[User] Please transcribe this text

[Assistant] The peptide binding pocket also is sort of shaped in different ways to accommodate the R groups of different amino acids.


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[Assistant] So here on this slide, you can see, you know, we've got a triangly one here and a circly one here.


[User] Please transcribe this text

[Assistant] I might think about it that really my peptide binding cleft has like a long skinny region.


[User] Please transcribe this text

[Assistant] Here, and then kind of a round one like this. And oh my gosh!


[User] Please transcribe this text

[Assistant] It can fit a lysine in that long, skinny pocket. And it could fit a phenylalanine in this pocket, and it wouldn't even have to be deformed. Uhm, and so,


[User] Please transcribe this text

[Assistant] We can think about the location of the pocket. Is it around where the first amino acid would be or the second or the fourth? As well as sort of the shape and the charge and the size of that pocket that will be specific for certain types of amino acids.


[User] Please transcribe this text

[Assistant] These amino acids are known as the anchor residues. So they are anchoring that peptide into the MHC class 1 binding pocket.


[User] Please transcribe this text

[Assistant] In fact, there was a very famous experiment. One reason why I like to tell you guys about this experiment is that this was actually done by two students as an undergraduate thesis. Uhm, back in the day, I don't remember what year it was. Uhm, but they,


[User] Please transcribe this text

[Assistant] Isolated the MHC molecules off of the surface of some cells. So basically they cut MHCs off the surface of cells.


[User] Please transcribe this text

[Assistant] And then they sequenced the peptides in those MHC molecules. And they found that if they looked at, you know, MHC number one, they could get all sorts of different peptides.


[User] Please transcribe this text

[Assistant] But those peptides always had certain amino acids in common, like they always had a G at position 2, and a P at position 3, and an either I or an L at position 9.


[User] Please transcribe this text

[Assistant] And if they looked at a diff- and so what they realized is, in order to bind to the pocket of MHC variance number one, there po- there must be a pocket that needs a G and a P.


[User] Please transcribe this text

[Assistant] And an L or an I at position 9. So that must be what the shape of the pocket is. These are the anchor residues that you need to have to anchor into that MHC, to bind in.


[User] Please transcribe this text

[Assistant] The rest of them can vary. The rest of the peptides can vary. So all sorts of peptides from all sorts of microbes can be presented as long as they have these common features.


[User] Please transcribe this text

[Assistant] And if they looked at the peptides that came from a different MHC molecule, they could see that now they often had a tyrosine at position 2 and an isoleucine or a valine at position 9. So each MHC type has, each MHC class 1 type had some specific unique anchor residues.


[User] Please transcribe this text

[Assistant] That were sort of characteristic for that, uhm, protein.


[User] Please transcribe this text

[Assistant] Uhm, you can also see that here, uhm, that any different MHC molecule will have some kind of, you know, peptide binding motif, like this one always binds something with an R position 2 and an R or K position 9.


[User] Please transcribe this text

[Assistant] And as a result, you can get a whole bunch of peptides from a whole bunch of different sources that combine to that MHC, as long as they have that one common motif, as long as they have those anchor residues.


[User] Please transcribe this text

[Assistant] Are different types of MHC molecules?


[User] Please transcribe this text

[Assistant] Also, get their peptides from different places.


[User] Please transcribe this text

[Assistant] So that's another big difference between class 1 and class 2, is where does the peptide come from? In the case of MHC class 1,


[User] Please transcribe this text

[Assistant] The peptides come from the cytoplasm of the cell.


[User] Please transcribe this text

[Assistant] So here we've got a cell making MHC class one. It's got some peptide and that peptide came from the cytoplasm.


[User] Please transcribe this text

[Assistant] Now let's imagine for a second that we're thinking about dealing with some microbes.


[User] Please transcribe this text

[Assistant] That might have its proteins in the cytoplasm of a cell. It's probably the, the...


[User] Please transcribe this text

[Assistant] Most straightforward way the proteins are going to be in the cytoplasm of the cell, as opposed to anywhere else.


[User] Please transcribe this text

[Assistant] From a virus. Viruses are taking over the cell or using the cell's machinery, including the ribosomes.


[User] Please transcribe this text

[Assistant] So the virus' proteins are all going to be in the cytoplasm of cells. And in fact, typically we think about MHC class 1 presenting viral proteins.


[User] Please transcribe this text

[Assistant] Though officially they are presenting any cytoplasmic protein, and you'll see that coming forward as well.


[User] Please transcribe this text

[Assistant] We talked, when we talked about the innate immune response, uhm, we talked about a little bit about how some of the PRRs


[User] Please transcribe this text

[Assistant] were cool cause they responded to a particular type of microbe and they also gave you a kind of response that was good for that kind of microbe.


[User] Please transcribe this text

[Assistant] And we sort of see the same thing with MHC class 1. Uhm, the MHC class 1 is largely presenting viral peptides and the responses, the immune responses that happen as a result of MHC class 1.


[User] Please transcribe this text

[Assistant] Uh, are going to be particularly good at, uh, virus, dealing with viruses.


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[Assistant] Before, and I want you to remember that thought, cause it comes up in a couple of slides, but I have to tell you something else first.


[User] Please transcribe this text

[Assistant] So the one, so right here we're, you know, we're really thinking about that MHC molecule plus peptide binding to the T cell receptor.


[User] Please transcribe this text

[Assistant] Remember this whole discussion of MHC is really so that we can think about T cells and how T cells work. So right now we're really trying to think about having a thing that can bind to the T cell receptor.


[User] Please transcribe this text

[Assistant] It has a little bit of a problem in that it's binding to, uhm, whatever it wants to bind to. Uh, in this case, MHC plus peptide is quite weak.


[User] Please transcribe this text

[Assistant] So this, uh, binding is really really weak, uhm, you can see that here, uhm, compared to some other types of biochemical interactions. So the T cell does not bind things very strongly.


[User] Please transcribe this text

[Assistant] To interact with MHC plus peptide.


[User] Please transcribe this text

[Assistant] We need to have some other proteins involved and those other proteins are really important for


[User] Please transcribe this text

[Assistant] Giving us more binding strength. So, you know, we don't hold with one hand, we hold with two hands. So we get better strength.


[User] Please transcribe this text

[Assistant] In the case of MHC Class 1,


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[Assistant] That other partner protein is called CD8.


[User] Please transcribe this text

[Assistant] So here you can see an MHC class 1 molecule.


[User] Please transcribe this text

[Assistant] With its peptide binding to a T cell receptor. It's a little bit of a weak interaction, but fortunately that T cell also has this protein CD8.


[User] Please transcribe this text

[Assistant] That can interact with the MHC molecule. So CD8 is interacting with this alpha 3 domain of the MHC heavy chain. And this is stabilizing the, uhm, MHC-TCR interaction. So you can see that here. And when we're thinking about MHC class 1, it's always interacting with CD8.


[User] Please transcribe this text

[Assistant] Pathogen, we are likely thinking about with MHC class 1.


[User] Please transcribe this text

[Assistant] Viruses, right? What do you think might be a good thing to do with a cell that is infected with a virus?


[User] Please transcribe this text

[Assistant] If you have a cell that's infected with the virus, what do you think is probably the best defense there?


[User] Please transcribe this text

[Assistant] MHC class one is going to be presenting peptides that were from the cytoplasm, which are usually viral.


[User] Please transcribe this text

[Assistant] And specifically, the T cells that MHC class 1 turns on are CD8 positive T cells. Cause they needed to have CD8 for this interaction.


[User] Please transcribe this text

[Assistant] CD8 positive T cells are the ones that do killing, are the killer type. So all of these pieces come together. We're going to present cytoplasmic peptides. That's going to turn on a CD8 positive T cell.


[User] Please transcribe this text

[Assistant] The CD8 positive T cell is going to kill that cell that had stuff in its cytoplasm.


[User] Please transcribe this text

[Assistant] Uhm, so we also have one other thing we should think about. Again, if you were in charge of designing the immune system, you had to think about this. Which cells of the body


[User] Please transcribe this text

[Assistant] Things on MHC Class 1 and show it off at the surface.


[User] Please transcribe this text

[Assistant] Which cells of your body maybe could get infected with a virus and should be able to show off peptides from their cytoplasm on their surface?


[User] Please transcribe this text

[Assistant] We thought about something similar when we thought about who should be able to respond to interferon. Yea, Brianna? All of them!


[User] Please transcribe this text

[Assistant] So when we actually look to see which cells have MHC class 1 on their surface, the answer is really all but one kind.


[User] Please transcribe this text

[Assistant] There's only one cell of your body that doesn't have MHC class 1 on its surface.


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[Assistant] Uhm, so MEC class 1 is shown here in this left column. Uhm, it's kind of trying to tell us if there's like a lot or a little. Just think about they all as yes, except for this one that is no.


[User] Please transcribe this text

[Assistant] What's the one cell that has, is a no, that doesn't have MHC class 1 on its surface? Yeah, Michael.


[User] Please transcribe this text

[Assistant] Red blood cells. Remember anything interesting about red blood cells from lab one?


[User] Please transcribe this text

[Assistant] They don't have a nucleus, right?


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[Assistant] Because they don't have a nucleus, viruses don't really care about them. They can't be useful for viruses.


[User] Please transcribe this text

[Assistant] So we often say when we ask the question, which cells express MHC class 1, that the answer is all nucleated cells.


[User] Please transcribe this text

[Assistant] Uhm, and a virus isn't going to use a red blood cell because it doesn't have a nuclear. So basically all of your cells have MHC class 1 on them.


[User] Please transcribe this text

[Assistant] So right now, every single cell of your body has-


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[Assistant] You're two different types of HLA-A, you're two different types of HLA-B, you're two different types of HLA-C on the surface. Right now, all the time, 24-7.


[User] Please transcribe this text

[Assistant] Uhm, we can contrast all of this with MHC class 2.


[User] Please transcribe this text

[Assistant] Uhm, MHC class 2 structurally looks a bit different than MHC class 1.


[User] Please transcribe this text

[Assistant] So the first thing that you should notice is that MHC class II molecules are actually made up of two proteins, uhm, that are sort of similar in size.


[User] Please transcribe this text

[Assistant] If you look back at a bunch of the genetics that I showed you in the past, uhm, so actually probably the best example is this one.


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[Assistant] You can see IA here, and you can see it actually shows two IAs. And here's IE, and there's two IEs.


[User] Please transcribe this text

[Assistant] If you look at, if you look very closely at any of the different versions of the, uh, genetics that you saw, there were often two genes for class two that I was kind of glossing over.


[User] Please transcribe this text

[Assistant] The reason why there are two is because we actually have two proteins that are coming together.


[User] Please transcribe this text

[Assistant] An alpha chain and a beta chain. They both have transmembrane domains. They both have, uhm,


[User] Please transcribe this text

[Assistant] Uhm, and it's the alpha 1 domain and the beta 1 domain, making that peptide binding cleft. Uhm, we do have the two transmembrane domains here.


[User] Please transcribe this text

[Assistant] Uhm, with MHC class 1, we had that beta 2m protein, which was non-covalently interacting with the heavy chain. It also didn't have a transmembrane domain.


[User] Please transcribe this text

[Assistant] Uhm, and one thing that I used to take advantage of in experiments in grad school is that MHC class 1 actually has a rate that we sometimes talk about as its breathing rate, where beta 2M goes on and off.


[User] Please transcribe this text

[Assistant] Um, and there's some ways you can play with that and it's really cool. MHC class two is a crazy stable protein by comparison.


[User] Please transcribe this text

[Assistant] It isn't gonna be folded correctly until you get, uh, the alpha chain, the beta chain, and the peptide. But when you have that, it is incredibly stable.


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[Assistant] This is going to become an issue that we have to think about a little bit more on Monday.


[User] Please transcribe this text

[Assistant] It is so stable. Again, those of you who think about some biochem will be surprised by this. It is known as SDS stable. So SDS is this chemical we use to unfold proteins.


[User] Please transcribe this text

[Assistant] If you put SDS on this whole quaternary structure complex, it doesn't come apart.


[User] Please transcribe this text

[Assistant] This is that stable. This is a crazy, crazy, crazy stable molecule. Uhm, when you have all three of these pieces together. So, just like we did with class 1, we're gonna pivot now and look down on the class 1 molecule.


[User] Please transcribe this text

[Assistant] And this is what we're going to see for our peptide binding cleft.


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[Assistant] So first of all, you will notice that the two sides of the peptide binding cleft are drawn in different colors in all of the different images.


[User] Please transcribe this text

[Assistant] That's because they're coming from different proteins. Part of it is coming from the alpha protein, part of it's coming from the beta protein. You get an alpha helix from each of them making up this peptide binding cleft.


[User] Please transcribe this text

[Assistant] The other thing that's super important is in this image from this textbook that I don't know why they discontinued this image because it's really good, is you can look at the ends of the peptide binding class. So again, you can see it's white and it's blue because it's coming from two different proteins. But you can also see that the end of the peptide isn't really covered. You don't see


[User] Please transcribe this text

[Assistant] Oftentimes, immunologists like to talk about how the class one, or the class two binding cleft looks like a hot dog bun.


[User] Please transcribe this text

[Assistant] With a hot dog, it's sort of sticking out the ends. Some textbooks even now at this point show a picture of a hot dog in a hot dog bun, but I was pretty sure you knew what that looked like and I didn't need to put it on the slide.


[User] Please transcribe this text

[Assistant] So with Class 2 Biden and Kluft, one thing that we think about is that there isn't that sort of constraint. For Class 1, it was 8 to 10 amino acids in length was all that would fit. For Class 2, we often talk about 10 to 20, but it really can be kind of any length.


[User] Please transcribe this text

[Assistant] Because the ends are open, the edges of the peptide can flop out.


[User] Please transcribe this text

[Assistant] Uhm, is shown here. So again, we can take a look.


[User] Please transcribe this text

[Assistant] At uhm, the biochemical interactions between the binding cleft and the peptide. And when we look at that, we see that the peptide binding cleft is mostly making interactions with the main chain atoms or the backbone. That NCC, NCC, NCC of the peptide.


[User] Please transcribe this text

[Assistant] We're not seeing the peptide binding cleft make a lot of interactions with the R groups.


[User] Please transcribe this text

[Assistant] So one thing that you should realize here is that with MHC class 2, that means we don't really see anchor residues in the same way that we do for class 1.


[User] Please transcribe this text

[Assistant] Because the R group isn't really making contacts with the MHC molecule, the MHC molecule doesn't care which R groups are there. Every amino acid has the same backbone.


[User] Please transcribe this text

[Assistant] Uhm, sometimes you can see, like, sort of patterns, and sometimes people talk about class 2 anchor residues. I always think they're baloney when I hear about them.


[User] Please transcribe this text

[Assistant] Because like, okay, so here, yeah, they, all these peptides have an L or an F or an I, which is not really that conserved.


[User] Please transcribe this text

[Assistant] And in this one it's the fifth, and this one it's the fourth, and this one it's the seventh, and


[User] Please transcribe this text

[Assistant] Because the peptides can be different lengths, so it doesn't matter exactly where the ends are and how much they flap out the side. And it's really not that strict in what amino acid it is because we're not making a ton of contacts with the, the mean chain. So, class 2 is not as strict about which peptides it binds compared to class 1.


[User] Please transcribe this text

[Assistant] We really don't see kind of a specific motif, a specific sequence, uhm, or anchor residues for class 2.


[User] Please transcribe this text

[Assistant] We will often see, we see our peptides coming from a different location in the cell.


[User] Please transcribe this text

[Assistant] We're class two, our peptides are coming from the endocytic pathway in the cell.


[User] Please transcribe this text

[Assistant] So specifically we are getting those types of peptides either from a phagosome.


[User] Please transcribe this text

[Assistant] So a compartment inside the cell that was made as a result of phagocytosis.


[User] Please transcribe this text

[Assistant] Or some other kind of compartment in the cell, like uhm, is being like an endosome or something like that.


[User] Please transcribe this text

[Assistant] Uh, Bio250, you learned about sort of the biosynthetic secretory pathway, also known as the endocytic pathway or the secretory pathway. You know, the Golgi, the endosome, the ER, all that business.


[User] Please transcribe this text

[Assistant] Class 2 is getting its peptides from that pathway, not from the cytoplasm.


[User] Please transcribe this text

[Assistant] As you will see so much more on Monday, immunologists in fact often think about the cell as having two big compartments, the cytoplasm, which is shown in yellow here, and the endocytic pathway or the compartments, which are shown here in white. And notice that the white is the same color as outside of the cell, both


[User] Please transcribe this text

[Assistant] Are across the membrane from the cytoplasm. So if something wants to get here, it has to solve the problem of crossing a membrane.


[User] Please transcribe this text

[Assistant] Something wants to get here, it has to solve the problem of crossing a membrane.


[User] Please transcribe this text

[Assistant] So, with immunology, the sort of, are you on the same side of the membrane as the cytoplasm, or are you on a different side of the membrane from the cytoplasm, ends up being a big deal. That's going to be a big deal on Monday.


[User] Please transcribe this text

[Assistant] Uhm, so class two is presenting from, basically, from places that are across a membrane from a cytoplasm.


[User] Please transcribe this text

[Assistant] For most cases, this is either going to be something living in a compartment in the cell, like one of those bacteria that I showed you about that could live in a phagocyte.


[User] Please transcribe this text

[Assistant] Or this is something that has been phagocytosed by maybe a macrophage. So it's something the macrophage ate from outside.


[User] Please transcribe this text

[Assistant] Uhm, and again, we need that partner, we need a partner protein, sort of a second hand to hold to give us good interaction.


[User] Please transcribe this text

[Assistant] And in this case, the partner protein is called CD4.


[User] Please transcribe this text

[Assistant] Again, you can see that CD4 is binding to, uhm, the back of the MHC class 2 molecule, this beta 2 subunit.


[User] Please transcribe this text

[Assistant] Uhm, one thing I didn't mention with class 1 and CD8 is also true here. Uhm, this back part of the MHC that in this case is being bound by CD4 and the other case was being bound by CD8 is not variable between different MHC molecules. So you don't have to worry about like,


[User] Please transcribe this text

[Assistant] Some MHCs bind CD4 well and some don't. That's like a super conserved, uh, readout. So, uh, CD4.


[User] Please transcribe this text

[Assistant] Is binding to class 2. CD8 is binding to class 1.


[User] Please transcribe this text

[Assistant] Someone on one of the podcasts I was on mentioned to me that the reason why they remember it.


[User] Please transcribe this text

[Assistant] That is that if you do the multiplication you always get 8. So 4 times 2 is 8 and 8 times 1 is 8. Uhm, so that's how they can remember which ones go together. Uhm, and uhm,


[User] Please transcribe this text

[Assistant] As a result, MHC plus peptide.


[User] Please transcribe this text

[Assistant] Uhm, so we're going to be now seeing our CD4 positive T cells specifically attacking things that are presenting peptide on MHC class 2.


[User] Please transcribe this text

[Assistant] And with MHC class two, we're generally looking at either something that we have endocytosed or phagocytosed or something that is living in a compartment in the cell.


[User] Please transcribe this text

[Assistant] In those cases, your best bet might not be to kill this whole cell.


[User] Please transcribe this text

[Assistant] It might be to do something, like if you kill this cell, well, that doesn't actually do anything against this little flowery guy that was hanging out outside. Whatever made it is still there making it.


[User] Please transcribe this text

[Assistant] Instead of just killing the cell. And so the CD4 cell is going to be a helper is going to influence other types of immune responses instead of killing the cell that it sees. So again, all these pieces are coming together.


[User] Please transcribe this text

[Assistant] We also can think about which cells are expressing our MHC molecules.


[User] Please transcribe this text

[Assistant] So if you recall with MHC class 1, we saw that all nucleated cells were presenting on MHC class 1. This is different for MHC class 2.


[User] Please transcribe this text

[Assistant] When I think about MHC class 2, I only think about three types of cells. So really only three types of cells in your body are presenting on MHC class 2.


[User] Please transcribe this text

[Assistant] This is a figure from your textbook. It is correct that there are some situations where T cells present.


[User] Please transcribe this text

[Assistant] We're never going to think about that ever again. Like yeaah, I know why they put that there, because that's correct.


[User] Please transcribe this text

[Assistant] I wish I almost put a white box over that, but I decided not to be lying.


[User] Please transcribe this text

[Assistant] So there are only three kinds of cells in your body that present class II. They are B cells, macrophages, and dendritic cells. So they are all types of immune cells.


[User] Please transcribe this text

[Assistant] Note, in fact, this is one of those differences between macrophages and neutrophils, so neutrophils don't present on class 2.


[User] Please transcribe this text

[Assistant] Remember I sort of think about macrophages as like fancy bonus neutrophils because they do PRR stuff. It's also because they can present on class too.


[User] Please transcribe this text

[Assistant] So there are only three types of cells that, uhm, present on class two, and they are known as the professional antigen presenting cells, or professional EPCs.


[User] Please transcribe this text

[Assistant] Uhm, and they are very important for helping to turn on that adaptive response. Uhm, the fact that B cells are professional antigen presenting cells is both important for uhm, thinking about how T cells work, but is also a key piece of B cell biology. So again, this is one of the reasons I had to tell you all this stuff before I told you what happened to our B cell.


[User] Please transcribe this text

[Assistant] There are a few other types of cells that can sometimes present on class two. I care that you are aware of one of them.


[User] Please transcribe this text

[Assistant] So yes, this shows a bunch of them. There's only one I actually care about.


[User] Please transcribe this text

[Assistant] And the one that I care about are thymic epithelial cells.


[User] Please transcribe this text

[Assistant] So really, when I think about presentation on class two, I think about four cell types. I think about B cells, macrophages, and dendritic cells, the professional APCs. And I think about thymic epithelial cells.


[User] Please transcribe this text

[Assistant] Thymic epithelial cells are cells of the thymus.


[User] Please transcribe this text

[Assistant] We've already seen the thymus. It is one of our primary lymphoid organs.


[User] Please transcribe this text

[Assistant] Uhm, and it is where, as you will see in a week or something, where T cells develop.


[User] Please transcribe this text

[Assistant] And so actually it's important that we have some class 2 around when T cells are developing. So yes, we do have some class 2 expression in the thymus to help support T cell development.


[User] Please transcribe this text

[Assistant] Uhm, but it's not, uh, for making an immune response, the one, the, for making an immune response, it's dendritic cells, macrophages, and B-cells.


[User] Please transcribe this text

[Assistant] Uh, so we can see our compare and contrast of class 1 and class 2 here. Uhm, the peptide binding domain in class 1 is made of


[User] Please transcribe this text

[Assistant] Two parts of the same protein, alpha 1 and alpha 2.


[User] Please transcribe this text

[Assistant] Uhm, in class 2, it's made of parts of two different proteins, the alpha and beta, alpha 1 and beta 1. Uhm, the nature of the peptide binding groove is close at both ends for class 1, open at both ends for class 2,


[User] Please transcribe this text

[Assistant] Uhm, you can see the size of the bound peptide varies pretty dramatically. For class 1, it is 8 to 10.


[User] Please transcribe this text

[Assistant] For class two, I always learned 10 to 20, this says 13 to 18, whatever.


[User] Please transcribe this text

[Assistant] With the, uh, class one, we have anchor residues, uhm, we have, uhm, some charges in the pocket, uhm,


[User] Please transcribe this text

[Assistant] And this does conserved residues, but


[User] Please transcribe this text

[Assistant] Uhm, and here you can also see the compare and contrast of the structure. Uhm, you can see our class 1 with this heavy chain and the conserved beta 2m as well as the peptide.


[User] Please transcribe this text

[Assistant] Uhm, and with class 2 you can see the, the, uh, polymorphic alpha and beta chains with the peptide.


[User] Please transcribe this text

[Assistant] Uhm, class 1 is on all nucleated cells, class 2 is only on


[User] Please transcribe this text

[Assistant] Uhm, the dendritic cells, macrophages, B cells, and, uh, thymus. Uhm, class 1 gets its peptide from, uh, the cytosol. Class 2 gets its peptides from endosome or lysosome. Class 1 turns on CD8 T cells. Class 2 turns on CD4 T cells.


[User] Please transcribe this text

[Assistant] Uhm, so, any questions about any of that?


[User] Please transcribe this text

[Assistant] Uhm, so I didn't have time to talk through this on Wednesday, so I wanted to just make sure we talked through this as well. Uhm, this is a question that I've asked students in the past. Uhm, question that I can ask myself in the past is where is the eraser?


[User] Please transcribe this text

[Assistant] Uhm, and so here I'm asking, uhm, to identify the MHC haplotypes.


[User] Please transcribe this text

[Assistant] Uhm, and you can also notice that this is listed as being four points, because guess what? There are four parts to the answer.


[User] Please transcribe this text

[Assistant] So remember that a haplotype


[User] Please transcribe this text

[Assistant] It is defined as a group of genes that are inherited together.


[User] Please transcribe this text

[Assistant] So what I want to know is which genes are inherited together. Sort of a fancy way of seeing which ones are on the same chromosome.


[User] Please transcribe this text

[Assistant] We have a father, a mother, and a child here. So the way that I would actually work this out


[User] Please transcribe this text

[Assistant] Is, I would think about, uhm, the child, and I would know that the child got half of its MHDs from its mom.


[User] Please transcribe this text

[Assistant] From one of Mom's chromosomes. We'll call that Mom chromosome 1. And that child got the other half of its MHCs from Dad. One of Dad's chromosomes. We'll call that Dad's chromosome 1.


[User] Please transcribe this text

[Assistant] If we look at the child, we can say, well,


[User] Please transcribe this text

[Assistant] Which HLA-A molecule did this child get from their mother?


[User] Please transcribe this text

[Assistant] Yeah, Michael. A2! That's one they have in common.


[User] Please transcribe this text

[Assistant] It couldn't have gotten A20 from their mother because their mother didn't have it to give to them. So the child must have had, so mom must have had A2 on one of her chromosomes.


[User] Please transcribe this text

[Assistant] Which bee did the child get from the mother?


[User] Please transcribe this text

[Assistant] B27 must have been on the same chromosome. Cause that's the one that mom gave. What DR was on that chromosome?


[User] Please transcribe this text

[Assistant] Okay, so that's one of the four haplotypes in this family. There is one chromosome being transmitted in this family that has this combo of A, B, and D, R.


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[Assistant] Yep, Carney. A20. Okay, what about the B?


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[Assistant] B57. Okay. DR5. Okay, so here's a second chromosome, but I told you there was four parts to the answer.


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[Assistant] Well we, we just listed what was on one of mom's chromosomes and what's on one of dad's chromosomes.


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[Assistant] We can figure out what's on mom's other chromosomes.


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[Assistant] So one of mom's chromosomes has A2, B27, and DR3. What does mom's other chromosome have on it?


[User] Please transcribe this text

[Assistant] Mom was unlucky that she has DR2, the same DR on both of her chromosomes. All right. What about dad? What was dad's other chromosome?


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[Assistant] Okay, so these would be the four haplotypes of the family. Basically these are the four chromosomes that are present in this family that could be passed around.


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[Assistant] Uhm, so that is how you would address a question like this, uhm, which like I said I ran out of time for on Wednesday, but here it is today. Uhm, I will see you guys on Monday.


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[Assistant] Oh my god, Vavini, I'm so happy you're here! Vavini.


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[Assistant] Yeah, he's my baby boy. He is my sweet baby baby boy.


[User] Please transcribe this text

[Assistant] Welcome to this video in learning Elasticsearch 5.0 entitled Kibana. In this video, we start with an introduction to Kibana. We then move to installation and setup steps and finally, during the implementation part of this video,


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[Assistant] We define index patterns and engage in data discovery. Two key elements to use in Kibana.


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[Assistant] Aside from being a tool for visualizing data in Elasticsearch, Kibana also serves as an interface for cluster management.


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[Assistant] When installing Kibana, the first thing you need to do is download the correct version based on your OS. Next.


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[Assistant] You then map to the directory. But, before starting Kibana.


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[Assistant] You will need to edit your configuration file, which is located in the config directory in your cabana source files.


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[Assistant] With the text editor, open the cabana.yml file and make sure that the elasticsearch.url is pointing at the location where elasticsearch is running. In this case, of course, we have been using the localhost on port 9200.


[User] Please transcribe this text

[Assistant] You can start Kibana with the appropriate command based on your OS and then navigate your browser to the localhost.


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[Assistant] Since we walked through the installation of Kibana in the implementation part of the introduction video, 1.3 to be specific,


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[Assistant] We will center our implementation segment on defining index patterns and data discovery.


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[Assistant] What we're going to do is first we're going to select management.


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[Assistant] From management, what we're going to do is we're going to select index patterns in Kibana because we want to set up an index pattern. Now, this is the interface.


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[Assistant] We're going to use our books index to illustrate this example. We've already set up our books index. We've done the mapping, etc.


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[Assistant] Now we have a choice. We can type in the direct name or we can use what's called a wildcard.


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[Assistant] If the name of your index is books, but you also have a book index, et cetera, you can use a wild card. And let's say you type BOO star or asterisk, then that will actually give you all the indices that come up as a result. But what we're going to do here.


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[Assistant] Right now is we're going to just directly name our index without using the wild card. So let's go books.


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[Assistant] And now, one key thing to note is up top, right here,


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[Assistant] We have index contains time based events. Sometimes your indices will have time based events that that means fields that contain timestamps, date stamps, etc.


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[Assistant] Kibana makes this easy for us because all we need to do is click discover and voila. Now when you look here, no problem, it says that


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[Assistant] Unfortunately, I cannot find any results, et cetera, based on the index you have. What you do is you go and you select Time Picker. If you ever see this, select Time Picker. And Time Picker gives you opportunities to select your data based on the timestamp. So, for example, pub underscore date. Well, that's our time data. So here, what I'm going to do


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[Assistant] Again, it's a limited data set but you can see here that it shows the number of books


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[Assistant] Finally note that one of the core things that can be achieved in Kibana is data visualization.


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[Assistant] DataViz is and can get quite involved and as a result is beyond the scope of this course. So that concludes this video. Up next, we look at LogStash, the elastic stack tool for log analysis.


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[Assistant] And be careful! Ugh.


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[Assistant] She is going to set out from the French coast at five o'clock in the morning.


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[Assistant] And she hopes to set up a new world record.


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[Assistant] Debbie's father will set out with her, in a small boat.


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[Assistant] Mr. Hart has trained his daughter for years.


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[Assistant] Tomorrow, he will be watching her anxiously.


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[Assistant] As she swims the long distance to England.


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[Assistant] Debbie intends to take short rests every two hours.


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[Assistant] She will have something to drink, but she will not eat any solid food.


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[Assistant] Who swam the channel herself when she was a girl.


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[Assistant] I twisted the heck out of my ankle, so I'm gonna sit while I teach today, uhm, instead of hobble. Uhm.


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[Assistant] So today I'm going to be talking about, uhm, some additional information about barrier immunity. Uh, these slides are a continuation of Wednesday's slides, so there is not a second set of slides posted.


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[Assistant] Also, please remember the, uhm, clinical assignment that is, uhm, posted on Moodle and due next week. Uhm, so be aware of that. Basically there are three cases to read about and each case has three questions. Uhm, it's the same three questions for all three cases.


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[Assistant] Uhm, and if you have questions or want to talk about things, I am more than happy to talk about them.


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[Assistant] One of the things we talked about on Wednesday or sort of the area that we got into on Wednesday was this idea of barrier immunity and thinking about the immune responses at barrier tissues. All of these tissues are sort of unique in that they are constantly in contact with microorganisms and are


[User] Please transcribe this text

[Assistant] But you might imagine they also need to be somewhat unique immunologically because if they were making


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[Assistant] Inflammatory responses or immune responses 24-7, that might not be something that made you feel great.


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[Assistant] One feature of all of these tissues that we talked about last time is that they all have a group of commensal microbes.


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[Assistant] Uhm, that provide a number of different benefits to you, including, uh, providing colonization resistance.


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[Assistant] So that other pathogenic organisms don't have a niche, uhm, to come into. And so that's actually one layer of defense at all of the barrier tissues.


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[Assistant] We also talked a little bit about how we can divide up the barrier tissues and I gave you sort of the simple definition.


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[Assistant] ...of things that are kind of wet versus things that are not, uhm, in terms of the skin versus other mucosal sites.


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[Assistant] For the rest of the time today, I'm going to be focusing on the other mucosal sites. There are plenty of really fascinating things about skin immunology, particularly how things like, um, wound healing,


[User] Please transcribe this text

[Assistant] Uhm, how having your hair regrow is related to immune responses in the skin. Uhm, so there's all sorts of cool stuff.


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[Assistant] So these are sort of the mucosal tissues. Uhm, most of the time, immunologists think about barrier organs. They are thinking about mucosal tissues. And so we're going to specifically, instead of just thinking about barrier tissue, uhm, zoom in on mucosal immune responses. And you can see the mucosal organs.


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[Assistant] Like the sinuses, the trachea, the lungs, parts of the GI tract, the oral cavity, esophagus, stomach, pancreas, intestine, the conjunctiva, so the eyes, the lacrimal gland, which is where tears come from, salivary gland. You can also see the urogenital tract.


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[Assistant] Uhm, as well as a lactating mammary gland, uhm, which is also known as a mucosal tissue.


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[Assistant] The way that your textbook described what mucosal tissues were and what was important about them. Uhm, so I quoted it here.


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[Assistant] Uhm, which is to say that all of these tissues are sites of communication where material and information are passed between the body and its environment. And so if you think about that, we think of these tissues as being a barrier to keep out microbes, but they also have to be able to let stuff in.


[User] Please transcribe this text

[Assistant] As you can see, there is this material and information passage there, and so you can't just have a gigantic wall.


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[Assistant] Uhm, I mean the skin is a gigantic wall in a lot of ways. But these have to be able to let stuff in. So you can see, because of their functions of gas exchange, food absorption, sensory activity, and reproduction,


[User] Please transcribe this text

[Assistant] Uhm, they're by necessity dynamic, so they've gotta be able to change quickly. They have to be relatively thin and they have to be relatively permeable.


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[Assistant] And how in the world you defend in those kind of areas can be a real challenge.


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[Assistant] Uhm, and they all have vital functions and they're also sometimes a bit fragile because they're thin and they have to let things through.


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[Assistant] Uhm, and so that has meant that these tissues tend to have


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[Assistant] Uhm, some really specific, uh, unique organization and unique aspects of defense.


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[Assistant] We've already talked about one aspect of a unique response at mucosal tissues earlier this semester. And that is secretory IGA.


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[Assistant] So if you remember when we talked about the different isotypes of antibodies,


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[Assistant] We talked about how IGA has a form. It is the major form that people study, so in fact I didn't even tell you really that IGA could do anything else.


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[Assistant] It can, but this is the main one that people think about.


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[Assistant] Here we've got a mucosal tissue. This is the surface that's sort of in contact with the outside world. Here is the inside part of the body.


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[Assistant] And what you can see is that our IgA is actually in that mucosal tissue. It's been secreted into the mucosal tissue where we can


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[Assistant] Neutralize pathogens or toxins before they get in.


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[Assistant] And so one of the unique features of the mucosal tissue is they have secretory IGA.


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[Assistant] So, we can see, uhm, if a microbe needs to be exported, uhm, or a toxin needs to be exported, you can see this here. Uhm, as secretory IGA is getting secreted, it can take stuff out with it.


[User] Please transcribe this text

[Assistant] Uhm, and bring those outside. So secretory IgA is one of the unique features of the mucosal immune system.


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[Assistant] Feature of the mucosal immune system that we can think about very broadly and uhm, this one is


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[Assistant] Obvious or implied in the name of the mucosal immune system.


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[Assistant] Which I am sure you are familiar with in some form.


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[Assistant] So mucus is basically a polymer, uhm, where there is this one little protein


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[Assistant] That gets a ton of glycosylation.


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[Assistant] And then when that one little protein is outside of cells, it polymerizes to make this super giant molecule. That's some proteins.


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[Assistant] That are making almost like a scaffold that are just covered with sugar.


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[Assistant] And so you can see all of this covering. It's basically a layer of goo.


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[Assistant] Uhm, the amount of water that's there can change to change how thick or thin that mucus is.


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[Assistant] And basically that mucus, again, you are probably familiar with mucus in some way or another.


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[Assistant] So that there is a bit of a barrier between the cells and any particular microbe.


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[Assistant] So this is showing different parts of the intestine, the small intestine and the large intestine. And in the grey, you can see the cells and their, uhm, absorptive capacity. And then in the green, you can actually see how much mucus sits on top of those cells. How much of this basically sugar


[User] Please transcribe this text

[Assistant] Big polymer sits on top of those cells. Notice here in the duodenum, it's about a hundred micrometers thick. That's almost the same thickness as the cell layer.


[User] Please transcribe this text

[Assistant] And so if a pathogen wanted to interact with or, uh, one of these cells for infection, it would have to get through this whole sugary goop layer.


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[Assistant] Uh, and you can see the specific details of those layers changing at different parts of the GI tract.


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[Assistant] But in any part of your mucosal immune system, you are going to have that layer of mucus helping to protect the cells from infection.


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[Assistant] You can see this here as well. So here is our layer of cells. We've got the immune cells underneath, inside the tissue, and outside the tissue we have our secreted IgA as well as all of our mucus.


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[Assistant] Giving us a nice layer of protection of the barrier.


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[Assistant] You can also see this in this other figure. I like this figure just because here you can see the cell layer and you can see all of this mucosal layer or this mucous layer outside of the cells and you can hopefully appreciate


[User] Please transcribe this text

[Assistant] layer of dead cells like the skin has, but it is some kind of physical blockade that is helping get rid of some of those microbes.


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[Assistant] And we act, we know about specific cells called goblet cells, whose job it is to just secrete mucus. Uhm, we also know that in uhm,


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[Assistant] Mice who have a certain, I guess a better way of doing it is if you first look at this, uhm, image, this microscopy image, the blue cells, the blue staining show you the cells of the intestine, and the green staining show you the micros.


[User] Please transcribe this text

[Assistant] And what you can see is there's a big gap where the microbes can't touch the cells of the intestine.


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[Assistant] And that gap, this empty looking place, this black part, is where all the mucus is, keeping these two apart.


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[Assistant] There are some situations where uhm, there will be mutations so that that mucus layer is


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[Assistant] Uh, gone, and so you can see in that situation the microbes are now going to be in contact with that barrier. And so at any part of the mucosal immune system, uhm, one of the things that we have protecting us is the mucus.


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[Assistant] These are not the only unique features of the mucosal immune system.


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[Assistant] So when we think about the mucosal immune system, some of the things that are unique have to do with anatomy.


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[Assistant] And in some ways I would say that the mucus is kind of an anatomy thing. Um, the presence of.


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[Assistant] Secretory IGA, you could, you can argue for yourself if that's anatomy or an effector function. Uhm, it's not clearly labeled as either one here, and I think that, you know, six of one, half dozen of the other could be some of either.


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[Assistant] But there are also some other types of anatomical features that we'll see.


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[Assistant] As well as some different types of effector mechanisms and some other unique features of the environment.


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[Assistant] And I'm going to show you some examples of each of these things in a mucosal immune response.


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[Assistant] As I mentioned a little bit ago, when immunologists study the mucosal immune system, if you look, for example,


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[Assistant] In your textbook, this chapter, chapter 10 is called the mucosal immune system.


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[Assistant] Uhm, in, uhm, some other immunology texts, uhm,


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[Assistant] This chapter is called the barrier immune system. It's because those texts have a little section on skin outside of mucosal immunity.


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[Assistant] But if you actually took chapter 10 of your book and looked at it really closely,


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[Assistant] You would see that when it is talking about the mucosal immune system, it pretty much always uses the same anatomic location as its example.


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[Assistant] And when most people think about mucosal immunity, they think about one particular mucosal immune organ instead of...


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[Assistant] Talking about what's up with all of the mucosal immune organs. Uhm, for a long time, we have really lumped them all together. Just all the mucosal immune system works the same way.


[User] Please transcribe this text

[Assistant] Uhm, I think that we are starting to understand that that's not totally true. Uhm, in fact, one thing that I learned during uh, COVID is that uhm, the,


[User] Please transcribe this text

[Assistant] Upper respiratory, like the nose immune system and the deep lung immune system are completely different. But your textbook just says they're all mucosal immunity.


[User] Please transcribe this text

[Assistant] Um, and so we're going to be talking about kind of the organ that everybody thinks about with the mucosal immune system. So if you were looking quickly at chapter 10, you would really think it was about one organ, not the whole mucosal immune system.


[User] Please transcribe this text

[Assistant] One reason why I laugh about this is I actually was on FaceTime with my sister last night. Uhm, my sister did her PhD on B-cell responses in the lung. And she thinks about mucosal immunity a lot.


[User] Please transcribe this text

[Assistant] This is sort of the way your textbook calls the mucosal immune system, but we are really picking one organ that we're focusing on. And that one organ is the GI tract, specifically the intestine.


[User] Please transcribe this text

[Assistant] That's the one that everybody talks about when they think about mucosal immunity.


[User] Please transcribe this text

[Assistant] Uhm, so know that we probably are leaving out a lot of things that go on in the mucosal immune system in some of these other organs. Uhm, I have another friend who works specifically on, uhm, the immune system in the mammary gland.


[User] Please transcribe this text

[Assistant] And there are many ways that what she studies is unique from what we're going to see today. But we're going to go big picture instead of zooming in on some of those little details.


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[Assistant] So we can look at uhm, some of our sites in the mucosal immune system.


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[Assistant] And one of the things that we see is on that list of anatomical changes.


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[Assistant] And so in any of our mucosal tissues, we actually find that there are organized lymphoid structures. So it's sort of like in each of these mucosal tissues, there are like mini lymph nodes.


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[Assistant] To help with the surveillance because there is so much encounter with microbes going on.


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[Assistant] And so here we can see, uhm, the wall of the GI tract. Uhm, you can see we've got the extended epithelium to give us lots of surface area for absorption. So here's our part of the intestine that is absorbing nutrients.


[User] Please transcribe this text

[Assistant] But you can also see that there are other little areas where we have these little lymphoid tissues.


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[Assistant] Uhm, that kind of look, that are officially secondary lymphoid organs and look like mini lymph nodes. And you can also see that we have lymphatics going through all of this tissue.


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[Assistant] So in one unique anatomical feature of our mucosal sites is they all have these organized lymphoid tissues. You can in fact see


[User] Please transcribe this text

[Assistant] This in cross section, you can even see some germinal centers.


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[Assistant] In some of these little lymphoid follicles. Some of them are so big, they get special names like the pyres patch. Sometimes there are just little lymphoid follicles that form in places as well.


[User] Please transcribe this text

[Assistant] There are some unique types of cells in some of these places. And one of those particular cells that's really important is called an M cell.


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[Assistant] Uhm, an M cell stands for a micro-fold cell. And you can see, uhm,


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[Assistant] An M cell in the wall of the intestine in an electron micrograph on the left.


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[Assistant] So what you should notice here is the area of the intestine where the M cell is looks different.


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[Assistant] M cells are, would also look different if we were somehow able to do our electron microscopy of the bottom and look at them from the inside. And this, of course, since that would be awfully hard to do, we instead have a cartoon.


[User] Please transcribe this text

[Assistant] And so here you can see the M cell in the lighter pink compared to the other cells of the intestine.


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[Assistant] In the darker pink. And you can see that the M cell, uhm, is shaped funny. And basically makes this little pocket internally.


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[Assistant] And that's a little pocket where immune cells can come hang out and take a look at antigens.


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[Assistant] The M cells can capture microbes.


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[Assistant] And bring them in just in sort of small numbers to show them to B cells and T cells.


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[Assistant] So that we can start to get a response. And so it's sort of like, instead of just letting in all of...


[User] Please transcribe this text

[Assistant] The microbes, instead of having an open wall where you just let the microbes come into the, the, uh, gut tissue, the M cell takes little samples.


[User] Please transcribe this text

[Assistant] And says, hey T cells and B cells, can you check these? See if they're okay? We're not gonna actually let them all in, cause they might be bad, and it would be really terrible if we let them all in.


[User] Please transcribe this text

[Assistant] But we're gonna bring a few in. We're gonna keep them in this secluded special zone. We're not going to actually let them go through the whole body. And we're gonna let you look at them. I'm sure we can come up with some, you know,


[User] Please transcribe this text

[Assistant] Like when they have this special screening area in the airport or something. They're like special little zone where they bring things to check it out.


[User] Please transcribe this text

[Assistant] Uhm, and this is all the job of the M cells, the things that will happen in this little pocket, and the sampling that the M cell is doing. We can also see


[User] Please transcribe this text

[Assistant] That there are actually dendritic cells that can reach between the cells of the intestinal wall to try to capture antigens outside.


[User] Please transcribe this text

[Assistant] Left, where you can see this yellow dendritic cell reaching in between the cells of the GI tract in order to phagocytose things that are actually in the GI lumen.


[User] Please transcribe this text

[Assistant] And you can also see this in the microscopy image on the right.


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[Assistant] The black area is the GI lumen, the green is some dendritic cell, and you can see that dendritic cell reaching up.


[User] Please transcribe this text

[Assistant] Uhm, really, and trying to go on the other side of the cell barrier in order to sample.


[User] Please transcribe this text

[Assistant] Uhm, so these are some of the important anatomic things going on here.


[User] Please transcribe this text

[Assistant] There are a couple of other important immunologic things as well. And one of them, to be honest with you, I would say that the next three slides are probably


[User] Please transcribe this text

[Assistant] Some of the things that are sort of, if you ask me, like,


[User] Please transcribe this text

[Assistant] It would be related to the stuff that's on the next few slides, the next three slides, because this is just to me, like, the thing that's super special about the mucosal immune system.


[User] Please transcribe this text

[Assistant] You actually see an image that's pretty similar to an image you've seen earlier in the semester.


[User] Please transcribe this text

[Assistant] Where you can see a, some kind of tissue. Here it's called, here we're saying it's the skin. I'm not gonna deal with exactly which tissue and whether I think the skin is the best tissue. Maybe it is the tissue in, well,


[User] Please transcribe this text

[Assistant] No, I won't go there. Uhm, it's some kind of tissue. Uhm,


[User] Please transcribe this text

[Assistant] You can see that that tissue has some kind of


[User] Please transcribe this text

[Assistant] Macrophage that lives locally in the tissue.


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[Assistant] You can see that something happens so that there are bacteria that come in.


[User] Please transcribe this text

[Assistant] And that local cell starts an inflammatory response.


[User] Please transcribe this text

[Assistant] And we get swelling and we get


[User] Please transcribe this text

[Assistant] And again, the top of this is basically the same figure you've already seen.


[User] Please transcribe this text

[Assistant] If you looked at the same process in a mucosal tissue, you would see something different happening.


[User] Please transcribe this text

[Assistant] There are still innate immune cells like macrophages that are living there. So here's a macrophage living.


[User] Please transcribe this text

[Assistant] In the mucosal tissue, just like the macrophage, a macrophage that we saw living in the skin.


[User] Please transcribe this text

[Assistant] That macrophage can sense some kind of microbe.


[User] Please transcribe this text

[Assistant] But when that macrophage senses that microbe, that macrophage


[User] Please transcribe this text

[Assistant] Won't induce the same kind of inflammatory cytokines. And won't induce an inflammatory response.


[User] Please transcribe this text

[Assistant] And so the response that we see will look pretty different than the response that we see in the mucosal tissue.


[User] Please transcribe this text

[Assistant] Um, a large part of that is because of, um, sort of different cytokines and different things coming from that original innate immune cell. Um, so here's the, here we can see some of those innate immune cells, either responding in the M cell pocket


[User] Please transcribe this text

[Assistant] Or doing some phagocytosis. They're not going to lead to a traditional inflammatory response. Those innate immune cells that live locally in this location are a bit different.


[User] Please transcribe this text

[Assistant] And they are often referred to as cells that have this sort of immunoregulatory ability.


[User] Please transcribe this text

[Assistant] And when I was putting this slide and the next couple of slides together, uhm,


[User] Please transcribe this text

[Assistant] I sort of was snickering to myself a little bit because I wrote the immunoregulatory environment and then I remembered that immunoregulatory is immunologist code, uhm, and that I probably was going to have to


[User] Please transcribe this text

[Assistant] Totally define for you what immunoregulatory means, or at least what an immunologist means when they say immunoregulatory.


[User] Please transcribe this text

[Assistant] I mentioned this a little bit, uhm, in one day in the past, and I'm not gonna go through the whole story now, but once upon a time,


[User] Please transcribe this text

[Assistant] Uhm, there was this idea of T cells that could turn off other T cells. They were called suppressor T cells.


[User] Please transcribe this text

[Assistant] And then for various reasons, people stopped believing suppressor T cells existed. Uhm, it's a whole big thing.


[User] Please transcribe this text

[Assistant] Uhm, and in fact when I was an undergraduate I was kind of taught that the word suppressor was a dirty word.


[User] Please transcribe this text

[Assistant] Later on, we found some T cells that turned some other T cells off.


[User] Please transcribe this text

[Assistant] There we go. But at this point, the word suppressor or suppression or suppress,


[User] Please transcribe this text

[Assistant] What is still thought of as a dirty word. You couldn't use that word. That word is BAD.


[User] Please transcribe this text

[Assistant] And so instead, we called the T cells that did the off stuff regulatory T cells.


[User] Please transcribe this text

[Assistant] Cause we didn't want to use this sort of bad word.


[User] Please transcribe this text

[Assistant] Immunologists have kind of taken on the idea of using regulatory to mean off. It's like, it's our code for suppression. I think when a lot of people think about such and such as regulatory,


[User] Please transcribe this text

[Assistant] They think they mean like, controls or something like that.


[User] Please transcribe this text

[Assistant] Immunologists have a little bit more, they mean a little bit more almost towards off or suppression when they say regulatory. And it's kind of because the idea of suppression got a bad name once upon a time. And so.


[User] Please transcribe this text

[Assistant] We say that the environment in mucosal tissues is immunoregulatory.


[User] Please transcribe this text

[Assistant] What that means is that those innate immune cells


[User] Please transcribe this text

[Assistant] Like this macrophage that we see in the mucosal immune tissue, like the GI tract, is going to make responses


[User] Please transcribe this text

[Assistant] That are not really inflammatory responses, that are instead responses that might lead towards, uhm,


[User] Please transcribe this text

[Assistant] More Tregs and other kind of suppressive types of responses. So this innate immune cell in the gut


[User] Please transcribe this text

[Assistant] Might specifically make cytokines to push T cells towards Tregs.


[User] Please transcribe this text

[Assistant] Uhm, whether it's a macrophage or whether it's a dendritic cell in that location. You can sort of imagine


[User] Please transcribe this text

[Assistant] That all of the innate immune cells in the GI tract


[User] Please transcribe this text

[Assistant] Know that they're in the GI tract, and when they say, when they see antigen,


[User] Please transcribe this text

[Assistant] Their response is sort of to be like, everybody calm down.


[User] Please transcribe this text

[Assistant] While in systemic tissue, we start this inflammatory response and we ring the alarm bells.


[User] Please transcribe this text

[Assistant] Instead, those same innate immune cells know that they live in the GI tract or in a mucosal tissue.


[User] Please transcribe this text

[Assistant] And they produce a different set of cytokines to sort of keep an immune response from getting too high.


[User] Please transcribe this text

[Assistant] This can, and this can be actually a number of different molecules.


[User] Please transcribe this text

[Assistant] Push us towards an immunoregulatory environment.


[User] Please transcribe this text

[Assistant] So let's think about this in terms of the good side, because there's a good side to this and a bad side to this. So let's think about the good side to this first. Why evolutionarily, or why sort of in general immunology terms?


[User] Please transcribe this text

[Assistant] Might it be a problem if you saw, had what happened at the top?


[User] Please transcribe this text

[Assistant] Happening in your mucosal tissue like in the intestine. Why might that be a problem?


[User] Please transcribe this text

[Assistant] Okay. So one of them is kind of a space problem of whether or not you have room to have that inflammation. And that is certainly related to kind of what I was thinking about. I hadn't thought about it that specifically. I thought about it more broadly, but that's totally like in that direction. What, yeah, Michael.


[User] Please transcribe this text

[Assistant] Basically, since we have all of these microbes, you can't, like, you don't live in a sterile box.


[User] Please transcribe this text

[Assistant] Your mucosal tissue is 24-7 in contact with microbes. If your mucosal tissue was inflamed 24-7, you would not feel good.


[User] Please transcribe this text

[Assistant] And in fact, you would probably have a fair amount of tissue damage.


[User] Please transcribe this text

[Assistant] You would also have blockade of the function of those tissues, like you could imagine with the space constraint that Karame mentions.


[User] Please transcribe this text

[Assistant] You would actually not be able to have your nose work correctly if it was always full of swelling and it was full of inflammation.


[User] Please transcribe this text

[Assistant] Uhm, if your lungs were 24-7 full of inflammation, they probably wouldn't be able to do gas exchange very well.


[User] Please transcribe this text

[Assistant] In an inflamed state, it probably wouldn't be doing food absorption very well.


[User] Please transcribe this text

[Assistant] T-for your normal physiology, and if there was tissue damage, you'd be in bad shape.


[User] Please transcribe this text

[Assistant] And if there was excess inflammation, you would actually stop the function of those organs. So one problem is you need to make sure that you don't have any kind of excess inflammation in those organs, because if you did, you'd be


[User] Please transcribe this text

[Assistant] In bad situations. So instead the innate immune cells are sort of saying, everybody calm down. We can't, we're in a location where we cannot have an excess type of response. If you have inflammation in your intestine all the time,


[User] Please transcribe this text

[Assistant] That is called Crohn's disease, or inflammatory bowel disease, or colitis.


[User] Please transcribe this text

[Assistant] Uhm, that's what's happening to you is that you have too much inflammation all the time in that location. Your immunoregulatory environment is not kind of working out. Uhm, there's one other reason


[User] Please transcribe this text

[Assistant] An immune response being made all the time in the GI tract.


[User] Please transcribe this text

[Assistant] So let's think about this a little bit more, kind of, big picture for a second. Big picture immunology is you respond to organisms that are foreign, right? You respond to organisms that are not you.


[User] Please transcribe this text

[Assistant] Uhm, I'm going to name some organisms that are not, that are different than me. They're not, that are foreign for me right now. Okay? Uhm, some organisms that I am not include a cow, a salmon, uhm, wheat,


[User] Please transcribe this text

[Assistant] Encountering foreign stuff. Even if it was totally sterile.


[User] Please transcribe this text

[Assistant] Yeah, I wouldn't have PRRs, but I'd still have some antigens that my B cells and T cells had never seen before.


[User] Please transcribe this text

[Assistant] In the case of whatever my food antigens are.


[User] Please transcribe this text

[Assistant] And so if we made an immune response to all of our foods, because all of our foods are unique organisms, except for maybe the Diet Coke I drank way too much of, uhm,


[User] Please transcribe this text

[Assistant] That again would be really bad evolutionarily. We would not survive or reproduce particularly well. And so what we've actually realized is that in


[User] Please transcribe this text

[Assistant] Uhm, mucosal tissues, and this is really well described in the GI tract. We have what's known as mucosal tolerance.


[User] Please transcribe this text

[Assistant] Uhm, and so when an antigen is first encountered, if the first time you ever see that antigen is in the, uhm,


[User] Please transcribe this text

[Assistant] GI tract, then you end up getting a.


[User] Please transcribe this text

[Assistant] When we look at food proteins or commensals, we largely will see, uhm, Tregs being induced instead of other T cells.


[User] Please transcribe this text

[Assistant] And we really see no other response in the system.


[User] Please transcribe this text

[Assistant] Uhm, this was actually one of the ways that Tregs were first described. Uhm, one of the first sort of places where people were like, oh right, these suppressing things kind of do exist, uhm, was in understanding Tregs. Tregs were originally called TH3s, uhm, before we understood a lot more about what was going on.


[User] Please transcribe this text

[Assistant] And we can, we've actually done a lot of experiments where we can take advantage of this. So one experiment that you can do is you can


[User] Please transcribe this text

[Assistant] Take some mice and you can inject a foreign protein. That foreign protein is called ovalbumin. Uhm, it comes from, uhm, a chicken. Uhm, it-


[User] Please transcribe this text

[Assistant] It's a protein that immunologists love to use as an antigen, so.


[User] Please transcribe this text

[Assistant] Do we just use it? It's basically the sample antigen in a lot of immunology. You can give some mice some ovalbumin in an injection. And it would sort of be like a vaccine.


[User] Please transcribe this text

[Assistant] Where you then looked to see, did those mice make an immune response to ovalbumin and they would make a huge immune response to ovalbumin.


[User] Please transcribe this text

[Assistant] Again, it would be like you basically gave the mice a vaccine against ovalbumin. So if ever they were attacked by chicken proteins, they would be safe.


[User] Please transcribe this text

[Assistant] Uhm, you can just make it, it's a foreign protein, inject it in, you make an immune response. If however,


[User] Please transcribe this text

[Assistant] Before you do that, you feed the mice some ovalbumin.


[User] Please transcribe this text

[Assistant] So that the first time the mice have encountered this antigen, they are encountering it in the GI tract. And then you immunize with ovalbumin. You actually don't get much of a response.


[User] Please transcribe this text

[Assistant] That initial immune response in the GI tract drove Tregs.


[User] Please transcribe this text

[Assistant] Uhm, and made this much more immunoregulatory response.


[User] Please transcribe this text

[Assistant] This is something that is taken, that we take advantage of in certain situations with some allergies in terms of trying to give uhm,


[User] Please transcribe this text

[Assistant] This is hypothesized to be involved in increasing numbers of peanut allergies in that a lot of little kids are


[User] Please transcribe this text

[Assistant] In the past, the first time you saw peanuts as an antigen, you saw them from eating peanuts.


[User] Please transcribe this text

[Assistant] More and more, the first time you see peanuts as an antigen, you're seeing lotion that has peanut oil in it.


[User] Please transcribe this text

[Assistant] Uhm, and so perhaps you're getting a slightly different response. That's very much hypothesized for a lot of what's going on with peanut allergy. So your first exposure gave you yes response instead of regulatory response. Uhm, sometimes people ask me,


[User] Please transcribe this text

[Assistant] Uhm, this is a question that I get asked pretty frequently and I want you guys to answer this question. Cause I get asked this question a lot when I'm giving talks to the lay public. I'm scared of needles.


[User] Please transcribe this text

[Assistant] I don't like needles. I want you to give me all my vaccines as pills that I take orally.


[User] Please transcribe this text

[Assistant] What do I usually say? Or what, what sort of is this something to be aware of in response to that?


[User] Please transcribe this text

[Assistant] Yeah, sometimes if you see an antigen for the first time in the GI tract, you're going to get a tolerance response. You're going to make Tregs.


[User] Please transcribe this text

[Assistant] So it's like that vaccine is actually going to make your life worse, not better, if we give it as a- through the mouth, as opposed to giving it systemically, uh, as a shot.


[User] Please transcribe this text

[Assistant] Obviously, uhm, there are...


[User] Please transcribe this text

[Assistant] Some exceptions and there are some ways that we're learning about these responses uhm, to try to figure out how we can start to sort of modulate them and work with them.


[User] Please transcribe this text

[Assistant] Uhm, there are lots of ways that working with them could be really important in thinking about how in the world we deal with uhm,


[User] Please transcribe this text

[Assistant] Allergy, but also how we could sort of do some of these vaccinations. But I, but one of the things I tell people is right now a lot of what we know about your GI immune response is about how you actually turn off immune responses when you see something in the GI tract.


[User] Please transcribe this text

[Assistant] The reason why you actually make sure that you don't make immune responses to cows and can eat a steak.


[User] Please transcribe this text

[Assistant] In the GI tract, with a pill, well yes, it might be


[User] Please transcribe this text

[Assistant] So you should realize mucosal tolerance is, uh, quite important.


[User] Please transcribe this text

[Assistant] Uhm, this also sometimes leads to one other detail. So we've talked about sort of the good side of mucosal tolerance.


[User] Please transcribe this text

[Assistant] Uhm, but what about the, uh, potential bad side? So do you have any questions or any sort of things that you look at here and say, wait a minute, there's still a piece missing. We still got a problem here.


[User] Please transcribe this text

[Assistant] Yeah, sometimes you actually do get infected with a pathogen in the infection, in the intestine. So what the heck happened there? Look, Christina, you even had the question on the next slide.


[User] Please transcribe this text

[Assistant] So we do kind of have to think about, okay, there are actually some pathogens that are going on here.


[User] Please transcribe this text

[Assistant] Uhm, some of this, uhm, will be, uh, a little bit of something that we deal with anatomically. So you think of the GI tract. You think about how the GI tract works. Nothing that's in the GI tract stays there forever. You are eventually forcing everything out at some point. And so part of it is that, you know,


[User] Please transcribe this text

[Assistant] We can have changes in how much we have things leaving in order to try to flush out potential pathogens.


[User] Please transcribe this text

[Assistant] Uhm, but we can also sometimes see a mucosal immune response to pathogens, and it is in fact important that we have this mucosal immune response to pathogens.


[User] Please transcribe this text

[Assistant] And so we will sometimes, you know, see a sort of more typical systemic response in response to pathogens.


[User] Please transcribe this text

[Assistant] And this table from, uhm, another immunology textbook, the Janeway immunology textbook, I think gets at this distinction really nicely. Uhm, so sometimes in the mucosal situation we get mucosal tolerance.


[User] Please transcribe this text

[Assistant] In other times we do get sort of the more traditional immune response, which is what they're calling here, protective immunity.


[User] Please transcribe this text

[Assistant] They make a nice distinction in this table If you look at this table


[User] Please transcribe this text

[Assistant] Particularly with regard to antigen, so I would say that the difference is in the antigen, and because the antigens are different, the response is different. But if you look at what this table says about the antigen,


[User] Please transcribe this text

[Assistant] What's different about the antigens in these two situations?


[User] Please transcribe this text

[Assistant] Yeah, notice that this says invasive bacteria.


[User] Please transcribe this text

[Assistant] And realize that viruses, again, are, as Michael says, are going to invade and get into other parts of the body. Toxins are going to get in. And so the difference is sort of, seems to be based on sort of whether or not the antigen seems to be trying to invade, whether or not there is invasiveness going on here.


[User] Please transcribe this text

[Assistant] Uhm, this just shows you a couple of examples, though there are so many examples of different types of microbes that can try to invade.


[User] Please transcribe this text

[Assistant] So here you can see organisms, I believe this is trying to show you shigella, but it could be shigella, it could be salmonella, it could be a type of E. coli, there's a bunch of them.


[User] Please transcribe this text

[Assistant] That will actually try to interact with the cells of the, uhm, GI tract.


[User] Please transcribe this text

[Assistant] And that will actually poke holes in them to try to get nutrients or other things. And so you can see.


[User] Please transcribe this text

[Assistant] That sort of formation where the cell is actually trying to get stuff.


[User] Please transcribe this text

[Assistant] Out of the cytoplasm of the cell. Here you can see some shigella that actually force their way in.


[User] Please transcribe this text

[Assistant] To different types of cells. Here you can see other microbes, Salmonella, forcing its way and trying to invade into other types of cells.


[User] Please transcribe this text

[Assistant] So what we might imagine here is that there is this distinction.


[User] Please transcribe this text

[Assistant] In terms of whether we're going to make an immune response that is more tolerance immune response.


[User] Please transcribe this text

[Assistant] More regulatory, if something is not invading.


[User] Please transcribe this text

[Assistant] And maybe those same innate immune cells are going to actually make the traditional inflammatory response if something tries to invade.


[User] Please transcribe this text

[Assistant] This is what we see in the bottom if we're looking at some non-invasive microbe. But the same macrophage, if the microbe was sort of trying to invade.


[User] Please transcribe this text

[Assistant] Could give us some information. It's just sort of trying to decide, is this an invasive or non-invasive thing?


[User] Please transcribe this text

[Assistant] Is this a thing we should be worried about trying to go big picture or not?


[User] Please transcribe this text

[Assistant] Uhm, I like this table because it talks about invasive things versus other things.


[User] Please transcribe this text

[Assistant] So that leads to one question on the side of the innate immune cell.


[User] Please transcribe this text

[Assistant] How might an innate immune cell know if a microbe is invasive or not? How in the world is that innate immune cell going to know whether or not a microbe is invasive?


[User] Please transcribe this text

[Assistant] How, you know, does it have the ability to ask, to interview the bacteria and be like, what are your thoughts and feelings?


[User] Please transcribe this text

[Assistant] Uhm, how's it supposed to, how's it gonna know the difference?


[User] Please transcribe this text

[Assistant] Okay, so, but remember MHT plus one and two is mostly going to be about what we present to T cells.


[User] Please transcribe this text

[Assistant] And we need to think about whether that innate immune cell is going to make an inflammatory response or not. Is it going to make inflammatory cytokines?


[User] Please transcribe this text

[Assistant] So that often is, in some ways, something we can think of.


[User] Please transcribe this text

[Assistant] In the immune cell, distinguish an invasive versus a non-invasive microbe.


[User] Please transcribe this text

[Assistant] Yeah, what if you took receptors and you had some of them on the cell surface?


[User] Please transcribe this text

[Assistant] Those would detect things that were outside, but not things that were inside yourself.


[User] Please transcribe this text

[Assistant] And what if you had some other receptors that were inside the cell?


[User] Please transcribe this text

[Assistant] We'd touch the ones on the outside of the cell, but not the ones on the inside of the cell, because it didn't try to get in. A microbe that was invasive?


[User] Please transcribe this text

[Assistant] Would be hitting both those outside receptors, but it would also hit the inside receptors. So you could imagine a way that


[User] Please transcribe this text

[Assistant] We could distinguish the invasive microbe versus not based on do we just detect it outside of cells or do we start to detect its products inside of cells too. Oh my gosh. Way back.


[User] Please transcribe this text

[Assistant] In the first couple weeks of class, when we talked about PRRs,


[User] Please transcribe this text

[Assistant] I told you that some were on the cell surface and some were inside of cells.


[User] Please transcribe this text

[Assistant] This is showing you that with toll-like receptors as an example, but there are others that are inside of cells like some of the different groups I told you about previously.


[User] Please transcribe this text

[Assistant] So right now we think that at least part of this has to do with whether the PRRs on the cell surface get triggered versus whether PRRs inside the cell get triggered.


[User] Please transcribe this text

[Assistant] In that macrophage in the GI tract. So that that


[User] Please transcribe this text

[Assistant] Genetics and other issues that may change the amount of mucus, the thickness of the mucus layer.


[User] Please transcribe this text

[Assistant] In terms of whether or not, uhm, those microbes can actually start to interact with those cells. Uhm, and so one of the things you'll notice is that one of the proteins that is involved in mucus is MyT88, which is part of toll-like receptor signaling.


[User] Please transcribe this text

[Assistant] And so the PRRs may be helping to control what's going on with the mucus, but also helping to allow the cell to know is this an invasive organism or is this an organism that is less problematic.


[User] Please transcribe this text

[Assistant] Uhm, and then of course we have the anatomical specializations to just flush stuff out.


[User] Please transcribe this text

[Assistant] Uhm, when we have a microbe uhm, that is causing a problem


[User] Please transcribe this text

[Assistant] There are, uh, we also can think about how exactly we deal with those microbes. So how do we deal with the fact that your GI tract is very likely to be in contact with pathogens from time to time, since it's in contact with microbes?


[User] Please transcribe this text

[Assistant] As we said, it would be pretty bad if you had damage to your GI tract, because then you couldn't absorb food and then you would not feel good. Or as Dunaway would say, then you get dead. Right?


[User] Please transcribe this text

[Assistant] So if you actually had a pathogen there, that would be bad.


[User] Please transcribe this text

[Assistant] You don't want to have so much inflammation there.


[User] Please transcribe this text

[Assistant] You also don't wanna like, let that pathogen go for a really long time.


[User] Please transcribe this text

[Assistant] And so one of the things that will happen when you try to make an adaptive response,


[User] Please transcribe this text

[Assistant] Is that we might cut out some of the steps.


[User] Please transcribe this text

[Assistant] That we talked about with the traditional adaptive response. Remember how we talked about what things take so long in making an adaptive immune response?


[User] Please transcribe this text

[Assistant] In the mucosal tissues, we cut out some of those steps.


[User] Please transcribe this text

[Assistant] To try to make that response not take as long and try to get rid of the microbes quicker in the situation where we need to get rid of those microbes.


[User] Please transcribe this text

[Assistant] One of the big things that took so long, one of the events that was part of our delay, was trafficking.


[User] Please transcribe this text

[Assistant] Trying to move all the stuff to the lymph nodes and to the lymphoid organ, right?


[User] Please transcribe this text

[Assistant] Well, that's why anatomically we put lymphoid tissue there.


[User] Please transcribe this text

[Assistant] So we don't really have to move things as far. We have a lymphoid organ right there.


[User] Please transcribe this text

[Assistant] Maybe first in a secondary lymphoid organ that's in a mucosal tissue like a pyre's patch.


[User] Please transcribe this text

[Assistant] That T-SAL is going to get specific types of


[User] Please transcribe this text

[Assistant] And that T cell or B cell is going to say, you know what, I'm not going to circulate through the whole body. I think I'm just going to live in the intestine. So that if my bacteria ever comes back.


[User] Please transcribe this text

[Assistant] We don't have to worry about the timing of moving this T cell back and forth. This T cell is just going to live in the intestine forever. Or live by the intestine forever.


[User] Please transcribe this text

[Assistant] Uhm, and so we see a lot of T cells that will specifically traffic to mucosal sites. And if you look at


[User] Please transcribe this text

[Assistant] The walls of the tissues in mucosal sites, you see that there are a lot of immune cells that live there.


[User] Please transcribe this text

[Assistant] And so we find effector T cells that just hang out in mucosal sites.


[User] Please transcribe this text

[Assistant] So that we can cut out some of the delays of trafficking and allow those cells to


[User] Please transcribe this text

[Assistant] Get rid of microbes ASAP if those problematic microbes are there. Uhm, you can see, uhm,


[User] Please transcribe this text

[Assistant] This in, this red layer is basically the wall of the intestine, the intestinal epithelium. And you can see that there are actually lymphocytes that live in the wall of the intestine.


[User] Please transcribe this text

[Assistant] As well as lymphocytes that, uh, live sort of in that intestinal tissue.


[User] Please transcribe this text

[Assistant] We call many of those cells that live in the wall of the intestine


[User] Please transcribe this text

[Assistant] Intraepithelial lymphocytes, or IELs.


[User] Please transcribe this text

[Assistant] So you can see they are living right in the walls of this tissue.


[User] Please transcribe this text

[Assistant] Uhm, some of them are like ILCs, the innate, uh, lymphoid cells. Some of them also have some weird kinds of TCRs like gamma delta cells or other kinds of weird T cells.


[User] Please transcribe this text

[Assistant] And they basically live in this organ and you can find similar types of T cells in other barrier organs that are ready to get rid of microbes.


[User] Please transcribe this text

[Assistant] Right away, instead of waiting for some of the parts of the delay of the, um, production of an adaptive immune response.


[User] Please transcribe this text

[Assistant] Uhm, you can see the IELs in cartoon form on the left side of this figure and you can actually see cells in the midst of the intestinal wall in an electron microscopy image as well.


[User] Please transcribe this text

[Assistant] Uhm, IELs are not particularly well understood.


[User] Please transcribe this text

[Assistant] Like, 5% of your T cells are IELs, and 95% of your T cells are IELs.


[User] Please transcribe this text

[Assistant] Both of those I think are probably wrong. Both a little extreme. But, in any case.


[User] Please transcribe this text

[Assistant] We don't know a lot about them. There's a lot of things we have not studied well about these cells.


[User] Please transcribe this text

[Assistant] Why might it be hard to study these cells? Let's imagine that you feel 100% fine in your GI tract today.


[User] Please transcribe this text

[Assistant] And I would like, and we would like to say, well okay, so what do your IELTS look like when you're perfectly, totally, 100% healthy?


[User] Please transcribe this text

[Assistant] Cause then we could compare that to what they look like in disease, right?


[User] Please transcribe this text

[Assistant] So how would we do an experiment to look at your IELTS when you are 100% perfectly GI tract healthy?


[User] Please transcribe this text

[Assistant] How am I going to study these T cells to just have a list of what they look like when you're healthy?


[User] Please transcribe this text

[Assistant] Is to actually cut out the wall of the intestine and pull those cells out.


[User] Please transcribe this text

[Assistant] A, it's gonna be hard to pull them out. And some of them are gonna die. So you're gonna get like three cells if you do this. You're gonna get very few cells.


[User] Please transcribe this text

[Assistant] B, if you feel 100% totally fine,


[User] Please transcribe this text

[Assistant] Would you like to give me some of the wall of your intestine today?


[User] Please transcribe this text

[Assistant] And have me grind it up in a tube to try to find three cells? Does that sound like a great idea? Not really.


[User] Please transcribe this text

[Assistant] It's very invasive if we actually want to get them out of an individual. So we know some stuff about mice, cause like we can do that experiment on mice a lot easier than getting a person to be like, oh sure, have my intestine.


[User] Please transcribe this text

[Assistant] And in many cases, the times where we get people's intestines.


[User] Please transcribe this text

[Assistant] Are when people are sick and they're willing to give us a biopsy to actually see what's up. And so we know much more about what these look like in, say,


[User] Please transcribe this text

[Assistant] In some cases, colitis patients actually have to have part of their intestine removed.


[User] Please transcribe this text

[Assistant] Uhm, as part of trading their colitis. Treats their colitis and then we have the intestinal. We can look at the IELs and see what IELs look like in the colitis, in a colitis patient. But we, we have a really hard time looking at a regular patient to see what they look like for comparison.


[User] Please transcribe this text

[Assistant] Uhm, and does, I mean this, you could imagine this would involve like a colonoscopy and this would involve like the biopsy and stuff and does


[User] Please transcribe this text

[Assistant] Do the IELTS get changed when you start sticking organs in places?


[User] Please transcribe this text

[Assistant] Like, you can imagine that this is going to be a really difficult thing to actually study when you start to think about the anatomy of all of this.


[User] Please transcribe this text

[Assistant] And this is one of the reasons why, like I said, I've seen super different numbers for even how many of them there are.


[User] Please transcribe this text

[Assistant] Uhm, the one kind of last thing we should just point out is who cares? Why do we even care about this?


[User] Please transcribe this text

[Assistant] Is probab- is in many cases probably pretty physiologic and pre-


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[Assistant] You know, important for what's really going on if we wanna understand health and disease.


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[Assistant] Even though these are very challenging things to study and things that we are only now realizing that maybe we shouldn't just look at the blood.


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[Assistant] Maybe we should, maybe we need to look at some of these more challenging to study tissues.


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[Assistant] Class on Monday is always an interesting place in the semester or the topic on Monday is a sort of interesting spot in the semester. Uhm, I think of Monday as our last sort of basic immunology class and then everything after that is being clinical.


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[Assistant] Many of the students think of Monday as the first clinical lecture. So Monday is sort of like on the border between clinical and not, because I'm going to talk about peripheral tolerance.


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[Assistant] Uhm, which segues us into how peripheral tolerance gets messed up and autoimmunity. So I'm going to largely talk about the peripheral tolerance mechanisms on Monday and then


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[Assistant] Start moving into autoimmunity and by Wednesday it will be totally about autoimmunity. Remember your clinical assignment is due on Monday and it's on Moodle. Please let me know if you have questions and I hope that you have a great weekend.


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[Assistant] You're the most done with life.


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[Assistant] God damn it, wrapping up right now!


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[Assistant] Whether you're tuning hyperparameters or trying out different ideas for learning algorithms or just trying out different options for building your machine learning system, you'll find that your progress will be much faster if you have a single real number evaluation metric that lets you quickly tell if the new thing you just tried is working better or worse than your last idea.


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[Assistant] So when teams are starting on the machine learning project, I often recommend that you set up a single real number evaluation metric for your problem. Let's look at an example.


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[Assistant] You've heard me say before that applying machine learning is a very empirical process where you often have an idea, code it up, run an experiment to see how well it did, and then use the outcome of the experiment to refine your ideas and then keep going around this loop as you keep on improving your algorithm.


[User] Please transcribe this text

[Assistant] So let's say for your CAD classifier, you have previously built some classifier A, and by changing the hyperparameters or the training sets or some other thing, you've now trained a new classifier B.


[User] Please transcribe this text

[Assistant] So one reasonable way to evaluate the performance of your classifiers is to look at this precision and recall.


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[Assistant] The exact details of what's precision and recall don't matter too much for this example, but briefly, the definition of precision is of the examples that your classifier recognized as cats.