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New tool in the genetic toolbox – Extended Play Audio

New tool in the genetic toolbox

Jill Wildonger, Assistant Professor
Department of Biochemistry
UW-Madison College of Agricultural and Life Sciences
wildonger@wisc.edu
(608) 890-4619

Kate O’Connor-Giles, Assistant Professor
Department of Genetics
UW-Madison College of Agricultural and Life Sciences
oconnorgiles@wisc.edu
(608) 265-4813, (608) 265-5428

23:00 – Total Time

0:17 – New tool, big name
0:21 – What CRISPR means
0:31 – Discovered in a yogurt factory
0:49 – Used to repair genes
1:28 – May repair genetic disorder
1;59 – Agriculture, biofuels, human health
2:42 – Like auto correct in a text message
3:23 – What it looks like
4:05 – Any way to see it
4:33 – How it’s applied
5:26 – What’s different from before
5:44 – The previous gene editing system
6:40 – Only available a couple years
7:40 – Useful for plants and animals
9:43 – What may we imagine
11:00 – People’s fears
11:32 – For more information
12:34 – Jill, your motivation for this research
13:15 – An ah ha moment
14:00 – Kate, why this line of work
15:23 – Research funding
15:66 – Difference between the labs
17:02 – Collaborations
18:20 – CRISPR center
18:42 – CRISPR in a box
20:00 – World wide coordination
20:50 – CRISPR changes everything
21:58 – Look back at this moment
22:49 – Lead out

Sevie Kenyon: A new tool in the genetic toolbox, we’re visiting today with Kate O’Connor-Giles and Jill Wildonger and I’m Sevie Kenyon. Jill can you tell us, does this tool have a name?
Jill Wildonger: This tool is named CRISPR
Sevie Kenyon: And what on Earth does CRISPR stand for?
Jill Wildonger: CRISPR, which stands for clustered regularly interspace short palindromic repeats, and that’s a long way of saying that the bacterial DNA that are part of the bacterial immune system to defend itself against viruses.
Sevie Kenyon: And Jill how is this new tool CRISPR discovered?
Jill Wildonger: It was actually discovered in a yogurt factory, so yogurt, rely upon bacteria and the bacteria were being invaded by viruses. The scientists at the factory found that the bacteria were using the CRISPR system to defend themselves against these viruses.
Sevie Kenyon: And Kate, perhaps you can tell us how CRISPR found its way into your genetic tool box?
Kate O’Connor-Giles: Once it was discovered how CRISPR was working in bacteria it became clear to scientists that it could potentially be used to do something scientists have always wanted to do which is to change the genomes of any organism.
Sevie Kenyon: Kate can you provide an example of how this might be used?
Kate O’Connor-Giles: So the CRISPR system works to cut DNA, that’s how the bacteria defend against viruses, they cut their DNA and destroy them. What we use it for is to cut the DNA and then repair it. So one can change a mistake to a correct gene.
Sevie Kenyon: And Jill, is it possible to provide an example we may recognize of how this is used?
Jill Wildonger: There are human developmental diseases and in my lab we’re using this technology to model those diseases and we’re using this to introduce the same mutations that we find in patients, into our model system. For example there is a human disease that affects brain development in children and we’re introducing the mutations that are found in human patients into our model system, the fruit fly, a very simple model system, to look at how the neurons develop within fruit flies. So we have little fruit flies that have the same mutations that are found in this devastating childhood disease.
Sevie Kenyon: Kate, look into your crystal ball, what is CRISPR going to do for us?
Kate O’Connor-Giles: The potential is huge. CRISPR has the potential to affect many areas from bioenergy, to agriculture, to personalized medicine. The long-term goal of CRISPR is that we’ll be able to sequence people’s genomes, identify mistakes that may be in their genomes, and potentially correct those if they’re causing those diseases.
Sevie Kenyon: Jill, we have a radio audience, can you paint a picture of how CRISPR works?
Jill Wildonger: Sure, think about when you’re typing out a text message and you make a mistake. You can go back and change that mistake. In the same way the cell may have a mistake in its genome and as researchers we’re using CRISPR to change that mistake, but the cells responsible for the repair. So just like when you’re sending a text message and autocorrect jumps in and tries to correct the word that you go back to, in the same way the cell can go back and maybe change the word that you’re trying to correct to a different word, so we don’t have full control over how the sequence is corrected.
Sevie Kenyon: For the audio audience, to actually tell me what it looks like when you’re working with it.
Kate O’Connor-Giles: So both of us work in fruit flies. What we do is there is an actual RNA that guides the enzyme to a specific sequence of DNA and cuts it and then we put back in different DNA and we include in with that something that makes the flies eyes florescent red. And so then we know if its happened by checking out the flies that come in the next generation to see if they have red florescent eyes and then that tells us that the change to the DNA has happened. We can’t actually see the RNA or the enzyme or the DNA.
Sevie Kenyon: Is there anyway to see it, laser microscopes?
Kate O’Connor-Giles: People are certainly crystalizing the protein to try to understand what it looks like, so they can figure out how it recognizes DNA because if they can understand that then they can potentially edit it to recognize DNA in slightly different ways for example, in more specific ways, so it doesn’t also recognize DNA that has a really close but not quite the same sequence.
Sevie Kenyon: How do you actually apply it to the fruit fly?
Kate O’Connor-Giles: So my lab studies how the genes that control how neurons communicate each other function. And these are genes that are disrupted in neurological disorders such as autism, major depressive disorder, and similar disorders, so understanding how they function is important for understanding the biological basis of these diseases and potentially identifying cures. So by knocking out these genes we can figure out what goes wrong when their gone. We also use CRISPR to knock into these genes, so we add to them a little tag that makes the proteins that they make florescent. And then we can follow where those proteins go in the cell and really see exactly what they do.
Sevie Kenyon: What is different about CRIPSR than what you have had in the past?
Jill Wildonger: CRISPR is much easier to work with it’s a two component system. The first component can be ordered by any scientist from a company, so it’s readily available, it’s very programmable. This is in contrast to previous systems, which were very labor intensive to generate and make.
Sevie Kenyon: Perhaps describe the previous system?
Kate O’Connor-Giles: CRISPR allows us to do something that we’ve actually been able to do in model organisms in particular for some time; it’s just been very labor intensive. In fact a former UW researcher Oliver Smithies won the Nobel Prize in 1970 for developing a technique to do exactly the kind of genome editing that CRIPSR allows us to do in mice, in order to create models for studying gene function. But what’s changed is that was an extremely labor intensive process that occurred very rarely and scientists had to select those rare cells where the genome editing had occurred. Now this is easy to do, it takes very little money, very little effort, and it’s highly efficient.
Sevie Kenyon: How long is the CRIPSR system been in use here, at the University?
Kate O’Connor-Giles: The CRIPSR system has been in use at UW-Madison since 2013, early 2013. In November of 2012 was the first demonstration that CRISPR could work to cut DNA in a tube, in a targeted manner. In January of 2013, the first demonstration that it could work in cells was published and then many groups started trying to use it in organisms. We were able to use it in fruit flies to alter their genomes by May of 2013. So that gives you an idea of how readily adaptable it is to different species.
Sevie Kenyon: Is CRISPR useful for both plants and animals?
Kate O’Connor-Giles: Yes, it has been used in many, many animals and plants, including crop plants, plants that aren’t generally considered to be model plants that are easy to study genetically can now be modified genetically and the same is true of animals. So animal’s genetic model organisms are limited to a small number of species whose genomes are easily manipulated by scientists but CRISPR is really opening the door to doing similar types of manipulations in other animals.
Jill Wildonger: And so I just wanted to add too that in early 2000 the genomes of different organisms were being sequenced and now we have a technology to utilize that information in a whole new way so, we’re taking the basis, we’re taking the sequences of all these different genomes, and now we’re able to use CRISPR to capitalize upon that information that we have.
Sevie Kenyon: So this is also symbiotic almost with other technology, the genome sequencing and other…
Jill Wildonger: Yes, very much so.
Kate O’Connor-Giles: Beyond the genome as well. For example we talked about inserting florescent tags into protein so we could follow them. Microscopy is advancing at a tremendous pace as well, so the combination of being able to insert tags into a cells genes combined with advances in imaging are allowing us to see things that we didn’t even imagine we could ever follow and to follow them live in a cell.
Sevie Kenyon: and the advantage to that is?
Kate O’Connor-Giles: The advantage of being able to do that is that this will really allow us to gain a dynamic picture of what the proteins in the cells are actually doing under different circumstances. For example at different stages during development, in a disease state, in a normal state.
Jill Wildonger: Protein function often times depends upon where the protein is within a cell, and by being able to follow its localization we can use that as a readout of its activity.
Sevie Kenyon: What might we imagine here, of how to resists disease, the end of genetic maladies in humans, with extremely drought tolerant corn plants, what kinds of things might we imagine if you let your imagination go?
Kate O’Connor-Giles: I think we can imagine this technology being used in a lot of tremendously useful ways. It could be used to engineer microbes to make synthetic products that we use, for example medicines that are useful to human beings. It could be used to correct mistakes in DNA that cause birth defects. It could be used to potentially cure disease. That said, there are a lot of details that still are absolutely critical that have to be worked out. We need to make sure that it is specific. We need to make sure that we are in complete control of what its doing, that we understand all of the consequences of the editing process and we also need to as a society decide what things we will and wont do with the technology as it evolves.
Jill Wildonger: And it should be clear that scientists are thinking about these issues and there have already been several meetings that have occurred where leaders in the field have come together to discuss the ramifications of this new technology.
Sevie Kenyon: is something new, and there’s almost always some fear and apprehension about new, do you care to address those fears?
Kate O’Connor-Giles: I think that the scientist community is well aware of both the, of the potential power of this technology, and with that kind of power comes a lot of decision making and so in our experience the scientific community is taking extremely seriously and trying to get ahead of the technology to make sure that those ethical decisions are addressed well before they need to be.
Sevie Kenyon: Is there a place people should go for more information about the technology?
Kate O’Connor-Giles: There are a number of websites about the technology, the University of Wisconsin has a genome engineering website called GEE Wisc, Genome Engineering and Editing at Wisconsin that you can go to, to see information about how scientists on campus are using the technology in their own research.
Sevie Kenyon: What would you Google search for if you wanted to find that?
Kate O’Connor-Giles: I think Genome Engineering Wisconsin should get you there. This has also been an incredibly popular topic in the lay press so there are lots of interesting articles. Wired has a really interesting article that has a flow chart that allows you to be an evil scientist and decide what you might engineer. For example, I think it was better tasting pizza was one of your options.
Sevie Kenyon: I’m curious too maybe grab the sail and turn it a little bit here, the microphone is right between you so I’m not sure I guess I’m looking at you, and I’ll get back to Kate in a second. Jill what motivates you to do this kind of research?
Jill Wildonger: What motivates me to do this research is there is a genetic basis for virtually everything that happens in a cell and by being able to modify the genome it gives us control over being the components of a cell and as a scientist I’m very interested in how a neuron functions and by being able to modify the genome I’m able to tinker with how proteins, organelles, or other components of a cell are functioning to understand how they normally function.
Sevie Kenyon: Did you just tell us you’re kind of a control freak?

Jill Wildonger: Ha Ha.
Sevie Kenyon: Was there an ah-ha moment in your life that set you down this career path, research path?
Jill Wildonger: I’ve always been very interested in how things work and I think that how the brain works is one of the biggest, largest, most outstanding questions there is in science.
Sevie Kenyon: That inspired you to follow this further?
Jill Wildonger: It did yes, and I have a parent whose a scientist as well, and so it was not just my own interest in science but seeing a parent who had a career in science made me realize that I could do this for a living and I am so excited, thrilled, happy, I just feel like the luckiest person in the world that I can do this as a career.
Sevie Kenyon: Wow, awesome. Same question for you, what caused you to take this line of work?
Kate O’Connor-Giles: I was driven into neuroscience actually by an undergraduate neuroscience class and I found neurobiology to be just a fascinating question. The question that’s always driven me is, how do you build a brain? How do you build a brain that can both carry out all of the functions it needs to carry out reliably but change itself throughout a life and in order to learn new things and adopt new behaviors, so that’s what my lab studies.
Sevie Kenyon: And was there an ah-ha moment where you woke up one day and needed to understand the brain, what inspired that to begin with?
Kate O’Connor-Giles: I always wanted to understand the brain. I got lucky and actually as a graduate student I was really wide open on how I thought I would go about that and I ended up rotating in a genetics lab and learned very rapidly the power of a genetic approach, where the way that we do this is essentially we break the genes that we think are important for building a brain and we see what happens when they’re gone. And so CRISPR allows us to do that much more efficiently and it really tells us exactly what all of the building blocks of a brain are doing and how they’re doing it.
Sevie Kenyon: How is this research with CRIPSR backed?
Kate O’Connor-Giles: Our research is backed by the NIH, the National Institute for Neurological Disease and Disorders as well as by the McKnight Foundation for Neuroscience and so we’re funded to do both basic research on the genes that control synapses, the connections between neurons, as well as research to develop genome engineering, CRISPR techniques, to make studying the brain easier.
Sevie Kenyon: What’s the difference between your two labs?
Jill Wildonger: I’m studying how different components of the cell are transported to different parts of the neuron and I would say I’m more on the architecture, building side of things and Kate a little bit more on the function side of things, but also thinking about how form and function combine.
Sevie Kenyon: Did you want to add to that Kate?
Kate O’Connor-Giles: So neurons have both a signal sending side and a signal receiving side and Jill studies how those different functions of the neuron develop by developing the different architecture of the neurons, so you need different things to end up at the signal receiving side than you need at the signal sending side. What we study then is how those signals are sent and received once the architecture of the neuron is established and it starts to form connections with other neurons to form circuits that then control different behaviors or store memories.
Sevie Kenyon: Become the brain.
Kate O’Connor-Giles: Become the brain!
Sevie Kenyon: There’s two of you here today and I know there’s a collaboration, do you care to talk about collaborations with other researchers here on campus or around the world?
Jill Wildonger: So I think it’s important to mention that the work that Kate and I have done also includes a third lab at UW, Melissa Harrison, and Melissa’s in the Bimolecular Chemistry Department and so it was the three of us working together that enabled this technology to develop within drosophila.
Kate O’Connor-Giles: And the fact that all three of us were interested in this despite the fact that we do different types of research really illustrates the general utility of this technology so the three of us came together knowing that if we could make this type, if we could make CRISPR work in drosophila, that it would advance all of our research tremendously so we came together to develop that technology.
Jill Wildonger: And shortly after we published our paper, we I think were each beseeched by requests from other researchers on campus using a variety of different organisms so it wasn’t just people working with flies and I think that we’ve had requests from people working with plants and cows and pigs and bacteria, and there’s now a new center on campus at the Biotech Center a translational genomics facility that is dedicated to helping researchers at UW use the CRISPR system.
Sevie Kenyon: Go ahead and describe that center for us that would be interesting to me.
Kate O’Connor-Giles: So the Center will help scientists figure out what they can do with CRISPR, figure out how to design an experiment from all of the molecules that are needed to do the editing and they will also help you with actually generating your edited organism.
Sevie Kenyon: Does CRISPR arrive in a box?
Kate O’Connor-Giles: No, so…
Sevie Kenyon: Is this like Amazon brings it?
Kate O’Connor-Giles: What a scientist needs to do to do CRISPR is to; you need to know the DNA sequence of the part of the genome that you want to edit. And from there you need to design the molecule, which happens to be the RNA that will guide the cutting enzyme to that sequence. So that requires a little bit of knowledge of the system, there are software programs out there some of which have been developed at UW, including from my lab, that help you figure out exactly how to make those components, but then once you get the molecules together which in this case its only two molecules, so its pretty easy, then you can carry out the experiment.
Jill Wildonger: So the facility’s goal is to make CRISPR a in the box system that you say, I want to edit this gene and then the facility can say this is how you do it. So its as close to in the box or on demand as possible.
Sevie Kenyon: How is all of this use of these tools either CRIPSR or anything before, how is this all coordinated among people around the world?
Kate O’Connor-Giles: So much of its coordinated the way science traditionally is through publication in journals that of course has been occurring on a much more rapid pace than normal. This technology has taken off very, very, very fast. But in many communities, in many research communities, including the drosophila research communities researchers have been sharing advances through websites and discussion groups and sharing resources because of how quickly this is developing and a desire to not duplicate each others efforts and to get the new information and new technologies out there as quickly as possible, so we can all apply them to our research.
Sevie Kenyon: You may have alluded to something here, how does this use of this new technology, how transformative is it to the research community?
Kate O’Connor-Giles: CRISPR changes everything. It makes what before was possible, now feasible to do and feasible to do on large scale. So, one can make pretty much any edit to the genome that they would like to make in many model organisms including fruit flies that we work in. So in that way it has really changed the way we think about our research and the way that we conduct our research.
Jill Wildonger: Yeah, I would say that it brings a lot of experiments within reach of many different researchers and that they’re advances in science that I might tell my family and friends about and this is one of those advances in science that I would tell all my family and friends about to follow. So pay attention to CRISPR it’s going to change everything.
Sevie Kenyon: I guess I’ve asked both of you the crystal ball question, but what happens at the look back, go ahead with your crystal ball you know 50 years and look back at this moment, what difference will there be, you know describe how this may look down the road? The past, you know, you’re living in the moment right now.
Kate O’Connor-Giles: It’s interesting, I think that it will be one of those changes, like sequencing the genome, that so rapidly and so thoroughly changes everything that it’s difficult to imagine the world before one could do it. Certainly as a basic scientist I think that’s already becoming true. I was a graduate student when the human genome was being sequenced, so I actually was a scientist before it was done but I can barely remember how we managed to do science without it and I think the same will be true of CRISPR.
Jill Wildonger: So if we go back to the word processing analogy, its like before computers, its before you could easily make corrections to what you were typing, it’s the manual type writer vs. the computer.
Sevie Kenyon: We’ve been visiting today with Kate O’Connor-Giles and Jill Wildonger University of Wisconsin Madison in the College of Agricultural and Life Sciences, and I’m Sevie Kenyon.