A quadri-fluorescence SARS-CoV-2 pseudovirus system for efficient antigenic characterization of multiple circulating variants.

The ongoing co-circulation of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains necessitates advanced methods such as high-throughput multiplex pseudovirus systems for evaluating immune responses to different variants, crucial for developing updated vaccines and neutralizing antibodies (nAbs). We have developed a quadri-fluorescence (qFluo) pseudovirus platform by four fluorescent reporters with different spectra, allowing simultaneous measurement of the nAbs against four variants in a single test. qFluo shows high concordance with the classical single-reporter assay when testing monoclonal antibodies and human plasma. Utilizing qFluo, we assessed the immunogenicities of the spike of BA.5, BQ.1.1, XBB.1.5, and CH.1.1 in hamsters. An analysis of cross-neutralization against 51 variants demonstrated superior protective immunity from XBB.1.5, especially against prevalent strains such as "FLip" and JN.1, compared to BA.5. Our finding partially fills the knowledge gap concerning the immunogenic efficacy of the XBB.1.5 vaccine against current dominant variants, being instrumental in vaccine-strain decisions and insight into the evolutionary path of SARS-CoV-2.

Combining an Enhanced Polyphosphate Kinase-Driven UDP-Glucose Regeneration System with the Screening of Key Glycosyltransferases for Efficient In Vitro Synthesis of Nucleoside Disaccharides.

Nucleoside disaccharides are essential glycosides that naturally occur in specific living organisms. This study developed an enhanced UDP-glucose regeneration system to facilitate the in vitro multienzyme synthesis of nucleoside disaccharides by integrating it with nucleoside-specific glycosyltransferases. The system utilizes maltodextrin and polyphosphate as cost-effective substrates for UDP-glucose supply, catalyzed by α-glucan phosphorylase (αGP) and UDP-glucose pyrophosphorylase (UGP). To address the low activity of known polyphosphate kinases (PPKs) in the UDP phosphorylation reaction, a sequence-driven screening identified RhPPK with high activity against UDP (>1000 U/mg). Computational design further led to the creation of a double mutant with a 2566-fold increase in thermostability at 50 °C. The enhanced UDP-glucose regeneration system increased the production rate of nucleoside disaccharide synthesis by 25-fold. In addition, our UDP-glucose regeneration system is expected to be applied to other glycosyl transfer reactions.

Cellular and Molecular Mechanisms of Chemoresistance for Gastric Cancer.

Gastric cancer (GC) is one of the most common malignant tumors in the digestive tract, and chemotherapy plays an irreplaceable role in the comprehensive treatment of GC. However, chemoresistance makes it difficult for patients with GC to benefit steadily from chemotherapy in the long term, which ultimately leads to tumor recurrence, metastasis, and patient death. Elucidating the detailed mechanism of chemoresistance in GC and identifying specific therapeutic targets will help to solve the difficult problem of chemoresistance and improve the prognosis of patients with GC. This review summarizes and clarifies the cellular and molecular mechanisms underlying chemoresistance for GC.

TCR-like bispecific antibodies toward eliminating infected hepatocytes in HBV mouse models.

Therapeutics for eradicating hepatitis B virus (HBV) infection are still limited and current nucleos(t)ide analogs (NAs) and interferon are effective in controlling viral replication and improving liver health, but they cannot completely eradicate the hepatitis B virus and only a very small number of patients are cured of it. The TCR-like antibodies recognizing viral peptides presented on human leukocyte antigens (HLA) provide possible tools for targeting and eliminating HBV-infected hepatocytes. Here, we generated three TCR-like antibodies targeting three different HLA-A2.1-presented peptides derived from HBV core and surface proteins. Bispecific antibodies (BsAbs) were developed by fuzing variable fragments of these TCR-like mAbs with an anti-CD3ϵ antibody. Our data demonstrate that the BsAbs could act as T cell engagers, effectively redirecting and activating T cells to target HBV-infected hepatocytes in vitro and in vivo. In HBV-persistent mice expressing human HLA-A2.1, two infusions of BsAbs induced marked and sustained suppression in serum HBsAg levels and also reduced the numbers of HBV-positive hepatocytes. These findings highlighted the therapeutic potential of TCR-like BsAbs as a new strategy to cure hepatitis B.

Association of textbook outcomes with improved survival in pancreatic ductal adenocarcinoma following pancreaticoduodenectomy: a retrospective study.

Background: Assessing the perioperative outcomes of pancreaticoduodenectomy (PD) based solely on individual complications is not comprehensive, and the association between perioperative outcomes and the long-term prognosis of individuals diagnosed with pancreatic ductal adenocarcinoma (PDAC) remains uncertain. Our study is designed to evaluate the impact of a novel composite indicator, textbook outcomes (TO), on the long-term prognosis of patients undergoing PD for PDAC. Methods: This study conducted a retrospective analysis of 139 patients who underwent PD for pathologically confirmed PDAC at our hospital between January 2018 and December 2021. After applying exclusion criteria, a total of 111 patients were included in the subsequent analysis. These patients were categorized into two groups: the non-TO group (n=42) and the TO group (n=69). The Kaplan-Meier survival curve was employed to describe the relationship between TO and disease-free survival (DFS) and overall survival (OS). Cox regression was employed to assess the impact of achieving TO on long-term survival. Logistic regression was employed to investigate the risk factors affecting the achievement of TO. Results: Out of the 111 PDAC patients, 69 (62.2%) achieved TO following PD. The achievement of TO significantly improved the OS of PDAC patients [P=0.03; hazard ratio (HR) =0.60; 95% confidence interval (CI): 0.37-0.83]. Cox regression analysis indicated that achieving TO was a protective factor for OS (P=0.04; HR =4.08; 95% CI: 1.07-15.61). Logistic regression analysis indicated that high amylase in drainage fluid on the third day after surgery (>1,300 U/L) was detrimental to achieve TO [odds ratio (OR) =0.10; 95% CI: 0.02-0.58; P=0.01], longer surgery durations (≥6.25 hours) was detrimental to achieve TO (OR =0.19; 95% CI: 0.06-0.54; P=0.002), and soft pancreatic texture was detrimental to achieve TO (OR =0.31; 95% CI: 0.10-0.93, P=0.04). Conclusions: Achievement of TO significantly improves the OS of PDAC patients and has the potential to serve as a robust prognostic indicator. Looking ahead, it is highly necessary for TO to become a standard surgical quality control measure in hospitals.

Exploring the clinical and biological significance of the cell cycle-related gene CHMP4C in prostate cancer.

BACKGROUND: Prostate cancer (PCa) stands as the second most prevalent malignancy impacting male health, and the disease's evolutionary course presents formidable challenges in the context of patient treatment and prognostic management. Charged multivesicular body protein 4 C (CHMP4C) participates in the development of several cancers by regulating cell cycle functions. However, the role of CHMP4C in prostate cancer remains unclear. METHODS: In terms of bioinformatics, multiple PCa datasets were employed to scrutinize the expression of CHMP4C. Survival analysis coupled with a nomogram approach was employed to probe into the prognostic significance of CHMP4C. Gene set enrichment analysis (GSEA) was conducted to interrogate the functional implications of CHMP4C. In terms of cellular experimentation, the verification of RNA and protein expression levels was executed through the utilization of qRT-PCR and Western blotting. Upon the establishment of a cell line featuring stable CHMP4C knockdown, a battery of assays, including Cell Counting Kit-8 (CCK-8), wound healing, Transwell, and flow cytometry, were employed to discern the impact of CHMP4C on the proliferation, migration, invasion, and cell cycle function of PCa cells. RESULTS: The expression of CHMP4C exhibited upregulation in both PCa cells and tissues, and patients demonstrating elevated CHMP4C expression levels experienced a notably inferior prognosis. The nomogram, constructed using CHMP4C along with clinicopathological features, demonstrated a commendable capacity for prognostic prediction. CHMP4C knockdown significantly inhibited the proliferation, migration, and invasion of PCa cells (LNcaP and PC3). CHMP4C could impact the advancement of the PCa cell cycle, and its expression might be regulated by berberine. Divergent CHMP4C expression among PCa patients could induce alterations in immune cell infiltration and gene mutation frequency. CONCLUSIONS: Our findings suggest that CHMP4C might be a prognostic biomarker in PCa, potentially offering novel perspectives for the advancement of precision therapy for PCa.

Constructing an artificial in vitro multi-enzyme cascade pathway to convert glycerol and CO2 into L-aspartic acid.

Developing utilization technologies for biomass resources, exploring their applications in the fields of energy and chemical engineering, holds significant importance for promoting sustainable development and constructing a green, low-carbon society. In this study, we designed a non-natural in vitro multi-enzyme system for converting glycerol and CO2 into L-aspartic acid (L-Asp). The coupled system utilized eight enzymes, including alditol oxidase (ALDO), catalase-peroxidase (CAT), lactaldehyde dehydrogenase (ALDH), glycerate 2-kinase (GK), phosphopyruvate hydratase (PPH), phosphoenolpyruvate carboxylase (PPC), L-aspartate dehydrogenase (ASPD), and polyphosphate kinase (PPK), to convert the raw materials into L-Asp in one-pot coupled with NADH and ATP regeneration. Under optimal reaction conditions, 18.6 mM of L-Asp could be produced within 2.0 h at a total enzyme addition of 4.85 mg/mL, demonstrating the high efficiency and productivity characteristics of the designed system. Our technological application provides new insights and methods for the development of biomass resource utilization technologies.

High-quality quasi-bound state in the continuum enabled single-nanoparticle virus detection.

Bound states in the continuum (BICs) have emerged as a powerful platform for boosting light-matter interactions because they provide an alternative way of realizing optical resonances with ultrahigh quality(Q-) factors, accompanied by extreme field confinement. In this work, we realized an optical biosensor by introducing a quasi-BIC (qBIC) supported by an elaborated all-dielectric dimer grating. Thanks to the excellent field confinement within the air gap of grating enabled by such a high-Q qBIC, the figure of merit (FOM) of a biosensor is up to 18,908.7 RIU-1. Furthermore, we demonstrated that such a high-Q grating can help push the limit of optical biosensing to the single-particle level. Our results may find exciting applications in extreme biochemical sensing like COVID-19 with ultralow concentration.

Engineering a Robust UDP-Glucose Pyrophosphorylase for Enhanced Biocatalytic Synthesis via ProteinMPNN and Ancestral Sequence Reconstruction.

UDP-glucose is a key metabolite in carbohydrate metabolism and plays a vital role in glycosyl transfer reactions. Its significance spans across the food and agricultural industries. This study focuses on UDP-glucose synthesis via multienzyme catalysis using dextrin, incorporating UTP production and ATP regeneration modules to reduce costs. To address thermal stability limitations of the key UDP-glucose pyrophosphorylase (UGP), a deep learning-based protein sequence design approach and ancestral sequence reconstruction are employed to engineer a thermally stable UGP variant. The engineered UGP variant is significantly 500-fold more thermally stable at 60 °C and has a half-life of 49.8 h compared to the wild-type enzyme. MD simulations and umbrella sampling calculations provide insights into the mechanism behind the enhanced thermal stability. Experimental validation demonstrates that the engineered UGP variant can produce 52.6 mM UDP-glucose within 6 h in an in vitro cascade reaction. This study offers practical insights for efficient UDP-glucose synthesis methods.

Gate-tunable subband degeneracy in semiconductor nanowires.

Degeneracy and symmetry have a profound relation in quantum systems. Here, we report gate-tunable subband degeneracy in PbTe nanowires with a nearly symmetric cross-sectional shape. The degeneracy is revealed in electron transport by the absence of a quantized plateau. Utilizing a dual gate design, we can apply an electric field to lift the degeneracy, reflected as emergence of the plateau. This degeneracy and its tunable lifting were challenging to observe in previous nanowire experiments, possibly due to disorder. Numerical simulations can qualitatively capture our observation, shedding light on device parameters for future applications.

Experimental investigation of acoustic moiré effect controlled by twisted bilayer gratings.

Recently, the moiré pattern has attracted lots of attention by superimposing two planar structures of regular geometries, such as two sets of metasurfaces or gratings. Here, we show the experimental investigation of acoustic moiré effect by using twisted bilayer gratings (i.e., one grating twisted with respect to the other). We observed the guided resonance that occurred when the incident ultrasound beam was coupled with the guiding modes in a meta-grating, significantly influencing the reflection and transmission. Tunable guided resonances from the moiré effect with complete ultrasound reflection at different frequencies were further demonstrated in experiments. Combining the measurements of transmission spectra and the Fast Fourier Transform analyses, we reveal the guided resonance frequencies of moiré ultrasonic metasurface can be effectively controlled by adjusting the twisting angle of the bilayer gratings. Our results can be explained in a simplified model based on the band folding theory, providing a reliable prediction on the precise control of ultrasound reflection via the twisting angle adjustment. Our work extends the moiré metasurface from optics into acoustics, which shows more possibilities for the ultrasound beam engineering from the moiré effect and enables the exploration of functional acoustic devices for ultrasound imaging, treatment and diagnosis.

Exploring the molecular mechanisms of Lrp/AsnC-type transcription regulator DecR, an L-cysteine-responsive feast/famine regulatory protein.

The Lrp/AsnC family of transcriptional regulators is commonly found in prokaryotes and is associated with the regulation of amino acid metabolism. However, it remains unclear how the L-cysteine-responsive Lrp/AsnC family regulator perceives and responds to L-cysteine. Here, we try to elucidate the molecular mechanism of the L-cysteine-responsive transcriptional regulator. Through 5'RACE and EMSA, we discovered a 15 bp incompletely complementary pair palindromic sequence essential for DecR binding, which differed slightly from the binding sequence of other Lrp/AsnC transcription regulators. Using alanine scanning, we identified the L-cysteine binding site on DecR and found that different Lrp/AsnC regulators adjust their binding pocket's side-chain residues to accommodate their specific effector. MD simulations were then conducted to explore how ligand binding influences the allosteric behavior of the protein. PCA and in silico docking revealed that ligand binding induced perturbations in the linker region, triggering conformational alterations and leading to the relocalization of the DNA-binding domains, enabling the embedding of the DNA-binding region of DecR into the DNA molecule, thereby enhancing DNA-binding affinity. Our findings can broaden the understanding of the recognition and regulatory mechanisms of the Lrp/AsnC-type transcription factors, providing a theoretical basis for further investigating the molecular mechanisms of other transcription factors.

Enhancing Electrocatalytic CO2-to-CO Conversion by Weakening CO Binding through Nitrogen Integration in the Metallic Fe Catalyst.

Metallic iron (Fe) typically demonstrates the unfavorable catalytic activity for the CO2 reduction reaction (CO2RR), mainly attributed to the excessively strong binding of CO products on Fe sites. Toward this end, we employed an effective approach involving electronic structure modulation through nitrogen (N) integration to enhance the performance of the CO2RR. Here, an efficient catalyst has been developed, composed of N-doped metallic iron (Fe) nanoparticles encapsulated in a porous N-doped carbon framework. Notably, this N-integrated Fe catalyst displays significantly enhanced performance in the electrocatalytic reduction of CO2, yielding the highest CO Faradaic efficiency of 97.5% with a current density of 6.68 mA cm-2 at -0.7 V versus the reversible hydrogen electrode. The theoretical calculations, combined with the in situ attenuated total reflection surface-enhanced infrared absorption spectroscopy study, reveal that N integration modulates the electron density around Fe, resulting in the weakening of the binding strength between the Fe active sites and *CO intermediates, consequently promoting the desorption of CO and the overall CO2RR process.

Engineering of the Lrp/AsnC-type transcriptional regulator DecR as a genetically encoded biosensor for multilevel optimization of L-cysteine biosynthesis pathway in Escherichia coli.

L-cysteine is an important sulfur-containing amino acid being difficult to produce by microbial fermentation. Due to the lack of high-throughput screening methods, existing genetically engineered bacteria have been developed by simply optimizing the expression of L-cysteine-related genes one by one. To overcome this limitation, in this study, a biosensor-based approach for multilevel biosynthetic pathway optimization of L-cysteine from the DecR regulator variant of Escherichia coli was applied. Through protein engineering, we obtained the DecRN29Y/C81E/M90Q/M99E variant-based biosensor with improved specificity and an 8.71-fold increase in dynamic range. Using the developed biosensor, we performed high-throughput screening of the constructed promoter and RBS combination library, and successfully obtained the optimized strain, which resulted in a 6.29-fold increase in L-cysteine production. Molecular dynamics (MD) simulations and electrophoretic mobility shift analysis (EMSA) showed that the N29Y/C81E/M90Q/M99E variant had enhanced induction activity. This enhancement may be due to the increased binding of the variant to DNA in the presence of L-cysteine, which enhances transcriptional activation. Overall, our biosensor-based strategy provides a promising approach for optimizing biosynthetic pathways at multiple levels. The successful implementation of this strategy demonstrates its potential for screening improved recombinant strains.

A circuitous route for in vitro multi-enzyme cascade production of cytidine triphosphate to overcome the thermodynamic bottleneck.

Cytidine triphosphate (CTP), as a substance involved in the metabolism of phospholipids, proteins and nucleic acids, has precise drug effects and is a direct precursor for the synthesis of drugs such as citicoline. In this study, we established an in vitro six-enzyme cascade system to generate CTP. To avoid thermodynamic bottlenecks, we employed a circuitous and two-stage reaction strategy. Using cytidine as the key substrate, the final product CTP is obtained via the deamination and uridine phosphorylation pathways, relying on the irreversible reaction of cytidine triphosphate synthase to catalyze the amination of uridine triphosphate. Several extremophilic microbial-derived deaminases were screened and characterized, and a suitable cytidine deaminase was selected to match the first-stage reaction conditions. In addition, directed evolution modification of the rate-limiting enzyme CTP synthetase in the pathway yielded a variant that successfully relieved the product feedback inhibition, along with a 1.7-fold increase in activity over the wild type. After optimizing the reaction conditions, we finally carried out the catalytic reaction at an initial cytidine concentration of 20 mM, and the yield of CTP exceeded 82% within 10.0 h.

Gaining insight into the effect of laccase expression on humic substance formation during lignocellulosic biomass composting.

The aim is to enhance lignin humification by promoting laccase activities which can promote lignin depolymerization and reaggregation during composting. 1-Hydroxybenzotriazole (HBT) is employed to conduct laccase mediator system (LMS), application of oxidized graphene (GO) in combination to strengthen LMS. Compared with control, the addition of GO, HBT, and GH (GO coupled with HBT) significantly improved laccase expression and activities (P < 0.05), with lignin humification efficiency also increased by 68.6 %, 36.7 %, and 107.8 %. GH treatment induces microbial expression of laccase by increasing the abundance and synergy of core microbes. The unsupervised learning model, vector autoregressive model and Mantel test function were combined to elucidate the mechanism of action of exogenous materials. The results showed that GO stabilized the composting environment on the one hand, and acted as a support vector to stabilize the LMS and promote the function of laccase on the other. In GH treatment, degradation of macromolecules and humification of small molecules were promoted simultaneously by activating the dual function of laccase. Additionally, it also reveals the GH enhances the humification of lignocellulosic compost by converting phenolic pollutants into aggregates. These findings provide a new way to enhance the dual function of laccase and promote lignin humification during composting. It could effectively achieve the resource utilization of organic solid waste and reduce composting pollution.

Design of Double Conductive Layer and Grid-Assistant Face-to-Face Structure for Wide Linear Range, High Sensitivity Flexible Pressure Sensors.

Recently, flexible pressure sensors have drawn great attention because of their potential application in human-machine interfaces, healthcare monitoring, electronic skin, etc. Although many sensors with good performance have been reported, researchers mostly focused on surface morphology regulation, and the effect of the resistance characteristics on the performance of the sensor was still rarely systematically investigated. In this paper, a strategy for modulating electron transport is proposed to adjust the linear range and sensitivity of the sensor. In the modulating process, we constructed a double conductive layer (DCL) and grid-assistant face-to-face structure and obtained the sensor with a wide linear range of 0-700 kPa and a high sensitivity of 57.5 kPa-1, which is one of the best results for piezoresistive sensors. In contrast, the sensor with a single conductive layer (SCL) and simple face-to-face structure exhibited a moderate linear range (7 kPa) and sensitivity (2.8 kPa-1). Benefiting from the great performance, the modulated sensor allows for clear pulse wave detection and good recognition of gait signals, which indicates the great application potential in human daily life.

Molecular mechanisms of circular RNA in breast cancer: a narrative review.

Background and Objective: Breast cancer is presently the most prevalent cancer and the leading cause of cancer-related deaths in women worldwide. Circular RNA (circRNA) is a class of closed circRNAs lacking a 5'-end cap structure and a 3'-end polyA tail, which is highly stable and widely involved in a variety of pathophysiological processes such as cell proliferation, differentiation, and apoptosis. In recent years, accumulating studies have shown that circRNAs play an important role in the development and prognosis of breast cancer, but there are fewer literature reviews on their intrinsic molecular mechanisms which is the aim of this study. Methods: This review synthesizes the findings of literature retrieved from searches of PubMed and Google Scholar databases, hand searches, and authoritative texts. Citations mainly originate from the past 3 years. The articles need to describe the role of circRNA in breast cancer; no language restrictions were imposed. Key Content and Findings: This review summarizes the latest relevant literature and systematically reviews the four main mechanisms of circRNA in breast cancer from the perspective of circRNA function. At the same time, we describe the formation mechanism, characterization, and biological functions of circRNAs. Conclusions: We reviewed the status of actual knowledge about circRNA biogenesis and functions and summarized novel findings regarding the molecular mechanism of circRNA in breast cancer. Meanwhile, this review explores the possibility of circRNAs for becoming new biodiagnostic indicators and therapeutic targets in breast cancer.

Ultrawide linear range, high sensitivity, and large-area pressure sensor arrays enabled by pneumatic spraying broccoli-like microstructures.

Large-area pressure sensor arrays with a wide linear response range and high sensitivity are beneficial to map the inhomogeneous interface pressure, which is significant in practical applications. Here, we demonstrate a pneumatic spraying method to prepare large-area microstructure films (PSMF) for high performance pressure sensor arrays. The sprayed surface morphology is designable by controlling the spraying parameters. It is worth noting that the constructed "broccoli" like morphology with a swollen top and shrunken bottom inspired a new mechanism to enlarge the linear response range by decreasing the series resistance with pressure increasing. At the same time, the pneumatic sprayed "broccoli" has a rough surface due to droplet stacking, which reduces the initial current effectively. Hence, the sensor achieves a 10 000 kPa ultrawide linear response range with a high sensitivity (98.71 kPa-1), and low detection (5 Pa). The prepared sensor has a small static response error (4.4%) and 5000 cycle full-range dynamic response durability. Finally, the constructed sensor arrays can distinguish the pressure distribution in different ranges clearly, which indicates a great potential in health care, motion detection, and the tire industry.