Ubiquitin-specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity.

Ubiquitin-specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met77 in linear diubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate "gatekeeper" residue in the S1' site of USP11 as a contributing feature for discriminating against linear diubiquitin. When mutated to a glycine, the corresponding residue in paralog USP15, USP11 acquired elevated activity toward linear diubiquitin in-gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralog-specific differences impacting diubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.

Zirconium-Directed Supramolecular Self-Assembly of Coenzyme A@GNCs with Enhanced Phosphorescence for Developing Ultrasensitive Tracer Probe of Dipicolinic Acid, a Biomarker of Bacterial Spores.

Luminescent gold nanoclusters (GNCs) are a class of attractive quantum-sized nanomaterials bridging the gap between organogold complexes and gold nanocrystals. They typically have a core-shell structure consisting of a Au(I)-organoligand shell-encapsulated few-atom Au(0) core. Their luminescent properties are greatly affected by their Au(I)-organoligand shell, which also supports the aggregation-induced emission (AIE) effect. However, so far, the luminescent Au nanoclusters encapsulated with the organoligands containing phosphoryl moiety have rarely been reported, not to mention their AIE. In this study, coenzyme A (CoA), an adenosine diphosphate (ADP) analogue that is composed of a bulky 5-phosphoribonucleotide adenosine moiety connected to a long branch of vitamin B5 (pantetheine) via a diphosphate ester linkage and ubiquitous in all living organisms, has been used to synthesize phosphorescent GNCs for the first time. Interestingly, the synthesized phosphorescent CoA@GNCs could be further induced to generate AIE via the PO32- and Zr4+ interactions, and the observed AIE was found to be highly specific to Zr4+ ions. In addition, the enhanced phosphorescent emission could be quickly turned down by dipicolinic acid (DPA), a universal and specific component and also a biomarker of bacterial spores. Therefore, a Zr4+-CoA@GNCs-based DPA biosensor for quick, facile, and highly sensitive detection of possible spore contamination has been developed, showing a linear concentration range from 0.5 to 20 µM with a limit of detection of 10 nM. This study has demonstrated a promising future for various organic molecules containing phosphoryl moiety for the preparation of AIE-active metal nanoclusters.

Correction: In situ synthesis of chiral AuNCs with aggregation-induced emission using glutathione and ceria precursor nanosheets for glutathione biosensing.

Correction for 'In situ synthesis of chiral AuNCs with aggregation-induced emission using glutathione and ceria precursor nanosheets for glutathione biosensing' by Mohamed Ibrahim Halawa et al., Analyst, 2022, https://doi.org/10.1039/d2an00939k.

In situ synthesis of chiral AuNCs with aggregation-induced emission using glutathione and ceria precursor nanosheets for glutathione biosensing.

In the present study, a mediator release test (MRT) strategy has been designed for the photoluminescent sensing of glutathione (GSH). On the basis of the redox reaction of GSH and cerium-based nanosheets (Ce(CO3)2 NSs), Ce3+ ions were released to act as a mediator for the photoluminescence emission of the Au-thiolate complexes through an aggregation-induced emission (AIE) process. Remarkably, AIE was also accompanied by high chirality for the in situ synthesis of AuNCs using Ce(CO3)2 NSs as a template and GSH as a releaser for oligomeric Au-thiolate complexes. Multiple characterization techniques, including high-resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM), selected-area electron diffraction (SAED), X-ray powder diffraction (XRD), and X-ray photoelectron spectroscopy (XPS), were employed to check the structure and morphology of the Ce(CO3)2 NSs as well as the successful in situ fabrication of the AuNCs. Using this new MRT strategy, an eco-friendly, selective, biocompatible and label-free AIE probe was established for the sensitive sensing of GSH with a limit of detection (LOD) of 1.02 µM. Moreover, this switch-on luminescent nanoplatform of the conjugate probe of Au-thiolate/Ce-based NSs was successfully applied for the selective and reliable GSH detection in human serum samples.

Detection of ascorbic acid based on its quenching effect on luminol-artemisinin chemiluminescence.

We find that luminol can react with artemisinin (ART) to produce chemiluminescence (CL) in the absence of a catalyst and ascorbic acid (AA) can quench luminol-ART CL. Based on its efficient inhibition effect on luminol-ART CL, a new AA detection method is established. The calibration curve for the determination of AA is in the linear range of 5 × 10-7 M to 1 × 10-4 M with a detection limit of 50 nM, which is more sensitive than many other reported methods. This CL approach was utilized to detect AA in vitamin C tablets by applying the standard addition method, and the recoveries of 104.0%, 96.8% and 103.4% were obtained, respectively, at concentrations of 1 µM, 5 µM and 10 µM with a RSD value of less than 3.6%. This developed method for AA assay is distinguished by its fastness, reproducibility, easy operation and good selectivity.

Development of luminol-based chemiluminescence approach for ultrasensitive sensing of Hg(II) using povidone-I2 protected gold nanoparticles as an efficient coreactant.

In this work, we fabricated gold nanoparticles (AuNPs) capped with both polyvinyl pyrrolidone (PVP) and iodine (I2) to act as efficient chemiluminescent coreactants for luminol. AuNPs synthesis was based on the direct chemical reduction of Au3+ with NaBH4 in the presence of PVP-I2 complex. The successful synthesis of PVP-I2@AuNPs was confirmed with scanning electron microscopy (SEM) and UV-vis spectrophotometry. Chemiluminescence (CL) intensity of luminol was greatly enhanced, upon its chemical reaction with chemisorbed I2 on AuNPs surfaces owing to the excellent catalytic activity of AuNPs. The PVP-I2@AuNPs/luminol CL sensing system was successfully applied for determination of Hg2+ ions and the results displayed linearity in a wide range from 0.5 to 2000 nM and an ultrasensitive response to 1.0 nM Hg2+. The detection limit of Hg2+ ions was 0.1 nM, which was 100 times lower than the limit value (10 nM) defined by the U.S. Environmental Protection Agency in drinkable water. This ultrasensitive luminogenic system for Hg2+ detection also exhibited excellent selectivity among 13 types of metals, suggesting that the luminol/PVP-I2@AuNPs system is a promising sensor for real-time detection of Hg2+. Graphical abstract.

Silicotungstic acid as a highly efficient coreactant for luminol chemiluminescence for sensitive detection of uric acid.

Herein, we report luminol-silicotungstic acid (STA) chemiluminescence (CL) for the first time. The luminol-STA system resulted in remarkable CL enhancement (65 times) compared with the known classical luminol-H2O2 system because of the generation of the strong oxidizing agent tungsten trioxide from STA. Based on the quenching effect of uric acid, the new CL system is applied for the sensitive and selective assay of uric acid in its pure state (LOD 0.75 nM) and in real human urine with excellent recoveries in the range of 99.6-102.3%. Furthermore, this system permits the efficient detection of STA (LOD, 0.24 µM).

Highly sensitive and selective non-enzymatic glucose detection based on indigo carmine/hemin/H2O2 chemiluminescence.

A new chemiluminescence (CL) system, indigo carmine/glucose/hemin/H2O2, has been found and developed for non-enzymatic detection of indigo carmine (IC) and glucose. The CL response increases linearly with IC concentrations from 3.2 µM to 10 mM and glucose concentrations from 0.06 µM to 3.5 mM. The detection limits are 1.45 µM and 15.0 nM for IC and glucose, respectively. This method allows the determination of glucose in blood and urine after simple dilution. The recoveries for the determination of glucose are between 98.5% and 101.0% in blood and between 98.5% and 101.3% in urine. This method shows good sensitivity, selectivity, simplicity, and is low cost, suggesting its promising broad applications.

Unsupervised KPIs-Based Clustering of Jobs in HPC Data Centers.

Performance analysis is an essential task in high-performance computing (HPC) systems, and it is applied for different purposes, such as anomaly detection, optimal resource allocation, and budget planning. HPC monitoring tasks generate a huge number of key performance indicators (KPIs) to supervise the status of the jobs running in these systems. KPIs give data about CPU usage, memory usage, network (interface) traffic, or other sensors that monitor the hardware. Analyzing this data, it is possible to obtain insightful information about running jobs, such as their characteristics, performance, and failures. The main contribution in this paper was to identify which metric/s (KPIs) is/are the most appropriate to identify/classify different types of jobs according to their behavior in the HPC system. With this aim, we had applied different clustering techniques (partition and hierarchical clustering algorithms) using a real dataset from the Galician computation center (CESGA). We concluded that (i) those metrics (KPIs) related to the network (interface) traffic monitoring provided the best cohesion and separation to cluster HPC jobs, and (ii) hierarchical clustering algorithms were the most suitable for this task. Our approach was validated using a different real dataset from the same HPC center.

Recent advances in nanomaterial-based capillary electrophoresis.

This review gives a summary of applications of different nanomateials, such as gold nanoparticles (AuNPs), carbon-based nanoparticles, magnetic nanoparticles (MNPs), and nano-sized metal organic frameworks (MOFs), in electrophoretic separations. This review also emphasizes the recent works in which nanoparticles (NPs) are used as pseudostationary phase (PSP) or immobilized on the capillary surface for enhancement of separation in CE, CEC, and microchips electrophoresis.

Pyridoxal 5'-phosphate assay based on lucigenin chemiluminescence.

The authors describe the first chemiluminescence (CL) based method for determination of pyridoxal 5'-phosphate (PLP). PLP is found to generate intense CL with lucigenin higher than that of the conventional lucigenin-H2O2 system by a factor of about 9.0. This new finding is used to be in a detection method for PLP via flow injection analysis (FIA). Response is linear in the 50 nM to 200 µM PLP concentration range with a correlation coefficient of 0.998, and the detection limit (at an S/N of 3) is 6.9 nM. The assay is highly selective over various amino acids, vitamins, sugars, coenzymes and metal ions cofactors. It exhibits advantages over the commonly employed HPLC methods in that it is rapid, more economic, eco-friendly and high throughput FIA detection of PLP without the need for toxic derivatization reagents, organic solvents, and HPLC instrumentation. The method was successfully applied to the determination of PLP in (spiked) human blood samples with recoveries in the range from 96.2-101.6% with % RSD < 4.0. The new system is also employed to determine lucigenin in the linear range of 0.3 to 100.0 µM with a correlation coefficient of 0.994 and the limit of detection is 0.04 µM. Graphical abstract Schematic of the chemiluminescent assay for pyridoxal 5'-phosphate (PLP). Lucigenin-PLP demonstrates 9-fold stronger chemiluminescence intensity than the lucigenin-H2O2 system. The detection limit of PLP is 6.9 nM. The method can detect PLP in human serum with good recoveries.

Chemiluminescence of Lucigenin-Allantoin and Its Application for the Detection of Allantoin.

Allantoin has been reported as a promising biomarker for monitoring of oxidative stress in humans and widely utilized in a variety of topical pharmaceuticals and cosmetics. Currently, the detection of allantoin is achieved by using chromatographic coupled techniques, which needs sample pre-extraction, derivatization, complex matrixes, and expensive instrumentation. Herein we report both the intense chemiluminescence of allantoin with lucigenin and the chemiluminescent detection of allantoin for the first time. The lucigenin-allantoin system demonstrated chemiluminescence emission intensity 17 times higher than that of the classic lucigenin-hydrogen peroxide system. Based on this fascinating phenomenon, a novel chemiluminescence method has been developed for the sensitive and selective allantoin determination with the combination of flow injection analysis. This method shows a linear calibration curve in the range 0.1-3000 µM with a detection limit (3σ/s) of 0.03 µM. Moreover, it was successfully utilized for the determination of allantoin in human eye drop and real urine samples after simple dilution with water. It shows excellent recoveries in the range 94.0-101.7%, and each measurement takes a very short time. This method exhibits potential advantages in the form of simplicity, rapidity, sensitivity, selectivity, and low cost. Allantoin could be an effective candidate for constructing new chemiluminescence systems, and it may provide a broad range of sensing applications.

Visual and Plasmon Resonance Absorption Sensor for Adenosine Triphosphate Based on the High Affinity between Phosphate and Zr(IV).

Zr(IV) can form phosphate and Zr(IV) (-PO32--Zr4+-) complex owing to the high affinity between Zr(IV) with phosphate. Zr(IV) can induce the aggregation of gold nanoparticles (AuNPs), while adenosine triphosphate(ATP) can prevent Zr(IV)-induced aggregation of AuNPs. Herein, a visual and plasmon resonance absorption (PRA)sensor for ATP have been developed using AuNPs based on the high affinity between Zr(IV)with ATP. AuNPs get aggregated in the presence of certain concentrations of Zr(IV). After the addition of ATP, ATP reacts with Zr(IV) and prevents AuNPs from aggregation, enabling the detection of ATP. Because of the fast interaction of ATP with Zr(IV), ATP can be detected with a detection limit of 0.5 µM within 2 min by the naked eye. Moreover, ATP can be detected by the PRA technique with higher sensitivity. The A520nm/A650nm values in PRA spectra increase linearly with the concentrations of ATP from 0.1 µM to 15 µM (r = 0.9945) with a detection limit of 28 nM. The proposed visual and PRA sensor exhibit good selectivity against adenosine, adenosine monophosphate, guanosine triphosphate, cytidine triphosphate and uridine triphosphate. The recoveries for the analysis of ATP in synthetic samples range from 95.3% to 102.0%. Therefore, the proposed novel sensor for ATP is promising for real-time or on-site detection of ATP.

Nanoscale Luminescence Imaging/Detection of Single Particles: State-of-the-Art and Future Prospects.

Single-particle-level measurements, during the reaction, avoid averaging effects that are inherent limitations of conventional ensemble strategies. It allows revealing structure-activity relationships beyond averaged properties by considering crucial particle-selective descriptors including structure/morphology dynamics, intrinsic heterogeneity, and dynamic fluctuations in reactivity (kinetics, mechanisms). In recent years, numerous luminescence (optical) techniques such as chemiluminescence (CL), electrochemiluminescence (ECL), and fluorescence (FL) microscopies have been emerging as dominant tools to achieve such measurements, owing to their diversified spectroscopy principles, noninvasive nature, higher sensitivity, and sufficient spatiotemporal resolution. Correspondingly, state-of-the-art methodologies and tools are being used for probing (real-time, operando, in situ) diverse applications of single particles in sensing, medicine, and catalysis. Herein, we provide a concise and comprehensive perspective on luminescence-based detection and imaging of single particles by putting special emphasis on their basic principles, mechanistic pathways, advances, challenges, and key applications. This Perspective focuses on the development of emission intensities and imaging based individual particle detection. Moreover, several key examples in the areas of sensing, motion, catalysis, energy, materials, and emerging trends in related areas are documented. We finally conclude with the opportunities and remaining challenges to stimulate further developments in this field.

Serum MicroRNA-146b Expression for Malignancy Prediction in Euthyroid Patients with Indeterminate Thyroid Nodules.

Thyroid nodules are frequently found, but the vast majority of them are benign. The difficulty in managing thyroid nodules is correctly diagnosing the minority of those who have malignancy. Thyroid fine-needle aspiration cytology (FNAC) with indeterminate cytology continues to raise doubts about the presence of thyroid cancer, leading to an unnecessary thyroidectomy. Circulating miRNAs may be useful as diagnostic and prognostic markers for a variety of cancers, including thyroid cancer. The goal of the present study was to determine the predictive value of serum miRNA-146b expression level for thyroid cancer by estimating its level in a group of euthyroid patients with thyroid nodules with indeterminate FNAC results. This cross-sectional study included 45 euthyroid patients with indeterminate thyroid nodules who visited the Endocrine Outpatient Clinic and Endocrine Surgical Ward at Ain Shams University Hospitals. For all patient thyroid profiles, ultrasound of the thyroid gland and FNAC of the thyroid nodule were performed. In addition, preoperative assessment of serum microRNA-146b expression by real-time PCR was achieved and the results correlated with post-operative thyroid histopathology. There was no difference in serum miRNA-146b expression between patients with benign thyroid nodules versus patients with malignant nodules (p= 0.789). The risk of malignancy increased with the increase in size of the dominant thyroid nodules, as larger nodules had a higher risk of malignancy (p= 0.027). In conclusion, in euthyroid patients with indeterminate thyroid nodules, serum miRNA-146b is a poor predictor of thyroid malignancy, however, the larger the nodule size, the higher the risk of cancer.

The winged helix domain of MORF binds CpG islands and the TAZ2 domain of p300.

Acetylation of histones by lysine acetyltransferases (KATs) provides a fundamental mechanism by which chromatin structure and transcriptional programs are regulated. Here, we describe a dual binding activity of the first winged helix domain of human MORF KAT (MORFWH1) that recognizes the TAZ2 domain of p300 KAT (p300TAZ2) and CpG rich DNA sequences. Structural and biochemical studies identified distinct DNA and p300TAZ2 binding sites, allowing MORFWH1 to independently engage either ligand. Genomic data show that MORF/MOZWH1 colocalizes with H3K18ac, a product of enzymatic activity of p300, on CpG rich promoters of target genes. Our findings suggest a functional cooperation of MORF and p300 KATs in transcriptional regulation.

Generation of Chemical Space of Compounds for Prostate Cancer Treatment: Biological Activity Prediction, Clustering, and Visualization of Chemical Space.

Designing molecules for pharmaceutical purposes has been a significant focus for several decades. The pursuit of novel drugs is an arduous and financially demanding undertaking. Nevertheless, the integration of computer-assisted frameworks presents a swift avenue for designing and screening drug-like compounds. Within the context of this research, we introduce a comprehensive approach for the design and screening of compounds tailored to the treatment of prostate cancer. To forecast the biological activity of these compounds, we employed machine learning (ML) models. Additionally, an automated process involving the deconstruction and reconstruction of molecular building blocks leads to the generation of novel compounds. Subsequently, the ML models were utilized to predict the biological activity of the designed compounds, and the t-SNE method was employed to visualize the chemical space covered by the novel compounds. A meticulous selection process identified the most promising compounds, and their potential for synthesis was assessed, offering valuable guidance to experimental chemists in their investigative endeavors. Furthermore, fingerprint and heatmap analysis were conducted to evaluate the chemical similarity among the selected compounds. This multifaceted approach, encompassing predictive modeling, compound generation, visualization, and similarity assessment, underscores our commitment to refining the process of identifying potential candidates for further exploration in prostate cancer treatment.

Unraveling Therapeutic Opportunities and the Diagnostic Potential of microRNAs for Human Lung Cancer.

Lung cancer is a major public health problem and a leading cause of cancer-related deaths worldwide. Despite advances in treatment options, the five-year survival rate for lung cancer patients remains low, emphasizing the urgent need for innovative diagnostic and therapeutic strategies. MicroRNAs (miRNAs) have emerged as potential biomarkers and therapeutic targets for lung cancer due to their crucial roles in regulating cell proliferation, differentiation, and apoptosis. For example, miR-34a and miR-150, once delivered to lung cancer via liposomes or nanoparticles, can inhibit tumor growth by downregulating critical cancer promoting genes. Conversely, miR-21 and miR-155, frequently overexpressed in lung cancer, are associated with increased cell proliferation, invasion, and chemotherapy resistance. In this review, we summarize the current knowledge of the roles of miRNAs in lung carcinogenesis, especially those induced by exposure to environmental pollutants, namely, arsenic and benzopyrene, which account for up to 1/10 of lung cancer cases. We then discuss the recent advances in miRNA-based cancer therapeutics and diagnostics. Such information will provide new insights into lung cancer pathogenesis and innovative diagnostic and therapeutic modalities based on miRNAs.

Regenerable sensor based on tris(4,7'-diphenyl-1,10-phenanthroline)ruthenium (II) for anodic and cathodic electrochemiluminescence applications.

Tris(4,7'-diphenyl-1,10-phenanthroline) ruthenium (II) dichloride [Ru(dpp)32+] was used for the first time to construct a regenerable electrochemiluminescence (ECL) sensor. The Ru(dpp)32+-modified carbon paste electrode (CPE) showed several unique features in comparison with commonly studied Ru(bpy)32+-modified electrodes. On the one hand, a quite reversible reduction peak was observed at -0.96 V where no obvious hydrogen evolution occured, enabling the sensitive detection of S2O82-. Moreover, our proposed S2O82- sensor showed a good linear range from 3 × 10-9 to 3 × 10-4 M with a detection limit of 2 nM, indicating higher sensitivity for the same analyte than previously reported ECL methods by about two orders of magnitude. On the other hand, the Ru(dpp)32+-modified electrode showed an irreversible oxidation peak because electrogenerated Ru(dpp)33+ is very reactive in aqueous solutions, while Ru(bpy)32+-modified electrode showed a reversible oxidation peak. Moreover, the present sensor showed a good linear range from 10-7 M to 10-3 M for oxalate with a detection limit of 60 nM. It detected oxalate in urine samples with nice recoveries. The regenerable ECL sensor presented good characteristics, such as low cost, simple fabrication procedure and fast response time. The Ru(dpp)32+ based regenerable sensor is an attractive alternative to Ru(bpy)32+-based regenerable sensor, as it can be used for both anodic and cathodic ECL analysis with high sensitivity in aqueous media.

Data mining and library generation to search electron-rich and electron-deficient building blocks for the designing of polymers for photoacoustic imaging.

Photoacoustic imaging is a good method for biological imaging, for this purpose, materials with strong near infrared (NIR) absorbance are required. In the present study, machine learning models are used to predict the light absorption behavior of polymers. Molecular descriptors are utilized to train a variety of machine learning models. Building blocks are searched from chemical databases, as well as new building blocks are designed using chemical library enumeration method. The Breaking Retrosynthetically Interesting Chemical Substructures (BRICS) method is employed for the creation of 10,000 novel polymers. These polymers are designed based on the input of searched and selected building blocks. To enhance the process, the optimal machine learning model is utilized to predict the UV/visible absorption maxima of the newly designed polymers. Concurrently, chemical similarity analysis is also performed on the selected polymers, and synthetic accessibility of selected polymers is calculated. In summary, the polymers are all easy to synthesize, increasing their potential for practical applications.