Environmental heterogeneity and dispersal limitation simultaneously determine the spatial scaling of different microbial functional groups

Uncovering the mechanisms driving patterns of diversity across space and through time is of critical importance in microbial community ecology. Previous studies suggest that microorganisms also follow the same spatial scaling patterns as macro-organisms. However, it remains unclear whether different microbial functional groups differ in spatial scaling and how different ecological processes may contribute to such differences. In this study, two typical spatial scaling patterns, taxa-area (TAR) and distance-decay relationships (DDR), were investigated for the whole prokaryotic community and seven microbial functional groups using marker genes, including amoA (AOA), amoA (AOB), aprA, dsrB, mcrA, nifH and nirS. Different microbial functional groups harbored different spatial scaling patterns. Microbial functional groups had weaker TAR slope coefficients than the whole prokaryotic community. The archaeal ammonia-oxidizing group, however, displayed a stronger DDR pattern than the bacterial ammonia-oxidizing group. For both TAR and DDR, rare subcommunities were mainly responsible for the observed microbial spatial scaling patterns. Significant associations between environmental heterogeneity and spatial scaling metrics were observed for multiple microbial functional groups. Dispersal limitation, which positively correlated with phylogenetic breadth, was also strongly associated with the strength of microbial spatial scaling. The results demonstrated that environmental heterogeneity and dispersal limitation simultaneously contributed to microbial spatial scaling patterns. This study links microbial spatial scaling patterns with ecological processes, providing mechanistic insights into the typical diversity patterns followed by microbes.

Impacts of co-exposure to zearalenone and trifloxystrobin on the enzymatic activity and gene expression in zebrafish

Although humans and animals are usually exposed to combinations of toxic substances, little is known about the interactive toxicity of mycotoxins and farm chemicals. Therefore, we can not precisely evaluate the health risks of combined exposure. In the present work, using different approaches, we examined the toxic impacts of zearalenone and trifloxystrobin on zebrafish (Danio rerio). Our findings showed that the lethal toxicity of zearalenone to embryonic fish with a 10-day LC₅₀ of 0.59 mg L^-1 was lower than trifloxystrobin (0.037 mg L^-1). Besides, the mixture of zearalenone and trifloxystrobin triggered acute synergetic toxicity to embryonic fish. Moreover, the contents of CAT, CYP450, and VTG were distinctly altered in most single and combined exposures. Transcriptional levels of 23 genes involved in the oxidative response, apoptosis, immune, and endocrine systems were determined. Our results implied that eight genes (cas9, apaf-1, bcl-2, il-8, trb, vtg1, erβ1, and tg) displayed greater changes when exposed to the mixture of zearalenone and trifloxystrobin compared with the corresponding individual chemicals. Our findings indicated that performing the risk assessment based on the combined impact rather than the individual dosage response of these chemicals was more accurate. Nevertheless, further investigations are still necessary to reveal the modes of action of mycotoxin and pesticide combinations and alleviate their effects on human health.

(NH4)2Mo3S13/MnFe2O4 hybrid with multiple active sites boosted activation of peroxymonosulfate for removal of tetracycline

Advanced oxidation processes (AOPs) based on peroxymonosulfate (PMS) activation have attracted much attention in wastewater treatment. Here, a series of (NH₄)₂Mo₃S₁₃/MnFe₂O₄ (MSMF) composites were prepared and used as PMS activators to remove tetracycline (TC) for the first time. When the mass ratio of (NH₄)₂Mo₃S₁₃ to MnFe₂O₄ was 4.0 (MSMF4.0), the composite showed remarkable catalytic efficiency for activating PMS to remove TC. Over 93% of TC was removed in MSMF4.0/PMS system in 20 min. The aqueous ^•OH as well as the surface SO₄^•- and ^•OH were the primary reactive species for TC degradation in MSMF4.0/PMS system, and the comprehensive experimental results excluded the contributions of aqueous SO₄^•-, O₂^•-, and ¹O₂, high-valent metal-oxo species, and surface-bound PMS. The Mn(II)/Mn(III), Fe(II)/Fe(III), Mo(IV)/Mo(VI), and S^2-/SO_x^2- all contributed to the catalytic process. MSMF4.0 also showed excellent activity and stability after five cycles and significant degradation efficiency for a variety of pollutants. This work will provide theoretical basis for applying MnFe₂O₄-based composites in PMS-based AOPs.

Lactobacillus coryniformis subsp. torquens inhibits bone loss in obese mice via modification of the gut microbiota

High-fat diet (HFD)-induced obesity results in bone loss associated with an imbalanced gut microbiota and altered immune status. Probiotics are live microorganisms that are beneficial to the host and are important in maintaining bone health and gut homeostasis. In this study, the probiotic Lactobacillus coryniformis subsp. torquens (T3L) was isolated from traditional yak milk cheese produced in Lhasa and showed distinct acid and bile salt resistance as potential probiotics. Our data indicated that T3L not only reversed HFD-induced gut dysbiosis, as indicated by decreased Firmicutes-to-Bacteroidetes ratios but also reduced bone loss. The anti-obesity, microbiome-modulating, and bone-protective effects were transmissible via horizontal faeces transfer from T3L-treated mice to HFD-fed mice. The protective effects of T3L on bone mass were associated with regulatory T (Treg) cell-mediated inhibition of osteoclast differentiation. Our data indicate that T3L is a regulator of the gut microbiota and bone homeostasis in an animal model.

Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling

The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated. The significant spatial scaling of biodiversity could be observed across all microbial domains, including archaea, bacteria, fungi, and protists. Among them, archaea and fungi were found with much stronger DDR slopes than those observed in bacteria and protists. For both TAR and DDR, rare subcommunities were mainly responsible for the observed spatial scaling patterns, except for the DDR of protists and bacteria. This was also evidenced by extending the TAR and DDR diversity metrics to Hill numbers. Further statistical analyses demonstrated that different microbial domains were influenced by different environmental factors and harbored distinct local community assembly processes. Of these, drift was mainly responsible for the compositional variations of bacteria and protists. Archaea were shaped by strong homogeneous selection, whereas fungi were more affected by dispersal limitation. Such differing ecological processes resulted in the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling and provides novel mechanistic insights into the diversity patterns of microbes that belong to different trophic levels. IMPORTANCE As the most diverse and numerous life form on Earth, microorganisms play indispensable roles in natural ecological processes. Revealing their diversity patterns across space and through time is of essential importance to better understand the underlying ecological mechanisms controlling the distribution and assembly of microbial communities. However, the diversity patterns and their underlying ecological mechanisms for different microbial domains and/or trophic levels require further exploration. In this study, the spatial scaling of different microbial domains and their associated ecological processes in a mudflat intertidal zone were investigated. The results showed different spatial scaling patterns for different microbial domains. Different ecological processes underlie the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling to provide novel mechanistic insights into the diversity patterns of microorganisms that belong to different trophic levels.

CircFOXK2 promotes hepatocellular carcinoma progression and leads to a poor clinical prognosis via regulating the Warburg effect

BACKGROUND

The Warburg effect is well-established to be essential for tumor progression and accounts for the poor clinical outcomes of hepatocellular carcinoma (HCC) patients. An increasing body of literature suggests that circular RNAs (circRNAs) are important regulators for HCC. However, few circRNAs involved in the Warburg effect of HCC have hitherto been investigated. Herein, we aimed to explore the contribution of circFOXK2 to glucose metabolism reprogramming in HCC.

METHODS

In the present study, different primers were designed to identify 14 circRNAs originating from the FOXK2 gene, and their differential expression between HCC and adjacent liver tissues was screened. Ultimately, circFOXK2 (hsa_circ_0000817) was selected for further research. Next, the clinical significance of circFOXK2 was evaluated. We then assessed the pro-oncogenic activity of circFOXK2 and its impact on the Warburg effect in both HCC cell lines and animal xenografts. Finally, the molecular mechanisms of how circFOXK2 regulates the Warburg effect of HCC were explored.

RESULTS

CircFOXK2 was aberrantly upregulated in HCC tissues and positively correlated with poor clinical outcomes in patients that underwent radical hepatectomy. Silencing of circFOXK2 significantly suppressed HCC progression both in vitro and in vivo. Mechanistically, circFOXK2 upregulated the expression of protein FOXK2-142aa to promote LDHA phosphorylation and led to mitochondrial fission by regulating the miR-484/Fis1 pathway, ultimately activating the Warburg effect in HCC.

CONCLUSIONS

CircFOXK2 is a prognostic biomarker of HCC that promotes the Warburg effect by promoting the expression of proteins and miRNA sponges that lead to tumor progression. Overall, circFOXK2 has huge prospects as a potential therapeutic target for patients with HCC.

Fascinating isomeric covalent organic frameworks

Isomeric covalent organic frameworks possessing the same chemical constitutions but different atomic arrangement structures and physicochemical properties are fascinating branches of covalent organic frameworks (COFs). However, the rational design and targeted synthesis of isomeric COFs remain conundrums, so the investigation of isomeric COFs is still in a fledging period. According to the diversity of frameworks, positional isomers with similar structures and framework isomers having distinct constructions are the main existing subspecies of isomeric COFs. In this review, we focus on the research progress and substantial achievements in this fascinating embranchment and systematically summarize and highlight the design principles of both positional isomeric and framework isomeric COFs, which will potentially facilitate further exploitation and investigation of novel isomeric COFs. The application and structure-property relationship of these isomeric COFs have been briefly introduced. Moreover, key constraints of current isomeric COFs and further advancement of this promising field are proposed and anticipated.

Emergent Majorana zero-modes in an intrinsic anti-ferromagnetic topological superconductor Mn2B2 monolayer

Topological superconductors (TSCs) are an exotic field due to the existence of Majorana zero-modes (MZM) in the edge states that obey non-Abelian statistics and can be used to implement topological quantum computations, especially for two-dimensional (2D) materials. Here we predict manganese diboride (Mn₂B₂) as an intrinsic 2D anti-ferromagnetic (AFM) TSC based on the magnetic and electronic structures of Mn and B atoms. Once Mn₂B₂ ML enters a superconducting state, MZM will be induced by the spin-polarized helical gapless edge states. The Z₂ topological non-trivial properties are confirmed by Wannier charge centers (WCC) and the platform of the spin Hall conductivity near the Fermi level. Phonon-electron coupling (EPC) implies s-wave superconductivity and the critical temperature (T_c) is 6.79 K.

Lab on a chip for a low-carbon future

Transitioning our society to a sustainable future, with low or net-zero carbon emissions to the atmosphere, will require a wide-spread transformation of energy and environmental technologies. In this perspective article, we describe how lab-on-a-chip (LoC) systems can help address this challenge by providing insight into the fundamental physical and geochemical processes underlying new technologies critical to this transition, and developing the new processes and materials required. We focus on six areas: (I) subsurface carbon sequestration, (II) subsurface hydrogen storage, (III) geothermal energy extraction, (IV) bioenergy, (V) recovering critical materials, and (VI) water filtration and remediation. We hope to engage the LoC community in the many opportunities within the transition ahead, and highlight the potential of LoC approaches to the broader community of researchers, industry experts, and policy makers working toward a low-carbon future.

Heterologous expression of cyclodextrin glycosyltransferase from Bacillus stearothermophilus in Bacillus subtilis and its application in glycosyl rutin production

In this paper, the cgt gene encoding cyclodextrin glycosyltransferase (CGTase) from Bacillus stearothermophilus was cloned into pWB980 plasmid for extracellular expression in Bacillus subtilis SCK6. Through adding a six-histidine affinity tag fused to the C-terminus, the recombinant CGTase could be purified by nickel ion affinity chromatography, and its molecular weight was approximately 76 kDa on SDS-PAGE. Then, the enzymatic properties were determined, and results were as follows: the optimum temperature and pH were identified as 40 ℃ and pH 5.0, respectively. CGTase had good tolerance to metal ions of Mn2+, Ca2+, and Mg2+. The enzyme activity was activated by Na+, Al3+, Fe3+, and Ni+, and it was remarkably inhibited by Cu2+ and Zn2+. To improve the aqueous solubility of rutin, CGTase was used to catalyze the transglycosylation reaction, and the conversion rate could reach as high as 80.13% under optimal conditions. Furthermore, the reaction mixture was treated with glucoamylase and microporous adsorbent resin. The yield of glycosyl-rutin was 56.1%, and its purity was 74.3%, which further improved the value of the product.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03510-5.

The Phytophthora sojae effector PsFYVE1 modulates immunity-related gene expression by targeting host RZ-1A protein

Oomycete pathogens secrete numerous effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of an FYVE domain-containing protein family that are highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora capsici infection in Nicotiana benthamiana and was necessary for Phytophthora sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conserved amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean (Glycine max), and silencing of NbRZ-1A/1B/1C genes attenuated plant immunity. NbRZ-1A was associated with the spliceosome complex that included three important components, glycine-rich RNA-binding protein 7 (NbGRP7), glycine-rich RNA-binding protein 8 (NbGRP8), and a specific component of the U1 small nuclear ribonucleoprotein complex (NbU1-70K). Notably, PsFYVE1 disrupted NbRZ-1A-NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only modulated pre-mRNA alternative splicing (AS) of the necrotic spotted lesions 1 (NbNSL1) gene, but also co-regulated transcription of hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (NbHCT), ethylene insensitive 2 (NbEIN2), and sucrose synthase 4 (NbSUS4) genes, which participate in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential uncharacterized effector types and also highlight that plant pathogen effectors can regulate plant immunity-related genes at both AS and transcription levels to promote disease.

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities

High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.

Structure, biochemical function, and signaling mechanism of plant NLRs

To counter pathogen invasion, plants have evolved a large number of immune receptors, including membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding and leucine-rich repeat receptors (NLRs). Our knowledge about PRR and NLR signaling mechanisms has expanded significantly over the past few years. Plant NLRs form multi-protein complexes called resistosomes in response to pathogen effectors, and the signaling mediated by NLR resistosomes converges on Ca²⁺-permeable channels. Ca²⁺-permeable channels important for PRR signaling have also been identified. These findings highlight a crucial role of Ca²⁺ in triggering plant immune signaling. In this review, we first discuss the structural and biochemical mechanisms of non-canonical NLR Ca²⁺ channels and then summarize our knowledge about immune-related Ca²⁺-permeable channels and their roles in PRR and NLR signaling. We also discuss the potential role of Ca²⁺ in the intricate interaction between PRR and NLR signaling.

Unique regulation of TiO2 nanoporous topography on macrophage polarization via MSC-derived exosomes

The comprehensive recognition of communications between bone marrow mesenchymal stem cells (bm-MSCs) and macrophages in the peri-implant microenvironment is crucial for implantation prognosis. Our previous studies have clarified the indirect influence of Ti surface topography in the osteogenic differentiation of bm-MSCs through modulating macrophage polarization. However, cell communication is commutative and multi-directional. As the immune regulatory properties of MSCs have become increasingly prominent, whether bm-MSCs could also play an immunomodulatory role on macrophages under the influence of Ti surface topography is unclear. To further illuminate the communications between bm-MSCs and macrophages, the bm-MSCs inoculated on Ti with nanoporous topography were indirectly co-cultured with macrophages, and by blocking exosome secretion or extracting the purified exosomes to induce independently, we bidirectionally confirmed that under the influence of TiO₂ nanoporous topography with 80-100 nm tube diameters, bm-MSCs can exert immunomodulatory effects through exosome-mediated paracrine actions and induce M1 polarization of macrophages, adversely affecting the osteogenic microenvironment around the implant. This finding provides a reference for the optimal design of the implant surface topography for inducing better bone regeneration.

The Role of Sarcopenia in Overactive Bladder in Adults in the United States: Retrospective Analysis of NHANES 2011-2018

PURPOSE

To investigate the association between sarcopenia and overactive bladder (OAB) in a United States adult population from 2011 to 2018, and whether sarcopenia can predict the risk of OAB.

MATERIALS AND METHODS

We analyzed data from the 2011-2018 National Health and Nutrition Examination Survey in a cross-sectional study(NHANES) of 8746 participants, of whom 1213 were diagnosed with OAB, we analyzed correlations by sex, age, race, education level, marital status, household income-to-poverty ratio, hypertension, diabetes, strenuous work activity, moderate work activity, strenuous recreational activity, moderate recreational activity, blood urea nitrogen, creatinine, and uric acid levels using restricted cubic spline plots of dose-response curves, univariate and multivariate Logistic regression. Models based on sex, age, education, household income to poverty ratio, hypertension, diabetes, sarcopenia index, and cotinine were developed and evaluated using Nomogram, calibration curves, receiver operating characteristic curves, and clinical decision curves.

RESULTS

Of the 1213 OAB patients, 388 (32.0%) were male and 825 (68.0%) were female. Univariate and multivariate Logistic regression analysis showed that sarcopenia index was negatively correlated with the prevalence of OAB (OR=0.084, 95% CI, 0.056 - 0.130, P <0.001;OR=0.456, 95%CI, 0.215-0.968, P= 0.0041). Dose curve analysis of the sarcopenia index and prevalence of OAB showed that the prevalence of OAB decreased significantly with increasing sarcopenia index. Sarcopenia was positively correlated with OAB (OR=2.400, 95%CI, 2.000 - 2.800, P <0.001;OR=1.46, 95%CI, 1.096 -1.953, P = 0.010). In addition, our model shows that sarcopenia can predict the prevalence of OAB (AUC = 0.750) and has some clinical decision-making implications.

CONCLUSION

Sarcopenia is positively associated with the risk of OAB in United States adults and can be used as a predictor of OAB prevalence.

Machine learning algorithms assist early evaluation of enteral nutrition in ICU patients

Background

This study applied machine learning (ML) algorithms to construct a model for predicting EN initiation for patients in the intensive care unit (ICU) and identifying populations in need of EN at an early stage.

Methods

This study collected patient information from the Medical Information Mart for Intensive Care IV database. All patients enrolled were split randomly into a training set and a validation set. Six ML models were established to evaluate the initiation of EN, and the best model was determined according to the area under curve (AUC) and accuracy. The best model was interpreted using the Local Interpretable Model-Agnostic Explanations (LIME) algorithm and SHapley Additive exPlanation (SHAP) values.

Results

A total of 53,150 patients participated in the study. They were divided into a training set (42,520, 80%) and a validation set (10,630, 20%). In the validation set, XGBoost had the optimal prediction performance with an AUC of 0.895. The SHAP values revealed that sepsis, sequential organ failure assessment score, and acute kidney injury were the three most important factors affecting EN initiation. The individualized forecasts were displayed using the LIME algorithm.

Conclusion

The XGBoost model was established and validated for early prediction of EN initiation in ICU patients.

Evolution of Benzimidazole Resistance Caused by Multiple Double Mutations of β-Tubulin in Corynespora cassiicola

Cucumber target leaf spot caused by Corynespora cassiicola has devastated greenhouse cucumber production. In our previous study, the resistance monitoring of C. cassiicola to carbendazim was carried out, and a large number of resistant populations carrying various mutations (M163I&E198A, F167Y&E198A, F200S&E198A, or E198A) in β-tubulin were detected. However, the single-point mutations M163I, F167Y, and F200S have remained undetected. To investigate the evolutionary mechanism of double mutations in β-tubulin of C. cassiicola resistance to benzimidazoles, site-directed mutagenesis was used to construct alleles with corresponding mutation genotypes in β-tubulin. Through PEG-mediated protoplast transformation, all the mutants except for the M163I mutation were obtained and conferred resistance to benzimidazoles. It was found that the mutants conferring the E198A or double-point mutations showed high resistance to carbendazim and benomyl, but the mutants conferring the F167Y or F200S mutations showed moderate resistance. Except, the F200S mutants showed low resistance, the resistance level of the other mutants to thiabendazole seemed no difference. In addition, compared to the other mutants, the F167Y and F200S mutants suffered a more severe fitness penalty in mycelial growth, sporulation, and virulence. Thus, combined with the resistance level, fitness, and molecular docking results, we concluded that the field double mutations (F167Y&E198A and F200S&E198A) evolved from the single mutations F167Y and F200S, respectively.

Nanotopographical cues for regulation of macrophages and osteoclasts: emerging opportunities for osseointegration

Nanotopographical cues of bone implant surface has direct influences on various cell types during the establishment of osseointegration, a prerequisite of implant bear-loading. Given the important roles of monocyte/macrophage lineage cells in bone regeneration and remodeling, the regulation of nanotopographies on macrophages and osteoclasts has arisen considerable attentions recently. However, compared to osteoblastic cells, how nanotopographies regulate macrophages and osteoclasts has not been properly summarized. In this review, the roles and interactions of macrophages, osteoclasts and osteoblasts at different stages of bone healing is firstly presented. Then, the diversity and preparation methods of nanotopographies are summarized. Special attentions are paid to the regulation characterizations of nanotopographies on macrophages polarization and osteoclast differentiation, as well as the focal adhesion-cytoskeleton mediated mechanism. Finally, an outlook is indicated of coordinating nanotopographies, macrophages and osteoclasts to achieve better osseointegration. These comprehensive discussions may not only help to guide the optimization of bone implant surface nanostructures, but also provide an enlightenment to the osteoimmune response to external implant.

Characteristics and background mucosa status of early gastric cancer after Helicobacter pylori eradication: A narrative review

Helicobacter pylori (H pylori) eradication treatment can reduce the risk of gastric cancer. However, early gastric cancer (EGC) can still be detected after eradication. Meanwhile, EGC after eradication is challenging to diagnose by an endoscopist in some cases due to the lack of apparent characteristics and the complex mucosal status. This review aims to summarize the endoscopic and histological characteristics and the mucosal risk factors for gastric cancer after H pylori eradication. The literature was searched for possible reported gastric cancer after eradication in "PubMed." These included related clinical studies and reviews, and unrelated or non-English articles were excluded. Endoscopically, EGC displays a small, reddish and depressed lesion, indistinct border, "gastritis-like" appearance and submucosal invasion. Histologically, it is divided into surface differentiation, nontumorous epithelium, and intestinal type. The risk factors include severe gastric atrophy, intestinal metaplasia in the corpus, and map-like redness. In conclusion, these studies on the characteristics and risk mucosal factors of patients with gastric cancer after H pylori eradication will drive the establishment of a novel endoscopic surveillance and diagnosis system for H pylori-eradicated patients.

Deep Reinforcement Learning for Solving the Heterogeneous Capacitated Vehicle Routing Problem

Existing deep reinforcement learning (DRL)-based methods for solving the capacitated vehicle routing problem (CVRP) intrinsically cope with a homogeneous vehicle fleet, in which the fleet is assumed as repetitions of a single vehicle. Hence, their key to construct a solution solely lies in the selection of the next node (customer) to visit excluding the selection of vehicle. However, vehicles in real-world scenarios are likely to be heterogeneous with different characteristics that affect their capacity (or travel speed), rendering existing DRL methods less effective. In this article, we tackle heterogeneous CVRP (HCVRP), where vehicles are mainly characterized by different capacities. We consider both min-max and min-sum objectives for HCVRP, which aim to minimize the longest or total travel time of the vehicle(s) in the fleet. To solve those problems, we propose a DRL method based on the attention mechanism with a vehicle selection decoder accounting for the heterogeneous fleet constraint and a node selection decoder accounting for the route construction, which learns to construct a solution by automatically selecting both a vehicle and a node for this vehicle at each step. Experimental results based on randomly generated instances show that, with desirable generalization to various problem sizes, our method outperforms the state-of-the-art DRL method and most of the conventional heuristics, and also delivers competitive performance against the state-of-the-art heuristic method, that is, slack induction by string removal. In addition, the results of extended experiments demonstrate that our method is also able to solve CVRPLib instances with satisfactory performance.

[Soft tissue reconstruction strategy for sacral tumor resection]

Objective: To investigate the clinical strategy and effect of soft tissue reconstruction after sacral tumor resection in different planes. Methods: The data of 27 consecutive patients who underwent primary or secondary sacral tumor resection and soft tissue reconstruction from June 2012 to June 2021 at Dongnan Hospital of Xiamen University (the 909th Hospital) were retrospectively analyzed. There were 11 males and 16 females, aged (M(IQR)) (46.2±23.6) years (range: 16 to 72 years). Sacrospinous muscle, gluteus maximus and vertical rectus abdominis muscle flap were selected for soft tissue reconstruction according to the tumor site and the size of tissue defect. the postoperative follow-up was performed. The operative methods, intraoperative conditions, complications and disease outcomes were summarized. Results: Among the 27 patients with sacral tumor, the tumor plane was located in S₁ in 8 cases, S₂ in 5 cases and S₃ or below in 14 cases. There were 12 patients with tumor volume≤400 cm³ and 15 patients with tumor volume>400 cm³. Operation time was 100(90) minutes (range: 70 to 610 minutes), intraoperative blood loss was 800(1 600) ml (range: 400 to 6 500 ml). Soft tissue reconstruction was performed by transabdominal rectus abdominis transfer repair in 2 cases, extraperitoneal rectus abdominis transfer repair in 1 case, gluteus maximus transfer repair in 5 cases, gluteus maximus advancement repair in 13 cases, and sacrospinous muscle transfer repair in 6 cases. Postoperative complications occurred in 6 cases, including 1 case of incision infection, 4 cases of skin border necrosis, and 1 case of delayed infection due to fracture of internal fixator 3 years after operation, all of them were cured. The follow-up time was (35±21) months. Among the patients, 6 patients had recurrence, 2 patients with Ewing sarcoma died of lung metastasis 1 year after operation, 4 patients with metastatic cancer died of primary disease, and the remaining patients survived without disease. Conclusion: Choosing different soft tissue reconstruction strategies according to sacral tumor location and tissue defect size can effectively fill the dead space after sacral tumor resection, reduce postoperative complications and improve the prognosis of patients.

Diverse mechanisms associated with cyhalofop-butyl resistance in Chinese sprangletop (Leptochloa chinensis (L.) Nees): Characterization of target-site mutations and metabolic resistance-related genes in two resistant populations

Resistance of Chinese sprangletop (Leptochloa chinensis (L.) Nees) to the herbicide cyhalofop-butyl has recently become a severe problem in rice cultivation. However, the molecular mechanisms of target-site resistance (TSR) in cyhalofop-butyl-resistant L. chinensis as well as the underlying non-target-site resistance (NTSR) have not yet been well-characterized. This study aimed to investigate cyhalofop-butyl resistance mechanisms using one susceptible population (LC-S) and two resistant populations (LC-1701 and LC-1704) of L. chinensis. We analyzed two gene copies encoding the entire carboxyltransferase (CT) domain of chloroplastic acetyl-CoA carboxylase (ACCase) from each population. Two non-synonymous substitutions were detected in the resistant L. chinensis populations (Trp²⁰²⁷-Cys in the ACCase1 of LC-1701 and Leu¹⁸¹⁸-Phe in the ACCase2 of LC-1704), which were absent in LC-S. As Trp²⁰²⁷-Cys confers resistance to ACCase-inhibiting herbicides, the potential relationship between the novel Leu¹⁸¹⁸-Phe mutation and cyhalofop-butyl resistance in LC-1704 was further explored by single-nucleotide polymorphism (SNP) detection. Metabolic inhibition assays indicated that cytochrome P450 monooxygenases (P450s) and glutathione S-transferases (GSTs) contributed to cyhalofop-butyl resistance in specific resistant populations. RNA sequencing showed that the P450 genes CYP71Z18, CYP71C4, CYP71C1, CYP81Q32, and CYP76B6 and the GST genes GSTF11, GSTF1, and GSTU6 were upregulated in at least one resistant population, which indicated their putative roles in cyhalofop-butyl resistance of L. chinensis. Correlation analyses revealed that the constitutive or inducible expression patterns of CYP71C4, CYP71C1, GSTF1, and GSTU6 in L. chinensis were strongly associated with the resistant phenotype. For this reason, attention should be directed towards these genes to elucidate metabolic resistance to cyhalofop-butyl in L. chinensis. The findings of this study improve the understanding of mechanisms responsible for resistance to ACCase-inhibiting herbicides in grass-weed species at the molecular level, thus aiding in the development of weed management strategies that delay the emergence of resistance to this class of pest control products.

In Situ Growth of Tunable Gold Nanoparticles by Titania Nanotubes Templated Electrodeposition for Improving Osteogenesis through Modulating Macrophages Polarization

Driving macrophages M2 polarization has attracted growing attention for improving osteogenesis. Here, the in situ growth of tunable gold nanoparticles (AuNPs) on titania nanotubes (TiNTs) array was realized by electrodeposition, with the guidance of TiNTs. The fabricated Au layer showed excellent biocompatibility with different osteoimmune effects. Briefly, the Au deposition on 5 and 10 V anodized TiNTs surface could induce RAW264.7 cells to M2 polarization, whereas the Au deposition on 20 V anodized TiNTs surface showed M1 polarization, as indicated by various markers determination through immunofluorescence staining, qPCR, Western blot, and ELISA. Furthermore, the osteogenic differentiation of MC3T3-E1 was significantly enhanced by the macrophages conditioned medium from the Au@10VNTs surface. The in vivo tests also confirmed denser and thicker new trabecula bone formation and more M2 macrophages infiltration both on and adjacent to the Au@10VNTs implant surface. In mechanism, the cytokine array analysis of macrophages conditioned medium from the Au@10VNTs surface revealed the upregulation of pro-healing cytokines such as IL-10 and VEGF and downregulation of pro-inflammatory cytokines such as IL-1β and MCSF. In addition, the NF-κB pathway was significantly inhibited. In conclusion, the electrodeposition of a Au layer guided by TiNTs is a promising strategy for reducing postoperative inflammatory reactions and improving osseointegration through modulating macrophages polarization.

From Ashes to Riches: Microscale Phenomena Controlling Rare Earths Recovery from Coal Fly Ash

Coal fly ash is an alternative source of rare earth elements (REEs), which are critical in modern energy and electronic technologies. Current hydrometallurgical processes, however, yield variable recovery rates because of the limited understanding of the microscale phenomena controlling the extraction of REEs from fly ash. This work investigates the microscale processes that dictate the recovery of REEs from ash particulates via a spatiochemical analysis. We find that REE-bearing minerals are hosted in three modes with distinct recovery mechanisms: (i) REEs encapsulated in dense particles are recovered via the cation exchange between matrix metals (Al, Ca, Mg, etc.) and solution cations, (ii) REEs within permeable particles are recovered via intraparticle pore-scale fluid flow, and (iii) discrete and surface-bound REE-bearing minerals are recovered via direct exposure to reagents. The role of metal content and the limiting transport mechanisms are further probed for dense particles, the predominant mode of occurrence. This study highlights, for the first time, how the morphology and the elemental makeup of the ash matrix play a critical role in the accessibility of REEs, furthering the knowledge base required for the design of cost-effective and environmentally benign REEs recovery techniques.

Activating Innate Immunity by a STING Signal Amplifier for Local and Systemic Immunotherapy

The number of patients who benefit from acquired immunotherapy is limited. Stimulator of interferon genes (STING) signal activation is a significant component to enhance innate immunity, which has been used to realize broad-spectrum immunotherapy. Here, M@P@HA nanoparticles, as a STING signal amplifier, are constructed to enhance innate immunotherapy. Briefly, when M@P@HA was targeted into tumor cells, the nanoparticles decomposed with Mn²⁺ and activated the release of protoporphyrin (PpIX). Under light irradiation, the generated reactive oxygen species disrupt the cellular redox homeostasis to lead cytoplasm leakage of damaged mitochondrial double-stranded (ds) DNA, which is the initiator of the STING signal. Simultaneously, Mn²⁺ as the immunoregulator could significantly increase the activity of related protein of a STING signal, such as cyclic GMP-AMP synthase (cGAS) and STING, to further amplify the STING signal of tumor cells. Subsequently, the STING signal of tumor-associated macrophages (TAM) is also activated by capturing dsDNA and Mn²⁺ that escaped from tumor cells, so as to enhance innate immunity. It is found that, by amplifying the STING signal of tumor tissue, M@P@HA could not only activate innate immunity but also cascade to activate CD8⁺ T cell infiltration even in a tumor with low immunogenicity.

Enhanced Immunotherapy Based on Combining the Pro-phagocytosis and Anti-phagocytosis Checkpoint Blockade for Tumor Eradication

Compared to the activation of acquired immunity by the immune checkpoint blockade, the activation of innate immunity via anti-phagocytosis checkpoint blockade could significantly increase the beneficiary population of immunotherapy. However, the activation of innate immunity and the occurrence of phagocytosis are only accomplished when the interaction between pro-phagocytosis signals and anti-phagocytosis signals is realized. Herein, a versatile nanoplatform (DHMR) based on mesoporous silicon nanoparticles (MSNPs) has been constructed. Two drugs, doxorubicin, a chemotherapeutic drug which could initiate tumor cells to release pro-phagocytosis signals, and RRx-001, an immunoadjuvant that could effectively implement the anti-phagocytosis checkpoint blockade, were loaded in MSNPs. Further decoration of hyaluronic acid encapsulation endows DHMR with the function of tumor targeting and long circulation. Ultimately, the DHMR system could efficiently and accurately target tumor tissue, release the drugs in the tumor microenvironment, achieve the activation of innate immunity, and finally dramatically inhibit the growth and metastasis of tumor cells.

[Comparative study of gap balancing and measured resection technique in patients receiving staged bilateral total knee arthroplasty]

Objective: To compare the clinical outcomes of staged total knee arthroplasty (TKA) performed on both knees in the same patient using gap balancing (GB) and measured resection (MR) techniques, respectively. Methods: The clinical data of 57 patients undergoing bilateral staged TKA at the Xi'an Jiaotong University Affiliated Honghui Hospital from July 2018 to January 2020 were analyzed. Using the random number table, MR or GB technique was selected when patients underwent primary TKA, and contralateral procedure was done with another technique. The procedures were performed by one chief surgeon, and the same prosthesis was chosen for all the procedures. The two osteotomy techniques for TKA were compared in terms of surgical status, radiographic data, functional recovery and satisfaction rate. Results: Total of 57 patients, including 16 males and 41 females, were included in the study with a mean age of (68.5±4.6) years (59-79 years) at primary TKA. All patients were followed up for (29.6±4.5) months (22-39 months). The interval between the two procedures was (4.7±3.0) months (0.5-12.0 months). Postoperative drainage was less in the GB side when compared with that in the MR side [(93.6±22.2) ml vs (109.9±36.9) ml, P=0.003]. At the 1-month postoperative follow-up, the visual analogue scale (VAS) of pain was lower on the GB side (3.0±0.8) than on the MR side (3.5±1.2), the range of motion (ROM) was higher on the GB side (105.7°±8.2° vs 100.2°±7.5°), the Knee Society Score (KSS) was higher on the GB side (78.5±5.4 vs 74.2±6.3), and the Western Ontario and McMaster University (WOMAC) score was lower on the GB side (35.4±5.5 vs 38.0±6.3), there were significant differences in the up-mentioned indexes between the two groups (all P<0.05). However, the repeated-measures analysis of variance indicated that there was no significant difference in VAS score, ROM, KSS score and WOMAC score between the two techniques (all P>0.05). The satisfactory rate of GB technique was 84.2%(48/57), ant it was 86.0%(49/57) with MR technique (P=0.446). There was also no significant difference between the two techniques in terms of complications (P=0.754). Conclusion: Both the GB and MR technique result in good knee function with similar clinical outcomes in patients receiving TKA in both knees for osteoarthritis without significant deformity.

Aptamer-Gold Nanocage Composite for Photoactivated Immunotherapy

Immune checkpoint blockade (ICB) has been hailed as the hope for conquering cancer as ICB could produce a significant and durable response to tumor cells. However, the high cost and severe side effects of ICB drugs limited their application for further anticancer therapy. Here, we developed a photoactivated immunotherapy nanoplatform (Apt@AuNC). This nanoplatform could target tumor tissues via enhanced penetration retention (EPR) effect and the aptamer (Apt) could be released from Apt@AuNC in tumor sites via illumination. The immune system in the tumor area was then activated after the combination of Apt and PD-1 protein. The heat generated from AuNC was able to continue killing tumor cells. This nanoplatform could not only achieve the precise immunotherapy but also significantly facilitate the anticancer efficacy.

A cuproptosis-related lncRNA signature identified prognosis and tumour immune microenvironment in kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC) is a heterogeneous malignant tumor with high incidence, metastasis, and mortality. The imbalance of copper homeostasis can produce cytotoxicity and cause cell damage. At the same time, copper can also induce tumor cell death and inhibit tumor transformation. The latest research found that this copper-induced cell death is different from the known cell death pathway, so it is defined as cuproptosis. We included 539 KIRC samples and 72 normal tissues from the Cancer Genome Atlas (TCGA) in our study. After identifying long non-coding RNAs (lncRNAs) significantly associated with cuproptosis, we clustered 526 KIRC samples based on the prognostic lncRNAs and obtained two different patterns (Cuproptosis.C1 and C2). C1 indicated an obviously worse prognostic outcome and possessed a higher immune score and immune cell infiltration level. Moreover, a prognosis signature (CRGscore) was constructed to effectively and accurately evaluate the overall survival (OS) of KIRC patients. There were significant differences in tumor immune microenvironment (TIME) and tumor mutation burden (TMB) between CRGscore-defined groups. CRGscore also has the potential to predict medicine efficacy.

Extracellular pH sensing by plant cell-surface peptide-receptor complexes

The extracellular pH is a vital regulator of various biological processes in plants. However, how plants perceive extracellular pH remains obscure. Here, we report that plant cell-surface peptide-receptor complexes can function as extracellular pH sensors. We found that pattern-triggered immunity (PTI) dramatically alkalinizes the acidic extracellular pH in root apical meristem (RAM) region, which is essential for root meristem growth factor 1 (RGF1)-mediated RAM growth. The extracellular alkalinization progressively inhibits the acidic-dependent interaction between RGF1 and its receptors (RGFRs) through the pH sensor sulfotyrosine. Conversely, extracellular alkalinization promotes the alkaline-dependent binding of plant elicitor peptides (Peps) to its receptors (PEPRs) through the pH sensor Glu/Asp, thereby promoting immunity. A domain swap between RGFR and PEPR switches the pH dependency of RAM growth. Thus, our results reveal a mechanism of extracellular pH sensing by plant peptide-receptor complexes and provide insights into the extracellular pH-mediated regulation of growth and immunity in the RAM.

PIF4 enhances DNA binding of CDF2 to co-regulate target gene expression and promote Arabidopsis hypocotyl cell elongation

How specificity is conferred within gene regulatory networks is an important problem in biology. The basic helix-loop-helix PHYTOCHROME-INTERACTING FACTORs (PIFs) and single zinc-finger CYCLING DOF FACTORs (CDFs) mediate growth responses of Arabidopsis to light and temperature. We show that these two classes of transcription factor (TF) act cooperatively. CDF2 and PIF4 are temporally and spatially co-expressed, they interact to form a protein complex and act in the same genetic pathway to promote hypocotyl cell elongation. Furthermore, PIF4 substantially strengthens genome-wide occupancy of CDF2 at a subset of its target genes. One of these, YUCCA8, encodes an auxin biosynthesis enzyme whose transcription is increased by PIF4 and CDF2 to contribute to hypocotyl elongation. The binding sites of PIF4 and CDF2 in YUCCA8 are closely spaced, and in vitro PIF4 enhances binding of CDF2. We propose that this occurs by direct protein interaction and because PIF4 binding alters DNA conformation. Thus, we define mechanisms by which PIF and CDF TFs cooperate to achieve regulatory specificity and promote cell elongation in response to light.

Learning Improvement Heuristics for Solving Routing Problems

Recent studies in using deep learning (DL) to solve routing problems focus on construction heuristics, whose solutions are still far from optimality. Improvement heuristics have great potential to narrow this gap by iteratively refining a solution. However, classic improvement heuristics are all guided by handcrafted rules that may limit their performance. In this article, we propose a deep reinforcement learning framework to learn the improvement heuristics for routing problems. We design a self-attention-based deep architecture as the policy network to guide the selection of the next solution. We apply our method to two important routing problems, i.e., the traveling salesman problem (TSP) and the capacitated vehicle routing problem (CVRP). Experiments show that our method outperforms state-of-the-art DL-based approaches. The learned policies are more effective than the traditional handcrafted ones and can be further enhanced by simple diversifying strategies. Moreover, the policies generalize well to different problem sizes, initial solutions, and even real-world data set.

Application of artificial intelligence in the diagnosis of subepithelial lesions using endoscopic ultrasonography: a systematic review and meta-analysis

Endoscopic ultrasonography (EUS) is the most common method for diagnosing gastrointestinal subepithelial lesions (SELs); however, it usually requires histopathological confirmation using invasive methods. Artificial intelligence (AI) algorithms have made significant progress in medical imaging diagnosis. The purpose of our research was to explore the application of AI in the diagnosis of SELs using EUS and to evaluate the diagnostic performance of AI-assisted EUS. Three databases, PubMed, EMBASE, and the Cochrane Library, were comprehensively searched for relevant literature. RevMan 5.4.1 and Stata 17.0, were used to calculate and analyze the combined sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and summary receiver-operating characteristic curve (SROC). Eight studies were selected from 380 potentially relevant studies for the meta-analysis of AI-aided EUS diagnosis of SELs. The combined sensitivity, specificity, and DOR of AI-aided EUS were 0.92 (95% CI, 0.85-0.96), 0.80 (95% CI, 0.70-0.87), and 46.27 (95% CI, 19.36-110.59), respectively). The area under the curve (AUC) was 0.92 (95% CI, 0.90-0.94). The AI model in differentiating GIST from leiomyoma had a pooled AUC of 0.95, sensitivity of 0.93, specificity of 0.88, PLR of 8.04, and NLR of 0.08. The combined sensitivity, specificity, and AUC of the AI-aided EUS diagnosis in the convolutional neural network (CNN) model were 0.93, 0.81, and 0.94, respectively. AI-aided EUS diagnosis using conventional brightness mode (B-mode) EUS images had a combined sensitivity of 0.92, specificity of 0.79, and AUC of 0.92. AI-aided EUS diagnosis based on patients had a combined sensitivity, specificity, and AUC of 0.95, 0.83, and 0.96, respectively. Additionally, AI-aided EUS was superior to EUS by experts in terms of sensitivity (0.93 vs. 0.71), specificity (0.81 vs. 0.69), and AUC (0.94 vs. 0.75). In conclusion, AI-assisted EUS is a promising and reliable method for distinguishing SELs, with excellent diagnostic performance. More multicenter cohort and prospective studies are expected to be conducted to further develop AI-assisted real-time diagnostic systems and validate the superiority of AI systems. Systematic Review Registration: PROSPERO (https://www.crd.york.ac.uk/PROSPERO/), identifier CRD42022303990.

A longitudinal study of COVID-19 disclosure stigma and COVID-19 testing hesitancy in the United States

Objectives

This study examines the relationship between COVID-19 disclosure stigma and COVID-19 testing hesitancy and assesses their changes between November 2020 and 2021.

Study design

This was a longitudinal cohort.

Methods

A total of 355 participants completed four study waves between November 2020 and November 2021. Factor analyses and Cronbach's alpha assessed the factor structure and internal consistency of the COVID-19 Disclosure Stigma scale. Paired t-tests and McNemar's Chi-squared test assessed change between the study waves. Multivariable logistic regression models examined the relationship between COVID-19 disclosure stigma and testing hesitancy at four study waves.

Results

COVID-19 disclosure stigma declined significantly between the last study waves (P = 0.030). The greatest disclosure concern was reporting a positive test to close contacts (range: 19%–21%) followed by disclosure to friends (range: 10%–15%) and family (range: 4%–10%). Over the course of the four study waves, COVID-19 testing hesitancy when symptomatic ranged from 23% to 30%. Older age, female gender, and having received a COVID-19 vaccine were associated with decreased odds of testing hesitancy. Greater COVID-19 disclosure stigma and more conservative political ideology showed a consistent relationship with increased odds of COVID-19 testing hesitancy.

Conclusions

Study findings suggest that many people anticipate feeling stigmatized when disclosing positive test results, especially to close contacts. A substantial percentage of study participants reported hesitancy to be tested when symptomatic. This study identifies a need for interventions that normalize COVID-19 testing (e.g. engaging leaders with conservative followings), provide strategies for disclosing positive results, and allow anonymous notification of potential COVID-19 exposure.

Case report: Bladder preserving after maximal transurethral resection of the bladder tumor combined with chemotherapy and immunotherapy in recurrent muscle-invasive bladder cancer patients: A report of two cases

Background

Cisplatin-based neoadjuvant chemotherapy combined with radical cystectomy (RC) plus pelvic lymph node dissection (PLND) is the preferred treatment option for muscle-invasive bladder cancer (MIBC). However, some patients are unable to tolerate RC or may have postoperative complications after RC. And most patients have a strong desire for bladder-preserving treatment. There are no reports on the efficacy of maximal transurethral resection of the bladder tumor (TURBT) in combination with chemotherapy plus tislelizumab for bladder-preserving in recurrent MIBC patients.

Case presentation

We report two cases diagnosed with recurrent MIBC who achieved pathological complete response (pCR) and bladder-preserving after maximal TURBT combined with chemotherapy plus tislelizumab.

Conclusion

Postoperative immunotherapy should be considered for all patients with recurrent MIBC who are eligible for immunotherapy. In addition, high programmed death ligand-1 (PD-L1) expression, high tumor mutation burden (TMB), and TP53 mutation level can be combined to predict tislelizumab efficacy.

[Effects of in situ cross-linked graphene oxide-containing gelatin methacrylate anhydride hydrogel on wound vascularization of full-thickness skin defect in mice]

Objective: To prepare graphene oxide (GO)-containing gelatin methacrylate anhydride (GelMA) hydrogel and to investigate the effects of in situ photopolymerized GO-GelMA composite hydrogel in wound vascularization of full-thickness skin defect in mice. Methods: The experimental study method was used. The 50 μL of 0.2 mg/mL GO solution was evenly applied onto the conductive gel, and the structure and size of GO were observed under field emission scanning electron microscope after drying. Human skin fibroblasts (HSFs) were divided into 0 μg/mL GO (without GO solution, the same as below) group, 0.1 μg/mL GO group, 1.0 μg/mL GO group, 5.0 μg/mL GO group, and 10.0 μg/mL GO group treated with GO of the corresponding final mass concentration, and the absorbance value was detected using a microplate analyzer after 48 h of culture to reflect the proliferation activity of cells (n=6). HSFs and human umbilical vein vascular endothelial cells (HUVECs) were divided into 0 μg/mL GO group, 0.1 μg/mL GO group, 1.0 μg/mL GO group, and 5.0 μg/mL GO group treated with GO of the corresponding final mass concentration, and the migration rates of HSFs at 24 and 36 h after scratching (n=5) and HUVECs at 12 h after scratching (n=3) were detected by scratch test, and the level of vascular endothelial growth factor (VEGF) secreted by HSFs after 4, 6, and 8 h of culture was detected by enzyme-linked immunosorbent assay method (n=3). The prepared GO-GelMA composite hydrogels containing GO of the corresponding final mass concentration were set as 0 μg/mL GO composite hydrogel group, 0.1 μg/mL GO composite hydrogel group, 1.0 μg/mL GO composite hydrogel group, and 5.0 μg/mL GO composite hydrogel group to observe their properties before and after cross-linking, and to detect the release of GO after soaking with phosphate buffer solution for 3 and 7 d (n=3). The full-thickness skin defect wounds were made on the back of 16 6-week-old female C57BL/6 mice. The mice treated with in situ cross-linked GO-GelMA composite hydrogel containing GO of the corresponding final mass concentration were divided into 0 μg/mL GO composite hydrogel group, 0.1 μg/mL GO composite hydrogel group, 1.0 μg/mL GO composite hydrogel group, and 5.0 μg/mL GO composite hydrogel group according to the random number table, with 4 mice in each group. The general condition of wound was observed and the wound healing rate was calculated on 3, 7, and 14 d of treatment, the wound blood perfusion was detected by laser Doppler flowmetry on 3, 7, and 14 d of treatment and the mean perfusion unit (MPU) ratio was calculated, and the wound vascularization on 7 d of treatment was observed after hematoxylin-eosin staining and the vascular density was calculated (n=3). The wound tissue of mice in 0 μg/mL GO composite hydrogel group and 0.1 μg/mL GO composite hydrogel group on 7 d of treatment was collected to observe the relationship between the distribution of GO and neovascularization by hematoxylin-eosin staining (n=3) and the expression of VEGF by immunohistochemical staining. Data were statistically analyzed with analysis of variance for repeated measurement, one-way analysis of variance, and Tukey's method. Results: GO had a multilayered lamellar structure with the width of about 20 μm and the length of about 50 μm. The absorbance value of HSFs in 10.0 μg/mL GO group was significantly lower than that in 0 μg/mL GO group after 48 h of culture (q=7.64, P<0.01). At 24 h after scratching, the migration rates of HSFs were similar in the four groups (P>0.05); at 36 h after scratching, the migration rate of HSFs in 0.1 μg/mL GO group was significantly higher than that in 0 μg/mL GO group, 1.0 μg/mL GO group, and 5.0 μg/mL GO group (with q values of 7.48, 10.81, and 10.20, respectively, P<0.01). At 12 h after scratching, the migration rate of HUVECs in 0.1 μg/mL GO group was significantly higher than that in 0 μg/mL GO group, 1.0 μg/mL GO group, and 5.0 μg/mL GO group (with q values of 7.11, 8.99, and 14.92, respectively, P<0.01), and the migration rate of HUVECs in 5.0 μg/mL GO group was significantly lower than that in 0 μg/mL GO group and 1.0 μg/mL GO group (with q values of 7.81 and 5.33, respectively, P<0.05 or P<0.01 ). At 4 and 6 h of culture, the VEGF expressions of HSFs in the four groups were similar (P>0.05); at 8 h of culture, the VEGF expression of HSFs in 0.1 μg/mL GO group was significantly higher than that in 0 μg/mL GO group and 5.0 μg/mL GO group (with q values of 4.75 and 4.48, respectively, P<0.05). The GO-GelMA composite hydrogels in the four groups were all red liquid before cross-linking, which turned to light yellow gel after cross-linking, with no significant difference in fluidity. The GO in the GO-GelMA composite hydrogel of 0 μg/mL GO composite hydrogel group had no release of GO at all time points; the GO in the GO-GelMA composite hydrogels of the other 3 groups was partially released on 3 d of soaking, and all the GO was released on 7 d of soaking. From 3 to 14 d of treatment, the wounds of mice in the 4 groups were covered with hydrogel dressings, kept moist, and gradually healed. On 3, 7, and 14 d of treatment, the wound healing rates of mice in the four groups were similar (P>0.05). On 3 d of treatment, the MPU ratio of wound of mice in 0.1 μg/mL GO composite hydrogel group was significantly higher than that in 0 μg/mL GO composite hydrogel group, 1.0 μg/mL GO composite hydrogel group, and 5.0 μg/mL GO composite hydrogel group (with q values of 10.70, 11.83, and 10.65, respectively, P<0.05 or P<0.01). On 7 and 14 d of treatment, the MPU ratios of wound of mice in the four groups were similar (P>0.05). The MPU ratio of wound of mice in 0.1 μg/mL GO composite hydrogel group on 7 d of treatment was significantly lower than that on 3 d of treatment (q=14.38, P<0.05), and that on 14 d of treatment was significantly lower than that on 7 d of treatment (q=27.78, P<0.01). On 7 d of treatment, the neovascular density of wound of mice on 7 d of treatment was 120.7±4.1 per 200 times of visual field, which was significantly higher than 61.7±1.3, 77.7±10.2, and 99.0±7.9 per 200 times of visual field in 0 μg/mL GO composite hydrogel group, 1.0 μg/mL GO composite hydrogel group, and 5.0 μg/mL GO composite hydrogel group (with q values of 12.88, 7.79, and 6.70, respectively, P<0.01), and the neovascular density of wound of mice in 1.0 μg/mL GO composite hydrogel group and 5.0 μg/mL GO composite hydrogel group was significantly higher than that in 0 μg/mL GO composite hydrogel group (with q values of 5.10 and 6.19, respectively, P<0.05). On 7 d of treatment, cluster of new blood vessels in wound of mice in 0.1 μg/mL GO composite hydrogel group was significantly more than that in 0 μg/mL GO composite hydrogel group, and the new blood vessels were clustered near the GO; a large amount of VEGF was expressed in wound of mice in 0.1 μg/mL GO composite hydrogel group in the distribution area of GO and new blood vessels. Conclusions: GO with mass concentration lower than 10.0 μg/mL had no adverse effect on proliferation activity of HSFs, and GO of 0.1 μg/mL can promote the migration of HSFs and HUVECs, and can promote the secretion of VEGF in HSFs. In situ photopolymerized of GO-GelMA composite hydrogel dressing can promote the wound neovascularization of full-thickness skin defect in mice and increase wound blood perfusion in the early stage, with GO showing an enrichment effect on angiogenesis, and the mechanism may be related to the role of GO in promoting the secretion of VEGF by wound cells.

TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity

Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/Interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded NADases produce signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR sub-classes. Here we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) via ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of ADPr-ATP or di-ADPR allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta . Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity

Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded NADase activity for immune signaling. TIR-NLR signaling requires helper NLRs N requirement gene 1 (NRG1) and Activated Disease Resistance 1 (ADR1), and Enhanced Disease Susceptibility 1 (EDS1) that forms a heterodimer with each of its paralogs Phytoalexin Deficient 4 (PAD4) and Senescence-Associated Gene101 (SAG101). Here, we show that TIR-containing proteins catalyze production of 2'-(5′'-phosphoribosyl)-5′-adenosine mono-/di-phosphate (pRib-AMP/ADP) in vitro and in planta . Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP/ADP, which allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP/ADP as a missing link in TIR signaling via EDS1-PAD4 and as likely second messengers for plant immunity.

A Dof-CLE circuit controls phloem organization

The phloem consists of sieve elements (SEs) and companion cells (CCs). Here we show that Dof-class transcription factors preferentially expressed in the phloem (phloem-Dofs) are not only necessary and sufficient for SE and CC differentiation, but also induce negative regulators of phloem development, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED25 (CLE25), CLE26 and CLE45 secretory peptides. CLEs were perceived by BARELY ANY MERISTEM (BAM)-class receptors and CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) co-receptors, and post-transcriptionally decreased phloem-Dof proteins and repressed SE and CC formation. Multiple mutations in CLE-, BAM- or CIK-class genes caused ectopic formation of SEs and CCs, producing an SE/CC cluster at each phloem region. We propose that while phloem-Dofs induce phloem cell formation, they inhibit excess phloem cell formation by inducing CLEs. Normal-positioned SE and CC precursor cells appear to overcome the effect of CLEs by reinforcing the production of phloem-Dofs through a positive feedback transcriptional regulation.

TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death

2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have the NADase function necessary but insufficient to activate plant immune responses. Here, we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data show that a TIR domain adopts distinct oligomers with mutually exclusive NADase and synthetase activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana (Nb), supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7, displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in Nb. Our study identifies a family of 2',3'-cAMP/cGMP synthetases and establishes a critical role for them in plant immune responses.

Characterization of 7-Methylguanosine Identified Biochemical Recurrence and Tumor Immune Microenvironment in Prostate Cancer

Prostate cancer (PCa) has a high incidence rate, mortality rate, and biochemical recurrence (BCR) rate. 7-Methylguanosine (m7G), as one of the RNA modifications, has been considered to be actively involved in cancer-related translation disorders in recent years. Therefore, we first used The Cancer Genome Atlas (TCGA) database to identify prognosis and m7G-related long non-coding RNAs (lncRNAs). Then we randomly divided the samples into the training set and test set and then constructed and verified the m7G lnRNA prognostic model (m7Gscore) by the least absolute shrinkage and selection operator (LASSO) regression analysis. The m7Gscore has been proved to be an independent marker of BCR-free survival in patients with PCa. Furthermore, the m7Gscore was significantly correlated with the tumor immune microenvironment (TIME) and somatic mutation of PCa patients and had the potential to be an indicator for the selection of drug treatment. We also clustered TCGA cohort into three m7G-related patterns (C1, C2, and C3). The Kaplan-Meier survival analysis revealed that C1 had the best BCR-free survival and C3 had the worst. The TIME was also significantly distinct among the three m7G-related patterns. According to the TIME characteristics of the patterns, we defined C1, C2, and C3 as immune-desert phenotype, immune-inflamed phenotype, and immune-excluded phenotype, respectively.

Single-Cell Transcriptomic Atlas of Gingival Mucosa in Type 2 Diabetes

The oral gingival barrier is a constantly stimulated and dynamic environment where homeostasis is often disrupted, resulting in inflammatory periodontal diseases. Type 2 diabetes (T2D) has been reported to be associated with gingival barrier dysfunction, but the effect and underlying mechanism are inconclusive. Herein, we performed single-cell RNA sequencing (scRNA-seq) of gingiva from leptin receptor-deficient mice (db/db) to examine the gingival heterogeneity in the context of T2D. Periodontal health of control mice is characterized by populations of Krt14⁺-expressing epithelial cells and Col1a1⁺-fibroblasts mediating immune homeostasis primarily through the enrichment of innate lymphoid cells. The db/db gingiva exhibited decreased epithelial/stromal ratio and dysfunctional barrier. We further observed stromal, particularly fibroblast immune hyperresponsiveness, linked to the recruitment of myeloid-derived cells at the db/db gingiva. Both scRNA-seq and histological analysis suggested the inflammatory signaling between fibroblasts and neutrophils as a potential driver of diabetes-induced periodontal damage. Notably, the "immune-like" stromal cells were wired toward the induction of gingival γδ T hyperresponsiveness in db/db mice. Our work reveals that the "immune-like" fibroblasts with transcriptional diversity are involved in the innate immune homeostasis at the diabetic gingiva. It highlights a potentially significant role of these cell types in its pathogenesis.

Bacteria-Elicited Specific Thrombosis Utilizing Acid-Induced Cytolysin A Expression to Enable Potent Tumor Therapy

Given the special microenvironment of solid tumors, live microorganisms have emerged as drug delivery vehicles and therapeutic agents. Here, an acid-induced therapeutic platform is constructed using attenuated Escherichia coli to express the cytolysin A protein. The bacteria can target and colonize tumor tissues without causing notable host toxicity. Bacterial infection can disrupt blood vessels and trigger thrombosis in tumor tissues, resulting in the cut-off of nutrient supply to tumor cells and the arrest of tumor growth. The expression of cytolysin A induced by the acidic tumor microenvironment further strengthens thrombosis and provides a complementary therapeutic option due to its pore-forming function. In a xenograft mouse tumor model, this strategy reduces tumor proliferation by 79% and significantly prevents tumor metastasis, thus paving a new avenue for bacteria-based tumor therapy.