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| 1 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 2 | The role of tocopherol cyclase in salt stress tolerance of rice(Oryza sativa)显示文摘Tocopherols synthesized exclusively by photosynthetic organisms are major antioxidants in biomembranes.In plants,tocopherol cyclase(TC/VTE1) catalyzes the conversion of 2,3-dimethyl-5-phytyl-1,4-benzoquinone(DMPBQ) to γ-tocopherol.In the present study,OsVTE1,which encodes a rice tocopherol cyclase ortholog,was cloned and characterized.OsVTE1 was induced significantly by abiotic stresses such as high salt,H2O2,drought,cold and by the plant hormones ABA and salicylic acid.The tissue-specific expression pattern and OsVTE1-promoter GUS activity assay showed that OsVTE1 was mainly expressed in the leaf,and also could be detected in the root,stem and panicle.Compared with control plants,transgenic plants with OsVTE1 RNA interference(OsVTE1-RNAi) were more sensitive to salt stress whereas,in contrast,transgenic plants overexpressing OsVTE1(OsVTE1-OX) showed higher tolerance to salt stress.The DAB in vivo staining showed that OsVTE1-OX plants accumulated less H2O2 than did control plants. | OUYANG ShouQiang HE SiJie LIU Peng ZHANG WanKe ZHANG JinSong CHEN ShouYi | 2011 | Science China(Life Sciences)2011，54，2： | 6 |
| 3 | D609 protects retinal pigmented epithelium as a potential therapy for age-related macular degeneration显示文摘Accumulated oxidative damage may lead to irreversible retinal pigmented epithelium(RPE)cell death,which is considered to be the primary cause of dry age-related macular degeneration(AMD),leading to blindness in the elderly.However,an effective therapy for this disease is lacking.Here,we described a robust high-content screening procedure with a library of 814 protective compounds and found that D609 strongly protected RPE cells from sodium iodate(SI)-induced oxidative cell death and prolonged their healthy survival.D609 effectively attenuated excessive reactive oxygen species(ROS)and prevented severe mitochondrial loss due to oxidative stress in the RPE cells.Surprisingly,the potent antioxidative effects of D609 were not achieved through its own reducibility but were primarily dependent on its ability to increase the expression of metallothionein.The injection of this small water-soluble molecule also showed an explicit protective effect of the RPE layer in an SI-induced AMD mouse model.These findings suggested that D609 could serve as a novel antioxidative protector of RPE cells both in vitro and in vivo and unveiled a novel antioxidative mechanism of D609,which may ultimately have clinical applications for the treatment of AMD. | Bowen Wang Li Wang Sijie Gu Yankun Yu Huaxing Huang Kunlun Mo He Xu Fanzhu Zeng Yichen Xiao Lulu Peng Chunqiao Liu Nan Cao Yizhi Liu Jin Yuan Hong Ouyang | 2020 | Signal Transduction and Targeted Therapy2020，5，1： | 2 |
| 4 | Study of the Sensing Characteristics of Irradiated Fiber Bragg Gratings and Fabry-Perot Interferometers Under Gamma Radiation显示文摘The sensing characteristics of irradiated fiber Bragg gratings(FBGs)and Fabry-Perot interferometers(FPIs)were investigated under a 2MGy dose of gamma radiation.The study found that the pressure sensitivity of FP sensors after irradiation was stable,while the temperature sensitivity of FBG sensors was unstable,and both wavelengths displayed a shift.These findings offer the possibility for the application of FP pressure sensors in the gamma radiation environments,and FBG sensors require further research to be suitable for application in the nuclear radiation environments. | Zhuoyue LI Zengling RAN Xianguo QING Zhengxi HE Yaqin XIAO Tingting YANG Xiu HE Jialiang ZHU Peng HE Sijie XU | 2022 | Photonic Sensors2022，12，1： | 1 |
| 5 | The microRNA-218 and ROBO-1 signaling axis correlates with the lymphaticmetastasis of pancreatic cancer显示文摘 | Hang He Yang Di Minrui Liang Feng Yang Lie Yao Sijie Hao Ji Li Yongjian Jiang Chen Jin Deliang Fu | 2013 | Oncology Reports2013，，2： | 1 |
| 6 | Rice transformation with a senescence-inhibition chimeric gene显示文摘A senescence-inhibition chimeric gene containing the specific promoter of SAG 12 and IPT gene was transferred into rice with the biolistic method. Results of PCR, Dot blotting and Southern blotting indicated that the chimeric gene had been integrated into rice genome. Analyses of GUS activity and cytokinin content in transgenic plants of rice and the observation of T 1 generation plant at grain formation stage indicated that the foreign gene was expressed. | Yongcai Fu Yueyun Ding Xinfang Liu Chuanqin Sun Souyun Cao Dongjiang Wang Sijie He Xiangkun Wang Liangcai Li Wenzhong Tian | 1998 | Chinese Science Bulletin1998，43，21： | 1 |
| 7 | Quick photofabrication of functional nanospheres from de novo designed peptides for NIR fluorescence and MR imaging显示文摘Combining the noncovalent and covalent interactions,a series of peptide amphiphiles were designed de novo and synthesized to architect functional assemblies by means of photochemistry.The strand of peptide sequence was structurally capped with photoactive tyrosine-tyrosine(YY)motifs at both termini,and the spacing was filled by alternating of hydrophilic D(L-aspartate)and hydrophobic X(ε-aminocaproic acid)structure.Upon visible-light irradiation,these de novo designed peptides underwent rapid photocrosslinking within merely 10 min.Interestingly,the modulation of alternating D-X pairs in occupying spacer would adjust molecular amphiphilicity,regulate charge distribution,and control particle size and loading capacity of peptide nanospheres(PNS)in aqueous media.With entirely peptide-based matrix,this PNS system could host cationic indicators of fluorescent rhodamine and magnetic GdIII for exemplar near infrared(NIR)fluorescence and magnetic resonance(MR)imaging,which paves a pathway to biomaterial and biomedical applications using de novo designed peptides. | Jingyi Zhao Chen Li Xue-Wang Gao Ke Feng Hao Liu Sijie He Wenhua Zhao Shumin Yang Jianqun Shao Ling Ye Bin Chen Nan Xie Chen-Ho Tung Li-Zhu Wu | 2023 | Nano Research2023，16，3： | 0 |
| 8 | Emerging strategies for nerve repair and regeneration in ischemic stroke:neural stem cell therapy显示文摘Ischemic stroke is a major cause of mortality and disability worldwide,with limited treatment options available in clinical practice.The emergence of stem cell therapy has provided new hope to the field of stroke treatment via the restoration of brain neuron function.Exogenous neural stem cells are beneficial not only in cell replacement but also through the bystander effect.Neural stem cells regulate multiple physiological responses,including nerve repair,endogenous regeneration,immune function,and blood-brain barrier permeability,through the secretion of bioactive substances,including extracellular vesicles/exosomes.However,due to the complex microenvironment of ischemic cerebrovascular events and the low survival rate of neural stem cells following transplantation,limitations in the treatment effect remain unresolved.In this paper,we provide a detailed summary of the potential mechanisms of neural stem cell therapy for the treatment of ischemic stroke,review current neural stem cell therapeutic strategies and clinical trial results,and summarize the latest advancements in neural stem cell engineering to improve the survival rate of neural stem cells.We hope that this review could help provide insight into the therapeutic potential of neural stem cells and guide future scientific endeavors on neural stem cells. | Siji Wang Qianyan He Yang Qu Wenjing Yin Ruoyu Zhao Xuyutian Wang Yi Yang Zhen-Ni Guo | 2024 | Neural Regeneration Research2024，19，11： | 0 |
| 9 | On-Chip Fabrication of Carbon Nanoparticle–Chitosan Composite Membrane显示文摘The on-chip fabrication of a carbon nanoparticle–chitosan composite membrane(i.e. a sorbent membrane or a mixed matrix membrane) using laminar flow-based interfacial deprotonation technology was presented in this paper. In addition, the effects of carbon nanoparticles and reactant flow rates on membrane formation were investigated. Finally, the permeability and adsorption capacities of the membrane were discussed. During fabrication, an acidic chitosan solution and a basic buffer solution that contained carbon nanoparticles were introduced into a microchannel. At the flow interface, a freestanding composite membrane with embedded carbon nanoparticles was formed due to the deprotonation of the chitosan molecules. The membrane growth gradually stopped with time from upstream to downstream and the thickness of the membrane increased rapidly and then slowly along the reactant flow direction.The formation of the membrane was divided into two stages. The average growth rate in the first stage was significantly larger than the average growth rate in the second stage. Carbon nanoparticles in the basic solution acted as nucleating agents and made the membrane formation much easier. As the flow rate of the chitosan solution increased, the averaged membrane thickness and the membrane hydraulic permeability initially increased and then decreased. Because of the addition of carbon nanoparticles, the formed membrane had adsorption abilities. The carbon nanoparticle–chitosan composite membrane that was fabricated in this study could be employed for simultaneous adsorption and dialysis in microdevices in the future. | Weiping Ding Cheng Liang Sijie Sun Liqun He Dayong Gao | 2015 | Journal of Materials Science & Technology2015，31，11： | 0 |
| 10 | Prognostic value of the 21-gene recurrence score in ER-positive,HER2-negative,node-positive breast cancer was similar in nodenegative diseases:a single-center study of 800 patients显示文摘Multi-gene assays have emerged as crucial tools for risk stratification in early-stage breast cancer.This study aimed to evaluate the prognostic significance of the 21-gene recurrence score(RS)in Chinese patients with pN0-l,estrogen receptor-positive(ER+),human epidermal growth factor receptor 2-negative(HER2)breast cancer.Among 800 patients recruited between 2009 and 2016,the median RS was 24(0-69),with 27.4%,46.8%,and 25.9%patients classified into low-,intermediate-,and high-risk groups.Cox regression analysis demonstrated that the high-risk category was associated with significantly higher odds of invasive disease-free survival(IDFS)and distant disease-free survival(DDFS)events compared with the low-risk category(IDFS:HR=2.450,95%Cl 1.017-5.902,P=0.046;DDFS:HR=2.829,95%Cl 1.013-7.901,P=0.047).No significant association between RS category and overall survival(OS)was found(intermediate vs.low:HR=1.244,95%Cl 0.292-5.297,P=0.768;high vs.low:HR=2.933,95%Cl 0.759-11.327,P=0.119).RS,as a continuous variable,was a highly significant predictor for IDFS(HR=1.028,95%Cl 1.010-1.047,P=0.002),DDFS(HR=1.030,95%Cl 1.010-1.051,P=0.003),and OS(HR=1.034,95%Cl 1.007-1.063,P=0.014).Our findings suggested that RS may predict IDFS in Chinese patients with ER+/HER2 breast cancer with NO or N1 disease. | Jiayi Wu Weiqi Gao Xiaosong Chen Chunxiao Fei Lin Lin Weiguo Chen Ou Huang Siji Zhu Jianrong He Yafen Li Li Zhu Kunwei Shen | 2021 | Frontiers of Medicine2021，15，4： | 0 |
| 11 | Development of a novel virus-like particle-based vaccine for preventing tick-borne encephalitis virus infection显示文摘Tick-borne encephalitis virus(TBEV)is an important tick-borne pathogen that poses as a serious public health concern.The coverage and immunogenicity of the currently available vaccines against TBEV are relatively low;therefore,it is crucial to develop novel and effective vaccines against TBEV.The present study describes a novel strategy for the assembly of virus-like particles(VLPs)by co-expressing the structural(core/prM/E)and non-structural(NS2B/NS3Pro)proteins of TBEV.The efficacy of the VLPs was subsequently evaluated in C57BL/6 mice,and the resultant IgG serum could neutralize both Far-Eastern and European subtypes of TBEV.These findings indicated that the VLP-based vaccine elicited the production of cross-subtype reactive antibodies.The VLPs provided protection to mice lacking the type I interferon receptor(IFNAR^(-/-))against lethal TBEV challenge,with undetectable viral load in brain and intestinal tissues.Furthermore,the group that received the VLP vaccine did not exhibit significant pathological changes and the inflammatory factors were significantly suppressed compared to the control group.Immunization with the VLP vaccine induced the production of multiple-cytokine-producing antiviral CD4+T cells in vivo,including TNF-α^(+),IL-2^(+),and IFN-γ^(+)T cells.Altogether,the findings suggest that noninfectious VLPs can serve as a potentially safe and effective vaccine candidate against diverse subtypes of TBEV. | Jielin Tang Muqing Fu Chonghui Xu Bao Xue Anqi Zhou Sijie Chen He Zhao Yuan Zhou Jizheng Chen Qi Yang Xinwen Chen | 2023 | Virologica Sinica2023，38，5： | 0 |
| 12 | A Simple Approach to Achieve Organic Radicals with Unusual Solid-State Emission and Persistent Stability显示文摘Sable organic radicals are promising materials for information storage,molecular magnetism,electronic devices,and biological probes.Many organic radicals have been prepared,but most are non-or weakly emissive and degrade easily upon photoexcitation.It remains challenging to produce stable and efficient luminescent radicals because of the absence of general guidelines for their synthesis.Herein,we present a photoactivation approach to generate a stable luminescent radical from tris(4-chlorophenyl)phosph ine(TCPP)with red emission in the crystal state.The mechanistic study suggests that the molecular symmetry breaking in the crystal causes changes of molecular conformation,redox properties,andmolecular packing that facilitates radical generation and stabilization.This design strategy demonstrates a straightforward approach to develop stable organic luminescent radicals that will open new doors to photoinduced luminescent radical materials. | Xueqian Zhao Junyi Gong Parvej Alam Chao Ma Yanpei Wang Jing Guo Zebin Zeng Zikai He Herman H.Y.Sung Ian D.Williams Kam Sing Wong Sijie Chen Jacky W.Y.Lam Zheng Zhao Ben Zhong Tang | 2022 | CCS Chemistry2022，4，6： | 0 |
| 13 | The Association between Vitamin D and Hashimoto Thyroiditis:An Upto-date Systematic Review and Meta-analysis显示文摘The objective of the surrent study was to summarize the up-to-date studies to investigate the relationship between vitamin D and Hashimoto thyroiditis(HT).An online search of English and Chinese databases was performed.The studies concerned the investigation of the relationship between vitamin D and HT including meta-analysis,meanwhile the heterogeneities were revealed by subgroup analysis.Fourty six elated studies containing 15,336 participants(HT:6,138 versus control:9,198)were included.HT patients had lower levels of 25(OH)D_(3)(standardised mean difference,−1.09;95%CI:[−1.42,−0.75];P<0.01),and were more likely to be deficient in 25(OH)D_(3)(OR,2.77;95%CI,[1.88,3.91];P<0.05).Obvious heterogeneities in the results of meta-analysis were down to the difference of detection methods and criteria of vitamin D insufficiency among studies.Vitamin D deficiency was colncluded to have a significant relation with HT. | Zhengrong Liu Linfei Feng Yanfang He Sijie Yuan Chao Xu | 2022 | Food Materials Research2022，2，1： | 0 |
| 14 | Structural genomics of the human dopamine receptor system显示文摘The dopaminergic system,including five dopamine receptors(D1R to D5R),plays essential roles in the central nervous system(CNS);and ligands that activate dopamine receptors have been used to treat many neuropsychiatric disorders,including Parkinson’s Disease(PD)and schizophrenia.Here,we report cryo-EM structures of all five subtypes of human dopamine receptors in complex with G protein and bound to the pan-agonist,rotigotine,which is used to treat PD and restless legs syndrome.The structures reveal the basis of rotigotine recognition in different dopamine receptors.Structural analysis together with functional assays illuminate determinants of ligand polypharmacology and selectivity.The structures also uncover the mechanisms of dopamine receptor activation,unique structural features among the five receptor subtypes,and the basis of G protein coupling specificity.Our work provides a comprehensive set of structural templates for the rational design of specific ligands to treat CNS diseases targeting the dopaminergic system. | Peiyu Xu Sijie Huang Brian E.Krumm Youwen Zhuang Chunyou Mao Yumu Zhang Yue Wang Xi-Ping Huang Yong-Feng Liu Xinheng He Huadong Li Wanchao Yin Yi Jiang Yan Zhang Bryan L.Roth H.Eric Xu | 2023 | Cell Research2023，33，8： | 0 |
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