So we're here with Dr. Caleb McMahan, who is the collection manager
of Fishes here at the Field Museum, and today we're going to be talking about
clearing and staining. What is clearing and staining?
Caleb: So, clearing and staining is a process where we take an entire specimen
and we clear that specimen down and use different stains to stain different parts of the skeleton.
Emily: So how is that process actually done -- how do you get from something that's, like
pickled in a jar like this, to something that you can literally see through?
Caleb: In general the process is that we start with a
specimen, so here we have a species of cichlid from Nicaragua and Costa Rica
and so we take this cichlid and the first thing we do -- and, again, some people
do things differently, but I -- a lot of times will take the eyes out. If it's a really thick
fish we might take the skin and scales off of it. And then we're going to take
out the the guts. We take the gonads out and we store those in a vial back in
the jar so that if later someone says I had the skeleton but I want to see what
sections of the reproductive tract look like they can still go back and do that
so then we're left with our fish and we first dehydrate them, in really strong
ethanol, like 95% ethanol, and then we start the process. And in general the two big
phases: one, we're going to stain them so we're going to take the fish and we're
going to use a stain called alcian blue. And we're going to put the fish in
this solution and it's going to stain the cartilage blue. And then we're going to
then use the red dye called alizarin red. Things with calcium -- calcium
phosphate -- will be stained red by this dye. The clearing of it to clear away
the tissue used trypsin which is an enzyme that digests proteins. It's found
commonly in in vertebrate digestive tracts. And trypsin eats away at the at
the tissue, the proteins, but it leaves the collagen. So you can see I can still
pick this fish up. So it's still an actual specimen.
Emily: It's like a jelly specimen!
Caleb: Right, right. It's still an actual fish specimen.. it's not just a pile of bones in
the tray. And then we store it in glycerin, so this -- Emily: That's what the gooey, syrup stuff...Caleb: The gooey kind of stuff. What's
really neat about storing it in glycerin is that glycerin and collagen have the
same refractive index. So, how light passes through - so when you put this on a
tray on a light box like this you just get the skeleton.
Emily: So... that's how-- that's how we'll get invisibility cloak technology.
Caleb: Probably coming from cleared and stained fish, yes.
Emily: Yeah, that will inspire how we develop that.
Why would you use this process over just
something like -- you know, creating an x-ray or CT scan? It seems like it would
be a little bit more evolved than that.
Caleb: we still use x-rays a lot, radiographs
for looking at skeletons. But the nice thing about cleared and stained specimens
is that we have a a 3D visualization of the skeleton, so X-rays don't give us that.
Sometimes the location of certain cartilages or how they vary across
different species or groups of species can tell you a lot about their evolution,
their development, and anatomy. And in fishes a lot of times the larve look
nothing like the adults and so you can track how certain bones change through
develop, and how the general morphology of the fish changes
and those make really interesting studies.
Emily: So you can try to essentially track the growth of an
animal, or a species throughout different stages.
Caleb: Right, right.
Emily: Are fish the only thing that you clear and stain?
Caleb: They're not the only thing. So
these are fish examples, but we also have a lot of examples from other vertebrate
groups as well. These are amphibians and reptiles. So here we have a snake you can
very nicely see the vertebral column wrapped up here. There's a frog, and the turtles
are interesting because they look about the same size but you can see the blue
one, there, is-- that's a cartilaginous skeleton, and so you've got an embryonic turtle there.
Emily: so that was a baby turtle. Caleb: That's a baby baby turtle.
Emily: Aww
Caleb: And then you have this smaller turtle -- the small turtle here with the red skeleton, that's, ah..
Emily: it's just a smaller -- small species of turtle, but it's an adult.
Caleb: Right.
Emily: So what are some of the
discoveries or novel concepts that have been learned from using this process?
Caleb: in my own research I've used cleared and stained specimens to look at their teeth
and morphology of their jaws, and how they look the same or different between
species, or across groups of fishes.
Emily: So kind of how something could move in relation to another thing?
Caleb: Ah, or in their appearance, but that's that's another
really, really interesting way that people are using cleared in stained
specimens for biomechanics, and understanding -- I mean, even here we had this incredible
diversity of morphology in fishes. And this particular species has this very
long -- it's called an ascending process -- off of this upper jaw bone.
Emily: It's like a big extra bone up its forehead?
Caleb: Right and so and what this fish does is you can see with the mouth closed
but to open the mouth you can use this specimen and you can see how the jaw opens.
Emily: Oh wow!
Caleb: Yeah, so using cleared and stained specimens allows us to look at how these
things move and how these things feed.
Emily: So does this process destroy the specimen at all? Because it -- obviously it
looks like it's kind of invasive.
Caleb: It doesn't destroy it -- it it changes the the
the form of the specimen. Instead of looking like this, or like this, it's now
a different appearance, and you can answer different questions with it. A lot
of times I think, you know, we associate to tell different species apart or or
groups of fishes -- that it's not all just always based on external anatomy or
morphology. So, sometimes the characteristics of their of their
skeleton which tell us what species it is. And- and so, sometimes - for instance - this
is one of the type specimens of a knife fish. And so- so- we clear that this was
cleared in stained as part of the description of the species to make sure
that the skeleton -- and show how the skeleton --was different from other species it related to.
Emily: Oh wow, so scientists don't don't see this process
is destructive at all the informative.
Caleb: Yes, absolutely.
Emily: Can you clear and stain a human? Like, can you clear and stain me when I die?
Caleb: it would take a lot of tripsin.
Emily: It would be very expensive.
Caleb: And a lot of glyserin.
Emily: But you could do it.
Caleb: It would be a bit expensive
Emily: Ok. I think that's a good use of scientific funds. .... probably not.
It still has brains on it.