Chirality Switching Via Rotation of Bilayer Fourfold Meta-Structure

Chiral effects have been observed from the interaction of chiral plasmonics nanostructures with light. Such nanostructures enhance the chiral response of molecules and provide an ideal platform for biological and chemical sensing. Here, we investigate the chiral switching effects of an array of subwavelength nanostructures with a unit cell composed of four double-layered nanostrips arranged to be rotationally symmetric. We observe chiral switching leading to a change in circular dichroism (CD) signature when the mutual angle between the first and second layer increases from 0° to 90° with respect to each other. This mutual angle can be manipulated to switch the handedness of the nanostructure and cause a change in the outgoing light. We also investigated the field distribution of each mode when circularly polarized light is normally incident into the structure. These modes can be categorized into longitudinal and transverse modes depending on the orientation of their dipole moments. The mode studies clearly show the nature of each plasmonics mode.     

Complex Polarization Response in Plasmonic Nanospirals

Archimedean nanospirals exhibit many far-field resonances that result from the lack of symmetry and strong intra-spiral plasmonic interactions. Here, we present a computational study, with corroborating experimental results, on the plasmonic response of the 4π Archimedean spiral as a function of incident polarization, for spirals in which the largest linear dimension is less than 550 nm. We discuss the modulation of the near-field structure for linearly and circularly polarized light in typical nanospiral configurations. Computational studies of the near-field distributions excited by circularly polarized light illustrate the effects of chirality on plasmonic mechanisms, while rotation of linearly polarized light provides a detailed view of the effects of broken symmetry on nanospiral fields in any given direction in the plane of the spiral. The rotational geometry exhibits a preference for circular polarization that increases near-field enhancement compared to excitation with linearly polarized light and exchanges near-field configurations and resonant modes. By analyzing the effects of polarization and wavelength on the near-field configurations, we also show how the nanospiral could be deployed in applications such as tunable near-field enhancement of nonlinear optical signals from chiral molecules.     

Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model

Abstract

Context: Accidental exposure to life-threatening radiation in a nuclear event is a major concern; there is an enormous need for identifying biomarkers for radiation biodosimetry to triage populations and treat critically exposed individuals.

Objective: To identify dose-differentiating miRNA signatures from whole blood samples of whole body irradiated mice.

Methods: Mice were whole body irradiated with X-rays (2?Gy–15?Gy); blood was collected at various time-points post-exposure; total RNA was isolated; miRNA microarrays were performed; miRNAs differentially expressed in irradiated vs. unirradiated controls were identified; feature extraction and classification models were applied to predict dose-differentiating miRNA signature.

Results: We observed a time and dose responsive alteration in the expression levels of miRNAs. Maximum number of miRNAs were altered at 24-h and 48-h time-points post-irradiation. A 23-miRNA signature was identified using feature selection algorithms and classifier models. An inverse correlation in the expression level changes of miR-17 members, and their targets were observed in whole body irradiated mice and non-human primates.

Conclusion: Whole blood-based miRNA expression signatures might be used for predicting radiation exposures in a mass casualty nuclear incident.     

Mode Controlling of Surface Plasmon Polaritons by Geometric Phases

Metasurfaces are made of two-dimensional arrays of subwavelength nanostructures that form a spatially varying optical response, to control the wave fronts of optical waves. As the feature size of its constituent materials is nanoscale, investigation of the light-nanostructure interactions in the near field is critical for understanding the novel properties of metasurfaces. Here, we used a scanning near-field optical microscope (SNOM) to observe the near-field distribution of surface plasmon polaritons (SPPs) from a ring-shaped metasurface under illumination of circularly polarized light. It was found that with an additional degree of freedom of the geometric phase provided by the regularly arranged metamolecules, control over the near-field interference of the SPPs can be achieved, which is governed by the metasurface geometric symmetry that can be tuned by its topological charge. Meanwhile, the planar chiral character of the metamolecules exerts a deep influence on the near-field interference patterns. Our results can pave the way for active control of SPP propagation in near fields and have potential applications in highly integrated optical communication systems.

     

Lanthanide Circularly Polarized Luminescence: Bases and Applications

Lanthanide (III) luminescence is very characteristic: it is characterized by narrow emission bands, large Stokes shift, and a long excited state lifetime. Moreover, chiral lanthanide complexes can emit strongly circularly polarized light in a way that is almost precluded to purely organic molecules. Thanks to the sensitivity and specificity of the Ln circularly polarized luminescence (CPL) signal, CPL‐active complexes are therefore employed as bioanalytical tools and other uses can be envisaged in many other fields. Here we present a brief overview of the most recently developed CPL‐active lanthanide complexes and a selected few examples of their applications. We briefly discuss the main mechanisms that can rationalize the observed outstanding CPL properties of these systems, and some practical suggestions on how to measure and report data. Chirality 27:1–13, 2015. © 2014 Wiley Periodicals, Inc.     

A new practical tool for deriving a functional signature for herbaceous vegetation

Hypothesis: For any one time and place a ‘functional signature’ can be derived for a sample of herbaceous vegetation in a way that concisely represents the balance between the different clusters of functional attributes that are present among component species. Methods: We developed a spreadsheet‐based tool for calculating functional signatures within the context of the C‐S‐R system of plant functional types. We used the tool to calculate and compare signatures for specimen British vegetation samples which differed in management regime and location in time. Conclusion: The integrative power of the ‘C‐S‐R signature’ is useful in comparative studies involving widely differing samples. Movements in the signature can be used to indicate degree of resistance, resilience, eutrophication and dereliction. Systems of plant functional types other than C‐S‐R might also be approached in this way. Availability: The tool can be downloaded free of charge from the first author's web pages or from the journal's electronic archive.     

Directional Excitation of Surface Plasmon Polaritons by Circularly Polarized Vortex Beams

We investigate the excitation of surface plasmon polaritons (SPPs) using a metallic nanoaperture array illuminated by circularly polarized Laguerre-Gaussian (LG) vortex beams. The direction of SPP excitation is tunable by changing the circular polarization and topological charge of LG beams. The left- or right-handed circular polarization determines SPP propagation on either side of the nanoaperture array. Furthermore, varying the topological charge of LG beam will result in beam splitting of SPPs. We also utilize a composite nanoaperture array with different periods to achieve unidirectional excitation of SPPs. The study provides an interesting approach to control the excitation direction of SPPs and may find great applications in SPP generators and optical switches.

     

Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins

Detecting similarities between local binding surfaces can facilitate identification of enzyme binding sites and prediction of enzyme functions, and aid in our understanding of enzyme mechanisms. Constructing a template of local surface characteristics for a specific enzyme function or binding activity is a challenging task, as the size and shape of the binding surfaces of a biochemical function often vary. Here we introduce the concept of signature binding pockets, which captures information on preserved and varied atomic positions at multiresolution levels. For proteins with complex enzyme binding and activity, multiple signatures arise naturally in our model, forming a signature basis set that characterizes this class of proteins. Both signatures and signature basis sets can be automatically constructed by a method called SOLAR (Signature Of Local Active Regions). This method is based on a sequence-order-independent alignment of computed binding surface pockets. SOLAR also provides a structure-based multiple sequence fragment alignment to facilitate the interpretation of computed signatures. By studying a family of evolutionarily related proteins, we show that for metzincin metalloendopeptidase, which has a broad spectrum of substrate binding, signature and basis set pockets can be used to discriminate metzincins from other enzymes, to predict the subclass of metzincins functions, and to identify specific binding surfaces. Studying unrelated proteins that have evolved to bind to the same NAD cofactor, we constructed signatures of NAD binding pockets and used them to predict NAD binding proteins and to locate NAD binding pockets. By measuring preservation ratio and location variation, our method can identify residues and atoms that are important for binding affinity and specificity. In both cases, we show that signatures and signature basis set reveal significant biological insight.     

Whole-animal Imaging and Flow Cytometric Techniques for Analysis of Antigen-specific CD8+ T Cell Responses after Nanoparticle Vaccination

Traditional vaccine adjuvants, such as alum, elicit suboptimal CD8+ T cell responses. To address this major challenge in vaccine development, various nanoparticle systems have been engineered to mimic features of pathogens to improve antigen delivery to draining lymph nodes and increase antigen uptake by antigen-presenting cells, leading to new vaccine formulations optimized for induction of antigen-specific CD8+ T cell responses. In this article, we describe the synthesis of a “pathogen-mimicking” nanoparticle system, termed interbilayer-crosslinked multilamellar vesicles (ICMVs) that can serve as an effective vaccine carrier for co-delivery of subunit antigens and immunostimulatory agents and elicitation of potent cytotoxic CD8+ T lymphocyte (CTL) responses. We describe methods for characterizing hydrodynamic size and surface charge of vaccine nanoparticles with dynamic light scattering and zeta potential analyzer and present a confocal microscopy-based procedure to analyze nanoparticle-mediated antigen delivery to draining lymph nodes. Furthermore, we show a new bioluminescence whole-animal imaging technique utilizing adoptive transfer of luciferase-expressing, antigen-specific CD8+ T cells into recipient mice, followed by nanoparticle vaccination, which permits non-invasive interrogation of expansion and trafficking patterns of CTLs in real time. We also describe tetramer staining and flow cytometric analysis of peripheral blood mononuclear cells for longitudinal quantification of endogenous T cell responses in mice vaccinated with nanoparticles.     

A Terahertz Tunable Metamaterial Reflective Polarization Converter Based On Vanadium Oxide Film

In this paper, on the basis of metamaterial, a simply single-layer and tunable reflective polarization converter has been numerically investigated, which is composed of vanadium dioxide film (VO₂) component combined with two-corner-cut square patch cut by a slit and reflective ground layer. Calculated results obtained by the CST Microwave Studio show that in the frequency of 2.22–5.42 THz, high polarization conversion efficiency (polarization conversion ratio (PCR) above 90%) can be normally achieved at the temperature about 25 °C for both the linearly and circularly polarized wave incidence. At the same time, the cross-polarization converter can be analyzed and obtained from the view on qualitative variable of polarization azimuth angle (θ) and ellipticity (η). Moreover, a tunable polarization conversion property can be realized by the designed device with vanadium dioxide utilizing changing different conductivities. Even so, to be demonstrated, the physical mechanism of the merits of controllability and uniqueness has been discussed by the distributions of current densities and E-field map, respectively. According to the prior results, the designed metamaterial could be applied in the area of temperature-controlled sensing, THz wireless communication, tunable polarized devices.

     

Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures

Background

DNA word frequencies, normalized for genomic AT content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a “genomic signature.” The genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled DNA. Genomic signatures can also be used to search for horizontally transferred DNA or DNA regions subjected to special selection forces. Thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. The factors associated with the stability of the genomic signatures are not known, and this motivated us to investigate further. We analyzed the intra-genomic variance of genomic signatures based on AT content normalization (0^th order Markov model) as well as genomic signatures normalized by smaller DNA words (1^st and 2^nd order Markov models) for 636 sequenced prokaryotic genomes. Regression models were fitted, with intra-genomic signature variance as the response variable, to a set of factors representing genomic properties such as genomic AT content, genome size, habitat, phylum, oxygen requirement, optimal growth temperature and oligonucleotide usage variance (OUV, a measure of oligonucleotide usage bias), measured as the variance between genomic tetranucleotide frequencies and Markov chain approximated tetranucleotide frequencies, as predictors.

Principal Findings

Regression analysis revealed that OUV was the most important factor (p<0.001) determining intra-genomic homogeneity as measured using genomic signatures. This means that the less random the oligonucleotide usage is in the sense of higher OUV, the more homogeneous the genome is in terms of the genomic signature. The other factors influencing variance in the genomic signature (p<0.001) were genomic AT content, phylum and oxygen requirement.

Conclusions

Genomic homogeneity in prokaryotes is intimately linked to genomic GC content, oligonucleotide usage bias (OUV) and aerobiosis, while oligonucleotide usage bias (OUV) is associated with genomic GC content, aerobiosis and habitat.     

Iron Oxide Nanoparticle Assisted Purification and Mass Spectrometry Based Proteolytic Mapping of Intact CD4+T Cells from Human Blood

Abstract

Iron oxide nanoparticles have been used for many years as clinical applications. We have developed a rapid immunoaffinity isolation method of CD4⁺T cells from a mixed cell population of human blood using iron oxide nanoparticles. Anti CD4-antibody has been attached to iron oxide nanoparticles after its surface modification. The antibody tagged iron oxide nanoparticle beads are simply incubated with the mixed cell population of human blood and CD4⁺T cells are purified using an external magnetic field. The purification level was checked by fluorescence microscopy and flow cytometry. The purified CD4⁺T cells were digested with trypsin with different time periods and the products were analyzed by MALDI-TOF mass spectrometry, without further fractionation or purification, to obtain its proteome pattern. A database search showed a number of peptide masses matched specific to T-cell peptide masses. These results indicate that iron oxide nanoparticles are useful for CD4⁺T cell purification, and mass spectrometry based proteolytic fingerprint is simple and swift for identifying putative surface biomarkers from the whole cell surfaces.     

Subwavelength Micro-Antenna for Achieving Slow Light at Microwave Wavelengths via Electromagnetically Induced Transparency in 2D Metamaterials

In this paper, a tunable slow light 2D metamaterial is presented and investigated. The metamaterial unit cell is composed of three metallic strips as radiative and non-radiative modes. Once introducing asymmetry, a transparency window induced by coupling between the dark and bright modes is observed. The transmission characteristics and the slow light properties of the metamaterial are verified by numerical simulation, which is in a good agreement with theoretical predictions. The impact of asymmetric parameter on transparency window is also investigated. Simulation results show the spectral properties and the group index of the proposed 2D metamaterial can be tunned by adjusting asymmetric structure parameter, temperature and also the metal used in the metamaterial. Furthermore, the electromagnetic field distributions, excited surface currents, induced electric dipole and quadruples, and slow light properties of the metamaterial are investigated in details as well as transmission spectral responses. The outstanding result is that, the 2D-metamaterial is in a high decrease of the group velocity and therefore slow light applications, because in the best state, the group velocity in our structure decreases by a factor of 221 at T=100 K using copper as metal in optimization asymmetric case.     

Structure Metallic Surface for Terahertz Plasmonics

Plasmonics is the field of study of the interaction between incident light and electrons in metals. It is used widely for developing nanophotonic devices. The structured metallic surface such as metamaterials can be used to produce spoof surface plasmons at any frequencies with the dimensions of unit cell less than the incident wavelength. Terahertz plasmonics is attracted to the field of research since it is used for sensing biological components even in a weak environment. The issue with planar metamaterials is a lower quality factor value. Several methods have been adopted for obtaining high Q-value in metamaterials. Among them, Fano- and Toroidal-based metamaterials offer high Q-factor and string localized field enhancement. This article discusses the importance and developments in the field of high-Q terahertz metamaterial for plasmonics applications. The nonlinear responses of terahertz metamaterial under high-intense THz pulses are also discussed.

     

On reliable discovery of molecular signatures

Background  

Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control error rates such as the false discovery rate (FDR) in signature discovery. Moreover, signatures for cancer gene expression have been shown to be unstable, that is, difficult to replicate in independent studies, casting doubts on their reliability.     

Individual Split Au Square Nanorings for Surface-Enhanced Raman and Hyper-Raman Scattering

In this paper, individual split Au square nanorings were numerically proposed as novel substrates for surface-enhanced Raman and hyper-Raman scattering (SERS and SEHRS) simultaneously. The peak wavelengths of their localized surface plasmon resonance (LSPR) fall in the near-infrared and visible light regions, respectively, which are able to be finely tuned to match well with the wavelengths of the incident laser and hyper-Raman scattered light beams. Their SEHRS and SERS performances along with electromagnetic (EM) field distributions are numerically investigated by finite element method. With the enhancement of near electric-fields generated by LSPRs, the maximum SEHRS and SERS enhancement factors are demonstrated to reach 1.22?×?10¹² and 10⁸, respectively. Meanwhile, the corresponding SERS-based refractive index (RI) sensitivity factor reaches as high as 258 nm/RIU and 893 nm/RIU, at visible and near-infrared wavelengths, respectively. The proposed structure holds great promise both for developing SEHRS- and SERS-based RI sensing substrates, which shows strong potential applications in nanosensing and enhanced Raman scattering.

     

A simple method for the computation of first neighbour frequencies of DNAs from CD spectra

A procedure for the computation of the first neighbour frequencies of DNA's is presented. This procedure is based on the first neighbour approximation of Gray and Tinoco. We show that the knowledge of all the ten elementary CD signals attached to the ten double stranded first neighbour configurations is not necessary. One can obtain the ten frequencies of an unknown DNA with the use of eight elementary CD signals corresponding to eight linearly independent polymer sequences. These signals can be extracted very simply from any eight or more CD spectra of double stranded DNA's of known frequencies. The ten frequencies of a DNA are obtained by least square fit of its CD spectrum with these elementary signals. One advantage of this procedure is that it does not necessitate linear programming, it can be used with CD data digitalized using a large number of wavelengths, thus permitting an accurate resolution of the CD spectra. Under favorable case, the ten frequencies of a DNA (not used as input data) can be determined with an average absolute error < 2%. We have also observed that certain satellite DNA's, those of Drosophila virilis and Callinectes sapidus have CD spectra compatible with those of DNA's of quasi random sequence; these satellite DNA's should adopt also the B-form in solution.     

Ring Gap Resonance Modes on Disk/Film Coupling System Caused by Strong Plasmon Interaction

Ring modes with large wave vectors cannot be easily excited on a single disk by the plane wave illumination with the polarization parallel to the disk interface. In this work, we show that special antisymmetric ring gap modes on the surface of the disk in close proximity to the metallic thin film can be excited in the visible light region of the electromagnetic spectrum. In the presence of the film, the strong plasmon interaction between disk and film causes ring gap modes to have lower energies and be more easily excited. We apply the plasmon hybridization method to illustrate the ring gap modes arising from the interaction between the localized disk plasmons and the continuum surface plasmons. The calculated hybridization data show good agreement with the results of finite element simulations. The excitation of ring gap modes provides further insight into the strong coupling of plasmons and the design of novel nanostructures.