Phytocomp - new computing tools for plant science

We are a group of collaborators from the Schools of Computing and Civil Engineering at the University of Dundee, the Department of Plant Sciences at the University of Cambridge, and the Environment-Plant Interactions Programme at SCRI in Dundee.   

We are developing a series of computational and modelling tools for use in plant science research, with particular emphasis on Image Analysis. If you are interested in using any of the tools, please email the contact listed at the bottom of the relevant page.

Who we are: Stephen McKenna, Glyn Bengough, Tracy Valentine, Jim Haseloff, Lionel Dupuy, Fraser Bransby. Our research interests range from computer vision and modelling through to root growth and development, and bioengineering.

Acknowledgements

Funding from BBSRC. The SCRI receives grant-in-aid from the Scottish Government Rural and Environment Research and 
Analysis Directorate.

Synthetic Biology and engineering of plant systems.

Synthetic Biology is an emerging field that employs engineering principles for constructing genetic systems. The approach is based on the use of well characterised and reusable components, and numerical models for the design of biological circuits – in a way that has become routine in other fields of engineering. This has proved a more robust way to construct novel regulatory networks in microbial systems, including synthetic oscillators, switches, logic gates, intercellular signaling systems and metabolic networks. Synthetic Biology is providing an conceptual and practical framework for the systematic engineering of gene expression and behaviour in microbes.

Synthetic Biology approaches show great potential for the engineering of multicellular systems. 
(1) The greatest diversity of cell types and biochemical specialisation is found in multicellular systems, 
(2) the molecular basis of cell fate determination is increasingly well understood, and 
(3) it is feasible to consider creating new tissues or organs with specialized biosynthetic or storage functions by remodelling the distribution of existing cell types.

Of all multicellular organisms, plants are the obvious first target for this type of approach. Plants possess indeterminate and modular body plans, have a wide spectrum of biosynthetic activities, can be genetically manipulated, and are widely used in crop systems for production of biomass, food, polymers, drugs and fuels.

Microanatomy of Plant Tissues 

A gallery of confocal microscopy images by Jim Haseloff at the University of Cambridge. A wide variety of staining techniques has been adopted for plant specimens over the past 150 years. Many of the synthetic dyes used for plant microtechniques are highly fluorescent and many classical histological techniques unintentionally produce specimens that are highly suited for confocal microscopy. The digital controls of a confocal microscope allow for the clean separation of different fluorescent emission signals and the balancing of signal levels in different channels. Thus, fluorescent images of exceptional clarity and vivid color can be easily obtained.

Image analysis techniques for intact tissues

Classical botanical microtechniques can be adapted for modern laser scanning confocal microscopy, to allow deep optical sectioning of intact plant tissues. The resulting large datasets can be visualised and converted to simple numerical descriptions of cell arrangement, shape and connectivity using 3D segmentation software.

High resolution optical microscopy for plants

The last twenty years have seen a revolution in the application of optical techniques to the study of biological systems. This largely due to the development of highly specific fluorescent labelling methods, and optical techniques such as confocal laser scanning microscopy. For example, different coloured fluorescent proteins are now used routinely to decorate cells and subcellular structures in living tissues, and optical sectioning techniques allow the precise visualisation of these labels.The techniques are being used to map gene expression and visualise signalling events within the 3D cellular architecture of developing organisms - developed in the Haseloff Lab.

Teaching material for Plant Development and Biotechnology

Link to handouts, slides and original references in PDF format for a variety of different courses on plant development and biotechnology that are given by Jim Haseloff at the University of Cambridge. While some illustrative material originates from our own lab, the the bulk of the material is culled from published sources. Additional background information about these and related courses is available from the Department of Plant Sciences website (www.plantsci.cam.ac.uk) at the University of Cambridge.

Coleochaete as a model system for plant morphogenesis

This genus of green algae shows some of the earliest and simplest features of multicellular plant growth. Haploid zoospores initiate the growth of discoid multicellular colonies. The colonies adhere to the substrate and grow as a cell monolayer. The circular morphology of the colonies is maintained by precisely coordinated sequences of anticlinal and periclinal divisions. Cultures are easy to maintain, and are ideal for microscopy. Coleochaete has been little studied as a developmental system, and we are transferring some of the molecular genetic and imaging tools that we have developed for Arabidopsis studies to Coleochaete.

Tools for Arabidopsis thaliana

Arabidopsis plants grow quickly, produce prolific seed, and are easy to transform. Its genome is completely sequenced and a large variety of experimental tools and genetic resources are available. The root meristem grows indeterminately, has a simple and transparent 3D architecture, and can be induced to form de novo in adult tissues. We have developed a combination of new genetic and microscopy techniques for Arabidopsis in order to visualise cell interactions and gene expression within plant tissues, and to reprogram plant gene expression. (GAL4 and HAP1 based expression systems from the Haseloff Lab).