Coen Lab - Research
From Flower Development, E Coen , Cell & Developmental Biology Department - JIC UK
Overview of Research Programme
Our research programme involves collaborations with several labs, including Computer scientists Andrew Bangham at the University of East Anglia and Przemyslaw Prusinkiewicz at the University of Calgary and ecological population geneticists Nick Barton at Vienna and Edinburgh and Christophe Thebaud at the University of Toulouse. We study developmental and evolutionary problems at a range of spatial and temporal scales, from subcellular events at minute intervals, to events at geographic scale over millions of years. Our long term goal is to link these different scales of analysis to give an integrated understanding of evolution and development. Each person in the lab has a main project while also working in collaboration with others in the group.
A major focus of our group is on leaf development in Arabidopsis, which has the advantage of good genetics and convenience for imaging. Starting at the subcellular scale, we are analysing the role of microtubules and nuclear movements in the control of leaf cell division and growth. This involves extensive confocal imaging, image processing and computational modelling1,2,3. This work is closely related to studies at the cellular scale on division, growth and differentiation in developing leaves, involving a combination of time-lapse imaging and modelling5,6. At the tissue scale we are studying leaf development through clonal analysis, time-lapse imaging7 and Optical Projection Tomography1,2,9. Leaf growth is also being modelled at this scale by treating the leaf as a growing sheet of material8,10,16. In addition to these studies on leaf development, we are analysing the growth of flowers using similar approaches in both Arabidopsis12 and Antirrhinum10,11,13.
Another major focus of our work is on the evolution of leaf and flower pattern and form, using the Antirrhinum species group as a model system. One aspect is to study evolutionary events over a few generations, at a naturally occuring hybrid zone in the Pyrenees. This uses a combination of DNA pedigree, phenotypic and pollinator studies13,14,15. We also aim to identify the key genes controlling flower colour that are under selection. On a longer evolutionary timescale we are studying variation in the function and structure of genes controlling flower colour between different Antirrhinum species using a combination of molecular and genetic approaches13,15. In addition to the work on flower colour, we are also studying genes underlying flower and leaf shape variation between species. These were identified through QTL analysis and are being studied at the molecular and phenotypic levels17.
Studies on the evolution of leaf shape are also being extended to carnivorous plants which have elaborate leaves that entice and digest animal prey, allowing them to thrive in nutrient poor environments. Carnivorous cup-shaped leaves with lids are effective animal traps very similar in structure to each other. They are found in four independent lineages; Asian pitcher plants (Nepenthes), Albany pitcher plants (Cephalotus), American pitcher plants (Sarracenia, Darlingtonia and Heliamphora) and bladderworts (Utricularia). This example of convergent evolution might hint at similar developmental mechanisms underlying the growth of these cup-shaped leaves. We are establishing Utricularia gibba as a model carnivorous plant to discover whether developmental rules discovered in Arabidopsis are adapted to grow cup-shaped leaf traps and whether these different plants are using similar genetic mechanisms to grow their traps9. We are using a combination of genetic analysis, imaging and mathematical modelling to understand how these leaves grow themselves.
- Our leaf growth work 'A Multiscale Approach to Genes Growth and Geometry' was funded by the BBSRC as part of the Systems Approaches to Biological Research (SABR) [2007 initiative]
- Our Antirrhinum work 'Evolutionary Dynamics Underlying Species Diversification' is funded by the BBSRC as part of the Longer and Larger Grants (LoLas) [2007-2013 initiative]
- Our carnivorous plant research is funded by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 323028 .
- We also receive funding for postdoctoral fellows from HSFP, EMBO and Marie Curie
1 - Modelling Microtubule Dynamics
Jacob Newman - email in collaboration with Jordi Chan
Microtubules in Arabidopsis leaf cells have been observed to undergo persistent reorientation. Much work has been done to quantify the dynamics and behaviour of microtubules, however little is known about the processes by which inter-microtubule interactions lead to the patterning observed in biological data. This work uses computer modelling software developed by Andrew Bangham and Richard Kennaway (MTtbox) to create a model which can reproduce the ordering and reordering of microtubule arrays, using realistic assumptions regarding microtubule dynamics.
In tandem with the modelling, an image processing project (in collaboration with Paul Southam) seeks to automatically quantify the dynamics and interactions of microtubules in time-lapsed, electron microscopy image data. This quantification serves to support the manual observations by Jordi Chan, to allow the processing of more data than could realistically be analysed by eye, and to extract parameters which will feed directly into our microtubule modelling.
2 - Image Processing for Biological Development
Paul Southam - email in collaboration with Scott Grandison and Jordi Chan
Extracting quantitative measurements from image data is a fundamental step towards understanding how biological forms develop and evolve. I work on a number of projects including:
Modelling microtubule dynamics during growth and division - Jordi Chan & Scott Grandison.
Modelling Dynamic Growth Maps of Leaf Development - Samantha Fox.
Capturing plant development in 3D with Optical Projection Tomography - Karen Lee.
I am also interested in cell segmentation, cell registration, leaf classification and texture analysis.
3 - Microtubule dynamics during growth and division
Jordi Chan - email in collaboration with Scott Grandison and Paul Southam
Microtubules are highly dynamic subcellular filaments that adopt different patterns of alignment during growth, division and differentiation. During growth, microtubules are found in close association with the plasma-membrane where they are needed to guide the movement of cellulose synthase to generate appropriate wall architectures. Like animal cells, microtubules are required for chromosome segregation during cell division via the spindle apparatus. However, unlike animal cells, plant microtubules bunch up at the onset of mitosis to form a cortical ring, known as the pre-prophase band (PPB), which is involved in determining the future plane of cell division. Since plant cells within tissues are immobilised by their own walls and can only respond to cellular and environmental cues by altering their directions of growth and division planes, microtubules are indispensible elements of plant morphogenesis.
How microtubules change alignment and construct different arrays during growth and cell division is unknown but is likely to reside within fundamental properties of the microtubules themselves, such as the dynamic behaviour of their filamentous ends, regulation of their sites and angles of nucleation (birth) and outcomes of encounters between themselves and the geometry of the cell. It is interesting to think that these simple subcellular behaviours or rules concerning microtubule dynamics may not only shape the cell but also be amplified during morphogenesis from cell-to-cell to shape the entire plant.
The aim of my work is to reconstitute microtubule dynamics and cortical array organisation in-silico to understand and test mechanisms behind microtubule reorientation and division plane alignment (PPB formation) in-planta. This will involve time-lapse microscopy of growing and dividing leaf cells expressing appropriate fluorescent reporter genes, the development of software to quantify microtubule dynamics at both subcellular and tissue levels, and computer modelling. Models will be tested using cytoskeletal-specific drugs and mutants harbouring defective cytoskeletal genes.
4 - Establishing a model for complex leaf development
Claire Bushell - email in collaboration with Karen Lee
Leaves are a fantastic example of the diversity of organ shape seen in nature and present us with a system in which development can be studied from the very early stages of growth. Our lab has generated a model for the growth and development of the relatively simple leaf shape seen in Arabidopsis thaliana. This model demonstrates how simple rules coordinated by a polarity system can generate leaf shape. The aim of my project is to see if these rules may underlie the development of complex leaf shapes seen in carnivorous plants. Interestingly, epiascidiate (cup-shaped) leaves have evolved four times independently; in the families Nepenthacea, Sarraceniaceae, Cephalotaceae (pitchers) and Lentibuleraceae (bladderworts). This may indicate that changes in an underlying developmental system may have taken place to give rise to the repeated evolution of form. We also have an understanding of a number of genes involved in the developmental program and their roles and interactions governing growth. Of particular interest are the HDZIPIII, KANADI and YABBY transcription factors which are known to play key roles in determining dorsoventral polarity of leaves. It is thought that the inside surface of epiascidiate leaves corresponds to the adaxial surface and the outside surface corresponds to the abaxial surface of a conventional leaf.
My work will expand on the knowledge we have by establishing a model system that will allow the study of complex leaf shapes. The organism of choice is the carnivorous bladderwort, Utricularia gibba, which has a number of key advantages as a novel model system. I will combine imaging, genetics, expression studies and computational modelling to explore the development of this leaf shape, comparing observations to those of Arabidopsis.
5 - The role of tissue cell polarity in Monocot organ development
Annis Richardson - email in collaboration with Xana Rebocho and Sarah Hake
There is huge diversity in organ shape in the plant kingdom, but how shape is defined during development is not yet fully understood. Growth is a key aspect of development and to generate non-uniform shapes, such as the complex leaf structure seen in many monocots, growth needs to be anisotropic (not equal in all directions). To define growth directionalities within biological tissues axial information is needed. Work within the lab has suggested that this axial information could be provided by tissue cell polarity (coordinated cell polarity across a tissue). We hypothesise that the establishment of tissue cell polarity could be mediated by the polar transport of Auxin, influenced by the activity of regions within the tissue called organisers. Plus organises are regions of high extracellular Auxin and minus organisers of low extracellular Auxin. Modulation of the position of these organisers could result in significant changes in organ shape during development. My work uses a combination of computer modelling and experimental work to test this model, focussing on monocot examples. In particular I am using the Hooded mutant in Barley to test the effect of ectopic BKn3 expression on tissue cell polarity. In addition to this I am investigating the role of tissue cell polarity in the development of the Maize leaf, with the aim of generating a model which describes the role of tissue cell polarity in the development of all ensheathing leaves found in the Poales order.
6 - Modelling and analysis of heteroblasty in Arabidopsis
Florent Pantin - email
My postdoctoral research project is a contribution to a mechanistic growth model of the Arabidopsis rosette. The Coen and Bangham group has recently shed light on the way a young leaf primordium acquires its typical leaf shape, through feedback between early patterns of oriented growth and tissue deformation (Kuchen et al., 2012). A model able to generate a leaf shape from a simple dome structure was developed using a limited set of hypotheses and validated against the spatial and temporal growth pattern of the first leaf of Arabidopsis. However, the first leaf is provided with juvenile features and its shape markedly differs from that of upper, adult leaves of the rosette. This is termed heteroblasty. I will test to what extent the central hypotheses underlying this growth model account for the growth pattern of adult leaves.
The long-standing aim of the project is to integrate the mechanistic bases of leaf growth into an earlier model of whole rosette development, which was based on a thorough description of shoot morphology and developmental events (Mündermann et al., 2005).
Marie Curie Intra-European Fellowship (call FP7-PEOPLE-2012-IEF, project n° 329784 HEMOTIONAL — HEteroblasty MOdelling: the TImetable of ONtogeny in Arabidopsis Leaves)
7 - Dynamic Growth Maps of Leaf Development
Samantha Fox - email
A major challenge in biology is to understand how buds comprising a few cells can give rise to complex plant and animal appendages, like leaves or limbs. We have addressed this problem through a combination of time-lapse imaging of growing leaf buds, clonal analysis and computational modelling. We have generated a model that shows how leaf shape can arise according to a few simple rules and that growth is coordinated by an in-built polarity system. Experimental tests through partial leaf ablation support this model, and allow re-evaluation of previous experimental studies. Our model allows a range of observed leaf shapes to be generated and predicts observed clone patterns in different species. Thus our experimentally validated model may underlie the development and evolution of diverse organ shapes.
Watch my Youtube movie to find out more: http://www.youtube.com/watch?v=G4lLGTiNe2A
8 - Differential Introgression and Genetic Incompatibilities in the Snapdragon Hybrid Zone
Our theoretical understanding of the evolutionary process is based on describing the fate of particular genetic variants in their internal (genomic) and external (environmental) context. Natural hybrid zones, which can be seen as contact zones or interfaces between different contexts, offer multifaceted opportunities to empirically investigate the resulting evolutionary dynamics. Differential introgression across the genome and geography can be related to internal or external selective barriers. My project addresses differential introgression at the genome-wide level in a hybrid zone between magenta- and yellow-flowered snapdragons (Antirrhinum) in the Pyrenees. The conspicuous flower colour difference has already been shown to relate to a lack of introgression of one particular locus (ROS/EL) involved in the regulation of the magenta pigment (Whibley et al. 2006), but what about further colour genes and the remainder of the genome? In collaboration with the lab of Nick Barton in Vienna, we aim at disentangling neutral gene flow from selective barriers to introgression, and at more closely characterising the spectrum of genetic loci subject to the latter. The results will help us to gain an empirically founded picture of the mechanisms underlying early stages of evolutionary divergence and the origins of genetic incompatibility in a flowering plant.
Whibley, A. C., Langlade, N. B., Andalo, C., Hanna, A. I., Bangham, A., Thébaud, C., Coen, E. (2006): Evolutionary paths underlying flower color variation in Antirrhinum. Science 313: 963-966.
My work is funded by an EMBO Fellowship.
9 - Exploring Inner Worlds of Plants in 3D with Optical Projection Tomography
Please see 3D Gallery for images of carnivorous plants and other beautiful plant specimens.
We have explored the use of Optical Projection Tomography (OPT) as a method for capturing 3D morphology and gene activity at a variety of developmental stages and scales from plant specimens, in collaboration with James Sharpe and Bioptonics . OPT can be conveniently applied to a wide variety of plant material including seedlings, leaves, flowers, roots, seeds, embryos and meristems. At the highest resolution large individual cells can be seen in the context of the surrounding plant structure. 3D domains of gene expression can be visualized using either marker genes such as β-glucuronidase, or more directly by whole-mount in situ hybridization. For naturally semi-transparent structures, such as roots or Bladderwort suction traps, live 3D imaging using OPT is possible. 3D gene expression patterns in living transgenic plants expressing fluorescent GFP markers can also be visualised. To interactively analyse and quantify OPT data, software was developed to visualise 3D volumes, accurately place points on volumes in 3D space and extract growth measurements.
Using these tools to capture leaf shape and growth, in combination with mathematical modelling, we are studying mechanisms controlling growth and shape from earliest stages of Arabidopsis leaf growth to maturity in 3D.
I am initiating a new project exploring carnivores. Carnivorous plants are amazing. They seem to turn the natural order around by being able to entice, capture and consume animal prey, when we normally think of plants as passive suppliers of nutrition for the animal world. Taking what we have learned from our Arabidopsis research we want to discover whether rules of growth underlying the development of simple leaves in Arabidopsis are are adapted to grow cup-shaped leaf traps of carnivorous plants. Using a combination of 3D imaging, genetic analysis and modelling, we aim to explore how these complex leaves develop.
Another project I am working on is a website showcasing the Inner World of Carnivorous Plants
Our carnivorous plant work is also featured in a Sightings article- 3D Carnivorous Plants, in American Science
Some of our images can also be found on the Cell Picture Show- Plant Biology
10 - Modelling Growth at the Tissue Scale
Richard Kennaway - email in collaboration with Erika Kuchen and Xana Rebocho
I am developing finite element methods for modelling the growth and development of curved two-dimensional tissues such as leaves and petals. The interactive software tool I am developing, called GFtbox, is available for download.
11 - Testing models for polarity and asymmetry in Antirrhinum
Xana Rebocho - email in collaboration with Des Bradley, Lucy Copsey, Andrew Bangham and Richard Kennaway
Bilateral symmetry of flowers has evolved several times independently from an ancient radially symmetrical condition. Antirrhinum’s flowers are comprised of 2 ventral, 2 lateral and 1 dorsal petal. One of the key genes involved in the control of dorsal identity is RADIALIS. RADIALIS is regulated by CYCLOIDEA and DICHOTOMA to be expressed in the primordial dorsal petals. One of the functions of RADIALIS is to prevent DIVARICATA, the ventral identity gene, expression in the lateral and dorsal domains. However, the way in which these genes act to control the asymmetry, shape and form of the flower remains to be unraveled. The establishment of ventral identity is also important for the development of petal specializations such as nectaries and spurs. I am studying an Antirrhinum mutant that produces a ventral outgrowth, similar to a spur, in order to understand how identity and polarity genes interplay to produce novel shapes. I am addressing these issues using a combination of genetic, developmental and computational approaches. The goal of my research will be to understand how genes act within and between cells to modify growth patterns that contributed to the final morphology of the flower and the evolution of new traits.
12 - Evolution and Development of Fruit Shape
Tilly Eldridge - email in collaboration with Lars Ostergaard
Fruit comes in diverse shapes across the flowering plant kingdom. In the family Brassicaceae alone there is much variation, for example three closely related species; Arabidopsis thaliana, Capsella rubella and Lepidium campestre. Arabidopsis has long thin pod-shaped fruit, Capsella has heart-shaped fruit and Lepidium has round flat fruit. Little is known about how these shapes are generated through growth and even less is known about the underlying genetic control of fruit shape. My project aims to answer these questions through a combination of genetic, clonal analysis, imaging and computational approaches.
Using a quantitative framework of flowering time developed by the lab we are able to carry out robust clonal analysis experiments on gynoecium/ fruit in Arabidopsis. We are developing a computational model to account for the growth rate and directions of growth observed in Arabidopsis from these experiments. To compare these growth patterns to a more complex shape I have also developed a clonal analysis line in C. rubella. I am also interested in identifying candidate genes that are important for controlling fruit shape and so I have developed a mutant population in C. rubella. As a result of this mutagenesis I have set up a TILLING population as a resource for others working with C. rubella.
13 - Evolution of organ size and shape between Antirrhinum species
Lucy Copsey - email in collaboration with Xana Rebocho, Des Bradley, Matt Couchman and Hugo Tavares.
The "old world" Antirrhinum species, found growing naturally in southern Europe and North Africa, show an extensive range of diversity in growth habit, organ size, shape and flower colour. This variation is important as it highlights differences between individuals which may be due to either environmental effects or differences at gene level, these genetic differences underpins how diversity in form is generated through evolutionary time and is the basis of evolution. By exploiting evolutionary variation in size we hope to identify genes controlling organ size in Antirrhinum species (allometry project).
I am using a classical genetics approach involving the production of a number of plant resources developed by crossing Antirrhinum species to both our cultivated JI stock 7 line and interspecies crosses to study natural variation and domestication effects. These resources are available for use by group members and for the wider Antirrhinum community.
14 - Evolutionary Dynamics Underlying Species Diversification
Matthew Couchman - email in collaboration with Xana Rebocho, Lucy Copsey, Des Bradley and Nick Barton
We are part of a collaboration investigating factors affecting gene flow across populations. The project focuses on flower colour in two distinct subspecies of Antirrhinum. Within the Spanish Pyrenees there are a number of hybrid zones that provide ideal environments for analysing how genes influence flower colour. For each individual within our chosen hybrid zone we are annually recording their GPS location and colour scores as well as taking samples for genotyping and other molecular analysis.
My role within the project is to develop a relational database to capture these and other collaborator outputs as well as a website to act as a gateway to this database. The website will include visual tools such as a configurable map of recorded GPS positions and genetic and physical maps.
15 - Natural variation of flower colour
Desmond Bradley - email
Collaborators: Christophe Thebaud, Xana Rebocho, Nick Barton, David Field, Christophe Andalo and Monique Burrus
Two subspecies of Antirrhinum (magenta and yellow), which generally occur in genetic isolation in the Pyrenees, have hybridized in nature to create a hybrid zone. Due to hybridization the Antirrhinum flowers display an array of parental as well as mixed flower colour phenotypes which are the result of genetic variation at three key loci ROSEA, ELUTA and SULFUREA. The two first genes are involved in the control of the magenta anthocyanin pigmentation while SULF is a repressor of aurone (yellow) pigmentation. As the HZ gives a great playground to study evolution in action, the goal of this research is to follow the genetic flow of these flower colour loci within the hybrid population as well as the fitness of each phenotype/genotype throughout several years.
16 - Interplay between axes during leaf development
Katie Abley - email in collaboration with Susana Sauret-Gueto, Richard Kennaway, Erika Kuchen, Pierre Barbier de Reuille, Emily Abrash
Leaf development involves different growth rates along three principle axes: the proximo-distal axis, the medio-lateral axis, and the adaxial-abaxial axis. For different growth rates to be specified along three axes, there must be at least two orthogonal axes of directional information, or polarity, within the leaf.
I am using a combination of computational modelling and experimental work in an attempt to elucidate the mechanisms underlying tissue polarity within the leaf. I am also trying to gain an understanding of how multiple axes of polarity can be established and co-ordinated within the leaf by testing the roles of known regulators of leaf development in these processes.
17 - The genetic basis for natural variation of organ shape and size
Desmond Bradley - email in collaboration with Xianzhong Feng and Lucy Copsey
Natural variation is one of the most striking features of the biological world; much of the variation between species and varieties involves correlated differences in shape and size (allometric variation). However, it is poorly understood the genetic, developmental and evolutionary basis of these variations. We addressed this problem by examining the genetic basis for organ size and shape differences between Antirrhinum species. Using statistical shape modeling, we quantified the differences of shape and size in both leaves and flowers . Allometry genes were identified by QTL analysis, and confirmed using recombinant inbred lines (RILs) and near isogenic lines (NILs). Key allometry loci is fine-mapped and transposon-mutagenesised with a view to isolating the corresponding genes. The allometry genes form different species are introgressed into a uniform background to compare their effects in evolution pathway.
18 - Evolutionary processes of trait diversity in the wild
Hugo Tavares - email in collaboration with Xana Rebocho, Des Bradley, Lucy Copsey, Matt Couchman and Louis Boell
Different species of Antirrhinum show conspicuous differences in flower color (see figure), a trait though to be under strong selective pressure in insect-pollinated species such as this one. To understand the molecular genetic basis of these differences I am focusing my work on two tightly-linked loci - ROSEA and ELUTA - which interact to regulate the intensity and pattern of red anthocyanin pigments. By combining genetic, molecular, and bioinformatic analysis I hope to understand how the different species' ROS and EL alleles (genotype) effectively contribute to their respective floral pigmentation patterns (phenotype), thus uncovering some of the evolutionary mechanisms that may lead to trait diversification in the wild.