Change In Emission Ratio Research Articles

Imaging of plant calcium-sensor kinase conformation monitors real time calcium-dependent decoding in planta.

Changes in cytosolic calcium (Ca2+) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca2+-permeable channels may generate distinct Ca2+ signatures and contribute to response specificities, the mechanisms by which Ca2+ signatures are decoded are poorly understood. Here, we developed a genetically encoded Förster resonance energy transfer (FRET)-based reporter that visualizes the conformational changes in Ca2+-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca2+-sensitivities, highly Ca2+-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca2+-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca2+ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca2+ changes, pointing to the isoform-specific Ca2+-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca2+ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca2+ decoding in a multitude of plant developmental and stress responses.

A Förster resonance energy transfer-based d-2-hydroxyglutarate biosensor

d-2-Hydroxyglutarate (d-2-HG) is an oncometabolite aberrantly accumulated in patients with d-2-hydroxyglutaric aciduria or various isocitrate dehydrogenases mutation-associated cancers. The detection of d-2-HG is of great significance for the diagnostic and therapeutic aspects of these diseases. Herein, a Förster resonance energy transfer (FRET)-based d-2-HG biosensor was developed. The d-2-HG-specific allosteric transcription factor DhdR from Achromobacter denitrificans NBRC 15125 was used as its biorecognition element and inserted between two fluorescent proteins Clover and mRuby2. The response magnitude of the biosensor was improved by truncation of the terminal amino acids of DhdR and addition of artificial linkers. The optimized variant DHGFR1.0 exhibited excellent sensitivity and specificity with a maximum emission ratio change (ΔRmax) of 30.77%, a half-maximal effective concentration (EC50) of 2.78 μM, and a dynamic detection range of 0.17–36.22 μM. It was able to detect the concentration of d-2-HG in body fluids and cell-related samples with high accuracy and precision in vitro. The ligand-binding site of DhdR was predicted and several biosensors with low affinity for d-2-HG were also generated by site-directed mutagenesis of DhdR.

A Selective Fluorescent l-Lactate Biosensor Based on an l-Lactate-Specific Transcription Regulator and Förster Resonance Energy Transfer.

Selective detection of l-lactate levels in foods, clinical, and bacterial fermentation samples has drawn intensive attention. Many fluorescent biosensors based on non-stereoselective recognition elements have been developed for lactate detection. Herein, the allosteric transcription factor STLldR from Salmonella enterica serovar Typhimurium LT2 was identified to be stereo-selectively respond to l-lactate. Then, STLldR was combined with Förster resonance energy transfer (FRET) to construct a fluorescent l-lactate biosensor FILLac. FILLac was further optimized by truncating the N- and C-terminal amino acids of STLldR between cyan and yellow fluorescent proteins. The optimized biosensor FILLac10N0C exhibited a maximum emission ratio change (ΔRmax) of 33.47 ± 1.91%, an apparent dissociation constant (Kd) of 6.33 ± 0.79 μM, and a limit of detection of 0.68 μM. FILLac10N0C was applied in 96-well microplates to detect l-lactate in bacterial fermentation samples and commercial foods such as Jiaosu and yogurt. The quantitation results of FILLac10N0C exhibited good agreement with that of a commercial l-lactate biosensor SBA-40D bioanalyzer. Thus, the biosensor FILLac10N0C compatible with high-throughput detection may be a potential choice for quantitation of l-lactate in different biological samples.

Bioluminescent RAPPID Sensors for the Single-Step Detection of Soluble Axl and Multiplex Analysis of Cell Surface Cancer Biomarkers.

Early diagnosis of cancer is essential for the efficacy of treatment. Our group recently developed RAPPID, a bioluminescent immunoassay platform capable of measuring a wide panel of biomarkers directly in solution. Here, we developed and systematically screened different RAPPID sensors for sensitive detection of the soluble fraction of Axl (sAxl), a cell surface receptor that is overexpressed in several types of cancer. The best-performing RAPPID sensor, with a limit of detection of 8 pM and a >9-fold maximal change in emission ratio, was applied to measure Axl in three different contexts: clinically relevant sAxl levels (∼0.5 and ∼1 nM) in diluted blood plasma, proteolytically cleaved Axl in the cell culture medium of A431 and HeLa cancer cells, and Axl on the membrane of A431 cells. We further extended the sensor toolbox by developing dual-color RAPPID for simultaneous detection of Axl and EGFR on A431 and HeLa cells, as well as an AND-gate RAPPID that measures the concurrent presence of these two cell surface receptors on the same cell. These new RAPPID sensors provide attractive alternatives for more laborious protein detection and quantification methods such as FACS and immunostainings, due to their simple practical implantation and low intrinsic background signal.

Concept of Fluorescent Transport Activity Biosensor for the Characterization of the Arabidopsis NPF1.3 Activity of Nitrate.

The NRT1/PTR FAMILY (NPF) in Arabidopsis (Arabidopsis thaliana) plays a major role as a nitrate transporter. The first nitrate transporter activity biosensor NiTrac1 converted the dual-affinity nitrate transceptor NPF6.3 into fluorescence activity sensors. To test whether this approach is transferable to other members of this family, screening for genetically encoded fluorescence transport activity sensor was performed with the member of the NPF family in Arabidopsis. In this study, NPF1.3, an uncharacterized member of NPF in Arabidopsis, was converted into a transporter activity biosensor NiTrac-NPF1.3 that responds specifically to nitrate. The emission ratio change of NiTrac-NPF1.3 triggered by the addition of nitrate reveals the important function of NPF1.3 in nitrate transport in Arabidopsis. A functional analysis of Xenopus laevis oocytes confirmed that NPF1.3 plays a role as a nitrate transporter. This new technology is applicable in plant and medical research.

Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca2+ Biosensor.

Ratiometric indicators with long emission wavelengths are highly preferred in modern bioimaging and life sciences. Herein, we elucidated the working mechanism of a standalone red fluorescent protein (FP)-based Ca2+ biosensor, REX-GECO1, using a series of spectroscopic and computational methods. Upon 480 nm photoexcitation, the Ca2+-free biosensor chromophore becomes trapped in an excited dark state. Binding with Ca2+ switches the route to ultrafast excited-state proton transfer through a short hydrogen bond to an adjacent Glu80 residue, which is key for the biosensor’s functionality. Inspired by the 2D-fluorescence map, REX-GECO1 for Ca2+ imaging in the ionomycin-treated human HeLa cells was achieved for the first time with a red/green emission ratio change (ΔR/R0) of ~300%, outperforming many FRET- and single FP-based indicators. These spectroscopy-driven discoveries enable targeted design for the next-generation biosensors with larger dynamic range and longer emission wavelengths.

Discrimination between Human Colorectal Neoplasms with a Dual-Recognitive Two-Photon Probe.

Colorectal cancer is a major cause of cancer-related deaths worldwide. Histologic diagnosis using biopsy samples of colorectal neoplasms is the most important step in determining the treatment methods, but these methods have limitations in accuracy and effectiveness. Herein, we report a dual-recognition two-photon probe and its application in the discrimination between human colorectal neoplasms. The probe is composed of two monosaccharides, d-glucosamine and β-d-galactopyranoside, in a fluorophore for the monitoring of both glucose uptake and β-gal hydrolysis. In vitro/cell imaging studies revealed the excellent selectivity and sensitivity of the probe for glucose transporter-mediated glucose uptake and β-gal activity. Cancer-specific uptake was monitored by increased fluorescence intensity, and additional screening of cancer cells was achieved by changes in emission ratio owing to the higher activity of β-gal. Using human colon tissues and two-photon microscopy, we found that the plot of intensity versus ratio can accurately discriminate between colorectal neoplasms in the order of cancer progression (normal, adenoma, and carcinoma).

Imaging Intracellular H2O2 with the Genetically Encoded PerFRET and OxyFRET Probes.

Hydrogen peroxide (H2O2) is an important signaling intermediate with various regulatory and effector functions. Despite its significance, the subcellular organization of H2O2 signals is poorly understood. Introducing novel techniques for the intracellular detection of H2O2 would be essential for a more complete understanding of its role in cellular signaling. We previously reported the development of two novel fluorescence resonance energy transfer (FRET)-based protein sensors that showed opposite emission ratio changes upon reaction with H2O2. In this chapter, we detail the methods for using OxyFRET and PerFRET for the assessment of changes in subcellular H2O2 levels.

Ratiometric Bioluminescent Sensor Proteins Based on Intramolecular Split Luciferase Complementation.

Bioluminescent sensor proteins provide attractive tools for applications ranging from in vivo imaging to point-of-care testing. Here we introduce a new class of ratiometric bioluminescent sensor proteins that do not rely on direct modulation of BRET efficiency, but are based on competitive intramolecular complementation of split NanoLuc luciferase. Proof of concept for the feasibility of this sensor principle was provided by developing a blue–red light emitting sensor protein for the detection of anti-HIV1-p17 antibodies with a 500% change in emission ratio and a Kd of 10 pM. The new sensor design also improved the dynamic response of a sensor for the therapeutic antibody cetuximab 4-fold, allowing the direct quantification of this anti-EGFR antibody in undiluted blood plasma. The modular sensor architecture allows easy and systematic tuning of a sensor’s dynamic range and should be generally applicable to allow rational engineering of bioluminescent sensor proteins.

EZinCh-2: A Versatile, Genetically Encoded FRET Sensor for Cytosolic and Intraorganelle Zn(2+) Imaging.

Zn2+ plays essential and diverse roles in numerous cellular processes. To get a better understanding of intracellular Zn2+ homeostasis and the putative signaling role of Zn2+, various fluorescent sensors have been developed that allow monitoring of Zn2+ concentrations in single living cells in real time. Thus far, two families of genetically encoded FRET-based Zn2+ sensors have been most widely applied, the eCALWY sensors developed by our group and the ZapCY sensors developed by Palmer and co-workers. Both have been successfully used to measure cytosolic free Zn2+, but distinctly different concentrations have been reported when using these sensors to measure Zn2+ concentrations in the ER and mitochondria. Here, we report the development of a versatile alternative FRET sensor containing a de novo Cys2His2 binding pocket that was created on the surface of the donor and acceptor fluorescent domains. This eZinCh-2 sensor binds Zn2+ with a high affinity that is similar to that of eCALWY-4 (Kd = 1 nM at pH 7.1), while displaying a substantially larger change in emission ratio. eZinCh-2 not only provides an attractive alternative for measuring Zn2+ in the cytosol but was also successfully used for measuring Zn2+ in the ER, mitochondria, and secretory vesicles. Moreover, organelle-targeted eZinCh-2 can also be used in combination with the previously reported redCALWY sensors to allow multicolor imaging of intracellular Zn2+ simultaneously in the cytosol and the ER or mitochondria.

Activation of α7 nicotinic acetylcholine receptors increases intracellular cAMP levels via activation of AC1 in hippocampal neurons

The activation of α7 nAChRs has been shown to improve hippocampal-dependent learning and memory. However, the molecular mechanism of α7 nAChRs' action remains elusive. We previously reported that activation of α7 nAChRs induced a prolonged enhancement of glutamatergic synaptic transmission in a PKA-dependent manner. Here, we investigated any connection between the activation of the α7 nAChR and cAMP signaling in hippocampal neurons. To address this question, we employed a FRET-based biosensor to measure the intracellular cAMP levels directly via live cell imaging. We found that application of the α7 nAChR-selective agonist choline, in the presence of the α7 nAChR positive allosteric modulator PNU-120596, induced a significant change in emission ratio of F535/F470, which indicated an increase in intracellular cAMP levels. This choline-induced increase was abolished by the α7 nAChR antagonist MLA and the calcium chelator BAPTA, suggesting that the cAMP increase depends on the α7 nAChR activation and subsequent intracellular calcium rise. The selective AC1 inhibitor CB-6673567 and siRNA-mediated deletion of AC1 both blocked the choline-induced cAMP increase, suggesting that calcium-dependent AC1 is required for choline's action. Furthermore, α7 nAChR activation stimulated the phosphorylation of synapsin, which serves as a downstream effector to regulate neurotransmitter release. Our findings provide the first direct evidence to link activation of α7 nAChRs to a cAMP rise via AC1, which defines a new signaling pathway employed by α7 nAChRs. Our study sheds light into potential molecular mechanisms of the positive cognitive actions of α7 nAChR agonists and development of therapeutic treatments for cognitive impairments.

Rational design of FRET sensor proteins based on mutually exclusive domain interactions

Proteins that switch between distinct conformational states are ideal to monitor and control molecular processes within the complexity of biological systems. Inspired by the modular architecture of natural signalling proteins, our group explores generic design strategies for the construction of FRET-based sensor proteins and other protein switches. In the present article, I show that designing FRET sensors based on mutually exclusive domain interactions provides a robust method to engineer sensors with predictable properties and an inherently large change in emission ratio. The modularity of this approach should make it easily transferable to other applications of protein switches in fields ranging from synthetic biology, optogenetics and molecular diagnostics.

Influence of Li+ doping on up-conversion and structural properties of Yb3+/Tm3+-doped cubic NaYF4 nanocrystals

The impact of Li+ doping on luminescence and structural properties of cubic NaYF4:Yb3+/Tm3+ colloidal nanocrystals was studied. The Yb3+/Tm3+ co-doped samples demonstrated significant red to blue emission ratio changes and high concentration quenching. By substituting Na+ with smaller Li+ ions within NaYF4 lattice, we expected to induce distortions in order to prevent the concentration quenching process, which is responsible for decrease of the luminescence intensity. The results indicated that the substitution of sodium ions by Li+ did not enhance Tm3+ up-conversion emission significantly in α-NaYF4:Yb3+/Tm3+. However, the influence of lithium ions on luminescence was not entirely the same in the case of 2% Tm3+ and 0.1% Tm3+ doped samples. The slight up-conversion intensity enhancement in the case of samples doped with 2% Tm3+ could result from the increase in the crystallites size and changes in the surface to volume ratio. The observed increase in lattice parameter and thus the increased distance between thulium ions in the lattice might also result in breaking apart of pairs responsible for cross-relaxation processes. Interestingly, in the 0.1% Tm3+ co-doped samples, initial luminescence intensity decrease followed by increase correlated with Li+ substitution was observed. Due to the existence of two different sites for incorporation of lithium ions into the host lattice, the changes in lattice parameters and resulting optical properties are not straightforward functions of variable amount of Li+.

Spatial and Temporal Analysis of NADPH Oxidase-Generated Hydrogen Peroxide Signals by Novel Fluorescent Reporter Proteins

Hydrogen peroxide (H2O2) is an emerging signaling molecule with diverse regulatory functions. Despite its significance, the spatial and temporal organization of H2O2 signals within cells is basically unknown. Our limited knowledge about H2O2 signals is largely due to the lack of appropriate techniques for measuring intracellular H2O2. The aim of the current study was to develop novel fluorescent reporter proteins for the measurement of intracellular H2O2. We developed two novel, fluorescence resonance energy transfer-based redox probes that undergo opposite emission ratio changes upon exposure to H2O2. We have successfully used these sensors to measure H2O2 production by NADPH oxidases (Nox). Moreover, we targeted these probes to specific cellular compartments or incorporated them into oxidase complexes to detect H2O2 at different, well-defined loci. Studying Nox2- and dual oxidase 1 (Duox1)-expressing cells, we provide the first analysis of how NADPH-oxidase generated H2O2 signals radiate within and between cells. Our results suggest that H2O2 produced by Noxs can induce redox changes in the intracellular milieu of Nox/Duox-expressing cells while simultaneously transmitting paracrine effects to neighboring cells.

도로 협곡에서 NOx와 VOCs에 대한 오존의 민감도

The sensitivity of ozone to and volatile organic compounds (VOCs) emission rates under different ventilation rates and emission ratios in a street canyon is investigated using a chemistry box model. The carbon bond mechanism IV (CBM-IV) with 36 gaseous species and 93 chemical reactions is incorporated. and VOCs emission rates considered range from 0.01 to with intervals of . Three different ventilation rates and three different emission ratios are considered. The simulation results show that the ozone concentration decreases with increasing emission rate but increases with increasing VOCs emission rate. When the emission ratio of VOCs to is smaller than about 4, the ozone concentration is lower in the street canyon than in the background. On average, the magnitude of the sensitivity of ozone to emission rate is significantly larger than that to VOCs emission rate. As the emission rate increases, the magnitude of the sensitivity of ozone to and VOCs emission rates decreases. Because the ozone concentration is lower in the street canyon than in the background, the increased ventilation rate enhances ozone inflow from the background. Therefore, the increase in ventilation rate results in the increase in ozone concentration and the decrease in the magnitude of the sensitivity of ozone to and VOCs emission rates when the emission ratio of VOCs to is smaller than about 4. On the other hand, the increase in emission ratio results in the increase in ozone concentration because the chemical ozone production due to the photolysis is enhanced. In the present experimental setup, the contribution of the change in emission ratio to the change in the sensitivity of ozone to emission rate is larger than that of the change in ventilation rate.

Improving FRET dynamic range with bright green and red fluorescent proteins

A variety of genetically encoded reporters use changes in fluorescence (or Förster) resonance energy transfer (FRET) to report on biochemical processes in living cells. The standard genetically encoded FRET pair consists of cyan and yellow fluorescent proteins (CFP and YFP), but many CFP-YFP reporters suffer from low FRET dynamic range, phototoxicity from the CFP excitation light, and complex photokinetic events such as reversible photobleaching and photoconversion. Here, we engineered two fluorescent proteins, Clover and mRuby2, which are the brightest green and red fluorescent proteins to date, and have the highest Förster radius of any ratiometric FRET pair yet described. Replacement of CFP and YFP in reporters of kinase activity, small GTPase activity, and transmembrane voltage significantly improves photostability, FRET dynamic range, and emission ratio changes. These improvements enhance detection of transient biochemical events such as neuronal action potential firing and RhoA activation in growth cones.

Förster Resonance Energy Transfer-Based Biosensors for Multiparameter Ratiometric Imaging of Ca2+ Dynamics and Caspase-3 Activity in Single Cells

As one of the principal cytoplasmic second messengers, the calcium ion (Ca(2+)) is central to a variety of intracellular signal transduction pathways. Accordingly, there is a sustained interest in methods for spatially- and temporally resolved imaging of the concentration of Ca(2+) in live cells using noninvasive methods such as genetically encoded biosensors based on Förster resonance energy transfer (FRET) between fluorescent proteins (FPs). In recent years, protein-engineering efforts have provided the research community with FRET-based Ca(2+) biosensors that are dramatically improved in terms of enhanced emission ratio change and optimized Ca(2+) affinity for various applications. We now report the development and systematic optimization of a pair of spectrally distinct FRET-based biosensors that enable the simultaneous imaging of Ca(2+) in two compartments of a single cell without substantial spectral crosstalk between emission channels. Furthermore, we demonstrate that these new biosensors can be used in conjunction with previously reported caspase-3 substrates based on the same set of FRET pairs.

A bacteria colony-based screen for optimal linker combinations in genetically encoded biosensors

BackgroundFluorescent protein (FP)-based biosensors based on the principle of intramolecular Förster resonance energy transfer (FRET) enable the visualization of a variety of biochemical events in living cells. The construction of these biosensors requires the genetic insertion of a judiciously chosen molecular recognition element between two distinct hues of FP. When the molecular recognition element interacts with the analyte of interest and undergoes a conformational change, the ratiometric emission of the construct is altered due to a change in the FRET efficiency. The sensitivity of such biosensors is proportional to the change in ratiometric emission, and so there is a pressing need for methods to maximize the ratiometric change of existing biosensor constructs in order to increase the breadth of their utility.ResultsTo accelerate the development and optimization of improved FRET-based biosensors, we have developed a method for function-based high-throughput screening of biosensor variants in colonies of Escherichia coli. We have demonstrated this technology by undertaking the optimization of a biosensor for detection of methylation of lysine 27 of histone H3 (H3K27). This effort involved the construction and screening of 3 distinct libraries: a domain library that included several engineered binding domains isolated by phage-display; a lower-resolution linker library; and a higher-resolution linker library.ConclusionApplication of this library screening methodology led to the identification of an optimized H3K27-trimethylation biosensor that exhibited an emission ratio change (66%) that was 2.3 × improved relative to that of the initially constructed biosensor (29%).

Development of an Indole-Based Boron-Dipyrromethene Fluorescent Probe for Benzenethiols

Discrimination between chemically related benzenethiols and aliphatic thiols represents a big problem. In this paper, a fluorescent probe, Bodipy-1, containing an indole-based Bodipy as a fluorophore and a 2,4-dinitrobenzenesulfonyl group as a recognition unit was constructed to achieve the selectivity between them. The Bodipy group in the prepared probe was selectively released through aromatic nucleophilic substitution by thiolate anions from benzenethiols, resulting in blue-red switching in the emission spectra in buffer solutions; that is, two new peaks of the phenol/phenolate state of Bodipy-2 at 565 and 629 nm appeared in emission spectra. By varying the pH value from 6.6 to 8.8, the intensity ratio of I(565)/I(629) varies from 2.0 to 0.3 after complete conversion to Bodipy-2, a ca. 7-fold emission ratio change. This ratiometric emission property by varying the pH value makes Bodipy-1 a promising probe to discriminate benzenethiols from aliphatic thiols by careful selection of the reaction pH.

Improved FRET Sensing Of Membrane Voltage With Voltage Sensitive Phosphatase And New Coral Fluorescence Proteins

Ciona voltage sensitive phosphatase (Ci-VSP) is an unique enzyme discovered first in asicdian genome, in which phosphatase activity is regulated by transmembrane potential. Ci-VSP consists of a phosphatase domain and a preceding voltage sensing domain (VSD) which is homologous to the S1-S4 transmembrane domain found in conventional voltage-gated ionic channels. Possible mechanism of Ci-VSP should be that changes in transmembrane potential elicit conformational changes in the VSD, which then induce conformational changes in the phosphatase domain, regulating enzymatic activity. Analogously, by replacing the phosphatase domain with two fluorescent proteins that act as fluorescence resonance energy transfer (FRET) donor and acceptor, it is expected that transmembrane potential can be optically probed as FRET readout. Using two new coral fluorescent proteins, we developed such a membrane potential reporter, named Mermaid, that displays 40% changes in emission ratio per 100 mV change, allowing for visualization of spatiotemporal dynamics in electrical activities of excitable cells. Notably, Mermaid has fast on-off kinetics at warm temperatures and can report voltage spikes comparable to action potentials.