About the Project
The growth of plants occurs through both cell division and expansion. The objective of this PhD project is to uncover the molecular pathways plant cells use to grow using a multidisciplinary approach (Bassel et al. 2012, Plant Cell).
Plant cell expansion is a mechanically-driven process that involves the co-ordination of increases in cellular turgor with the loosening of their rigid surrounding cells walls. While many genes involved in the modification of cell walls have been identified, it is not yet clear how these multi-gene families are regulated.
Seed germination is an ideal system to understand how changes in gene expression drive cell expansion. Following their development, seeds remain dormant in the soil and the cells within the plant embryo arrest their growth. During dormancy, genes involved in cell wall modification are not expressed. This system provides an opportunity to understand how individual factors drive plant cell growth through the targeted induction of cell wall modifying gene expression.
This PhD project will develop and analyse novel gene network models using new data types and link these predicted interactions with changes in 3D embryo cell shape. The student will learn how to generate networks, identify candidate genes driving cell expansion, and experimentally validate these hypotheses using a combination of molecular biology, generation of transgenic plants, plant physiology and computational quantitative analysis of 3D images.
Using a combination of genome-wide network analyses (Bassel et al, 2011 PNAS; Bassel et al. 2011, Plant Cell) and targeted molecular screens, key factors regulating plant cell wall modifying gene expression will be identified. Candidate genes will be functionally validated using transgenic molecular-based approaches.
The ability of these newly identified factors to drive plant cell expansion will be quantified using a newly developed quantitative 3D image analysis pipeline. High resolution 3D images of plant cells will be captured and changes in plant cell shape and size driven by the newly identified factors will be determined (Bassel et al. 2014, PNAS)
The final phase of the project will use the regulatory factors identified together with a synthetic biology approach to apply targeted modifications to the plant cell wall. This will be achieved through the computational design of novel molecular pathways, and can be used to both manipulate the growth of plants and also lead to novel technologies to enhance the efficiency in the production of cellulose-based biofuels.
Applicants should have a background in molecular biology and be willing to learn new computer software.
Given that seeds directly comprise 70% of the world’s calorie intake, and are the starting point for the vast majority of world agriculture, outputs of this project will have significant implications in terms of crop establishment and food security in addition to enhancing bioenergy production.
For more details please visit www.GeorgeBasselLab.com
Key experimental skills involved:
Molecular biology, confocal microscopy, plant growth analysis and transformation, computer analyses including quantitative 3D image analysis and gene functional network inference.
Please find additional funding text below. For further funding details, please see the ‘Funding’ section.
The School of Biosciences offers a number of UK Research Council (e.g. BBSRC, NERC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for research council studentships is 31 January each year.
Each year we also have a number of fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this scheme is also 31 January each year.
Funding Notes
All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students and encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).
The postgraduate funding database provides further information on funding opportunities available http://www.birmingham.ac.uk/postgraduate/funding/FundingFilter.aspx and further information is also available on the School of Biosciences website http://www.birmingham.ac.uk/schools/biosciences/courses/postgraduate/phd.aspx
References
Bassel GW, Stamm P, Mosca G, Barbier de Reuille P, Gibbs DJ, Winter R, Janka A, Holdsworth MJ, Smith RS (2014) Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo. Proc Natl Acad Sci U S A.
Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ (2011) Genome-wide network model capturing seed germination revealscoordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A. 108:9709-14
Bassel GW, Glaab E, Marquez J, Holdsworth MJ, Bacardit J. (2011) Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. The Plant Cell 23:3101-16.
Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I (2012) Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks. The Plant Cell 24(10):3859-3875