3D Organ design in plants

Project Outline

Across evolutionary history, multicellularity has arisen multiple times independently. By having cells co-operate together, multicellular organisms developed adaptive advantages over their unicellular counterparts. The manner with which cells organize themselves to give organs these advantages is not well understood.

This project seeks to understand how cells are organized within the organs of plants. Unlike in animal systems, plant cells do not move relative to one another within organs. This is a key advantage as the associations between cells do not change over time, facilitating the analysis of their relationships.

Using a combination of 3D confocal laser microscopy and computer image analysis, the way cells are connected to one another in plants will be captured. These data will in turn be analysed to reveal the organizing principles of multicellular life. The project will make use of both primitive land plants and more complex plant forms including crop species. In this way the changes in cellular organization that occurred over the course of evolution across to our current agricultural species will be determined.

The project will further develop approaches to re-engineer cell organization in plant organs to create novel plant organs using synthetic biology approaches.

Applicants need no prior experience, just a willingness to learn.

Techniques

Confocal microscopy, plant growth, 3D computational image analysis, mathematical science.

Improving plant establishment in Bambara groundnut using CRISPR/Cas9

Project Outline

The Bambara groundnut (Vigna subterranea (L.) Verdc.), an underused African legume, has the potential to contribute to better food and nutrition security. It also offers solutions for maintaining environmental sustainability and ensuring fair access to affordable food, while increasing the crop diversity humans rely upon.

A major issue limiting the production of Bambara is uneven seed germination. Seeds retain residual dormancy such that they do not germinate uniformly or at all. This presents a formidable obstacle towards the cultivation of this crop, and realizing the full food security potential it holds. The lack of reliability in crop establishment limits the adoption of this nutritious species by farmers.

This project will develop and implement strategies to improve the germination properties of Bambara groundnut. This will be achieved through a combination of gene expression analyses using next-generation sequencing and CRISPR/Cas9. Using a candidate gene approach, the expression of key genes will be modulated using CRISPR as guided by the gene expression analysis. In this way, new varieties of Bambara can be created which have an improved germination profile, which can both leader to a greater adoption of the crop combined with greater yields.

This will contribute towards wider global food security and the diversification of agriculture through the consumption of underutilized crops.

Techniques

Gene expression analysis, tissue culture, gene editing using CRISPR and physiological analyses of seed germination.

Integration of environmental signals in plants

Project Outline

Plants use a diversity of signals from the environment to make decisions during their life cycle. This project will focus on understanding how multiple signals from the environment are integrated to control seed dormancy. This trait determines where and when plants are established, and enabling their movement through time and space.

Following their development, seeds remain dormant in the soil. Here they receive a variety of cues from their environment, including light temperature and nutrients, which are used to inform their decision when to germinate. This represents a system where multiple inputs (light, temperature, nutrients) converge into a single output (dormancy/germination). This process is not unlike the decision of a student to pursue this project, whereby multiple factors are considered before making a single yes/no decision (Bassel (2016) Trends in Plant Science). Understanding this complex logic in plants remains enigmatic.

This PhD project will identify molecular pathways used by seeds to integrate signals from the environment. The student will identify and characterize the molecular factors which directly regulate these targets through the analysis of both genome-wide network models (Bassel et al, 2011 PNAS; Bassel et al. 2011, Plant Cell) and targeted molecular screens (Bassel et al, 2012, Plant Cell).

The student will learn how to generate gene regulatory networks to identify candidate genes, and experimentally validate these hypotheses using a combination of molecular biology, bioinformatics, generation of transgenic plants, plant physiology and computational approaches.

The final phase of the project will use identified signal integration factors and a synthetic biology approach to re-engineer seed responses to the environment. These pathways will be “rewired” such that their behaviour is altered in targeted ways. The development of this technology is of critical importance in light of the need for food security during rapid climate change.

Seeds are the direct source of 70% of the world's calorie intake, and are the starting point for the vast majority of world agriculture. The significance of this this project lies with the enhancement of crop establishment and food security.

Applicants need no prior experience, just a willingness to learn.

Techniques

Molecular biology, plant growth analysis and transformation, computer analyses of gene expression and network design.

Mapping 3D communication networks in plants

Project Outline

The cytoplasm of plant cells is connected through specialized channels called plasmodesmata. These provide a major route for cell-to-cell communication in plants, and control a wide range of developmental processes.

The mechanisms which control plasmodesmata opening and closing are being uncovered, definig how cells control their communication. Much less is known about how they are distributed across the interfaces between cells in plant tissues

Using a combination of 3D confocal laser microscopy and computer image analysis, the distribution of plasmodesmata will be captured. These data will in turn be analysed to reveal the organizing principles of multicellular life and communication between their cells. The project will make cutting edge molecular, imaging and computational tools in both model and crop species to understand the relationship between plant cell communication and organization.

Applicants need no prior experience, just a willingness to learn.

Techniques

Confocal microscopy, plant growth, 3D computational image analysis, mathematical science.