Multilevel Modelling of Plant Morphogenesis

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

This project focuses on using mathematical and computational methods to understand plant cell polarity control and multicellular organisation. In particular, we aim to unravel the complexity of the feedbacks between subcellular mechanisms of cell polarity and tissue-level patterning mechanisms, focusing on auxin patterning and biophysical interactions. From a theoretical standpoint, this translates in gaining insights on mechanisms of biological spatial pattern formation and auto-organisation
through multi-level modelling. Such modelling basically captures biological processes at different levels – molecular and genetic levels, subcellular properties, cells and organs – allowing them to interact. The objective is to investigate whether level cross-talk yields results that are not present at the lower level and whether essential patterns
for developmental regulation emerge on mesoscopic levels which are not coded for explicitly. This approach is developed in close collaboration with several experimental groups. Examples of these experiment-model cycles are: exploring the mechanics of cellular growth by quantifying the dynamics of single cell shape changes and relating this to organ growth; analysing biochemical pathways (such as cytokinin-auxin interactions) and their influence on cell polarity and plant development (e.g. valve formation through auxin minima in fruit development, radial patterning and specification of transition zones of the roots and root nodulation); and studying cell fate through genetic regulatory networks (e.g. stem cell maintenance).

Publications

10 25 50
 
Description Our recent findings are focused on understanding how plants can be both robust to fluctuations (internal and external), while also respond rapidly and sensitively to certain environmental cues. This has been demonstrated for the response of root growth via auxin-cytokinin interactions, as well as to the subcellular mechanisms of nutrient sensing to enable optimal nutrient uptake. Our work has demonstrated new paradigms which will be important to cross-bridge plant physiology to plant development. Moreover, we have established a new plateform for cell shape phenotyping, making this available for a broad scientific community (also applicable for organisms or subcellular compoenents).
Exploitation Route Our method of cell shape quantification can be used for studied of evo-devo. Our data on cellular topologies can be used for broader questions on biophysics. Our insights and model of Boron transport can be extended to other essential minerals. And finally, our theory of meristem control through cytokinin-auxin interactions can be extrapolated to other phytohormone interactions that impinge on auxin transport.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment

 
Description OpenPlant Advancing the ability to image single RNA molecules at the cellular level
Amount £4,000 (GBP)
Funding ID Grant BB/ L014130/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2016 
End 01/2017
 
Description Collaboration with the Department of Physiology and Cell Biology of IPK, Gatersleben. 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution Grieneisen Lab is setting up large-scale metameric models to investigate Root Architecture.
Collaborator Contribution Dr. Ricardo Giehl from IPK is setting up heterogeneous nutrient conditions in soil. Auxin and cytokinin signalling is being investigated.
Impact Multi-disciplinary partnership, including Bioinformatics (IPK), Plant Physiology (IPK) and Computational Modelling (Grieneisen Lab, JIC).
Start Year 2018
 
Description Mersitem Zone Regulation in Roots through Phytohormone crosstalk 
Organisation Sapienza University of Rome
Country Italy 
Sector Academic/University 
PI Contribution Modelling phytohormone interactions and feedbacks that are involved in positioning the transition between meristematic and differentiating cells in the Arabidopsis Root. Generating experimental predictions for to gain better insights in the development of the Arabidopsis root.
Collaborator Contribution Performed experiments with phytohormone manipulations and signalling manipulations. Generated mutants for important key players of the model.
Impact PhD on the subject, performed by visiting student to the Grieneisen Lab. We are resubmitting a manuscript on this work.
Start Year 2013
 
Description Nutrient uptake and transport in roots: a case study on Boron 
Organisation University of Tokyo
Country Japan 
Sector Academic/University 
PI Contribution We have developed predictive computational models of nutrient patterning in Arabidopsis roots. We have performed mathematical analysis on transport regulation in polarized tissues. We have discussed and helped design new experiments regarding Boron sensors and measurments. Developed software to use with LA-ICP-MS to enable cellular resolution elemental measurements. We have gained insights on the constraints that polarized tissues face to avoid instabilities in substrate concentrations.
Collaborator Contribution Performed experimental measurments to confirm modelling predictions. Constructing lines to enable in vivo spatio-temporal tracking of Boron dynamics and Boron transporter dynamics. PhD students have spent many months at our Lab to perform simulations; multiple experamentalists working on developing model-driven predictions. Tokyo University has invited myself and Stan Maree for visits in Japan.
Impact Collaboration is multidisciplinary, as a combination of mathamatical modelling and computational modelling is used together with molecular genetics and plant physiological studies. This collaboration has fostered a master thesis a completed PhD thesis. We have a publication already, and are working on future submissions.
Start Year 2011
 
Description OpenPlant Fund for Development of a Low-Cost Micro-Environment Device for Root-Nutrient Interaction 
Organisation University of Cambridge
Department Department of Plant Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Designing a Low-Cost Micro-Environment Device for Root-Nutrient Interaction. Testing root growth in the diverse prototypes.
Collaborator Contribution Helping to engineer the devices.
Impact Multi-disciplinary study, in which biophysics and plant biology meet.
Start Year 2016
 
Description OpenPlant Fund for RNA FISH studies 
Organisation University of Cambridge
Department Department of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution JIC side obtained an OpenPlant fund which was used to enhance current techniques of Fluorescence in situ hybridization for RNA in planta. This work was performed by the Grieneisen lab through Susan Duncan, in collaboration with Hasselhof lab in Cambridge. It has generated data which is incorporated in a manuscript to be submitted. Susan also extended this method, successfully, to the model species Marchantia.
Collaborator Contribution Hosted and provided lab infrastructure for Susan. Susana Sauret-Gueto, from Hasselhoff lab, visited the JIC.
Impact Multidisciplinary collaboration.
Start Year 2016
 
Description SwarmOrgan Partnership 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution We have developed simulators for swarm robotics, that can specifically use biologically inspired genetic regulatory networks. This has been made available to the open source community, and we also are working on submitting a manuscript on the simulator. We contribute to the understanding of morphogenesis in self-propelling and locally stimulated agents. We have a paper accepted in Current Opinion in Cell Biology, in which we make an analogy between root architecture plasticity and swarm behaviour, linking molecular details to local and global signalling.
Collaborator Contribution They have efficiently employed our strategies for network evolution and patterning studies. We continue to interact on ideas and projects which emerged from this EC grant.
Impact http://arxiv.org/abs/1511.04285 http://jic-csb.github.io/kilombo/
Start Year 2012
 
Description vasculature development 
Organisation University of Helsinki
Country Finland 
Sector Academic/University 
PI Contribution Model to predict patterning of phytohormone interactions and signalling in the vascular development of Arabidopsis roots.
Collaborator Contribution Performed experiments to verify models predictions.
Impact Published article in PloS Computational Methods.
Start Year 2011
 
Description 1ST INTERNATIONAL PLANT SYSTEMS BIOLOGY MEETING Roscoff, France 10 - 14 September 2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact First meeting of Systems Biology focused on Plant Biology. Many impactful discussions and collaborative initiatives were stimulated. Also, we organised in this meeting a special issue for Journal of Plant Molecular Biology.
Year(s) Of Engagement Activity 2018
 
Description BBC radio 4 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview on BBC radio 4 "Frontiers" programme: Swarming Robots, 2 Jul 2014.
Year(s) Of Engagement Activity 2014
URL http://www.bbc.co.uk/programmes/b047zrlc
 
Description Collective dynamics and self-organization in biological sciences 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Self-organization is pervasive in biology as living organisms are by essence systems that have self-assembled and self-organized in the course of their development. Self-organization refers to the ability of systems made of a large number of independent agents interacting through rather simple and local rules to generate large scale spatio-temporal coherent structures with typical dimensions orders of magnitude larger than those associated with each individual agent.

By bringing together mathematicians and biologists, this workshop provided a broad overview of the various self-organization mechanisms that prevail at the various scales and the mathematical models by which they can be described or even explained. Through this interaction between experts from different disciplines, the workshop made progress towards determination of the key biological mechanisms that enable self-organisation at each scale and across the scales, and towards the derivation of suitable `universal' mathematical models able to describe them across the scales.

The value of this workshop is twofold. For the biologists, it reinforced their link with mathematicians and, by this strengthened relationship, enlarged the range of models that they can use to probe observed biological complexity. For the mathematicians, it broadend the repertoire of case studies with which to confront their methodologies and practice. It suggested new systems where models are still preliminary if not existent and which may require the development of new mathematical frameworks. For the two communities, it offered the opportunity of building trans-disciplinary teams that can easily share knowledge, models and data and apply to major research councils in UK and in Europe for large grant funding.
Year(s) Of Engagement Activity 2018
URL https://www.icms.org.uk/collectivedynamics.php
 
Description Interview with national news (BBC Radio 4) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interview on the legacy of D'Arcy W. Thompsons' showcasing the research of my Lab (Grieneisen) and this ISP in "On Growth and Form", for BBC radio 4 "ScienceStories". Interviewer was Philip Ball, programme name:
The Man Who Found Physics in Shells, Seeds and Bees, 28 Jun 2017.
Year(s) Of Engagement Activity 2017
URL https://www.bbc.co.uk/programmes/b06vy2jd/episodes/downloads
 
Description JIC Interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview that was put on the main page of the John Innes Centre about my lab's interest in Plant Adaptability and Swarm Robotics, being Curiosity-driven Science at the JIC.
Year(s) Of Engagement Activity 2015
URL https://www.jic.ac.uk/news/2015/09/curiosity-driven-science-jic/
 
Description Norwich High School Visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact "Lunch and Learning" session with the sixth form girls from the Norwich High School for Girls, "Self-
organization in biological development: how computational sciences, mathematics and physics (and
robots!) can help us understand how organisms make themselves", 28 Jan 2015. The girls engaged with the scientific questions and also asked questions related to being a scientist.
Year(s) Of Engagement Activity 2015
 
Description Paris Biological Physics Community Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Postgraduate and undergraduate students from mathematics and physics attended this event to understand how they could contribute to biology.
Discussions about the role of physics in biology was discussed, and students were encouraged to network with the invited speakers and ask career questions.
Also, interested general audience also atteneded.
Year(s) Of Engagement Activity 2018
URL http://www.lcqb.upmc.fr/parisyoung/2018/
 
Description Plenary talk for the International Union of Pure and Applied Physics, 9th International Conference on Biological Physics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Plenary talk about Root Growth and Function. Attracted a lot of interest from a wide community of biophysicists that were unaware of the challenges of developmental plasticity in plants.
Year(s) Of Engagement Activity 2017
URL http://www.if.ufrgs.br/icbp2017/
 
Description Podcast interview with GARNET. 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Interview of the "Weeding the Gems" series, highlighting our publication showing the mechanism by which phytohormones auxin and cytokinin control root growth. The research was described in a general manner, aimed for any public interested.
Year(s) Of Engagement Activity 2017
URL http://blog.garnetcommunity.org.uk/veronica-grieneisen-talks-garnet/
 
Description Talk and debates in Workshop in Leiden 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Computational Scientists, Biologists, Historians, Artists and Architects came together to discuss overlaps concerning the legacy of "on Growth and Form". Computational methods were reviewed, and applications of science to the arts were discussed.
Year(s) Of Engagement Activity 2017
URL https://www.lorentzcenter.nl/lc/web/2017/930/info.php3?wsid=930
 
Description The Naked Scientists 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview by "The Naked Scientists", "Which way is up?", in which I describe the basic research interests of my group
focussing on Cell and Tissue Polarity.
Year(s) Of Engagement Activity 2013,2015
URL http://www.thenakedscientists.com/HTML/interviews/interview/1000529/
 
Description talk for EMBO conference in Heidelberg 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited speaker for the EMBO led conference "Quatitative Principles in Biology".
Year(s) Of Engagement Activity 2017
URL https://www.embl.de/training/events/2017/QUN17-01/