From fa192d90ee567285005187133de01697bd7504e7 Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Thu, 29 Jul 2021 15:07:29 -0400
Subject: [PATCH] ADD results section for il2 curves

---
 tex/thesis.tex | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index 154331b..821ce76 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -2193,7 +2193,18 @@ Venn diagram from the venn R package.
 
 \subsection{T cells can be grown on DMSs with lower IL2 concentrations}
 
+Prior to the main experiments in this aim, we performed a preliminary experiment
+to assess the effect of lowering the \gls{il2} concentration on the T cells
+grown with either bead or \gls{dms}. One of the hypotheses for the \gls{dms}
+system was that the higher cell density would enable more efficient cross-talk
+between T cells. Since \gls{il2} is secreted by activated T cells themselves,
+T cells in the \gls{dms} system may need less or no \gls{il2} if this hypothesis
+were true.
+
+
 % TODO this plots proportions look dumb
+% TODO explain what the NLS lines are in b
+% TODO plot the differences in lower IL2 concentrations to better show this
 \begin{figure*}[ht!]
   \begingroup
 
@@ -2217,6 +2228,29 @@ Venn diagram from the venn R package.
   \label{fig:il2_mod}
 \end{figure*}
 
+% TODO the nls stuff is a bit iffy
+We varied the concentration of \gls{il2} from \SIrange{0}{100}{\IU\per\ml} and
+expanded T cells as described in \cref{sec:tcellculture}. T cells grown with
+either method expanded robustly as \gls{il2} concentration was increased
+(\cref{fig:il2_mod_timecourse}). Surprisingly, neither the bead or the \gls{dms}
+group expanded at all with \SI{0}{\IU\per\ml} \gls{il2}. When examining the
+endpoint fold change after \SI{14}{\day}, we observe that the difference between
+the bead and \gls{dms} appears to be greater at lower \gls{il2} concentrations
+(\cref{fig:il2_mod_total}). This is further supported by fitting a non-linear
+least squares equation to the data following a hyperbolic curve (which should be
+a plausible model given that this curve describes receptor-ligand kinetics,
+which we can assume \gls{il2} to follow). Furthermore, the same trend can be
+seen when only examining the \ptmem{} cell expansion at day 14
+(\cref{fig:il2_mod_mem}). In this case, the \ptmemp{} of the T cells seemed to
+be relatively close at higher \gls{il2} concentrations, but separated further at
+lower concentrations (\cref{fig:il2_mod_flow})
+
+Taken together, these data do not support the hypothesis that the \gls{dms}
+system does not need \gls{il2} at all; however, it appears to have a modest
+advantage at lower \gls{il2} concentrations compared to beads. For this reason,
+we decided to investigate the lower range of \gls{il2} concentrations starting
+at \SI{10}{\IU\per\ml} throughout the remainder of this aim.
+
 % TODO this is not consistent with the next section since the responses are
 % different
 \subsection{DOE shows optimal conditions for expanded potent T cells}