Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein.

Protein surfaces have pivotal roles in interactions between proteins and other biological molecules. However, the structural dynamics of protein surfaces have rarely been explored and are poorly understood. Here, the surface of a single-stranded DNA (ssDNA) binding protein (SSB) with four DNA binding domains that bind ssDNA in binding site sizes of 35, 56, and 65 nucleotides per tetramer is investigated. Using oligonucleotides as probes to sense the charged surface, NaCl induces a two-state structural transition on the SSB surface even at moderate concentrations. Chelation of sodium ions with charged amino acids alters the network of hydrogen bonds and/or salt bridges on the surface. Such changes are associated with changes in the electrostatic potential landscape and interaction mode. These findings advance the understanding of the molecular mechanism underlying the enigmatic salt-induced transitions between different DNA binding site sizes of SSBs. This work demonstrates that monovalent salt is a key regulator of biomolecular interactions that not only play roles in non-specific electrostatic screening effects as usually assumed but also may configure the surface of proteins to contribute to the effective regulation of biomolecular recognition and other downstream events.

Pestiorosins A-F, New Papulacandins Isolated from the Fungus Pestalotiopsis rosea YNJ21.

Six previously unreported papulacandins, namely pestiorosins A-F (1-6), were isolated from the fermentation products of the fungus Pestalotiopsis rosea YNJ21 isolated from the fruitbody of Amanita exitialis. The structures of these compounds, along with a known compound called pestiocandin (7), were determined using MS, NMR data, and modified Mosher's method. All compounds exhibited significant antifungal activity against Candida albicans, with MIC values ranging from 0.06 to 2.00 µg/mL. In terms of cytotoxicity assays, compounds 3 and 6 demonstrated moderate inhibitory activity against human breast cancer MCF-7 cells with IC50 values of 24.50 and 16.83 µM, respectively. On the other hand, compound 7 displayed similar levels of inhibitory activity against mice microglial BV2 cells with an IC50 value of 24.51 µM.

Scene-Dependent Prediction in Latent Space for Video Anomaly Detection and Anticipation.

Video anomaly detection (VAD) plays a crucial role in intelligent surveillance. However, an essential type of anomaly named scene-dependent anomaly is overlooked. Moreover, the task of video anomaly anticipation (VAA) also deserves attention. To fill these gaps, we build a comprehensive dataset named NWPU Campus, which is the largest semi-supervised VAD dataset and the first dataset for scene-dependent VAD and VAA. Meanwhile, we introduce a novel forward-backward framework for scene-dependent VAD and VAA, in which the forward network individually solves the VAD and jointly solves the VAA with the backward network. Particularly, we propose a scene-dependent generative model in latent space for the forward and backward networks. First, we propose a hierarchical variational auto-encoder to extract scene-generic features. Next, we design a score-based diffusion model in latent space to refine these features more compact for the task and generate scene-dependent features with a scene information auto-encoder, modeling the relationships between video events and scenes. Finally, we develop a temporal loss from key frames to constrain the motion consistency of video clips. Extensive experiments demonstrate that our method can handle both scene-dependent anomaly detection and anticipation well, achieving state-of-the-art performance on ShanghaiTech, CUHK Avenue, and the proposed NWPU Campus datasets.

Genotype selection identified elite lines through quantitative trait loci mapping of agronomically important traits in wheat.

Wheat is one of the most important staple foods in the world. Genetic characterization of wheat agronomically important traits is crucial for yield improvement through molecular breeding. In this study, a recombinant inbred line (RIL) population was developed by crossing a local adapted high yield variety Jimai 22 (JM22) with an external variety Cunmai no.1 (CM1). A high-density genetic map containing 7,359 single nucleotide polymorphism (SNP) markers was constructed. Quantitative trait loci (QTL) mapping identified 61 QTL for eight yield-related traits under six environments (years). Among them, 17 QTL affecting spike number per plant, grain number per spike and thousand grain weight showed high predictability for theoretical yield per plant (TYP), of which, 12 QTL alleles positively contributed to TYP. Nine promising candidate genes for seven of the 12 QTL were identified including three known wheat genes and six rice orthologs. Four elite lines with TYP increased by 5.6%-15.2% were identified through genotype selection which carried 7-9 favorable alleles from JM22 and 2-3 favorable alleles from CM1 of the 12 QTL. Moreover, the linked SNPs of the 12 QTL were converted to high-throughput kompetitive allele-specific PCR (KASP) markers and validated in the population. The mapped QTL, identified promising candidate genes, developed elite lines and KASP markers are highly valuable in future genotype selection to improve wheat yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01496-3.

Intimal Injury Potentially Plays a Key Role in the Formation of Carotid Artery Dissection: A Novel Animal Model Establishing.

Research on the pathophysiological mechanism of carotid artery dissection and its clinical translation is limited due to the lack of effective animal models to simulate the occurrence of this condition. Assuming that intimal injury is an important factor in the formation of carotid dissection, we established a novel method for inducing carotid dissection models by scraping the carotid intima using a fine needle. Scraping the carotid intima with fine needles can induce the rapid formation of carotid dissection. Magnetic resonance imaging and hematoxylin-eosin staining suggest the presence of false lumens and mural hematomas in the vessels. Our model-induction technique, inspired by iatrogenic catheter-induced artery dissections (carotid, coronary, aortic), significantly mimics the pathological process of clinical carotid dissection. The results suggest that mechanical injury may be a significant cause of carotid dissection and that intimal injury is a major factor in the formation of arterial dissections. This approach will provide assistance in the understanding of medically induced arterial dissection.

Epitaxial Growth of Monolayer WS2 Single Crystals on Au(111) Toward Direct Surface-Enhanced Raman Spectroscopy Detection.

The epitaxial growth of wafer-scale two-dimensional (2D) semiconducting transition metal dichalcogenides (STMDCs) single crystals is the key premise for their applications in next-generation electronics. Despite significant advancements, some fundamental factors affecting the epitaxy growth have not been fully uncovered, e.g., interface coupling strength, adlayer-substrate lattice matching, substrate step-edge-guiding effects, etc. Herein, we develop a model system to tackle these issues concurrently, and realize the epitaxial growth of wafer-scale monolayer tungsten disulfide (WS2) single crystals on the Au(111) substrate. This epitaxial system is featured with good adlayer-substrate lattice matching, obvious step-edge-guiding effect for the unidirectionally aligned nucleation/growth, and relatively weaker interfacial interaction than that of monolayer MoS2/Au(111), as evidenced by the evolution of a uniform Moiré pattern and an intrinsic band gap, according to on-site scanning tunneling microscopy/spectroscopy (STM/STS) characterizations and density functional theory calculations. Intriguingly, the unidirectionally aligned monolayer WS2 domains along the Au(111) steps can behave as ultrasensitive templates for surface-enhanced Raman scattering detection of organic molecules, due to the obvious charge transfer occurred at substrate step edges. This work should hereby deepen our understanding of the epitaxy mechanism of 2D STMDCs on single-crystal substrates, and propel their wafer-scale production and applications in various cutting-edge fields.

Objective Analysis of Predictive Value of Ultrasound Quantitative Scoring System for Treatment Method Selection in Cesarean Scar Pregnancy.

ABSTRACT: This study aimed to explore the feasibility of using the ultrasound quantitative scoring system to guide the selection of surgical methods for a cesarean scar ectopic pregnancy (CSEP). A retrospective analysis was conducted of the medical records of 117 cases of patients with a CSEP. All patients underwent transvaginal ultrasound examination before treatment, and the ultrasound results were compared with the results of surgical exploration. The treatment methods that were delivered for the 2 patient groups with CSEP were analyzed, and agreement between the predicted and actual treatment protocols was tested using the kappa consistency test. Residual myometrial thickness at the scar site was mainly concentrated above 3 mm in the low-risk group, with 70 cases accounting for 76.9%, while in the high-risk group, this was primarily in the range of 1-3 mm with 18 cases accounting for 69.2%. The grading of nourishing blood supply to the gestational sac showed that 96.7% of patients in the low-risk group had Grade I and Grade II blood flow, while 84.6% of the high-risk group had Grade I and Grade II blood flow; Grade II blood flow was predominant in the high-risk group. The majority of patients in both the low- and high-risk groups experienced intraoperative blood loss of ≤50 mL (93.9% vs 80.6%, respectively). The consistency test between the actual and predicted treatment methods yielded a kappa coefficient of 0.644, indicating consistency between the two. For patients with CSEP in the low-risk group (score <4), the ultrasound quantitative scoring system could provide individualized assessment and offer clinically valuable treatment protocols.

Gut microbiota, circulating inflammatory proteins and sepsis: a bi-directional Mendelian randomization study.

Background: Gut microbiota is closely related to the occurrence and development of sepsis. However, the causal effects between the gut microbiota and sepsis, and whether circulating inflammatory proteins act as mediators, remain unclear. Methods: Gut microbiota, circulating inflammatory proteins, and four sepsis-related outcomes were identified from large-scale genome wide association studies (GWAS) summary data. Inverse Variance Weighted (IVW) was the primary statistical method. Additionally, we investigated whether circulating inflammatory proteins play a mediating role in the pathway from gut microbiota to the four sepsis-related outcomes. Results: There were 14 positive and 15 negative causal effects between genetic liability in the gut microbiota and four sepsis-related outcomes. Additionally, eight positive and four negative causal effects were observed between circulating inflammatory proteins and the four sepsis-related outcomes. Circulating inflammatory proteins do not act as mediators. Conclusions: Gut microbiota and circulating inflammatory proteins were causally associated with the four sepsis-related outcomes. However, circulating inflammatory proteins did not appear to mediate the pathway from gut microbiota to the four sepsis-related outcomes.

How can the microbial community in watershed sediment maintain its resistance in the presence of shifting antibiotic residuals?

The widespread presence of antibiotics in global watershed environments poses a serious threat to public health and ecosystems. It is essential to examine the resistance of microbial communities in watershed environments in response to shifting antibiotic residues. Sediment samples were collected from seven sites across a watershed, encompassing surface sediment (0-10 cm) and bottom sediment (30-40 cm) depths. The aim was to replicate exposure scenarios to different antibiotics (oxytetracycline (OTC) and sulfadiazine (SD)) at varying concentrations (0, 10, and 100 µg/L) in sediment overlying water, within controlled laboratory settings. The study findings revealed significant variations in the microbial community structure of sediments between different treatments, with distinct differences observed in the upper stream and top sediment layers compared to the sediments located downstream and in the bottom layers. After the introduction of antibiotics, a significant decrease in microbial nodes was observed in the genus-level co-occurrence network analysis of the bottom sediment layer, particularly in the OTC treatment groups. In contrast, the downstream region displayed more robust correlations among the top 20 genera than the upstream area. There was no significant variance observed in the expression of Antibiotic resistance genes (ARGs), consisting of tetracycline resistance genes (tetC, tetG, tetM, tetW, and tetX) and sulfonamide resistance genes (sul1, sul2, and sul3), between sediments in the top and bottom layers. Nevertheless, downstream samples exhibited significantly higher levels of ARGs when compared to upstream samples. Network correlation analysis indicated notably lower correlations between ARGs and bacterial genera in sediments from upstream or surface layers compared to those in downstream or deeper layers. Moreover, correlations in the sediments from surface layers and upstream regions showed a decreasing trend with increasing SD exposure concentrations, while those in deeper layers and downstream areas remained relatively stable. The presence of antibiotics notably enhanced the correlation between sediment properties and ARGs, particularly emphasizing associations with total carbon, nitrogen, and sulfur content. However, the introduction of SD and OTC resulted in a decrease in the influence of these sediment factors on microbial community functions related to sulfur and nitrogen metabolism, as indicated by KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation. The research provided empirical evidence on how microbial resistance responds to changes in antibiotics in sediment samples taken from various depths and locations within a watershed. It emphasized the urgent need for heightened awareness of the movement and alteration of antibiotic resistance patterns in watershed ecosystems.

Surficial Reconstruction of Pt-Ni/NiS and Its Effect on Electrocatalytic Hydrogen Evolution in Alkaline Medium.

Cyclic voltammetry pretreatment of Pt-based electrocatalysts has been proven to be a normal activation process on achieving the optimal alkaline hydrogen evolution performance. Until now, the congruent relationship between the microstructural evolution and performance improvement during this process has rarely been reported. Herein, when the in situ transmission electron microscopy and in situ Raman analyses are employed, a self-reconstruction process from crystalline NiS into amorphous nickel hydroxide hydrate [Ni(OH)2-x·H2O, where x ≈ 0.3] on the surface of platinum-nickel nanowires has first been captured, which is the critical water dissociation active site to offer a sufficient proton supply. Furthermore, such a surficial reconstruction triggers an increase in the current density from -2.3 to -38.8 mA/cm2 (at -70 mV), which is nearly 17 times. These observations point to the fact that it is essential to consider the fundamental mechanisms of hydrogen evolution on the active sites when the process is scaled up.

The impact of cue and preparation prompts on attention guidance in goal-directed tasks.

Introduction: In goal-directed tasks, visual prompts before the appearance of goals can make people ready in advance, which helps them to complete the movement better, and the presentation type of the visual prompt is very important. In previous studies, it has not been clear how different types of visual prompts guide attention in goal-directed tasks. Methods: According to the characteristics of goal-directed tasks, our research designed three different prompts: the cue prompt (featuring static arrow), the preparation prompt (involving dynamic countdown), and the combination prompt of cue and preparation information (simultaneously incorporating arrow and countdown). We used event-related potential components (CNV and P300) and graph theory indicators (clustering coefficient and characteristic path length) under the brain function connection to analyze the attention state of the brain. Results: The results showed that the combination prompts better guided the participants' sustained attention during the prompt stage, making them well prepared for the movement. Thus, after the target appeared, the participants had better executive control and achieved a faster response to the target. However, under the combination prompt, the participants consumed more attention resources during the prompt stage. Discussion: We believe that for the participants with impaired cognitive function, cue prompts or preparation prompts can be considered, which also play a role in guiding the participants' attention and helping them make motor preparations when less attention resources are consumed. This study provides a neurophysiological and behavioral foundation for the design of visual prompts in goal-directed tasks.

ITGB3-enriched extracellular vesicles mediate the formation of osteoclastic pre-metastatic niche to promote lung adenocarcinoma bone metastasis.

The regulatory mechanisms underlying bone metastasis in lung adenocarcinoma (LUAD) are not yet fully understood despite the frequent occurrence of bone involvement. This study aimed to examine the involvement and mechanism of integrin subunit beta 3 (ITGB3) in the process of LUAD bone metastasis. Our findings indicate that ITGB3 facilitates the migration and invasion of LUAD cells in vitro and metastasis to the bone in vivo. Furthermore, ITGB3 stimulates osteoclast production and activation, thereby expediting osteolytic lesion progression. Extracellular vesicles (EVs) isolated from the conditioned medium (CM) of LUAD cells overexpressing ITGB3 determined that ITGB3 facilitates osteoclastogenesis and enhances osteoclast activity by utilizing EVs-mediated transport to RAW264.7 cells. Our in vivo findings demonstrated that ITGB3-EVs augmented the population of osteoclasts, thereby establishing an osteoclastic pre-metastatic niche (PMN) conducive to the colonization and subsequent growth of LUAD cells in the bone. ITGB3 is enriched in serum EVs of patients diagnosed with LUAD bone metastasis, potentially facilitating osteoclast differentiation and activation in vitro. Our research illustrates that ITGB3-EVs derived from LUAD cells facilitate osteoclast differentiation and activation by modulating the phosphorylation level of p38 MAPK. This process ultimately leads to the generation of osteolytic PMN and accelerates the progression of bone metastasis.

Enhanced osteogenesis and antibacterial activity of dual-functional PEEK implants via biomimetic polydopamine modification with chondroitin sulfate and levofloxacin.

Polyetheretherketone (PEEK) implants have emerged as a clinically favored alternative to titanium alloy implants for cranial bone substitutes due to their excellent mechanical properties and biocompatibility. However, the biological inertness of PEEK has hindered its clinical application. To address this issue, we developed a dual-functional surface modification method aimed at enhancing both osteogenesis and antibacterial activity, which was achieved through the sustained release of chondroitin sulfate (CS) and levofloxacin (LVFX) from a biomimetic polydopamine (PDA) coating on the PEEK surface. CS was introduced to promote cell adhesion and osteogenic differentiation. Meanwhile, incorporation of antibiotic LVFX was essential to prevent infections, which are a critical concern in bone defect repairing. To our delight, experiment results demonstrated that the SPKD/CS-LVFX specimen exhibited enhanced hydrophilicity and sustained drug release profiles. Furthermore, in vitro experiments showed that cell growth and adhesion, cell viability, and osteogenic differentiation of mouse calvaria-derived osteoblast precursor (MC3T3-E1) cells were significantly improved on the SPKD/CS-LVFX coating. Antibacterial assays also confirmed that the SPKD/CS-LVFX specimen effectively inhibited the growth of Escherichia coli and Staphylococcus aureus, attributable to the antibiotic LVFX released from the PDA coating. To sum up, this dual-functional PEEK implant showed a promising potential for clinical application in bone defects repairing, providing excellent osteogenic and antibacterial properties through a synergistic approach.

Regulating the Scaling Relations in Ammonia Synthesis through a Light-driven Bendable Seesaw Effect on Tailored Iron Catalyst.

Advancing the energy-intensive Haber-Bosch process faces significant challenges due to the intrinsic constraints of scaling relations in heterogeneous catalysis. Herein, we reported an approach of bending the "seesaw effect" to regulate the scaling relations over a tailored α-Fe metallic material (α-Fe-110s), realizing highly efficient light-driven thermal catalytic ammonia synthesis rate of 1260 µmol gcatalyst-1 h-1 without additional heating. Specifically, the thermal catalytic activity of α-Fe-110s was significantly enhanced by the novel stepped {110} surface, exhibiting a 3.8-fold increase compared to the commercial fused-iron catalyst with promoters at 350 °C. The photo-induced hot electron transfer further accelerates the dinitrogen dissociation and hydrogenation simultaneously, effectively overcoming the limitation of scaling relation over identical sites. Consequently, the ammonia production rate of α-Fe-110s was further enhanced by 30 times at the same temperature with irradiation. This work designs an efficient and sustainable system for ammonia synthesis and provides a novel approach for regulating the scaling relations in heterogeneous catalysis.

The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA.

CDCA7, encoding a protein with a carboxyl-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.

The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma.

Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse, and clonal heterogeneity in MM, but our knowledge on epigenetic mechanisms underlying MM development is far from complete. The SAGA complex serves as a coactivator in transcription and catalyzes acetylation and deubiquitylation. Analyses of data sets in the Cancer Dependency Map Project revealed that many SAGA components are selective dependencies in MM. To define SAGA-specific functions, we focused on ADA2B, the only subunit in the lysine acetyltransferase (KAT) module that specifically functions in SAGA. Integration of RNA sequencing (RNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), and cleavage under targets and release using nuclease assay (CUT&RUN) results identified pathways directly regulated by ADA2B including MTORC1 signaling and oncogenic programs driven by MYC, E2F, and MM-specific MAF. We discovered that ADA2B is recruited to MAF and MYC gene targets, and that MAF shares a majority of its targets with MYC in MM cells. Furthermore, we found that the SANT domain of ADA2B is required for interaction with both GCN5 and PCAF acetyltransferases, incorporation into SAGA, and ADA2B protein stability. Our findings uncover previously unknown SAGA KAT module-dependent mechanisms controlling MM cell growth, revealing a vulnerability that might be exploited for future development of MM therapy.

Identification and Functional Analysis of Novel Long Intergenic RNA in Chicken Macrophages Infected with Avian Pathogenic Escherichia coli.

Avian pathogenic E. coli (APEC), a widespread bacterium, results in serious economic losses to the poultry industry annually, and it poses a threat to human health due to the contaminated retail poultry meat and eggs. Recently, it has been demonstrated that long non-coding RNAs played important roles in regulating gene expression and the animal immune response. This study aimed to systematically explore the function of the novel long intergenic non-coding transcript, lincRNA-73240, upon APEC infection. A bioinformatics analysis indicated that lincRNA-73240 had no coding ability and a relative stable secondary structure with multiple hairpin rings. Moreover, the RT-qPCR results showed that lincRNA-73240 was highly expressed in lungs, heart, liver, spleen, cecum tonsils, thymus, ileum, bursa of Fabricius, harderian gland, and muscles in comparison to the cerebrum. Additionally, overexpression of lincRNA-73240 can promote the expression levels of inflammation, apoptosis, autophagy, and oxidative stress-related genes, as well as the production of reactive oxygen species (ROS), malondialdehyde (MDA), and nitric oxide (NO) upon APEC infection, which lead to cellular injury and apoptosis. These findings collectively establish a foundation for the study of the biological function of chicken lincRNA-73240 and provide a theoretical basis for further research on the molecular mechanisms of the chicken immune response.

Downregulation of PRKCI inhibits osteosarcoma cell growth by inactivating the Akt/mTOR signaling pathway.

PRKCI is abnormally expressed in various cancers, but its role in osteosarcoma is unknown. This study aimed to explore the biological function of PRKCI in osteosarcoma and its potential molecular mechanism. PRKCI expression was evaluated in osteosarcoma cell lines using Western blot analysis and reverse transcription PCR. The CCK-8 assay, colony formation assay, flow cytometry, Transwell assay, and wound-healing assay were used to detect the proliferation, colony-forming capacity, cell cycle, migration, and invasion of osteosarcoma cells when PRKCI was overexpressed or knocked down. The interaction between PRKCI and SQSTM1 was explored using immunoprecipitation. Finally, the protein molecule expression of the Akt/mTOR signaling pathway in osteosarcoma was detected when PRKCI was knocked down. Our study found that PRKCI was overexpressed in osteosarcoma cell lines. The overexpression of PRKCI promoted the proliferation and colony-forming capacity of osteosarcoma cells, while silencing PRKCI inhibited the proliferation, colony-forming capacity, migration, and invasion of osteosarcoma cells and arrested the cell cycle at the G2/M phase. Both PRKCI and SQSTM1 were overexpressed in osteosarcoma. The expression of PRKCI was only related to histological type, while that of SQSTM1 was not related to clinical characteristics. The expression of PRKCI and SQSTM1 in osteosarcoma was higher than that in chondrosarcoma. Knockdown of PRKCI inhibited the proliferation of osteosarcoma cells by inactivating the Akt/mTOR signaling pathway, suggesting that PRKCI was a potential target for osteosarcoma therapy.