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\begin{document}

\title{Undergraduate project 1: path to dormancy}



\author[1]{Daphne}%
\affil[1]{Affiliation not available}%


\vspace{-1em}



  
  \date{May 08, 2024}


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\section*{Background and motivation}

{\label{489918}}

Many plants use the change in day length as an indicator of the change
in seasons.~ Arabidopsis adjusts its phenotype in response to day length
through a regulatory network centred on a number of photoperiodic genes,
including FT and CO, whose expression levels depend both on the time of
day and the season.~ ~Previously, Nagano et al collected RNA-seq data
(i) weekly for two years and (ii) every two hours for two days in each
equinox and solstice, from~\emph{Arabidopsis halleri
(\url{https://www.nature.com/articles/s41477-018-0338-z?WT.feed\_name=subjects\_plant-sciences})}.~
Using this data, we can show that many seasonal fluctuations in gene
expression are due to seasonal phase shifts in diurnal gene expression
patterns.~ This means that an experiment would reveal~\emph{opposite
patterns in seasonal fluctuations depending on the time of day samples
are collected:}

\par\null\par\null\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Figure-season-2D/Figure-season-2D}
\caption{{The columns show the box-plots of gene expression when samples are
exclusively collected at 4am,~ 12pm (noon) and 8pm, respectively.~ The
rows show the gene expression values for LHY, COL9, and AST12,
respectively.~ Gene expression is in terms of TPM.~ Note that there are
different y-scales-- but the point is that if you only sampled at that
time point, you would have no idea that your results were time-of-day
dependent.
{\label{110166}}%
}}
\end{center}
\end{figure}

~

And this is true for almost all of the genes that are both circadian and
seasonal.~ In particular, we think that the `odd season out' is winter,
where it looks like there is not a very substantial circadian cycle of
gene expression, possibly caused by winter dormancy:

\par\null\par\null\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Figure-season-1B/Figure-season-1B}
\caption{{(Note: Rows are samples, columns are genes, values are z-scores-- I
don't know why the labels disappeared when I converted it from a pdf to
png\ldots{}need to fix)
{\label{396140}}%
}}
\end{center}
\end{figure}

\par\null

You will investigate how gene expression transitions from autumn to
winter.~ For instance, we don't know if there is a certain time point
that is a `switch' or whether the transition is smooth.~ We also don't
know whether all genes transition into winter dormancy at once or
whether they do so in multiple waves.~ Also, are there a core set of
genes that continue to cycle during winter dormancy?~ Finally, a similar
analysis can be performed about moving out of winter dormancy into
spring and summer.~~

\section*{}

{\label{367083}}

\section*{Research aims and questions}

{\label{718314}}\par\null

\textbf{Main aim}: to describe the path to winter dormancy in
\emph{Arabidopsis halleri}

\par\null

Questions to start with:

\begin{itemize}
\tightlist
\item
  How does gene expression change for diurnal genes during the autumn to
  winter transition and are there groups of genes that behave the same
  way?~ How about in the winter to spring transition?~ Are there
  groupings of genes (clusters) the same in both cases?~~
\item
  Instead of doing the above analysis on a set of genes in which we
  observe circadian cycles, how about we do it in genes that are
  homologous to Arabidopsis thaliana genes that exhibit circadian
  cycles?~ Or that have GO terms associated with photoperiod in
  Arabidopsis thaliana?
\item
  Is there a relationship between the
\end{itemize}

\par\null

\section*{Approaches}

{\label{454734}}

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