Revisions in the intro

presentation.mkdn

@@ -48,31 +48,47 @@ A graft is categorized based on the relationship between donor and recipient:
 
 :::
 
-## Allograft rejection is a major long-term problem
+## Recipient T-cells reject allogenic MHCs
 
-![Kidney allograft survival rates in children by transplant year[^kim-marks]](graphics/presentation/kidney-graft-survival.png){ height=65% }
+::::: {.columns}
 
-[^kim-marks]:[ Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
+::: {.column width="75%"}
 
-## Graft rejection is an adaptive immune response
+:::: incremental
 
-<!-- TODO: Need a graphic for this -->
+<!-- Vertical alignment hacks -->
 
-::: incremental
+\rule{\linewidth}{0pt}
+
+\vspace*{36pt}
 
-* The host's adaptive immune system identifies and attacks cells
-  bearing non-self antigens
+* TCR binds to both antigen *and* MHC surface \vspace{10pt}
 
-* An allograft contains differnet genetic variants from the host,
-  resulting in protein-coding differences
+* HLA genes encoding MHC proteins are highly polymorphic \vspace{10pt}
 
-* Left unchecked, the host immune system eventually notices these
-  alloantigens and begins attacking (rejecting) the graft
+* Variants in donor MHC can trigger the same T-cell response as a
+  foreign antigen
 
-* Rejection is the major long-term threat to organ allografts
+\vspace*{36pt}
+
+\rule{\linewidth}{0pt}
+
+::::
 
 :::
 
+::: {.column width="25%"}
+![\footnotesize Janeway's Immunobio- logy (2012), Fig. 9.19](graphics/presentation/janeway-fig9.19-TCR.png){ height=70% }
+:::
+
+:::::
+
+## Allograft rejection is a major long-term problem
+
+![Kidney allograft survival rates in children by transplant year[^kim-marks]](graphics/presentation/kidney-graft-survival.png){ height=65% }
+
+[^kim-marks]:[ Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
+
 ## Rejection is treated with immune suppressive drugs
 
 <!-- TODO: Need a graphic, or maybe a table of common drugs +
@@ -80,19 +96,19 @@ mechanisms, or a diagram for periodic checking. -->
 
 ::: incremental
 
-* To prevent rejection, a graft recipient must take immune suppressive
-  drugs for the rest of their life
+* Graft recipient must take immune suppressive drugs indefinitely
 
-* The graft is periodically checked for signs of rejection, and immune
-  suppression dosage is adjusted accordingly
+* Graft is monitored for rejection and dosage adjusted over time
+
+* Immune suppression is a delicate balance: too much and too little
+  are both problematic.
 
-* Immune suppression is a delicate balance: too much leads to immune
-  compromise; too little leads to rejection.
-  
 :::
 
 ## My thesis topics
 
+<!-- Needs revision -->
+
 ### Topic 1: Immune memory
 Genome-wide epigenetic analysis of H3K4 and H3K27 methylation in naïve
 and memory $\mathsf{CD4}^{+}$ T-cell activation

slides-notes.org

@@ -49,18 +49,18 @@
 - [X] Slide with organ bar chart: Adjust title to 'Organ donation
   statistics for the USA in 2018', remove from bottom and make image
   itself bigger
-- [ ] What's the connection between organ transplant, graft rejection,
+- [X] What's the connection between organ transplant, graft rejection,
   and immune response? Make that clear in the transition between
   slides. We now want to know about graft rejection because.... why?
   what about what we just learned with the organ transplants directly
   connects?
-- [ ] Condense these bullet points. The previous set of bullet points
+- [X] Condense these bullet points. The previous set of bullet points
   is a perfect example of spacing and length readable in a short
   amount of time for the audience
-- [ ] More time on allografting and less time on graft rejection. What
+- [X] More time on allografting and less time on graft rejection. What
   is it? How does it work? Provide a brief example/image right before
   the chart
-- [ ] Rejection and immmuno suppressive drugs -- this is a great
+- [X] Rejection and immmuno suppressive drugs -- this is a great
   transition (well explained) but again the bullet points need to be
   condensed. Bring in an image with these as well to give the audience
   'a visual break' before you intro your topics