θ-Nanopore Ratiometry

Developing nanoscale ratiometric techniques capable of biochemical response should prove of significance for precise applications with stringent spatial and biological restrictions. Here we present and devise the concept of θ-nanopore ratiometry, which uses ratiometric signals that could well address the serious concerns about device deviation in fabrication and nonspecific adsorption in the detection. As exemplified by a 200 nm θ-nanopore toward miRNA detection, the ±20 nm aperture drift could be mitigated and the issue of nonspecific adsorption could be minimized in the complex cytosolic environment. Practical application of this θ-nanopore ratiometry realizes the measurements of cytosolic miRNA-10b. This work has not only established a nanoscopic ratiometric technique but also enriched the extant armory of nanotools for single-cell studies and beyond.

Optical mapping of contracting hearts

Optical mapping is a widely used tool to record and visualize the electrophysiological properties in a variety of myocardial preparations such as Langendorff-perfused isolated hearts, coronary-perfused wedge preparations, and cell culture monolayers. Motion artifact originating from the mechanical contraction of the myocardium creates a significant challenge to performing optical mapping of contracting hearts. Hence, to minimize the motion artifact, cardiac optical mapping studies are mostly performed on non-contracting hearts, where the mechanical contraction is removed using pharmacological excitation-contraction uncouplers. However, such experimental preparations eliminate the possibility of electromechanical interaction, and effects such as mechano-electric feedback cannot be studied. Recent developments in computer vision algorithms and ratiometric techniques have opened the possibility of performing optical mapping studies on isolated contracting hearts. In this review, we discuss the existing techniques and challenges of optical mapping of contracting hearts.

A Selective Excited-State Intramolecular-Proton-Transfer (ESIPT) Sensor for Copper(II) Based on Chelation-Enhanced Quenching and "Off-On" Detection of Amino Acids

We report the synthesis of 2-(4,5-diphenyl-1H-imidazole-2-yl)phenol (TPI-9) as an interesting fluorescent molecule displaying Excited-State Intramolecular-Proton-Transfer (ESIPT) with stokes shift of 120 nm. Phenolic compounds with the ability to form intramolecular hydrogen bonds and subsequent proton transfer are known as ESIPT fluorophores. Proton accepting ability can increase significantly by tailoring electron-donating groups. With the assistance of an environment-friendly organocatalyst, 10-camphor sulfonic acid (10-CSA), TPI-9 was synthesized to introduce substituents with electron-donating abilities to develop an efficient ESIPT mechanism. Factors influencing the emission, such as solvent, pH, and metal ions, are investigated. Quenching of fluorescence by Cu²⁺ through chelation enhancement quenching effect with a high selectivity allowed the establishment of a Cu²⁺ sensor with an LoD of 0.57 ppm and a ratiometric estimation with an LoD of 0.73 ppm. Metal binding (2 : 1) stoichiometry and quenching constant (0.0072 mol^-1 s^-1 ) are calculated from Job's and Stern-Volmer plots. Density functional theory (DFT) calculations are in accordance with the experimental results. Competitive replacement of TPI-9 by amino acids restores ESIPT, consequently, the fluorescence. Thus, an "off-on" fluorescence sensor for amino acid estimation is developed under 1 minute incubation. A linear relationship between amino acid concentration and fluorescence intensity is in 0-20 μg/mL range, and the LoD is less than 2.2 μg/mL.

MXene with Great Adsorption Ability toward Organic Dye: An Excellent Material for Constructing a Ratiometric Electrochemical Sensing Platform

Ratiometric electrochemical sensors coupled with an intrinsic built-in correction have received much attention in biochemical analysis, which can effectively avoid potential impacts from both intrinsic and extrinsic factors. However, the complex modification procedure and the unstable reference signal limit development and application of ratiometric sensing. To address these issues, we proposed a novel ratiometric electrochemical platform based on MXene. Introduction of built-in correction was realized via simple one-step incubation of MXene in solution containing the reference molecule methylene blue (MB), and their firm electrostatic interaction ensures the strong adsorption capability of MXene toward MB. Remarkable enhancement in repeatibility and stability compared with nonratio sensor was proved by detecting the model analyte piroxicam. Furthermore, compatibility of the ratio sensor was demonstrated by integrating copper nanoparticles (CuNPs) into the platform. It turned out that sensing performance of the hybrid electrochemical sensor was significantly improved owing to synergistic effect of MXene and CuNPs, where the former affords a large specific surface area as well as quick electron transport, and the latter possess decent electrical catalytic ability. In all, the proposed ratiometric sensor based on MXene features easy preparation, superb reproducibility, robustness, and broad applicability, affording the platform highly competitive and reliable in the determination of a wide range of substances.

A Mass-Ratiometry-Based CD45 Barcoding Method for Mass Cytometry Detection

Mass cytometry (CyTOF) is a critical cell profiling tool in acquiring multiparameter proteome data at the single-cell level. A major challenge in CyTOF analysis is sample-to-sample variance arising from the pipetting process, staining variation, and instrument sensitivity. To reduce such variations, cell barcoding strategies that enable the combination of individual samples prior to antibody staining and data acquisition on CyTOF are often utilized. The most prevalent barcoding strategy is based on a binary scheme that cross-examines the existence or nonexistence of certain mass signals; however, it is limited by low barcoding efficiency and high cost, especially for large sample size. Herein, we present a novel barcoding method for CyTOF application based on mass ratiometry. Different mass tags with specific fixed ratios are used to label CD45 antibody to achieve sample barcoding. The presented method exponentially increases the number of possible barcoded samples with the same amount of mass tags compared with conventional methods. It also reduces the overall time for the labeling process to 40 min and avoids the need for expensive commercial barcoding buffer reagents. Moreover, unlike the conventional barcoding process, this strategy does not pre-permeabilize cells before the barcoding procedure, which offers additional benefits in preserving surface biomarker signals.

Ultrabright Red-Emitting Photostable Perylene Bisimide Dyes: New Indicators for Ratiometric Sensing of High pH or Carbon Dioxide

New pH-sensitive perylene bisimide indicator dyes were synthesized and used for fabrication of optical sensors. The highly photostable dyes show absorption/emission bands in the red/near-infrared (NIR) region of the electromagnetic spectrum, high molar absorption coefficients (up to 100 000 m-1  cm-1 ), and fluorescence quantum yields close to unity. The absorption and emission spectra show strong bathochromic shifts upon deprotonation of the imidazole nitrogen atom, which makes the dyes promising as ratiometric fluorescent indicators. Physical entrapment of the indicators into a polyurethane hydrogel enables pH determination at alkaline pH values. It is also shown that a plastic carbon dioxide solid-state sensor can be manufactured by immobilization of the pH indicator in a hydrophilic polymer, along with a quaternary ammonium base. The influences of the plasticizer, different lipophilic bases, and humidity on the sensitivity of the sensor material are systematically investigated. The disubstituted perylene, particularly, features two deprotonation equilibria, enabling sensing over a very broad pCO2 range of 0.5 to 1000 hPa.

Latent pH-responsive ratiometric fluorescent cluster based on self-assembled photoactivated SNARF derivatives

We have developed a self-assembled fluorescent cluster comprising a seminaphthorhodafluor (SNARF) derivative protected by a photoremovable o-nitrobenzyl group. Prior to UV irradiation, a colorless and nonfluorescent cluster was spontaneously assembled in aqueous solution. After UV irradiation, the self-assembled cluster remained intact and showed a large enhancement in pH-responsive fluorescence. The unique pH responsive fluorescent cluster could be used as a dual-emissive ratiometric fluorescent pH probe not only in the test tube but also in HeLa cell cultures.

A smart "sense-act-treat" system: combining a ratiometric pH sensor with a near infrared therapeutic gold nanocage

Herein, we design a "sense-act-treat" system via the combination of a ratiometric pH sensor with a therapeutic gold nanocage. Our design could "sense" the tumor through two-state switching of fluorescence and further provide chemotherapy and hyperthermia for "treating" the tumor, showing the potential for future biomedical applications.

Simultaneous optical mapping of transmembrane potential and wall motion in isolated, perfused whole hearts

Optical mapping of cardiac propagation has traditionally been hampered by motion artifact, chiefly due to changes in photodetector-to-tissue registration as the heart moves. We have developed an optical mapping technique to simultaneously record electrical waves and mechanical contraction in isolated hearts. This allows removal of motion artifact from transmembrane potential (V(m)) recordings without the use of electromechanical uncoupling agents and allows the interplay of electrical and mechanical events to be studied at the whole organ level. Hearts are stained with the voltage-sensitive dye di-4-ANEPPS and ring-shaped markers are attached to the epicardium. Fluorescence, elicited on alternate frames by 450 and 505 nm light-emitting diodes, is recorded at 700 frames∕ per second by a camera fitted with a 605 ± 25 nm emission filter. Marker positions are tracked in software. A signal, consisting of the temporally interlaced 450 and 505 nm fluorescence, is collected from the pixels enclosed by each moving ring. After deinterlacing, the 505 nm signal consists of V(m) with motion artifact, while the 450 nm signal is minimally voltage-sensitive and contains primarily artifacts. The ratio of the two signals estimates V(m). Deformation of the tissue enclosed by each set of 3 rings is quantified using homogeneous finite strain.

Mapping Functional Connectivity between Neuronal Ensembles with Larval Zebrafish Transgenic for a Ratiometric Calcium Indicator

The ability to map functional connectivity is necessary for the study of the flow of activity in neuronal circuits. Optical imaging of calcium indicators, including FRET-based genetically encoded indicators and extrinsic dyes, is an important adjunct to electrophysiology and is widely used to visualize neuronal activity. However, techniques for mapping functional connectivities with calcium imaging data have been lacking. We present a procedure to compute reduced functional couplings between neuronal ensembles undergoing seizure activity from ratiometric calcium imaging data in three steps: (1) calculation of calcium concentrations and neuronal firing rates from ratiometric data; (2) identification of putative neuronal populations from spatio-temporal time-series of neural bursting activity; and then, (3) derivation of reduced connectivity matrices that represent neuronal population interactions. We apply our method to the larval zebrafish central nervous system undergoing chemoconvulsant-induced seizures. These seizures generate propagating, central nervous system-wide neural activity from which population connectivities may be calculated. This automatic functional connectivity mapping procedure provides a practical and user-independent means for summarizing the flow of activity between neuronal ensembles.

Improved cytoplasmic pH measurements in SNARF-1 stained plant cells by image processing

Cytoplasmic pH has long been considered to act as a secondary messenger of various cellular responses by affecting the ionization state of proteins. In plant biology, cytoplasmic pH has traditionally been measured, especially in guard cells and as a response to plant microorganism interactions, with pH-sensitive microelectrodes. More recently, the development of fluorescent pH markers, such as BCECF and SNARF-1, has allowed us to monitor cytoplasmic pH without the need for electrophysiological equipment. However, because of vacuolar structures that occupy a large volume of plant cells, simple measurements of fluorescent intensities are insufficient to provide precise cytoplasmic pH values. In this addendum, we describe our improved method to monitor cytoplasmic pH in plant cells stained by SNARF-1 by image processing using a noise-reducing filter after determination of an optimal ROI size. In addition, further developments for automated region extraction are proposed.