DNA in Space! w/ Astronaut Kate Rubins #ScienceGoals


Don’t mess with
a bench scientist when she’s busy
doing work on orbit. How can DNA help us
keep astronauts healthy and also help us search
for life on other planets? Well, today with the help
of some NASA scientists and an astronaut, we’re
going to find out. They let me talk
to an astronaut. But first let’s talk
to some NASA scientists about DNA sequencing,
the process of reading all the different
letters of DNA, and about why NASA is
interested in doing this aboard the International
Space Station. I’m Sara Wallace, and
I am a microbiologist at the Johnson Space Center. We are responsible
for making sure that the ISS stays
relatively microbially clean, and so we screen the food and
the hardware and the cargo. So why then is NASA interested
in sequencing in space? There’s a lot of reasons. So first from my standpoint
as a microbiologist, right now we’re able to quantify the types
of– the amount of organisms on the ISS, and we do that
by the astronauts actually culture them. So think old school, think
in your basic micro 101 class when you have your Petri
dish and you’re growing up your bacteria and your fungi,
that’s what the astronauts do. That gives us a count
of how many’s there, but we have no idea what they
are until those samples get back to my lab. So at that point we
then identify them. We use biochemical
methods or sequencing. So if we had a
sequence or in flight, we would know what was growing
before– without having to send the samples back. We also don’t have any way to
diagnose infectious disease. So if a crew member gets
sick, it’s up to them to talk with their
flight surgeon and figure out what it is. If we have the sequencer,
it could help diagnose that. That would, of course, lead
to what kind of treatment and all those things. We think an instrument like
a miniaturized DNA sequencer might have practical
applications for the search for life. We have every reason with
the numbers of planets that are being discovered
almost on a daily basis by the Kepler mission and
other planned missions from NASA that are
looking to other sources– we have every reason to believe
that we’re not really special in terms of at least
the number of planets in the galaxy in the universe. I don’t think it’s a great
leap to therefore assume that if there are
lots of planets and the same sort of ingredients
are available on those planets that you might have the right
circumstances to allow life to emerge. The question is how do we
go about detecting that. So DNA sequencing can help us
keep astronauts healthy onboard and also help us to find
life beyond our own planet. But before we go
any further, let’s back up to talk about what
DNA sequencing really means. DNA is like the
instruction book for life, and it’s in every living thing– you, your dog, a potato,
bacteria, a fungus, everything. And it’s the instructions
coded in that DNA that make you you and your dog a
dog and a potato a potato. Your DNA codes all
these instructions with just four letters– A, T, C, and G. Each
of these letters is actually a different
little molecule or base all hooked together
into long strands of DNA. So if you were to read down
a strand of your own DNA, it would just be A, T, A, C, C,
G, A, T, T, C, A, G, G, A, T, C, A, G, G, A, T, T, C,
A, G, G, G, and on and on for billions of letters. No we can’t read all
these letters of DNA just by looking at it. Instead, we have to do something
called DNA sequencing where we use special machines
or sequencers to do the reading for us. By figuring out the sequence
of letters in a DNA sample, we can start to figure out
what that DNA encodes for. It’s a lot like reading a book
letter by letter by letter. Once you know what
all the letters are and what order
they’re in, you can start to figure out what words
and sentences and paragraphs they make up and figure
out whether or not that book is about you
or your dog or a potato. So tell me a little bit more
about the sequencer itself. Out of all the sequencers, why
was it the one that was chosen? So– could we grab it? Yeah. Is it in my purse? Oh, OK. So I just pulled the
sequencer out of my purse. So that should answer the
question as to why this one. So this is the MinION from
Oxford Nanopore Technologies, and we really chose it
because it’s portable. So this is the MinION
Nanopore DNA sequencer that we’ve been using on the
International Space Station. And then here is the
conventional state of the art benchtop
sequencer the MiSeq. So this weighs I think on
the order of about 100 grams, and this one weighs
about 120 pounds. So there’s a ballpark estimate
that costs about $10,000 a pound to fly something into
space or deliver it to orbit. For that reason and
many others, the MinION is really the only
sequencer that we could have flown to the ISS. So within the sequencer,
there’s this little window. And within it in
this flow cell, this is where all the sequencing
chemistry takes place. There are 2,048
nanopore proteins. And so there are actually
these little pores that are within this membrane
that the DNA passes through. It’s in a buffer, and that
buffer contains some salts. We also have an electric
current that’s applied, and so it creates
a current of what’s going through those pores. Whenever DNA molecule
passes through the pore, it blocks it, and therefore
changes the current. So that change in
current is detected, and it’s changed into– we have software that
changes it into whether it’s an A, a G, a T,
or a C, and that’s how we get our DNA sequence. Last year with
this tiny sequencer aboard the International
Space Station, NASA successfully
sequenced DNA in space for the very first time. And the astronaut who did this
sequencing was Dr. Kate Rubins. And for some crazy
reason, NASA let me fly on down to the Johnson
Space Center in Houston to actually meet Dr. Rubins
and sequence DNA with her. The hardware that
we have on orbit is actually just the
MinION sequencer itself, and you can see this
hardware right here. And it just got a little
bit of Velcro on it. We can’t– on orbit, you
can’t really put anything down on the benchtop, but this
actually allowed these guys– they did the sequencing
almost on the wall. And so is a little
computer laptop desk that comes out from an arm. And both the tablet
and the sequencer are just stuck on
this laptop desk. When I did the loading, it
was actually interesting because when you do the
loading on the ground, you would just get your
pipette, and you would come up and you would load the sample. And you wouldn’t really think
about the reaction force that you put into your loading. But when you’re loading
sequencing reaction in space, anything
that you press down, it wants to shoot you way
with the equal and opposite reaction. So I actually had
to find a handrail underneath the
sequencer and tuck my feet into that handrail. And then I could crouch down
and offset my pipetting forces. You don’t really
understand actually how much force that
you put when you’re pipetting and trying
to keep air bubbles out of the reaction mixture. So this is what we used onboard. And the syringe came
in two versions. The first one was
just an empty syringe, and we actually would use
that to withdraw any air. And so you’re just pulling
back on the syringe, and you can see here I’m
using gravity to brace. It’s actually much easier on
the planet than it is on board. And you’re just pulling
back a little bit until you see some
fluid in the tip so that you make sure
that all the– there’s no air bubbles in here at all. So then once you’ve
withdrawn liquid, you’ll just take your sample. And then it’s just a matter– the library is prepped of
getting all of your liquid down in and then just
loading the sample. So this is actually
the first time I’ve loaded a cell
back on the ground. It is lovely to
load on the ground. Now you can tell this
thing is actually designed for Earth because
you can hold this firmly in your knot. I’m not flying up
towards the ceiling. If I was in space, I
would be up in the ceiling tiles with just this
amount of force. We didn’t want people to think,
oh, this is only for microbes. It’s bacteria and weird things. It’s anything. At the level of sequencing,
DNA is DNA is DNA. It doesn’t matter
where it came from. So what we included
in the sample was DNA from a bacteria,
a virus, and a mouse, just to really– all-in-one sample, all three
organisms, whole genomic DNA. We had folks here on the
ground that prep that and split the samples and then sent
identical replicates onboard and at the same time performed
the sequencing on the ground as we were doing it in space. And you can start to see
the data come in right away. And it’s a histogram. And I was incredibly
nervous the first time when I was on the loop
set with these guys here, and I was calling down and I
was like, is it working yet? Is it working–
how is it working? What’s the quality score? And so they were
giving me– they were pretty excited
when they saw the data come through and
were giving us updates that, yeah, it was
actually working. You can see the
histogram in real time. So we let the reaction
go for about six hours. I tried to go eat
dinner, and then I kept coming back and checking
it to see how it was going. And I was babysitting
it until I went to bed to make sure things good. And you start to
see data right away, and it start showing
you the distribution and the [INAUDIBLE] length– a lot of what I was looking
at was the number of events, and so that’s roughly
equivalent to the bases that you’ve sequenced before
it’s gone through all the data processing. And so you can see
that number tick up, and we’d be looking
at say 30,000. We come back the next
day, it’d say 70,000. And so that was pretty
exciting to see that grow and to know that we
were actually generating huge amounts of data. It just these you know
six-hour runs or 48-hour runs. So the next step and
what we’re focusing on flying in the
spring frame this year is being able to take, say,
microbial cells or something and be able to lice
them and do a library prep in a very simple process. In principle, we’re
envisioning that the workflow from collecting the sample
to starting the sequester will take on the
order of like three to four hours for a
sample, and then you start getting the
data right away. And so Kate had mentioned the
process of bringing samples down every three
months and then having to get them and
analyze them in lab. And then you say, OK,
so three months ago this was what was in the
potable water supply or this was what
was on that surface. Now we can say in
a matter of hours that, oh, this is what’s
there, and it’s no big deal or, yeah, we should
probably clear that up. And this is the best way
to actually treat that. So my long-term interest
is to use sequencing to look for life elsewhere. The nice thing
about the hardware is it’s very small architecture. You’ve got the little nanopores
that do the sequencing. And so I’d like to
send it to, say, Mars or Europa or some
planetary surface where we think life might exist. It’s pretty funny. Jeff floated past actually. He knew I was doing
something big that day, and I’m like, Jeff, we’re
going to sequence DNA space. And he’s like, OK, that’s cool. And then he actually
had the video camera, and he was trying
to film something. And it’s like, back off. I’m doing science here. Don’t disturb me what
I’m concentrating on loading this channel. He’s like, you were– this was probably
the most serious I’ve seen you in
spaceflight as trying to make sure that when you
load it, it happens perfectly. I said, don’t mess with
a bench scientist when she’s busy doing work on orbit. Huge, huge thank you’s to
everybody who’s involved in the making of this video. First and foremost, the
Google Making and Science team and their hashtag
Science Goals campaign for supporting this video. You guys rock. Second of all, of course, to
all of the NASA scientists and astronauts who talked
to me for this video. I appreciate that
you guys sat down and let me geek out about
genetics with you for hours. That was fantastic. And also huge thank you’s to
all the people behind the scenes at NASA, especially
in the public affairs office who helped to
make this video possible. Also a special shout out to
Destin of Smarter Every Day. Without his pep
talks and support, this video would not be
nearly as cool as it is. And also to all of you for
watching and subscribing and sharing these videos
and to my Patreon supporters for helping me to continue
to create stuff like this. I appreciate your
support of all forms. So much more than
you can imagine. I could not do any of
this without you guys watching and subscribing
and sharing all the time. And I appreciate it so, so much. Huge thank you. Go forth and do
science in space.

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