Advanced biotechnology最新文献

{"title":"The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.","authors":"Dongdong Wei, Chengguang Xing, Shenzheng Zeng, Dongwei Hou, Zhixuan Deng, Xinghai Long, Hao Wang, Renjun Zhou, Lingfei Yu, Nana Shu, Zhonghu Tao, Xi Zhou, Shaoping Weng, Jianguo He, Zhijian Huang","doi":"10.1007/s44307-026-00106-x","DOIUrl":"https://doi.org/10.1007/s44307-026-00106-x","url":null,"abstract":"<p><p>Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13121677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147794229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EYA4 promotes cellular senescence by enhancing P21 transcription through interaction with SIX2.","authors":"Xiaolin Li, Pingsu Mao, Dandan Chen, Lin Li, Hehua Fang, Junjiu Huang, Haiying Liu","doi":"10.1007/s44307-026-00109-8","DOIUrl":"10.1007/s44307-026-00109-8","url":null,"abstract":"<p><p>During the aging process, the expression levels of numerous genes undergo significant changes, some of which in turn regulate the progression of aging. In this study, we identified the expression of EYA4 is upregulated during aging and demonstrated its critical role in modulating cellular senescence. Knockdown of EYA4 significantly delays both replicative and stress-induced cellular senescence. Mechanistic investigations showed that EYA4 interacts with the transcription factor SIX2 to promote the expression of p21, a key molecule in the senescence-signaling pathway, which accelerates cellular senescence. Interestingly, EYA4 possesses both transcriptional activation and phosphatase activities, yet experiments using phosphatase-deficient mutants revealed that its ability to enhance p21 expression is independent of its phosphatase activity. Further analysis demonstrated that the EYA4-SIX2-mediated regulation of p21 expression is p53-dependent, as the absence of p53 abolished this regulatory effect. In conclusion, our findings uncover a novel role of the EYA4-SIX2 complex in promoting cellular senescence through the transcriptional activation of p21. Targeting EYA4 may represent a promising strategy for delaying the aging process.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147701471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The potential of metabolic engineering for sustainable phytosterol production.","authors":"Runmeng Hu, Xueni Di, Guangli Li, Hubert Schaller, Andréa Hemmerlin, Pan Liao","doi":"10.1007/s44307-026-00108-9","DOIUrl":"10.1007/s44307-026-00108-9","url":null,"abstract":"<p><p>Phytosterols, essential components pivotal to plant membrane stability and celebrated for their extensive pharmacological benefits, have garnered considerable attention across industries, including food fortification, nutraceuticals, and pharmaceuticals. The escalating demand for phytosterols, fueled by their myriad health advantages, underscores the urgent need for more efficient synthesis methodologies. Among these, metabolic engineering stands out as a promising approach due to its biologically driven process, which operates under stable conditions, thereby enhancing reaction specificity and drastically reducing the production of undesirable by-products. This review consolidates the latest research endeavors focused on enhancing phytosterol accumulation, providing a comprehensive analysis of strategies including gene manipulation, enzyme engineering, metabolic engineering, and the utilization of diverse host organisms such as bacteria, algae, and yeast. We explore recent advancements in phytosterol biosynthesis and engineering, providing a comprehensive overview of the field's current state and examining promising methodologies for future research and applications.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13083469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Duckweeds: from fundamental biology to a sustainable plant chassis for biotechnology.","authors":"Gui-Min Yin, Lin Yang, Sha Li, Yan Zhang","doi":"10.1007/s44307-026-00110-1","DOIUrl":"10.1007/s44307-026-00110-1","url":null,"abstract":"<p><p>Duckweeds (Lemnaceae), the smallest and fastest-growing flowering plants, have emerged as a transformative platform for sustainable biotechnology. This review synthesizes recent advances that underpin their potential as a next-generation plant chassis. We discuss duckweed's unique biology, characterized by reductive evolution, extreme phenotypic plasticity, and a simplified epigenome that favors transgene expression. The decoding of its minimalist genome, along with the establishment of efficient genetic tools including optimized transformation and CRISPR-Cas9 editing, enables precise genetic and metabolic engineering. While traditional uses in phytoremediation and animal feed validate its utility, duckweed's rapid growth in contained, soil-free culture and its edibility offer distinct advantages for molecular farming over established systems like tobacco. We highlight progress in engineering duckweeds to produce vaccines, therapeutic proteins, and high-value metabolites. To transition from proof-of-concept to an industrial workhorse, future efforts must focus on integrated omics databases, universal genetic toolkits, and scalable cultivation. Converging fundamental insights with synthetic biology principles positions duckweed as a versatile and powerful chassis for the bioeconomy.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147701490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering a robust IsPETase for energy-efficient PET depolymerization in natural seawater at ambient temperatures.","authors":"Xin Huang, Qian Jia, Guang Li, Xiangpeng Yang, Shujing Xu, Jianzhong Liu, Wenjun Li, Yuhuan Liu, Wei Xie, Lichuang Cao","doi":"10.1007/s44307-026-00104-z","DOIUrl":"10.1007/s44307-026-00104-z","url":null,"abstract":"<p><p>Enzymatic depolymerization of polyethylene terephthalate (PET), the world's most widely used polyester, in seawater at ambient temperature offers a promising and energy-efficient route for freshwater-free plastic recycling. While a number of PET hydrolases have been reported in recent years, their potential under saline conditions remains largely unexplored. Here, we screened eight enzymes in artificial seawater at 30 °C and engineered the most active one, IsPETase, using a semi-rational strategy focused on rigidifying flexible sites. The resulting variant M8 showed simultaneous enhancementsin thermostability (ΔT_m = + 27.3 °C), activity (1.14-fold increase) and soluble expression yield (14.3-fold increase). The overall depolymerization efficiency of M8 surpassed that of the thermostable benchmark enzymes DuraPETase and LCC-ICCG by 32.2- and 10.4-fold, respectively. Notably, M8 achieved continuous and efficient depolymerization of 15% (w/v) PET powder in natural seawater at 37 °C, yielding monomers at a rate of 15.4 mM/day, a concentration sufficient to support downstream bacterial assimilation. This work provides an efficient enzymatic platform and paves the way for fully integrated, seawater-based plastic bioconversion processes.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13083688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EVmiRED: a curated database of miRNA editing landscape in extracellular vesicles.","authors":"KaHei Kou, Lanqi Wen, Luo Yang, Zhoufeng Gao, Bei Jin, Jingxuan Pan, Rui Zhang","doi":"10.1007/s44307-026-00107-w","DOIUrl":"10.1007/s44307-026-00107-w","url":null,"abstract":"<p><p>Metastasis accounts for the vast majority of tumor-related mortality. Certain populations of tumor cells exhibit organotropism by preferentially colonizing specific distant organs. The organ specificity of metastatic cells is determined by unique interactions between tumor cells and the microenvironment in target organs. Tumor extracellular vesicles (EVs), particularly exosomes, delivering tumor cell components including nucleic acid complexes, proteins, and lipids, play a crucial role in mediating intercellular communication between tumor cells and their microenvironment. ADAR-mediated microRNA (miRNA) editing has emerged as a crucial mechanism influencing miRNA stability, processing, and target specificity. Although EVs are increasingly recognized as important vehicles of intercellular signaling and promising biomarkers for cancer, the landscape of miRNA editing within EVs remains largely unexplored. Here, we present EVmiRED (Extracellular Vesicle miRNA Editing Database), a resource that integrates miRNA expression and editing profiles from tumor-derived EVs. The current release includes data from 683 samples across 12 tumor types and cell lines. EVmiRED provides detailed information on miRNA abundance, editing frequency, and the predicted functional impact of specific editing events. EVmiRED enables users to query individual miRNAs, visualize expression and editing patterns, and access raw datasets for customized analyses. Together, EVmiRED offers a valuable platform to advance our understanding of RNA editing-mediated regulation in intercellular communication, tumor progression, and cancer immunology.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13065891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147640816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning-driving optimization and spatial assembly of a cell-free system for high-yield liquiritigenin production.","authors":"Fei Liu, Si-Bo Zhao, Yan-Hua Liu, Jun-Feng Li, Nuo-Qiao Lin, Meihereayi Mutailifu, Pei Xu, Jian-Zhong Liu","doi":"10.1007/s44307-026-00103-0","DOIUrl":"10.1007/s44307-026-00103-0","url":null,"abstract":"<p><p>Liquiritigenin is a medicinal flavonoid whose production is constrained by inefficient plant extraction and complex chemical synthesis. To overcome this, we developed a modular cell-free multi-enzyme system for its efficient biosynthesis from tyrosine, integrating spatial enzyme assembly with machine learning-guided optimization. Using a combined cell-free metabolic engineering (CFME) and cell-free protein synthesis-driven metabolic engineering (CFPS-ME) approach, we screened and optimized five key pathway enzymes to establish a one-pot reaction. The optimal enzyme combination (phenylalanine ammonia-lyase from Zea mays, 4-coumarate-coenzyme A ligase 4 from Arabidopsis thaliana, chalcone synthase from Glycine max, chalcone reductase from Medicago sativa, chalcone flavonone isomerase from Zea mays) was identified through systematic screening and ratio optimization. After Plackett-Burman and steepest-ascent experiments, three rounds of iterative machine learning fine-tuned key parameters, including enzyme ratios and cofactor concentrations, yielding 155.32 ± 14.39 mg/L. Spatial enzyme assembly was further enhanced via covalent peptide tags and scaffold proteins (γPFD-SpyCatcher) under CFME. Combining CFPS-ME with scaffold-assisted co-immobilization significantly boosted production, reaching a final titer of 439.42 ± 19.53 mg/L. This study demonstrates that machine learning-driven optimization and spatial assembly of multienzyme complexes is a powerful approach for cell-free biosynthesis.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147535287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural pharmacology of Chinese medicine: technological breakthroughs in decoding multi-target synergy and precision mechanisms.","authors":"Caiyan Wang, Yanling Li, Lin Zhuo, Songzhu Xu, Mengyao Wang, Zhongqiu Liu","doi":"10.1007/s44307-026-00095-x","DOIUrl":"10.1007/s44307-026-00095-x","url":null,"abstract":"<p><p>Traditional Chinese Medicine (TCM) offers valuable therapeutic strategies for chronic and infectious diseases, yet the inherent complexity of its multi-component, multi-target formulations and synergistic effects presents substantial challenges to pharmacological mechanistic understanding. Structural pharmacology of Chinese Medicine has emerged as a transformative discipline, integrating structural biology, computational chemistry, and pharmacology to elucidate the precise mechanisms underlying TCM efficacy. This review synthesizes technological advancements that enable the characterization of synergistic mechanisms and dynamic molecular interactions in TCM. Key advancements include high-resolution structural techniques such as X-ray crystallography, cryo-electron microscopy, sophisticated computational approaches such as AI-driven predictive modeling, and advanced analytical platforms. We critically examine persistent technical hurdles, such as capturing transient binding events and modeling complex multi-component system dynamics. Finally, we outline future research trajectories to establish a predictive and adaptable scientific foundation for TCM modernization, facilitating its evidence-based global integration and application in precision medicine.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12988076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147461350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acriflavine-empowered IR780-PTX albumin nanoparticles for reinforced synergistic photochemotherapy.","authors":"Dazhao Li, Tong Wang, Hongchao Liu, Yao Yao, Taiyuan Lu, Rong Wang, Xinyi Jiang, Xiaoyang Zhang, Minjie Sun, Ya Peng, Yilin Yang, Naiyuan Shao, Dawei Ding, Feng Zhi","doi":"10.1007/s44307-026-00097-9","DOIUrl":"10.1007/s44307-026-00097-9","url":null,"abstract":"<p><p>Traditional chemotherapy and radiotherapy for glioma are challenging due to the hypoxia in tumor microenvironment and the inability of chemotherapeutic agents to enter into tumor cells. Phototherapy is a novel therapeutic approach against various tumors in recent years. When combined with chemotherapy, the antitumor efficacy of phototherapy is superior than each alone. However, the combination of chemotherapy and phototherapy is still hampered by the hypoxic tumor microenvironment which upregulates the expression of hypoxia-inducible factor 1 (HIF-1) and its downstream pathways, as well as the thermoresistance caused by the overexpression of heat shock proteins (HSPs). To solve this, the biocompatible albumin-based nanoparticles (NPs) are developed to co-deliver IR780 iodine (IR780) and paclitaxel (PTX) simultaneously at an optimized ratio (IR780-PTX NPs) for synergistic photochemotherapy. Moreover, acriflavine (ACF), a chemical inhibitor of HIF-1, is formulated into intratumorally formed hydrogels to reinforce synergistic photochemotherapy. The continuously released ACF from hydrogel not only relieves the impact of photodynamic therapy-exacerbated tumor hypoxia by suppressing HIF-1 activity, but also efficiently attenuates HSP70 upregulation. The collaboration between IR780-PTX NPs and ACF hydrogels leads to an extraordinary antitumor effect in vitro and in vivo. The reinforced synergistic photochemotherapy via a single molecule by overcoming HIF-1 activity and HSP overexpression provides an effective therapeutic example to treat tumors, especially in those undergone severe hypoxia and/or therapy-induced thermoresistance.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12979732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147438964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.","authors":"Zhixing Wu, Jiayi Li, Rong Xia, Jiayin Dai, Jionglong Su, Jia Meng, Yuxin Zhang","doi":"10.1007/s44307-025-00093-5","DOIUrl":"10.1007/s44307-025-00093-5","url":null,"abstract":"<p><p>Recent advancements in sequencing technologies have transformed the characterization of genomic and transcriptomic complexity. In this review, we present a comprehensive overview of Oxford Nanopore Technologies (ONT), emphasizing its unique capability for real-time, long-read, and direct RNA sequencing. We begin by outlining the core ONT analytical workflow-base calling, alignment, re-squiggling, and quality control-and summarize the major computational tools applied at each stage. Then extensive illustrations of various RNA modification detection techniques are provided, spanning from statistical models, machine learning and deep learning frameworks to advanced strategies incorporating large language models. To assess methodological performance, additional benchmark analyses of m6A and pseudouridine (Ψ) are carried out across two publicly available datasets. These results demonstrate substantial variability across different tools, underscoring the inherent difficulties in reliably detecting modifications from ONT signals. We further examine the biological roles of key RNA modifications and contrast ONT-based approaches with conventional detection technologies. Finally, we discuss persistent limitations such as sequencing error rates, data and computational demands, and the complexity of multi-modification inference, and further propose future directions aimed at improving accuracy, robustness, and biological interpretability in ONT-based epitranscriptomic research.</p>","PeriodicalId":519913,"journal":{"name":"Advanced biotechnology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12976157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147438994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}