Probe Design Research Articles

Nanoprobe Based on Novel NIR-II Quinolinium Cyanine for Multimodal Imaging.

NIR-II imaging has the advantages of high sensitivity, spatiotemporal resolution, and high penetration depth, thereby serving as a potential alternative to conventional imaging methods. Herein, a novel NIR-II dye IR-1010 (λex/λem = 1010/1058nm) is reported with high quantum yield (3.08%) and good stability, by incorporating p-methoxyphenyl groups into a quinolinium cyanine dye. Then a multifunctional nanoprobe, termed IUFP NPs, is developed by the incorporation of upconversion (UC) nanoparticles (NPs), perfluoro-15-crown-5-ether (PFCE), and IR-1010, to display the novel performance of multimodal imaging. Under the single-wavelength excitation (980nm), IUFP NPs simultaneously emit the NIR-II fluorescence of IR-1010 and visible UC luminescence of UCNPs, and thus realize the UC imaging for cells, and NIR-II fluorescence/photoacoustic/19F magnetic resonance imaging for blood vessels, lymph nodes and tumor in mice. This work affords a novel approach to NIR-II dyes and a general strategy for the design of multimodal imaging probes.

Luminescent lanthanide metallopeptides for biomolecule sensing and cellular imaging.

Lanthanide ions display unique luminescent properties that make them particularly attractive for the development of bioprobes, including long-lived excited states that allow the implementation of time-gated experiments and the elimination of background fluorescence associated with biological media, as well as narrow emission bands in comparison with typical organic fluorophores, which allow ratiometric and multiplex assays. These luminescent complexes can be combined with peptide ligands to endow them with additional targeting, responsiveness, and selectivity, thus multiplying the opportunities for creative probe design. In this feature article we will present some of the main strategies that researchers have used to develop lanthanide metallopeptide probes for the detection of proteins and nucleic acids, as well as for monitoring enzymatic activity and cellular imaging.

Simple design of fluorescein-based probe for rapid and in situ visual monitoring of histamine levels in food spoilage

With the emergence of numerous food safety problems, rapid and accurate detection of histamine in food spoilage remains a challenge. To this end, we developed a simple design and easy synthesis of fluorescein-based probe FCHO to achieve specific and rapid (<1 s) quantitative detection of histamine through “imine formation” reaction. Significant enhanced fluorescence signal in response to histamine enabled our probe with high sensitivity as low as 51 nM. Utilizing the visualized fluorescence color changes of the probe as histamine increasing, we combined it with paper-based test chip to construct a color-resolved and highly selective recognition system. In addition, our proposed probe has been successfully used to visually imaging histamine changes in fish samples. Finally, for the first time, we have proved it possesses reliable ability to directly in situ imaging the distribution of histamine in whole spoiled fish. Thus, our strategy will provide great potential for monitoring food spoilage.

A General Method for Calibration of Active Scanning Thermal Probes

Scanning thermal microscopy (SThM) is a scanning probe technique aimed at quantitative characterization of local thermal properties at the length scale down to tens of nanometers. With many probe designs and approaches to interpretation of probe responses, there is a need for a universal framework, which would allow probe calibration and comparison of probe performance. Herein, a calibration framework based on an abstracted, formal, probe model for active SThM probes is developed. The calibration can be accomplished through measurements with two or three calibration samples. Requirements for calibration samples are described with examples of structures of suitable samples identified in published literature. A link to a published experimental work indirectly verifying the proposed procedure is provided. The calibration does not require knowledge of internal probe properties and yields a small and universal set of parameters that can be used to quantify thermal resistance presented to the probe by samples as well as to characterize active‐mode SThM probes of any type and at any measurement frequency. How the probe calibration parameters can be used to guide probe design is illustrated. When the calibration approach can be used directly to measure the thermal conductivity of unknown samples is also analyzed.

Research Note: Development of a reverse transcriptase recombinase-aided amplification method for detection of Parrot Borna Virus 4

The Parrot Borna virus 4 (PaBV-4) is the primary causative agent of parrot developmental disorder (PDD), leading to symptoms such as bloating, undigested feed in stool, decreased appetite, diarrhea, and weight loss. Its impact on the parrot industry has been significant, therefore, it is imperative to develop a rapid detection method for PaBV-4. The detection of PaBV-4 was achieved through the development of an RT-RAA assay, which involved the design of specific probes and primers targeting the N gene. This method allows for detection at 41°C within 30 min and has a minimum detection threshold of 8.56 × 101 copies/μL. The RT-RAA method demonstrated specific detection of PaBV-4 without any cross-reactivity observed with H5N6, H7N9, H9N2 avian influenza virus, newcastle disease virus (NDV), avian infectious bronchitis virus (IBV) and Parrot Borna virus 2 (PaBV-2). The coefficient of variation for the 3 repeatability experiments was below 10%. Tissue samples from 28 suspected cases of PaBV related deaths in parrots were analyzed using both RT-RAA and RT-qPCR methods. The sensitivity and specificity of both methods were 100%, demonstrating perfect agreement between them as indicated by a kappa value of 1. In conclusion, this study created a RT-RAA method for PaBV-4 detection successfully.

Near-Infrared Emissive π-Conjugated Oligomer Nanoparticles for Three- and Four-Photon Deep-Brain Microscopic Imaging Beyond 1700 nm Excitation.

High-resolution visualization of the deep brain is still a challenging and very significant issue. Multiphoton microscopy (MPM) holds great promise for high-spatiotemporal deep-tissue imaging under NIR-III and NIR-IV excitation. However, thus far, their applications have been seriously restricted by the scarcity of efficient organic probes. Herein, we designed and synthesized two donor-acceptor-donor-type conjugated small molecules (TNT and TNS) for in vivo mouse deep-brain imaging with three- and four-photon microscopy under 1700 and 2200 nm excitation. With a selenium (Se) substitution, we synthesized two conjugated small molecules to promote their emission into the deep near-infrared region with high quantum yields of 55% and 20% in THF solvent, respectively, and their water-dispersive nanoparticles have relatively large absorption cross-sections in the 1700 and 2200 nm windows, respectively, with good biosafety. With these superiorities, these organic NPs achieve high-resolution deep-brain imaging via three-photon and four-photon microscopy with excitation at 1700 and 2200 nm windows, and 1620 μm deep in the brain vasculature can be visualized in vivo. This study demonstrates the efficiency of NIR-emissive conjugated small molecules for high-performance MPM imaging in the NIR-III and NIR-IV window and provides a route for the future design of organic MPM probes.

Engineering two-in-one DNA nanohybrids to evaluate anti-cancer effects through activatable RNA imaging

The development of DNA-based imaging techniques provides a promising way for theranostic applications. However, the dramatic chemical difference between DNA probes and therapeutics significantly hinders the construction of an ideal theranostic system for evaluation of therapeutic effects via in situ molecular imaging. In this work, we report a simple approach for the construction of a two-in-one DNA nanohybrid via one-step assembly of DNA probes and small molecular drugs, enabling evaluation of therapeutic effects via sensitive imaging of apoptosis-related mRNA. The nanohybrid was self-assembled from a rationally designed molecular beacon (MB) probe, doxorubicin (DOX, a chemotherapeutic drug) and Fe (II) ions through coordination interactions, which possesses anti-cancer effects from chemotherapeutics and the capability of efficient co-delivery of DNA probes without transfection agents. By tracking pro-apoptotic Bax mRNA expression with the MB, this system allows real-time monitoring of cell apoptotic process in response to drug treatment, enabling assessment of therapeutic effects of small molecular drugs. In addition, the approach is extended to the imaging of target microRNA in the drug treatment based on flexible DNA probe design, demonstrating the universality of this strategy. Moreover, the modular design of this DNA nanohybrid allows the introduction of photosensitizers into this system for efficient photodynamic therapy and simultaneous mRNA monitoring. This strategy expands the theranostic toolbox for the in situ evaluation of treatment response and screening anticancer drugs.

Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales

Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.

Tuning and Matching Error-Compensated, Quantitative Solid-State Nuclear Magnetic Resonance.

NMR spectroscopy has long been recognized as a powerful quantitative analytical tool. Quantification is commonly done against internal and external standards. A third approach is to quantify against an electronic reference, which combines the advantages of the two methods. The implementation of this approach in solid-state NMR is more challenging due to the single-coil design of double resonance probes. In this study, a novel approach for implementing the electronic referencing method in solid-state NMR by injecting the reference signal using a broadband antenna installed near the NMR receiver coil is presented. This method demonstrates excellent accuracy and precision, as it remains robust to changes in the electronic conditions of the probe, including tuning and matching errors.

Cyano-determined mercury (II) ion selective fluorescence assay over polymeric carbon nitride

Selective response is the key index to evaluate the performance of polymeric carbon nitride (PCN)-based heavy metal ion fluorescence sensors. Herein, to explore the role of cyano groups on selectivity, four kinds of PCN, including PCN-Cl, PCN-Ac, PCN-B and PCN-K were prepared by the molten salt method of sodium chloride and sodium acetate, the reduction method of sodium borohydride and the etching method of potassium hydroxide, respectively. These PCNs exhibited different surface cyano characteristics, but all of them had significant blue emission under ultraviolet excitation. It is proved that the assistant of sodium chloride or potassium hydroxide is an effective method to prepare PCNs with abundant surface cyano group. A series of fluorescence quenching experiments of metal ions showed that the cyano-rich degree of PCN is closely related to its selective response to mercury (II) ions. PCN-Cl and PCN-K emerged good selective quenching of mercury (II) ions, which may be related to the soft acid-soft base strong interaction between mercury (II) ions and cyano groups. Both PCN-Cl and PCN-K fluorescent probes for mercury (II) ions had a linear range of 5 ∼ 50 μmol L−1, and PCN-Cl exhibited a lower detection limit of 0.38 μmol L−1. This work confirmed the selective fluorescence response of cyano-rich PCN to mercury (II) ions, proposed the mechanism of selective fluorescence quenching response of mercury (II) ions, and provided a new idea for the design of efficient and accurate PCN-based fluorescence probes.

Design and synthesis of a TICT-based red-emissive fluorescent probe for the rapid and selective detection of HSA in human biofluids and live cell imaging.

Here, we report the design and synthesis of a D⋯π⋯A-based fluorescent probe, (E)-4-(4-(dibutylamine)-2-hydroxystyryl)-1-methylquinolin-1-ium (DHMQ), which is nonfluorescent in ∼100% PBS buffer medium due to a twisted intra molecular charge transfer (TICT) phenomenon and it becomes highly fluorescent (∼149 fold) in the presence of human serum albumin (HSA), owing to the restriction of its intramolecular free rotation inside the hydrophobic binding cavity of HSA. The site-selective fluorescence displacement assay and molecular docking studies clearly reveal that DHMQ selectively binds at subdomain IB of HSA. The 3σ/slope method was adopted to determine the limit of detection (LOD) value, which was as low as 2.39 nM in ∼100% PBS medium, indicating its high sensitivity towards HSA. The low dissociation constant value [Kd = (1.066 ± 0.017) μM] suggests a strong complexation between the DHMQ and HSA. Importantly, it has been demonstrated that DHMQ is capable of detecting HSA in real human serum and urine samples and was found to be suitable for live cell imaging of HSA.

A novel dual-site fluorescent probe for the one-step detection of Cys and SO2 in living cells

BackgroundCysteine (Cys) is the major intracellular thiol and plays a key role in human pathology. Furthermore, endogenous sulfur dioxide (SO2) is produced in mammals. Abnormal levels of SO2 are commonly associated with a variety of respiratory, cardiovascular, and neurological diseases. Therefore, given their important role in life activities, it is significant to construct a fluorescent probe that can detection between Cys and SO2. ResultsWe have designed and synthesized a two-site fluorescent probe CUM with coumarin derivative and benzaldehyde molecules, which can detect and differentiate between Cys and SO2 through dual excitation wavelengths. Its carbon-carbon double bond reacts with Cys and undergoes a nucleophilic reaction, emitting green fluorescence at 520 nm, while SO32− reacts with benzaldehyde molecules in the probe CUM and undergoes a blue fluorescence at 460 nm. SO32− reacts with the benzaldehyde molecule of probe CUM and fluoresces blue at 460 nm. Thus, the probe CUM with two reaction sites can distinguish between Cys and SO2 and shows good selectivity and fast reaction speed. In addition, we successfully utilized probe CUM to image Cys and SO2 in human breast cancer cells (MDA-MB-231). SignificanceThis work provides an effective method for the molecular design of coumarin-based fluorescent probes. Probe CUM as a promising and reliable tool for the meticulous discrimination and quantification of Cys and SO2 in diverse biological matrices, thereby opening up new avenues for various biological systems.

Tailoring near-infrared amyloid-β probes with high-affinity and low background based on CN and amphipathic regulatory strategies and in vivo imaging of AD mice

Amyloid-β (Aβ) species (Aβ fibrils and Aβ plaques), as one of the typical pathological markers of Alzheimer's disease (AD), plays a crucial role in AD diagnosis. Currently, some near-infrared I (NIR I) Aβ probes have been reported in AD diagnosis. However, they still face challenges such as strong background interference and the lack of effective probe design. In this study, we propose molecular design strategy that incorporates CN group and amphiphilic modulation to synthesize a series of amphiphilic NIR I Aβ probes, surpassing the commercial probe ThT and ThS. Theoretical calculations indicate that these probes exhibit stronger interaction with amino acid residues in the cavities of Aβ. Notably, the probes containing CN group display the ability of binding two distinct sites of Aβ, which dramatically enhanced the affinity to Aβ species. Furthermore, these probes exhibit minimal fluorescence in aqueous solution and offer ultra-high signal-to-noise ratio (SNR) for in vitro labeling, even in wash-free samples. Finally, the optimal probe DM-V2CN-PYC3 was utilized for in vivo imaging of AD mice, demonstrating its rapid penetration through the blood-brain barrier and labelling to Aβ species. Moreover, it enabled long-term monitoring for a duration of 120 min. These results highlight the enhanced affinity and superior performance of the designed NIR I Aβ probe for AD diagnosis. The molecular design strategy of CN and amphiphilic modulation presents a promising avenue for the development Aβ probes with low background in vivo/in vitro imaging for Aβ species.

Bin2cell reconstructs cells from high resolution Visium HD data.

Visium HD by 10X Genomics is the first commercially available platform capable of capturing full scale transcriptomic data paired with a reference morphology image from archived FFPE blocks at sub-cellular resolution. However, aggregation of capture regions to single cells poses challenges. Bin2cell reconstructs cells from the highest resolution data (2 μm bins) by leveraging morphology image segmentation and gene expression information. It is compatible with established Python single cell and spatial transcriptomics software, and operates efficiently in a matter of minutes without requiring a GPU. We demonstrate improvements in downstream analysis when using the reconstructed cells over default 8 μm bins on mouse brain and human colorectal cancer data. Bin2cell is available at https://github.com/Teichlab/bin2cell, along with documentation and usage examples, and can be installed from pip. Probe design functionality is available at https://github.com/Teichlab/gene2probe.

Eddy Currents Probe Design for NDT Applications: A Review.

Eddy current testing (ECT) is a crucial non-destructive testing (NDT) technique extensively used across various industries to detect surface and sub-surface defects in conductive materials. This review explores the latest advancements and methodologies in the design of eddy current probes, emphasizing their application in diverse industrial contexts such as aerospace, automotive, energy, and electronics. It explores the fundamental principles of ECT, examining how eddy currents interact with material defects to provide valuable insights into material integrity. The integration of numerical simulations, particularly through the Finite Element Method (FEM), has emerged as a transformative approach, enabling the precise modeling of electromagnetic interactions and optimizing probe configurations. Innovative probe designs, including multiple coil configurations, have significantly enhanced defect detection capabilities. Despite these advancements, challenges remain, particularly in calibration and sensitivity to environmental conditions. This comprehensive overview highlights the evolving landscape of ECT probe design, aiming to provide researchers and practitioners with a detailed understanding of current trends in this dynamic field.

Chromogenic probes featuring hydroxyethyl acetate as metal ion binding site: Selective dual-mode response and quantitative analysis of Ag+ at micellar interface

This study presents the design and synthesis of Charge Transfer-based chromogenic probes utilizing hydroxyethyl acetate (HEA) as a metal ion chelating site, and anthraimidazoldione (1) and bisindolyl methane (2) as signalling moieties. Both compounds demonstrated pH-sensitive nanoaggregate formation in aqueous solutions, as confirmed by various spectroscopic studies, dynamic light scattering (DLS) analysis, and field emission scanning electron microscopy (FESEM) imaging. Despite containing the HEA unit, compound 1 displayed no interaction with metal ions either in water or acetonitrile medium. However, in Brij-58 micelles, compound 1 exhibited a selective color-changing response to Ag+ ions accompanied by fluorescence enhancement. Mechanistic investigations revealed that Ag+ ions bound to the HEA unit, altering the charge transfer state of the probe. Compound 2, with bisindolyl methane as signalling moiety, demonstrated a superior response to Ag+ ions, attributed to differences in the pKa values of coordinating tertiary nitrogen centers and aggregation behavior. The developed sensory system was applied for silver ion estimation in Silverex ionic gel and diluted human urine samples, demonstrating high recovery values (~100 %) with low standard deviation (<5 %). These results suggest suitability of the present method for quantitative analysis of real-life samples.

Investigation of musculoskeletal symptoms, work postures, quantification of muscle activity, and estimation of grip/push forces among sonographers

AbstractDue to the physical nature of their work, sonographers are exposed to many musculoskeletal disorder risk factors, including awkward posture, repetitive movements, forceful manual exertion, and static muscle contractions, especially in the upper limbs. The current study is an investigation of musculoskeletal disorders among sonographers, caused by various occupational risk factors via different sonographic scan types. During the first phase of this study, the musculoskeletal symptoms and work postures of 29 subjects were investigated. During the second phase, muscle activity was quantified, and grip/push forces were estimated using the data obtained from 10 volunteer sonographers. 82% of sonographers experienced musculoskeletal symptoms. Based on the final scores and action levels obtained via rapid upper limb assessment, while performing scans of left regions; ergonomic changes and interventions were found necessary, to relieve stress on the sonographer's body. The results of muscular activity per muscle and scan type, showed that the mean muscle activity of the middle deltoid muscle was significantly higher during the right abdominal scan (17.64% maximum voluntary contraction [MVC]), compared to those of thyroid (12.54% MVC) and left abdominal (7.32% MVC) scans. Additionally, mean grip and push forces during both abdominal scans were significantly higher than those during the thyroid scan. Despite an injury risk during all scans, risk factor impact was different among scan types. This groundbreaking study represents the first that captures and measures both grip and push forces simultaneously, which may prove helpful while investigating corrective interventions or optimizing design of sonography robots and ergonomic probes in future studies.

Quantitative Optimization of Handheld Probe External Pressure on Dermatological Microvasculature Using Optical Coherence Tomography-Based Angiography.

Optical Coherence Tomography (OCT)-based angiography (OCTA) is a high-resolution, high-speed, and non-invasive imaging method that can provide vascular mapping of subcutaneous tissue up to approximately 2 mm. In dermatology applications of OCTA, handheld probes are always designed with a piece of transparent but solid contact window placed at the end of the probe to directly contact the skin for achieving better focusing between the light source and the tissue, reducing noise caused by minor movements. The pressure between the contact window and the skin is usually uncontrollable, and high external pressure affects the quality of microvascular imaging by compressing the vessels and obstructing the underlying blood flow. Therefore, it is necessary to determine a pressure range to ensure that the vessels can be fully imaged in high-quality images. In this paper, two pressure sensors were added to the existing handheld OCT probe, and the imaging probe was fixed to a metal stand and adjusted vertically to change the pressure between the probe and the tested skin site, a gradient of roughly 4 kPa (with 1-2 kPa error) increase was applied in each experiment, and the impact of pressure to the vessel was calculated. The experiment involved a total of five subjects, three areas of which were scanned (palm, back of the hand, and forearm). The vessel density was calculated to evaluate the impact of external pressure on angiography. In addition, PSNR was calculated to ensure that the quality of different tests was at a similar level. The angiography showed the highest density (about 10%) when the pressure between the contact window on the probe and the test area was between 3 and 5 kPa. As the pressure increased, the vascular density decreased, and the rate of decrease varied in different test areas. After fitting all the data points according to the different sites, the slope of the fitted line, i.e., the rate of decrease in density per unit value of pressure, was found to be 4.05% at the palm site, 6.93% at the back of the hand, and 4.55% at the forearm site. This experiment demonstrates that the pressure between the skin and contact window is a significant parameter that cannot be ignored. It is recommended that in future OCTA data collection processes and probe designs, the impact of pressure on the experiment be considered.

The Effects of Using Adapted Science eBooks Within Shared Reading on Comprehension and Task Engagement of Students with Autism Spectrum Disorder.

The purpose of this study was to examine the effects of using adapted science eBooks within shared reading on comprehension and task engagement of high school students with autism spectrum disorder (ASD). A grade-level science textbook was selected and converted into an eBook format, incorporating various visual and auditory features (e.g., text-to-speech, summarized sentences, highlighted keywords) and presented on an iPad. The shared reading intervention included before, during, and after reading strategies (i.e., pre-teaching target vocabulary words, sharing information, retelling), with direct instruction on locating literal information. The intervention effects on reading comprehension and task engagement were evaluated using a single-case multiple probe design. The results of this study indicated that all participants demonstrated improvements in reading comprehension. Despite the longer intervention sessions compared to the baseline, all participants exhibited similar or enhanced levels of task engagement during the intervention sessions. The findings of this study provide empirical evidence supporting the use of adapted eBooks within shared reading as a means to increase access to grade-level science texts for high school students with ASD while maintaining a high level of task engagement. This intervention holds promise for improving the learning outcomes for students with ASD in science content area.

Synthesis and photophysical properties of 3-aryl-2-cyanoacrylamides: Design of a turn-on fluorescent probe for cyanide ion detection

Three 3-aryl-2-cyanoacrylamide derivatives were synthesised in 71−79 % yields from cheap reagents and mild reaction conditions using the Et3N-mediated Knoevenagel condensation of fluorescent arylaldehydes (e.g., triphenylamine and anthracene) with cyanoacetamide. These dyes' photophysical properties and anions-recognizing behaviour were studied, revealing that the 9-anthracenyl derivative can "turn on" fluorescence in cyanide presence, with high selectivity and a detection limit (LOD) of 710 nM. Initially, there is fluorescence quenching by the energy transfer (ET) from the anthracene ring to the 2-cyanoacrylamide moiety due to the non-coplanarity of these fragments and, upon the cyanide addition to Cβ of the receptor unit, the intrinsic fluorescence of anthracene is restored. HRMS and NMR experiments and TD-DFT calculations were performed to confirm the detection mechanism and fluorescence properties of the design chemodosimeter; fluorescent test paper was also used to detect cyanide in an aqueous medium.