knew this when I was already in this field, is that working with bacillus is so easy. (laughter) It’s so easy to make a genetic manipulations.
Vincent: Easier than E. coli?
Xindan: Yeah, a lot easier, because of the natural competence. You grow the cells, you take the DNA in.
Vincent: So you don’t have to make them competent as you do E. coli?
Xindan: You just grow them to a certain 4 hours median and you add the DNA and they take it. So it’s just so easy.
Vincent: What is the, listen to how I phrase this, what is the reason that they are, she’s laughing because she knows how I’m doing it, what is the reason that they are competent all the time and not some times like other bacteria? Do you know?
Xindan: So they are not competent all the time, so when they grow exponentially they are not, only when they are sort of stressed, there are some signaling pathways to go down and then they start a little change.
Vincent: So tell us what happens to the chromosome during a growth cycle of Bacillus, so when they’re growing and they divide and all that and how that relates to what you are interested in.
Xindan: Right, so I need to step back a little, so most bacteria has a single chromosome and it’s a circular DNA molecule. It has a replication origin here, the terminus here, and the tool replication arms like this.
Vincent: It’s circular, though.
Xindan: Yeah, it’s one circle, you have the origin, terminus, and the two arms.
Vincent: And for B. subtilis, how long is it, roughly?
Xindan: It is around 4 million base pairs, so the first study, a systematic study of a bacterial chromosomal segregation was in a model organism called Caulobacter crescentus. So this DNA molecule in a rod shaped cell is compacted 1000 fold. But we need to think about it, it’s really like 10,000 kilometers, or 1,000 kilometers in your backpack. It needs to be compacted a lot but the cells are growing very fast and then they have to constantly make new proteins in response to all these different stresses. So it needs ot be organized. When people look at the chromosome organization using this bacterium, they found that this chromosome has the replication origin located to one end of the cell and the terminus to the other end, and the two replication arms are aligned linearly from one end to the other.
Vincent: So there’s one origin.
Xindan: Yeah, so one origin to one end terminus to the other end, the two arms are just aligned.
Vincent: You say two arms, you mean the replication is bidirectional?
Xindan: Yeah, right, yeah. So and then this was just a very intuitive organization. You have the chromosome and you just organize it like this. And this was thought to be true for all the bacteria. So when I started my PhD some of the regions in E. coli didn’t fit this regime at all, so I decided to look into the chromosome organization in E. coli, I found that in E. coli this organization is rotated 90 degrees. So basically the origin instead of at the pole is now in the middle of the cell and the two replication arms are on the cell halves. And this is quite, very different from what we thought before. And then during my post doc I moved on to bacillus. I found out that in bacillus, the chromosome actually adopts an unusual dance. So at the beginning of the cell cycle the two arms are like this, but at some point in the cell cycle it is rotated like this. So every cell cycle it does this oscillation. So then later and right now I am trying to find what is contributing to this different organization? Actually, all these bacteria use very similar sets of factors and they use a slightly differently and now they result in this seemingly diverse organization patterns, but basically they have a very fundamental similarity between them, and that is that they are compacted in a certain way and they are localized linearly and all the DNA replication segregation and cell divisions are happening at the same time and they have to find a way to coordinate these.
Vincent: So is the chromosome attached at all to the cell wall or anything like that?
Xindan: In some bacteria it is very well studied that the origins are attached to the cell pole and it might be attached to the membrane but we don’t know this for sure, for bacillus there is attachment at a certain point in the development but it is not clear when the attachment is happening all the time.
Vincent: I know in E. coli at least, when growing there is an understanding there is a cytoskeleton and that is involved in division and partitioning. Is this the case with bacillus as well?
Xindan: It can be. So, seemingly everything is connected, and we are just now trying to find the connections and trying to find these connections and we discover it more and more, but it’s not…
Vincent: Alright, we’ll come back to you. Let’s move on to Ankur. So everyone can talk. So you work on Vibrio?
Ankur: I do, yeah.
Vincent: Tell us just a little about Vibrio cholerae, right?
Vincent: It’s a pathogen, right?
Ankur: It is a pathogen, yeah, so it is the causative agent of the diarrheal disease caused cholera so it is a devastating disease. Normally it is only affecting populations in the developing countries really where people lack access to clean drinking water and so if the bacteria is ingested by a human host, it will colonize the small intestine, it will elaborate a toxin called cholera toxin which causes the disease, basically. It is a main component of the disease.
Vincent: So where would you acquire it, you said contaminated water, right?
Ankur: Correct, food or drinking water is a common route for infection.
Vincent: But it lives in the environment also, is that right?
Ankur: Yeah, it’s normally environmental and lives in brackish water environments is where it kind of likes it the best, and when it is in the environment one of the things it likes to associate with is the chitinous shells of crustaceans. So and that compound of that cells is called chitin so if you’ve ever had lobsters or crabs the shells of those organisms are made up of chitin. And so if Vibrio is kind of in the environment floating around, it will find a piece of chitin, latch on to it, form a biofilm, divide and grow on that surface.
Vincent: You said they are mainly in brackish environments, right, so you wouldn’t find them in the open ocean at all?
Ankur: Vibrio cholerae I think could also definitely be found in the open ocean. It can tolerate high salinity but I think it thrives in brackish water environments.
Vincent: So if you could show me a picture of the Earth and tell me where Vibrio cholera was, where would it most likely be?
Ankur: I guess I have to disclaimer this a little bit. So Vibrio cholera, there are two types of Vibrio cholerae. There are Vibrio cholerae that are completely environmental, will not cause any disease, and then there are toxinogenic Vibrio cholerae that have a specific element which is a phage which is lysogenising vibrio that encodes the cholera toxin, and so those are called toxinogenic vibrio cholera strains.
Vincent: That’s what you work on.
Ankur: Correct. And so normal Vibrio cholera are very broadly distributed across the globe. Toxinogenic Vibrio cholerae are much more limited in their distribution.
Vincent: Julie is nodding because she also works on a Vibrio, right, but it’s a different Vibrio. So make sure he says everything correctly (laughter) Because I can’t catch it, that’s for sure. So this phage that was acquired happened a long time ago presumably and does it confer some advantage to Vibrio?
Ankur: It’s a great question, actually. It confers the ability to cause disease, whether or not that is a selective advantage or not I guess is a question.
Vincent: If you take the environmental vibrio and put this phage in them will it make them pathogens?
Ankur: So they need to have the right receptor on the bacterium for them to take the phage in, so I don’t know if that experiment has been done. Actually, I’m sure it has, I just don’t know the paper that describes it. So I don’t know the answer to that question, actually.
Vincent: So the toxinogenic vibrios, they live mainly in brackish waters, is that right?
Ankur: They can, they’ll thrive in brackish water environments but they can also survive in basically straight water as well, but they’ll also survive in higher salinity, so they kind of have a salt tolerance that allows them to live wherever.
Vincent: So one more general question. When there is an outbreak of cholera, so in Haiti it was brought there, right, but are there any instances where someone actually acquires an infection not from a human to human transmission but from an environmental source?
Ankur: Absolutely, that can certainly happen, and that actually happens cyclically every year in Bangladesh, there is an area where cholera is endemic and so it is thought that Vibrio cholera is sticking around in the water and every year a new outbreak comes out. If you look at the strains that are causing disease every year, they can differ from year to year, suggesting that they are acquired from the environment.
Vincent: Now, from what I understand from your website, you are interested in how the Vibrio take up DNA.
Ankur: That’s right.
Vincent: Tell us what you’re interested in there.
Ankur: Sure, yeah. So this process that they use to take up DNA is called natural competence, as Xindan alluded to, and so this is a way these bacteria when they are in the environment, they will induce themselves for this process. They’ll make this protein apparatus to take up DNA that is sitting outside of the cell, bring it into the cytoplasm or inside the cell, and then recombine that DNA in the chromosome, and they can use this as ways to acquire novel traits or to introduce mutations to existing genes. So my interest is really pretty broad in terms of this process. I really want to know how it works in a fine detail way. So we are really interested in what are the mechanisms these bacteria use to take up the DNA, what are the mechanisms that they are using to actually integrate in the chromosome, and even further back, we are really interested in looking at the regulation of this process, how are they controlling the processes that allow this to happen.
Vincent: So this uptake of DNA, this implies that there is DNA everywhere, right, is that true if you go into the environmental niche of Vibrio, there’s lots of DNA around?
Ankur: So the way that, I will back up and describe I guess, when they are turning this system on. They are normally turning this system on when they are forming biofilms on chitin, which is that thing that I mentioned they are interacting with in the environment. And so I guess the idea there is that when they are colonizing chitin, it is very likely that you will be surrounded by neighbors, potentially other Vibrio species or other Vibrio cholerae isolates, and it is a great environment in which they can start to share DNA potentially.
Vincent: So if they are in someones intestine, are they forming a biofilm and turning on this DNA uptake?
Ankur: Great question. I don’t think anyone knows the answer to that yet. In terms of thinking about chitin as an inducer for this process or normal chitin biofilm formation is what normally turns this system on. If there is a chitin biofilm in the gut it could potentially turn on this system, I would say. But it is also known that if you give the bacteria other carbon sources, that will prevent them from turning this system on. So if there are other preferred pieces of food around, they will actively not turn this system on. So it is hard to say whether or not it would turn on in the human gut or not.
Vincent: We don’t have chitin in our gut, do we?
Ankur: We do not, no.
Vincent: So it’s not going to be a chitin dependent process, but it could be dependent on something else as you say.
Ankur: That’s possible, sure.
Vincent: So would Vibrio be on the lobster shell for example? Or is it not likely to be there.
Ankur: It certainly could be. If you’re getting that lobster from the wrong water source, I guess, yeah, that’s entirely possible.
Vincent: In the ocean, what other sources of chitin besides crustaceans, for example?
Ankur: It is mainly crustaceans, but it’s not going to be the macroscopic huge crustaceans like lobsters and crabs. They are also colonizing microscopic crustaceans like zooplankton as well.
Vincent: So the transfer of DNA, is that from other Vibrios or other species entirely different?
Ankur: It could be from potentially other closely related species as well, so the way the DNA is actually integrated in the chromosome is using homologous recombination which actually means that DNA has to be somewhat similar to the host chromosome for it to actually be crossed in and integrated. So it could be other Vibrio cholera isolates that are out there in nature, or it could be other Vibrio species that have similar genetic content.
Vincent: So if you look at the genome sequence can you tell sort of the origin of different parts of the genome?
Ankur: Actually there is not a ton of examples of movement of the DNA among Vibrio cholera isolates in nature. So it is hard for us to get a consensus on where pieces are coming from currently.
Vincent: So you are interested in how chitin regulates this, is that right? Tell us about that.
Ankur: So these bugs, when they are sitting on a piece of chitin, they basically have to degrade this compound. So chitin is an insoluble polymer of N-acetylglucosamine which is just a sugar, so it’s really just a chain of sugars that is normally insoluble. So for Vibrio to kind of gain access to this awesome carbon source or this sugar to eat they need to degrade that carbon source into soluble sugars and then they eat that, basically. And so in order to regulate that process, they don’t want to turn on the enzymes to break that sugar down all the time, they have a system in place where they can sense some of those sugars and then crank on the expression of these genes that are important for eating the chitin but also turning on this process of natural competence. And so we are really interested in trying to figure out what exactly are the enzymes that mediate this process, how are they sensing those sugars to turn on these distinct processes of eating the chitin vs turning on competence and is there interplay between those two systems.
Vincent: So the use of chitin as a source and the uptake of DNA are both linked.
Vincent: Is that coincidental or do you think–
Ankur: I think it comes back tot he question of when should you turn this mechanism of DNA uptake and integration on? And I think that in terms of the ecology of the organism, it might make sense to do it under conditions when they might be surrounded by neighbors, and growing on a chitin biofilm is a great environment for them, I mean, this is anthropomorphizing the bacteria, so I don’t really know if Vibrio cholera is really trying to do, but it makes sense in the sense that it could be a good environment to share.
Vincent: So how do you study this? Do you grow Vibrio on crustacea in the lab?
Ankur: That’s right, yeah. So basically we actually order from Sigma, very very fancy compound, crushed shrimp cells that we use in the lab setting (laughter) and actually the batch of shrimp cells that we get, they have to meet certain criteria, we had a scare in the lab where we thought our shrimp shells were going off, so, we had to find a new lot of shrimp cells. But basically we grow them up in some nutrient broth and transfer them over to a tube containing just some crushed shrimp shells and they turn on this competence machinery.
Vincent: And so you study what genes are going on?
Ankur: That’s right, so what genes are going on, what are the genes that then turn those genes on, and what is the mechanism of everything in between, basically.
Vincent: So if you met someone in an elevator who wasn’t a scientist and they asked you what is the relevance of this work to me, what would you tell them?
Ankur: Well, I would say that natural transformation is a great way for dissemination of pieces of DNA, which could be antibiotic resistance determinants, they could be virulence factors, they could be other things that some pathogens use to increase their virulence. So in terms of human health and biology certainly pathogens have this capacity, we should probably try and understand it, because if we can understand it we might be able to stop it. So that is I think one aspect of this, for sure.
Vincent: So there is no crustacean DNA in the Vibrio genome, right, I guess?
Ankur: I don’t know that I’ve looked for that, actually. But I am going to say tentatively no. (laughter)
Vincent: Someone once told us years ago DNA is a real problem, it’s everywhere. If you are doing very sensitive sequencing it gets contaminants all the time of all sorts of things. So I have this vision that it’s all over and whatever environment that you look at, there’s DNA, so eukaryotes take up DNA as well, right, we’re just beginning to realize that. I think it is a really interesting way to look at it. We’ll get back to you. Julia, you also work on a Vibrio but a different one, right?
Julia: That’s correct. We work on Vibrio harveyi mostly in the lab, although we work on Vibrio cholera occasionally sometimes some of the other marine vibrios as well.
Vincent: You guys talk to each other?
Julia: All the time.
Ankur: Absolutely, yeah.
Vincent: Are you near each other physically?
Ankur: Only one floor away, yeah.
Julia: And there’s a third Vibrio lab here, too, which is Dean Rowe-Magnus’s lab, so, we have a great Vibrio community at IU.
Ankur: A quorum.
Julia: We have a quorum. (laughter)
Vincent: We have a quorum, that’s a good title, right? We got to somehow put Indiana in the title. (laughter) But what Vibrio is that third lab?
Julia: They usually work on vulnificus, sometimes parahaemolyticus, as well.
Vincent: So harveyi is not a pathogen.
Julia: It’s not a pathogen to humans, it is a pathogen of shrimp and fish and so is more of a concern for aquaculture, but that’s right. We get to work on a non pathogenic one for the most part. We work on them however because they are bioluminescent and that is one of the more important traits that we study in the lab.
Vincent: So what’s the function of bio luminescence in their life?
Julia: That’s a great question that nobody knows the answer to.
Julia: Yeah. Most of the ones that you hear about are from Vibrio fischeri which we have as a community studied Vibro fischeri bio luminescence and its role in symbiosis with the bobtail squid. Vibrio harveyi, it is not clear why they bioluminesce, there are a lot of hypotheses, I don’t think anyone has actually determined the actual reason.
Vincent: But for fischeri, the luminescence helps the squid, right? Do we know what it does for fischeri at all?
Julia: The bio luminescence? The luminescence in fischeri is important for the squid to counter illumination strategy. So they are in the ocean in Hawaii and the picture this nice moonlight on the beach in Hawaii and they’re in very shallow water and the moonlight makes a shadow and the squid needs to hide from its prey, the predator also hides from its prey, and it makes a shadow and so the light from the bacteria that it has in its light organ hides the shadow.
Vincent: So the bacteria get a place to live.
Julia: And food, most importantly.
Vincent: And they exchange light for the squid and that’s the symbiosis there, but we don’t know for harveyi, it must do something, though.
Julia: There are some ideas, one of them is that it is the bioluminescent bacteria, when they infect, say, shrimp, and the shrimp might then be bioluminescent, which they are, might be another way that the shrimp are then prey for other predators and that might disseminate the bacteria more. Some people have hypothesized that it is just an accident of its enzymatic light reaction, it just produces light as part of other metabolic processes. It could be that there is a symbiosis with an organism that we just have not studied very well.
Vincent: But you and others in the field use it to study quorum sensing, so can you explain quorum sensing for us?
Julia: Sure. So quorum sensing is our technical term for how bacteria communicate, it’s how bacteria secrete molecules called autoinducers, these are usually specific to the bacteria but they can also be more general to many bacteria can detect, and it is their way of counting their numbers. So the number of these autoinducers in their environment is a proxy for how many cells are in the environment. More molecules means more cells and the cells can bind these autoinducers and detect them and change their gene expression so they change their behavior. If they are in different environments under different situations or around different bacteria, they can modify their behaviors accordingly. We often think about bacteria as individuals perhaps swimming around in the ocean alone, right? Or like Ankur was talking about, living on a chitinous shell in a biofilm and how their behaviors change under those circumstances.
Vincent: The idea that bacteria live in communities is not very old, is it?
Julia: No and it is really one of the first things I talk about when I introduce the idea. We always think about bacteria as these single celled organisms, or at least that was how I was taught way back then, but we now know they exist in these really complex multicellular communities and they are interacting and they are sometimes fighting each other and they are sometimes beneficial to each other and it just depends on the environment.
Vincent: There is now some evidence that viruses might induce cells to secrete substances that cause quorums, as well.
Julia: Yes, it’s a very interesting new development in the field. There have been a couple very recent papers that have been very fun to read about that topic.
Vincent: But you use luminescence as kind of a readout for quorum formation, right?
Julia: It is one of the best readouts for sure.
Vincent: There are other things that happen as well in response to these molecules, right?
Julia: Right. So that’s actually one of the reasons we use Vibrios as models, because they do fascinating things responding to quorum sensing. Competence is one of them, like Ankur was just talking about, biofilm formation, multiple types of secretion systems, motility, there are a number of things that change.
Vincent: Are there many molecules that are produced, that are used to sense quorums?
Julia: Yeah, so in every bacterium it is different, the structure can be different, anything from things with lactone rings to long carbon chains to peptides, depending on the organism. In Vibrios, there are even every Vibrio has multiple autoinducers, multiple molecules, multiple proteins that detect those molecules, it can be quite complicated in certain species.
Vincent: Do most people who study biofilms use these model systems like harveyi?
Julia: So the best biofilm model is Vibrio cholerae, actually, so it forms very nice biofilms and it is something that is highly studied, there are people doing some really fascinating work looking at how bacteria change gene expression in different parts of the biofilm and how those cells align in the biofilm and things like that.
Vincent: So tell us what aspect of quorum sensing you are working on?
Julia: Sure, so actually after I tell you everything about those molecules, we actually don’t work with them at all (laughter) So we are actually interested in what happens downstream after all of the communication has occurred, so we are interested in the proteins, the transcription factors specifically, that enact all those changes in gene expression.
Vincent: So when these, how do these molecules do that? Do they bind receptors?
Julia So in Vibrio it is somewhat different than in most Gram negative bacteria. In most Gram negative bacteria, you have a molecule that is diffusing through the membrane and is bound inside the cytoplasm by a transcription factor. In Vibrio, we have those but there are others and some of the molecules are detected on the surface and then have a signal transduction cascade that then changes gene expression of a very important transcription factor at the center of the pathway. So that is where we have been focusing our research, on the center transcription factor, and really one remarkable protein changes hundreds of genes, turns them on, turns them off, there’s a massive cascade that happens. We are very interested in when those genes are turned on and off, and also how that ties in to other signaling systems, so changes in nutrients or salts or different growth conditions, surfaces or not surfaces, and how that intersects with quorum sensing.
Vincent: So one of these genes under the control of this protein must be the luminescence gene, right?
Julia: Absolutely, the bio luminescence gene was one of the first ones that was discovered so we know a lot about the bioluminescent genes, we know a lot about their enzymatic activity, we actually still don’t know a lot about how they are regulated, so one part of my lab focuses very closely on the mechanism of gene regulation in quorum sensing in Vibrios, and the bioluminescent promoter is a great example that we work with.
Vincent: And what does the other half do?
Julia: The other half thinks more about the downstream phenotype. So I have people who are interested in how after quorum sensing signaling what changes happen, so let’s say osmotic stress response genes, for example. These are bacteria that are marine organisms, they exhibit, they experience different changes in salinity all the time, and they turn on the osmotic stress genes when they are doing quorum sensing. We don’t know why but we are very interested in why the salt signaling and why the quorum signaling intersect at these genes. There are other people that are interested in motility, and biofilms, type 3 secretion is another one that we study, so really looking at how multiple pathways intersect.
Vincent: Do you think you could study this the rest of your career or do you think you could be distracted if you found a particular downstream operon that was really interesting and had nothing to do with quorum sensing?
Julia: I do get distracted a lot, actually (laughter) so I think that the mechanism work is always going to be at the heart, the regulation mechanism will always be at the heart of our work. It has really been driven a lot by what the individuals in my lab are interested in, so they kind of have their own favorite pathway and what physiological question they want to ask. So it might be that they will get fascinated with one thing and will go with that for a while.
Vincent: So you’re okay with that, if someone came and said oh, this is really cool, I want to work on this, yeah?
Vincent: Good, yeah. Now let me ask you the same question I asked Ankur. If you’re in an elevator and someone asks you what is the importance of glowing bacteria what would you say??
Julia: So I always say this metaphor, if bacteria are alone in their environment, let’s say they are bioluminescent, it is not going to do much good, but if there are a trillion of them in one area and they turn on bio luminescence, what does that do? For Vibrio harveyi we might not know, but we know a lot about pathogenesis, right? So bacteria that are alone tend not to cause disease, but we know when there is a million of them in the human host that they cause disease. So our research has relevance for studying pathogenesis in humans as well as other animals and plants. What we are hoping to learn is how to turn off quorum sensing so that they cannot use their quorum sensing strategy to act and secrete virulence factors and make good biofilms, so if we can turn that off maybe we can turn off pathogenesis. And what is really important about that is that molecules, and these are being developed now, molecules that block quorum sensing don’t have a very strong selective advantage for the bacteria to generate resistance, so this has been pretty carefully studied that antibiotics have a very strong selective advantage to generate resistance. Molecules that target quorum sensing would ideally not do that, so there might be a lower rate of resistance.
Vincent: Do we understand why that is? Why there is very little selection for resistance?
Julia: So generally, even if you knock out these quorum sensing proteins, the strains don’t have that much effect. There is a slight growth disadvantage but it is nearly as bad obviously as a bacteriocidal antibiotic would be.
Vincent: I didn’t ask you, Xindan, that question. So let me ask you now, if you were in an elevator and someone overheard you talking about studying chromosome movement, what would you tell them if they said why does this matter?
Xindan: Well, in every cell, every cell faces this problem if they want to make two daughters. They have to copy the DNA and distribute them evenly to the daughter cells. In bacteria they do it very fast, every 20 minutes they have to do this. So it is very important for the bacteria to preserve the genetic material and so from bacteria, one cell is the whole organism, and for us, every cell has our genetic material and is doing exactly the same thing. We face the same challenge. So chromosome organization and segregation is very important.
Vincent: Of course, you don’t have to explain any of this to me or us in this room, but I think it is really important to let the general non science public understand why we are doing what we do, because we know that you could work on the most obscure thing and it would be cool and it might lead to something great one day and we get that, but I think it is really good to put your work in terms of an elevator talk. I think that is essential. So I want to ask you all some fun questions, maybe. Julia, you’re all pretty early on in your careers, so some of these are less compelling than we will ask later on TWIV, on TWIV we have mostly old folk, I think (laughter)
Julia: Adam’s offended.
Vincent: Mostly old, yeah. I’m old, too.
Adam: I’m very young.
Vincent: Mentally, sure. (laughter) So Julia, if you hadn’t been a scientist, what else would you have done, you ever think about that?
Julia: Just like Xindan, I love math, I’ve always loved math. I actually wish I had taken more of it in college because I had apparently forgotten it all. But yeah, I really loved math.
Vincent: What would you do with math, though?
Julia Oh, you know, I really like balancing checkbooks. Probably accounting. (laughter)
Vincent: Cool, accounting, great. How about you, Ankur?
Ankur: So when I was going to undergrad, I was either going to go for science or go into medical school or I was going to become an architect was my other idea, because my dad is an architect, so that’s what he did and he really enjoyed it. So either an architect or an engineer would be my other career I would have considered, something I could still tinker with every day.
Vincent: So you like to take things apart?
Ankur: That’s right. Yeah, that’s the other half of my lab, we develop methods for genetic engineering, so I’m not actually an engineer but I can at least mess with the bacteria.
Vincent: When I was a kid I also liked taking apart TVs, and I would take them apart, never put them back together. (laughter)
Ankur: We had very similar youths, I think.
Vincent: It’s New Jersey. (laughter) In those days, TVs were huge boxes with big tubes and I would cut out all the components and put them in drawers and my mother would say, what are you doing? And at the end we threw it all out, but the best part, we would take the picture tubes and put them in the woods and throw rocks at them and they would explode. How about you, I think you kind of mentioned you always wanted to be a scientist and nothing else, but is there anything else?
Xindan: So, maybe a more realistic question you would ask is what happens if you burn all your startup money, you don’t get (laughter) you don’t get your funding and you have to close your lab and you can’t do any science related things, what would you do? So this is more realistic, and I actually think about it. I think I would want to become a math teacher and I would like to teach middle school students when they are still quite young and fresh and don’t know too much about life. (laughter) I like to plant this seed in their head when they are young and I like to inspire them to find their talent and to be aware of their talent and to find what they are curious about and to pursue it. I hope to let them know that there is something bigger than yourself and try to do a degree in STEM, so to get curious and try to ask questions and even if, I will try to get them to do a PhD, I will get into science, I want to let them know even if what we are doing is not immediately related to human health, I will try to make it into applications, but what we are doing with any science, with any discovery, will be useful maybe not in our lifetime but it will be useful one day to actually make a difference in this world. This is my dream, it’s kind of ideal, I feel that I can actually try to influence the younger people and make them realize this very early on in their life. I hope to do this.
Vincent: It’s good to dream, always, right?
Vincent: You’ll be fine, you’ll stay a scientist, I have no doubt. Julia, have you read any good books lately?
Julia: So truth be told, I’m in a book club, and I did not read the last book (laughter) Which was supposed to be “Exit West” and I’ve heard it is very good. But I am supposed to be reading “Ready Player One” which I’ve heard is very good, so that’s on my nightstand.
Vincent: Ankur, you’ve been here the longest of the three, right?
Ankur: Nope, Julia.
Vincent: Julia has been here the longest? Alright, then well, anyway, I’ll ask you, what do you do for fun?
Ankur: What do I do for fun? I always tell people that my job and my number one hobby is doing science. So if I can I am trying to be at the bench as much as possible. Every day it is getting harder and harder which means I am not doing anything at home basically, I am doing a lot of science. So yeah, main hobby is that, but if I get time I like to go rock climbing, as well, so that’s the other hobby I try to keep up.
Vincent: Xindan, a new student comes to your lab, what’s the best advice you can give them?
Xindan: This is a hard question. What’s the best advice I can give them? So maybe, this is something I learned at the very beginning of my PhD. Our conclusions are only as strong as our data, so it is very important to have high quality data. On the other hand, we don’t have to do every experiment in the most perfect way. Let me tell you one example. So at some point, I knew this at the beginning of my PhD and I tried to do everything perfect. I would find the best controls and do the controls first and wait until I have everything to do my real experiment, find the most elegant way to do a test and only in the end fund that. It wasn’t so interesting. So my advice to my students is it is very important to have high quality data, but when you are doing some exploratory research, when you are not sure whether it will work, it is okay to do a pilot experiment to see if it works. And you will have the opportunity to do your perfect experiment if there is something interesting to pursue.
Vincent: Alright, well, we are out of time. So let me just tell you that you can find this podcast and all of our others at microbe.tv. You can send questions and comments to firstname.lastname@example.org. If you’d like to support us, which some people do financially, you can go to microbe.tv/contribute and you can find ways to do that. And I want to thank my guests for today, Xindan Wang, thank you so much.
Xindan: Thank you.
Vincent: Ankur Dalia, thank you so much.
Ankur: Thanks for having me.
Vincent: Julia Van Kessel, thank you.
Julia: Thank you.
Vincent: I also want to thank this young lady who is standing here, Jolene Ramsey, for getting this all initiated (applause) I met her at ASM in New Orleans earlier this year, she said would you like to come to Bloomington and that was the beginning, and she really organized it all and made sure it happened and made a great poster and everything, so thank you very much. I want to thank the departments here that have participated in my day and so forth. I want to thank the American Society for Microbiology for their support of TWIM as well as Ray Ortega who does a lot of post production for us. Thanks for listening everyone, oh, by the way, I’m Vincent Racaniello, you can find me at virology.ws. Thanks for listening everyone, we will see you next time on This Week in Microbiology.
Content on This Week in Microbiology (microbe.tv/twim) is licensed under a Creative Commons Attribution 3.0 License.
Transcribed by Sarah Morgan.