The Microphenotron: developing an automated microphenotyping platform to unlock the potential of chemical biology in plants

Chemical biology is the scientific discipline that harnesses the ability of small molecules to perturb biological processes. It is used to improve our understanding of those biological processes, to identify the genes that control them and to discover novel compounds that can be used to improve human health or increase crop productivity. Whilst chemical biology is widely exploited in other fields, and despite its proven power as a gene discovery tool in plants, it has been slow to gain acceptance amongst plant biologists. A primary reason for this is that the methods previously available to screen small molecules for their effects on the plant phenotype are laborious and limited in the number of traits they can monitor. At Lancaster University a novel technology has recently been developed that for the first time allows Arabidopsis seedlings to be grown under conditions suitable for studying the effects of small molecules on the development of both roots and shoots. However, it is still a laborious process to screen more than a few hundred molecules using the current version of this technology, and there are some intrinsic problems that preclude reliable quantitative analysis of root architecture.

In this 15 month multidisciplinary project, a team of biologists, engineers and computer scientists will address these problems to develop the 'Microphenotron', a robotic version of the phenotyping system that will automate the process of image capture and analysis. The development of the Microphenotron will greatly expand the accessibility and utility of chemical biology approaches to the wider plant biology community, leading to a greater understanding of plant gene function. It will also provide a new tool for the development of synthetic and natural molecules for improved agricultural sustainability, with resulting benefits for farmers, the environment and society.

Chemical biology is a powerful tool for gene discovery and for the development of chemical probes for investigating and manipulating biological processes. However, a major limiting factor in the adoption of chemical biology approaches by plant biologists has been the lack of effective and accessible phenotypic screening methods that can be applied to whole seedlings. At Lancaster, a novel technique has been devised that for the first time allows simultaneous phenotyping of both roots and shoots in a 96-well format compatible with chemical screens. The methodology has recently been validated by using it to identify, from a collection of 1600 small molecules bioactive in yeast, two classes of compound able to antagonise the characteristic effect of exogenous glutamate on root architecture. However, in its current form, the technique is too laborious to be used to screen the larger numbers of small molecules required for most screening programmes. The goal of this project is therefore to develop a robotic version of the technique that is able to fully exploit and expand its phenotyping power, but in combination with automated image capture and analysis.

To achieve this goal a number of technical hurdles will have to be overcome. The first will be to develop a modified version of the FrameStrips currently used as growth devices, but which were designed for PCR reactions. The new 'Phytostrips' will make it possible to reliably generate images of the root system that are suitable for automated extraction of the root phenotype. The second will be to develop a robotic platform that can process the Phytostrips individually through an imaging station, where images of whole seedlings are automatically captured from the side and above, and return them to their microtitre plates for continued growth. The third will be to develop a version of Nottingham's RootNav software that automatically extracts comprehensive phenotypic data from these composite images.

Direct Impacts (1-5 years)
The technology to be developed in this project is expected to have a direct impact on plant research within and beyond academia. It is designed to enable small- to medium-sized labs in universities, research institutes and the agrochemical industry to pursue chemical biology approaches that have previously been largely inaccessible to them. The attached letters of support demonstrate the breadth of interest and enthusiasm from the scientific community in this technology.

As chemical biology is a generic approach applicable to most fields of biological research, the academic beneficiaries extend across the whole breadth of plant science disciplines and all parts of the world. To illustrate this, the letters of support we have received have come from plant scientists working on a wide range of subjects, many of which address topics of direct relevance to key agronomic traits, including control of root architecture, abiotic stress tolerance, plant-microbial interactions, ethylene signalling, sugar signalling and programmed cell death. As evidence of the geographical spread of interest, we have received letters of support from five UK academic research groups, one private research institute and two universities in the US, two European labs, one lab in Malaysia and one in Saudi Arabia.

As an example from the public sector, chemical genetics is written into the JIC's Institute Strategic Programme on Understanding and Exploiting Metabolism (supported in part by the BBSRC Crop Improvement Industry Club) and Prof. Robert Field has provided a letter of support indicating his group's strong interest in using our technology in this research programme.

In the commercial sector we expect the technology to be used (under licence) by agrochemical companies, both as part of their screening programmes for candidate molecules with novel bioactivity and in bioassays for natural compounds that may have beneficial effects on plant growth. We have recently been collaborating with a US company, Agricen Sciences (Texas), to explore the use of the technology in metabolomic and metagenomic projects aimed at identifying microbial products that improve the yield and the sustainability of agricultural systems (see their letter of support).

To access the technology, researchers will have the option to reproduce the phenotyping system in their own labs, using our published designs, or to use our facilities on a service or a collaborative basis. The Phytostrips will be available for sale from 4titude Ltd and the RootNav V2 software will be available for free download. If the level of interest from other laboratories is sufficient we will evaluate the possibility of setting up a spin-off company offering access to the Microphenotron as a commercial service.

Specialist image analysis software from the commercial sector is expensive, so that providing a custom open-source solution to accompany the technology will benefit both the industrial and academic sectors. Additionally, the novel developments in image analysis theory that will be needed in elaborating the RootNav V2 software will be of benefit to other image analysis researchers.

Indirect, longer term impacts (5-15 years)
Farmers can expect to benefit from the use of the technology to develop novel agrochemicals that enhance crop yields or reduce the costs of inputs e.g. through novel and more effective pesticides, or additives to improve nutrient-use efficiency or abiotic stress tolerance.

Societal benefits in the form of improved quality of life would arise from the development of more environmentally friendly agrochemicals and improvements in nutrient-use efficiency, leading to reduced impacts on the environment and improvements in agricultural sustainability.

As an outcome of its use as a tool for gene discovery, the technology could lead to the identification of novel genes that would be the basis for breeding of improved crop varieties.