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| 1 | Large-field high-resolution two-photon digital scanned light-sheet microscopy显示文摘 | Weijian Zong Jia Zhao Xuanyang Chen Yuan Lin Huixia Ren Yunfeng Zhang Ming Fan Zhuan Zhou Heping Cheng Yujie Sun Liangyi Chen | 2015 | Cell Research2015，25，2： | 12 |
| 2 | Super-resolution fluorescence-assisted diffraction computational tomography reveals the threedimensional landscape of the cellular organelle interactome显示文摘The emergence of super-resolution(SR)fluorescence microscopy has rejuvenated the search for new cellular substructures.However,SR fluorescence microscopy achieves high contrast at the expense of a holistic view of the interacting partners and surrounding environment.Thus,we developed SR fluorescence-assisted diffraction computational tomography(SR-FACT),which combines label-free three-dimensional optical diffraction tomography(ODT)with two-dimensional fluorescence Hessian structured illumination microscopy.The ODT module is capable of resolving the mitochondria,lipid droplets,the nuclear membrane,chromosomes,the tubular endoplasmic reticulum,and lysosomes.Using dual-mode correlated live-cell imaging for a prolonged period of time,we observed novel subcellular structures named dark-vacuole bodies,the majority of which originate from densely populated perinuclear regions,and intensively interact with organelles such as the mitochondria and the nuclear membrane before ultimately collapsing into the plasma membrane.This work demonstrates the unique capabilities of SR-FACT,which suggests its wide applicability in cell biology in general. | Dashan Dong Xiaoshuai Huang Liuju Li Heng Mao Yanquan Mo Guangyi Zhang Zhe Zhang Jiayu Shen Wei Liu Zeming Wu Guanghui Liu Yanmei Liu Hong Yang Qihuang Gong Kebin Shi Liangyi Chen | 2020 | Light(Science & Applications)2020，9，1： | 7 |
| 3 | Graded activation of CRAC channel by binding of different numbers of STIM1 to Orail subunits显示文摘Ca2+ 激活版本的 Ca2+(CRAC ) 隧道毛孔被 STIM1 被 Orai1 和 gated 在细胞内部的 Ca2+ 店弄空以后形成。为了解决分子被要求到多少 STIM1,打开一条 CRAC 隧道,我们与 STIM1 的功能的二双人脚踏车的细胞质的领域熔化了 Orai1 子单元的不同数字(残余 336-485,指定了领域为 S ) 。整个房间的补丁夹钳揭示的这些妄想的分子的记录在四 Orai1 和八个 S 领域的 stoichiometry 最大的到达的那 CRAC 水流。进一步的实验显示二双人脚踏车的 S 领域明确地与一个 Orai1 子单元,和 CRAC 电流的 C 终点交往当更多的 Orai1 子单元能与 S 领域或 STIM1 蛋白质交往,能逐渐地被增加。我们的数据建议一条 CRAC 隧道的那最大的开始要求八个 STIM1 分子,并且支持 CRAC 隧道激活不以一种鈥渁l l-or-none 鈥 ? 方式,但是经历的一个模型经由 STIM1 的不同数字的绑定的分级的进程。 | Zhengzheng Li Lin Liu Yongqiang Deng Wei Ji Wen Du Pingyong Xu Liangyi Chen Tao Xu | 2011 | Cell Research2011，21，2： | 5 |
| 4 | A protocol for structured illumination microscopy with minimal reconstruction artifacts显示文摘The imaging rate of structured illumination microscopy (SIM) reached 188 Hz recently. As the exposure time decreases, the camera detects fewer virtual photons, while the noise level remains the same. As a result, the signal-to-noise ratio (SNR) decreases sharply. Furthermore, the SNR decreases further because of photobleaching and phototoxicity. This decreased quality of SIM raw data may lead to surprising artifacts with various causes, which may confuse a new user of SIM microscopy. We summarize three significant possible sources of severe artifacts in reconstructed super-resolution (SR) images. Ultrafast motion of a biological sample or an uneven illumination pattern is the most difficult to be identified. The estimated parameter could also be incorrect, leading to artifact of regular patterns. Furthermore, rec on struction with the Wiener method generates stochastic artifacts due to the amplification of noise during the deconvolution process. To deal with these problems, we have established a protocol to reconstruct ultrafast SIM raw data obtained in low SNR conditions. First, we checked the quality of the raw data with the ImageJ plugin SIMcheck before rec on struction. Then, a modified parameter estimation method was used to improve the precision of the parameters. Finally, an iterative algorithm was used for SIM reconstruction under low signal-to-noise ratio cond让ions. This procedure effectively suppressed the artifacts in the super-resoluti on images rec on structed from raw data of low signal-to-noise ratio. | Junchao Fan Xiaoshuai Huang Liuju Li Shan Tan Liangyi Chen | 2019 | Biophysics Reports2019，5，2： | 4 |
| 5 | A new type of ERGIC–ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis显示文摘Under stress,the endomembrane system undergoes reorganization to support autophagosome biogenesis,which is a central step in autophagy.How the endomembrane system remodels has been poorly understood.Here we identify a new type of membrane contact formed between the ER-Golgi intermediate compartment(ERGIC)and the ER-exit site(ERES)in the ER-Golgi system,which is essential for promoting autophagosome biogenesis induced by different stress stimuli.The ERGIC-ERES contact is established by the interaction between TMED9 and SEC12 which generates a short distance opposition(as close as 2-5 nm)between the two compartments.The tight membrane contact allows the ERES-located SEC12 to transactivate COPII assembly on the ERGIC.In addition,a portion of SEC12 also relocates to the ERGIC.Through both mechanisms,the ERGIC-ERES contact promotes formation of the ERGIC-derived COPII vesicle,a membrane precursor of the autophagosome.The ERGIC-ERES contact is physically and functionally different from the TFG-mediated ERGIC-ERES adjunction involved in secretory protein transport,and therefore defines a unique endomembrane structure generated upon stress conditions for autophagic membrane formation. | Shulin Li Rui Yan Jialu Xu Shiqun Zhao Xinyu Ma Qiming Sun Min Zhang Ying Li Jun-Jie Gogo Liu Liangyi Chen Sai Li Ke Xu Liang Ge | 2022 | Cell Research2022，32，2： | 3 |
| 6 | Miniature Fluorescence Microscopy for Imaging Brain Activity in Freely-Behaving Animals显示文摘An ultimate goal of neuroscience is to decipher the principles underlying neuronal information processing at the molecular,cellular,circuit,and system levels.The advent of miniature fluorescence microscopy has furthered the quest by visualizing brain activities and structural dynamics in animals engaged in self-determined behaviors.In this brief review,we summarize recent advances in miniature fluorescence microscopy for neuroscience,focusing mostly on two mainstream solutions-miniature single-photon microscopy,and miniature two-photon microscopy.We discuss their technical advantages and limitations as well as unmet challenges for future improvement.Examples of preliminary applications are also presented to reflect on a new trend of brain imaging in experimental paradigms involving body movements,long and complex protocols,and even disease progression and aging. | Shiyuan Chen Ziehen Wang Dong Zhang Aiming Wang Liangyi Chen Heping Cheng Runlong Wu | 2020 | Neuroscience Bulletin2020，36，10： | 2 |
| 7 | Ultrafast,accurate,and robust localization of anisotropic dipoles显示文摘The resolution of single molecule localization imaging techniques largely depends on the precision of localization algorithms.However,the commonly used Gaussian function is not appropriate for anisotropic dipoles because it is not the true point spread function.We derived the theoretical point spread function of tilted dipoles with restricted mobility and developed an algorithm based on an artifi cial neural network for estimating the localization,orientation and mobility of individual dipoles.Compared with fi tting-based methods,our algorithm demonstrated ultrafast speed and higher accuracy,reduced sensitivity to defocusing,strong robustness and adaptability,making it an optimal choice for both two-dimensional and threedimensional super-resolution imaging analysis. | Yongdeng Zhang Lusheng Gu Hao Chang Wei Ji Yan Chen Mingshu Zhang Lu Yang Bei Liu Liangyi Chen Tao Xu | 2013 | Protein & Cell2013，4，8： | 2 |
| 8 | Alterations of the Ca2+ signaling pathway in pancreatic beta-cells isolated from db/db mice显示文摘 | Kuo Liang Wen Du Jingze Lu Fei Li Lu Yang Yanhong Xue Bertil Hille Liangyi Chen | 2014 | Protein & Cell2014，5，10： | 2 |
| 9 | Hessian single-molecule localization microscopy using sCMOS camera显示文摘 | Fudong Xue Wenting He Fan Xu Mingshu Zhang Liangyi Chen Pingyong Xu | 2018 | Biophysics Reports2018，4，4： | 2 |
| 10 | 3D Hessian deconvolution of thick light-sheet z-stacks for high-contrast and high-SNR volumetric imaging显示文摘Due to its ability of optical sectioning and low phototoxicity,z-stacking light-sheet microscopy has been the tool of choice for in vivo imaging of the zebrafish brain.To image the zebrafish brain with a large field of view,the thickness of the Gaussian beam inevitably becomes several times greater than the system depth of field(DOF),where the fluorescence distributions outside the DOF will also be collected,blurring the image.In this paper,we propose a 3D deblurring method,aiming to redistribute the measured intensity of each pixel in a light-sheet image to in situ voxels by 3D deconvolution.By introducing a Hessian regularization term to maintain the continuity of the neuron dis-tribution and using a modified stripe removal algorithm,the reconstructed z stack images exhibit high contrast and a high signal-to-noise ratio.These performance characteristics can facilitate subsequent processing,such as 3D neuron registration,segmentation,and recognition. | ZHE ZHANG DONGZHOU GOU FAN FENG RUYI ZHENG KE DU HONGRUN YANG GUANGYI ZHANG HUITAO ZHANG LOUIS TAO LIANGYI CHEN HENG MAO | 2020 | Photonics Research2020，8，6： | 1 |
| 11 | Dynamics of calcium clearance in mouse pancreatic β-cells显示文摘 | Liangyi Chen Duk-Su Koh Bertil Hill | 2003 | Diabetes2003，52，： | 1 |
| 12 | Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation显示文摘In fluorescence microscopy,computational algorithms have been developed to suppress noise,enhance contrast,and even enable super-resolution(SR).However,the local quality of the images may vary on multiple scales,and these differences can lead to misconceptions.Current mapping methods fail to finely estimate the local quality,challenging to associate the SR scale content.Here,we develop a rolling Fourier ring correlation(rFRC)method to evaluate the reconstruction uncertainties down to SR scale.To visually pinpoint regions with low reliability,a filtered rFRC is combined with a modified resolution-scaled error map(RSM),offering a comprehensive and concise map for further examination.We demonstrate their performances on various SR imaging modalities,and the resulting quantitative maps enable better SR images integrated from different reconstructions.Overall,we expect that our framework can become a routinely used tool for biologists in assessing their image datasets in general and inspire further advances in the rapidly developing field of computational imaging. | Weisong Zhao Xiaoshuai Huang Jianyu Yang Liying Qu Guohua Qiu Yue Zhao Xinwei Wang Deer Su Xumin Ding Heng Mao Yaming Jiu Ying Hu Jiubin Tan Shiqun Zhao Leiting Pan Liangyi Chen Haoyu Li | 2023 | Light(Science & Applications)2023，12，12： | 0 |
| 13 | Bulk-like endocytosis plays an important role in the recycling of insulin granules in pancreatic beta cells显示文摘Although bulk endocytosis has been found in a number of neuronal and endocrine cells,the molecular mechanism and physiological function of bulk endocytosis remain elusive.In pancreatic beta cells,we have observed bulk-like endocytosis evoked both by flash photolysis and trains of depolarization.Bulk-like endocytosis is a clathrin-independent process that is facilitated by enhanced extracellular Ca^(2+) entry and suppressed by the inhibition of dynamin function.Moreover,defects in bulklike endocytosis are accompanied by hyperinsulinemia in primary beta cells dissociated from diabetic KKAy mice,which suggests that bulk-like endocytosis plays an important role in maintaining the exo-endocytosis balance and beta cell secretory capability. | Du Wen Yanhong Xue Kuo Liang Tianyi Yuan Jingze Lu Wei Zhao Tao Xu Liangyi Chen | 2012 | Protein & Cell2012，3，8： | 0 |
| 14 | Superresolution live-cell imaging reveals that the localization of TMEM106B to filopodia in oligodendrocytes is compromised by the hypomyelination-related D252N mutation显示文摘Hypomyelination leukodystrophies constitute a group of heritable white matter disorders exhibiting defective myelin development.Initially identified as a lysosomal protein,the TMEM106B D252N mutant has recently been associated with hypomyelination.However,how lysosomal TMEM106B facilitates myelination and how the D252N mutation disrupts that process are poorly understood.We used superresolution Hessian structured illumination microscopy(Hessian-SIM)and spinning discconfocal structured illumination microscopy(SD-SIM)to find that the wild-type TMEM106B protein is targeted to the plasma membrane,filopodia,and lysosomes in human oligodendrocytes.The D252N mutation reduces the size of lysosomes in oligodendrocytes and compromises lysosome changes upon starvation stress.Most importantly,we detected reductions in the length and number of filopodia in cells expressing the D252N mutant.PLP1 is the most abundant myelin protein that almost entirely colocalizes with TMEM106B,and coexpressing PLP1 with the D252N mutant readily rescues the lysosome and filopodia phenotypes of cells.Therefore,interactions between TMEM106B and PLP1 on the plasma membrane are essential for filopodia formation and myelination in oligodendrocytes,which may be sustained by the delivery of these proteins from lysosomes via exocytosis. | Shijia Xing Xiaolu Zheng Huifang Yan Yanquan Mo Ruoyu Duan Zhixing Chen Kunhao Wang Kai Gao Tongsheng Chen Shiqun Zhao Jingmin Wang Liangyi Chen | 2023 | Science China(Life Sciences)2023，66，8： | 0 |
| 15 | Mitochondria determine the sequential propagation of the calcium macrodomains revealed by the super-resolution calcium lantern imaging显示文摘Despite the wide application of super-resolution(SR)microscopy in biological studies of cells,the technology is rarely used to monitor functional changes in live cells.By combining fast spinning disc-confocal structured illumination microscopy(SD-SIM)with loading of cytosolic fluorescent Ca2+indicators,we have developed an SR method for visualization of regional Ca2+dynamics and related cellular organelle morphology and dynamics,termed SR calcium lantern imaging.In COS-7 cells stimulated with ATP,we have identified various calcium macrodomains characterized by different types of Ca2+release from endoplasmic reticulum(ER)stores.Finally,we demonstrated various roles of mitochondria in mediating calcium signals from different sources;while mitochondria can globally potentiate the Ca2+entry associated with store release,mitochondria also locally control Ca2+release from the neighboring ER stores and assist in their refilling processes. | Yulin Zhang Jianyong Wang Shijia Xing Liuju Li Shiqun Zhao Wenzhen Zhu Kuo Liang Yanmei Liu Liangyi Chen | 2020 | Science China(Life Sciences)2020，63，10： | 0 |
| 16 | Mining Cross-Transaction Web Usage Patterns显示文摘 | Jian Chen Jian Yin Jin Huang Liangyi Ou | 2005 | 通讯和计算机(中英文版)2005，2，5： | 0 |
| 17 | Diffusion behavior of polyelectrolytes in dilute solution: coupling effects of hydrodynamic and Coulomb interactions显示文摘The diffusion behavior of polyelectrolytes in dilute salt-free solution is studied through a hybrid mesoscale simulation technique that combines the molecular dynamics method and the multiparticle collision dynamics approach.To elucidate the effects of hydrodynamic interactions(HI),we compare results for hydrodynamic and random solvents.When HI are taken into account,we find that the chain diffusivity decreases initially and then increases gradually with the increasing strength of the Coulomb interaction.By contrast,when HI are switched off,the electrostatic-dependent diffusivity shows three distinct regions,and a plateau of approximately constant diffusivity manifests between two decreasing regions.The findings reveal that the dynamics of polyelectrolytes in dilute solution depend on the coupling effects of hydrodynamic and Coulomb interactions,and that these dynamics can be understood by considering the conformational changes of chains,the counterion condensation,and the dynamics of counterions. | LIU LiJun CHEN JiZhong CHEN WenDuo LI LiangYi AN LiJia | 2014 | Science China Chemistry2014，57，7： | 0 |
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