Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prospective Use of High-Refractive Index Materials for Single Molecule Detection in Flow Cytometry.

ABSTRACT: Phenotyping extracellular vesicles (EVs), where surface receptor expression is often as low as one molecule per EV, remains problematic due to the inability of commercial flow cytometers to provide single-fluorescent molecule sensitivity. While EVs are widely considered to be of great potential as diagnostic, prognostic and theranostic biomarkers, their use is currently hindered by the lack of tools available to accurately and reproducibly enumerate and phenotype them. Herein, we propose a new class of labels that leverage the biophysical properties of materials with unique complex refractive indices and demonstrate that this class of labels has the possibility of allowing single-epitope detection using conventional flow cytometry.

SUBMITTER: Welsh JA

PROVIDER: S-EPMC6111846 | biostudies-other | 2018 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Prospective Use of High-Refractive Index Materials for Single Molecule Detection in Flow Cytometry.

Welsh Joshua A JA Kepley Julia J Rosner Ariel A Horak Peter P Berzofsky Jay A JA Jones Jennifer C JC

Sensors (Basel, Switzerland) 20180801 8

Phenotyping extracellular vesicles (EVs), where surface receptor expression is often as low as one molecule per EV, remains problematic due to the inability of commercial flow cytometers to provide single-fluorescent molecule sensitivity. While EVs are widely considered to be of great potential as diagnostic, prognostic and theranostic biomarkers, their use is currently hindered by the lack of tools available to accurately and reproducibly enumerate and phenotype them. Herein, we propose a new c ...[more]

PMID: 30071576

Similar Datasets

Strong coupling of single quantum dots with low-refractive-index/high-refractive-index materials at room temperature.

Project description:Strong coupling between a cavity and transition dipole moments in emitters leads to vacuum Rabi splitting. Researchers have not reported strong coupling between a single emitter and a dielectric cavity at room temperature until now. In this study, we investigated the photoluminescence (PL) spectra of colloidal quantum dots on the surface of a SiO2/Si material at various collection angles at room temperature. We measured the corresponding reflection spectra for the SiO2/Si material and compared them with the PL spectra. We observed PL spectral splitting and regarded it as strong coupling between colloidal quantum dots and the SiO2/Si material. Upper polaritons and lower polaritons exhibited anticrossing behavior. We observed Rabi splitting from single-photon emission in the dielectric cavity at room temperature. Through analysis, we attributed the Rabi splitting to strong coupling between quantum dots and bound states in the continuum in the low-refractive-index/high-refractive-index hybrid material.

| S-EPMC7679155 | biostudies-literature

Designing High-Refractive Index Polymers Using Materials Informatics.

Project description:A machine learning strategy is presented for the rapid discovery of new polymeric materials satisfying multiple desirable properties. Of particular interest is the design of high refractive index polymers. Our in silico approach employs a series of quantitative structure⁻property relationship models that facilitate rapid virtual screening of polymers based on relevant properties such as the refractive index, glass transition and thermal decomposition temperatures, and solubility in standard solvents. Exploration of the chemical space is carried out using an evolutionary algorithm that assembles synthetically tractable monomers from a database of existing fragments. Selected monomer structures that were further evaluated using density functional theory calculations agree well with model predictions.

| S-EPMC6415069 | biostudies-literature

Greatly Enhanced Single Particle Fluorescence Detection Using High Refractive Index Liquid-Core Waveguides.

Project description:High sensitivity and easy integration with microfabrication techniques has made silicon photonics one of the leading technologies used to build biosensors for diagnostic applications. Here we introduce a new silicon dioxide based optofluidic platform having a planar solid-core (SC) waveguide orthogonally intersecting a liquid-core (LC) waveguide with high refractive index ZnI2 salt solution as core. This enables both more uniform collection of particle fluorescence by the core mode and its propagation to an off-chip detector. This approach results in ultra-high sensitivity performance, demonstrated by achieving 8X enhancement in signal-to-noise ratio, a 45x increase in detection efficiency, and a 100x lower detection limit of 80 aM of fluorescent nanobeads. This represents a key step towards an ultrasensitive biosensor system for analyzing pathogens at clinical concentrations.

| S-EPMC8117828 | biostudies-literature

Topological phase singularities in atomically thin high-refractive-index materials.

Project description:Atomically thin transition metal dichalcogenides (TMDCs) present a promising platform for numerous photonic applications due to excitonic spectral features, possibility to tune their constants by external gating, doping, or light, and mechanical stability. Utilization of such materials for sensing or optical modulation purposes would require a clever optical design, as by itself the 2D materials can offer only a small optical phase delay - consequence of the atomic thickness. To address this issue, we combine films of 2D semiconductors which exhibit excitonic lines with the Fabry-Perot resonators of the standard commercial SiO2/Si substrate, in order to realize topological phase singularities in reflection. Around these singularities, reflection spectra demonstrate rapid phase changes while the structure behaves as a perfect absorber. Furthermore, we demonstrate that such topological phase singularities are ubiquitous for the entire class of atomically thin TMDCs and other high-refractive-index materials, making it a powerful tool for phase engineering in flat optics. As a practical demonstration, we employ PdSe2 topological phase singularities for a refractive index sensor and demonstrate its superior phase sensitivity compared to typical surface plasmon resonance sensors.

| S-EPMC9019097 | biostudies-literature

Profiling T cell activation using single-molecule fluorescence in situ hybridization and flow cytometry.

Project description:Flow cytometric characterization of Ag-specific T cells typically relies on detection of protein analytes. Shifting the analysis to detection of RNA would provide several significant advantages, which we illustrate by developing a new host immunity-based platform for detection of infections. Cytokine mRNAs synthesized in response to ex vivo stimulation with pathogen-specific Ags are detected in T cells with single-molecule fluorescence in situ hybridization followed by flow cytometry. Background from pre-existing in vivo analytes is lower for RNAs than for proteins, allowing greater sensitivity for detection of low-frequency cells. Moreover, mRNA analysis reveals kinetic differences in cytokine expression that are not apparent at the protein level but provide novel insights into gene expression programs expected to define different T cell subsets. The utility of probing immunological memory of infections is demonstrated by detecting T cells that recognize mycobacterial and viral Ags in donors exposed to the respective pathogens.

| S-EPMC4350577 | biostudies-literature

Colossal magnetic fields in high refractive index materials at microwave frequencies.

Project description:Resonant scattering of electromagnetic waves is a widely studied phenomenon with a vast range of applications that span completely different fields, from astronomy or meteorology to spectroscopy and optical circuitry. Despite being subject of intensive research for many decades, new fundamental aspects are still being uncovered, in connection with emerging areas, such as metamaterials and metasurfaces or quantum and topological optics, to mention some. In this work, we demonstrate yet one more novel phenomenon arising in the scattered near field of medium sized objects comprising high refractive index materials, which allows the generation of colossal local magnetic fields. In particular, we show that GHz radiation illuminating a high refractive index ceramic sphere creates instant magnetic near-fields comparable to those in neutron stars, opening up a new paradigm for creation of giant magnetic fields on the millimeter's scale.

| S-EPMC8648870 | biostudies-literature

Flow cytometry assay for the detection of single-copy DNA in human lymphocytes.

Project description:Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization, flow cytometric detection of specific genomic DNA sequences has not been established. Here, we present a flow cytometry assay for detection of single-copy genomic sequences in human lymphocytes using in situ PCR with universal energy transfer-labelled primers.

| S-EPMC7470942 | biostudies-literature

Mapping the refractive index with single plasmonic nanoantenna.

Project description:As the size of the state-of-the-art optical devices shrinks to nanoscale, the need for tools allowing mapping the local optical properties at deep sub-diffraction resolution increases. Here we demonstrate successful mapping the variations of the refractive index of a smooth dielectric surface by detecting spectral response of a single spherical-shape Ag nanoparticle optically aligned with a supporting optical fiber axicon microlens. We propose and examine various excitation schemes of the plasmonic nanoantenna to provide efficient interaction of its dipolar and quadrupolar modes with the underlying sample surface and to optimize the mapping resolution and sensitivity. Moreover, we demonstrate an lithography-free approach for fabrication of the scanning probe combining the high-quality fiber microaxicon with the Ag spherical nanoparticle atop. Supporting finite-difference time-domain calculations are undertaken to tailor the interaction of the plasmonic nanoantenna and the underlying dielectric substrate upon various excitation conditions demonstrating good agreement with our experimental findings and explaining the obtained results.

| S-EPMC5832779 | biostudies-literature

Refractive index measurement using single fiber reflectance spectroscopy.

Project description:A method using single fiber reflectance spectroscopy to measure the refractive indices of transparent and turbid media over a broad wavelength range is presented and tested. For transparent liquid samples, the accuracy is within 0.2%, and the accuracy increases with increasing wavelength. For liquid turbid media, the accuracy is within 0.3% and increases with decreasing wavelength. For solid turbid samples, such as human skin, the accuracy critically depends on the optical contact between the fiber and sample surface. It is demonstrated that this technique has the potential to measure refractive indices of biological tissue in vivo.

| S-EPMC7065624 | biostudies-literature

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.

Project description:The DNA base modification N6-methyladenine (m6A) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method to detect base modifications. Here, we show that a neural network can improve m6A detection at trained sequence contexts compared to previously published methods using deviations between measured and expected current values as each adenine travels through a pore. The model, implemented as the mCaller software package, can be extended to detect known or confirm suspected methyltransferase target motifs based on predictions of methylation at untrained contexts. We use PacBio, Oxford Nanopore, methylated DNA immunoprecipitation sequencing (MeDIP-seq), and whole-genome bisulfite sequencing data to generate and orthogonally validate methylomes for eight microbial reference species. These well-characterized microbial references can serve as controls in the development and evaluation of future methods for the identification of base modifications from single-molecule sequencing data.

| S-EPMC6362088 | biostudies-other

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