Imperial College London

DrNaomiNakayama

Faculty of EngineeringDepartment of Bioengineering

Senior Lecturer
 
 
 
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Contact

 

n.nakayama Website

 
 
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Location

 

B213bBessemer BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

8 results found

Certini D, Fazan L, Nakayama N, Viola IM, Kozlowski Get al., 2020, Velocity of the falling dispersal units in Zelkova abelicea: remarkable evolutionary conservation within the relict tree genus, AMERICAN JOURNAL OF BOTANY, Vol: 107, Pages: 1831-1838, ISSN: 0002-9122

Journal article

Nakayama N, 2020, Naomi Nakayama, New Phytologist, Vol: 226, Pages: 1548-1549, ISSN: 0028-646X

Journal article

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.

Journal article

Andreou AI, Nakayama N, 2020, Mobius Assembly., Methods Mol Biol, Vol: 2205, Pages: 201-218

Mobius Assembly is a versatile and user-friendly DNA Assembly method, which facilitates rapid and simple generation of DNA constructs. Mobius Assembly combines high cloning capacity and vector toolkit simplicity to streamline combinatorial assemblies. It is a two-level hierarchical modular cloning system that enables quadruple assembly augmentation. It adopts the 4 bp standard overhangs defined by Phytobricks to promote standard part sharing, and it can be made compatible with different chassis. Furthermore, Mobius Assembly reduces domestication requirements and uses chromogenic proteins to facilitate the identification of positive assemblies.

Journal article

Cummins C, Seale M, Macente A, Certini D, Mastropaolo E, Viola IM, Nakayama Net 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.

Journal article

Seale M, Cummins C, Viola IM, Mastropaolo E, Nakayama Net 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.

Journal article

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.

Journal article

Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson Oet 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.

Journal article

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