Coming from the biological sciences background I had very little bioinformatics experience before the start of the project. I graduated from a 4 year integrated masters degree MBiolSci Biochemistry and Genetics at the University of Sheffield with First Class and decided to stay for my PhD project at the same university. After familiarizing myself with programming and coding, I now enjoy learning and writing in R and Python. Upon successful completion of my PhD I plan to search for a job that combines biology and IT the same way my PhD does.
Light is an extremely important resource to plants. Not only it is necessary for photosynthesis and thus nutrient production, but it also serves as a complex and detailed signal, informing the plant about its environment and driving developmental changes. It has been determined that almost one-third of the whole Arabidopsis genome is regulated by light and affect as many as 26 different cellular pathways (Ma et al., 2001). Whole seedling and leaf extracts are routinely investigated in the microarray or RNA sequencing experiments to provide an insight into the changing levels of transcription of many genes in response to light.
However, plants are complex organisms with many specialised tissues and organs, which have been shown to express unique patterns of gene expression (Bruex et al., 2012, Pillitteri et al., 2011). In 2014 it was shown that whole leaf extract primarily consists of mesophyll tissues (~80%) and the overall gene expression patterns resemble that of the mesophyll (Endo et al., 2014). This poses questions on the extent of the differences between light signalling gene expression in various organs and tissues as well as how much of the tissue or organ specific information we lose when looking at the whole seedlings or leaf extracts.
In my work, I show that many light signalling genes exhibit differential expression between at least two different organs in Arabidopsis thaliana. I further test the behaviour of the tissue specific light signalling network in red/far-red light receptor mutants, which express the receptor only in the epidermal tissue or the mesophyll. This investigation reveals the fundamental importance of the epithelial tissue in light-driven inter-tissue communication, necessary for the correct functioning of a developing seedling and its ability to respond to changing light stimulus.