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The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

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Plant Communications 2023年第1期4卷 148-166页

作者： Zhen Zeng Yang liu xing-Yu Feng sai-xi li xing-Mei Jiang Jian-Qun Chen Zhu-Qing Shao State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China

Arbuscular mycorrhizal symbiosis(AMS)is an ancient plant-fungus relationship that is widely distributed in terrestrial *** formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous ***,the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly *** this study,a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato,an emerging AMS *** annotation of the tomato genome was improved by a multiple-platform sequencing strategy.A total of 3,174 protein-coding genes were upregulated during AMS,42%of which were alternatively ***-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant *** additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host ***,these orthogroups were absent or not induced in monocots and/or non-AMS hosts,suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory ***,we detected 587 lncRNAs,ten miRNAs,and 146 circRNAs that responded to AMS,which were incorporated to establish a tomato AMSresponsive,competing RNA-responsive endogenous RNA(ceRNA)***,a tomato symbiotic transcriptome database(TSTD,https://***/TSTD)was constructed to serve as a resource for deep deciphering of the AMS regulatory *** results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.

关键词： tomato RNAome landscape arbuscular mycorrhizal symbiosis evolution ceRNA network

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Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

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Horticulture Research 2023年第9期10卷 13-23页

作者： Jia-Yu Xue Hai-Yun Fan Zhen Zeng Yu-Han Zhou Shuai-Ya Hu sai-xi li Ying-Juan Cheng xiang-Ru Meng Fei Chen Zhu-Qing Shao Yves Van de Peer College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China College of Tropical Crops Sanya Nanfan Research InstituteHainan UniversityHaikou 570228China Hainan Yazhou Bay Seed Laboratory Sanya 572025China Department of Plant Biotechnology and Bioinformatics VIB-UGent Center for Plant Systems BiologyGhent UniversityB-9052 GhentBelgium Department of Biochemistry Genetics and MicrobiologyUniversity of PretoriaPretoria 0028South Africa

MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe ***,with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments,we constructed multiple gene co-expression networks,which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth,*** mycorrhizal symbiosis and fruit ***,non-coding RNAs,including miRNAs,lncRNAs,and circRNAs were also identified,together with their potential *** networks between different types of non-coding RNAs(miRNA-lncRNA),and non-coding RNAs and genes(miRNA-mRNA and lncRNA-mRNA)were constructed as *** results and data will provide valuable information for the study of organ differentiation and development of this important ***,we established a database(http://***/microTomBase/)with genomic and transcriptomic data,as well as details of gene co-expression and interacting networks on MicroTom,and this database should be of great value to those who want to adopt MicroTom as a model plant for research.

关键词： metabolism organs networks

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Constraints on holographic QCD phase transitions from PTA observations

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 71-78页

作者： Song He li li sai Wang Shao-Jiang Wang Center for Theoretical Physics and College of Physics Jilin University School of Physical Science and Technology Ningbo University Max Planck Institute for Gravitational Physics (Albert Einstein Institute) CAS Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences School of Fundamental Physics and Mathematical Sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences (UCAS) School of Physical Sciences University of Chinese Academy of Sciences (UCAS) Theoretical Physics Division Institute of High Energy Physics Chinese Academy of Sciences

The underlying physics of QCD phase transition in the early Universe remains largely unknown due to its strong-coupling nature during the quark-gluon plasma/hadron gas transition, yet a holographic model has been proposed to quantitatively fit the lattice QCD data while with its duration of the first-order phase transition(FoPT) left undetermined. At specific baryon chemical potential, the first-order QCD phase transition agrees with the observational constraint of baryon asymmetry. It, therefore, provides a scenario for phase transition gravitational waves(GWs) within the standard model of particle physics. If these background GWs could contribute dominantly to the recently claimed common-spectrum red noise from pulsar timing array(PTA) observations, the duration of this FoPT can be well constrained, and the associated primordial black holes are still allowed by current observations.

关键词： pulsar timing array QCD phase transition gravitational waves primordial black holes

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FUBP3 mediates the amyloid-β-induced neuronal NLRP3 expression

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Neural Regeneration Research 2025年第7期20卷 2068-2083页

作者： Jing Yao Yuan li xi liu Wenping liang Yu li liyong Wu Zhe Wang Weihong Song The National Clinical Research Center for Geriatric Disease Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Neurology The First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Pediatrics The Second Affiliated Hospital and Yuying Children’s HospitalKey Laboratory of Alzheimer’s Disease of Zhejiang ProvinceInstitute of AgingWenzhou Medical UniversityWenzhouZhejiang ProvinceChina Oujiang Laboratory(Zhejiang Laboratory for Regenerative Medicine Visionand Brain Health)WenzhouZhejiang ProvinceChina

Alzheimer's disease is characterized by deposition of amyloid-β,which forms extracellular neuritic plaques,and accumulation of hyperphosphorylated tau,which aggregates to form intraneuronal neurofibrillary tangles,in the *** NLRP3 inflammasome may play a role in the transition from amyloid-βdeposition to tau phosphorylation and *** NLRP3 is primarily found in brain microglia,and tau is predominantly located in neurons,it has been suggested that NLRP3 expressed by microglia indirectly triggers tau phosphorylation by upregulating the expression of pro-inflammatory ***,we found that neurons also express NLRP3 in vitro and in vivo,and that neuronal NLRP3 regulates tau *** biochemical methods,we mapped the minimal NLRP3 promoter and identified FUBP3 as a transcription factor regulating NLRP3 expression in *** primary neurons and the neuroblastoma cell line Neuro2A,FUBP3 is required for endogenous NLRP3 expression and tau phosphorylation only when amyloid-βis *** the brains of aged wild-type mice and a mouse model of Alzheimer's disease,FUBP3 expression was markedly increased in cortical *** analysis suggested that FUBP3 plays a role in neuron-mediated immune *** also found that FUBP3 trimmed the 5′end of DNA fragments that it bound,implying that FUBP3 functions in stress-induced *** findings suggest that neuronal NLRP3 may be more directly involved in the amyloid-β-to–phospho-tau transition than microglial NLRP3,and that amyloid-βfundamentally alters the regulatory mechanism of NLRP3 expression in *** that FUBP3 was only expressed at low levels in young wild-type mice and was strongly upregulated in the brains of aged mice and Alzheimer's disease mice,FUBP3 could be a safe therapeutic target for preventing Alzheimer's disease progression.

关键词： 5′end trimming Alzheimer's disease amyloid-beta amyloid-β-dependent transcription FUBP3 inflammasome inflammation neuron NLRP3 tau transcription factor

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Deciphering Water Oxidation Catalysts:The Dominant Role of Surface Chemistry over Reconstruction Degree in Activity Promotion

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Nano-Micro Letters 2025年第3期17卷 340-354页

作者： li An Jianyi li Yuanmiao Sun Jiamin Zhu Justin Zhu Yeow Seow Hong Zhang Nan Zhang Pinxian xi * Zhichuan JXu Chun‑Hua Yan State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu ProvinceFrontiers Science Center for Rare IsotopesCollege of Chemistry and Chemical EngineeringLanzhou UniversityLanzhou 730000People’s Republic of China School of Materials Science and Engineering Nanyang Technological UniversitySingapore 639798Singapore Faculty of Materials Science and Energy Engineering Institute of Technology for Carbon NeutralityShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055People’s Republic of China Key Laboratory of Electromagnetic Materials and Devices National Center for International Research On Photoelectric and Energy MaterialsSchool of Materials and EnergyElectron Microscopy CenterYunnan UniversityKunming 650091People’s Republic of China State Key Laboratory of Baiyunobo Rare Earth Resource Researches and Comprehensive Utilization Baotou Research Institute of Rare EarthsBaotou 014030People’s Republic of China Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and ApplicationsPKU‑HKU Joint Laboratory in Rare Earth Materials and Bioinorganic ChemistryPeking UniversityBeijing 100871People’s Republic of China

Water splitting hinges crucially on the availability of electrocatalysts for the oxygen evolution *** surface reconstruction has been widely observed in perovskite catalysts,and the reconstruction degree has been often correlated with the activity ***,a systematic study on the roles of Fe substitution in activation of perovskite LaNiO_(3)is *** substituting Fe content influences both current change tendency and surface reconstruction ***_(0.9)Fe_(0.1)O_(3)is found exhibiting a volcano-peak intrinsic activity in both pristine and reconstructed among all substituted perovskites in the LaNi_(1-x)Fe_(x)O_(3)(x=0.00,0.10,0.25,0.50,0.75,1.00)*** reconstructed LaNi_(0.9)Fe_(0.1)O_(3)shows a higher intrinsic activity than most reported NiFe-based ***,density functional theory calculations reveal that Fe substitution can lower the O 2p level,which thus stabilize lattice oxygen in LaNi0.9Fe0.1O3 and ensure its long-term ***,it is vital interesting that activity of the reconstructed catalysts relied more on the surface chemistry rather than the reconstruction *** effect of Fe on the degree of surface reconstruction of the perovskite is decoupled from that on its activity enhancement after surface *** finding showcases the importance to customize the surface chemistry of reconstructed catalysts for water oxidation.

关键词： Oxygen evolution reaction Perovskite oxides Doping Activation and reconstruction

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Distinct MLT asymmetry of auroral kilometric radiation observed by the FAST satellite

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Earth and Planetary Physics 2025年第1期9卷 188-193页

作者： JiaWen Tang sai Zhang Fuliang xiao HongMing Yang Si liu YiHua He Chang Yang YuYue Jin ZhouKun Deng Ping li Archie James Johnston School of Physics and Electronic Sciences Changsha University of Science and TechnologyChangsha 410114China Hunan Province Higher Education Key Laboratory of Modeling and Monitoring on the Near-Earth Electromagnetic Environments Changsha University of Science and TechnologyChangsha 410114China School of Electrical and Information Engineering Changsha University of Science and TechnologyChangsha 410114China

Auroral Kilometric Radiation (AKR) is a common radio emission,which can contribute to the magnetosphere-ionosphereatmosphere co u *** emissions have been observed in all magnetic planet magnetospheres of the solar *** this study,using observations from the FAST satellite from 30 August 1996 to 9 September 2001,the distribution of AKR in altitude=500-4500 km and invariant latitude (|ILAT|)=60°-80°has been analyzed.63045 AKR samples have been identified with~48%(52%) samples on the dayside (nightside).Of considerable interest,there is a distinct MLT asymmetry with the high occurrence rate in MLT=05-08 and 18-22(02-05 and 12-17) in the northern (southern) *** distinct MLT asymmetry is associated with the direction of Bxof the interplaneta ry magnetic *** addition,the occurrence rate on the nightside clearly increases as the AE^(*) index *** study further enriches the information and understanding of AKR in the magnetosphere as well as other similar radio emissions.

关键词： asymmetry auroral kilometric radiation interplanetary magnetic field

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Tranylcypromine upregulates Sestrin 2 expression to ameliorate NLRP3-related noise-induced hearing loss

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Neural Regeneration Research 2025年第5期20卷 1483-1494页

作者： xihang Chen Zhifeng Chen Menghua li Weiwei Guo Shuolong Yuan liangwei Xu Chang lin xi Shi Wei Chen Shiming Yang Senior Department of Otolaryngology Head and Neck Surgery Chinese PLA General HospitalChinese PLA Medical SchoolBeijingChina State Key Laboratory of Hearing and Balance Science BeijingChina National Clinical Research Center for Otolaryngologic Diseases BeijingChina Key Laboratory of Hearing Science Ministry of EducationBeijingChina Beijing Key Laboratory of Hearing Impairment Prevention and Treatment BeijingChina Department of Otorhinolaryngology Head and Neck Surgery The First Affiliated Hospital of Fujian Medical UniversityFuzhouFujian ProvinceChina Department of Otolaryngology Head and Neck Surgery The 940th Hospital of Joint Logistics Support Force of Chinese PLALanzhouGansu ProvinceChina Key Laboratory of Tropical Biological Resources of Ministry of Education School of Pharmaceutical SciencesHainan UniversityHaikouHainan ProvinceChina Academician Workstation of Hainan University School of Pharmaceutical SciencesYazhou BaySanyaHainan ProvinceChina

Noise-induced hearing loss is the primary non-genetic factor contributing to auditory ***,there are currently no effective pharmacological interventions for patients with noise-induced hearing ***,we present evidence suggesting that the lysine-specific demethylase 1 inhibitor–tranylcypromine is an otoprotective agent that could be used to treat noise-induced hearing loss,and elucidate its underlying regulatory *** established a mouse model of permanent threshold shift hearing loss by exposing the mice to white broadband noise at a sound pressure level of 120 d B for 4 *** found that tranylcypromine treatment led to the upregulation of Sestrin2(SESN2)and activation of the autophagy markers light chain 3B and lysosome-associated membrane glycoprotein 1 in the cochleae of mice treated with *** noise exposure group treated with tranylcypromine showed significantly lower average auditory brainstem response hearing thresholds at click,4,8,and 16 k Hz frequencies compared with the noise exposure group treated with *** findings indicate that tranylcypromine treatment resulted in increased SESN2,light chain 3B,and lysosome-associated membrane glycoprotein 1 expression after noise exposure,leading to a reduction in levels of 4-hydroxynonenal and cleaved caspase-3,thereby reducing noise-induced hair cell ***,immunoblot analysis demonstrated that treatment with tranylcypromine upregulated SESN2 expression via the autophagy *** treatment also reduced the production of NOD-like receptor family pyrin domaincontaining 3(NLRP3)*** conclusion,our results showed that tranylcypromine treatment ameliorated cochlear inflammation by promoting the expression of SESN2,which induced autophagy,thereby restricting NLRP3-related inflammasome signaling,alleviating cochlear hair cell loss,and protecting hearing *** findings suggest that inhibiting lysine-specific demethylase 1 is a

关键词： 4-hydroxynonenal apoptosis autophagy cleaved caspase-3 inflammation NOD-like receptor family pyrin domain-containing 3(NLRP3) noise-induced hearing loss oxidative stress Sestrin2 tranylcypromine

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Ni-catalyzed cross-electrophile alkyl-alkyl coupling reactions

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Science China Chemistry 2025年

作者： li-Xu You Lan Tian Chun-ling Guo Shun-xi li Yu-Cheng liu Yu-Long li Wei Shu College of Chemistry and Environmental Engineering Key Laboratory of Green Catalysis of Higher Education Institutes of Sichuan Sichuan University of Science and Engineering Guangming Advanced Research Institute Shenzhen Grubbs Institute Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology

Introducing saturated carbon-carbon bonds into organic molecules significantly increases the three-dimensional configuration,thus altering the physical and chemical properties as well as the functions of molecules. Transition-metal-catalyzed carboncarbon cross-couplings represent one of the most straightforward, efficient and modular alternatives to build saturation in a single step. However, the efficient construction of alkyl-alkyl bonds remains a formidable challenge due to the precise manipulation of multiple alkyl metallic intermediates as well as associated competitive side reactions and selectivity control. Over the past years, Ni-catalyzed cross-coupling under reductive conditions has gained more and more attention for alkyl-alkyl crosscoupling partially attributing to the low-valent state of metal centers under reducing conditions, which suppresses the competitive β-hydride elimination process, thus facilitating the formation of alkyl-alkyl bonds. In this review, the initiative and progress of Ni-catalyzed cross-electrophile alkyl-alkyl cross-coupling, including the efforts in racemic and enantioselective formation of alkyl-alkyl bonds, have been summarized and discussed. Moreover, the challenges and further opportunities in this area have also been discussed.

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EZH2-dependent myelination following sciatic nerve injury

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Neural Regeneration Research 2025年第8期20卷 2382-2394页

作者： Hui Zhu li Mu xi Xu Tianyi Huang Ying Wang Siyuan Xu Yiting Wang Wencong Wang Zhiping Wang Hongkui Wang Chengbin Xue Research Center of Clinical Medicine Affiliated Hospital of Nantong UniversityKey Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationCo-innovation Center of NeuroregenerationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsNantong UniversityNantongJiangsu ProvinceChina Medical School of Nantong University NantongJiangsu ProvinceChina Department of Neurology Affiliated Hospital of Nantong UniversityNantongJiangsu ProvinceChina Department of Rehabilitation Medicine Affiliated Hospital of Nantong UniversityNantongJiangsu ProvinceChina Department of Critical Care Medicine Nantong Fourth People’s HospitalNantongJiangsu ProvinceChina

Demyelination and remyelination have been major focal points in the study of peripheral nerve regeneration following peripheral nerve ***,the gene regulatory network of regenerated myelin differs from that of native *** of enhancer of zeste homolog 2(EZH2)hinders the differentiation,maturation,and myelination of Schwann cells in *** further determine the role of EZH2 in myelination and recovery post-peripheral nerve injury,conditional knockout mice lacking Ezh2 in Schwann cells(Ezh2^(fl/fl);Dhh-Cre and Ezh2^(fl/fl);Mpz-Cre)were *** results show that a significant proportion of axons in the sciatic nerve of Ezh2-depleted mice remain *** highlights the crucial role of Ezh2 in initiating Schwann cell ***,we observed that 21 days after inducing a sciatic nerve crush injury in these mice,most axons had remyelinated at the injury site in the control nerve,while Ezh2^(fl/fl);Mpz-Cre mice had significantly fewer remyelinated axons compared with their wild-type *** suggests that the absence of Ezh2 in Schwann cells impairs myelin formation and *** conclusion,EZH2 has emerged as a pivotal regulatory factor in the process of demyelination and myelin regeneration following peripheral nerve *** EZH2 activity during these processes may offer a promising therapeutic target for the treatment of peripheral nerve injuries.

关键词： demyelination EZH2 myelination peripheral nerve injury PRC2 remyelination Schwann cells sciatic nerve crush sciatic nerve transection

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Modular assembly of complex C-alkyl glycoside enabled via cooperative NHC and photoredox catalysis

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Science China Chemistry 2025年

作者： Rui-Qiang Jiao Ming li xi Chen Mei-Ze Xu Tian Ding xiao-Ping Gong Zhuo-Mei li Xue-Yuan liu Yong-Min liang State Key Laboratory of Applied Organic Chemistry Lanzhou University College of Chemistry and Chemical Engineering Northwest Normal University

C-Alkyl glycosides are found in natural products and are indispensable in drug development programs,owing to their diverse range of medicinal ***-component reactions involving glycosyl radical addition are well documented and proved efficient for the C-alkyl glycosides ***,multicomponent reactions for the rapid and controllable construction of structurally diversified C-alkyl glycosides in a single step remains a significant challenge due to the issues associated with balancing reactivity,compatibility,and ***,we report an NHC and photoredox co-catalyzed three-component method to access complex and valuable C-alkyl *** protocol exhibits broad substrate scope and excellent chemoand ***,nine types of sugars are compatible with this *** addition,the generality of this catalytic strategy was further highlighted by the potential for scalable production,the feasibility of further modifications of the products and its successful application in the late-stage functionalization of pharmaceutical skeletons.

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