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Toward understanding the role of genomic repeat elements in neurodegenerative diseases

Neural Regeneration Research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen institute of Science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina MOE Frontiers Center for Brain Science Fudan UniversityShanghaiChina MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan UniversityShanghaiChina zhangjiang Fudan International Innovation Center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

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Observation of cavitation and water-refilling processes in plants with X-ray phase contrast microscopy

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Nuclear Science and Techniques 2013年第6期24卷 1-6页

作者： XUE Yanling XIAO Tiqiao DU Guoha TONG Yajun LIU Huiqiang DENG Biao XIE Honglan XU Hongjie Shanghai institute of Applied Physics Chinese Academy of SciencesZhangjiang Campus

With the spatial coherence of X-rays and high flux and brightness of the 3rd generation synchrotron radiation facility,X-ray phase contrast microscopy(XPCM)at Shanghai Synchrotron Radiation Facility(SSRF)can provide high resolution dynamic imaging of low electron density materials in *** this paper,we investigated the cavitation and water-refilling processes in rice and bamboo leaves utilizing XPCM at *** occurrence of xylem cavitation was recorded in *** study also revealed that under different dehydration conditions,cavitation occurs in different degrees,and therefore,the refilling process is *** results demonstrate that SSRF can provide high enough fluxes to study dynamic processes in plants in real-time,and XPCM is expected to be a promising method to reveal the mechanisms of cavitation and its repair in plants nondestructively.

关键词：相衬显微镜显微镜观察植物 X-射线填充过程气蚀上海同步辐射装置水稻

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Scan system for arbitrary-shaped samples at the synchrotron radiation facility

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Nuclear Science and Techniques 2017年第5期28卷 18-27页

作者： Xu-Ying Lan Dong-Xu Liang Cheng-Wen Mao Shanghai institute of Applied Physics Chinese Academy of Sciences Zhangjiang Campus Shanghai 201204 China

X-ray fluorescence(XRF) scan methodology is important for elemental mapping of samples at a synchrotron radiation facility. To save the experiment time and improve the experiment efficiency, one should develop an efficient XRF scan method. In this paper, a new scan mode is presented. It can map arbitrary-shaped areas withou stopping the motors. The control and data acquisition system integrates motor controlling, detector triggering, and data acquisition and storage. The system realizes the arbitrary-shaped 2D-mapping and fluorescence data acquisition synchronously. SR-XRF mapping has been performed with a standard gold mask to verify the validity of this method a beamline BL15U1 of the Shanghai Synchrotron Radiation Facility. The results show that this method reduces the tota scan time and improves the experiment efficiency.

关键词： Synchrotron radiation X-ray fluorescence mapping EPICS XPS controller

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Synthesis,Crystal Structure and Biological Activity of(2,4-Dihydroxy-3,6-dimethoxyphenyl)-((1R,2S,3S,4R,7R)-7-isopropyl-5-methyl-3-phenylbicyclo[2.2.2]-oct-5-en-2-yl)methanone

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Chinese Journal of Structural Chemistry 2018年第11期37卷 1718-1722页

作者：孙振亮杜鹏严雪冰李豪黄林生屈潇孔程吕志良秦环龙 Medical College Tongji University zhangjiang Branch institute of Chinese State institute of Pharmaceutical Industry

The crystal structure of the natural terpene derivative（2,4-dihydroxy-3,6-dimethoxyphenyl）(（1 R,2 S,3 S,4 R,7 R）-7-isopropyl-5-methyl-3-phenylbicyclo[2.2.2]oct-5-en-2-yl)-methanone was determined by single-crystal X-ray diffraction method. The compound crystallizes in triclinic,space group P21/c with a = 16.1444（9）, b = 16.5294（9）, c = 19.7875（11） ?, V = 5280.4（5） ?3, Z = 4,Dc = 1.209 g/cm;, F（000） = 2064, μ（Cu Kα） = 0.675 mm-1, S = 1.069, R = 0.0520 and wR(I > 2σ（I）)= 0.1392. The spiro structure constructed by Diels-Alder reaction was highly symmetric. In addition,the title compound showed inhibitory activities against cancer cell line with varied potencies.

关键词： monoterpene total synthesis crystal structure biological activity

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The protein complex crystallography beamline(BL19U1)at the Shanghai Synchrotron Radiation Facility

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Nuclear Science and Techniques 2019年第11期30卷 30-40页

作者： Wei-Zhe Zhang Jian-Chao Tang Si-Sheng Wang Zhi-Jun Wang Wen-Ming Qin Jian-Hua He National Facility for Protein Science in Shanghai Shanghai Advanced Research Institute(Zhangjiang Laboratory)Chinese Academy of SciencesShanghai 201210China Shanghai Synchrotron Radiation Facility Shanghai Advanced Research Institute(Zhangjiang Laboratory)Chinese Academy of SciencesShanghai 201204China

The protein complex crystallographic beamline BL19U1 at the Shanghai Synchrotron Radiation Facility is one of the five beamlines dedicated to protein sciences operated by National Facility for Protein Science(Shanghai,China).The beamline,which features a small-gap invacuum undulator,has been officially open to users since March *** beamline delivers X-ray in the energy range 7–15 *** its high flux,low divergence beam and a large active area detector,BL19U1 is designed for proteins with large molecular weight and large crystallographic unit cell *** performance and stable operation of the beamline have allowed the number of Protein Data Bank(PDB)depositions and the number of articles published based on data collected at this beamline to increase *** date,over 300 research groups have collected data at the *** than 600 PDB entries have been deposited at the PDB(***).More than 300 papers have been published that include data collected at the beamline,including 21 research articles published in the top-level journals Cell,Nature,and Science.

关键词： MX beamlines Macromolecular crystallography Shanghai Synchrotron Radiation Facility SSRF-BL19U1

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Cyano migration-mediated radical-polar crossover cyclopropanation

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Science China Chemistry 2025年第1期 241-248页

作者： Ziqiang Wang Yasu Chen Jie Li Chen Zhu Key Laboratory of Organic Synthesis of Jiangsu Province College of Chemistry Chemical Engineering and Materials ScienceSoochow University Frontiers Science Center for Transformative Molecules Zhangjiang Institute for Advanced Study and Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University

We report a novel cyano migration-mediated radical-polar crossover process, whereby both the sulfonylcyanation of aliphatic alkenes and the formation of cyclopropanes are concurrently achieved. This transformation yields a diverse array of multisubstituted cyclopropanes under mild photocatalytic conditions. Mechanistic studies elucidate that the reaction proceeds via intramolecular nucleophilic substitution, leading to the formation of the cyclopropane derivatives.

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An S-band solid-state radio frequency power amplifier used at Shanghai soft X-ray FEL facility

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Nuclear Science and Techniques 2016年第6期27卷 86-92页

作者： Hong-Li Ding Ming-Hua Zhao Cheng-Cheng Xiao Shao-Peng Zhong Jun-Qiang Zhang Shanghai institute of Applied Physics Chinese Academy of SciencesZhangjiangShanghai 201800China University of Chinese Academy of Sciences Beijing 100049China

In this paper,we present the general design methods and parameter measurements of a 1-k W solidstate radio frequency(RF) power amplifier at 2856 MHz,for the soft X-ray free electron laser ***-stage amplification with a 4-way combination is *** RF switch module is integrated with the solid-state RF power amplifier to convert the continuous wave(CW) signal into pulse signal,with adjustable pulse *** power gain is measured at 57.7 d B at 60 d Bm *** RF phase noise,which is measured by the low-level RF system,is\0.015 degree(RMS),while the pulse frontier jitter is\5 ns.

关键词：射频功率放大器激光装置自由电子软X射线固态 S波段上海参数测量

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Local structural evolutions of CuO/ZnO/Al2O3 catalyst for methanol synthesis under operando conditions studied by in situ quick X-ray absorption spectroscopy

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Nuclear Science and Techniques 2017年第2期28卷 35-43页

作者： Xue-Ping Sun Fan-Fei Sun Song-Qi Gu Jing Chen Xian-Long Du Jian-Qiang Wang Yu-Ying Huang Zheng Jiang Shanghai institute of Applied Physics Chinese Academy of Sciences Zhangjiang Campus Shanghai 201204 China University of Chinese Academy of Sciences Beijing 100049China

In situ quick X-ray absorption spectroscopy(QXAFS) at the Cu and Zn K-edge under operando conditions has been used to unravel the Cu/Zn interaction and identify possible active site of CuO/ZnO/Al_2O_3 catalyst for methanol synthesis. In this work, the catalyst, whose activity increases with the reaction temperature and pressure, was studied at calcined, reduced, and reacted conditions. TEM and EDX images for the calcined and reduced catalysts showed that copper was distributed uniformly at both conditions. TPR profile revealed two reduction peaks at 165 and 195 °C for copper species in the calcined catalyst. QXAFS results demonstrated that the calcined form consisted mainly of a mixed Cu O and Zn O, and it was progressively transformed into Cu metal particles and dispersed Zn O species as the reduction treatment. It was demonstrated that activation of the catalyst precursor occurred via a Cu^+intermediate, and the active catalyst predominantly consisted of metallic Cu and Zn O evenunder higher pressures. Structure of the active catalyst did not change with the temperature or pressure, indicating that the role of the Zn was mainly to improve Cu *** indicates the potential of QXAFS method in studying the structure evolutions of catalysts in methanol synthesis.

关键词： In situ Quick X-ray absorption spectroscopy CuO/ZnO/Al2O3 catalyst Operando condition

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A novel heating area design of temperature-jump microfluidic chip for synchrotron radiation solution X-ray scattering

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Nuclear Science and Techniques 2016年第4期27卷 115-119页

作者： Yi-Wen Li Feng-Gang Bian Jie Wang Shanghai institute of Applied Physics Chinese Academy of Sciences Zhangjiang Campus Shanghai 201204 China University of Chinese Academy of Sciences Beijing 100049 China

In this paper, we present a novel design scheme of temperature-jump(T-jump) area for microfluidic *** simulation and experimental research of thermal characteristics of the solution in microchannels is *** simulation of the temperature-jump microchannel is analyzed to study the heat transfer characteristics by comparing performance of three proposed *** of the power requirement is discussed in the dimensional design of microheater. Temperature-sensitive fluorescent dye is applied to investigate the temperature field of microchannel heated by a designed microheater. It is found that the T-jump microfluidic device can provide rapid heating for solutions with strong convection heat transfer ability.

关键词：微流控芯片温升设计温度场 X射线散射同步辐射溶液微流体装置跳变

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Improving Touschek lifetime and synchrotron frequency spread by passive harmonic cavity in the storage ring of SSRF

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Nuclear Science and Techniques 2017年第8期28卷 41-46页

作者： Thanapong Phimsen Bo-Cheng Jiang Hong-Tao Hou Shun-Qiang Tian Man-Zhou Zhang Qing-Lei Zhang Zhen-Tang Zhao Shanghai institute of Applied Physics Chinese Academy of Sciences Zhangjiang Campus Shanghai 201800 China University of Chinese Academy of Sciences Beijing 100049China

Beam lifetime of a synchrotron is dominated by Touschek *** the beamline Phase II project of Shanghai synchrotron radiation facility,a passive third harmonic cavity is to be installed for bunch lengthening and instability *** this paper,the beam dynamics of the cavity is *** parameters of passive operation are optimized to cancel the slope of RF voltage and lengthen the *** Touschek lifetime increases are estimated for optimum and non-optimum voltage flattening.A tolerance of the operation is studied in case that there is a shift on detuning *** effect caused by reduction in harmonic voltage generated by lengthened bunch distribution is also estimated using iteration *** increase in synchrotron frequency spread due to nonlinearity of the voltage giving to the bunch is found by using tracking *** spread can help in damping coupled bunch instability through Landau damping.

关键词：同步加速器束流寿命谐波上海储存环同步辐射光束线电压降低扩频

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