Webinar: DNA Barcoding
Aired May 28, 2020
Maggy Benson:
Hey everybody. Welcome, welcome, welcome. Thanks for joining us here on Smithsonian Science How. I'm Maggy Benson, and I'm a museum educator at the Smithsonian's National Museum of Natural History. I'm coming to you virtually from my home in Washington, D.C., along with several other of our scientists from the Smithsonian. Before we begin, I want to give a special thanks to our generous donors, our volunteers, and other important partners who enable our team at the Natural History Museum to discover, create, and share new knowledge with the world, like we're doing today, and do every day free of charge. While we wait for some more friends to join us. Take a moment to find the Q and A button on your screen. It should be located either at the bottom or the top. Use that Q and A button to tell us where you're joining in from. I'm going to read some of those responses in a minute here.
All right, now you're going to use that same Q and A button to send all of your questions and comments throughout today's program. Today's webinar is going to be about 45 minutes long, and I'm going to share my screen here. It's going to be about 45 minutes long, and during that time, we are going to meet Dr. Sarah Luttrell, and then we're going to take some of your questions. Then she's going to teach us all about DNA barcoding. Once she's done that, we'll have a big chunk of time at the end of our program to take even more of your questions. Now during today's program, we have questions planned for you as well, and you're going to use that same Q and A box to send those responses. You'll notice when you use the Q and A that you won't be able to see your friends' comments.
That's okay. Our team here at the Smithsonian can see everything. I also want to point out a new feature in our webinars. We have live captions. So next to your Q and A button, you should see an icon with two C's cc. That's our closed caption box, and you can click on that to either hide or display the captions. You can also go into the caption settings to make those live captions larger or smaller, whatever you prefer. Now, these are live, and so there will be a slight delay to them. Don't worry about that. It's normal. All right, so I'm going to take a moment to welcome some of our friends, and it looks like you're joining from all over the country. We have Connecticut, Arizona, Texas, New Mexico, New York, Virginia, England, South Carolina, more Virginia, lots of Virginia, Texas, Kentucky, Minnesota, more New York, Massachusetts, Maryland, lots of Maryland, New York City, Georgia, Canada, Michigan. All right, More Maryland, Indianapolis. All right.
Sarah Luttrell:
Oh, I see Denver. Hey, Denver. I have family out there.
Maggy Benson:
All right. New Jersey, Colorado, Grand Junction, California, Seattle. All right. A lot more in Georgia, Maryland and Virginia.
Sarah Luttrell:
Oh, all right, Ohio, California. Wow.
Maggy Benson:
Utah. Welcome. We are so happy to be able to bring people together from all over the country and even the world through our video programs, and we're really excited that you are here joining us today. Now that you know how to use the Q and A, remember that's the same space that you're going to use throughout the whole program to answer the questions we ask you and to send us questions. You see all of these lovely scientists on your screen here. These are some of the scientists that you're going to meet today, and several of them are going to be in that Q and A box, answering your questions directly by text. So let's take a minute and introduce them now. All right. Hey guys.
Carla:
Hi.
Maggy Benson:
All right, let's quickly hear from each of you and what kinds of questions you're going to be answering in our Q and A today. Faridah let's start with you up. We can't hear you. You're muted. That's okay.
Faridah:
Hi, I'm Faridah, I work with Carla, Sarah, and everybody from the lab, and I'll be answering questions on the molecular, the DNA part.
Maggy Benson:
Awesome. Thanks for joining us.
Lee:
Hi, I'm Lee. I work in the DNA lab also, and I'll be answering questions on DNA. Joining you from Edgewater, Maryland.
Amy:
Hi, I'm Amy. I also work in the DNA lab and do a lot of DNA barcoding projects. I'll be answering questions about DNA and DNA barcoding today.
Carla:
Hi, I'm Carla from Virginia. I work in the Feather lab and I will be answering questions about birdstrikes and feathers today.
Jim:
Hi, I'm Jim. I work in the Feather Lab as well, and I'll be in answering any general bird questions or birdstrike feather identification questions from you today.
Sahas:
I'm Sahas from DC and I'll be answering questions about birds and their feathers.
Maggy Benson:
Wonderful. Thank you all so much for joining us. So all of our experts, they're going to be in that Q and A. When you're submitting questions, there's going to be two tabs on top. One will say All Questions, and the other will say My Questions. Make sure to check that My Questions tab to see if one of our experts has responded to you directly, and you can see the responses to all the questions that they get to in that space. We will of course be taking some of those questions in the Q and A to our featured expert, expert, Dr. Sarah Luttrell answer today. Without much more ado, let's move along and meet Sarah now. So hey Sarah, how are you?
Sarah Luttrell:
Hey Maggy. Hey everybody. I am doing so well. Thank you guys all for coming. I am super excited to talk to you today about DNA barcoding. Just to get started, to tell you a little bit about myself, I have loved science and outdoors for as long as I can remember, and birds, my mom tells me that I identified my first bird at the age of two and it was blue jay, but I didn't really know that you could make a career out of studying birds until I went to college. That's when I learned how to really write and read and work critically as a scientist. I got to meet a lot of amazing people and go on some pretty cool adventures, like the Galapagos Islands. You can see that picture down below where I'm actually inside a Galapagos turtle shell. They're so big. Then eventually I earned my Ph.D. studying how animals evolve in extreme environments by looking at birds' song and color and DNA in salt marshes, which is a really hard place for birds to live. Can I go on here? There we go.
Maggy Benson:
Sounds like you had an interest in natural history from a very early age.
Sarah Luttrell:
For sure. I definitely spent a lot of time like collecting bugs and rocks and all kinds of things, so you never know where that's going to take you. So now I work at the Smithsonian Feather Identification Lab with an awesome team of people, some of whom you already met just now. We identify birds that get hit by airplanes. Ever since people have been flying, since the Wright brothers first started flying, birds and airplanes have unfortunately been colliding, and that is bad news for the birds and it's bad news for the people. What we do at the Feather Identification Lab is use some different techniques to try and figure out what kind of birds are getting hit by planes so that people that operate the planes and the airfields can help keep the birds and the planes apart.
Maggy Benson:
Very important work for our safety and the safety of the birds.
Sarah Luttrell:
That's right. We have three different techniques that we use to try and identify birds. The first is whole feathers. If we get nice big feathers in a sample, we can take them out to this amazing reference collection that we have in the National Museum of Natural History and match those feathers up and make an identification for that species. Sometimes we get much smaller fragments of feathers, and in that case we can use the microscopic characters of feathers that you can see on the bottom of this screen in order to make an identification, not to species, but to the larger group of birds like ducks or seabirds or songbirds. If you're really interested about this, because it's a super cool technique, you can go to the Science How website and see the talk that Dr. Carla Dove did on using microscopy to identify birds a couple weeks ago. It's really fun. Sometimes though, we don't even get little tiny scraps of feathers, we just get bird ick off the plane. Which we very technically call snarge. That is a combination of the word snot and garbage. Even though snot and garbage, snarge, is a little bit icky, there is so much information that we can get out of that snarge and we can use DNA, specifically DNA barcoding to figure out what species of bird that snarge came from.
Maggy Benson:
Very cool.
Sarah Luttrell:
That's what we're going to be talking about today.
Maggy Benson:
All right. So Sarah, before we move on, we do have a couple quick questions, but I have a question myself. You work in a lab that identifies species based on their DNA. Has there ever been an instance where you've gotten a really weird result?
Sarah Luttrell:
For sure, Maggy. Every now and then we get really bizarre things. The case that jumps to mind specifically that happened recently was one that we got from a remote island in the North Pacific Ocean from a Marine Corps airplane. When we got it back from DNA, it said we had hit a buccaneer anchovy.
Now we're pretty sure that plane did not hit an anchovy. We tried it again. Sometimes we get funny results the first time. We tried it again, we still got anchovy. Okay, what's going on here? Did the person that took the sample off of that plane have pizza for lunch? What is going on? So we dipped into our toolkit and we looked microscopically at the feathers from that sample and we found some teeny teeny little fragments. Those fragments led us to a group of birds called seabirds. All right, we're getting closer, but at the Feather lab we really like to get a species-level identification. We wrote back to the people that sent us a sample and said, "Please, do you have any more evidence you can send to us?" And they did. They sent us another sample and it turned out that sample had feathers big enough that we were able to identify the species involved in that strike as a sooty tern, which is a seabird that lives in the Pacific and probably ate anchovies as its last meal.
Maggy Benson:
Oh, wow. So Sophie actually asked, "Did the bird have the fish in its mouth?" Close to that, right?
Sarah Luttrell:
It's possible. We don't actually know. The bird could have been carrying the fish or maybe the bird had already eaten the fish. We weren't there. We just know the bird and the fish were both on that plane.
Maggy Benson:
So interesting. Let's pause for a moment and get to some of our student questions and then we're going to move on to see what technique allowed you to identify both that bird and that fish. This question's from Jade. "You have been studying DNA for your whole career? What is one thing about DNA you wish everyone should know?"
Sarah Luttrell:
Oh, Jade, that's an interesting question. Well, I think that the one thing that I would like everyone to know about DNA is something we're going to talk about today, and that is quickly just the fact that the way the DNA is built and the way that it replicates means that we can take advantage of that to try and build copies and actually read that DNA. We're going to go over that today.
Maggy Benson:
All right. "Can you get bird identification from bird poop?" That one's from Claire.
Sarah Luttrell:
Oh Claire, that is another good question. In fact, you can get bird identification from bird poop, although it's a lot harder because there's not as much DNA in bird poop as there is in say, a feather. But, that is one of the ways that other scientists use DNA barcoding, especially if they want to study an animal that's either really uncommon or really endangered. So instead of actually bothering that animal, you can grab that animal's poop and get a lot of information about their DNA from the poop.
Maggy Benson:
All right, we're going to ask just a couple more and then move on. Montana asks, "Are bird strikes really a big problem and how can we coexist with birds?"
Sarah Luttrell:
Awesome. So I hesitate to use the word problem, but yes, bird strikes are a really persistent occurrence. At the Feather Identification Lab, we get about 10,000 bird strike cases every year. If you think of the number of airplanes that are just taking off at your airfield alone and the number of birds that are around, you can imagine that they get in each other's way pretty often. Now, most of those strikes aren't problematic at all. A lot of that is because we're able to identify the species of birds involved in those strikes, and we can work together as a big team of people. Biologists on the airfield that can do things like change the habitat to make the birds not want to be there anymore. Engineers designing the planes that can make it so that if a bird does hit a plane, it doesn't do major damage to the plane. And even especially in the case of military, thinking about what times of day particular birds might be active and just not flying when those birds are moving.
Maggy Benson:
Right. And so Isabelle asked, "Do all birds get hit by things or only some types of birds?" It sounds like a lot of different types of birds, but depending on the habitat and the location of the airport, those species of birds change.
Sarah Luttrell:
That is absolutely true. Yeah.
Maggy Benson:
Let's move on to the topic of our program today, which is how you use DNA barcoding to identify those birds involved in the strike. We did have a question from Agatha who asked, "How can you tell whose DNA is whose?" Perhaps that's illuminated by DNA barcoding. DNA barcoding helps us solve that puzzle.
Sarah Luttrell:
A little bit. Yeah, so DNA barcoding is basically an idea that scientists have been kicking around for a really long time, and about 20 years ago, they started to figure out a good way to do it. The idea is just like you can go to the store and you can scan a barcode, and that barcode can tell you lots of information about an item, that there might be some feature about a living thing. In this case we're going to talk about animals that you could scan and it could tell you say, what kind of species that is. Scientists focused on DNA as their barcoding key, their unique identifier, because if you have the animal in your hand, you can look at them and see whether they're different. Sometimes you don't have the whole animal, but also sometimes your animals look and behave really similar and maybe there'd be some clue in their DNA that could help us flag groups of species that look really the same, but may not actually be the same.
Maggy Benson:
Interesting. So you're using its DNA to be able to compare animals?
Sarah Luttrell:
That's right. That's what we're going to talk about today.
Maggy Benson:
All right. Where do we start?
Sarah Luttrell:
Well, let's start by backing up a little bit and talking about what DNA actually is. You guys have maybe seen this picture before or something like it, right? DNA is a string of chemical molecules that are the blueprints for how a cell builds and operates. Basically the instructions for how to make you. We get all these pretty pictures of DNA that show us a lot of the key features, like the fact that there are two strands that wind around each other and these rungs on the ladder that connect the two strands. Those rungs are the really important parts that we're going to talk about today. Those are called bases, and there are four of them: adenine, thymine, cytosine, and guanine. Those bases are kind of like computer code, the way a computer reads ones and zeroes and gives you instructions for how it's going to work.
The DNA is made up of these four letters, these four bases, and those are the instructions for how the DNA works. One thing you can't see from this really nice picture is the coolest thing about this DNA. This is kind of the question we got asked earlier. What do you want everybody to know? Well, the coolest thing about DNA is the fact that each of these bases, they're like chemical puzzle pieces and they only fit together one way. The adenine only fits with the thymine. If you try to add a guanine to it, they just don't stick. What that means is if you take those two pieces of the ladder apart, you can rebuild the second piece of the ladder because only one piece will fit. That's how DNA replicates and makes new copies of itself. It's actually also how we're going to harness in order to make new copies of our barcode and figure out what a species is.
Maggy Benson:
There are four bases, and those four bases are arranged in a way where the A only fits with the T and the C only fits with the G. Those repeat over and over again in our DNA to be able to write kind of instructions for how animals, the traits that we have, and even all of our functions to keep us alive.
Sarah Luttrell:
Yeah, that's exactly it. It's so cool, isn't it?
Maggy Benson:
It's so cool. Yes. All right. So here we just learned a little bit about DNA. All right, now, where do we go to next?
Sarah Luttrell:
Now, because we work on animals in the Feather Identification Lab, we're going to specifically talk about animal cells. First, we need to understand where the DNA is. In an animal cell, DNA is found in two places. It's found in the nucleus, which is this blue region. And in the mitochondria, which are the yellow things here. Each of these regions has their own DNA, and they have slightly different jobs, but they work together in order for your cell to function. Now, the nucleus has two copies of all of your DNA, and each mitochondria has a couple different copies of its DNA. The other interesting thing you should know here is that in this picture, I've only shown three mitochondria just to make it easier to see. It turns out that each animal cell has hundreds or even thousands of mitochondria packed in there. A lot of DNA.
Maggy Benson:
That's a lot of DNA.
Sarah Luttrell:
We need to pick a section of DNA to be our unique identifier in order to barcode animals. Maybe right off the bat, if we know we only have a couple copies of nuclear DNA, but we have a lot of copies of mitochondrial DNA, which one might we start to target to pick our barcode?
Maggy Benson:
Let's ask our students that. Students take a look at this image and consider what Sarah just told us about how many copies of DNA are in these cells. We know that there's mitochondrial DNA in each one of the mitochondria, the powerhouse of the cell, and those are illustrated in this orangeish-yellow color. And there can be hundreds or thousands of those in each cell. Whereas in that nuclear DNA, there may just be one copy, right, Sarah?
Sarah Luttrell:
Well, technically it's two because you have one copy of each gene, one you get from each parent, but it's one copy of your whole genome.
Maggy Benson:
If you were to pick which one that you want to study to be able to start this DNA barcoding process, which would you pick? One from the mitochondrial DNA or the nuclear DNA? Okay. Use the Q and A to tell us, and we already have people using that. Some people have said the blue one, the nuclear DNA, others have said mitochondrial DNA. All right.
Sarah Luttrell:
There's definitely interesting things we can learn from nuclear DNA.
Maggy Benson:
One from the nuclear, but we have kind of a mix from nuclear and mitochondrial. I think at this point, from what I'm seeing, it looks like it is half and half.
Sarah Luttrell:
Neck and neck. You guys just can't decide.
Maggy Benson:
Neck and neck, we get blue, nuclear, mitochondrial. Mitochondrial might be a better target. What do you think?
Sarah Luttrell:
Well, there are definitely lots more copies of mitochondrial DNA in each cell. That's an advantage for us because DNA is really, really little, so we're going to have to make a lot of copies in order to read it. That's one advantage. And it turns out there's actually a couple advantages to using mitochondrial DNA that scientists have zeroed in on.
Maggy Benson:
We're looking at the mitochondrial DNA because there's already so much more of it per cell.
Sarah Luttrell:
Exactly.
Maggy Benson:
All right. So well done, everybody. Way to go in looking at that picture and making a prediction. All right, so where do we go to next?
Sarah Luttrell:
All right. Well now we know where the DNA is in the cells. We have to get it out. And at the Smithsonian, I do that in the Smithsonian Laboratories of Analytical Biology, which is pictured here. And the Laboratory of Analytical Biology is an amazing resource with lots of equipment and lots of scientists that share all of that space. It is fancy and it looks fancy, but it might be a little intimidating for you and it shouldn't be because really a lab is a lot a really fancy kitchen. Just like when you make cookies, you're really doing chemistry. In the lab, when we're sequencing DNA, we are actually doing chemistry. And the really great thing about being in the lab is that we have all these other scientists around that are working on similar kinds of questions. And so we have all these other people to ask for recipe suggestions or help us solve problems if we run into a problem and this kind of thing, we are going to extract DNA in the laboratory, but actually there's some pretty simple processes to it. You can find some links online to extract DNA in your very own kitchen. We're going to share one with you at the end of this presentation.
Maggy Benson:
Very cool. Some people might think that scientists work alone by themselves, but it's very much a team sport, having all of those people there to ask questions of support you in different ways.
Sarah Luttrell:
Yeah, absolutely. You saw that we in the Feather Lab are a team of five that work hard to solve these cases together, but there's also this big extra team of scientists working on other projects that we collaborate with all the time.
Maggy Benson:
You said this is like one giant kitchen. What kind of DNA processes are you doing in this big lab?
Sarah Luttrell:
Good question. Well, we'll kind of go through it step by step for what we do in the Feather Lab. First thing we have to do is get that DNA out of the cells. And we have some pretty fancy kitchen equipment that helps us do that for a couple of reasons. The biggest one is we get thousands of samples every year, so we have to be able to process and extract DNA from a lot of different cells at once. In order to get the DNA out of the cells we use some special chemicals, but they're pretty analogous to stuff that you have around your house. We use detergent and salt to help break down the cell and release that DNA to a place that we can get to. We have a nice robot that helps us do all of those chemical reactions to release the DNA from the cells and wash away all the bits of the cell that we don't care about and end up with a purified DNA product at the end.
Then once we have all that DNA, we have to move on to the next step, the next baking chemical reaction. You remember that when we extracted DNA, we extracted all the DNA. In a chicken that's about a billion base pairs. A billion of those A's and T's and C's and G's. That's so many. There are definitely ways that scientists can sequence and read every single one of those base pairs. But remember, we just want to barcode. We just want a unique identifier, a little tiny piece. We have to figure out how to focus on that little tiny piece. That's our next baking step. We have two secret ingredients for that. The first is called a primer, and a primer is a manmade piece of DNA that's going to fit like a puzzle onto the section of DNA that we care about. Then the second piece, a second secret ingredient is an enzyme called taq that is going to help us do that special thing the DNA does and build additional copies based on that first template piece of DNA.
Maggy Benson:
Okay, so just to recap here, you have all of the DNA that you're getting has up to a billion base pairs, all of those A, C, Gs and Ts, and you only need one small section of those to be able to compare all animal life to be able to identify different species. And so these special ingredients, this primer, it's actually helping you target that one special area in all of the DNA that you sequence so that you can compare those animals.
Sarah Luttrell:
That's exactly right. It's helping us target just one little piece of mitochondrial DNA out of all that DNA. And that piece turns out to be 648 base pairs long. It's like 0.0000001 percent of all the DNA in that cell. And that should be able to tell us what species we have.
Maggy Benson:
So interesting. Comparing that buccaneer anchovy to that tern that was living out at sea, there's enough differences between that combination of 648 base pairs to differentiate them using that section between a fish and a bird.
Sarah Luttrell:
Yeah.
Maggy Benson:
Cool.
Sarah Luttrell:
But in order to do that, first we have to make more copies, even though we started with hundreds or thousands of copies of that piece of DNA from the mitochondria, DNA's really little and we need to be able to read it. We have to make some more copies. And we do that in a step called polymerase chain reaction or PCR. And the chain reaction part is going to be the important part of this. This is kind of taking advantage of the way cells duplicate DNA naturally and the way those bases fit together, like puzzle pieces. The first thing we're going to do is we're going to heat the DNA up and we're going to melt the two strands apart. So now we have access to those puzzle piece bases. Next, our primer, our first secret ingredient is going to come in and latch up with those puzzle pieces at just the right spot.
And then our taq, our second secret ingredient is going to help us build the opposite side of that DNA strand. We started with one copy and now we have two. Then we heat the DNA up again and melt it apart again and cool our reaction down and our primer and our taq make more copies and now we have four. And then we heat it up again and melt it apart and cool it down. And our primer and our taq make eight, this chain reaction doubles every time we heat it up and cool it down. If we do this 30 times, we have over a billion copies of that little piece of DNA that we wanted.
Maggy Benson:
Wow. Why on Earth would you need 1 billion copies?
Sarah Luttrell:
Right? A billion is so many.
Maggy Benson:
I thought identifying that special section was so that you didn't have to read 1 billion copies.
Sarah Luttrell:
That's a good point. But it turns out that we need the extra copies in order to do the reading. Thank goodness we're not making a billion copies of a billion base pairs, because that'd be a lot more reading.
Maggy Benson:
Too much.
Sarah Luttrell:
Too much. We have one more chemical reaction, one more baking step to do in order to read those billion copies. And that is something called Sanger Sequencing. What we do there is make one more copy of each of those billion that we already copied, but this time we have a new secret ingredient. That secret ingredient are that some of the bases that we're going to use to rebuild that DNA are fluorescent. That means they glow when you hit them with light, like a glow-in-the-dark star or something you might have at home. We're going to recopy all of our billions and every now and then we're going to add in one of these glowing fluorescent bases. Another cool thing about this ingredient is when we add it, that particular strand is going to stop being built. We're going to end up with all these pieces that are a bunch of copies of the same little 600 base pair fragment, but some of them are going to be like one base pair and some of them are going to be like 200.
And at the end of every one is going to be a glowing base pair. Then our sequencer can line up all of those pieces according to their size. Thank goodness, again, that a machine is doing this. We don't have to line up a billion copies and we can start to see the sequence of the genes. G, A, C, A. There we go. This is what that data looks like. Another reason we have a billion copies, aside from the fact that we're cutting it up randomly and we want to make sure we have enough copies in order to get all the sizes that we want, is that again, that fluorescent tag is super cool, but it's little. So the more copies of each length we have, the stronger the light is going to be and the better the machine can read that sequence. Now you have a billion copies.
Maggy Benson:
That billion copies is on that very small section of the DNA, that 648-base-pair section. It's amplifying, It's making all of the signals for each one of those bases stronger so that you can read it.
Sarah Luttrell:
Exactly. Kind of like if you made a zillion Xeroxes and then had to use a magnifying glass to read them. What you're seeing here is just a little section, it's just 20 of those bases. If you zoom out so you can see all 648 at once, bam. It even looks like a barcode. How fun is that?
Maggy Benson:
That is very cool. Each species of animal has a unique barcode in the same way that if we go to the store and scan something. It even looks the same.
Sarah Luttrell:
That's right. Yeah. It's pretty nice that we can even look at them and think of them in the same way.
Maggy Benson:
Those colors are cool, but how do you read that?
Sarah Luttrell:
Yeah, so each of the colors you remember corresponds to a letter. You can see here at the bottom we have the color at the top. It tells us the letter. We can just copy and paste the letter part. Now we have 648 letters and we have to figure out what species that scans to basically. Well, thankfully, scientists have agreed that this is a really good section of DNA to use for barcoding and scientists all across the world have been sequencing all kinds of animals for this one section of gene and putting all of their sequences into a program called the Barcode of Life Data System. In the Barcode of Life Data System right now, there are over 3 million copies of this little gene region, this little DNA region, that represent more than 50 percent of the animal species on earth. Hopefully when we put our sequence into the database, there is somebody out there that has already sequenced something that matches our sequence. Now, if I had to do this by hand, I could spend basically my whole career just trying to compare this sequence against 3 million others. Thankfully there are computer programs that do that for us. We plop it in and then we have our little CSI moment where the computer churns for a couple of seconds and then compares them, compares and compares, bam.
Our species that hit that plane was an American robin.
Maggy Benson:
Wow, that's so incredible. It's so cool to see how several steps that you take in the lab to be able to take the DNA out, make copies of it, and do different things to it chemically so that you can read it, can then be put into a database and tell you exactly what kind of species of animal.
Sarah Luttrell:
Yeah. It's really awesome that we can use chemistry in this way to go from snarge to species.
Maggy Benson:
That is just incredible. It's kind of like this magic box that I think people think is really complicated and really hard, but as you've taken us through the whole process and kind of use that analogy, it's kind of like baking. You can see how several of these key steps when they're put in order, it's not so scary.
Sarah Luttrell:
That's right. Thankfully lots of very smart people have figured this out and now we can all benefit from that and it's really a pretty easy idea overall. Now we have completed our DNA journey. We've done all the steps necessary to get our barcode, but at the Feather Lab we have one more thing to do. We always check our work. Remember that anchovy? Okay, it was pretty obvious something was wrong there, but it's not always obvious when we have more than two things or something funky is going on. So we always, always double check that the answer we get from DNA matches with other information we know about the case. So where was that plane when it hit that bird? What time of day was it? What time of year was it? All these other clues and maybe even other clues in the bag, if there's teeny little feathers that we couldn't identify earlier. Now do those feathers support the identification that we have? We use all of that to check our work and make sure when we send a species ID out to somebody that we are really, really certain, we know what hit that plane.
Maggy Benson:
Very cool. It sounds like a really fascinating place to work in the Feather Identification Lab and in the Laboratory of Analytical Biology where Amy and Lee who are answering questions today, work where all of the DNA processing happens. Sarah, I know that you have an activity prepared for us and maybe we can go through that now. You have helped us understand that there are a couple steps between when you get that snarge into your lab and when you are able to put that sequence into a database to identify which species it is. I think it would be a great exercise now for all of you watching to help us put the steps in order that Sarah shared with us today.
Sarah Luttrell:
Oh, right, those are the steps.
Maggy Benson:
All right, so here are the main steps. There are pretty much four main steps in DNA bar coding that you just walked us through right now. And so I want to ask everyone to use the Q and A box to tell us what step is first. Which step is first in the process of DNA barcoding? Our options are PCR, we copy just one gene. Is it searching the database, extracting the DNA, or is it labeling the bases and sequencing the gene? Okay. We do have a unanimous responses here. Everyone selected extract DNA. Well done. Yes, the first step is extracting the DNA. Now what happens after you have that DNA? What is the next step? Is it searching the database, labeling the bases, or is it PCR? Oh, some people have jumped ahead and labeled all four steps. Well done. We do have unanimous responses here where people are saying, copying and PCR. Are we on the right track?
Sarah Luttrell:
Yeah, absolutely. First you got that DNA out. Now you have to make copies of just the part you care about reading.
Maggy Benson:
Okay, so what is the next step? What do we do next? Do we label the bases and sequence the gene or do we search the database? What do we do after we've extracted the DNA and done the PCR?
Sarah Luttrell:
All right, what do you guys think?
Maggy Benson:
All right. We have label bases and sequence gene. Label, label, label. So many people are saying that we label, which makes for one last step.
Sarah Luttrell:
Yep. Good job guys. You label it next and then you have that whole sequence and last you...
Maggy Benson:
Database. Yeah.
Sarah Luttrell:
Search the database.
Maggy Benson:
Well done.
Sarah Luttrell:
All right. Good job guys. You definitely put those all in the correct order. Hopefully today we sort of took the magic out of how we get a species DNA ID.
Maggy Benson:
Yes, Well done everyone. You did such a great job following along there and putting those steps in order. I think you've all had a primer in DNA barcoding. Now you're ready to move on to some lab work. What do you think, Sarah?
Sarah Luttrell:
I could definitely take some assistants. That would be awesome. We got migration coming up. We're going to be busy.
Maggy Benson:
Well, that takes us to our student questions right now. We have a lot of time left here at the end here to take some of your questions. We have a lot of them. Speaking of things like bird migration making you busier, someone asked earlier, "How many samples has the Feather ID Lab received recently with a lot of flights delayed during Covid?"
Sarah Luttrell:
That is a good question. I don't know the numbers off the top of my head, but I know that our caseload is definitely down from this same time last year. But even though there's not a lot of commercial air traffic right now, there's still some planes flying and there's definitely still military planes doing all of their practicing and maneuvering. We still are getting pretty much the same volume from the military that we always get, we're just getting a lot less from commercial air travel.
Maggy Benson:
Now, a couple of people have asked, Can DNA be broken or destroyed? What happens if DNA breaks in your body?
Sarah Luttrell:
Oh, okay. Well first of all, I will talk about the fact that yes, DNA can be broken and destroyed. And we are always really sad in the Feather ID Lab when we get a sample where the DNA has been broken or destroyed. Because once it's really broken, there's not a lot you can do to sequence it well. It's just too busted up. In our case, DNA is broken if it maybe has gotten rotten in the mail on its way to us, which also makes the mail room people really sad, or if it wasn't sampled properly. That means that we have a hard time getting a species-level ID. And to the second part of that question, yes, DNA can get broken or damaged in your body too, but luckily your body has a lot of mechanisms for fixing and repairing DNA. A good example of this is when you get a sunburn, your DNA in those skin cells has actually been damaged. Getting a tan is a way that your body then protects you from further damage.
Maggy Benson:
Okay, this one is from Ronin. "What chemical is included in the fluorescent DNA? Is it the same chemical that makes underwater animals glow? Is it chemical fluorescent?"
Sarah Luttrell:
Ronin, that is a really good question. It is not exactly the same chemical, but the chemical that makes underwater animals glow is something that scientists use in the lab a lot to label cells and proteins. Mostly I think that fluorescent chemical comes from jellyfish.
Maggy Benson:
Cool. From Claire, "Is the equipment that showed in the photos earlier special for bird DNA or can you use it for all DNA?"
Sarah Luttrell:
Hmm. That equipment can be used for all DNA, which is really good because like I said, there are lots of scientists that are working together in the Smithsonian Lab of Analytical Biology and we are studying all kinds of life. There are people studying plants and people studying insects and people studying mammals and people studying all kinds of stuff where they're not even sure what it is on a coral reef. They're doing DNA barcoding also to find out how many and what kinds of animals there are in coral reefs.
Maggy Benson:
Fabulous. Several people have asked, can you do the same process with plants and other animals? So, the answer there is yes.
Sarah Luttrell:
Yes. Yeah.
Maggy Benson:
Sue would like to know how long does the process of DNA barcoding take?
Sarah Luttrell:
That sort of depends on how fast you're working and how fast your machines are. But in our lab we can turn around from snarge to species identification in three days if we're really got our nose to the grindstone. It's not as fast as CSI where they cut to commercial and then they have their answer. But we're pretty efficient.
Maggy Benson:
Several people have asked, how do you extract DNA at home?
Sarah Luttrell:
Oh yeah. There are some really fun videos of how to do this and we've got one in the very last, so you'll be able to find links for this at the end. Basically what you do is, and strawberries are a good example for this, you take something that you can kind of crush up. Strawberries are nice and soft and they have lots of DNA, so they're good example. Then you add a little bit of water to make them runny and a little bit of soap and a little bit of salt to break up those cells and smash them up and then drain out the liquid. Because like we did in our lab, we don't want all the other gunk in the cells, we just want the DNA and the DNA's going to be in the liquid that's left from that. Then you can add rubbing alcohol to that liquid. And the rubbing alcohol, the DNA doesn't want to stay in a liquid in the rubbing alcohol. It binds together into this gooey snot that you can see. If you have enough of it, you can even pull it out of the glass.
Maggy Benson:
It's kind of like the good snarge.
Sarah Luttrell:
Yes.
Maggy Benson:
Making snarge at home. All right. Montana asks, "How do you identify species when you don't know what you're looking for? If it is a new species or you have no idea what to search for?"
Sarah Luttrell:
Yeah, that is a problem that scientists still kind of come up against. Basically the start of that question is you put it into the database and you don't get a good match and that's when you know have something really exciting and then you just kind of have to start to be a sleuth and try and figure out where that DNA came from and can you get another sample and can you actually see that animal and try and figure out what it is.
Maggy Benson:
All right. From Ashley, can DNA barcoding help fight crime?
Sarah Luttrell:
Yes, it can. We don't do crime-fighting DNA barcoding in our lab, but there are lots of wildlife forensics labs that use DNA barcoding to understand whether in wildlife poaching or maybe whether there was some kind of animal present at a crime scene. It's not really used for humans because in that case we know the species involved. We're using a slightly different piece of DNA to look at human crime. But in wildlife forensics, they use barcoding all the time.
Maggy Benson:
They even use it in epidemiology. When we study viruses and other infectious diseases, are they doing DNA sequencing and barcoding for Covid?
Sarah Luttrell:
They are definitely doing DNA sequencing for Covid 19, but they're not doing barcoding. In this case, scientists want to know not just about a little piece of the virus's genome, but they want the whole thing so that they can understand how it mutates and how it interacts with humans. It's a slightly different process, but amazingly, scientists have already sequenced 30,000 copies of the virus genome for Covid 19.
Maggy Benson:
Wow. Wow. Now we'll just take a couple more questions before we wrap up. Several people have asked about the primers and this one's from Kathleen. "How do you know the primer when you don't know?" Oh, it just flipped off my screen. "How do you know the primer when you don't know the exact sequence that you're looking for?"
Sarah Luttrell:
Yeah, that's tricky. In the case of the barcode, we are lucky because the primer region is actually a part of the DNA that doesn't change very much. That's one of the powerful things that lets us be able to figure out all the downstream changes that are unique to that animal. That upstream part, it is really similar among a lot of animal species, but when you first are trying to figure out what your primer is going to be, you have to use a slightly different technique to look at a large part of the gene and figure and choose a region that you want to read and then you can design that region yourself, design copies of it.
Maggy Benson:
Lots of our friends today have asked it about using DNA for cloning. Ryan asked specifically, "Can you take DNA from an endangered animal to keep it just in case the animal goes extinct? Also, can you use DNA to bring other animals back to life by cloning?"
Sarah Luttrell:
A complicated question. At the Smithsonian, we are now saving tissue samples from most of the new animals that come into our collection. We're not doing it because we want to clone those animals to keep them from going extinct. We're doing it because we're recognizing that this might be one of the last chances for scientists to get DNA from those animals. We keep them in really deep freezers so that they can be studied in the future to learn something more about those animals. There are a few people that are trying to use cloning to bring animals back from extinction, but we aren't participating in that because there's a lot of good reasons to focus your energy on the animals that are still around instead of trying to bring back ones that are already gone.
Maggy Benson:
Yes, very good point. Amelia wants to know what inspired you to become a scientist?
Sarah Luttrell:
Oh, that is a good question. You know what? I think the moment that I really wanted to become a scientist was when I was in the fourth grade and I had this really awesome mentor and a summer program and she took us bird banding and I get to hold an actual live wild bird in my hand. And that that is the moment that I always look back on to think like, "Oh my gosh, how cool is this that I could do that?"
Maggy Benson:
So cool. Thinking back, working at the Natural History Museum, so many scientists have a moment in which they look back and they had one teacher, one mentor, that really made a strong impression or gave a really special experience just like that. It really shows how important our teachers are and our colleagues.
Sarah Luttrell:
Yeah, absolutely. I am forever grateful for those kind of teachers that I've had in my life. I hope you guys all have somebody like that, too.
Maggy Benson:
Well, Sarah, I think that you've done that for a lot of our viewers today. Judging on the quality of our questions about the process of DNA barcoding and all of your in-depth questions about what we can learn from DNA, I think you've given us a great head start. Thank you for being that inspiring mentor that we all need. Do you have any advice for additional resources where our friends today can go to learn a little bit more about DNA barcoding and the work you do?
Sarah Luttrell:
Yeah, I sure do. You know what? Let's throw up some websites here really quick that you guys can look at. There you go. So there's some sites that you can learn how to extract DNA in your very own kitchen or maybe just learn some more about DNA and genomes or color some cells. Some really fun ways for you guys to learn more.
Maggy Benson:
All right, So we're going to keep that up for a moment so that you can jot those sites down. Also, if you look in the answered column or in the all questions column, I did respond to one of the questions with some of those links there. Take a moment and you can see how to extract DNA in your kitchen. I've done this with my children, It's very fun. We have the National Institutes of Health Cell Diagram, coloring sheets, very cool, and the Barcode of Life database student portal. All right, Sarah, thank you so much for joining us today and teaching us the process of DNA barcoding. It's been really lovely to see all of the steps lined up so simply and so easy to understand. And we really appreciate that. Thank you too to all of our chat experts who have been answering your questions behind the scenes in that Q and A space.
Thanks especially to all of our viewers who joined us today to learn about DNA barcoding and the important work that Sarah and her colleagues here at the Natural History Museum do. So thank you all.
Sarah Luttrell:
Thanks guys. I'm so glad you joined us today. Thank you everybody.
Maggy Benson:
I do want to mention that we have live video webinars with our Natural History Museum scientists nearly every day. If you go to our website, naturalhistory.si.edu, you can see our full schedule of programming and all of our recorded webinars too. That's where you can find Carla Dove's program on identifying birds from bird strikes, from their feathers. Check that out. Tomorrow we will be back at 2:00 PM with Dr. Gene Hunt, exploring some fossils for Fossil Friday. And on Saturday, we will be showing you how to make a plant press. Check out our website to get more information about those upcoming programs. For now, thank you so much for joining us. When you exit, a survey will pop up on your Zoom browser window. We would love to hear back from you to hear how you like this program so that we can continue giving you programs that are valuable to you. Thank you all so much for joining us. Thanks again, Sarah. This was great.
Sarah Luttrell:
Thanks guys. Have a good rest of your day.
Maggy Benson:
Bye everyone.
