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| 1 | 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 |
| 2 | Microblog Burst Keywords Detection Based on Social Trust and Dynamics Model显示文摘Microblog has emerged as a popular medium for providing new sources of information and rapid communications, particularly during burst topics. Burst keywords detection from real-time microblog streams is important for burst topics detection. The exiting algorithms may detect fake burst keywords without taking into account the trustworthiness of the users and human's daily timetable. Our work is the first to combine the trustworthiness of the users with burst keywords detection. We propose a novel approach to detect burst keywords based on social trust and dynamics model. We adapt basic notions of dynamics from physics and model keywords bursts as momentum change of the keywords. On the analogy of physical dynamics model, this approach defines mass as the trustworthiness of user and position as the frequency of keywords. We compute each keyword's burst value by using Moving average convergence/divergence(MACD) and determine whether it is a burst keyword in a given time window. The experimental results on large-scale Sina microblog dataset show that the proposed approach can avoid detecting fake burst keywords. | DONG Guozhong LI Ruiguang YANG Wu WANG Wei GONG Liangyi SHEN Guowei YU Miao LV Jiguang | 2014 | Chinese Journal of Electronics2014，23，4： | 6 |
| 3 | Functional Analysis of Slow Myosin Heavy Chain 1 and Myomesin-3 in Sarcomere Organization in Zebrafish Embryonic Slow Muscles显示文摘Myofibrillogenesis, sarcomere 形成的过程,要求 sarcomeric 蛋白质的靠近的相互作用和 sarcomere 结构的各种各样的部件。肌浆球蛋白厚细丝和 M 线是 sarcomere 的二个关键部件。M 线的 myomesin 蛋白质与肌浆球蛋白和 titin 蛋白质交往并且使,这被建议了厚并且有序的 titin 细丝。然而,在 myofibrillogenesis 和 sarcomere 组织的 myomesin 的功能仍然保持大部分神秘。没有猛烈或击倒的动物模型被报导了阐明在 sarcomere 组织 in vivo 的 myomesin 的角色。在这研究,由在 zebrafish 胚胎使用基因特定的击倒的途径,我们执行了 myomesin-3 和慢肌浆球蛋白的 loss-of-function 分析重链(smyhc1 ) 1 在慢肌肉明确地表示了。我们表明了那废除的 smyhc1 击倒在慢肌肉的 myomesin-3 的 sarcomeric 本地化。相反, myomesin-3 的损失没在厚、薄的细丝以及 M 线和 Z 线结构的 sarcomeric 组织上有效果。一起,这些研究显示那肌浆球蛋白厚细丝为 M 线组织和 myomesin-3 的 M 线本地化被要求。相反, myomesin-3 为在慢肌肉的 sarcomere 组织是非必需的。 | Jin Xu Jie Gao Junling Li Liangyi Xue Kan J. Clark Stephen C. Ekker Shao Jun Du | 2012 | Journal of Genetics and Genomics2012，39，2： | 6 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | Optimization of Protectant, Salinity and Freezing Condition for Freeze-Drying Preservation of Edwardsiella tarda显示文摘Novel preservation condition without ultra-low temperature is needed for the study of pathogen in marine fishes. Freeze-drying is such a method usually used for preservation of terrigenous bacteria. However, studies using freeze-drying method to preserving marine microorganisms remain very limited. In this study, we optimized the composition of protectants during the freeze-drying of Edwardsiella tarda, a fish pathogen that causes systemic infection in marine fishes. We found that the optimal composition of protectant mixture contained trehalose(8.0%), skim milk(12.0%), sodium citrate(2.0%), serum(12.0%) and PVP(2.0%). Orthogonal and interaction analyses demonstrated the interaction between serum and skim milk or sodium citrate. The highest survival rate of E. tarda was observed when the concentration of Na Cl was 10.0, 30.0 and between 5.0 and 10.0 g L^(-1) for preparing TSB medium, E. tarda suspension and protectant mixture, respectively. When E. tarda was frozen at-80℃ or-40℃ for 6 h, its survival rate was higher than that under other tested conditions. Under the optimized conditions, when the protectant mixture was used during freeze-drying process, the survival rate(79.63%–82.30%) of E. tarda was significantly higher than that obtained using single protectant. Scanning electron microscopy(SEM) image indicated that E. tarda was embedded in thick matrix with detectable aggregation. In sum, the protectant mixture may be used as a novel cryoprotective additive for E. tarda. | YU Yongxiang ZHANG Zheng WANG Yingeng LIAO Meijie LI Bin XUE Liangyi | 2017 | Journal of Ocean University of China2017，16，5： | 3 |
| 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 | Effect of fasting on protein metabolism in muscle tissue of Larimichthys crocea revealed by transcriptome and proteome显示文摘The large yellow croaker(Larimichthys crocea)is an important mariculture fish in China.Farmed large yellow croaker undergo periods of fasting to adapt to the environment or to improve meat quality.To better understand the physiological responses of their muscle tissues to fasting stresses,we analyzed the transcriptomes and proteome s of both normally-fed and fasting fish groups and identified 7578 differentially expressed genes(DEGs)and 297 differentially expressed proteins(DEPs)among them.Gene ontology and KEGG analysis showed that the enriched biological pathways were mainly involved in various synthetic and catabolic pathways,especially the protein metabolism.Based on the omics data,nine DEGs related to muscle composition(CAN3,MYL3,and TNNC2),growth(MSTN and MYF5),autophagy(TSC2 and ULK1),and the ubiquitin proteasome pathway(PRS6 B and UCHL3)were examined using qPCR.In response to fasting stress,MYL3 and TNNC2 were significantly downregulated,while genes associated with autophagy and the ubiquitin proteasome pathway were significantly upregulated.In re sponse to fasting stres s,MYL3,TNNC2,and MYF5 positively correlated with muscle growth were significantly downregulated,while inhibiting growth MSTN and genes associated with autophagy and the ubiquitin proteasome pathways were significantly upregulated.These results clarify the effects of fasting on metabolic changes in their muscle components and growth at the molecular level. | Yu ZHANG Weiliang SHEN Juan LI Baoxiao ZHENG Zhengjia LOU Mohammad Aslam HOSAIN Baoying QIAN Liangyi XUE | 2021 | Journal of Oceanology and Limnology2021，39，5： | 1 |
| 10 | Co3O4 nanocrystals on graphene as a synergistic catalyst for oxygen reduction reaction 显示文摘 | LiangYY Li Y G Wang H L Zhou J G Wang J Regier T Dai H J | 2011 | Nature Materials2011，10，10： | 1 |
| 11 | 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 |
| 12 | Germplasm of breeding Pseudosciaena crocea as revealed by microsatellite markers显示文摘The germplasm of breeding large yellow croaker(Pseudosciaena crocea Richardson)was revealed using 12 microsatellite markers.The results showed that the genetic diversities were on a mediated level in the bred Daiqu and Min-Yue stocks and two hybrid groups,as represented by 4.83 of the mean number of alleles and 0.561 of the average observed heterozygosity.The value of pairwise differentiation coefficient(FST)was only 13.1% between Daiqu and Min-Yue stocks,demonstrating the low level of differentiation and a close relationship.However,STRUCTURE simulations and phylogenetic tree based on the UPGMA method supported that they are geographically different populations of the same species with distinct genetic structures.Examinations of individual admixture showed that Min-Yue stock had been contaminated by alien individuals.Moreover,the genetic structures of the two hybrid groups resembled those of their parents,especially affected more by their female parents.Finally,the values of average observed heterozygosity between parents and their ascendants were compared and tested,as a result of no detectable differences(P>0.05). | CHANG Yumei DING Lei LI Mingyun XUE Liangyi LIANG Liqun HE Jianguo LEI Qingquan | 2008 | Acta Oceanologica Sinica2008，27，4： | 0 |
| 13 | 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 |
| 14 | The Impact of Digital Finance on High-Quality Development of the Chengdu-Chongqing Economic Circle显示文摘This paper developed a comprehensive evaluation system that was able to quantify the levels of high-quality development across the cities within the Chengdu-Chongqing economic circle,and investigate the impact that digital finance had on the cities’high-quality development and the underlying mechanisms through which it achieved this.This comprehensive evaluation system was constructed using statistical data from these cities for the period 2014 to 2020 while also taking China’s high-quality development philosophy into account.The key findings revealed that:(a)Digital finance was able to significantly promote high-quality development in the Chengdu-Chongqing economic circle;(b)Digital finance had a significant positive effect in promoting innovative,coordinated,green,open,and shared development;(c)Digital finance was able to stimulate the high-quality development in the Chengdu-Chongqing economic circle by boosting entrepreneurial dynamism;(d)Digital finance had a significant impact on the high-quality development of the axis areas,while its impact was less discernible in non-axis areas.The insights from this research offer a deeper understanding of the factors that drive high-quality development,the role digital finance plays,and the mechanisms through which digital finance is able to propel high-quality development at the city cluster scale. | Wei Liangyi Bai Xiaobo Li Qin | 2024 | Contemporary Social Sciences2024，9，2： | 0 |
| 15 | 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 |
| 16 | Expression of human hepatitis C virus core antigen in tobacco plants by tobacco mosaic virus-based vector system显示文摘Tobacco mosaic virus (TMV) has the potential to highly express foreign gene. A novel TMV-based in trans expression system was constructed. A TMV mutant TSHc had its coat protein replaced with hepatitis C vir黶 (HCV) core antigen gene. Anotherr TMV mutant TSBD was repli-case-defective. Coinfection of the two mutants could cause systemic infection in tobacco plants by in trans complementation of their functions. TSHc could effectively replicate and assemble to viral particles, which were a little longer than that of wild-type TMV. HCV core antigen was expressed in whole tobacco plants. A similar expression level of HCV core antigen was detected on serial passages, which suggested that this viral expression system be stable. | HAN Aidong LIU Yule XIAO Li KANG Liangyi ZHANG Yuman LI Dongtian TIAN Bo | 2000 | Chinese Science Bulletin2000，45，1： | 0 |
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