Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes.

Nonsense mutations create premature termination codons (PTCs), activating the nonsense-mediated mRNA decay (NMD) pathway to degrade most PTC-containing mRNAs. The undegraded mRNA is translated, but translation terminates at the PTC, leading to no production of the full-length protein. This work presents targeted PTC pseudouridylation, an approach for nonsense suppression in human cells. Specifically, an artificial box H/ACA guide RNA designed to target the mRNA PTC can suppress both NMD and premature translation termination in various sequence contexts. Targeted pseudouridylation exhibits a level of suppression comparable with that of aminoglycoside antibiotic treatments. When targeted pseudouridylation is combined with antibiotic treatment, a much higher level of suppression is observed. Transfection of a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene targeting the PTC also leads to nonsense suppression. Thus, targeted pseudouridylation is an RNA-directed gene-specific approach that suppresses NMD and concurrently promotes PTC readthrough.

Transcriptome-wide dynamics of RNA pseudouridylation.

Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

Activin A-Expressing Polymorphonuclear Myeloid-Derived Suppressor Cells Infiltrate Skeletal and Cardiac Muscle and Promote Cancer Cachexia.

Cachexia is a major cause of death in cancer and leads to wasting of cardiac and skeletal muscle, as well as adipose tissue. Various cellular and soluble mediators have been postulated in driving cachexia; however, the specific mechanisms behind this muscle wasting remain poorly understood. In this study, we found polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) to be critical for the development of cancer-associated cachexia. Significant expansion of PMN-MDSCs was observed in the cardiac and skeletal muscles of cachectic murine models. Importantly, the depletion of this cell subset, using depleting anti-Ly6G Abs, attenuated this cachectic phenotype. To elucidate the mechanistic involvement of PMN-MDSCs in cachexia, we examined major mediators, that is, IL-6, TNF-α, and arginase 1. By employing a PMN-MDSC-specific Cre-recombinase mouse model, we showed that PMN-MDSCs were not maintained by IL-6 signaling. In addition, PMN-MDSC-mediated cardiac and skeletal muscle loss was not abrogated by deficiency in TNF-α or arginase 1. Alternatively, we found PMN-MDSCs to be critical producers of activin A in cachexia, which was noticeably elevated in cachectic murine serum. Moreover, inhibition of the activin A signaling pathway completely protected against cardiac and skeletal muscle loss. Collectively, we demonstrate that PMN-MDSCs are active producers of activin A, which in turn induces cachectic muscle loss. Targeting this immune/hormonal axis will allow the development of novel therapeutic interventions for patients afflicted with this debilitating syndrome.

Pseudouridylation-mediated gene expression modulation.

RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.

Enhanced N2 Adsorption and Activation by Combining Re Clusters and In Vacancies as Dual Sites for Efficient and Selective Electrochemical NH3 Synthesis.

The electrochemical N2 reduction reaction (NRR) is a green and energy-saving sustainable technology for NH3 production. However, high activity and high selectivity can hardly be achieved in the same catalyst, which severely restricts the development of the electrochemical NRR. In2Se3 with partially occupied p-orbitals can suppress the H2 evolution reaction (HER), which shows excellent selectivity in the electrochemical NRR. The presence of VIn can simultaneously provide active sites and confine Re clusters through strong charge transfer. Additionally, well-isolated Re clusters stabilized on In2Se3 by the confinement effect of VIn result in Re-VIn active sites with maximum availability. By combining Re clusters and VIn as dual sites for spontaneous N2 adsorption and activation, the electrochemical NRR performance is enhanced significantly. As a result, the Re-In2Se3-VIn/CC catalyst delivers a high NH3 yield rate (26.63 µg h-1 cm-2) and high FEs (30.8%) at -0.5 V vs RHE.

Hydrodynamics-Controlled Single-Particle Electrocatalysis.

Electrocatalysis is considered promising in renewable energy conversion and storage, yet numerous efforts rely on catalyst design to advance catalytic activity. Herein, a hydrodynamic single-particle electrocatalysis methodology is developed by integrating collision electrochemistry and microfluidics to improve the activity of an electrocatalysis system. As a proof-of-concept, hydrogen evolution reaction (HER) is electrocatalyzed by individual palladium nanoparticles (Pd NPs), with the development of microchannel-based ultramicroelectrodes. The controlled laminar flow enables the precise delivery of Pd NPs to the electrode-electrolyte interface one by one. Compared to the diffusion condition, hydrodynamic collision improves the number of active sites on a given electrode by 2 orders of magnitude. Furthermore, forced convection enables the enhancement of proton mass transport, thereby increasing the electrocatalytic activity of each single Pd NP. It turns out that the improvement in mass transport increases the reaction rate of HER at individual Pd NPs, thus a phase transition without requiring a high overpotential. This study provides new avenues for enhancing electrocatalytic activity by altering operating conditions, beyond material design limitations.

UCHL-3 as a potential biomarker of ovarian cancer.

OBJECTIVE: This study explored promising prognostic and immune therapeutic candidate biomarkers for OC and determined the expression, prognostic value, and immune effects of UCHL3. METHODS: UCHL3 expression and clinical data were investigated using bioinformatic analysis. CCK8 and transwell assays were conducted to evaluate the impact of UCHL3 on proliferation and migration, and the effects of UCHL3 were further validated in a mouse model. Univariate and least absolute shrinkage and selection operator regression analyses were performed to construct a novel UCHL3-related prognostic risk model. Gene set enrichment analysis (GSEA) and immune analysis were performed to identify the significantly involved functions of UCHL3. Finally, bioinformatic analysis and immunohistochemistry were performed to explore the effect of UCHL3 on chemotherapy. RESULTS: UCHL3 expression was upregulated and associated with worse overall survival (OS) in OC. UCHL3 depletion repressed cell proliferation and migration both in vitro and in vivo. Furthermore, 237 genes were differentially expressed between the high and low UCHL3 expression groups. Subsequently, a UCHL3-related prognostic signature was built based on six prognostic genes (PI3, TFAP2B, MUC7, PSMA2, PIK3C2G, and NME1). Independent prognostic analysis suggested that age, tumor mutational burden, and RiskScore can be used as independent prognostic factors. The immune infiltration analysis and GSEA suggested that UCHL3 expression was related to the immune response. In addition, UCHL3 expression was higher in platinum-resistant OC patients than in platinum-sensitive patients. UCHL3 overexpression was associated with poorer OS. CONCLUSION: UCHL3 overexpression contributes to aggressive progression, poor survival, and chemoresistance in OC. Therefore, UCHL3 may be a candidate prognostic biomarker and potential target for controlling progression and platinum resistance in OC.

HFM-Tracker: a cell tracking algorithm based on hybrid feature matching.

Cell migration is known to be a fundamental biological process, playing an essential role in development, homeostasis, and diseases. This paper introduces a cell tracking algorithm named HFM-Tracker (Hybrid Feature Matching Tracker) that automatically identifies cell migration behaviours in consecutive images. It combines Contour Attention (CA) and Adaptive Confusion Matrix (ACM) modules to accurately capture cell contours in each image and track the dynamic behaviors of migrating cells in the field of view. Cells are firstly located and identified via the CA module-based cell detection network, and then associated and tracked via a cell tracking algorithm employing a hybrid feature-matching strategy. This proposed HFM-Tracker exhibits superiorities in cell detection and tracking, achieving 75% in MOTA (Multiple Object Tracking Accuracy) and 65% in IDF1 (ID F1 score). It provides quantitative analysis of the cell morphology and migration features, which could further help in understanding the complicated and diverse cell migration processes.

Observation of an isothermal glass transition in metallic glasses.

Glass transition, commonly manifested upon cooling a liquid, is continuous and cooling rate dependent. For decades, the thermodynamic basis in liquid-glass transition has been at the center of debate. Here, long-time isothermal annealing was conducted via molecular dynamics simulations for metallic glasses to explore the connection of physical aging in supercooled liquid and glassy states. An anomalous two-step aging is observed in various metallic glasses, exhibiting features of supercooled liquid dynamics in the first step and glassy dynamics in the second step, respectively. Furthermore, the transition potential energy is independent of initial states, proving that it is intrinsic for a metallic glass at a given temperature. We propose that the observed dynamic transition from supercooled liquid dynamics to glassy dynamics could be glass transition manifested isothermally. On this basis, glass transition is no longer cooling rate dependent, but is shown as a clear phase boundary in the temperature-energy phase diagram. Hence, a modified out-of-equilibrium phase diagram is proposed, providing new insights into the nature of glass transition.

Three-Dimensional Magnetic Resonance Imaging Fast Field Echo Resembling a Computed Tomography Using Restricted Echo-Spacing Sequence Is Equivalent to 3-Dimensional Computed Tomography in Quantifying Bone Loss and Measuring Shoulder Morphology in Patients With Shoulder Dislocation.

PURPOSE: To evaluate the equivalence of 3-dimensional (3D) magnetic resonance imaging (MRI) (FRACTURE [Fast field echo Resembling A CT Using Restricted Echo-spacing]) and 3D computed tomography (CT) in quantifying bone loss in patients with shoulder dislocation and measuring morphologic parameters of the shoulder. METHODS: From July 2022 to June 2023, patients with anterior shoulder dislocation who were aged 18 years or older and underwent both MRI and CT within 1 week were included in the study. The MRI protocol included an additional FRACTURE sequence. Three-dimensional reconstructions of MRI (FRACTURE) and CT were completed by 2 independent observers using Mimics software (version 21.0) through simple threshold-based segmentation. For bone defect cases, 2 independent observers evaluated glenoid defect, percentage of glenoid defect, glenoid track, Hill-Sachs interval, and on-track/off-track. For all cases, glenoid width, glenoid height, humeral head-fitting sphere radius, critical shoulder angle, glenoid version, vault depth, and post-processing time were assessed. The paired t test was used to assess the differences between 3D CT and 3D MRI (FRACTURE). Bland-Altman plots were constructed to evaluate the consistency between 3D CT and 3D MRI (FRACTURE). Interobserver and intraobserver agreement was evaluated with the interclass correlation coefficient. The paired χ2 test and Cohen κ statistic were used for binary variables (on-track/off-track). RESULTS: A total of 56 patients (16 with bipolar bone defect, 5 with only Hill-Sachs lesion, and 35 without bone defect) were ultimately enrolled in the study. The measurements of 21 bone defect cases showed no statistically significant differences between 3D CT and 3D MRI: glenoid defect, 4.05 ± 1.44 mm with 3D CT versus 4.16 ± 1.39 mm with 3D MRI (P = .208); percentage of glenoid defect, 16.21% ± 5.95% versus 16.61% ± 5.66% (P = .199); glenoid track, 18.02 ± 2.97 mm versus 18.08 ± 2.98 mm (P = .659); and Hill-Sachs interval, 14.29 ± 1.93 mm versus 14.35 ± 2.07 mm (P = .668). No significant difference was found between 3D CT and 3D MRI in the diagnosis of on-track/off-track (P > .999), and diagnostic agreement was perfect (κ = 1.00, P < .001). There were no statistically significant differences between the 2 examination methods in the measurements of all 56 cases, except that the post-processing time of 3D MRI was significantly longer than that of 3D CT: glenoid height, 34.56 ± 1.98 mm with 3D CT versus 34.67 ± 2.01 mm with 3D MRI (P = .139); glenoid width, 25.32 ± 1.48 mm versus 25.45 ± 1.47 mm (P = .113); humeral head-fitting sphere radius, 22.91 ± 1.70 mm versus 23.00 ± 1.76 mm (P = .211); critical shoulder angle, 33.49° ± 2.55° versus 33.57° ± 2.51° (P = .328); glenoid version, -3.25° ± 2.57° versus -3.18° ± 2.57° (P = .322); vault depth, 37.43 ± 1.68 mm versus 37.58 ± 1.75 mm (P = .164); and post-processing time, 89.66 ± 10.20 seconds versus 360.93 ± 26.76 seconds (P < .001). For all assessments, the Bland-Altman plots showed excellent consistency between the 2 examination methods, and the interclass correlation coefficients revealed excellent interobserver and intraobserver agreement. CONCLUSIONS: Three-dimensional MRI (FRACTURE) is equivalent to 3D CT in quantifying bone loss in patients with shoulder dislocation and measuring shoulder morphologic parameters. LEVEL OF EVIDENCE: Level II, development of diagnostic criteria (consecutive patients with consistently applied reference standard and blinding).

Pore confined time-of-flight secondary ion electrochemical mass spectrometry.

Molecular structure conversion concomitant with mass transfer processes at the electrode-electrolyte interfaces plays a central role in energy electrochemistry. Mass spectrometry, as one of the most intuitive, sensitive techniques, provides the capability to collect transient intermediates and products and uncover reaction mechanisms and kinetics. In situ time-of-flight secondary ion electrochemical mass spectrometry with inherent high mass and spatiotemporal resolution has emerged as a promising strategy for investigating electrochemical processes at the electrode surface. This review illustrates the recent advancements in coupling time-of-flight secondary ion mass spectrometry and electrochemistry to visualize and quantify local dynamic electrochemical processes, identify solvated species distribution, and disclose hidden reaction pathways at the molecular level. Moreover, the key challenges in this field are further discussed to promote new applications and discoveries in operando studying the dynamic electrochemical interfaces of advanced energy systems.

Multiscale Synergetic Bandgap/Structure Engineering in Semiconductor Nanofibrous Aerogels for Enhanced Solar Evaporation.

Solar-driven interface evaporation has been identified as a sustainable seawater desalination and water purification technology. Nonetheless, the evaporation performance is still restricted by salt deposition and heat loss owing to weak solar spectrum absorption, tortuous channels, and limited plane area of conventional photothermal material. Herein, the semiconductor nanofibrous aerogels with a narrow bandgap, vertically aligned channels, and a conical architecture are constructed by the multiscale synergetic engineering strategy, encompassing bandgap engineering at the atomic scale and structure engineering at the nano-micro scale. As a proof-of-concept demonstration, a Co-doped MoS2 nanofibrous aerogel is synthesized, which exhibits the entire solar absorption, superhydrophilic, and excellent thermal insulation, achieving a net evaporation rate of 1.62 kg m-2 h-1 under 1 sun irradiation, as well as a synergistically efficient dye ion adsorption function. This work opens up new possibilities for the development of solar evaporators for practical applications in clean water production.

Confined-Enhanced Raman Spectroscopy.

In 1997, the discovery of single molecule-surface enhanced Raman spectroscopy (SM-SERS) rekindled broad interests owing to its ultrahigh enhancement factor up to the 1014-1015 level. However, regretfully, the advantage of SM-SERS with an ultralow detection limit has not yet been fully utilized in commercialized applications. Here, we report a strategy, which we name confined-enhanced Raman spectroscopy, in which the overall Raman properties can be remarkably improved with in situ-formed active nanoshell on the surface of silver or gold nanoparticles. The nanoshell can confine and anchor molecules onto the surface of plasmonic nanoparticles and avoid desorption from hot spots so that the "on and off" blinking effect can be eliminated. It is the first time the single-molecule detection of analytes with super sensitivity, high stability, and reproducibility based on gold nanoparticles has been realized. In addition, this strategy is suitable for SERS detection in diverse molecule systems, including biomedical diagnosis, catalytic reaction, etc.

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.

In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4-6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.

Hydrophilic Cocrystals with Water Switched Luminescence.

Utilizing water molecules to regulate the luminescence properties of solid materials is highly challenging. Herein, we develop a strategy to produce water-triggered luminescence-switching cocrystals by coassembling hydrophilic donors with electron-deficient acceptors, where 1,2,4,5-Tetracyanobenzene (TCNB) was used as the electron acceptor and pyridyl benzimidazole derivatives were used as the electron donors enabling multiple hydrogen-bonds. Two cocrystals, namely 2PYTC and 4PYTC were obtained and showed heat-activated emission, and such emission could be quenched or weakened by adding water molecules. The cocrystal structure exhibited the donor molecule that can form multiple hydro bonds with water and acceptor molecules due to the many nitrogen atoms of them. The analyses of the photophysical data, powder X-ray diffraction, and other data confirmed the reversible fluorescence "on-off" effects were caused by eliminating and adding water molecules in the crystal lattice. The density functional theory calculations indicate that the vibration of the O-H bond of water molecules in the cocrystal can absorb the excitation energy and suppress fluorescence. Furthermore, the obtained cocrystals also showed temperature, humidity, and H+ /NH4 + responsive emission behavior, which allows their applications as thermal and humidity sensors, and multiple information encryptions. This research paves the way for preparing intelligent hydrophilic organic cocrystal luminescent materials.

Unlocking Single Particle Anisotropy in Real-Time for Photoelectrochemistry Processes at the Nanoscale.

The key to rationally and rapidly designing high-performance materials is the monitoring and comprehension of dynamic processes within individual particles in real-time, particularly to gain insight into the anisotropy of nanoparticles. The intrinsic property of nanoparticles typically varies from one crystal facet to the next under realistic working conditions. Here, we introduce the operando collision electrochemistry to resolve the single silver nanoprisms (Ag NPs) anisotropy in photoelectrochemistry. We directly identify the effect of anisotropy on the plasmonic-assisted electrochemistry at the single NP/electrolyte interface. The statistical collision frequency shows that heterogeneous diffusion coefficient among crystal facets facilitates Ag NPs to undergo direction-dependent mass transfer toward the gold ultramicroelectrode. Subsequently, the current amplitudes of transient events indicate that anisotropy enables variations in dynamic interfacial electron transfer behaviors during photothermal processes. The results presented here demonstrate that the measurement precision of collision electrochemistry can be extended to the sub-nanoparticle level, highlighting the potential for high-throughput material screening with comprehensive kinetics information at the nanoscale.

Electrochemical Monitoring of Real-Time Vesicle Dynamics Induced by Tau in a Confined Nanopipette.

The microtubule-associated protein tau participates in neurotransmission regulation via its interaction with synaptic vesicles (SVs). The precise nature and mechanics of tau's engagement with SVs, especially regarding alterations in vesicle dynamics, remain a matter of discussion. We report an electrochemical method using a synapse-mimicking nanopipette to monitor vesicle dynamics induced by tau. A model vesicle of ~30 nm is confined within a lipid-modified nanopipette orifice with a comparable diameter to mimic the synaptic lipid environment. Both tau and phosphorylated tau (p-tau) present two-state dynamic behavior in this biomimetic system, showing typical ionic current oscillation, induced by lipid-tau interaction. The results indicate that p-tau has a stronger affinity to the lipid vesicles in the confined environment, blocking the vesicle movement to a higher degree. Taken together, this method bridges a gap for sensing synaptic vesicle dynamics in a confined lipid environment, mimicking vesicle movement near the synaptic membrane. These findings contribute to understanding how different types of tau protein regulate synaptic vesicle motility and to underlying its functional and pathological behaviours in disease.

Emerging Data Processing Methods for Single-Entity Electrochemistry.

Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.

Multiphase Chemistry under Nanoconfinement: An Electrochemical Perspective.

Most relevant systems of interest to modern chemists rarely consist of a single phase. Real-world problems that require a rigorous understanding of chemical reactivity in multiple phases include the development of wearable and implantable biosensors, efficient fuel cells, single cell metabolic characterization techniques, and solar energy conversion devices. Within all of these systems, confinement effects at the nanoscale influence the chemical reaction coordinate. Thus, a fundamental understanding of the nanoconfinement effects of chemistry in multiphase environments is paramount. Electrochemistry is inherently a multiphase measurement tool reporting on a charged species traversing a phase boundary. Over the past 50 years, electrochemistry has witnessed astounding growth. Subpicoampere current measurements are routine, as is the study of single molecules and nanoparticles. This Perspective focuses on three nanoelectrochemical techniques to study multiphase chemistry under nanoconfinement: stochastic collision electrochemistry, single nanodroplet electrochemistry, and nanopore electrochemistry.

Data-driven discovery of a universal indicator for metallic glass forming ability.

Despite the importance of glass forming ability as a major alloy characteristic, it is poorly understood and its quantification has been experimentally laborious and computationally challenging. Here, we uncover that the glass forming ability of an alloy is represented in its amorphous structure far away from equilibrium, which can be exposed by conventional X-ray diffraction. Specifically, we fabricated roughly 5,700 alloys from 12 alloy systems and characterized the full-width at half-maximum, Δq, of the first diffraction peak in the X-ray diffraction pattern. A strong correlation between high glass forming ability and a large Δq was found. This correlation indicates that a large dispersion of structural units comprising the amorphous structure is the universal indicator for high metallic glass formation. When paired with combinatorial synthesis, the correlation enhances throughput by up to 100 times compared to today's state-of-the-art combinatorial methods and will facilitate the discovery of bulk metallic glasses.