I submitted by PhD thesis entitled "Cell type specific transcriptomic analyses of immunity in Arabidopsis thaliana roots" in October 2018.

I performed the research for my thesis under the supervision of Dr Patrick Schäfer and Dr Sascha Ott at the School of Life Sciences as part of a Doctoral Training Programme (DTP): MIBTP (Midlands Integrative Biosciences Training Partnership).

Following my PhD, I am changing my research interests toward human immunology. I will be working with Professor Tao Dong and Dr Hashem Koohy investigating T cell receptors in a cancer immune therapy context at the Weatherall Institute for Molecular Medicine at the University of Oxford. I will be in this post until Autumn 2021, more details here.

My PhD research: Cell type specific transcriptomic analyses of immunity in Arabidopsis thaliana roots

Plant roots represent a complex organ consisting of different cell types with highly varied functions. Thus, the response of plant roots to environmental stresses, such as pathogen infection, require the concerted action of many cell-types. To understand stress resistance signalling in such a complex organ, cell type-specific transcriptomic studies are essential.

In this thesis, the transcriptomic response to immunity elicitation is examined at the resolution of tissues and individual cell types in two large scale RNA-seq experiments. Firstly, Fluorescence-Activated Cell Sorting combined with RNA-seq was used to produce the first high-resolution gene expression atlas of plant root immunity. The resulting data set encompassed the transcriptomes of three root cell types which had been treated by two immunity elicitors. Differential gene expression analysis newly revealed that both immunity elicitors induced a largely cell-type specific response with a comparatively small set of genes differentially expressed in all three cell types. This strong specificity indicates that cell identity is a strong driver of the transcriptomic immune response.

Secondly, gene expression in root tips was analysed using the single cell technique Drop-seq. Clustering methods were used to identify cells from three developmental stages and multiple cell types, and the immune responses in these tissues were characterised.

In an effort to interpret and predict immunity network regulation in different cell types, a novel tool entitled the Paired Motif Enrichment Tool (PMET) was developed to investigate gene regulation by combinatorial transcription factor groups. The tool identifies enriched pairs of known regulatory motifs within immune-responsive gene sets and revealed that each cell-type/immune response combination has a largely unique regulatory landscape. Furthermore, PMET has predicted new roles of transcription factors within immunity networks.

 

Non-academic interests:

I am involved with the Warwick Folk society, playing violin and piano in the university ceilidh band and running the dance club. I am also a keen ceilidh/barn dance caller working both with the university and outside of it.

Professional development MIBTP Training year

Mini-Project 1 (Jan-Mar 2015)

Supervisor: Dr George Bassel, School of Biosciences, University of Birmingham

Project: Graph theory as a tool to analyse patterning during embryo development in Arabidopsis thaliana

Mini-Project 2 (Jul-Sep 2015)

Supervisor: Dr Sascha Ott, Systems Biology, University of Warwick

Project: Developing the methods to investigate chromatin modifications in immune signalling in Arabidopsis thaliana

Professional Internship Placement (Apr-Jun 2015)

Host: Widening Patricipation and Outreach, University of Warwick.

This placement gave me insight into a wide range of outreach activities that take place at the University of Warwick. My responsibilities included:

• Planning and co-coordinating a 'Headstart' summer school in the School of Life Sciences
• Demonstrating for school groups at the Cheltenham Science Festival
• Developing a nature trail for 7-10 year olds, to both teach about ecosystems and introduce the concept of university to primary school children
• Rewriting a guide to Higher Education for Parents to be distributed by the Outreach department.

Charlotte Rich

Charlotte dot s dot rich at gmail dot com

C dot S dot Rich at warwick dot ac dot uk