My name is Charlotte Rich and I am a second year PhD student studying in the School of Life Sciences as part of a Doctoral Training Programme (DTP): MIBTP (Midlands Integrative Biosciences Training Partnership).
My research title: Using cell type-specific transcriptomics to understand immune responses in Arabidopsis thaliana roots
Each year crop losses due to pathogen attack are devastating worldwide, and so one of the most important aims of crop science is to enhance plant immunity to reduce crop losses. However, immune activation in plants inhibits growth and development. In order to reduce crop losses without adversely affecting crop yields, we must deconstruct immune and growth responses on a cell-type specific level. This immunity-triggered growth inhibition is demonstrated in Arabidopsis thaliana roots after treatment by immunity elicitors such as flg22 (the active epitope of bacterial flagellin) and Pep1 (an endogenous ‘danger’ peptide). However, by pre-inoculating these roots with the mutualistic fungus Piriformospora indica, we are able to rescue the growth inhibition phenotype caused by flg22 but by Pep1 implying that there are multiple pathways inducing this growth inhibition. Additionally, since roots have been shown to respond to flg22 in a cell type-specific manner, we aim to determine how different cell types contribute to the phenotypic effects using cell-type specific RNA-seq. We inoculated the roots of fluorescent cell-type marker lines with Piriformospora indica and after 3 days treated with either flg22 or Pep1. We then used FACS to isolate 3 individual cell-types prior to RNAseq.
My PhD project is to analyse this RNAseq data and to establish first whether different cell-types play different roles within the Arabidopsis root and secondly to understand the differences between flg22 and Pep1 stress signalling by examining the differences between the datasets inoculated with P. indica and the control inoculated data.
Other research interests: I have recently begun a second project (supervised by Miriam Gifford) to look for a key regulator of nodulation in Medicago trunculata using motif analysis of nodulation-induced genes.
Other non-academic interests: I am heavily 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 as a
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.
C dot S dot Rich at warwick dot ac dot uk