Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Confocal, three-dimensional tracking of individual quantum dots in high-background environments.

ABSTRACT: We demonstrate a custom confocal fluorescence-microscope that is capable of tracking individual quantum dots undergoing three-dimensional Brownian motion (diffusion coefficient approximately 0.5 microm(2)/s) in environments with a signal-to-background ratio as low as 2:1, significantly worse than observed in a typical cellular environment. By utilizing a pulsed excitation source and time-correlated single photon counting, the time-resolved photon stream can be used to determine changes in the emission lifetime as a function of position and positively identify single quantum dots via photon-pair correlations. These results indicate that this microscope will be capable of following protein and RNA transport throughout the full three-dimensional volume of a live cell for durations up to 15 s.

SUBMITTER: Wells NP

PROVIDER: S-EPMC4337952 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Confocal, three-dimensional tracking of individual quantum dots in high-background environments.

Wells Nathan P NP Lessard Guillaume A GA Werner James H JH

Analytical chemistry 20081201 24

We demonstrate a custom confocal fluorescence-microscope that is capable of tracking individual quantum dots undergoing three-dimensional Brownian motion (diffusion coefficient approximately 0.5 microm(2)/s) in environments with a signal-to-background ratio as low as 2:1, significantly worse than observed in a typical cellular environment. By utilizing a pulsed excitation source and time-correlated single photon counting, the time-resolved photon stream can be used to determine changes in the em ...[more]

PMID: 19072277

Similar Datasets

High-Resolution Three-Dimensional Imaging of Individual Astrocytes Using Confocal Microscopy.

Project description:Astrocytes play numerous vital roles in the central nervous system. Accordingly, it is of merit to identify structural and functional properties of astrocytes in both health and disease. The majority of studies examining the morphology of astrocytes have employed immunoassays for markers such as glial fibrillary acidic protein, which are insufficient to encapsulate the considerable structural complexity of these cells. Herein, we describe a method utilizing a commercially available and validated, genetically encoded membrane-associated fluorescent marker of astrocytes, AAV5-GfaABC1D-Lck-GFP. This tool and approach allow for visualization of a single isolated astrocyte in its entirety, including fine peripheral processes. Astrocytes are imaged using confocal microscopy and reconstructed in three dimensions to obtain detailed morphometric data. We further provide an immunohistochemistry procedure to assess colocalization of isolated astrocytes with synaptic markers throughout the z-plane. This technique, which can be utilized via a standard laboratory confocal microscope and Imaris software, allows for detailed analysis of the morphology and synaptic colocalization of astrocytes in fixed tissue. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Microinjection of AAV5-GfaABC1D-Lck-GFP into the nucleus accumbens of rats Basic Protocol 2: Tissue processing and immunohistochemistry for post-synaptic density-95 Basic Protocol 3: Single-cell image acquisition Basic Protocol 4: Three-dimensional reconstruction of single cells Basic Protocol 5: Three-dimensional colocalization analysis.

| S-EPMC7216730 | biostudies-literature

Three-Dimensional Superlattice of PbS Quantum Dots in Flakes.

Project description:In the last two decades, many experiments were conducted in self-organization of nanocrystals into two- and three-dimensional (3D) superlattices and the superlattices were synthesized and characterized by different techniques, revealing their unusual properties. Among all characterization techniques, X-ray diffraction (XRD) is the one that has allowed the confirmation of the 3D superlattice formation due to the presence of sharp and intense diffraction peaks. In this work, we study self-organized superlattices of quantum dots of PbS prepared by dropping a monodispersed colloidal solution on a glass substrate at different temperatures. We showed that the intensity of the low-angle XRD peaks depends strongly on the drying time (substrate temperature). We claim that the peaks are originated from the 3D superlattice. Scanning electron microscopy images show that this 3D superlattice (PbS quantum dots) is formed in flake's shape, parallel to the substrate surface and randomly oriented in the perpendicular planes.

| S-EPMC6641286 | biostudies-literature

3-Dimensional Tracking of Non-blinking 'Giant' Quantum Dots in Live Cells.

Project description:While semiconductor quantum dots (QDs) have been used successfully in numerous single particle tracking (SPT) studies due to their high photoluminescence efficiency, photostability, and broad palette of emission colors, conventional QDs exhibit fluorescence intermittency or 'blinking,' which causes ambiguity in particle trajectory analysis and limits tracking duration. Here, non-blinking 'giant' quantum dots (gQDs) are exploited to study IgE-Fc?RI receptor dynamics in live cells using a confocal-based 3D SPT microscope. There is a 7-fold increase in the probability of observing IgE-Fc?RI for longer than 1 min using the gQDs compared to commercially available QDs. A time-gated photon-pair correlation analysis is implemented to verify that selected SPT trajectories are definitively from individual gQDs and not aggregates. The increase in tracking duration for the gQDs allows the observation of multiple changes in diffusion rates of individual IgE-Fc?RI receptors occurring on long (>1 min) time scales, which are quantified using a time-dependent diffusion coefficient and hidden Markov modeling. Non-blinking gQDs should become an important tool in future live cell 2D and 3D SPT studies, especially in cases where changes in cellular dynamics are occurring on the time scale of several minutes.

| S-EPMC4366348 | biostudies-literature

Three-dimensional reconstruction of cell nuclei, internalized quantum dots and sites of lipid peroxidation.

Project description:BackgroundThe purpose of the study was to develop and illustrate three-dimensional (3-D) reconstruction of nuclei and intracellular lipid peroxidation in cells exposed to oxidative stress induced by quantum dots. Programmed cell death is characterized by multiple biochemical and morphological changes in different organelles, including nuclei, mitochondria and lysosomes. It is the dynamics of the spatio-temporal changes in the signalling and morphological adaptations which will ultimately determine the 'shape' and fate of the cell.ResultsWe present new approaches to the 3-D reconstruction of organelle morphology and biochemical changes in confocal live-cell images. We demonstrate the 3-D shapes of nuclei, the 3-D intracellular distributions of QDs and the accompanying lipid-membrane peroxidation, and provide methods for quantification.ConclusionThis study provides an approach to 3-D organelle and nanoparticle visualization in the context of cell death; however, this approach is also applicable more generally to investigating changes in organelle morphology in response to therapeutic interventions, stressful stimuli and internalized nanoparticles. Moreover, the approach provides quantitative data for such changes, which will help us to better integrate compartmentalization of subcellular events and to link morphological and biochemical changes with physiological outcomes.

| S-EPMC1635722 | biostudies-literature

Multi-color single particle tracking with quantum dots.

Project description:Quantum dots (QDs) have long promised to revolutionize fluorescence detection to include even applications requiring simultaneous multi-species detection at single molecule sensitivity. Despite the early promise, the unique optical properties of QDs have not yet been fully exploited in e. g. multiplex single molecule sensitivity applications such as single particle tracking (SPT). In order to fully optimize single molecule multiplex application with QDs, we have in this work performed a comprehensive quantitative investigation of the fluorescence intensities, fluorescence intensity fluctuations, and hydrodynamic radii of eight types of commercially available water soluble QDs. In this study, we show that the fluorescence intensity of CdSe core QDs increases as the emission of the QDs shifts towards the red but that hybrid CdSe/CdTe core QDs are less bright than the furthest red-shifted CdSe QDs. We further show that there is only a small size advantage in using blue-shifted QDs in biological applications because of the additional size of the water-stabilizing surface coat. Extending previous work, we finally also show that parallel four color multicolor (MC)-SPT with QDs is possible at an image acquisition rate of at least 25 Hz. We demonstrate the technique by measuring the lateral dynamics of a lipid, biotin-cap-DPPE, in the cellular plasma membrane of live cells using four different colors of QDs; QD565, QD605, QD655, and QD705 as labels.

| S-EPMC3498293 | biostudies-literature

Transcriptome Profile of Quantum Dots on Saccharomyces cerevisiae

Project description:Transcriptome Profile of CdSe/ZnS and InP/ZnS Quantum Dots on Saccharomyces cerevisiae

2021-01-30 | GSE165805 | GEO

Hydrothermal Synthesis of Graphene Quantum Dots Supported on Three-Dimensional Graphene for Supercapacitors.

Project description:Incorporation of new functional components into a three-dimensional graphene (3DG) framework improves the performance of supercapacitors based on 3DG as electrodes by tailoring the framework's structure and properties. In this work, graphene quantum dots (GQDs) were incorporated into 3DG via one-step hydrothermal treatment of GQDs and graphene oxide (GO). By simply adjusting the GQDs/GO feeding ratio by weight, various GQDs/3DG composites were formed. The maximum feeding ratio was 80%, and the prepared composites possessed saturated GQDs loading on the 3DG framework, whereas composites obtained with a GQDs/GO feeding ratio of 40% as electrodes exhibited optimal specific capacitance of 242 F·g-1 for supercapacitors, an increase of 22% compared with that of pure 3DG electrodes (198 F·g-1). This improved performance was mainly due to better electrical conductivity and larger surface area for GQDs/3DG composites with moderate GQDs content. The fabricated GQDs/3DG composites as electrodes for supercapacitors revealed high electrochemical stability. Their capacitance kept 93% of the initial value after 10,000 charge-discharge cycles.

| S-EPMC6409901 | biostudies-other

Parallax: high accuracy three-dimensional single molecule tracking using split images.

Project description:Three-dimensional (3D) tracking can provide valuable biological insights that are missing in conventional microscopy. Here we developed a single molecule 3D tracking microscopy technique, named Parallax, with high localization precision and temporal resolution. We demonstrated its capabilities by studying the 3D trafficking of glucose-transporter-4 containing vesicles in living adipocytes as well as the walking path of single myosin VI molecules along actin filaments.

| S-EPMC2728077 | biostudies-literature

Three-dimensional motion tracking for high-resolution optical microscopy, in vivo.

Project description:When conducting optical imaging experiments, in vivo, the signal to noise ratio and effective spatial and temporal resolution is fundamentally limited by physiological motion of the tissue. A three-dimensional (3D) motion tracking scheme, using a multiphoton excitation microscope with a resonant galvanometer, (512 × 512 pixels at 33 frames s(-1)) is described to overcome physiological motion, in vivo. The use of commercially available graphical processing units permitted the rapid 3D cross-correlation of sequential volumes to detect displacements and adjust tissue position to track motions in near real-time. Motion phantom tests maintained micron resolution with displacement velocities of up to 200 ?m min(-1), well within the drift observed in many biological tissues under physiologically relevant conditions. In vivo experiments on mouse skeletal muscle using the capillary vasculature with luminal dye as a displacement reference revealed an effective and robust method of tracking tissue motion to enable (1) signal averaging over time without compromising resolution, and (2) tracking of cellular regions during a physiological perturbation.

| S-EPMC3799900 | biostudies-literature

Lighting up individual DNA binding proteins with quantum dots.

Project description:The ability to determine the precise loci and occupancy of DNA-binding proteins is instrumental to our understanding of cellular processes like gene expression and regulation. We propose a single-molecule approach for the direct visualization of proteins bound to their template DNA. Fluorescent quantum dots (QD) are used to label proteins bound to DNA, allowing multicolor, nanometer-resolution localization. Protein-DNA complexes are linearly extended and imaged to determine the precise location of the protein binding sites. The method is demonstrated by detecting individual QD-labeled T7-RNA polymerases on the T7 bacteriophage genome. This work demonstrates the potential of this approach to precisely read protein binding position or, alternatively, "write" such information on extended DNA with QDs via sequence-specific molecular recognition.

| S-EPMC3084662 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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