Arash Komeili, Part 2 of 2

Spectrum

Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part 2.

Transcript

Speaker 1: Spectrum's next

Speaker 2: [inaudible] [inaudible].

Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news.

Speaker 3: Hello and good afternoon. My name is Renee Rao. I'll be hosting today's show. Today we present part two of our interview with a Rosh Kamali. Dr [inaudible] is a cell biologist and associate [00:01:00] professor of plant and microbial biology at UC Berkeley. Previously on spectrum, he discussed his work with magneto tactic bacteria. Here's Dr Camilia explaining why these bacteria so interesting.

Speaker 4: We work with a specific type of bacteria. They're called magneto is tactic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you [00:01:30] take their shape or if you look at even the genes they have, you can't really group them into one specific group as opposed to many other bacteria that you can do that, but unites them together as a group is that they're able to orient in magnetic fields. And some along magnetic fields

Speaker 3: today. In part two of his interview, Dr [inaudible] explains how these discoveries might be applied and discusses the scientific outreach he does in our community. Here is Brad swift interviewing a Kamali,

Speaker 4: [00:02:00] so how is it that you're trying to leverage what you're learning about the magnetic zone? You're trying to apply it in any way. Are you still really in the pure research mode? I think we're starting to move out or at least branch out to try to do some applications as well. This has been a really, one of the areas of research that's been the most active, or at least the most thought about for Magna [inaudible] bacteria for the last 40 years or so of that people have been working on it. You have two [00:02:30] features of the magnesiums that immediately can be thought of as being very useful for applications, but one is that they're making something that's nanometers size. Very small is magnetic and it has very, very irregular dimensions, quite free of impurities. So you can make magnetic particles in the lab and people have gotten very good at it actually, but it's often very hard to control some of their features.

Speaker 4: Maybe contaminants can kind of bind my net [00:03:00] particles pretty easily. And then on top of that you have to sort of use certain types of chemical conditions that are not so favorable. Maybe the Ph has to be a little bit high or chemicals that you don't want to use. And that's one of the reasons why the bacteria are so great. Right? Then as I said, they make an Organelle in this case to magnetism. So then within this tiny 50 nanometers sphere, they can just make what is otherwise a toxic condition inside of that and make this magnetic particle. But the cells are [00:03:30] growing in relatively harmless growth media at 30 degrees centigrade. So you can make magnetic particles under what are not toxic conditions because the bacteria are taking care of that inside of the cell. So that's one of the reasons people have been really fascinated by them.

Speaker 4: So how can we take these sort of perfect crystals out of these bacteria and apply them to something else? The other aspect of it that's really important to recognize is that it's not just that the bacteria are randomly making magnetic particles. [00:04:00] They actually have a whole set of genes that they're used to build a magnetism and build the magnetic particle. So the ability to make a magnetic crystal is in coated in jeans, so you can not only extract the magnets out of these bacteria to use it for applications. Maybe you can extract the genes and put them into another organism and now give that other organism the capability to make magnetic nanoparticles. They're [00:04:30] magnetic properties, mixed them, really useful for many different kinds of applications. One of them, they can be potentially contrast agents for magnetic resonance imaging or MRI. When you get an MRI, does a lot of structures that are easily seen, but a lot of things are sort of invisible to the MRI and if you had a little magnetic particle in that region, you'd be able to see it better. One idea is can we put the genes as we learn more about them, can we sort of gather [00:05:00] up a minimum set of genes that are sort of sufficient to make a magnetism and a magnetic particle and then just put those into some other cell types and then see if that's enough to make a magnetic particle and that settle and they can we track it by MRI or something so that that's actually the focus of a grant that we recently got with a few other groups on campus. As a large collaborative grant,

Speaker 4: how will you start to [00:05:30] prove that concept? I think we're taking many parallel approaches for it. You know, both to show the utility or the different ways that you would have to image them. One group is working on essentially technologies for imaging, magnetic nanoparticles and animals, and then we are sort of at the very other end of the spectrum and the collaboration, we're trying to say, we think we have a set of genes that are sufficient. This process, let's start taking baby steps [00:06:00] and move them to other types of cells, whether they're bacteria or other cells. And see if we can produce magnetic particles in those cells. Are other collaborators they're focusing more on, well, if we know these genes, can we start transferring them to mammalian cells and then in animal studies we could track cells using magnetic resonance imaging. Each group has focusing on a different aspect of the project.

Speaker 4: Some of the other applications are really fascinating too. There's one where [00:06:30] particles hold their magnetic properties very stably and if you give a very strong magnetic field then you can kind of flip the dipole moment of the crystal. You can do this back and forth, keeps switching it, and if the pulse is switching faster than the dipole man can flip on the magnetic protocol. The difference in energies essentially released as heat. We can in that way heat the particle. There's a lot of anticancer treatments to try to essentially have the particles adhere to [00:07:00] a tumor and then heat the particles using this method. Just have the heat of the particles, kill the cells locally. There's been quite a few papers on it and some of these types of studies are in clinical trials to see how effective that could be for different kinds of tumors.

Speaker 4: Yeah. Bacteria seems to get used that way. More and more to go into a tumor and linger just on the tumor and continue to just be very local in terms of very specific. And that's, you know, [00:07:30] local drug delivery or local attacking of tumor cells would be something that's very, this bacteria have this great access that other organisms don't have. If you can localize them and direct them. And that's sort of some, there's some other work which I think is also really interesting is to thinking about the magna detected bacteria as a vehicle for delivering drugs. You know, one of the things you can imagine is that you could guide them with a magnetic fields so you can have them guided to some [00:08:00] areas in the body by an external magnetic field. And there's definitely some people who are working on that. Can they move the bacteria through vasculature to a certain area because they can swim along magnetic field.

Speaker 4: So if you want to localize it somewhere, you would have to instigate that field there. Yeah, exactly. To direct it. Right. The stuff I was telling you about with the heat treatment, I think all of that is trying to, right now at least because there's not much known about how to target the bacteria, they work with kinds of tumors that are accessible [00:08:30] so that you could inject the particles into the tumor directly directly to the tumor as opposed to try to do a systemic thing. Yeah, exactly. But you can imagine that maybe one benefit of the is is that they are surrounded by biological membrane and you can have proteins on them and people have done this pretty, you can display specific proteins on the surface of magnesiums, so then you could customize your, I need a zone to have affinity for certain types of proteins [00:09:00] or certain types of cells. Some proof of concept of that has been done for sure.

Speaker 5: Mm MM.

Speaker 3: Our guest on spectrum today, is it rush Molly, I cell biologist and associate professor at UC Berkeley. In the next segment. Dr Camelli speaks more about some of his collaborative. This is k a l x Berkeley. [00:09:30] [inaudible].

Speaker 4: The work you're doing with a sequencing is a lot of it. Trying to catalog everything. Keep track of what's, what sort of explain the sequencing side of what you're doing. The sequencing side, we are fortunate that the organism that we work with is in pure culture. Our lab rat essentially has been already sequenced by someone else. When we sequence, [00:10:00] it's more to make sure if we're going to put some gene fusion into the bacteria or that what we have is correct. Our sequencing is relatively limited. We are trying to branch out more and say nowadays technologies for sequencing the whole genome are much more accessible, affordable, certain types of genetics that we do where we try to delete genes or randomly mutate them. Then we can just start identify what's changed by going back and just sequencing the whole [00:10:30] genome or the bacteria. We are doing a little bit of that.

Speaker 4: We do it on campus very accessible and affordable, but it's really something that was unthinkable even five, six years ago that you could do this on a large scale, do it affordably. And it could be a pretty routine tool in research. Sorry, I mean it's a really exciting, actually you're not gonna necessarily have to be restricted to these lab rats that do represent some of the general features of the process you're interested [00:11:00] in, but not the diversity of fitness necessarily. And so you can say, instead of studying just one organism, maybe I can study many other ones. There's still a lot that I can do with my model system in the law that I can't do with some of these other unconventional organisms, but they're at least visible to me. Their genes are visible to me and I don't have to isolate them away from everybody else to get an understanding of [00:11:30] what their genetic makeup is and where they are.

Speaker 4: And for things like microbiome studies is revolutionize the whole field. They were, they were always just looking at such a small sliver of what they could isolate. Yeah. And now you can look at everything, you know, they can do lots of really interesting experiments like what's on your fingers, what's on your, you know, how's your right hand different from your left hand and microbial content. Yeah. You know, so that's really interesting. Yeah, it gets very refined. Is synthetic [00:12:00] biology involved in what you're doing in some way? Yeah, definitely. So what I was telling you about the applications, you know, essentially, I mean synthetic biology, I guess there's different ways of defining it. For me, you have inspiration from some biological system and now you're trying to extrapolate that and put it in a new context to do something new or something different than it normally does.

Speaker 4: Though. What I was telling you about this, this project that we have on campus or does not support [00:12:30] it by the Keck foundation to put the magnetism genes into other organisms, but that's essentially synthetic biology. So yeah, we are really relying on that and trying to see if we're going to move these genes, how are they going to be more, how can we customize them so that they work better in the new organisms they go to? Can we add on things to them or take things away and doing this using synthetic biology essentially that it would fall under the category of synthetic biology. Sort started like mixing and matching genes and in [00:13:00] new contexts that you wouldn't have naturally. And what sort of safety protocols do you have to abide by in your research? For? For our research, we are working with something that's non-pathogenic that's quite harmless.

Speaker 4: We follow the, the university has pretty strict guidelines for even for nonpathogenic organisms. Anytime you're working with recombinant DNA, even those things I was telling you where we are making a fluorescent protein fusion, we really [00:13:30] have to be careful about how we get rid of things and you know, don't just dump it down the drain. Safety-Wise. We don't really use anything harmful in the lab. I think maybe you're getting more into like what do you do with the hybrid organisms somehow and there we have to be, you know, we're always careful about how we dispose of materials. Eat cultures are always killed by bleach or heating before we dispose of it. You know, often people [00:14:00] say imagination runs wild with them. Right. You know? Yeah. And a lot of that has to do with fiction. Yeah. Books and movies and things. But I think it's important to sort of sort of what prompts me to ask.

Speaker 4: And I think a lot of times maybe scientists think about that too late, you know, so, so maybe it may not be the first thing you say. That'd be the first thing you think about. And then it may also, it may not be in your training expertise or whatever to even know what would be dangerous. So I, I, [00:14:30] is that something that the university is helping with in the sense of certainly providing those kinds of resources to you so you don't have to be expert, right? We don't. Yeah, exactly. How can you be, and also you know, we have to comply with not just handling of biological organisms, but just how the lab functions. We have not only have to comply with university rules, but we have federal rules for worker safety, city rules that are different. So we have five or six different sort of safety protocols that we have to [00:15:00] abide by and we do get inspections once a year and I know people who work with animals, they have even more extensive things. I'd have to go through a whole separate set of protocols to just the sort of ethical treatment of the animals approved by independent boards and things like that. And the funding agencies have a lot of rules, so they give us money, but they expect us to follow certain types of rules.

Speaker 2: [inaudible] [00:15:30] you're listening to spectrum on k a Alex Berkeley. Our guest is a Raj Chameleon. In the next segment he speaks about his work on outreach to the broader public [inaudible] [inaudible] [inaudible]

Speaker 4: I noticed you've got a Twitter account. I do, yeah. And is that sort of part [00:16:00] of an outreach effort on your part to get the community involved or people interested in what you're doing? How do you view outreach going forward for your projects? Yeah, so the Twitter thing is you'd asked me that outreach are fun and I think it's both. It's not anonymous. You can be social, my name, you can find it. We have one for the lab also, which not very active at all by mine. A lot of people that I follow are other scientists. I think it is not known so well that there are many scientists on Twitter and there's great outreach [00:16:30] because often is a great way to share new findings and research or things that are exciting to people or having a discussion within the community, but this all accessible.

Speaker 4: None of it is anonymous, so you can really see that. It's also fun obviously. For example, I encourage people to look out there. There's a lot of great science writers who take research findings and they in science blogs turn it into very accessible stories to understand the latest developments in research for [00:17:00] outreach. We try to do a lot of things. Members of my lab go out to, there's different events where scientists can interact with the community. I've done a few microbiology experiments with my son's classroom and you know, kindergarten, first, second grade. For me it's been really eye opening to do that because you see you all, sometimes you think what you're doing is so inaccessible on out there. But when you go and just talk to people you see that they can get really excited about, especially kids, [00:17:30] kids can get really excited about micro was, which is kind of funny because it's not something they can see and they really only heard about bad germs.

Speaker 4: They've only heard about things that can hurt them and it's just great to go out there and talk about things that are good germs and on their bodies and everything. So we do a little experiment where we take the little auger played, which has the growth for the bacteria. They put their little fingerprints on it or they can see over the course of few days, bacteria grow on there. They washed her hands and they can see that that changes whether they can grow, [00:18:00] and I do the exact same experiment. I teach undergraduate microbiology lab here. You know, the questions that the undergrads ask are almost exactly the same questions that the third graders ask. So it's great to see that they have the insight and the excitement to learn about science. It just has to be, I think, encouraged and followed up more as they go through schooling.

Speaker 4: I think another reason for us to go and do outreaches to just sort of, I get more excited about my work when I go and talk to other people and see that it's not so out there [00:18:30] and the university provides a lot of chances for us to do outreach to it. I mean, just recently we had cal day. There was lots of science on campus. Other blogs that you follow because you'd want to mention some colleagues at Berkeley have blogs, but I think people are more active through Twitter than they are through blogs. The scientific American blogs in general are pretty good. You mentioned the Keck Foundation that's brought together this collaboration that you're going to try to do the applied research on. Are there other collaborations [00:19:00] that you're trying to pursue? Yeah. You know our work, we rely on a lot of collaborations mainly because the bacteria do this really amazing thing of building these magnetic particles and we're always just like the example I told you about with the more high resolution electron microscopy where we were able to see something that we hadn't seen before.

Speaker 4: There was a lot of people who were interested in imaging magnetic particles. They're developing instruments all the time that you would be able to look at these things in new ways and [00:19:30] we can't build the same instruments, but it ends up being a really great interaction all the time to find these groups that are developing technologies for imaging bacteria or imaging particles and then see how what we've learned can be applied to their technologies. One great collaboration we've had recently is with the walls worth group at Harvard and they have these, essentially there is a way you can treat diamonds so that there's certain defects on the surface of the diamonds and then you can detect magnetic [00:20:00] fields close to the surface of the diamond can actually essentially image these bacteria that we've worked with sitting on the surface of these diamonds because of their magnetic properties.

Speaker 4: It's been great for us because working with them, hopefully we're able to fine tune some aspects of their technique to then study the magnetic particles and the magnetic chains in a different way than we had been so far and learn new things. Basically at any given point we might have seven or eight active collaboration's going on. [00:20:30] A lot of it on our part is not that difficult. We just provide a sample of the bacteria and then they work on it and if it goes somewhere then we go and get more involved in the collaboration. You start iterating with them. Yeah, exactly. This Keck collaboration was out of a brainstorming session. Went from there and we have another collaboration. Also synthetic biology that was just funded by the office of naval research and that's between two or three groups that are in different universities. We had always just talked here and there to each other and all of a sudden we realized that we could do something [00:21:00] together.

Speaker 4: And that's how that came about. It's a huge part of science I think is even more now with funding situation and you have to really look for more creative ways of doing your science and your sense is that the funding environment is dwindling. Is that good? Yeah. Yeah. I think it was already bad and the sequester just sort of pushed it down even further. For example, you look at NIH, the amount of money is that increasing, which means it's not keeping up with inflation. So your purchasing power is much less and then all of [00:21:30] a sudden the sequester takes out a few percentages off of what was getting funded to you. So I think both the success rates for getting a grant and the amount of money that you get from that grant are lower. Even if you're lucky enough to be able to get the grant. What you could do with the money is less than before. Obviously, you know, I'm biased, but I don't think it's that great. You're essentially sacrificing the next generation of scientists, limiting [00:22:00] it, limiting it big time.

Speaker 4: Was there anything that you wanted to mention? One thing I was going to say is that we've talked a lot about these bacteria, but obviously the visual is the easiest way to really appreciate what they do. And we have a, on my lab website, we have a page of videos where you can see how these bacteria migrate along magnetic fields and you can see images of them and you can see the structures within the solid with the magnesium. So clinic. So, so people go to [inaudible] [00:22:30] lab.org they can actually see videos of the bacteria. Great. Yeah, that'd be good. Yeah. Arash Kamali. Thanks very much for being on spectrum. Thank you so much. This was a lot of fun.

Speaker 2: [inaudible]. You can follow Rajkot Maley on Twitter at micro magnet or you can watch them. Fantastic [00:23:00] sell videos on his website Oh Maley, that is k o n e I l I e lab.org and now a few of the science and technology events happening locally over the next few weeks and Rick chronicity joins me in presenting the calendar

Speaker 3: this Monday. The California Academy of Sciences will host a talk by Dr. John Jenkins, [00:23:30] senior research scientist at the Seti Institute. Dr. Jenkins will speak about NASA search for other habitable planets. In 2009 NASA launched the space cough known as Kepler into orbit in order to survey our own region of the Milky Way. Kepler's has been looking for planets that are similar in size and distance from a son to our owners. In those four years. The probe has collected data on over 190,000 stars and confirmed over 130 new planets. Dr. Jenkins [00:24:00] will discuss the exciting you dated that capital has provided as well as a few of the technical and scientific challenges that went into building a vessel at Kepler. He will also give a brief overview of tests. NASA's next mission to detect earth's closest cousins. This event will be held Monday, July 15th at 7:30 PM in the planetarium of the California Academy of Sciences. Go to cal academy.org to reserve a ticket in advance.

Speaker 6: The theme for July is adult science, happy hour science, [00:24:30] neat. His brains, brains, grains, everything you've always wanted to know about your brain and more. There'll be talks in demos on memory, truth and tricks, neurobiology, human brains, a sheep brain dissection and illusions. Science neat takes place at the El Rio bar. Three one five eight mission street in San Francisco and mission for those 21 and over is $4 this month's [00:25:00] science need is on Tuesday, July 16th with doors at six and then talks at six 30

Speaker 3: every Sunday. This month the UC Berkeley Botanical Gardens will be hosting special be explained explainer lectures about the importance of wild bees in the care and maintenance of all gardens and especially in the native California Habitat. The botanical garden also features and amazing collection of plants from nearly every continent. Although there is a focus on plants that thrive in our Mediterranean climate. [00:25:30] The Asian, Californian and South American collections are currently blooming. The garden will be open from 9:00 AM to 5:00 PM most days. Although bee explainer tours are only offered from 11 to one 30 on Sundays, admission is $10 for adults and $8 for students.

Speaker 6: On Saturday, July 20th at 11:00 AM Dr Steve Croft. We'll give the free public science at cal lecture on snacking gorgeous and cannibalizing the [00:26:00] feeding habits of black holes. Learn about the latest telescopes and how they are giving more information about how black holes grow and merge. Steve Leads the science at cal lecture series and as an assistant project astronomer working on large radio surveys and transient and variable astronomical sources. He helps commission the Allen Telescope Array for science operations and develop data analysis pipelines. He is an expert in the use of data at [00:26:30] a wide range of wavelengths from many different telescopes. The talk [e-mail] for more information and now

Speaker 3: spectrum brings you some of our favorite stories in science and technology news. Rick Kaneski joins me again for the news science news summarized an article published on July 3rd in the proceedings of the royal society a about how surface [00:27:00] tension can lead to upstream contamination. Sebastian BN. Connie observed this when watching the preparation of Argentinian Montay t when hot water was poured from a pot into a container of leaves below some of the tea leaves float upward against the force of gravity and upstream of the water flow being Kinney and his colleagues from the University of Havana and from Rutgers showed through both experiments and simulations. [00:27:30] The particles can flow upstream several meters and up central meter high waterfalls because the downstream flow of clean water creates a gradient. What the container of t or other particles lowering the surface tension of the water, the particles are thus pulled into the clean water which has a greater surface tension.

Speaker 3: The team also demonstrated that these results could have practical applications such as through the discharge of a standard pipette in other lab work [00:28:00] or in the simulated release of waste into larger scale channels. Indiana University scientist have transformed mouse embryonic stem cells into key structures of the inner ear. The discovery provides new insight into the sensory Oregon's developmental process and sets the stage for laboratory models of disease, drug discovery, and potential treatments for hearing loss and balance disorders. A research team led by ear. He has Chino Phd and Russi Holton. A professor [00:28:30] at the school of Medicine reported that by using a three dimensional cell culture method, they were able to Koch stem cells to develop into inner ear sensory epithelia containing hair cells, supporting cells and neurons that collectively detect sound had movement and gravity. The researchers reported online Wednesday in the journal Nature, Karl Kohler, the papers first author and a graduate student at the medical school said the three dimensional culture allows the cells to self [00:29:00] organize into complex tissues using mechanical cues that are found during embryonic development. Additional research is needed to determine how exactly inner ear cells involved in auditory sensing might develop as well as how these processes can be applied to develop human inner ear cells.

Speaker 7: [inaudible] music heard during the shows witness produced by Alex. Thanks to Rick krones for contributing [00:29:30] to our news and calendar section and to Rene Rao for editing systems. Thank you for listening to spectrum. If you have comments about [inaudible] about

Speaker 3: the show, please send them to us via email

Speaker 1: or email address is spectrum. Doug k a l [e-mail] join us in two weeks at the same time.

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