Skin wound healing is a multi-stage and complex process frequently compromised by bacterial infection, a major global health concern exacerbated by the limitations of conventional treatments, such as invasive procedures and antibiotic resistance driven by systemic drug use. This has spurred the exploration of alternative strategies, with two-dimensional nanomaterials (2DNMs) emerging as a highly promising platform. This review comprehensively analyzes recent advancements in various 2DNMs, including graphene and its derivatives, transition metal dichalcogenides (TMDs), MXenes, carbon nitrides (CN), metal-organic frameworks (MOFs), and covalent organic frameworks (COFs), for wound management. We focus on their exceptional properties, such as high specific surface area, mechanical flexibility, and tunable surface chemistry, which underpin capabilities in drug loading, targeted delivery, reactive oxygen species (ROS) scavenging, and immunomodulation. The discussion critically assesses integration strategies like functionalized traditional dressings, composite hydrogels, and microneedles, which leverage synergistic antibacterial mechanisms (e.g., physical disruption, chemical, and photothermal interactions) to modulate the wound microenvironment and promote healing. Despite this significant potential, key challenges persist, including the need to fully elucidate multi-mechanistic synergies, ensure the long-term biosafety of composite systems, and overcome barriers to the scalable manufacturing of these systems. By systematically evaluating material classifications, functional properties, and pathophysiological interactions from an interdisciplinary perspective, this review identifies these critical bottlenecks and proposes forward-looking strategies to guide the development of next-generation, clinically translatable wound healing platforms.

The enrichment of hydrophilic nanomaterials on polymer membrane surfaces was crucial for enhancing both antifouling capability and separation efficiency. This study presented a facile strategy to drive carbon quantum dots (CQDs) directionally to the membrane surface via an electrostatic enhanced surface segregation strategy. Specifically, CQDs modified with positively charged polyethyleneimine (PEI) were added into the polyethersulfone (PES) casting solution, while negatively charged poly(sodium 4-styrenesulfonate) (PSS) was dissolved in coagulation bath. During the non-solvent induced phase separation (NIPS) process, the strong electrostatic and hydrophilic interaction between PEI@CQDs and PSS propelled PEI@CQDs to migrate and enrich towards PES membrane surface, and a composite antifouling layer was constructed in situ. The optimal membrane (MPC-P) achieved a water flux of 127.4 L•m−2•h−1, with exceptional rejection ratios of 99.35% for bovine serum albumin (BSA) and 98.80% for humic acid (HA). Accordingly, after five filtration cycles, the water flux recovery ratios (FRR) for BSA and HA remained high at 90.86% and 91.35%, while the total permeance decline ratios (DRt) were 11.01% and 6.85%, respectively. Meanwhile, it exhibited a remarkably high inhibition rate of 84.21% against S. aureus, which was approximately 5.7 times higher than that of the pure PES membrane. During a continuous filtration for model foulants lasting 400 min, the membrane exhibited outstanding sustained antifouling and permeation stability. The underlying interaction mechanisms between the pollutants and the membrane surface were successfully revealed by molecular dynamics (MD) simulations. This research offered a robust paradigm for developing high-performance antifouling membranes and promoting their practical application in water treatment.

Potato powdery scab is a soilborne disease caused by the fungus Spongospora subterranea, which belongs to the class of Plasmodiophorids and cannot be cultured. In this study, a species-specific genomic DNA fragment of Spongospora subterranea (2494 bp) was identified using comparative genomics methods. Polymerase chain reaction (PCR) and recombinase-aided amplification-lateral flow dipstick (RAA-LFD) base assays were then developed for the specific detection of this pathogen. Both detection methods effectively distinguished Spongospora subterranea from other common potato pathogens, and Polymyxa graminis and Plasmodiophora brassicae, the primary pathogens of the intercropping cruciferous and gramineous plants. The detection sensitivity of the three PCR primer pairs (SsF1/R1, SsF2/R2, and SsF3/R3) under the optimal conditions (60.5 °C; 40 cycles in a 20 μL reaction system) were 10.8 copies, 10.3 copies, and 10.6 copies, respectively. Using amplification durations of 10, 15, 20, and 25 min, the detection limits of the RAA primer and probe set (RS1F1/RI and RS1-Probe) in a 25 μL optimal reaction system were 2.51 × 103, 2.51 × 102, 2.51 × 102, and 2.51 × 101 copies, respectively. The PCR assays positively detected Spongospora subterranea DNA in all diseased tubers (41/41) and most samples of infested soil (27, 28, and 25 out of 31, corresponding to SsF1/R1, SsF2/R2, and SsF3/R3), whereas the RAA-LFD assay positively detected the pathogen in all tuber and soil samples when amplified at 37 °C for 20 min. The RAA-LFD outperformed PCR specifically in soil samples, mentioning performance metrics. The RAA-LFD isothermal detection assay developed herein provides a rapid, specific, and field-deployable method for diagnosing potato powdery scab in tubers and soil.

Linking spatial transcriptomic data to clinically relevant phenotypes is essential for advancing spatially informed precision oncology. Here, we present SpaPheno, an interpretable machine learning framework that integrates spatial transcriptomics with clinically annotated bulk RNA-seq to identify spatially resolved biomarkers predictive of patient outcomes, including survival, tumor stage, and immunotherapy response. SpaPheno provides multi-scale interpretability from tissue regions to cell types and individual spatial spots, enabling clear biological insights from complex spatial data. We validate SpaPheno through extensive simulations and applications to multiple cancer cohorts—primary liver cancer, clear cell renal cell carcinoma, breast cancer, and melanoma—demonstrating robust predictive performance alongside biologically meaningful spatial patterns. SpaPheno offers a generalizable strategy to translate spatial omics data into clinically actionable knowledge, facilitating precision oncology informed by tumor spatial architecture. SpaPheno is available at https://github.com/Duan-Lab1/SpaPheno.

Bacterial blight (caused by Xanthomonas oryzae pv. oryzae, Xoo) reduces rice yields by 10-50 %, threatening global food security. Current control relies on resistant cultivars and chemical pesticides, but pathogen evolution and environmental risks limit efficacy. This study demonstrates that g-C₃N₄-a stable carbon-based nanomaterial-inhibits Xoo via photocatalysis. Optimal inhibition (1.5 mg/mL) suppressed strains Pxo99A and Y8, disrupting membrane integrity, changing ROS/ATP levels, causing DNA and Protein damage, ultimately, alterations in bacterial morphology and structure. Moreover, by disrupting biofilm formation and flagellar motility, g-C₃N₄ interfered with the ability of Xoo to colonize and infect the host plant. Transcriptomics revealed g-C₃N₄ impaired bacterial function by suppressing the type III secretion system (T3SS), virulence genes, ATP synthesis, and RNA degradation, while triggering a stress response marked by upregulation of flagellar genes. Plants applications showed dual foliar sprays (24 h pre-and post-inoculation) reduced disease severity by 62.7 %. In plants, g-C₃N₄ induced disease resistance through enhanced antioxidant enzymes, PAL activity, stomatal closure. Additionally, early regulation of genes associated with the salicylic acid(SA) and Jasmonic acid (JA) pathways and ubiquitination system was accompanied by systemic acquired resistance (SAR), with no adverse effects on rice growth or photosynthesis observed throughout the process. Together, these results illustrate a two-tiered mechanism: g-C₃N₄ not only directly disrupts bacterial virulence and viability but also primes rice immunity through enzymatic, stomatal, and genetic pathways, offering a multifaceted strategy for disease control.

The emergence of spatial transcriptomics (ST) technology offers unprecedented opportunities to elucidate the complexity and heterogeneity of the tumor microenvironment (TME). However, quantitatively linking spatially resolved features with clinical phenotypes remains challenging due to the scarcity of clinical annotations of spatial sequencing samples. Herein, we introduce SpaLinker, an innovative integrated framework that utilizes ST data to decipher spatially resolved TMEs at molecular, cellular, and tissue structure levels. Specifically, it assesses the prognostic significance of spatially defined features by integrating well-accumulated bulk RNA sequencing (RNA-seq) data, using a phenotype-driven computational framework. Applying SpaLinker to diverse tumor ST datasets demonstrated its utility and effectiveness in recognizing spatial architectures, including tertiary lymphoid structures and tumor-normal interfaces, and in establishing links to distinct clinical outcomes. Overall, this study presents a valuable and comprehensive pan-cancer analytical platform to de novo identify phenotype-associated spatial TME features, significantly enhancing the clinical utility of spatial sequencing technology.

Biodegradable mulching films are promoted as alternatives to traditional polyethylene films, but their environmental impacts remain controversial. This study investigates how biodegradable films affect microplastic pollution of soil, fungal community structure, and ecological network stability. We conducted a maize field experiment comparing conventional polyethylene (CF, PE) and biodegradable (BF, PLA + PBAT) film residues. We used scanning electron microscopy and high-throughput sequencing of fungal ITS genes. We assessed soil properties, microplastic release, fungal communities, and network stability through co-occurrence analysis. BF degraded rapidly, releasing microplastic concentrations much higher than CF. BF increased soil carbon and nitrogen and substantially enhanced maize biomass. However, it significantly reduced soil pH and decreased key functional fungi (saprotrophs and symbionts) abundance. The fungal ecological network complexity and stability declined significantly. Correlation analysis revealed positive associations between saprotrophic and symbiotic fungi abundance and network stability. In contrast, CF reduced some nutrient levels but improved fungal network complexity and stability. This study reveals that biodegradable films create an “ecological trap.” Short-term nutrient benefits mask systematic damage to soil microbial network stability. Our findings challenge the notion that “biodegradable equals environmentally friendly.” Environmental assessments of agricultural materials must extend beyond degradability to include microplastic release, functional microbial responses, and ecological network stability.

BACKGROUND:Spatial transcriptomics preserves spatial context of tissues while capturing gene expression. As the technology advances, researchers are increasingly generating data from multiple tissue sections, creating a growing demand for multi-slice integration methods. These methods aim to generate spatially aware embeddings that jointly capture spatial and transcriptomic information, preserving biological signals while mitigating technical artifacts such as batch effects. However, the reliability of these methods varies, and the growing diversity of technologies makes integration even more challenging. This underscores the need for a comprehensive benchmark to evaluate their performance, which is still lacking. RESULTS:To systematically evaluate the performance of multi-slice integration methods, we propose a comprehensive benchmarking framework covering four key tasks that form an upstream-to-downstream pipeline: multi-slice integration, spatial clustering, spatial alignment, slice representation. For each task, we perform detailed analyses of the methods and provide actionable recommendations. Our results reveal substantial data-dependent variation in performance across tasks. We further investigate the relationships between upstream and downstream tasks, showing that downstream performance often depends on upstream quality. CONCLUSIONS:Our study provides a comprehensive benchmark of 12 multi-slice integration methods across four key tasks using 19 diverse datasets. Our results reveal that method performance is highly dependent on application context, dataset size, and technology. We also identified strong interdependencies between upstream and downstream tasks, highlighting the importance of robust early-stage analysis.

The escalating demand for lithium necessitates the development of advanced separation technologies to efficiently extract and recover lithium from saline lake brines determined by high Mg2+/Li+ ratios. Herein, we report a dual interfacial polymerization strategy incorporating benzo-15-crown-5 (B15C5) ether to fabricate nanofiltration membranes with hierarchically structured Li+ transport channels. Systematic optimization of the secondary interfacial polymerization (SIP) parameters synergistically combined with B15C5 functionalization endowed the membrane with exceptional Mg2+ rejection (> 99 %) while maintaining stable water permeance (8.2 L·m⁻2·h⁻1·bar⁻1). The membrane achieved ultra-high Mg2+/Li+ separation factors (SLi, Mg) of 57.2, outperforming most of the previously reported membranes. Practical validation using actual saline lake brine (Qarhan Salt Lake, China; initial Mg2+/Li+ ratio is 928.6) demonstrated a two-stage separation efficiency that reduced the Mg2+/Li+ ratio to 1.9 with 488.7-fold lithium enrichment. Density functional theory (DFT) calculations and static diffusion tests further revealed that the B15C5-modified membrane exhibited a strong binding affinity for Li+ and significantly enhanced Li+ permeation ability. Additionally, X-ray photoelectron spectroscopy (XPS) depth etching and Time-of-flight secondary ion mass spectrometry (TOF-SIMS) resolved the spatially graded bilayer architecture of the membrane. These findings established a molecular-scale design paradigm for ion-selective membranes, addressing critical challenges in energy-efficient lithium extraction from high Mg2+/Li+ ratio brines.

With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection, reference-based annotation, and multiple slice clustering at both single-cell and spot resolutions. We demonstrate SpaDo’s effectiveness with over 40 multi-slice spatial transcriptome datasets from 7 sequencing platforms. Our findings highlight SpaDo’s potential to reveal novel biological insights in multi-slice spatial transcriptomes.

The application of antibiotics has advanced modern medicine significantly. However, the abuse and discharge of antibiotics have led to substantial antibiotic residues in water, posing great harm to natural organisms and humans. To address the problem of antibiotic degradation, this study developed a novel catalytic membrane by depositing Co catalysts onto MXene nanosheets and fabricating the polyethersulfone composite (Co@MXene/PES) using vacuum-assisted self-assembly. The dual role of MXene as both a carrier for Co atoms and an enhancer of interlayer spacing led to improved flux and catalytic degradation capabilities of the membrane. Experimental results confirmed that the Co@MXene/PES membrane effectively degraded antibiotics through peroxymonosulfate activation, achieving up to 95.51% degradation at a cobalt concentration of 0.01 mg/mL. The membrane demonstrated excellent antibacterial properties, minimal flux loss after repeated use, and robust anti-fouling performance, making it a promising solution for efficient antibiotic removal and stable water treatment.

Cytochrome P450s represent one of the largest protein families across all domains of life. In plants, biotic stress can regulate the expression of some P450 genes. However, the CYPome (cytochrome P450 complement) in Solanum tuberosum and its response to Phytophthora infestans infection remains unrevealed. In this study, 488 P450 genes were identified from potato genome, which can be divided into 41 families and 57 subfamilies. Responding to the infection of P. infestans, 375 potato P450 genes were expressed in late blight resistant or susceptible cultivars. A total of 14 P450 genes were identified as resistant related candidates, and 81 P450 genes were identified as late blight responsive candidates. Several phytohormone biosynthesis, brassinosteroid biosynthesis, and phenylpropanoid biosynthesis involved P450 genes were differentially expressed during the potato-pathogen interactions. This study firstly reported the CYPome in S. tuberosum, and characterized the expression patterns of these P450 genes during the infection of P. infestans.

BACKGROUND:The precise characterization of individual tumors and immune microenvironments using transcriptome sequencing has provided a great opportunity for successful personalized cancer treatment. However, the cancer treatment response is often characterized by in vitro assays or bulk transcriptomes that neglect the heterogeneity of malignant tumors in vivo and the immune microenvironment, motivating the need to use single-cell transcriptomes for personalized cancer treatment. METHODS:Here, we present comboSC, a computational proof-of-concept study to explore the feasibility of personalized cancer combination therapy optimization using single-cell transcriptomes. ComboSC provides a workable solution to stratify individual patient samples based on quantitative evaluation of their personalized immune microenvironment with single-cell RNA sequencing and maximize the translational potential of in vitro cellular response to unify the identification of synergistic drug/small molecule combinations or small molecules that can be paired with immune checkpoint inhibitors to boost immunotherapy from a large collection of small molecules and drugs, and finally prioritize them for personalized clinical use based on bipartition graph optimization. RESULTS:We apply comboSC to publicly available 119 single-cell transcriptome data from a comprehensive set of 119 tumor samples from 15 cancer types and validate the predicted drug combination with literature evidence, mining clinical trial data, perturbation of patient-derived cell line data, and finally in-vivo samples. CONCLUSIONS:Overall, comboSC provides a feasible and one-stop computational prototype and a proof-of-concept study to predict potential drug combinations for further experimental validation and clinical usage using the single-cell transcriptome, which will facilitate and accelerate personalized tumor treatment by reducing screening time from a large drug combination space and saving valuable treatment time for individual patients. A user-friendly web server of comboSC for both clinical and research users is available at www.combosc.top . The source code is also available on GitHub at https://github.com/bm2-lab/comboSC .

Novel MXene-based two-dimensional (2D) membranes are widely used for water purification due to their highly controllable structure and antibacterial properties. However, in the process of membrane separation, the problems of membrane fouling, especially biological fouling, limits the further application of MXene-based membranes. In this study, in order to improve the antibacterial and separation properties of membranes, three kinds of MXene-based 2D–2D composite membranes (M2~M4) were prepared using polyethersulfone (PES) as the substrate, which were GO@MXene, O-g-C3N4@MXene and BiOCl@MXene composite membranes respectively. The results showed that the antibacterial activity of M2~M4 against Escherichia coli and Staphylococcus aureus was further improved, especially the antibacterial ratio of M4 against Escherichia coli and Staphylococcus aureus was up to 50% and 82.4%, respectively. By comparing the surface morphology of MXene membrane and modified membrane treated bacteria through scanning electron microscopy (SEM), it was found that the cell density on modified membrane was significantly lower than that of pure MXene membrane.

Due to their unique microstructure and physical and chemical properties, two-dimensional（2D）materials have gradually become a research hotspot in the cross-fields of environment, biology and energy. In this experiment, MoS 2 powder is synthesized by a hydrothermal method with thiourea and ammonium paramolybdate as raw materials, and Mo S2 nanosheets are obtained by liquid phase ultrasonic stripping. Further, the precursor solution composed of MoS 2 and MXene 2D materials is filtered on PES substrate by vacuum filtration, and a novel 2D MXene@MoS 2 composite membrane is constructed. The characterizations of XRD and TEM prove the successful preparation of MoS 2 nanosheets, and the surface and cross-sectional morphologies of the composite membranes are observed by SEM. The experimental results indicate that the addition of MoS 2 nanosheets can improve the separation performance of membrane significantly. Compared with pure MXene membrane, the rejection ratios of novel composite membrane for Congo red and Rhodamine B in water increases from 86.7%～88.4% to 98%～98.8%, respectively. In addition, MXene@MoS 2 composite membrane also shows a good antibacterial activity on E.coli and S. aureus in water. The development of new membrane is expected to solve the key problem that the membrane is easy to be polluted by bacteria in its practical application.

Membrane separation has been widely used for water treatment, but the accumulation of pollutants on mem-brane surface is still inevitable during practical applications. Photocatalytic technology is an effective and environmentally friendly method for the degradation of pollutants. Here, we reported a simple method to prepare novel two-dimensional (2D) Bi2O2CO3@MXene photocatalytic composite membranes as well as their multi-functional abilities for water treatment. The experimental results exhibited that the composite membrane has ultrahigh water flux after incorporation of N-doped Bi2O2CO3 nanoparticles (815.3 L.m(-2).h(-1)). In addition, the rejection ratio for three different types of oil/water emulsions was all over 99 %, and excellent dyes removals were obtained by membrane separation, adsorption and photodegradation abilities, which were approximately 99.9 % (Congo red), 98 % (Trypan blue) and 98.4 % (Rhodamine B), respectively. Most importantly, the com-posite membrane maintained a stable permeability and selectivity after five consecutive cycles with visible light irradiation. Density functional theory (DFT) calculation and Finite Element Method (FEM) analysis were carried out to reveal the mechanisms for the improvement of photocatalytic activity and membrane permeability, respectively.

Membrane separation technology has been widely used in the field of industrial dye wastewater treatment. In this work, a series of new composite membranes were fabricated by modifying MXene two-dimensional (2D) materials with polydopamine (PDA) from the mussel biological inspiration via vacuum filtration on cellulose acetate (CA) support. Scanning electron microscope (SEM), transmission electron microscope (TEM), atomic force microscope (AFM), X-ray diffraction technique (XRD), energy spectrum analysis (EDS), have been utilized to evident the successful synthesis of MXene and the modification of MXene by PDA. The resultant PDA@MXene/CA membrane was found to have good hydrophilicity, and the pure water flux reached up to 271.2 L.m(-2).h(-1), which was 277% more than the unmodified membrane. An improvement in dye separation capability has also been noticed using PDA@MXene/CA membranes. The rejection ratio of direct red 28 reached 88.9%, and that of direct black 38 reached 88.6%. Moreover, a strong anti-fouling characteristic with good antibacterial ability of resultant membrane was demonstrated. Therefore, the new modified membrane showed the potential for good application prospects in the field of small molecule separation.

The oily wastewater is one of the major waste streams generated due to industrialization. The membrane technology has prominent advantages in the field of oily wastewater treatment. In present investigation, halloysite nanotubes (Hal) and polydopamine (PDA) were utilized to synergistically modify MXene followed by the fabrication of a series of Hal@MXene-PDA two-dimensional (2D) composite membranes by vacuum filtration. Observing the morphology of the membrane and exploring the change in interlayer space by scanning electron microscope (SEM), atomic force microscope (AFM) and X-ray diffraction (XRD), it was confirmed that, the composite membrane was successfully modified. The results revealed that, the Hal@MXene-PDA composite membrane exhibits higher hydrophilicity compared to the virgin membrane. The pure water flux using the composite membrane was found to be 5036.2 L.m(-2).h-(1).bar(-1), and the rejections of petroleum ether and lubricating oil were evaluated as 99.8%. The modified membrane(M6) also shows good anti-fouling ability in the anti-fouling cycle test and hence can be considered as a potential candidate for oil-water separation.

Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.

Cordycepin is a major bioactive compound found in Cordyceps militaris (C. militaris) that exhibits a broad spectrum of biological activities. Hence, it is potentially a bioactive ingredient of pharmaceutical and cosmetic products. However, overexploitation and low productivity of natural C. militaris is a barrier to commercialization, which leads to insufficient supply to meet its existing market demands. In this study, a preliminary study of distinct concentrations of salt treatments toward C. militaris was conducted. Although the growth of C. militaris was inhibited by different salt treatments, the cordycepin production increased significantly accompanied by the increment of salt concentration. Among them, the content of cordycepin in the 7% salt-treated group was five-fold higher than that of the control group. Further transcriptome analysis of samples with four salt concentrations, coupled with Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, several differentially expressed genes (DEGs) were found. Finally, dynamic changes of the expression patterns of four genes involved in the cordycepin biosynthesis pathway were observed by the quantitative real-time PCR. Taken together, our study provides a global transcriptome characterization of the salt treatment adaptation process in C. militaris and facilitates the construction of industrial strains with a high cordycepin production and salt tolerance.