Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optical visualization and quantification of enzyme activity using dynamic droplet lenses.

ABSTRACT: In this paper, we describe an approach to measuring enzyme activity based on the reconfiguration of complex emulsions. Changes in the morphology of these complex emulsions, driven by enzyme-responsive surfactants, modulate the transmission of light through a sample. Through this method we demonstrate how simple photodetector measurements may be used to monitor enzyme kinetics. This approach is validated by quantitative measurements of enzyme activity for three different classes of enzymes (amylase, lipase, and sulfatase), relying on two distinct mechanisms for coupling droplet morphology to enzyme activity (host-guest interactions with uncaging and molecular cleavage).

SUBMITTER: Zarzar LD

PROVIDER: S-EPMC5393242 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Optical visualization and quantification of enzyme activity using dynamic droplet lenses.

Zarzar Lauren D LD Kalow Julia A JA He Xinping X Walish Joseph J JJ Swager Timothy M TM

Proceedings of the National Academy of Sciences of the United States of America 20170327 15

In this paper, we describe an approach to measuring enzyme activity based on the reconfiguration of complex emulsions. Changes in the morphology of these complex emulsions, driven by enzyme-responsive surfactants, modulate the transmission of light through a sample. Through this method we demonstrate how simple photodetector measurements may be used to monitor enzyme kinetics. This approach is validated by quantitative measurements of enzyme activity for three different classes of enzymes (amyla ...[more]

PMID: 28348236

Similar Datasets

Sub-wavelength Laser Nanopatterning using Droplet Lenses.

Project description:When a drop of liquid falls onto a screen, e.g. a cell phone, the pixels lying underneath appear magnified. This lensing effect is a combination of the curvature and refractive index of the liquid droplet. Here, the spontaneous formation of such lenses is exploited to overcome the diffraction limit of a conventional laser direct-writing system. In particular, micro-droplets are first laser-printed at user-defined locations on a surface and they are later used as lenses to focus the same laser beam. Under conditions described herein, nanopatterns can be obtained with a reduction in spot size primarily limited by the refractive index of the liquid. This all-optics approach is demonstrated by writing arbitrary patterns with a feature size around 280 nm, about one fourth of the processing wavelength.

| S-EPMC4635425 | biostudies-literature

Visualization and quantification of dynamic STAT3 homodimerization in living cells using homoFluoppi.

Project description:Dimerization in signal transduction is a dynamically regulated process and a key regulatory mechanism. Signal transducer and activator of transcription 3 (STAT3) dimerizes after tyrosine phosphorylation upon cytokine stimulation. Because only the STAT3 dimer possesses the trans-activation activity, dimerization is an indispensable process for cytokine signaling. Here we report the detection of dynamic STAT3 dimerization in living cells using the homoFluoppi system. This method allowed us to validate the presence of an intact Src homology 2 domain and STAT3 Tyr705 phosphorylation, which facilitate puncta formation and homodimerization. Puncta formation was reversible, as determined by a decreased punctate signal after washout of oncostatin M. We analyzed STAT3 mutants, which have been reported in patients with hyper IgE syndrome and inflammatory hepatocellular adenoma (IHCA). Analysis of the IHCA mutants using homoFluoppi revealed constitutive activity independent of cytokine stimulation and novel insight into kinetics of dimer dissociation process. Next, we used homoFluoppi to screen for inhibitors of STAT3 dimerization, and identified 3,4-methylenedioxy-?-nitrostyrene as a novel inhibitor. The results of this study show that homoFluoppi is a useful research tool for the analysis of proteins like STAT3 that dynamically dimerize, and is applicable for the screening of dimerization modulators.

| S-EPMC5799161 | biostudies-other

Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv

Project description:The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility, due to its simplicity, speed, and low input material requirements. However, it can be difficult to evaluate data quality, particularly when processing many samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing ATAC-seq quality control results. We perform controlled ATAC-seq experiments and utilize ataqv to show that the ratio of Tn5 transposase to nuclei and sequencing flowcell cluster density induce reproducible technical bias in ATAC-seq results, significantly changing the fragment length distribution and enrichment of reads in promoter and enhancer chromatin states.

2020-03-23 | GSE130450 | GEO

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

Project description:We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

| S-EPMC4558716 | biostudies-literature

Quantitative telomerase enzyme activity determination using droplet digital PCR with single cell resolution.

Project description:The telomere repeat amplification protocol (TRAP) for the human reverse transcriptase, telomerase, is a PCR-based assay developed two decades ago and is still used for routine determination of telomerase activity. The TRAP assay can only reproducibly detect ? 2-fold differences and is only quantitative when compared to internal standards and reference cell lines. The method generally involves laborious radioactive gel electrophoresis and is not conducive to high-throughput analyzes. Recently droplet digital PCR (ddPCR) technologies have become available that allow for absolute quantification of input deoxyribonucleic acid molecules following PCR. We describe the reproducibility and provide several examples of a droplet digital TRAP (ddTRAP) assay for telomerase activity, including quantitation of telomerase activity in single cells, telomerase activity across several common telomerase positive cancer cells lines and in human primary peripheral blood mononuclear cells following mitogen stimulation. Adaptation of the TRAP assay to digital format allows accurate and reproducible quantification of the number of telomerase-extended products (i.e. telomerase activity; 57.8 ± 7.5) in a single HeLa cell. The tools developed in this study allow changes in telomerase enzyme activity to be monitored on a single cell basis and may have utility in designing novel therapeutic approaches that target telomerase.

| S-EPMC4117742 | biostudies-literature

Optical bench simulation for intraocular lenses using field-tracing technology.

Project description:PurposeTo evaluate the image quality of intraocular lenses (IOLs) using field-tracing optical simulation and then compare it with the image quality using conventional ray-tracing simulation.MethodsWe simulated aspheric IOLs with a decenter, tilt, and no misalignment using an aspheric corneal eye model with a positive spherical aberration. The retinal image, Strehl ratio, and modulation transfer function (MTF) were compared between the ray-tracing and field-tracing optical simulation and confirmed by the results reported in an in vitro experiment using the same eye model.ResultsThe retinal image showed interference fringes from target due to diffraction from the object in a field-tracing simulation. When compared with the experimental results, the field tracing represented the experimental results more precisely than ray tracing after passing over 400 μm of the decentration and 4 degrees of the tilt of the IOLs. The MTF values showed similar results for the case of no IOL misalignment in both the field tracing and ray tracing. In the case of the 200-μm decentration or 8-degree tilt of IOL, the field-traced MTF shows lower values than the ray-traced one.ConclusionsThe field-tracing optical bench simulation is a reliable method to evaluate IOL performance according to the IOL misalignment. It can provide retinal image quality close to real by taking into account the wave nature of light, interference and diffraction to explain to patients having the IOL misalignment.

| S-EPMC8673660 | biostudies-literature

Visualization and quantification of dynamic intercellular coupling in human embryonic stem cells using single cell sonoporation.

Project description:Gap junctions (GJs), which are proteinaceous channels, couple adjacent cells by permitting direct exchange of intracellular molecules with low molecular weights. GJ intercellular communication (GJIC) plays a critical role in regulating behaviors of human embryonic stem cells (hESCs), affecting their proliferation and differentiation. Here we report a novel use of sonoporation that enables single cell intracellular dye loading and dynamic visualization/quantification of GJIC in hESC colonies. By applying a short ultrasound pulse to excite single microbubbles tethered to cell membranes, a transient pore on the cell membrane (sonoporation) is generated which allows intracellular loading of dye molecules and influx of Ca2+ into single hESCs. We employ live imaging for continuous visualization of intercellular dye transfer and Ca2+ diffusion in hESC colonies. We quantify cell-cell permeability based on dye diffusion using mass transport models. Our results reveal heterogeneous intercellular connectivity and a variety of spatiotemporal characteristics of intercellular Ca2+ waves in hESC colonies induced by sonoporation of single cells.

| S-EPMC7589565 | biostudies-literature

Dynamic near-infrared carbon dioxide leak visualization detection during surgery using the FLIR GF343 optical imaging system.

Project description: Not available

| S-EPMC7545813 | biostudies-literature

Reconfigurable and responsive droplet-based compound micro-lenses.

Project description:Micro-scale optical components play a crucial role in imaging and display technology, biosensing, beam shaping, optical switching, wavefront-analysis, and device miniaturization. Herein, we demonstrate liquid compound micro-lenses with dynamically tunable focal lengths. We employ bi-phase emulsion droplets fabricated from immiscible hydrocarbon and fluorocarbon liquids to form responsive micro-lenses that can be reconfigured to focus or scatter light, form real or virtual images, and display variable focal lengths. Experimental demonstrations of dynamic refractive control are complemented by theoretical analysis and wave-optical modelling. Additionally, we provide evidence of the micro-lenses' functionality for two potential applications-integral micro-scale imaging devices and light field display technology-thereby demonstrating both the fundamental characteristics and the promising opportunities for fluid-based dynamic refractive micro-scale compound lenses.

| S-EPMC5344304 | biostudies-literature

Four human Plasmodium species quantification using droplet digital PCR.

Project description:Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection. The ddPCR assay was developed based on primers and probes specific to the Plasmodium genus 18S rRNA gene. Using ddPCR for ultra-sensitive P. falciparum assessment, the lower level of detection from concentrated DNA obtained from a high volume (1 mL) blood sample was 11 parasites/mL. For species identification, in particular for samples with mixed infections, a duplex reaction was developed for detection and quantification P. falciparum/ P. vivax and P. malariae/ P. ovale. Amplification of each Plasmodium species in the duplex reaction showed equal sensitivity to singleplex single species detection. The duplex ddPCR assay had higher sensitivity to identify minor species in 32 subpatent parasitaemia samples from Cambodia, and performed better than real-time PCR. The ddPCR assay shows high sensitivity to assess very low parasitaemia of all human Plasmodium species. This provides a useful research tool for studying the role of the asymptomatic parasite reservoir for transmission in regions aiming for malaria elimination.

| S-EPMC5396971 | 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