Bidirectional waveguide coupling with plasmonic Fano nanoantennas

We introduce the concept of a bidirectional, compact single-element Fano nanoantenna that allows for directional coupling of light in opposite directions of a high-index dielectric waveguide for two different operation wavelengths. We utilize a Fano resonance to tailor the radiation phases of a gold nanodisk and a nanoslit that is inscribed into the nanodisk to realize bidirectional scattering. We show that this Fano nanoantenna operates as a bidirectional waveguide coupler at telecommunication wavelengths and, thus, is ideally suitable for integrated wavelength-selective light demultiplexing

Electro-optical switching by liquid-crystal controlled metasurfaces

We study the optical response of a metamaterial surface created by a lattice of split-ring resonators covered with a nematic liquid crystal and demonstrate millisecond timescale switching between electric and magnetic resonances of the metasurface. This is achieved due to a high sensitivity of liquid-crystal molecular reorientation to the symmetry of the metasurface as well as to the presence of a bias electric field. Our experiments are complemented by numerical simulations of the liquid-crystal reorientation.Comment: 6 pages, 3 figure

High-efficiency light-wave control with all-dielectric optical Huygens' metasurfaces

Optical metasurfaces have developed as a breakthrough concept for advanced wave-front engineering enabled by subwavelength resonant nanostructures. However, reflection and/or absorption losses as well as low polarisation-conversion efficiencies pose a fundamental obstacle for achieving high transmission efficiencies that are required for practical applications. Here we demonstrate, for the first time to our knowledge, highly efficient all-dielectric metasurfaces for near-infrared frequencies using arrays of silicon nanodisks as meta-atoms. We employ the main features of Huygens' sources, namely spectrally overlapping electric and magnetic dipole resonances of equal strength, to demonstrate Huygens' metasurfaces with a full transmission-phase coverage of 360 degrees and near-unity transmission, and we confirm experimentally full phase coverage combined with high efficiency in transmission. Based on these key properties, we show that all-dielectric Huygens' metasurfaces could become a new paradigm for flat optical devices, including beam-steering, beam-shaping, and focusing, as well as holography and dispersion control.Comment: 17 pages, 5 figure

Hybrid nanoantennas for directional emission enhancement

Plasmonic and dielectric nanoparticles offer complementary strengths regarding their use as optical antenna elements. While plasmonic nanoparticles are well-known to provide strong decay rate enhancement for localized emitters, all-dielectric nanoparticles can enable high directivity combined with low losses. Here, we suggest a hybrid metal-dielectric nanoantenna consisting of a gold nanorod and a silicon nanodisk, which combines all these advantages. Our numerical analysis reveals a giant enhancement of directional emission together with simultaneously high radiation efficiency (exceeding 70%). The suggested hybrid nanoantenna has a subwavelength footprint, and all parameters and materials are chosen to be compatible with fabrication by two-step electron-beam lithography.The authors acknowledge a support from the Australian Research Council

Analysis of the Host Transcriptome from Demyelinating Spinal Cord of Murine Coronavirus-Infected Mice

Persistent infection of the mouse central nervous system (CNS) with mouse hepatitis virus (MHV) induces a demyelinating disease pathologically similar to multiple sclerosis and is therefore used as a model system. There is little information regarding the host factors that correlate with and contribute to MHV-induced demyelination. Here, we detail the genes and pathways associated with MHV-induced demyelinating disease in the spinal cord. High-throughput sequencing of the host transcriptome revealed that demyelination is accompanied by numerous transcriptional changes indicative of immune infiltration as well as changes in the cytokine milieu and lipid metabolism. We found evidence that a Th1-biased cytokine/chemokine response and eicosanoid-derived inflammation accompany persistent MHV infection and that antigen presentation is ongoing. Interestingly, increased expression of genes involved in lipid transport, processing, and catabolism, including some with known roles in neurodegenerative diseases, coincided with demyelination. Lastly, expression of several genes involved in osteoclast or bone-resident macrophage function, most notably TREM2 and DAP12, was upregulated in persistently infected mouse spinal cord. This study highlights the complexity of the host antiviral response, which accompany MHV-induced demyelination, and further supports previous findings that MHV-induced demyelination is immune-mediated. Interestingly, these data suggest a parallel between bone reabsorption by osteoclasts and myelin debris clearance by microglia in the bone and the CNS, respectively. To our knowledge, this is the first report of using an RNA-seq approach to study the host CNS response to persistent viral infection

Enhancing Eu3+ magnetic dipole emission by resonant plasmonic nanostructures

We demonstrate the enhancement of magnetic dipole spontaneous emission from Eu3?ions by an engineered plas-monic nanostructure that controls the electromagnetic environment of the emitter. Using an optical microscope setup, an enhancement in the intensity of the Eu3?magnetic dipole emission was observed for emitters located in close vicinity to a gold nanohole array designed to support plasmonic resonances overlapping with the emission spectrum of the ions

HAMR: High-Throughput Annotation of Modified Ribonucleotides

RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, when converted to cDNA in the course of RNA sequencing, can produce sequence patterns that are distinguishable from simple base-calling errors. To determine whether these modifications can be detected in RNA sequencing data, we developed a method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications. Using small RNA-seq data we were able to detect 92% of all known human tRNA modification sites that are predicted to affect RT activity. We also found that different modifications produce distinct patterns of cDNA sequence, allowing us to differentiate between two classes of adenosine and two classes of guanine modifications with 98% and 79% accuracy, respectively. To show the robustness of this method to sample preparation and sequencing methods, as well as to organismal diversity, we applied it to a publicly available yeast data set and achieved similar levels of accuracy. We also experimentally validated two novel and one known 3-methylcytosine (3mC) sites predicted by HAMR in human tRNAs. Researchers can now use our method to identify and characterize RNA modifications using only RNA-seq data, both retrospectively and when asking questions specifically about modified RNA

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in \u3cem\u3eArabidopsis\u3c/em\u3e

The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we marry classical nuclease-based structure mapping techniques with high-throughput sequencing technology to interrogate all base-paired RNA in Arabidopsis thaliana and identify ∼200 new small (sm)RNA–producing substrates of RNA–DEPENDENT RNA POLYMERASE6. Our comprehensive analysis of paired RNAs reveals conserved functionality within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs, as well as a novel population of functional RNAs, many of which are the precursors of smRNAs. Finally, we identify intra-molecular base-pairing interactions to produce a genome-wide collection of RNA secondary structure models. Although our methodology reveals the pairing status of RNA molecules in the absence of cellular proteins, previous studies have demonstrated that structural information obtained for RNAs in solution accurately reflects their structure in ribonucleoprotein complexes. Furthermore, our identification of RNA–DEPENDENT RNA POLYMERASE6 substrates and conserved functional RNA domains within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs using this approach strongly suggests that RNA molecules are correctly folded into their secondary structure in solution. Overall, our findings highlight the importance of base-paired RNAs in eukaryotes and present an approach that should be widely applicable for the analysis of this key structural feature of RNA