Vertical-stage confocal microscopy for live imaging of growing plants

Lead Research Organisation: University of Leeds
Department Name: Sch of Biology


As all gardeners know, plant roots grow vertically downwards, and they do this by responding to gravity. Understanding how this happens, how roots develop and respond to their environment is essential to improving nutrient and water uptake in plants, which will ultimately help us improve agricultural productivity to feed the world. Plant growth and development are complex processes that are regulated by several proteins and other molecules within cells. Understanding where in the cells these proteins normally reside, and how they move within cells either during normal developmental processes or in response to environmental stimuli is an important first step in understanding the molecular pathways that regulate plant growth responses, and microscopy is a common tool used to study this. However, most microscopes are only equipped with a horizontal stage, which means that plants cannot be imaged in their natural vertical orientiation. As plants respond to gravity, placing them in a horizontal orientation perturbs their normal behaviour, making it difficult to draw valid conclusions about the normal plant response to gravity. The new horizontally-mounted confocal microscope will allow us, for the first time, to use powerful confocal microscopy to image vertical plant roots in their natural orientation at high resolution (with fine detail). This cutting edge vertical microscope will enable us to image proteins and other molecules in their native orientation within cells, as well as allow the dynamic live imaging of movement of these molecules in response to different environmental signals and during growth and development.

Technical Summary

The main objective of our proposed research is to implement and use cutting edge techniques in vertical-stage confocal microscopy for novel high resolution dynamic live cell imaging of plant root cells in their native vertical orientation. Being the first of its kind in the UK, this microscope will be situated in the Bioimaging suite at the University of Leeds and be made available to all researchers from the 14 plant science groups at Leeds, and more broadly to plant science groups across the UK, as well as researchers in other fields needing to utilize vertical confocal microscopy. It will enable us to address a number of key questions such as how changes in auxin distribution and PIN polarity affect different regulatory processes such as lateral root growth angle and root cap patterning and development as well as explore the effects of mechanical impedance on root growth and morphology. Other important applications of this technology will be to study the role of class 11 myosins in root gravitropic and developmental responses and image novel cell cycle markers in real time during the processes of lateral root initiation. Additionally, this microscope will enable live imaging of the effect of callose deposition on plasmodesmal connectivity within root cells and its effect on root growth. All of these studies form the basis of key aspects of translational plant science research that are being addressed by groups across the UK, and in the world.

Planned Impact

Who will benefit from this research?

The Zeiss vertical confocal microscope will be a novel piece of equipment that will impact a range of beneficiaries. Firstly, researchers at the Centre for Plant Sciences will have access to a specially engineered cutting edge technology that will dramatically enhance research output. Secondly, plant science researchers from across the UK, as well as the private sector will benefit from this microscope, which in turn will foster collaborative research with the University of Leeds, further enhancing research potential. The new microscope will become a useful tool in knowledge dissemination to the general public through generation of high resolution, attractive images showcasing our research. The general public will also benefit from our improved knowledge in the plant science field in terms of addressing problems such as food security in a rapidly changing environment.

How will they benefit from this research?

Researchers at the Centre of Plant Sciences will have access to novel ground breaking technology and develop new skills in high resolution dynamic live cell imaging and automation methods. This in turn will impact research output at the University of Leeds. Moreover, plant science based research across the UK will benefit from this microscope, which in turn will increase economic competitiveness of the UK as well as foster new collaborative interdisciplinary research not only in the academic field, but also between the public and private industry sector. Finally, in the long term, the general public will benefit from new insights into plant growth and behavior in order to improve agricultural productivity and improve resource and water uptake.


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Roychoudhry S (2022) Auxin in Root Development. in Cold Spring Harbor perspectives in biology

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Roychoudhry S (2022) The Analysis of Gravitropic Setpoint Angle Control in Plants. in Methods in molecular biology (Clifton, N.J.)

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Vain T (2019) Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development. in Proceedings of the National Academy of Sciences of the United States of America

Description BBSRC responsive mode
Amount £576,766 (GBP)
Funding ID BB/N010124/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2016 
End 06/2019
Description Friml Collaboration 
Organisation Institute of Science and Technology Austria
Country Austria 
Sector Academic/University 
PI Contribution We share an interest in gravitropism and PIN biology with this group. We have supplied the Friml group we molecular genetic tools.
Collaborator Contribution The Friml lab has hosted PDRAs from my group to allow them to use the vertical-stage confocal microscope they have at IST, Vienna
Impact Papers are being prepared
Start Year 2013