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construction of a CRISPR-based paired-sgRNA library for chromosomal deletion of long non-coding RNAs

Quantitative Biology 2020年第1期8卷 31-42页

作者： Minzhen Tao Qiaochu Mu Yurui Zhang Zhen Xie MOE Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic and System BiologyDepartment of AutomationBeijing National Research Center for Information Science and TechnologyTsinghua UniversityBeijing 100084China Zhejiang Tmall Techonogy co. LtdYuhang DistrictHangzhou 311121China beiing syngentech co..ltd Zhongguancun Life Science ParkChangping DistrictBeijing 102206China

Background:Derived from an adaptive bacterial immune system,the clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated 9(Cas9)system has shown great potential in high-throughput functional genomic screening,especially for protein-coding genes.However,it is still challenging to apply the similar strategy to study non-coding genomic elements such as long non-coding RNAs(lncRNAs)or clusters of microRNAs,because short insertions or deletions may not be sufficient to generate loss-of-function phenotypes.Methods:Here,we presented a systematic strategy for designing a CRISPR-based paired-sgRNA library for highthroughput screening in non-coding regions.Due to the abundance of lncRNAs and their diverse regulatory roles in vivo,we repurposed microarray datasets to select 600 highly expressed lncRNAs in non-small-cell lung cancer and designed two schemes for lncRNA deletion with^20 paired-sgRNAs for each lncRNA.Through Golden-Gate assembly,we generated a pooled CRISPR-based library with a total of 12,878 sgRNA pairs.Results:Over 80%of paired-sgRNAs were recovered from final pooled library with a relarively even distribution.Cleavage efficiency of sgRNA pairs was validated through experiments of transient transfection and viral infection.Moreover,randomly selected paired-sgRNAs showed that efficient deletion of genomic DNA could be achieved with a deletion size within the range of 500 to 3000 bp.conclusions:In summary,we have demonstrated a strategy to design and construct a pooled paired-sgRNA library to generate genomic deletion in the lncRNA regions,validated their deletion efficiency and explored the relationship of deletion efficiency with respect to deletion size.This method would be also suitable for investigation of other uncharacterized non-coding genomic regions in mammalian cells in an efficient and cost-efTective manner.

关键词： CRISPR/Cas9 paired-sgRNA chromosomal deletion non-coding genomic elements lncRNA

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Molecular cloning and functional characterization of multiple ApOSCs from Andrographis paniculata

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Chinese Journal of Natural Medicines 2020年第9期18卷 659-665页

作者： WANG Jian LIN Hui-Xin ZHAO Huan GUO Juan SU Ping YANG Jian WU Xiao-Yi HUANG Lu-Qi GAO Wei School of Traditional Chinese Medicine Shenyang Pharmaceutical UniversityShenyang 100016China State Key Laboratory Breeding Base of Dao-di Herbs National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China School of Traditional Chinese Medicine Capital Medical UniversityBeijing 100069China Geneis(Beijing)co..ltd Beiing 100102Chind.

Triterpenoids have been described in Andrographis paniculata. Oleanolic acid exhibits high biological activity and is widely used in the clinic, and β-sitosterol not only has good biological activity but also plays an important physiological role in plants.However, analysis of the biosynthetic pathway of triterpenoids in Andrographis paniculata has not been reported. Here, we provide the first report of the isolation and identification of nine 2, 3-oxidosqualene cyclases(ApOSC3 to ApOSC11) from A. paniculata. The results showed that ApOSC4 represented a monofunctional synthase that could convert 2, 3-oxidosqualene to β-amyrin. ApOSC5 as a bifunctional 2, 3-oxidosqualene cyclases, could transfer 2, 3-oxidosqualene to β-amyrin and α-amyrin. ApOSC6 to ApOSC8 composed the multifunctional 2, 3-oxidosqualene cyclases that could convert 2, 3-oxidosqualene to β-amyrin, α-amyrin and one or two undetermined triterpenoids. This study provides a better understanding of the biosynthetic pathway of triterpenoids in A. paniculata, and the discovery of multifunctional 2, 3-oxidosqualene cyclases ApOSC5 to ApOSC8 of the facilitates knowledge of the compounds diversity in A. paniculata.

关键词： Triterpenoids 2 3-Oxidosqualene cyclases A.paniculata β-Amyrin α-Amyrin

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HDR-Net-Fusion:Real-time 3D dynamic scene reconstruction with a hierarchical deep reinforcement network

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computational Visual Media 2021年第4期7卷 419-435页

作者： Hao-Xuan Song Jiahui Huang Yan-Pei Cao Tai-Jiang Mu BNRist Department of Computer Science and TechnologyTsinghua UniversityBeiing 100084China Kuaishou Technology co. Ltd.Beijing 100085China

Reconstructing dynamic scenes with commodity depth cameras has many applications in computer graphics,computer vision,and robotics.However,due to the presence of noise and erroneous observations from data capturing devices and the inherently ill-posed nature of non-rigid registration with insufficient information,traditional approaches often produce low-quality geometry with holes,bumps,and misalignments.We propose a novel 3D dynamic reconstruction system,named HDR-Net-Fusion,which learns to simultaneously reconstruct and refine the geometry on the fly with a sparse embedded deformation graph of surfels,using a hierarchical deep reinforcement(HDR)network.The latter comprises two parts:a global HDR-Net which rapidly detects local regions with large geometric errors,and a local HDR-Net serving as a local patch refinement operator to promptly complete and enhance such regions.Training the global HDR-Net is formulated as a novel reinforcement learning problem to implicitly learn the region selection strategy with the goal of improving the overall reconstruction quality.The applicability and efficiency of our approach are demonstrated using a large-scale dynamic reconstruction dataset.Our method can reconstruct geometry with higher quality than traditional methods.

关键词： dynamic 3D scene reconstruction deep reinforcement learning point cloud completion deep neural networks

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Study on the Effect of Two-Step Saturated Steam Heat Treatment Process on the Properties of Reconstituted Bamboo

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Journal of Renewable Materials 2022年第12期10卷 3313-3334页

作者： Xin Han Zhichao Lou Chenglong Yuan Xinwu Wu Jie Liu Fujin Weng Yanjun Li Jiangsu co-Innovaton Center of Eficient Processing and Utilization of Forest Resources Nanjing Forestry UniversityNanjingChina Zhejiang Academy of Forestry Sciences HangzhouChina Key Laboratory of National Forestry and Grassland Admini stration/Beijng for Bamboo&Rattan Science and Technology BeiingChina college of Materials Science and Engineering Nanjing Forestry UniversityNanjingChina

With the aim of utilizing reconstituted bamboo as a carbon cycle oriented material,the improvement of physical and mechanical properties has been actively studied to solve using problems The saturated steam heat treatment process has been widely used in worldwide.With the development and exploration of this technology,two step satu-rated steam heat treatment process appears in some practical production,that is,affer a period of saturated steam heat treatment at a lower temperature,the bamboo bundles are taken out and seasoned for a period of time,and then put back into the heat tank again,and heated at a higher temperature for another period of time.During the two-step saturated steam heat treatment,the physical and mechanical properties of bamboo changed.However,the mechanism of two step saturated steam heat treatment has not been thoroughly discussed.For purpose that this paper all discuss and find out the mechanism of two step saturated steam heat treatment on the change of physical and mechanical properties of reconstituted bamboo.In this work,the one and two step saturated steam heat treat-ments were carried out according to the actual production parameters,and the physical and mechanical properties of the reconstituted bamboo board made of treated bamboo bundles were analyzed,including the color change,the thickness swelling(TS),modulus of elasticity(MOE),modulus of rupture(MOR)and shear strength.The results indicate that two-step saturated steam heat treatment is better than one step.Based on the detailed study of the chemical composition,crytalinity and micro morphologial characteristics of the heated bamboo bundles,it is further revealed that during two-step saturated steam heat treatment,oxygen air is added to the reaction system between the two heat treatment processes to further catalyze the oxidation of hemicellulose and enhance the crystal-linity of cellulose,so as to improve the properties of the final products.Our work has optimized the saturated steam heat treatment process which is widely used i

关键词： Modulus of elasticity modulus of rupture thickness swelling oxidation

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Enhancement of electrochemical performance in lithium-ion battery via tantalum oxide coated nickel-rich cathode materials

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Chinese Physics B 2022年第5期31卷 683-690页

作者：陈峰岭林建楠陈一帆董彬彬尹楚君田飔莹孙大鹏解婧张振宇李泓李超波 Institute of Microelectronics Chinese Academy of SciencesBeiing 100029China University of Chinese Academy of Sciences Beijing 100049China Institute of Physics Chinese Academy of SciencesBeijing 100190China Beijing Welion New Energy Technology co. LtdBeijing 102402China

Nickel-rich cathode materials are increasingly being applied in commercial lithium-ion batteries to realize higher specific capacity as well as improved energy density.However,low structural stability and rapid capacity decay at high voltage and temperature hinder their rapid large-scale application.Herein,a wet chemical method followed by a post-annealing process is utilized to realize the surface coating of tantalum oxide on LiNi_(0.88)Mn_(0.03)co_(0.09)O_(2),and the electrochemical performance is improved.The modified Li Ni_(0.88)Mn_(0.03)co_(0.09)O_(2)displays an initial discharge capacity of~233 m Ah/g at0.1 C and 174 m Ah/g at 1 C after 150 cycles in the voltage range of 3.0 V–4.4 V at 45℃,and it also exhibits an enhanced rate capability with 118 m Ah/g at 5 C.The excellent performance is due to the introduction of tantalum oxide as a stable and functional layer to protect the surface of LiNi_(0.88)Mn_(0.03)co_(0.09)O_(2),and the surface side reactions and cation mixing are suppressed at the same time without hampering the charge transfer kinetics.

关键词： LiNi0.88Mn0.03co0.09O2 tantalum oxide surface coating lithium-ion battery cathode material

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correction to:Rescue of premature aging defects in cockayne syndrome stem cells by CRISPR/Cas9-mediated gene correction

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Protein & Cell 2022年第8期13卷 623-625页

作者： Si Wang Zheying Min Qianzhao Ji Lingling Geng Yao Su Zunpeng Liu Huifang Hu Lixia Wang Weiqi Zhang Keiichiro Suzuiki Yu Huang Puyao Zhang Tie-Shan Tang Jing Qu Yang Yu Guang-Hui Liu Jie Qiao Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking University Third HospitalBeiing 100191China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBejing 100101China University of Chinese Academy of Sciences Bejjing 100049China Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China Institute for Stem cell and Regeneration Chinese Academy of SciencesBeijing 100101China Key Laboratory of Genomic and Precision Medicine Beiing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Beijing Institute for Brain Disorders Beijing 100069China Institute for Advanced co-Creation Studies Osaka UniversityOsaka 560-8531Japan Graduate School of Engineering Science Osaka UniversityOsaka 560-8531Japan Department of Medical Genetics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeiing 100101China Peking-Tsinghua Center for Life Sciences Academy forAdvancedInterdisciplinary StudiesPeking UniversityBeijing 100871China

coRRECTION TO:PROTEIN CELL HTTPS://***/10.1007/S13238-019-0623-2 In Fig.7C,we used the ERCC6mut.iPSCs(CS iPSCs)as NANOG positive control pluripotent cells in the upper pan-els.However,these cells were inadvertently labeled as ERCC6^(GC)-iPSCs.In the revised version of Fig.7C,we have updated the high-quality images along with the corrected mark.In addition,we have also made corresponding chan-ges in the figure legend.

关键词： CRISPR/Cas9 Rescue correction

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Effect of Modified Xijiao Dihuang Decoction (加味犀角地黄汤) on Intestinal Flora and Th17/Treg in Rats with Radiation Enteritis

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Chinese Journal of Integrative Medicine 2021年第3期27卷 198-205页

作者： WANG Yu-guo GAO Yue FENG Jian DOU Yong-qi Medical School of Chinese People's Liberation Army The General Hospital of People's Liberation ArmyBeiing 100853China Beijing Institute of Radiation Medicine Beiing 100850China

Objective To observe the effect of Modified Xijiao Dihuang Decoction(加味犀角地黄汤,MXDD)on rats with radiation enteritis,and explore its action mechanism.Methods Thirty female Sprague Dawley rats were divided into the control,model,dexamethasone(DXM),golden bifid(GB)and MXDD groups using random number table,6 rats in each group.Except the control group,the other rats were developed into radiation enteritis model by exposing to a single 60co-γray at a dose of 11 Gy.The rats in the DXM,GB and MXDD groups were treated with DXM(1.425 mg/kg),GB(0.8 g/kg)and MXDD(36.0 g/kg)for 3 days,respectively.Body weight and diarrhea condition of rats were evaluated daily.On day 3,the feces of rats were collected for intestinal flora detection and the small intestinal tissues were also collected.Bacterial species annotation,alpha and beta diversities as well as composition of intestinal flora were detected and compared.The protein and mRNA expressions of interleukin 17(IL-17),retinoid-related orphan nuclear receptor gamma t(ROR-γt)and forkhead/winged helix transcription factor p3(FoxP3)were determined by Western blot and polymerase chain reaction,respectively.The abundance and diversity of intestinal flora as well as the proportion at the phylum and genus levels were assayed by 16S rRNA metagenome sequencing.correlation between intestinal flora and Th17/Treg was analyzed by heatmap method.Results On day 1 to 3 after radiation,compared with the control group,the body weight in model group was decreased(Pcompared with the model group,MXDD could alleviate weight loss and diarrhea caused by irradiation.At the phylum level,MXDD cause a significant increase in Firmicutes,and a decrease in Proteobacteria(Pcorrelated with FoxP3(r=0.73,0.79,respecti

关键词： Modified Xijiao Dihuang Decoction radiation enteritis intestinal flora Th17/Treg Chinese medicine

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Deciphering the Role of Fluoroethylene Carbonate towards Highly Reversible Sodium Metal Anodes

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Research 2022年第2期2022卷 259-269页

作者： Xueying Zheng Suting Weng Wei Luo Bo Chen Xiao Zhang Zhenyi Gu Haotian Wang Xiaolu Ye Xuyang Liu Liqiang Huang Xinglong Wu Xuefeng Wang Yunhui Huang Institute of New Energy for Vehicdes Shanghai Key Laboratory of Developmrent&Apication for Metali Functional MaterialsSchool of Materials Science and EngineringTongji UniversitShanghai 201804China Instiute of Physics Chinese Academy of SciencesSchoo of Plhysical SciencesUniversity of Chinese Academy of SciencesBeiing 100190China Key Laboratory of Advanced Civil Engineering Materials(Tongji University) Ministry of EducationShanghai 201804China Key Laboratory for UV Light Emiting Materials and TechnologyNortheast Normal UniversilyMinistry of EducationChangchumJilin 130024China Tianmu Lake Institute of Advanced Energy Storage Technologies co. LtdLiyangJiangsu 213300China State Key Laboratory of Materials Procssing and Die&Mould Technology Schoo of Materials Science and Engineering Huazhong University of Science and TechnologyWuhanHubei 430074China

Sodium metal anodes(SMAs)sufer from extremely low reversibility(95%with conventional NaPF。salt at a regular concentration(1.0M).The peculiar role of FEC is firstly.unraveled via its involvement into the solvation str... 详细信息

Sodium metal anodes(SMAs)sufer from extremely low reversibility(conclusion by incorporating fluoroethylene carbonate(FEC)as cosolvent that renders a Na plating/stripping fficiency of>95%with conventional NaPF。salt at a regular concentration(1.0M).The peculiar role of FEC is firstly.unraveled via its involvement into the solvation structure,where a threshold FEC concentration with a coordination number>1.2 is needed in guaranteeing high Na reversibility over the long-term.Specifially,by incorporating an average number of 1.2 FEC molecules into the primary Na*solvation sheath,lowest unoccupied molecular orbital(LUMO)levels of such Nat-FEC solvates undergo further decrease,with spin electrons residing either on the O=C 0(O)moiety of FEC or sharing between Na*and its C=:O bond,which ensures a prior FEC decomposition in passivating the Na surface against other carbonate molecules.Further,by adopting cryogenic tranmission electron microscopy(cryo-TEM),we found that the Na filaments grow into substantially larger diameter from-400nm to>1 pum with addition of FEC upon the threshold value.A.highly crstalline and much thiner(-40 nm)slid-electrolyte interphase(SED)is consequently observed to uniformly wrap the Na surface,in contrast to the severely corroded Na as retrieved from the blank electrolyte.The potence of FEC is further demonstrated in a series of"corrosive solvents"such as ethy!l acetate(EA)。trimethyl phosphate(TMP),and actonitrile(AN)enabling highly reversible SMAs in the otherwise unusable solvent systems.

关键词： electrolyte otherwise Highly

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Influence of the convective mixing-length parameterαon the chemical abundances in the case of metal-poor giant HD 122563

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Research in Astronomy and Astrophysics 2020年第8期20卷 181-192页

作者： Nan Song Sofya Alexeeval Gang Zhao Key Laboratory of Optical Astronomy National Astronomical ObservatoriesChinese Academy of SciencesBejjing 100101China School of Astronomy and Space Science University of Chinese Academy of SciencesBeiing 100049China

One-dimensional(1 D)model atmospheres are still the most commonly used tool for the determination of stellar chemical composition.convection in the model is usually treated by mixing-length theory(MLT).The mixing-length parameterαis generally calibrated from the Sun and applied to all other stars.The metal-poor giant,HD 122563,is an important benchmark star to test stellar atmosphere and interior physics.We investigate the influence of the convection mixing-length parameterαon the determination of chemical abundances of Na,Mg,Al,Si,Ca,Sc,Ti,Cr,Mn,co,Ni,Sr,Y,Zr and Ba in the case of HD 122563,taking advantage of a high resolution and high signal-to-noise ratio HARPS spectrum.The abundance discrepanciesΔ[X/H]that occur due toαvariation rarely exceed 0.05 dex and most are less than 0.03 dex.We calculate the discrepancyΔ[X/H]using a line-by-line differential analysis.The abundance discrepancies do not have direct relation with either line strength or the excitation potential.For 1 D stellar atmospheric analysis of HD 122563,the accuracy of abundance determination does not strongly depend on the choice of mixing-length parameterα(causing average discrepancies of<0.03 dex),while the uncertainties in the effective temperature and surface gravity play a more important role.

关键词： stars:abundances convection stars:atmospheres line:profiles

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Role of CD8^(+) T lymphocyte cells:Interplay with stromal cells in tumor microenvironment

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Acta Pharmaceutica Sinica B 2021年第6期11卷 1365-1378页

作者： Qin Xie Jian Ding Yi Chen college of Pharmaceutical Sciences Zhejiang UniversityHangZhou 310012China Division of Anti-Tumor Pharmacology Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beiing 100049China State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Shanghai Hai He Pharmaceutical co. Ltd.Shanghai 201203China

CD8^(+) T lymphocytes are pivotal cells in the host response to antitumor immunity.Tumordriven microenvironments provide the conditions necessary for regulating infiltrating CD8^(+) T cells in favor of tumor survival,including weakening CD8^(+) T cell activation,driving tumor cells to impair immune attack,and recruiting other cells to reprogram the immune milieu.Also in tumor microenvironment,stromal cells exert immunosuppressive skills to avoid CD8^(+) T cell cytotoxicity.In this review,we explore the universal function and fate decision of infiltrated CD8^(+) T cells and highlight their antitumor response within various stromal architectures in the process of confronting neoantigen-specific tumor cells.Thus,this review provides a foundation for the development of antitumor therapy based on CD8^(+)T lymphocyte manipulation.

关键词： CD8+T lymphocyte Stromal cell Tumor microenvironment Immunosuppression Immunotherapy Antitumor

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