Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes.

The characterization of protein complex is vital for unraveling biological mechanisms in various life processes. Despite advancements in biophysical tools, the capture of non-covalent complexes and deciphering of their biochemical composition continue to present challenges for low-input samples. Here we introduce SNAP-MS, a Stationary-phase-dissolvable Native Affinity Purification and Mass Spectrometric characterization strategy. It allows for highly efficient purification and characterization from inputs at the pico-mole level. SNAP-MS replaces traditional elution with matrix dissolving during the recovery of captured targets, enabling the use of high-affinity bait-target pairs and eliminates interstitial voids. The purified intact protein complexes are compatible with native MS, which provides structural information including stoichiometry, topology, and distribution of proteoforms, size variants and interaction states. An algorithm utilizes the bait as a charge remover and mass corrector significantly enhances the accuracy of analyzing heterogeneously glycosylated complexes. With a sample-to-data time as brief as 2 hours, SNAP-MS demonstrates considerable versatility in characterizing native complexes from biological samples, including blood samples.

Complex structure and activation mechanism of arginine kinase McsB by McsA.

Protein phosphorylation is a pivotal post-translational modification modulating various cellular processes. In Gram-positive bacteria, the protein arginine kinase McsB, along with its activator McsA, has a key role in labeling misfolded and damaged proteins during stress. However, the activation mechanism of McsB by McsA remains elusive. Here we report the cryo-electron microscopy structure of a tetrameric McsA-McsB complex at 3.41 Å resolution. Biochemical analysis indicates that the homotetrameric assembly is essential for McsB's kinase activity. The conserved C-terminal zinc finger of McsA interacts with an extended loop in McsB, optimally orienting a critical catalytic cysteine residue. In addition, McsA binding decreases the CtsR's affinity for McsB, enhancing McsB's kinase activity and accelerating the turnover rate of CtsR phosphorylation. Furthermore, McsA binding also increases McsB's thermostability, ensuring its activity under heat stress. These findings elucidate the structural basis and activation mechanism of McsB in stress response.

Unravelling the antioxidant behaviour of self-assembly ß-Sheet in silk fibroin.

Local oxidative stress in diseases or injury severely hinders cell homeostasis and organ regeneration. Antioxidant therapy is an effective strategy for oxidative stress treatment. Biomaterials with good biocompatibility and reactive oxygen species (ROS) scavenging ability are good choices for antioxidant therapeutics. However, there are few natural biomaterials that are identified with both biocompatibility and strong antioxidant activity. Here, we show, for the first time, that silk fibroin (SF) is a strong antioxidant, which can eliminate ROS in both cells and zebrafish. We further demonstrate that the ß-sheet structures turn into a random coiled structure when SF is treated with hydrogen peroxide. The content of ß-sheet structures can be increased by heating, thus enhancing the antioxidation properties of SF. Therefore, SF can serve as a good antioxidant biomaterial for therapeutics, and its ß-sheet structure-based antioxidation mechanism provides a novel theoretical basis, which could be a new cue for more antioxidant biomaterial discovery and identification.

Multi-modal mass spectrometry imaging of a single tissue section.

Mass spectrometry imaging (MSI) was developed to visualize spatial chemical information within tissues, thereby facilitating spatial multi-omic analysis. However, due to the limited spatial information provided by individual modal MSI, correlating various chemical data within tissues remains a significant challenge. In recent years, multimodal MSI has garnered considerable attention due to its ability to visualize the spatial distributions of multiple biomolecules within tissues. Among the strategies employed in this field, multimodal imaging on a single tissue section circumvents multiple issues introduced by integration of images of consecutive tissue sections. In this minireview, we provide an overview of multimodal MSI on a single tissue section, with a particular focus on the use of Matrix-Assisted Laser Desorption/Ionization-MSI for spatial multi-omic investigations that offer a comprehensive and in-depth elucidation of the biological state and activities, aiming to inspire the development of new approaches in this field.

Structured learning in time-dependent Cox models.

Cox models with time-dependent coefficients and covariates are widely used in survival analysis. In high-dimensional settings, sparse regularization techniques are employed for variable selection, but existing methods for time-dependent Cox models lack flexibility in enforcing specific sparsity patterns (ie, covariate structures). We propose a flexible framework for variable selection in time-dependent Cox models, accommodating complex selection rules. Our method can adapt to arbitrary grouping structures, including interaction selection, temporal, spatial, tree, and directed acyclic graph structures. It achieves accurate estimation with low false alarm rates. We develop the sox package, implementing a network flow algorithm for efficiently solving models with complex covariate structures. sox offers a user-friendly interface for specifying grouping structures and delivers fast computation. Through examples, including a case study on identifying predictors of time to all-cause death in atrial fibrillation patients, we demonstrate the practical application of our method with specific selection rules.

Construction of Monolayer Ti3C2Tx MXene on Nickel Foam under High Electrostatic Fields for High-Performance Supercapacitors.

Ti3C2Tx MXene, as a common two-dimensional material, has a wide range of applications in electrochemical energy storage. However, the surface forces of few-layer or monolayer Ti3C2Tx MXene lead to easy agglomeration, which hinders the demonstration of its performance due to the characteristics of layered materials. Herein, we report a facile method for preparing monolayer Ti3C2Tx MXene on nickel foam to achieve a self-supporting structure for supercapacitor electrodes under high electrostatic fields. Moreover, the specific capacitance varies with the deposition of different-concentration monolayer Ti3C2Tx MXene on nickel foam. As a result, Ti3C2Tx/NF has a high specific capacitance of 319 mF cm-2 at 2 mA cm-2 and an excellent long-term cycling stability of 94.4% after 7000 cycles. It was observed that the areal specific capacitance increases, whereas the mass specific capacitance decreases with the increasing loading mass. Attributable to the effect of the high electrostatic field, the self-supporting structure of the Ti3C2Tx/NF becomes denser as the concentration of the monolayer Ti3C2Tx MXene ink increases, ultimately affecting its electrochemical performance. This work provides a simple way to overcome the agglomeration problem of few-layer or monolayer MXene, then form a self-supporting electrode exhibiting excellent electrochemical performance.

Design and performance of an epithermal neutron detector based on PFN.

In this paper, an epithermal neutron detector suitable for the Prompt Fission Neutron (PFN) uranium logging method is designed by Monte Carlo simulation. According to the simulation results, the epithermal neutron detector composed of a 1 mm cadmium (Cd) layer, a 5 mm high-density polyethylene (HDPE) layer, and a 3He tube is sensitive to epithermal neutrons. Through the simulation test of Monte Carlo in formations with different uranium content, the results show that the uranium content in the formation has an obvious linear relationship with E/T, and the detection limit can meet the minimum standard for uranium ore detection. It meets the design expectation and provides a basis for the optimal design of an epithermal neutron detector.

Association between Sitting Time and Urinary Incontinence in the US population: Data from the National Health and Nutrition Examination Survey (NHANES) 2007 to 2018.

Background: Urinary incontinence (UI) is a common health problem that affects the quality of life and health of millions of people in the United States (US). We aimed to investigate the association between sitting time and UI symptoms in the US population. Methods: A cross-sectional survey of participants aged 20 and above from the National Health and Nutrition Examination Survey 2007-2018 was performed. A self-report questionnaire that reported complete data on UI, sitting time and covariates was included. Weighted multivariable logistic and regression models were used to assess the association between sitting time and UI symptoms. Results: A total of 22,916 participants were enrolled. Prolonged sitting time was associated with urgency UI (UUI, odds ratio [OR] = 1.2, 95% confidence interval [CI] = 1.1 to 1.3, p = 0.001). Compared with patients with sitting a time shorter than 7 hours (h), moderate recreational activity modified the association between sitting time and mixed UI in males in the fully adjusted model (OR = 2.5, 95% CI = 1.4 to 4.5, p = 0.002). A sitting time over 7 h was related to mixed UI (MUI, OR = 1.6, 95% CI = 1.1 to 2.2, p = 0.01) in males, and stress UI (SUI, OR = 0.9, 95% CI = 0.8 to 0.98, p = 0.03) in females. However, no significant difference was found among the UI, SUI, and MUI groups in fully adjusted model. Conclusions: A prolonged sitting time (≥7 h) was associated with UUI symptoms in all populations, SUI symptoms in females and MUI symptoms in males compared with sitting time lower than 7 h. Compared with those sit shorter than 7 h, moderate recreational activity may be a modifier between prolonged sitting and MUI symptoms in male participants, which warrants further studies for confirmation.

Using Effect Scores to Characterize Heterogeneity of Treatment Effects.

This JAMA Guide to Statistics and Methods article explains effect score analyses, an approach for evaluating the heterogeneity of treatment effects, and examines its use in a study of oxygen-saturation targets in critically ill patients.

Role of BcSfb3, the subunit of COPII vesicles, in fungal development and pathogenicity, ER-phagy and autophagy in the gray mold fungus Botrytis cinerea.

Cytoplasmic coat protein complex II (COPII) plays a multifunctional role in the transport of newly synthesized proteins, autophagosome formation, and endoplasmic reticulum (ER)-ER-phagy. However, the molecular mechanisms of the COPII subunit in ER-phagy in plant pathogens remain unknown. Here, we identified the subunit of COPII vesicles (BcSfb3) and explored the importance of BcSfb3 in Botrytis cinerea. BcSfb3 deletion affected vegetative growth, conidiation, conidial morphology, and plasma membrane integrity. We confirmed that the increase in infectious hyphal growth was delayed in the ΔBcSfb3 mutant, reducing its pathogenicity in the host plant. Furthermore, the ΔBcSfb3 mutant was sensitive to ER stress, which caused massive ER expansion and induced the formation of ER whorls that were taken up into the vacuole. Further examination demonstrated that BcSfb3 deletion caused ER stress initiated by unfolded protein response, and which led to the promotion of ER-phagy and autophagy that participate in sclerotia formation. In conclusion, these results demonstrate that BcSfb3 plays an important role in fungal development, pathogenesis, ER-phagy and autophagy in B. cinerea.

Galectin-3 is involved in inflammation and fibrosis in arteriogenic erectile dysfunction via the TLR4/MyD88/NF-κB pathway.

Galectin-3 (Gal-3) is a multifunctional protein that has been linked to fibrosis and inflammation in the cardiovascular system. In this study, we examined the impact of Gal-3 on inflammation and fibrosis in patients with arteriogenic erectile dysfunction (A-ED) and the underlying mechanisms involved. To induce arterial injury, we utilized cuffs on the periaqueductal common iliac arteries of Sprague‒Dawley (SD) rats and administered a high-fat diet to co-induce local atherosclerosis. Our results showed that we successfully developed a novel A-ED model that was validated based on histological evidence. In vivo, the vascular lumen of rats subjected to a high-fat diet and cuff placement exhibited significant narrowing, accompanied by the upregulation of Gal-3, Toll-like receptor 4 (TLR4), and myeloid differentiation primary response protein 88 (MyD88) expression in the penile cavernosa. This led to the activation of nuclear factor kappa B 65 (NF-κB-p65), resulting in reduced intracavernosal pressure, endothelial nitric oxide synthase expression, and smooth muscle content, promoting inflammation and fibrosis. However, treatment with Gal-3 inhibitor-modified citrus pectin (MCP) significantly normalized those effects. In vitro, knocking down Gal-3 led to a significant reduction in TLR4, MyD88, and NF-κB-p65 expression in corpus cavernosum smooth muscle cells (CCSMCs), decreasing inflammation levels. In conclusion, inhibiting Gal-3 may improve A-ED by reducing inflammation, endothelial injury, and fibrosis in the penile corpus cavernosum through the TLR4/MyD88/NF-κB pathway. These findings highlight the potential therapeutic target of Gal-3 in A-ED.

Microfluidic-assisted single-cell RNA sequencing facilitates the development of neutralizing monoclonal antibodies against SARS-CoV-2.

As a class of antibodies that specifically bind to a virus and block its entry, neutralizing monoclonal antibodies (neutralizing mAbs) have been recognized as a top choice for combating COVID-19 due to their high specificity and efficacy in treating serious infections. Although conventional approaches for neutralizing mAb development have been optimized for decades, there is an urgent need for workflows with higher efficiency due to time-sensitive concerns, including the high mutation rate of SARS-CoV-2. One promising approach is the identification of neutralizing mAb candidates via single-cell RNA sequencing (RNA-seq), as each B cell has a unique transcript sequence corresponding to its secreted antibody. The state-of-the-art high-throughput single-cell sequencing technologies, which have been greatly facilitated by advances in microfluidics, have greatly accelerated the process of neutralizing mAb development. Here, we provide an overview of the general procedures for high-throughput single-cell RNA-seq enabled by breakthroughs in droplet microfluidics, introduce revolutionary approaches that combine single-cell RNA-seq to facilitate the development of neutralizing mAbs against SARS-CoV-2, and outline future steps that need to be taken to further improve development strategies for effective treatments against infectious diseases.

Evaluating hybrid controls methodology in early-phase oncology trials: A simulation study based on the MORPHEUS-UC trial.

Phase Ib/II oncology trials, despite their small sample sizes, aim to provide information for optimal internal company decision-making concerning novel drug development. Hybrid controls (a combination of the current control arm and controls from one or more sources of historical trial data [HTD]) can be used to increase statistical precision. Here we assess combining two sources of Roche HTD to construct a hybrid control in targeted therapy for decision-making via an extensive simulation study. Our simulations are based on the real data of one of the experimental arms and the control arm of the MORPHEUS-UC Phase Ib/II study and two Roche HTD for atezolizumab monotherapy. We consider potential complications such as model misspecification, unmeasured confounding, different sample sizes of current treatment groups, and heterogeneity among the three trials. We evaluate two frequentist methods (with both Cox and Weibull accelerated failure time [AFT] models) and three different commensurate priors in Bayesian dynamic borrowing (with a Weibull AFT model), and modifications within each of those, when estimating the effect of treatment on survival outcomes and measures of effect such as marginal hazard ratios. We assess the performance of these methods in different settings and the potential of generalizations to supplement decisions in early-phase oncology trials. The results show that the proposed joint frequentist methods and noninformative priors within Bayesian dynamic borrowing with no adjustment on covariates are preferred, especially when treatment effects across the three trials are heterogeneous. For generalization of hybrid control methods in such settings, we recommend more simulation studies.

Rapid and signal crowdedness-robust in situ sequencing through hybrid block coding.

Spatial transcriptomics technology has revolutionized our understanding of cell types and tissue organization, opening possibilities for researchers to explore transcript distributions at subcellular levels. However, existing methods have limitations in resolution, sensitivity, or speed. To overcome these challenges, we introduce SPRINTseq (Spatially Resolved and signal-diluted Next-generation Targeted sequencing), an innovative in situ sequencing strategy that combines hybrid block coding and molecular dilution strategies. Our method enables fast and sensitive high-resolution data acquisition, as demonstrated by recovering over 142 million transcripts using a 108-gene panel from 453,843 cells from four mouse brain coronal slices in less than 2 d. Using this advanced technology, we uncover the cellular and subcellular molecular architecture of Alzheimer's disease, providing additional information into abnormal cellular behaviors and their subcellular mRNA distribution. This improved spatial transcriptomics technology holds great promise for exploring complex biological processes and disease mechanisms.

Multi-omics for COVID-19: driving development of therapeutics and vaccines.

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.

Dealloying-Induced Zeolite-like Metal Framework of AB2 Laves Phase Intermetallic Electrocatalysts.

Exploring an efficient and robust electrocatalyst for hydrogen evolution reaction (HER) at high pH and temperature holds the key to the industrial application of alkaline water electrolysis (AWE). Herein, we design an open tunnel structure by dealloying a series of Laves phase intermetallics, i.e., MCo2 and MRu0.25Co1.75 (M = Sc and Zr). The dealloying process can induce a zeolite-like metal framework for ScCo2 and ScRu0.25Co1.75 by stripping Sc metal from the center of a tunnel structure. This structural engineering significantly lowers their overpotentials at a current density of 500 mA/cm2 (η500) ca. 80 mV in 1.0 M KOH. Through a simple process, ScRu0.25Co1.75 can be easily decorated on a carbon cloth substrate and only requires 132 mV to reach 500 mA/cm2. More importantly it can maintain activity over 1000 h in industrial conditions (6.0 M KOH at 333 K), showing its potential for practical industrial applications.

Perillaldehyde Functions as a Potential Antifungal Agent by Triggering Metacaspase-Independent Apoptosis in Botrytis cinerea.

Botrytis cinerea, the causal agent of gray mold, is an important plant pathogen causing preharvest and postharvest diseases. Due to the extensive use of commercial fungicides, fungicide-resistant strains have emerged. Natural compounds with antifungal properties are widely present in various kinds of organisms. Perillaldehyde (PA), derived from the plant species Perilla frutescens, is generally recognized as a potent antimicrobial substance and to be safe to humans and the environment. In this study, we demonstrated that PA could significantly inhibit the mycelial growth of B. cinerea and reduced its pathogenicity on tomato leaves. We also found that PA had a significant protective effect on tomato, grape, and strawberry. The antifungal mechanism of PA was investigated by measuring the reactive oxygen species (ROS) accumulation, the intracellular Ca2+ level, the mitochondrial membrane potential, DNA fragmentation, and phosphatidylserine exposure. Further analyses revealed that PA promoted protein ubiquitination and induced autophagic activities and then triggered protein degradation. When the two metacaspase genes, BcMca1 and BcMca2, were knocked out from B. cinerea, all mutants did not exhibit reduced sensitivity to PA. These findings demonstrated that PA could induce metacaspase-independent apoptosis in B. cinerea. Based on our results, we proposed that PA could be used as an effective control agent for gray mold management. IMPORTANCE Botrytis cinerea causes gray mold disease, is considered one of the most important dangerous pathogens worldwide, and leads to severe economic losses worldwide. Due to the lack of resistant varieties of B. cinerea, gray mold control has mainly relied on application of synthetic fungicides. However, long-term and extensive use of synthetic fungicides has increased fungicide resistance in B. cinerea and is harmful to humans and the environment. In this study, we found that perillaldehyde has a significant protective effect on tomato, grape, and strawberry. We further characterized the antifungal mechanism of PA on B. cinerea. Our results indicated that PA induced apoptosis that was independent of metacaspase function.

Oxidative Stress Induced by Selenium Deficiency Contributes to Inflammation, Apoptosis and Necroptosis in the Lungs of Calves.

Selenium is an essential trace element for health that can only be obtained through food. However, the pathological processes of selenium deficiency in cattle have received little attention. This study investigated the effects of selenium deficiency on oxidative stress, apoptosis, inflammation, and necroptosis in the lungs of weaning calves compared with healthy calves as controls. The lung selenium content and the expression of 11 selenoproteins mRNA in selenium-deficient calves were substantially reduced compared with the controls. Pathological results showed engorged alveolar capillaries, thickened alveolar septa, and diffuse interstitial inflammation throughout the alveolar septa. The levels of GSH and T-AOC, as well as the CAT, SOD, and TrxR activities, were significantly decreased compared with healthy calves. MDA and H2O2 were significantly elevated. Meanwhile, the apoptosis activation in the Se-D group was validated. Next, in the Se-D group, several pro-inflammatory cytokines showed higher expression. Further research revealed that the lungs in the Se-D group experienced inflammation via hyperactive NF-κB and MAPK pathways. The high level of expression of c-FLIP, MLKL, RIPK1, and RIPK3 indicated that necroptosis also causes lung damage during selenium deficiency.

Regulation of Released Alkali from Gel Polymer Electrolyte in Quasi-Solid State Zn-Air Battery.

Gel polymer electrolyte (GPE) in quasi-solid state Zn-air battery (QSZAB) will release alkali during cycling, resulting in gradual dehydration of GPE, corrosion of Zn electrode, Zn dendrites growth, and therefore inferior performance. Here, hollow Sn microspheres are prepared on Zn substrate by the technique of colloidal self-assembly. The inner surfaces of hollow Sn microspheres are modified by 2-hydroxypropyl-ß-cyclodextrin (hollow Sn-inner HPßCD) to regulate the released alkali at GPE|anode interface. The hollow Sn-inner HPßCD can lessen the leakage of released alkali, make stored alkali diffuse back to GPE during the charging process, and mitigate the loss of soluble Zn(OH)4 2- to suppress Zn dendrites growth. Resultantly, GPE in QSZAB with hollow Sn-inner HPßCD exhibits a high retention capacity for alkaline solution. The cell also exhibits a long cyclic lifespan of 127 h due to the effective regulation of released alkali, which outperforms QSZAB without hollow Sn-inner HPßCD by 7.94 times. This work rivets the regulation of released alkali at GPE|anode interface, providing new insight to improve QSZABs' performance.

SAV Nsp2 regulates NF-κB signaling to induce inflammatory responses by targeting host DDX3.

Salmon alphavirus (SAV) infection leads to severe pancreas disease (PD) with typical inflammatory responses in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Nsp2, an important nonstructural protein of SAV, can activate NF-κB signaling pathway to reduce inflammatory responses. However, the molecular mechanism remains unclear. In this study, the ML (279-421aa) of Nsp2 was revealed to be the key domain for activating NF-κB. We focused on a host protein, DEAD-box RNA helicase 3 (DDX3), that may interact with Nsp2 to regulate NF-κB-induced inflammatory. The interaction between DDX3 and Nsp2 was confirmed in vitro. Overexpression of DDX3 inhibited the activation of NF-κB by Nsp2. SAV Nsp2 relieves the inhibitory effect of DDX3 on NF-κB, thereby initiating the innate immune response. This study revealed the molecular mechanism of Nsp2-induced inflammatory response by targeting DDX3 to activate NF-κB, providing a theoretical basis for revealing the underlying infection mechanism and pathogenesis of SAV.