Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanodisk codes.

ABSTRACT: We report a new encoding system based upon dispersible arrays of nanodisks prepared by on-wire lithography and functionalized with Raman active chromophores. These nanodisk arrays are encoded both physically (in a "barcode" pattern) and spectroscopically (Raman) along the array. These structures can be used in covert encoding strategies because of their small size or as biological labels with readout by scanning confocal Raman spectroscopy. As proof-of-concept, we demonstrate their utility in DNA detection in a multiplexed format at target concentrations as low as 100 fM.

SUBMITTER: Qin L

PROVIDER: S-EPMC3200538 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nanodisk codes.

Qin Lidong L Banholzer Matthew J MJ Millstone Jill E JE Mirkin Chad A CA

Nano letters 20071128 12

We report a new encoding system based upon dispersible arrays of nanodisks prepared by on-wire lithography and functionalized with Raman active chromophores. These nanodisk arrays are encoded both physically (in a "barcode" pattern) and spectroscopically (Raman) along the array. These structures can be used in covert encoding strategies because of their small size or as biological labels with readout by scanning confocal Raman spectroscopy. As proof-of-concept, we demonstrate their utility in DN ...[more]

PMID: 18041858

Similar Datasets

Lasing in Ni Nanodisk Arrays.

Project description:We report on lasing at visible wavelengths in arrays of ferromagnetic Ni nanodisks overlaid with an organic gain medium. We demonstrate that by placing an organic gain material within the mode volume of the plasmonic nanoparticles both the radiative and, in particular, the high ohmic losses of Ni nanodisk resonances can be compensated. Under increasing pump fluence, the systems exhibit a transition from lattice-modified spontaneous emission to lasing, the latter being characterized by highly directional and sub-nanometer line width emission. By breaking the symmetry of the array, we observe tunable multimode lasing at two wavelengths corresponding to the particle periodicity along the two principal directions of the lattice. Our results are relevant for loss-compensated magnetoplasmonic devices and topological photonics.

| S-EPMC6543507 | biostudies-literature

ApoE enhances nanodisk-mediated curcumin delivery to glioblastoma multiforme cells.

Project description:To evaluate the effect of incorporating the polyphenol, curcumin, into nanodisk (ND) particles on its biological activity.Curcumin-NDs formulated with different scaffold proteins were incubated with cultured glioblastoma multiforme cells.When ApoE was employed as the ND scaffold protein, enhanced curcumin uptake was observed. Furthermore, ApoE curcumin-NDs induced greater cell death than either free curcumin or ApoAI curcumin-NDs. A total of 1 h after exposure of glioblastoma multiforme cells to ApoE curcumin-NDs, significant curcumin uptake was detected while ApoE was localized at the cell surface. After 2 h, a portion of the curcumin had migrated to the nucleus, giving rise to enhanced fluorescence intensity in discrete intranuclear sites.ApoE-mediated interaction of curcumin-NDs with glioblastoma multiforme cells leads to enhanced curcumin uptake and increased biological activity.

| S-EPMC3904962 | biostudies-literature

Neural burst codes disguised as rate codes.

Project description:The burst coding hypothesis posits that the occurrence of sudden high-frequency patterns of action potentials constitutes a salient syllable of the neural code. Many neurons, however, do not produce clearly demarcated bursts, an observation invoked to rule out the pervasiveness of this coding scheme across brain areas and cell types. Here we ask how detrimental ambiguous spike patterns, those that are neither clearly bursts nor isolated spikes, are for neuronal information transfer. We addressed this question using information theory and computational simulations. By quantifying how information transmission depends on firing statistics, we found that the information transmitted is not strongly influenced by the presence of clearly demarcated modes in the interspike interval distribution, a feature often used to identify the presence of burst coding. Instead, we found that neurons having unimodal interval distributions were still able to ascribe different meanings to bursts and isolated spikes. In this regime, information transmission depends on dynamical properties of the synapses as well as the length and relative frequency of bursts. Furthermore, we found that common metrics used to quantify burstiness were unable to predict the degree with which bursts could be used to carry information. Our results provide guiding principles for the implementation of coding strategies based on spike-timing patterns, and show that even unimodal firing statistics can be consistent with a bivariate neural code.

| S-EPMC8342467 | biostudies-literature

Morphing a plasmonic nanodisk into a nanotriangle.

Project description:We morph a silver nanodisk into a nanotriangle by producing a series of nanoparticles with electron beam lithography. Using electron energy loss spectroscopy (EELS), we map out the plasmonic eigenmodes and trace the evolution of edge and film modes during morphing. Our results suggest that disk modes, characterized by angular order, can serve as a suitable basis for other nanoparticle geometries and are subject to resonance energy shifts and splittings, as well as to hybridization upon morphing. Similar to the linear combination of atomic orbitals (LCAO) in quantum chemistry, we introduce a linear combination of plasmonic eigenmodes to describe plasmon modes in different geometries, hereby extending the successful hybridization model of plasmonics.

| S-EPMC4133183 | biostudies-other

Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers.

Project description:Experimental characterization of membrane proteins often requires solubilization. A recent approach is to use styrene-maleic acid (SMA) copolymers to isolate membrane proteins in nanometer-sized membrane disks, or so-called SMA lipid particles (SMALPs). The approach has the advantage of allowing direct extraction of proteins, keeping their native lipid environment. Despite the growing popularity of using SMALPs, the molecular mechanism behind the process remains poorly understood. Here, we unravel the molecular details of the nanodisk formation by using coarse-grained molecular dynamics simulations. We show how SMA copolymers bind to the lipid bilayer interface, driven by the hydrophobic effect. Due to the concerted action of multiple adsorbed copolymers, large membrane defects appear, including small, water-filled pores. The copolymers can stabilize the rim of these pores, leading to pore growth and membrane disruption. Although complete solubilization is not seen on the timescale of our simulations, self-assembly experiments show that small nanodisks are the thermodynamically preferred end state. Our findings shed light on the mechanism of SMALP formation and on their molecular structure. This can be an important step toward the design of optimized extraction tools for membrane protein research.

| S-EPMC6084417 | biostudies-literature

Plasmon-Coupled Whispering Gallery Modes on Nanodisk Arrays for Signal Enhancements.

Project description:Metallic nanostructures including single and double nanodisks are successfully used to enhance the localized electric field in vicinity of microcavity in whispering gallery mode (WGM) sensor. We demonstrate numerical calculations of plasmonic coupling of WGMs to single and double nanodisk arrays on a planar substrate. We then experimentally confirmed that the resonance wavelength of WGM sensor was dramatically shifted by adoption of single and double nanodisks on the surface of microcavity in the WGM sensor. Thus, our approach provides the tunable sensitivity of WGM sensor, and has a great potential to be used in numerous areas where the single biomolecule, protein-protein folding and biomolecular interactions are involved.

| S-EPMC5601917 | biostudies-literature

Forming individual magnetic biskyrmions by merging two skyrmions in a centrosymmetric nanodisk.

Project description:When two magnetic skyrmions - whirl-like, topologically protected quasiparticles - form a bound pair, a biskyrmion state with a topological charge of NSk?=?±2 is constituted. Recently, especially the case of two partially overlapping skyrmions has brought about great research interest. Since for its formation the individual skyrmions need to posses opposite in-plane magnetizations, such a biskyrmion cannot be stabilized by the Dzyaloshinskii-Moriya-interaction (DMI), which is the interaction that typically stabilizes skyrmions in non-centrosymmetric materials and at interfaces. Here, we show that these biskyrmions can be stabilized by the dipole-dipole interaction in centrosymmetric materials in which the DMI is forbidden. Analytical considerations indicate that the bound state of a biskyrmion is energetically preferable over two individual skyrmions. As a result, when starting from two skyrmions in a micromagnetic simulation, a biskyrmion is formed upon relaxation. We propose a scheme that allows to control this biskyrmion formation in nanodisks and analyze the individual steps.

| S-EPMC6606756 | biostudies-literature

Ambiguous genetic codes

Project description:Crammed, ambiguous genetic codes

| PRJEB9019 | ENA

Optical and electrical properties of the nanodisk-shaped SnS layers grown by sputtering.

Project description:In this data article, we presented the structural, optical, and electrical data of the nanodisk-shaped SnS layers. A facile formation of orthorhombic SnS derived from SnS2 particles was discussed in our previous study (Patel et al., 2017) [1]. The data includes the standard XRD patterns supercell structure of the Orthorhombic SnS material, the photograph of prepared samples, thickness dependent absorbance spectra, and temperature dependent carrier concentration and its mobility estimated from the hall measurement of SnS samples.

| S-EPMC5635201 | biostudies-literature

Protective and antifungal properties of Nanodisk-Amphotericin B over commercially available Amphotericin B.

Project description:ObjectiveAmphotericin B (AMB), a potent antifungal agent, has been employed as topical and systemic therapy for sinonasal fungal infections. A novel formulation of nanodisc (ND) containing super aggregated AMB (ND-AMB) for the treatment of fungal infections has been recently developed to provide greater protection from AMB toxicity than current, clinically approved lipid-based formulations. The objective of the current study was to evaluate the safety and potency of ND-AMB for sinonasal delivery using an in vitro model.MethodsHuman sinonasal tissue was harvested during endoscopic sinus surgery and grown at air-liquid interface until well-differentiated. Cultures were exposed to ND-AMB vs AMB and changes in K+ permeability and resistance were measured and recorded via Ussing chamber assay. Ciliary beat frequency (CBF) was analyzed in parallel as well as cytotoxic assay. Potency was assessed using real-time PCR measurement of the Aspergillus fumigatus 18S rRNA.ResultsUssing chamber studies revealed K+ currents that increased rapidly within 30 s of adding AMB (10 μg/mL) to the apical side, indicating apical membranes had become permeable to K+ ions. In contrast, negligible induction of K+ current was obtained following addition of ND-AMB [AMB = (107.7 ± 15.9) μA/cm2 AMB vs ND-AMB = (2.3 ± 0.7) μA/cm2 ND-AMB; P = 0.005]. ND-AMB also protected nasal epithelial cells from cytotoxicity of AMB (P < 0.05). There was no difference in ciliary beat frequency between the two groups (P = 0.96). The expression of A. fumigatus 18S rRNA with exposure of lower dose of ND-AMB was significantly lower compared to that with AMB (P < 0.05).ConclusionsData from the present study suggests ND-AMB protects human nasal epithelia membranes from AMB toxicity by protecting against apical cell K+ permeability while maintaining uncompromised antifungal property compared to AMB. ND-AMB could provide a novel topical therapy for sinonasal fungal diseases.

| S-EPMC5683641 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data