T Cell Development – Selection and More Selection

For Immunology Chapter 9 Day 2

1. After jumping through the hoops necessary to make functional α and β chains of their TCRs, ~95% of CD4+CD8+ (DP) thymocytes die from what? Because of this fact, why are quotes necessary when someone says thymocytes “learn” or are “educated” in the thymus?
2. What stages of T-cell development (DN1, DN2, DN3, DN4, DP, CD4 SP, or CD8 SP) would be affected in mice with the following genetic modifications? Justify your answers.
   1. Mice that do not express MHC class II
   2. Mice that do not express AIRE.
   3. Mice that do not express the TCRα chain.
3. You stain thymocytes with PE-conjugated anti-CD3 and FITC-conjugated anti-TCRβ. Most cells stain with both.  However, you find a proportion of cells that stain with neither antibody.  You also find a small population that stain with anti-CD3, but not with anti-TCRβ.  What thymocyte populations might each of these populations represent?
4. The overview figure for this chapter (9-1) shows that “Positive and negative selection” occurs in the thymic cortex and that “Negative selection” occurs in the thymic medulla. Compare and contrast the two forms of negative selection.  (Hint: In which negative selection step does “AIRE” play a role?)
5. Describe the experiments where Hogquist and colleagues made use of 1) the fetal thymic organ culture (FTOC) system and 2) mice deficient in TAP-1. From these experiments, what is the estimated difference in binding affinity between cells that are negatively vs. positively selected?