Publications
17 results found
Kocaoglan EG, Radhakrishnan D, Nakayama N, 2023, Synthetic developmental biology: molecular tools to re-design plant shoots and roots, Journal of Experimental Botany, Vol: 74, Pages: 3864-3876, ISSN: 0022-0957
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable - subtle or pleiotropic in the resulting effect. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would likely benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with the suite of gene regulation tools (e.g., cell-type specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
Mason SE, Nakayama N, 2023, Self-burying robot morphs wood to sow seeds, Nature, Vol: 614, Pages: 415-416, ISSN: 0028-0836
Ohlendorf R, Tan NY-H, Nakayama N, 2023, Engineering Themes in Plant Forms and Functions, ANNUAL REVIEW OF PLANT BIOLOGY, Vol: 74, Pages: 777-801, ISSN: 1543-5008
Seale M, Zhdanov O, Soons M, et al., 2022, Environmental morphing enables informed dispersal of the dandelion diaspore, eLife, Vol: 11, ISSN: 2050-084X
Animal migration is highly sensitised to environmental cues, but plant dispersal is considered largely passive. The common dandelion, Taraxacum officinale, bears an intricate haired pappus facilitating flight. The pappus enables the formation of a separated vortex ring during flight; however, the pappus structure is not static but reversibly changes shape by closing in response to moisture. We hypothesised that this leads to changed dispersal properties in response to environmental conditions. Using wind tunnel experiments for flow visualisation, particle image velocimetry, and flight tests we characterised the fluid mechanics effects of the pappus morphing. We also modelled dispersal to understand the impact of pappus morphing on diaspore distribution. Pappus morphing dramatically alters the fluid mechanics of diaspore flight. We found that when the pappus closes in moist conditions, the drag coefficient decreases and thus the falling velocity is greatly increased. Detachment of diaspores from the parent plant also substantially decreases. The change in detachment when the pappus closes increases dispersal distances by reducing diaspore release when wind speeds are low. We propose that moisture-dependent pappus-morphing is a form of informed dispersal allowing rapid responses to changing conditions.
Nakayama N, Seale M, Kiss A, et al., 2022, Dandelion pappus morphing is actuated by radially patterned material swelling, Nature Communications, Vol: 13, Pages: 1-13, ISSN: 2041-1723
Plants generate motion by absorbing and releasing water. Many Asteraceae plants, such as the dandelion, have a hairy pappus that can close depending on moisture levels to modify dispersal. Here we demonstrate the relationship between structure and function of the underlying hygroscopic actuator. By investigating the structure and properties of the actuator cell walls, we identify the mechanism by which the dandelion pappus closes. We developed a structural computational model that can capture observed pappus closing and used it to explore the critical design features. We find that the actuator relies on the radial arrangement of vascular bundles and surrounding tissues around a central cavity. This allows heterogeneous swelling in a radially symmetric manner to co-ordinate movements of the hairs attached at the upper flank. This actuator is a derivative of bilayer structures, which is radial and can synchronise the movement of a planar or lateral attachment. The simple, material-based mechanism presents a promising biomimetic potential in robotics and functional materials.
Viola IM, Nakayama N, 2022, Flying seeds, CURRENT BIOLOGY, Vol: 32, Pages: R204-U95, ISSN: 0960-9822
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- Citations: 1
Jha SG, Borowsky AT, Cole BJ, et al., 2021, Science forum: vision, challenges and opportunities for a Plant Cell Atlas, eLife, Vol: 10, ISSN: 2050-084X
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
Autran D, Bassel GW, Chae E, et al., 2021, What is quantitative plant biology?, Quantitative Plant Biology, Vol: 2, Pages: 1-16, ISSN: 2632-8828
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
Certini D, Fazan L, Nakayama N, et al., 2020, Velocity of the falling dispersal units in <i>Zelkova abelicea</i>: remarkable evolutionary conservation within the relict tree genus, AMERICAN JOURNAL OF BOTANY, Vol: 107, Pages: 1831-1838, ISSN: 0002-9122
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- Citations: 6
Cummins C, Viola IM, Mastropaolo E, et al., 2020, The effect of permeability on the flow past permeable disks at low Reynolds numbers (vol 29, 097103, 2017), Physics of Fluids, Vol: 32, ISSN: 1070-6631
Nakayama N, 2020, Naomi Nakayama, New Phytologist, Vol: 226, Pages: 1548-1549, ISSN: 0028-646X
Seale M, Nakayama N, 2020, From passive to informed: mechanical mechanisms of seed dispersal, New Phytologist, Vol: 225, Pages: 653-658, ISSN: 0028-646X
Plant dispersal mechanisms rely on anatomical and morphological adaptations for the use of physical or biological dispersal vectors. Recently, studies of interactions between the dispersal unit and physical environment have uncovered fluid dynamic mechanisms of seed flight, protective measures against fire, and release mechanisms of explosive dispersers. Although environmental conditions generally dictate dispersal distances, plants are not purely passive players in these processes. Evidence suggests that some plants may enact informed dispersal, where dispersal‐related traits are modified according to the environment. This can occur via developmental regulation, but also on shorter timescales via structural remodelling in relation to water availability and temperature. Linking interactions between dispersal mechanisms and environmental conditions will be essential to fully understand population dynamics and distributions.
Andreou AI, Nakayama N, 2020, Mobius Assembly, DNA CLONING AND ASSEMBLY, Vol: 2205, Pages: 201-218, ISSN: 1064-3745
Cummins C, Seale M, Macente A, et al., 2018, A separated vortex ring underlies the flight of the dandelion, Nature, Vol: 562, Pages: 414-418, ISSN: 0028-0836
Wind-dispersed plants have evolved ingenious ways to lift their seeds1,2. The common dandelion uses a bundle of drag-enhancing bristles (the pappus) that helps to keep their seeds aloft. This passive flight mechanism is highly effective, enabling seed dispersal over formidable distances3,4; however, the physics underpinning pappus-mediated flight remains unresolved. Here we visualized the flow around dandelion seeds, uncovering an extraordinary type of vortex. This vortex is a ring of recirculating fluid, which is detached owing to the flow passing through the pappus. We hypothesized that the circular disk-like geometry and the porosity of the pappus are the key design features that enable the formation of the separated vortex ring. The porosity gradient was surveyed using microfabricated disks, and a disk with a similar porosity was found to be able to recapitulate the flow behaviour of the pappus. The porosity of the dandelion pappus appears to be tuned precisely to stabilize the vortex, while maximizing aerodynamic loading and minimizing material requirements. The discovery of the separated vortex ring provides evidence of the existence of a new class of fluid behaviour around fluid-immersed bodies that may underlie locomotion, weight reduction and particle retention in biological and manmade structures.
Seale M, Cummins C, Viola IM, et al., 2018, Design principles of hair-like structures as biological machines, Journal of The Royal Society Interface, Vol: 15, Pages: 1-16, ISSN: 1742-5689
Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas.
Andreou AI, Nakayama N, 2018, Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly, PLoS One, Vol: 13, Pages: 1-18, ISSN: 1932-6203
Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile—simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
Reimegård J, Kundu S, Pendle A, et al., 2017, Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana, Nucleic Acids Research, Vol: 45, Pages: 3253-3265, ISSN: 0305-1048
Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation.
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