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Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae

Genome Biology 2025年第1期26卷 1-26页

作者： Wang, Yubo Zhao, Lulu Wang, Deyan Chen, Kai Luo, Tiannan Luo, Jianglin Jiang, Chengzhi He, Zhoujian Huang, Heng Xie, Jiaxiao Jiang, Yuanzhong Liu, Jianquan Ma, Tao Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station College of Life Science Sichuan University Chengdu China School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem College of Ecology Lanzhou University Lanzhou 730000 China

Background: Centromeres play a crucial role in maintaining genomic stability during cell division. They are typically composed of large arrays of tandem satellite repeats, which hinder high-quality assembly and complicate our efforts to understand their evolution across species. Here, we use long-read sequencing to generate near-complete genome assemblies for two Populus and two Salix species belonging to the Salicaceae family and characterize the genetic and epigenetic landscapes of their centromeres. Results: The results show that only limited satellite repeats are present as centromeric components in these species, while most of them are located outside the centromere but exhibit a homogenized structure similar to that of the Arabidopsis centromeres. Instead, the Salicaceae centromeres are mainly composed of abundant transposable elements, including CRM and ATHILA, while LINE elements are exclusively discovered in the poplar centromeres. Comparative analysis reveals that these centromeric repeats are extensively expanded and interspersed with satellite arrays in a species-specific and chromosome-specific manner, driving rapid turnover of centromeres both in sequence compositions and genomic locations in the Salicaceae. Conclusions: Our results highlight the dynamic evolution of diverse centromeric landscapes among closely related species mediated by satellite homogenization and widespread invasions of transposable elements and shed further light on the role of centromere in genome evolution and species diversification. © The Author(s) 2025.

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Single-cell RNA sequencing reveals the heterogeneity and interactions of immune cells and Müller glia during zebrafish retina regeneration

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Neural Regeneration Research 2025年第12期20卷 3635-3648页

作者： Hui Xu Lining Cao Yuxi Chen Cuiping Zhou Jie Xu Zhuolin Zhang Xiangyu Li Lihua Liu Jianfeng Lu Shanghai YangZhi Rehabilitation Hospital(Shanghai Sunshine Rehabilitation Center) Frontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina Key Lab of Neuroregeneration of Jiangsu and Ministry of Education Co-innovation Center of NeuroregenerationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsNantong UniversityNantongJiangsu ProvinceChina

Inflammation plays a crucial role in the regeneration of fish and avian ***,how inflammation regulates Müller glia(MG)reprogramming remains ***,we used single-cell RNA sequencing to investigate the cell heterogeneity and interactions of MG and immune cells in the regenerating zebrafish *** first showed that two types of quiescent MG(resting MG1 and MG2)reside in the uninjured *** retinal injury,resting MG1 transitioned into an activated state expressing known reprogramming genes,while resting MG2 gave rise to rod *** further showed that retinal microglia can be categorized into three subtypes(microglia-1,microglia-2,and proliferative)and pseudotime analysis demonstrated dynamic changes in microglial status following retinal *** of cell–cell interactions indicated extensive crosstalk between immune cells and MG,with many interactions shared among different immune cell ***,we showed that inflammation activated Jak1–Stat3 signaling in MG,promoting their transition from a resting to an activated *** study reveals the cell heterogeneity and crosstalk of immune cells and MG in zebrafish retinal repair,and may provide valuable insights into future mammalian retina regeneration.

关键词： immune cells inflammation Jak1-Stat3 signaling microglia Müller glia regeneration reprogramming retina single-cell RNAseq zebrafish

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Cyclodextrin-boosted photocatalytic oxidation for efficient bisphenol A removal

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Chinese Chemical Letters 2025年第3期36卷 156-163页

作者： Qinwei Lu Jinjie Lu Juying Lei Xubiao Luo Yanbo Zhou State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process East China University of Science and TechnologyShanghai 200237China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China School of Life Science Jinggangshan UniversityJi’an 343009China

Wastewater contains various high-risk trace organic pollutants,such as antibiotics and endocrine disruptors,which seriously restrict wastewater ***-based functional materials show great potential in the removal of trace pollutants because of their adsorption catalytic *** the synergistic mechanism of cyclodextrin in oxidation is the key issue in confined catalytic oxidation process *** this work,we fabricated a BiOIO_(3)@BiOBr/β-CD heterojunction photocatalyst to study the synergistic mechanism of cyclodextrin in the photocatalytic oxidation *** synergistic mechanism of cyclodextrin was investigated by combining radical chemistry,electrochemistry,spectroscopy,and timedependent density functional *** showed that the excited intermediate free radicals played an important role in promoting the photocatalytic degradation *** heterojunction photocatalyst loaded withβ-cyclodextrin(β-CD)at the electronic end(C[Cat.]=0.2mg/mL)removed about 97%of bisphenol A(BPA)within 30min,and the first-order kinetic constant(k_(CDBIB)=0.112 min^(−1))was about twice that of the unloadedβ-CD(k_(BIB)=0.057 min^(−1)).Cyclodextrin loading improved the photocatalytic performance of the heterojunction and stimulated the intermediate to increase the free radical yield and regulate the reaction path.

关键词： Photocatalysis β-Cyclodextrin Bisphenol A Confined catalysis Organic free radical

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Spatiotemporal characteristics and dynamic prediction of agricultural carbon compensation potential in the middle and lower reaches of the Yellow River Basin

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Environmental science and Pollution Research 2025年第4期32卷 1903-1917页

作者： Luo, Jikang Zhao, Zhen Pang, Jing College of Science Inner Mongolia University of Technology Hohhot015000 China School of Mathematics and Statistics Ningbo University Ningbo315000 China Inner Mongolia Key Laboratory of Statistical Analysis Theory for Life Data and Neural Network Modelling Inner Mongolia University of Technology Hohhot015000 China

Climate change, driven by carbon emissions, has emerged as a pressing global ecological and environmental challenge. Here, we leverage the panel data of five provinces and above prefecture-level cities in the middle and lower reaches of the Yellow River Basin to estimate the agricultural carbon emissions (CEs), carbon sinks (CSs), carbon compensation rate (CCR), and carbon compensation potential (CCP) from 2001 to 2022 and investigate the spatiotemporal evolution characteristics for this region. We propose an improved GLM-stacking ensemble learning method for CE prediction with limited sample data. The findings indicate the following: (i) From 2001 to 2022, the overall CEs show a trend of "development - decline - stabilization" and reach a peak of 172.54 Mt in 2005. CCR first exceeded the "CCR = 1" in 2008, which also indicates that reducing CEs and increasing CSs are the paths to achieving agricultural carbon neutrality. (ii) Although each province has achieved "net-zero emissions," the CCP of most urban agglomerations is about 0.5 and shows a certain agglomeration trend, indicating significant room for further carbon offset. (iii) The novel GLM-stacking model has higher prediction accuracy when compared to a single model. These findings provide scientific and technological support to realize the provincial dual carbon goals in China. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Carbon capture and utilization

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Time-Dependent Transcriptional Dynamics of Contextual Fear Memory Retrieval Reveals the Function of Dipeptidyl Peptidase 9 in Reconsolidation

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Neuroscience Bulletin 2025年第1期41卷 16-32页

作者： Wen-Ting Guo Wen-Xing Li Yu-Chen Liu Ya-Bo Zhao Lin Xu Qi-Xin Zhou Key Laboratory of Animal Models and Human Disease Mechanisms Laboratory of Learning and MemoryKunming Institute of ZoologyThe Chinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China CAS Centre for Excellence in Brain Science and Intelligent Technology Shanghai 200031China Jiangsu Key Laboratory of Neuropsychiatric Diseases College of Pharmaceutical SciencesSoochow UniversitySuzhou 215123China

Numerous studies on the formation and consolidation of memory have shown that memory processes are characterized by phase-dependent and dynamic *** retrieval,as the only representation of memory content and an active form of memory processing that induces memory reconsolidation,has attracted increasing attention in recent *** the molecular mechanisms specifc to memory retrievalinduced reconsolidation have been gradually revealed,an understanding of the time-dependent regulatory mechanisms of this process is still *** this study,we applied a transcriptome analysis of memory retrieval at diferent time points in the recent memory *** expression analysis and Short Time-series Expression Miner(STEM)depicting temporal gene expression patterns indicated that most diferential gene expression occurred at 48 h,and the STEM cluster showing the greatest transcriptional upregulation at 48 h demonstrated the most significant *** then screened the diferentially-expressed genes associated with that met the expression patterns of those cluster-identifed genes that have been reported to be involved in learning and memory processes in addition to dipeptidyl peptidase 9(DPP9).Further quantitative polymerase chain reaction verifcation and pharmacological intervention suggested that DPP9 is involved in 48-h fear memory retrieval and viral vector-mediated overexpression of DPP9 countered the 48-h retrieval-induced attenuation of fear *** together,our fndings suggest that temporal gene expression patterns are induced by recent memory retrieval and provide hitherto undocumented evidence of the role of DPP9 in the retrieval-induced reconsolidation of fear memory.

关键词： Transcriptome analysis Temporal gene expression Fear memory retrieval Reconsolidation DPP9

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Engineered platelets-based nano-aircraft system for precise tumor chemo-immunotherapy with graded drug delivery and self-recognized tumor targeting

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science Bulletin 2025年第9期70卷 1462-1477页

作者： Geng, Meijuan Du, Huiping Wei, Xuan Chen, Siyu Cheng, Jiamin Meng, Siyu Gong, Liyang Yang, Hui Cai, Kaiyong Dai, Liangliang Institute of Medical Research Northwestern Polytechnical University Xi'an710072 China School of Life Science Northwestern Polytechnical University Xi'an710072 China Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University Chongqing400044 China

Metastasis and heterogeneity pose major challenges in cancer treatment. Although chemoimmunotherapy shows promising efficacy, its therapeutic impact is limited by off-target effects and differences in the delivery sites of chemotherapeutic drugs and immunosuppressants. In this study, an engineered platelets (Pts)-based nano-aircraft, Pts@DOX/HANGs@Gal, was constructed with an internally loaded chemotherapeutic drug, doxorubicin, and externally grafted reduction-responsive hyaluronidase-cross-linked nanospheroids loaded with the immunosuppressant galunisertib for precise tumor chemo-immunotherapy. The normal physiological features of host Pts, including their excellent targeting capability for both metastatic and orthotopic tumors, are not disturbed by functional nanosystems. The interaction between Pts@DOX/HANGs@Gal and tumors gives rise to Pts activation, achieving the continuous targeted delivery of DOX to tumors, inducing the transition from cold to hot tumors, and promoting the recruitment of immune cells. Simultaneously, the external nanospheres disintegrate from Pts@DOX/HANGs@Gal, releasing galunisertib and hyaluronidase into the extracellular matrix to relieve immune tolerance and open up a high-speed channel for the tumor infiltration of immune cells and deep tumor penetration of the nanosystem. Consequently, Pts@DOX/HANGs@Gal not only effectively reinforced the antitumor immune response through self-recognized tumor-targeting chemo-immunotherapy and graded drug delivery but also reduced tumor metastasis in vivo. This study presents promising Pt-based nanovesicles for precise cancer treatment. © 2025 science China Press

关键词： Platelets

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Nonglycosidic C–O bond formation catalyzed by a bifunctional pseudoglycosyltransferase ValL

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Synthetic and Systems Biotechnology 2025年第3期10卷 846-857页

作者： Guo, Ziyue Zhang, Xin Zhou, Lin Huang, Qungang Kang, Qianjin Bai, Linquan State Key Laboratory of Microbial Metabolism School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 China College of Life Science and Technology Tarim University Xinjiang Alar 843300 China

The C7N antibiotic validamycin A is an antifungal agent widely used as a crop protectant. It comprises a validoxylamine A unit linked to a glucose moiety, which is formed through a nonglycosidic C–N bond connecting a... 详细信息

The C₇N antibiotic validamycin A is an antifungal agent widely used as a crop protectant. It comprises a validoxylamine A unit linked to a glucose moiety, which is formed through a nonglycosidic C–N bond connecting a valienol moiety and a validamine moiety, a reaction catalyzed by the pseudoglycosyltransferase ValL. In this study, we analyzed the chemical composition of validamycins in Streptomyces hygroscopicus var. jinggangensis TL01. A series of novel oxygen-bridged analogues, namely, validenomycin, validomycin, and 1,1′-bis-valienol, were identified in the culture supernatants, and their chemical structures were elucidated using a combination of one- and two-dimensional nuclear magnetic resonance and mass spectrometry. Gene disruption and complementation experiments revealed that valL is essential for the biosynthesis of these new oxygen-bridged analogues of validamycins. Biochemical assays further demonstrated that ValL catalyzed the C–O bond formation between GDP-valienol and valienol-7-phosphate, producing 1,1′-bis-valienol-7-phosphate, which was subsequently dephosphorylated by ValO and glycosylated by ValG to yield validenomycin. Collectively, our findings revealed the unique ability of ValL to catalyze nonglycosidic C–O coupling, potentially enabling the generation of various chemical scaffolds for C₇N family antibiotics. © 2025 The Authors

关键词： C7N antibiotics Nonglycosidic C–O bond Pseudoglycosyltransferase Validamycin A

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VCP downstream metabolite glycerol-3-phosphate(G3P)inhibits CD8+T cells function in the HCC microenvironment

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Signal Transduction and Targeted Therapy 2025年第2期10卷 1040-1057页

作者： Cheng Cheng Qingrui Zha Linmao Sun Tianming Cui Xinyu Guo Changjian Xing Zhengxiang Chen Changyong Ji Shuhang Liang Shengwei Tao Junhui Chu Chenghui Wu Qi Chu Xuetian Gu Ning Zhang Yumin Fu Shumin Deng Yitong Zhu Jiabei Wang Yao Liu Lianxin Liu Department of Hepatobiliary Surgery Centre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230001China Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery HefeiAnhui 230001China Anhui Provincial Clinical Research Center for Hepatobiliary Diseases HefeiAnhui 230001China Department of Gastrointestinal Surgery Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230001China

CD8+T cells within the tumor microenvironment(TME)are often functionally impaired,which limits their ability to mount effective anti-tumor ***,the molecular mechanisms behind this dysfunction remain incompletely ***,we identified valosin-containing protein(VCP)as a key regulator of CD8+T cells suppression in hepatocellular carcinoma(HCC).Our findings reveal that VCP suppresses the activation,expansion,and cytotoxic capacity of CD8+T cells both in vitro and in vivo,significantly contributing to the immunosuppressive nature of the ***,VCP stabilizes the expression of glycerol-3-phosphate dehydrogenase 1-like protein(GPD1L),leading to the accumulation of glycerol-3-phosphate(G3P),a downstream metabolite of *** accumulated G3P diffuses into the TME and directly interacts with SRC-family tyrosine kinase LCK,a critical component of the T-cell receptor(TCR)signaling pathway in CD8+T *** interaction heightens the phosphorylation of Tyr505,a key inhibitory residue,ultimately reducing LCK activity and impairing downstream TCR ***,CD8+T cells lose their functional capacity,diminishing their ability to fight against ***,we demonstrated that targeting VCP in combination with anti-PD1 therapy significantly suppresses HCC tumor growth and restores the anti-tumor function of CD8+T cells,suggesting synergistic therapeutic *** findings highlight a previously unrecognized mechanism involving VCP and G3P in suppressing T-cell-mediated immunity in the TME,positioning VCP as a promising upstream target for enhancing immunotherapy in HCC.

关键词： molecular mechanisms valosin containing protein glycerol phosphate dehydrogenase protein hepatocellular carcinoma CD T cells hepatocellular carcinoma hcc our immunosuppression tumor microenvironment tme

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Salinity-responsive key endophytic bacteria in the propagules of Kandelia obovata enhance salt tolerance in rice

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Journal of Integrative Agriculture 2025年第5期24卷 1738-1753页

作者： Zhian Dai Rongwei Yuan Xiangxia Yang Hanxiao Xi Ma Zhuo Mi Wei School of Agriculture and Biotechnology Shenzhen Campus of Sun Yat-sen University Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province/College of Life Science and Technology Hubei Engineering University

Salinity is a major environmental stress affecting crop growth and productivity globally. The application of halotolerant plant growth-promoting bacteria（HT-PGPB） has been widely recognized to promote crop growth and reduce the adverse effects of salt stress. In this study, key endophytic bacteria that can respond to salinity changes were identified by analyzing the microbial community in propagules of Kandelia obovata. Delftia tsuruhatensis DYX29, a strain that can grow normally under high salinity conditions with a sodium chloride（NaCl） concentration of 5%（w/v）,was obtained by pure culture. DYX29 can produce siderophores with a siderophore unit value of 87.6% and 1-aminocyclopropane-1-carboxylate（ACC） deaminase with 29 UL–1, and its synthesis of intracellular amino acids and auxin can be induced by high salinity. Inoculation with DYX29 can remarkably promote the salt tolerance of rice. Under salt stress, the addition of DYX29 was shown to effectively promote the growth of rice seedlings through a variety of approaches. It increased the biomass of rice seedlings by 32.9%（dry weight） and promoted the accumulation of soluble sugars by 23.1%. It also increased catalase（CAT） and peroxidase（POD） activities in rice leaves by 37.8 and 88.2%, respectively. Moreover, it maintained the ionic homeostasis in rice roots and leaves. In addition, it upregulated the expression of growth-promoting hormones, such as indole-3-acetic acid（IAA）, brassinolide（BL）, abscisic acid（ABA）, and salicylic acid（SA）, in rice roots by 27.8, 69.5, 123.7 and 28.6%, respectively. This study provides inspiration for screening valuable salt-tolerant pro-biotic bacteria from mangrove ecosystems and their use for crop growth promotion under salt stress. It can also provide useful references for the development of new salt-tolerant and pro-biotic biofertilizers, as well as the investigation of the related mechanisms.

关键词： salt stress halo-tolerant plant growth-promoting bacteria Delftia tsuruhatensis microbial community

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Regulating crystallization and retarding oxidation in Sn-Pb perovskite via 1D cation engineering for high performance all-perovskite tandem solar cells

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Journal of Energy Chemistry 2025年第1期100卷 646-652页

作者： Ranran Liu Xin Zheng Zaiwei Wang Miaomiao Zeng Chunxiang Lan Shaomin Yang Shangzhi Li Awen Wang Min Li Jing Guo Xuefei Weng Yaoguang Rong Xiong Li Michael Grätzel Center for Mesoscopic Solar Cells Wuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan 430074HubeiChina Institute of Technology for Carbon Neutrality Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055GuangdongChina School of Chemistry Chemical Engineering and Life SciencesState Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology430070HubeiChina Suzhou Institute of Nano-Tech and Nano-Bionics(SINANO) Chinese Academy of SciencesSuzhou 215123JiangsuChina School of Physics and Optoelectronic Engineering Hainan UniversityHaikou 570228HainanChina

All-perovskite tandem solar cells have the potential to surpass the theoretical efficiency limit of single junction solar cells by reducing thermalization ***,the challenges encompass the oxidation of Sn^(2+)to Sn^(4+)and uncontrolled crystallization kinetics in Sn-Pb perovskites,leading to nonradiative recombination and compositional heterogeneity to decrease photovoltaic efficiency and operational ***,we introduced an ionic liquid additive,1-ethyl-3-methylimidazolium iodide (EMIMI) into Sn-Pb perovskite precursor to form low-dimensional Sn-rich/pure-Sn perovskites at grain boundaries,which mitigates oxidation of Sn^(2+)to Sn^(4+)and regulates the film-forming dynamics of Sn/Pb-based perovskite *** optimized single-junction Sn-Pb perovskite devices incorporating EMIMI achieved a high efficiency of 22.87%.Furthermore,combined with wide-bandgap perovskite sub-cells in tandem device,we demonstrate 2-terminal all-perovskite tandem solar cells with a power conversion efficiency of 28.34%,achieving improved operational stability.

关键词： All-perovskite tandem solar cells Sn-Pb perovskite 1D Regulated crystallization Antioxidation

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