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Clathrin light chains negatively regulate plant immunity by hijacking the autophagy pathway

Plant Communications 2024年第8期5卷 172-188页

作者： Hu-Jiao Lan Jie Ran Wen-Xu Wang Lei Zhang Ni-Ni Wu Ya-Ting Zhao min-jun huang min Ni Fen Liu Ninghui Cheng Paul A.Nakata Jianwei Pan Steven A.Whitham Barbara J.Baker Jian-Zhong Liu Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants Zhejiang Normal UniversityJinhua 321004China Institute of Plant Genetics and Developmental Biology College of Chemistry and Life SciencesZhejiang Normal UniversityJinhua 321004China College of Life Sciences Lanzhou UniversityLanzhou 730000China Department of Plant Pathology and Microbiology Iowa State UniversityAmesIA 50011USA Department of Plant and Microbial Biology University of CaliforniaBerkeleyBerkeleyCA 94720USA Plant Gene Expression Center U.S.Department of Agriculture-Agricultural Research ServiceAlbanyCA 94706USA Lushan Botanical Garden Chinese Academy of SciencesJiujiang 332000China U.S.Department of Agriculture-Agricultural Research Service Children’s Nutrition Research CenterDepartment of PediatricsBaylor College of MedicineHoustonTX 77030USA

The crosstalk between clathrin-mediated endocytosis(CME)and the autophagy pathway has been reported in mammals;however,the interconnection of CME with autophagy has not been established in ***,we report that the Arabidopsis CLATHRIN LIGHT CHAIN(CLC)subunit 2 and 3 double mutant,clc2-1 clc3-1,phenocopies Arabidopsis AUTOPHAGY-RELATED GENE(ATG)mutants in both autoimmunity and nutrient ***,the autophagy pathway is significantly compromised in the clc2-1 clc3-1 ***,multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific *** expected,both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation,and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 ***,simultaneous knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum,supporting the functional relevance of the CLC2-ATG8h/8i *** conclusion,our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis.

关键词： autophagy clathrin light chain immunity clathrin-mediated endocytosis senescence cell death

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Physiological and pathological functions of circular RNAs in the nervous system

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Neural Regeneration Research 2024年第2期19卷 342-349页

作者： min Zhou Shi Li Chuan huang School of Life Sciences Chongqing UniversityChongqingChina

Circular RNAs(circRNAs)are a class of covalently closed single-stranded RNAs that are expressed during the development of specific cells and *** play crucial roles in physiological and pathological processes by sponging microRNAs,modulating gene transcription,controlling the activity of certain RNA-binding proteins,and producing functional peptides.A key focus of research at present is the functionality of circRNAs in the nervous system and several advances have emerged over the last 2 ***,the precise role of circRNAs in the nervous system has yet to be comprehensively *** this review,we first summarize the recently described roles of circRNAs in brain development,maturity,and ***,we focus on the involvement of circRNAs in various diseases of the central nervous system,such as brain cancer,chronic neurodegenerative diseases,acute injuries of the nervous system,and neuropathic pain.A better understanding of the functionality of circRNAs will help us to develop potential diagnostic,prognostic,and therapeutic strategies to treat diseases of the nervous system.

关键词： Alzheimer’s disease amyotrophic lateral sclerosis brain development circRNAs neuropathic pain Parkinson’s disease

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Rheum palmatum L. and Salvia miltiorrhiza Bge. Alleviates Acute Pancreatitis by Regulating Th17 Cell Differentiation: An Integrated Network Pharmacology Analysis, Molecular Dynamics Simulation and Experimental Validation

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Chinese Journal of Integrative Medicine 2024年第5期30卷 408-420页

作者： FENG min-chao LUO Fang huang Liang-jiang LI Kai CHEN Zu-min LI Hui YAO Chun QIN Bai-jun CHEN Guo-zhong The First Clinical Medical College Guangxi University of Traditional Chinese MedicineNanning 530000China Guangxi Key Laboratory of Molecular Biology of Traditional Chinese Medicine and Preventive Medicine Nanning 530000China Graduate School Guangxi University of Traditional Chinese MedicineNanning 530000China Department of Gastroenterology the First Affiliated Hospital of Guangxi University of Traditional Chinese MedicineNanning 530023China

Objective: To identify the core targets of Rheum palmatum L. and Salvia miltiorrhiza Bge.,(Dahuang-Danshen, DH-DS) and the mechanism underlying its therapeutic efficacy in acute pancreatitis(AP)using a network pharmacology approach and validate the findings in animal experiments. Methods: Network pharmacology analysis was used to elucidate the mechanisms underlying the therapeutic effects of DH-DS in AP. The reliability of the results was verified by molecular docking simulation and molecular dynamics ***, the results of network pharmacology enrichment analysis were verified by immunohistochemistry,Western blot analysis and real-time quantitative PCR, respectively. Results: Sixty-seven common targets of DH-DS in AP were identified and mitogen-activated protein kinase 3(MAPK3), Janus kinase 2(JAK2), signal transducer and activator of transcription 3(STAT3), protein c-Fos(FOS) were identified as core targets in the protein interaction(PPI) network analysis. Gene ontology analysis showed that cellular response to organic substance was the main functions of DH-DS in AP, and Kyoto Encyclopedia of Genes and Genomes analysis showed that the main pathway included Th17 cell differentiation. Molecular docking simulation confirmed that DH-DS binds with strong affinity to MAPK3, STAT3 and FOS. Molecular dynamics simulation revealed that FOS-isotanshinone Ⅱ and STAT3-dan-shexinkum d had good binding capacity. Animal experiments indicated that compared with the AP model group, DH-DS treatment effectively alleviated AP by inhibiting the expression of interleukin-1β, interleukin-6 and tumor necrosis factor-α, and blocking the activation of Th17 cell differentiation(P<0.01). Conclusion: DH-DS could inhibit the expression of inflammatory factors and protect pancreatic tissues,which would be functioned by regulating Th17 cell differentiation-related m RNA and protein expressions.

关键词： Rheum palmatum L. Salvia miltiorrhiza Bge. molecular docking simulation network pharmacology acute pancreatitis Th17 cell differentiation

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Chimeric Monkey Born Alive with a High Contribution of Donor Cells

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Neuroscience Bulletin 2024年第6期40卷 849-851页

作者： Jia huang jun Wu Department of Molecular Biology University of Texas Southwestern Medical CenterDallasTX75390USA Hamon Center for Regenerative Science and Medicine University of Texas Southwestern Medical CenterDallasTX75390USA Cecil H.and Ida Green Center for Reproductive Biology Sciences University of Texas Southwestern Medical CenterDallasTX75390USA

Chimeras,which consist of cells from different individuals or different species,represent an important tool in biological *** in the early twentieth century,studies on chimeras have been focusing on understanding fundamental genetic and cellular developmental *** the advances in genetic engineering and embryonic stem cell(ESC)technology,chimeras have become an important tool for the generation of transgenic animals.

关键词： mechanisms advances developmental

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A proteomic landscape of pharmacologic perturbations for functional relevance

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Journal of Pharmaceutical Analysis 2024年第1期14卷 128-139页

作者： Zhiwei Liu Shangwen Jiang Bingbing Hao Shuyu Xie Yingluo Liu Yuqi huang Heng Xu Cheng Luo min huang minjia Tan jun-Yu Xu State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China School of Chinese Materia Medica Nanjing University of Chinese MedicineNanjing210023China Zhongshan Institute for Drug Discovery Shanghai Institute of Materia MedicaChinese Academy of SciencesZhongshanGuangdong528400China State Key Laboratory of Pharmaceutical Biotechnology Nanjing UniversityNanjing210023China

Pharmacological perturbation studies based on protein-level signatures are fundamental for drug discovery. In the present study, we used a mass spectrometry (MS)-based proteomic platform to profile the whole proteome of the breast cancer MCF7 cell line under stress induced by 78 bioactive compounds. The integrated analysis of perturbed signal abundance revealed the connectivity between phenotypic behaviors and molecular features in cancer cells. Our data showed functional relevance in exploring the novel pharmacological activity of phenolic xanthohumol, as well as the noncanonical targets of clinically approved tamoxifen, lovastatin, and their derivatives. Furthermore, the rational design of synergistic inhibition using a combination of histone methyltransferase and topoisomerase was identified based on their complementary drug fingerprints. This study provides rich resources for the proteomic landscape of drug responses for precision therapeutic medicine.

关键词： Proteomics Drug Perturbation Drug target Drug combination

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Energy-information trade-off induces continuous and discontinuous phase transitions in lateral predictive coding

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Science China(Physics,Mechanics & Astronomy) 2024年第6期67卷 79-85页

作者： Zhen-Ye huang Ruyi Zhou Miao huang Hai-jun Zhou Key Laboratory for Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China School of Optics and Photonics Beijing Institute of TechnologyBeijing 100081China minjiang Collaborative Center for Theoretical Physics Minjiang UniversityFuzhou 350108China

Lateral predictive coding is a recurrent neural network that creates energy-efficient internal representations by exploiting statistical regularity in sensory ***,we analytically investigate the trade-off between information robustness and energy in a linear model of lateral predictive coding and numerically minimize a free energy *** observed several phase transitions in the synaptic weight matrix,particularly a continuous transition that breaks reciprocity and permutation symmetry and builds cyclic dominance and a discontinuous transition with the associated sudden emergence of tight balance between excitatory and inhibitory *** optimal network follows an ideal gas law over an extended temperature range and saturates the efficiency upper bound of energy *** results provide theoretical insights into the emergence and evolution of complex internal models in predictive processing systems.

关键词： predictive coding recurrent neural network phase transition internal model free energy

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Demonstration of controlled high-dimensional quantum teleportation

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Science China(Physics,Mechanics & Astronomy) 2024年第3期67卷 1-6页

作者： min-Yu Lv Xiao-min Hu Neng-Fei Gong Tie-jun Wang Yu Guo Bi-Heng Liu Yun-Feng huang Chuan-Feng Li Guang-Can Guo CAS Key Laboratory of Quantum Information University of Science and Technology of ChinaHefei 230026China CAS Centerfor Excellence in Quantum Information and Quantum Physics University of Science and Technology of ChinaHefei230026China Hefei National Laboratory University of Science and Technology of ChinaHefei 230088China State Key Laboratory of Information Photonics and Optical Communications School of ScienceBeijing University of Posts and TelecommunicationsBeijing 100876China

Controlled quantum teleportation(CQT), which is regarded as the prelude and backbone for a genuine quantum internet, reveals the cooperation, supervision, and control relationship among the sender, receiver, and controller in the quantum network within the simplest unit. Compared with low-dimensional counterparts, high-dimensional CQT can exhibit larger information transmission capacity and higher superiority of the controller's authority. In this article, we report a proof-of-principle experimental realization of three-dimensional(3D) CQT with a fidelity of 97.4% ± 0.2%. To reduce the complexity of the circuit, we simulate a standard 4-qutrit CQT protocol in a 9×9-dimensional two-photon system with high-quality operations. The corresponding control powers are 48.1% ± 0.2% for teleporting a qutrit and 52.8% ± 0.3% for teleporting a qubit in the experiment, which are both higher than the theoretical value of control power in 2-dimensional CQT protocol(33%). The results fully demonstrate the advantages of high-dimensional multi-partite entangled networks and provide new avenues for constructing complex quantum networks.

关键词： high dimension quantum information quantum teleportation quantum nonlocality

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Discovering deaminases using AlphaFold2:a strategy to search for tool proteins for gene editing

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Signal Transduction and Targeted Therapy 2024年第3期9卷 822-824页

作者： Yongye huang Jianxin Jiang min Wu Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health SciencesNortheastern UniversityShenyang 110169China Wound Trauma Medical Center State Key Laboratory of TraumaBurns and Combined InjuryDaping HospitalArmy Medical UniversityChongqing 400042China Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University WenzhouZhejiang 325000China Wenzhou Institute University of Chinese Academy of SciencesWenzhou 325000China The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical UniversityNingboChina

A recent study by huang et *** in Cell reported the application of AlphaFold2 to forecast the structures of deaminase proteins and cluster them based on structural similarity,creating a truncated Sdd that can be used as a cytosine base editor(CBE)to be integrated into a single adeno-associated virus(AAV)1 This ground-breaking study aided by the artificial intelligence system would largely broaden the utility of tool proteins for gene editing.

关键词： CBE Alpha editor

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Quantum vector DC magnetometry via selective phase accumulation

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Science China(Physics,Mechanics & Astronomy) 2024年第10期67卷 12-22页

作者： min Zhuang Sijie Chen Jiahao huang Chaohong Lee Institute of Quantum Precision Measurement State Key Laboratory of Radio Frequency Heterogeneous IntegrationCollege of Physics and Optoelectronic EngineeringShenzhen UniversityShenzhen 518060China Quantum Science Center of Guangdong-Hong Kong-Macao Greater Bay Area(Guangdong) Shenzhen 518045China Laboratory of Quantum Engineering and Quantum Metrology School of Physics and AstronomySun Yat-sen University(Zhuhai Campus)Zhuhai 519082China

Precision measurement of magnetic fields is a crucial issue in both fundamental scientific research and practical sensing *** sensitive detection of a vector magnetic field poses a significant challenge in quantum magnetometry,particularly in estimating a vector DC magnetic field with high ***,we propose a comprehensive protocol for quantum vector DC magnetometry,utilizing selective phase accumulation in both non-entangled and entangled quantum *** upon the principles of Ramsey interferometry,our protocol enables the selective accumulation of phase for a specific magnetic field component by incorporating a meticulously designed pulse *** the individual measurement scheme,we employ three individual quantum interferometries to independently estimate each of the three magnetic field ***,in the simultaneous measurement scheme,the application of a pulse sequence along different directions enables the simultaneous estimation of all three magnetic field components using only one quantum ***,by employing an entangled state(such as the Greenberger-Horne-Zeilinger state)as the input state,the measurement precisions of all three components may reach the Heisenberg *** study not only establishes a general protocol for measuring vector magnetic fields using quantum probes,but also presents a viable pathway for achieving entanglement-enhanced multi-parameter estimation.

关键词： magnetometry quantum interferometry entanglement-enhanced quantum metrology

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Joint Sample Position Based Noise Filtering and Mean Shift Clustering for Imbalanced Classification Learning

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Tsinghua Science and Technology 2024年第1期29卷 216-231页

作者： Lilong Duan Wei Xue jun huang Xiao Zheng School of Computer Science and Technology Anhui University of TechnologyMaanshan 243032China Institute of Artificial Intelligence Hefei Comprehensive National Science CenterHefei 230088China

The problem of imbalanced data classification learning has received much *** classification algorithms are susceptible to data skew to favor majority samples and ignore minority *** weighted minority oversampling technique(MWMOTE)is an effective approach to solve this problem,however,it may suffer from the shortcomings of inadequate noise filtering and synthesizing the same samples as the original minority *** this end,we propose an improved MWMOTE method named joint sample position based noise filtering and mean shift clustering(SPMSC)to solve these ***,in order to effectively eliminate the effect of noisy samples,SPMsC uses a new noise filtering mechanism to determine whether a minority sample is noisy or not based on its position and distribution relative to the majority *** that MWMOTE may generate duplicate samples,we then employ the mean shift algorithm to cluster minority samples to reduce synthetic replicate ***,data cleaning is performed on the processed data to further eliminate class *** on extensive benchmark datasets demonstrate the effectiveness of SPMsC compared with other sampling methods.

关键词： imbalanced data classification oversampling noise filtering clustering

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