ADD a bunch of figures

tex/thesis.tex

@@ -61,6 +61,7 @@
 \newacronym{bca}{BCA}{bicinchoninic acid assay}
 \newacronym{bsa}{BSA}{bovine serum albumin}
 \newacronym{stp}{STP}{streptavidin}
+\newacronym{stppe}{STP-PE}{streptavidin-phycoerythrin}
 \newacronym{snb}{SNB}{sulfo-nhs-biotin}
 \newacronym{cug}{CuG}{Cultispher G}
 \newacronym{cus}{CuS}{Cultispher S}
@@ -132,6 +133,8 @@
 
 \newcommand{\inlinecode}{\texttt}
 
+\newcommand{\subcap}[2]{\subref{#1}) #2}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % ditto for environments
 
@@ -662,6 +665,16 @@ better retention of memory phenotype compared to current bead-based methods.
 \section{methods}
 \subsection{dms functionalization}
 
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_flowchart.png}
+
+  \endgroup
+  \caption[\gls{dms} Flowchart]{Overview of \gls{dms} manufacturing process.}
+  \label{fig:dms_flowchart}
+\end{figure*}
+
 Gelatin microcarriers (\gls{cus} or \gls{cug}, GE Healthcare, DG-2001-OO and
 DG-0001-OO) were suspended at \SI{20}{\mg\per\ml} in 1X \gls{pbs} and
 autoclaved. All subsequent steps were done aseptically, and all reactions were
@@ -781,7 +794,7 @@ threshold. Media glucose was measured using a \product{GlucCell glucose
 % added to a final concentration of \SI{50}{\ug\per\ml} during media addition.
 
 Cells on the \glspl{dms} were visualized by adding \SI{0.5}{\ul}
-\product{\gls{stp}-\gls{pe}}{\bl}{405204} and \SI{2}{ul}
+\product{\gls{stppe}}{\bl}{405204} and \SI{2}{ul}
 \product{\acd{45}-\gls{af647}}{\bl}{368538}, incubating for \SI{1}{\hour}, and
 imaging on a spinning disk confocal microscope.
 
@@ -868,21 +881,113 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
 
 \subsection{DMSs can be fabricated in a controlled manner}
 
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_coating.png}
+  \phantomsubcaption\label{fig:stp_carrier_fitc}
+  \phantomsubcaption\label{fig:mab_carrier_fitc}
+  \phantomsubcaption\label{fig:cug_vs_cus}
+  \phantomsubcaption\label{fig:biotin_coating}
+  \phantomsubcaption\label{fig:stp_coating}
+  \phantomsubcaption\label{fig:mab_coating}
+
+  \endgroup
+  \caption[\gls{dms} Coating]
+  {\gls{dms} functionalization results.
+    \subcap{fig:stp_carrier_fitc}{\gls{stp}-coated or uncoated \glspl{dms}
+      treated with biotin-FITC and imaged using a lightsheet microscope.}
+    \subcap{fig:mab_carrier_fitc}{\gls{mab}-coated or \gls{stp}-coated
+      \glspl{dms} treated with \anti{\gls{igg}} \glspl{mab} and imaged using a
+      lightsheet microscope.} \subcap{fig:cug_vs_cus}{Bound \gls{stp} surface
+      density on either \gls{cus} or \gls{cug} microcarriers. Surface density
+      was estimated using the properties in~\cref{tab:carrier_props}} Total
+    binding curve of \subcap{fig:biotin_coating}{biotin},
+    \subcap{fig:stp_coating}{\gls{stp}}, and
+    \subcap{fig:mab_coating}{\glspl{mab}} as a function of biotin added. }
+  \label{fig:dms_flowchart}
+\end{figure*}
+
+% TODO these caption titles suck
+% TODO combine this DOE figure into one interaction plot
 \begin{table}[!h] \centering
   \caption{Properties of the microcarriers used}
-  \label{tab:ci_treat}
+  \label{tab:carrier_props}
   \input{../tables/carrier_properties.tex}
 \end{table}
 
-% fabrication flow chart
+\begin{figure*}[ht!]
-% microcarrier properties
+  \begingroup
-% green carrier figure
+
-% quality control figure
+  \includegraphics{../figures/dms_qc.png}
-% DMS manufacturing timing figure
+  \phantomsubcaption\label{fig:dms_qc_doe}
+  \phantomsubcaption\label{fig:dms_qc_ph}
+  \phantomsubcaption\label{fig:dms_qc_washes}
+  \phantomsubcaption\label{fig:dms_snb_decay_curves}
+
+  \endgroup
+  \caption[\gls{dms} Quality Control]
+  {\gls{dms} quality control investigation and development
+    \subcap{fig:dms_qc_doe}{\gls{doe} investigating the effect of initial mass
+      of microcarriers, reaction temperature, and biotin concentration on
+      biotin attachment.}
+    \subcap{fig:dms_qc_ph}{Effect of reaction ph on biotin attachment.}
+    \subcap{fig:dms_qc_washes}{effect of post-autoclave washing of the
+      microcarriers on biotin attachment.}
+    \subcap{fig:dms_snb_decay_curves}{Hydrolysis curves of \gls{snb} in
+      \gls{pbs} of differing pH.}
+    All statistical tests where p-values are noted are given by two-tailed t
+    tests.
+  }
+  \label{fig:dms_flowchart}
+\end{figure*}
+
+\begin{table}[!h] \centering
+  \caption{Properties of the microcarriers used}
+  \label{tab:carrier_props}
+  \input{../tables/carrier_properties.tex}
+\end{table}
+
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_timing.png}
+  \phantomsubcaption\label{fig:dms_biotin_rxn_mass}
+  \phantomsubcaption\label{fig:dms_biotin_rxn_frac}
+  \phantomsubcaption\label{fig:dms_stp_per_time}
+
+  \endgroup
+  \caption[\gls{dms} Reaction timing]
+  {Reaction kinetics for microcarrier functionalization.
+    \subcap{fig:dms_biotin_rxn_mass}{Biotin mass bound per time}
+    \subcap{fig:dms_biotin_rxn_frac}{Fraction of input biotin bound per time}
+    \subcap{fig:dms_stp_per_time}{\Gls{stp} bound per time.}
+  }
+  \label{fig:dms_flowchart}
+\end{figure*}
 
 \subsection{DMSs can efficiently expand T cells compared to beads}
 
-% cells growing on DMSs
+% TODO make sure the day on these is correct
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/cells_on_dms.png}
+  \phantomsubcaption\label{fig:dms_cells_phase}
+  \phantomsubcaption\label{fig:dms_cells_fluor}
+
+  \endgroup
+  \caption[\gls{dms} Reaction timing]
+  {Cells grow in tight clusters in and around functionalized \gls{dms}.
+    \subcap{fig:dms_cells_phase}{Phase-contrast image of T cells growing on
+      \glspl{dms} on day 7}
+    \subcap{fig:dms_cells_fluor}{Confocal images of T cells in varying z-planes
+      growing on \glspl{dms} on day 9. \Glspl{dms} were stained using
+      \gls{stppe} (red) and T cells were stained using \acd{45}-\gls{af647}.}
+  }
+  \label{fig:dms_flowchart}
+\end{figure*}
+
 % 3-donor expansion figure
 
 \subsection{DMSs lead to greater expansion and memory and CD4+ phenotypes}