A plant disease extension of the Infectious Disease Ontology

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism

Electromagnetic properties of anisotropic plasmonic metamaterials

In this dissertation we study the electromagnetic properties of plasmonic metamaterials. We develop an analytical description to solve the fundamental problem of free-space scattering in planar plasmonic systems by utilizing anisotropic metamaterials. We show with exact numerical simulations that these manufactured materials do completely eliminate the scattering, and even in the case of fabrication defects the scattering is greatly minimized. We further show that the standard effective medium theory calculations for the cases of anisotropic metamaterials constructed of metal-dielectric layers fails to account for nonlocal effects in the cases where the constituent materials have large differences in permittivity. We show how it is possible to construct a plasmon waveguide out of such a structure and describe a new naming scheme based on the bulk plasmon modes that are supported. Finally, we study the effective medium theory applied to the case of plasmonic wires embedded in a dielectric host. We describe the effect the geometric properties of the structure has on effective permittivities. For example, we show that a 10% stretching/compression of the distance between nanowires can change the sign of elements of the permittivity tensor. These results can be applied to high-performance optical sensing, optical polarizers, novel lenses including the hyper- and superlenses, and subdiffraction imaging

Scattering-free plasmonic optics with anisotropic metamaterials

We develop an approach to utilize anisotropic metamaterials to solve one of the fundamental problems of modern plasmonics -- parasitic scattering of surface waves into free-space modes, opening the road to truly two-dimensional plasmonic optics. We illustrate the developed formalism on examples of plasmonic refractor and plasmonic crystal, and discuss limitations of the developed technique and its possible applications for sensing and imaging structures, high-performance mode couplers, optical cloaking structures, and dynamically reconfigurable electro-plasmonic circuits

The Plant Ontology: A common reference ontology for plants

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms

Nanowire metamaterials with extreme optical anisotropy

We study perspectives of nanowire metamaterials for negative-refraction waveguides, high-performance polarizers, and polarization-sensitive biosensors. We demonstrate that the behavior of these composites is strongly influenced by the concentration, distribution, and geometry of the nanowires, derive an analytical description of electromagnetism in anisotropic nanowire-based metamaterials, and explore the limitations of our approach via three-dimensional numerical simulations. Finally, we illustrate the developed approach on the examples of nanowire-based high energy-density waveguides and non-magnetic negative index imaging systems with far-field resolution of one-sixth of vacuum wavelength.Comment: Updated version; accepted to Appl.Phys.Let

The Plant Ontology facilitates comparisons of plant development stages across species

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution

Highly Confined Optical Modes in Nanoscale Metal-Dielectric Multilayers

We show that a stack of metal-dielectric nanolayers, in addition to the long- and short-range plasmons, guides also an entire family of modes strongly confined within the multilayer - the bulk plasmon modes. We propose the classification scheme that reflects specific properties of these modes. We report experimental verification of the bulk plasmon modes by measuring modal indices in a structure made of three pairs of silica(29nm)/gold(25nm) layers.Comment: 4 pages, 4 figure

Plasmonic Nanolayer Composites: Coupled Plasmon Polaritons, Effective-Medium Response, and Subdiffraction Light Manipulation

We analyze the evolution of the modes in nanoplasmonic multilayered structures and study the transition of the optical properties of these systems to the effective-medium regime. We derive the effective-medium parameters and study the validity of our analytical results with exact numerical solutions of Maxwell equations. Finally, we explore the applications of multilayered systems for subwavelength light confinement in planar and circular waveguides

Quasi-planar optics: computing light propagation and scattering in planar waveguide arrays

We analyze wave propagation in coupled planar waveguides, pointing specific attention to modal cross-talk and out-of-plane scattering in quasi-planar photonics. An algorithm capable of accurate numerical computation of wave coupling in arrays of planar structures is developed and illustrated on several examples of plasmonic and volumetric waveguides. An analytical approach to reduce or completely eliminate scattering and modal cross-talk in planar waveguides with anisotropic materials is also presented

Nonlocal effects in effective-medium response of nanolayered metamaterials

The authors analyze electromagnetic modes in multilayered nanocomposites and demonstrate that the response of a majority of realistic layered structures is strongly affected by the nonlocal effects originating from strong field oscillations across the system, and is not described by conventional effective-medium theories. They develop the analytical description of the relevant phenomena and confirm their results with numerical solutions of Maxwell equations. Finally, the authors use the developed formalism to demonstrate that multilayered plasmonic nanostructures support high-index volume modes, confined to deep subwavelength areas, opening a wide class of applications in nanoscale light management