00-preface.Rmd

 \phantomsection
 \pdfbookmark[0]{Title Page}{title}
  <!-- Title, name and date -->
- \title{\LARGE {\bf My awesome thesis dissertaion title}\\
+ \title{\LARGE \textbf {Investigation of the selective toxicity of neonicotinoids using the nematode worm \textit {\textbf {Caenorhabditis elegans}}}\\
   \vspace*{6mm}}
  \author{Monika Kudelska}
 \maketitle

05-discussion.Rmd

-# Discussion {#discussion}
-
-Discussion chapter.
\ No newline at end of file

21-appendix-a.Rmd

-# Title of appendix
+# Pharmacophore of the nicotinic acetylcholine receptor 
+
+\newpage
+
+```{r echo=FALSE, fig.pos='H', fig.align='center', out.width="70%"}
+knitr::include_graphics("fig/appendix/seq_align_1a.png")
+```
+
+(ref:pharacophore-seq) Sequence alignment of the binding pocket of the ligand binding protein and nicotinic acetylcholine receptors. Amino acid sequences from the principal (a) and complementary (b) binding site loops, which form the ligand binding pocket. Residues important for agonist binding are highlighted and color coded as in Figure \@ref(fig:binding-pocket-label). Numbering corresponds to the sequence of the great pond snail acetylcholine binding protein (AChBP). Alignment was generated with MUSCLE [@edgar2004]. Abbreviations used: Ls - *Lymnaela stagnalis* (great pond snail), Am- *Apis mellifera* (honeybee), Mz- *Myzus persicae* (peach aphid), Hs- *Homo sapiens* (human), Gg- *Gallus gallus* (chicken), Ce - *C. elegans*.
+
+```{r pharacophore-seq-label, fig.cap="(ref:pharacophore-seq)", fig.scap="Sequence alignment of the ligand binding pocket of the AchBPs and nAChRs.", fig.align='center', echo=FALSE, fig.pos='H'}
+knitr::include_graphics("fig/appendix/seq_align_1b.png")
+```
 
-First appendix

Analysis/Data/Exported/24_hrs_assay/Avoidance/% worms present.csv

+Cond,%_on_plate,%_on_plate,%_on_plate,%_on_plate,%_on_plate,%_on_plate
+Nicotine 0,100,100,100,100,100,100
+ Nicotine 0.5,100,100,90,100,,
+Nicotine 1,100,100,87,,,
+Nicotine 10,66.66,100,100,75,,
+Nicotine 25,0,25,70,25,,
+Nicotine 50,0,50,,,,
+Nicotine 100,0,25,,,,