Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

New sensors for quantitative measurement of mitochondrial Zn(2+).

ABSTRACT: Zinc (Zn(2+)) homeostasis plays a vital role in cell function, and the dysregulation of intracellular Zn(2+) is associated with mitochondrial dysfunction. Few tools exist to quantitatively monitor the buffered, free Zn(2+) concentration in mitochondria of living cells ([Zn(2+)](mito)). We have validated three high dynamic range, ratiometric, genetically encoded, fluorescent Zn(2+) sensors that we have successfully used to precisely measure and monitor [Zn(2+)](mito) in several cell types. Using one of these sensors, called mito-ZapCY1, we report observations that free Zn(2+) is buffered at concentrations about 3 orders of magnitude lower in mitochondria than in the cytosol and that HeLa cells expressing mito-ZapCY1 have an average [Zn(2+)](mito) of 0.14 pM, which differs significantly from other cell types. These optimized mitochondrial Zn(2+) sensors could improve our understanding of the relationship between Zn(2+) homeostasis and mitochondrial function.

SUBMITTER: Park JG

PROVIDER: S-EPMC3477250 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

New sensors for quantitative measurement of mitochondrial Zn(2+).

Park J Genevieve JG Qin Yan Y Galati Domenico F DF Palmer Amy E AE

ACS chemical biology 20120810 10

Zinc (Zn(2+)) homeostasis plays a vital role in cell function, and the dysregulation of intracellular Zn(2+) is associated with mitochondrial dysfunction. Few tools exist to quantitatively monitor the buffered, free Zn(2+) concentration in mitochondria of living cells ([Zn(2+)](mito)). We have validated three high dynamic range, ratiometric, genetically encoded, fluorescent Zn(2+) sensors that we have successfully used to precisely measure and monitor [Zn(2+)](mito) in several cell types. Using ...[more]

PMID: 22850482

Similar Datasets

New alternately colored FRET sensors for simultaneous monitoring of Zn²⁺ in multiple cellular locations.

Project description:Genetically encoded sensors based on fluorescence resonance energy transfer (FRET) are powerful tools for reporting on ions, molecules and biochemical reactions in living cells. Here we describe the development of new sensors for Zn²⁺based on alternate FRET-pairs that do not involve the traditional CFP and YFP. Zn²⁺ is an essential micronutrient and plays fundamental roles in cell biology. Consequently there is a pressing need for robust sensors to monitor Zn²⁺ levels and dynamics in cells with high spatial and temporal resolution. Here we develop a suite of sensors using alternate FRET pairs, including tSapphire/TagRFP, tSapphire/mKO, Clover/mRuby2, mOrange2/mCherry, and mOrange2/mKATE. These sensors were targeted to both the nucleus and cytosol and characterized and validated in living cells. Sensors based on the new FRET pair Clover/mRuby2 displayed a higher dynamic range and better signal-to-noise ratio than the remaining sensors tested and were optimal for monitoring changes in cytosolic and nuclear Zn²⁺. Using a green-red sensor targeted to the nucleus and cyan-yellow sensor targeted to either the ER, Golgi, or mitochondria, we were able to monitor Zn²⁺ uptake simultaneously in two compartments, revealing that nuclear Zn²⁺ rises quickly, whereas the ER, Golgi, and mitochondria all sequester Zn²⁺ more slowly and with a delay of 600-700 sec. Lastly, these studies provide the first glimpse of nuclear Zn²⁺ and reveal that nuclear Zn²⁺ is buffered at a higher level than cytosolic Zn²⁺.

| S-EPMC3500285 | biostudies-literature

A New Measurement Approach for Small Deformations of Soil Specimens Using Fiber Bragg Grating Sensors.

Project description:A measurement approach for small deformations of soil specimens has been proposed in this study. The proposed approach consists of a small deformation transducer (SDT) based on fiber Bragg grating sensors which could provide an alternative tool to measure local small deformations of a soil specimen with high accuracy. The working principle, design procedures, calibrations and applications of the SDT are presented. An analytical solution is derived to obtain the relationship between the small deformation of the transducer and the wavelength shift of the FBG sensor, which was further evident in the laboratory calibration tests. The measurement range and resolution of the SDT can be adjusted by choosing different length and thickness of the material. The SDT can achieve a strain resolution of 4.45 micro-strains for a soil specimen with 80 mm in height. Measurement errors and stability were also examined and the results show that the maximum measurement error was around 0.01 mm. The designed SDT was further installed in a modified triaxial apparatus. Three shearing tests under different confining pressures were conducted. Results measured by the newly developed SDT are analyzed with comparisons to the results using external linear variable differential transformer (LVDT) transducers. The results provide evidence that this measurement approach is suitable for measuring the local deformations of soil specimens with high accuracy and stability.

| S-EPMC5469539 | biostudies-literature

High-performance gas sensors with temperature measurement.

Project description:There are a number of gas ionization sensors using carbon nanotubes as cathode or anode. Unfortunately, their applications are greatly limited by their multi-valued sensitivity, one output value corresponding to several measured concentration values. Here we describe a triple-electrode structure featuring two electric fields with opposite directions, which enable us to overcome the multi-valued sensitivity problem at 1 atm in a wide range of gas concentrations. We used a carbon nanotube array as the first electrode, and the two electric fields between the upper and the lower interelectrode gaps were designed to extract positive ions generated in the upper gap, hence significantly reduced positive ion bombardment on the nanotube electrode, which allowed us to maintain a high electric field near the nanotube tips, leading to a single-valued sensitivity and a long nanotube life. We have demonstrated detection of various gases and simultaneously monitoring temperature, and a potential for applications.

| S-EPMC3569919 | biostudies-literature

Quantitative Model for Reversibly Photoswitchable Sensors.

Project description:Composed of a reversibly photoswitchable unit allosterically linked to a sensing module, reversibly photoswitchable sensors (rs-sensors) represent a new and attractive strategy to quantitatively read-out analyte concentrations. However, their kinetic response to illumination is complex, and much attention is required from the design to the application steps. Here, we exploit a generic kinetic model of rs-sensors which enables us to point to key thermokinetic parameters, such as dissociation constants and kinetic rates for exchange toward the analyte, and cross-sections for photoswitching. The application of the model allows to evaluate the robustness of the analyzed parameters and to introduce a methodology for their reliable use. Model and methodology have been experimentally tested on a newly reported calcium sensor based on a reversibly photoswitchable green fluorescent protein allosterically linked to a calcium-sensing module integrating calmodulin and an RS20 peptide.

| S-EPMC8008439 | biostudies-literature

Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells.

Project description:In this chapter, we describe a gene-specific quantitative PCR (QPCR)-based assay for the measurement of DNA damage, using amplification of long DNA targets. This assay has been used extensively to measure the integrity of both nuclear and mitochondrial genomes exposed to different genotoxins and has proven to be particularly valuable in identifying reactive oxygen species-mediated mitochondrial DNA damage. QPCR can be used to quantify both the formation of DNA damage as well as the kinetics of damage removal. One of the main strengths of the assay is that it permits monitoring the integrity of mtDNA directly from total cellular DNA without the need for isolating mitochondria or a separate step of mitochondrial DNA purification. Here we discuss advantages and limitations of using QPCR to assay DNA damage in mammalian cells. In addition, we give a detailed protocol of the QPCR assay that helps facilitate its successful deployment in any molecular biology laboratory.

| S-EPMC4407362 | biostudies-literature

Light sensors for objective light measurement in ambulatory polysomnography.

Project description:Ambulatory polysomnography (PSG) does not commonly include an objective measure of light to determine the time of lights off (Loff), and thus cannot be used to calculate important indices such as sleep onset latency and sleep efficiency. This study examined the technical specifications and appropriateness of a prototype light sensor (LS) for use in ambulatory Compumedics Somte PSG.Two studies were conducted. The first examined the light measurement characteristics of the LS when used with a portable PSG device, specifically recording trace range, linearity, sensitivity, and stability. This involved the LS being exposed to varying incandescent and fluorescent light levels in a light controlled room. Secondly, the LS was trialled in 24 home and 12 hospital ambulatory PSGs to investigate whether light levels in home and hospital settings were within the recording range of the LS, and to quantify the typical light intensity reduction at the time of Loff. A preliminary exploration of clinical utility was also conducted. Linearity between LS voltage and lux was demonstrated, and the LS trace was stable over 14 hours of recording. The observed maximum voltage output of the LS/PSG device was 250 mV, corresponding to a maximum recording range of 350 lux and 523 lux for incandescent and fluorescent light respectively. At the time of Loff, light levels were within the recording range of the LS, and on average dropped by 72 lux (9-245) in the home and 76 lux (4-348) in the hospital setting. Results suggest that clinical utility was greatest in hospital settings where patients are less mobile. The LS was a simple and effective objective marker of light level in portable PSG, which can be used to identify Loff in ambulatory PSG. This allows measurement of additional sleep indices and support with clinical decisions.

| S-EPMC5690677 | biostudies-literature

Smartphone-based quantitative measurements on holographic sensors.

Project description:The research reported herein integrates a generic holographic sensor platform and a smartphone-based colour quantification algorithm in order to standardise and improve the determination of the concentration of analytes of interest. The utility of this approach has been exemplified by analysing the replay colour of the captured image of a holographic pH sensor in near real-time. Personalised image encryption followed by a wavelet-based image compression method were applied to secure the image transfer across a bandwidth-limited network to the cloud. The decrypted and decompressed image was processed through four principal steps: Recognition of the hologram in the image with a complex background using a template-based approach, conversion of device-dependent RGB values to device-independent CIEXYZ values using a polynomial model of the camera and computation of the CIEL*a*b* values, use of the colour coordinates of the captured image to segment the image, select the appropriate colour descriptors and, ultimately, locate the region of interest (ROI), i.e. the hologram in this case, and finally, application of a machine learning-based algorithm to correlate the colour coordinates of the ROI to the analyte concentration. Integrating holographic sensors and the colour image processing algorithm potentially offers a cost-effective platform for the remote monitoring of analytes in real time in readily accessible body fluids by minimally trained individuals.

| S-EPMC5687774 | biostudies-literature

Measurement of foot placement and its variability with inertial sensors.

Project description:Gait parameters such as stride length, width, and period, as well as their respective variabilities, are widely used as indicators of mobility and walking function. Foot placement and its variability have thus been applied in areas such as aging, fall risk, spinal cord injury, diabetic neuropathy, and neurological conditions. But a drawback is that these measures are presently best obtained with specialized laboratory equipment such as motion capture systems and instrumented walkways, which may not be available in many clinics and certainly not during daily activities. One alternative is to fix inertial measurement units (IMUs) to the feet or body to gather motion data. However, few existing methods measure foot placement directly, due to drift associated with inertial data. We developed a method to measure stride-to-stride foot placement in unconstrained environments, and tested whether it can accurately quantify gait parameters over long walking distances. The method uses ground contact conditions to correct for drift, and state estimation algorithms to improve estimation of angular orientation. We tested the method with healthy adults walking over-ground, averaging 93 steps per trial, using a mobile motion capture system to provide reference data. We found IMU estimates of mean stride length and duration within 1% of motion capture, and standard deviations of length and width within 4% of motion capture. Step width cannot be directly estimated by IMUs, although lateral stride variability can. Inertial sensors measure walks over arbitrary distances, yielding estimates with good statistical confidence. Gait can thus be measured in a variety of environments, and even applied to long-term monitoring of everyday walking.

| S-EPMC4284057 | biostudies-literature

A New Method for the Measurement of the Diffusion Coefficient of Adsorbed Vapors in Thin Zeolite Films, Based on Magnetoelastic Sensors.

Project description:In the current work an experimental method is used in order to calculate the diffusivity D (diffusion coefficient) of various vapors in thin zeolite films. The method is based on adsorption data from magnetoelastic sensors on top of which a zeolite layer was synthesized, and the diffusivity is extracted by fitting the data to Fick's laws of diffusion. In particular, the method is demonstrated for two volatile organic compound (VOC) vapors on two different zeolites, the p-Xylene adsorption in Faujasite type zeolite with D=1.89×10-13 m2/s at 120 °C and the propene adsorption in Linde Type A type zeolite with D=5.9×10-14 m2/s at 80 °C, two diffusion coefficients which are extracted experimentally for first time. Our results are within the order of magnitude of other VOC/zeolite values reported in literature.

| S-EPMC7309032 | biostudies-literature

Glucose Concentration Measurement in Human Blood Plasma Solutions with Microwave Sensors.

Project description:Three microwave sensors are used to track the glucose level of different human blood plasma solutions. In this paper, the sensors are evaluated as glucose trackers in a context close to real human blood. Different plasma solutions sets were prepared from a human blood sample at several added glucose concentrations up to 10 wt%, adding also ascorbic acid and lactic acid at different concentrations. The experimental results for the different sensors/solutions combinations are presented in this work. The sensors show good performance and linearity as glucose level retrievers, although the sensitivities change as the rest of components vary. Different sensor behaviors depending upon the concentrations of glucose and other components are identified and characterized. The results obtained in terms of sensitivity are coherent with previous works, highlighting the contribution of glucose to the dielectric losses of the solution. The results are also consistent with the frequency evolution of the electromagnetic signature of glucose found in the literature, and are helpful for selecting frequency bands for sensing purposes and envisioning future approaches to the challenging measurement in real biological contexts. Discussion of the implications of the results and guidelines for further research and development of more accurate sensors is offered.

| S-EPMC6749577 | 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