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| 1 | High-efficiency and multiplex adenine base editing in plants using new TadA variants显示文摘Recently reported adenine base editors(ABEs)exhibit powerful potential for targeted gene correction as well as developing gain-of-function mutants and novel germplasms for both gene function studies and crop breeding.However,editing efficiency varies significantly among different target sites.Here,we investigated the activities of three evolved E.coli adenosine deaminase TadA variants(TadA8e,TadA8.17,and TadA8.20)side-by-side in transgenic rice.We found that TadA8e outperforms TadA8.17 and TadA8.20,and induces efficient A-to-G conversion at all tested sites in the rice genome,including those that were un-editable by ABE7.10 in our previous experiments.Furthermore,V82S/Q154R mutations were incorporated into TadA8e,resulting in a new variant that we named TadA9.Our data show that TadA9 is broadly compatible with CRISPR/SpCas9,CRISPR/SpCas9-NG,and CRISPR/SpRY,as well as CRISPR/ScCas9 nickase systems,achieving comparable or enhanced editing in a larger editing window at diverse PAM sites as compared with TadA8e.Finally,TadA9 was used to simultaneously install novel SNPs in four endogenous herbicide target genes in the commercial rice cultivar Nangeng 46 for potential field application in.weed control.Collectively,we successfully generated a series of novel ABEs that can efficiently edit adenosines in the rice genome.Our findings suggest that TadA9 and TadA8e have great potentials in the development of plant base editors and crop molecular breeding. | Daqi Yan Bin Ren Lang Liu Fang Yan Shaofang Li Guirong Wang Wenxian Sun Xueping Zhou Huanbin Zhou | 2021 | Molecular Plant2021，14，5： | 8 |
| 2 | Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV显示文摘The tomato encode four functional DCL families,of which DCL2 is poorly studied.Here,we generated loss-of-function mutants for a tomato DCL2 gene,dcl2b,and we identified its major role in defending against tomato mosaic virus in relation to both natural and manual infections.Genome-wide small RNA expression profiling revealed that DCL2b was required for the processing 22-nt small RNAs,including a few species of miRNAs.Interestingly,these DCL2b-dependent 22-nt miRNAs functioned similarly to the DCL1-produced 22-nt miRNAs in Arabidopsis and could serve as triggers to generate a class of secondary siRNAs.In particular,the majority of secondary siRNAs were derived from plant defense genes when the plants were challenged with viruses.We also examined differentially expressed genes in dcl2b through RNA-seq and observed that numerous genes were associated with mitochondrial metabolism and hormone signaling under virus-free conditions.Notably,when the loss-of-function dcl2b mutant was challenged with tomato mosaic virus,a group of defense response genes was activated,whereas the genes related to lipid metabolism were suppressed.Together,our findings provided new insights into the roles of tomato DCL2b in small RNA biogenesis and in antiviral defense. | Tian Wang Zhiqi Deng Xi Zhang Hongzheng Wang Yu Wang Xiuying Liu Songyu Liu Feng Xu Tao Li Daqi Fu Benzhong Zhu Yunbo Luo Hongliang Zhu | 2018 | Horticulture Research2018，5，1： | 4 |
| 3 | Glucocorticoid receptor modulates myeloid-derived suppressor cell function via mitochondrial metabolism in immune thrombocytopenia显示文摘Myeloid-derived suppressor cells(MDSCs)are a heterogeneous population of immature cells and natural inhibitors of adaptive immunity.Intracellular metabolic changes in MDSCs exert a direct immunological influence on their suppressive activity.Our previous study demonstrated that high-dose dexamethasone(HD-DXM)corrected the functional impairment of MDSCs in immune thrombocytopenia(ITP);however,the MDSC population was not restored in nonresponders,and the mechanism remained unclear.In this study,altered mitochondrial physiology and reduced mitochondrial gene transcription were detected in MDSCs from HD-DXM nonresponders,accompanied by decreased levels of carnitine palmitoyltransferase-1(CPT-1),a rate-limiting enzyme in fatty acid oxidation(FAO).Blockade of FAO with a CPT-1 inhibitor abolished the immunosuppressive function of MDSCs in HD-DXM responders.We also report that MDSCs from ITP patients had lower expression of the glucocorticoid receptor(GR),which can translocate into mitochondria to regulate the transcription of mitochondrial DNA(mtDNA)as well as the level of oxidative phosphorylation.It was confirmed that the expression of CPT-1 and mtDNA-encoded genes was downregulated in GR-siRNA-treated murine MDSCs.Finally,by establishing murine models of active and passive ITP via adoptive transfer of DXM-modulated MDSCs,we confirmed that GR-silenced MDSCs failed to alleviate thrombocytopenia in mice with ITP.In conclusion,our study indicated that impaired aerobic metabolism in MDSCs participates in the pathogenesis of glucocorticoid resistance in ITP and that intact control of MDSC metabolism by GR contributes to the homeostatic regulation of immunosuppressive cell function. | Yu Hou Jie Xie Shuwen Wang Daqi Li Lingjun Wang Haoyi Wang Xiaofei Ni Shaoqiu Leng Guosheng Li Ming Hou Jun Peng | 2022 | Cellular & Molecular Immunology2022，19，7： | 4 |
| 4 | Treatment of autosomal recessive hearing loss via in vivo CRISPR/Cas9-mediated optimized homology-directed repair in mice显示文摘Dear Editor,Hearing loss is the most common sensory disorder in the world.Among cases of non-syndromic hearing loss,which account for 70%of all cases of genetic hearing loss,around 80%of cases arise from autosomal recessive loss-of-function mutations that require repair,rather than disruption,of the mutant allele.1 CRISPR/Cas9-mediated homology-directed repair(HDR)-based therapies have the potential to cure many genetic diseases because this class of therapeutics can achieve arbitrary base changes as well as the insertion or deletion of DNA fragments/However. | Xi Gu Xinde Hu Daqi Wang Zhijiao Xu Fang Wang Di Li Geng-lin Li Hui Yang Huawei Li Erwei Zuo Yilai Shu | 2022 | Cell Research2022，32，7： | 3 |
| 5 | Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach显示文摘Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants.Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism.L-Ascorbic acid(AsA),which is an essential nutrient component for human health and plant metabolism,plays key roles in diverse biological processes such as cell cycle,cell expansion,stress resistance,hormone synthesis,and signaling.Here,we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato(Solanum lycopersicum L.)fruit with different AsA content levels,which leads to identifcation of AsA relevant modules and vital genes in AsA regulatory pathways.Twenty-four modules were compartmentalized according to gene expression profling.Among these modules,one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed.The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit,and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level. | Chao Gao Zheng Ju Shan Li Jinhua Zuo Daqi Fu Huiqin Tian Yunbo Luo Benzhong Zhu | 2013 | Journal of Integrative Plant Biology2013，55，11： | 3 |
| 6 | Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis显示文摘Major evolutionary transitions are enigmas,and the most notable enigma is between invertebrates and vertebrates,with numerous spectacular innovations.To search for the molecular connections involved,we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans.We focused on gametes and early embryos,where the methylomes are known to evolve divergently between fish and mammals.Here,we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects,but clearly presents in deuterostomes such as echinoderms and invertebrate chordates,and then becomes more evident in vertebrates.Functional association analysis suggests that DNA methylation reprogramming is associated with development,reproduction and adaptive immunity for vertebrates,but not for invertebrates.Interestingly,the single HOX cluster of invertebrates maintains unmethylated status in all stages examined.In contrast,the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis.Notably,the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals.Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution,especially after the evolutionary transitions from invertebrates to vertebrates,and then to mammals. | Xiaocui Xu Guoqiang Li Congru Li Jing Zhang Qiang Wang David KSimmons Xuepeng Chen Naveen Wijesena Wei Zhu Zhanyang Wang Zhenhua Wang Bao Ju Weimin Ci Xuemei Lu Daqi Yu Qian-fei Wang Neelakanteswar Aluru Paola Oliveri Yong EZhang Mark QMartindale Jiang Liu | 2019 | National Science Review2019，6，5： | 2 |
| 7 | Synthesis, Characterization, DNA-binding Properties and DNA Cleavage of a New Ternary Copper(ll) Complex with Mixed-ligands of Tridentate Schiff Base and 1,10-Phenanth roline显示文摘新铜(II ) 建筑群,[Cu (naph 列伊) phen ] CH3OH 牥 ??? 浯汰硥眠瑩 ? 楍數 ? 楬慧摮 ? 景吠楲敤瑮瑡 ? 罉 E 晦 ? 獡 ? 湡 ??? 倭敨慮瑮牨汯湩? | Dong Jianfang Li Lianzhi Li Linwei Xu Tao Wang Daqi | 2011 | Chinese Journal of Chemistry2011，29，2： | 2 |
| 8 | Molecular Similarity: Methods and Performance显示文摘分子的类似长是一个热话题,它被各种各样的途径和戏在 protein-ligand 和蛋白质蛋白质相互作用识别评估了并且比较一个重要角色。当前有有他们的自己的优点和劣势的分子的类似评估方法的许多类型。分子的指纹是为仅仅关于快速的 2D 使普通基础检索担心,但是缺乏能力关于 3D conformers 编码信息的分子的类似评估的最普通的方法。分子的描述符基于的 3D 方法忍受表示 conformer 的结构信息,而是描述符没被保证精确描述分子的优点。基于的方法试着附加二个分子并且用通常比分子的描述符更精确,但是要求费时间的优化进程的最佳的姿势评估类似的分子的排列。基于的方法仅仅在化学药品上集中的 Pharmacophore 关于一个分子展示并且不能够处理分子的形状类似。为了评估分子的类似的表演,基于屏蔽,许多种度量标准是可得到的,例如,跳跃的视觉表示,量的大小和支架能力大小。分子的类似的进一步的应用包括分子相互作用网络的建设或多样的混合物图书馆的产生。 | Chaoqian Cai Jiayu Gong Xiaofeng Liu Daqi Gao Honglin Li | 2013 | Chinese Journal of Chemistry2013，31，9： | 1 |
| 9 | Efficient large fragment deletion in plants:double pairs of sgRNAs are better than dual sgRNAs显示文摘Dear Editor,Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)is a powerful and versatile gene editing system that has been extensively utilized in various animals and plants,which holds enormous potential and value for scientific research and breeding.However,single-targeted CRISPR can only induce a few base deletions,insertions,or substitution.Ideally,thesemutations result in premature termination of the protein encoded by the target gene,leading to a loss of function[1]. | Guoning Zhu Lingling Zhang Liqun Ma Qing Liu Kejian Wang Jinyan Li Guiqin Qu Benzhong Zhu Daqi Fu Yunbo Luo Hongliang Zhu | 2023 | Horticulture Research2023，10，10： | 1 |
| 10 | Modeling Herschel- Bulkely drilling fluid flow in a variable radial fracture显示文摘 | Li Song Kang Yili Li Daqi | 2014 | Journal of Porous Media2014，17，3： | 1 |
| 11 | Preventing autosomal-dominant hearing loss in Bth mice with CRISPR/CasRx-based RNA editing显示文摘CRISPR/RfxCas13d(CasRx)editing system can specifically and precisely cleave single-strand RNAs,which is a promising treatment for various disorders by downregulation of related gene expression.Here,we tested this RNA-editing approach on Beethoven(Bth)mice,an animal model for human DFNA36 due to a point mutation in Tmc1.We first screened 30 sgRNAs in cell cultures and found that CasRx with sgRNA3 reduced the Tmc1^(Bth)transcript by 90.8%,and the Tmc1 wild type transcript(Tmc1^(+))by 44.3%.We then injected a newly developed AAV vector(AAV-PHP.eB)based CasRx into the inner ears of neonatal Bth mice,and we found that Tmc1^(Bth)was reduced by 70.2%in 2 weeks with few off-target effects in the whole transcriptome.Consistently,we found improved hair cell survival,rescued hair bundle degeneration,and reduced mechanoelectrical transduction current.Importantly,the hearing performance,measured in both ABR and DPOAE thresholds,was improved significantly in all ages over 8 weeks.We,therefore,have validated the CRISPR/CasRx-based RNA editing strategy in treating autosomal-dominant hearing loss,paving way for its further application in many other hereditary diseases in hearing and beyond. | Ziwen Zheng Guo Li Chong Cui Fang Wang Xiaohan Wang Zhijiao Xu Huiping Guo Yuxin Chen Honghai Tang Daqi Wang Mingqian Huang Zheng-Yi Chen Xingxu Huang Huawei Li Geng-Lin Li Xiaoxiang Hu Yilai Shu | 2022 | Signal Transduction and Targeted Therapy2022，7，4： | 1 |
| 12 | Single-walled carbon nanotube based SERS substrate with single molecule sensitivity显示文摘In single molecule study,surface-enhanced Raman scattering(SERS)has the advantage of specifically providing structural information of the molecules targeted.The main challenge in single molecule SERS is developing reusable plasmonic substrates that ensures single molecule sensitivity and acquires intrinsic information of molecules.Here,we proposed a strategy to utilize single-walled carbon nanotubes(SWNTs)to construct SERS substrates.Employing ultrasonic spray pyrolysis,we prepared in situ polyhedral gold nanocrystals closely spaced and attached to nanotubes,ensuring valid hot spots formed along the tube-walls.With such SERS substrates,we proved the single molecule detection by the statistical analysis based on the natural abundance of isotopes.Since SWNTs provide non-chemical bonding adsorption sites,our SERS substrates are easily reusable and have a unique advantage of preserving the intrinsic property of the molecules detected.Using SWNTs to build SERS substrates may become a powerful general strategy in various static and dynamic studies of single molecules. | Chenmaya Xia Daqi Zhang Henan Li Sheng Li Haoming Liu Li Ding Xiyan Liu Min Lyu Ruoming Li Juan Yang Yan Li | 2022 | Nano Research2022，15，1： | 0 |
| 13 | Radial deformation of single-walled carbon nanotubes on quartz substrates and the resultant anomalous diameter-dependent reaction selectivity显示文摘Owing to the unique conjugated structure, the chemical-reaction selectivity of single-walled carbon nanotubes (SWNTs) has attracted great attention. By utilizing the radial deformation of SWNTs caused by the strong interactions with the quartz lattice, we achieve an anomalous diameter-dependent reaction selectivity of quartz lattice-oriented SWNTs in treatment with iodine vapor; this is distinctly different from the widely reported and well accepted higher reaction activity in small-diameter tubes compared to large-diameter tubes. The radial deformation of SWNTs on quartz substrate is verified by detailed Raman spectroscopy and mappings in both G-band and radial breathing mode. Due to the strong interaction between SWNTs and the quartz lattice, large-diameter tubes present a larger degree of radial deformation and more delocalized partial electrons are distributed at certain sidewall sites with high local curvature. It is thus easier for the carbon--carbon bonds at these high-curvature sites on large-diameter tubes to break down during reaction. This anomalous reaction activity offers a novel approach for selective removal of small-band^aD large-diameter tubes. | Juan Yang Yu Liu Daqi Zhang Xiao Wang Ruoming Li Yan Li | 2015 | Nano Research2015，8，9： | 0 |
| 14 | Classification of Rice Yield Using UAV-Based Hyperspectral Imagery and Lodging Feature显示文摘High-yield rice cultivation is an effective way to address the increasing food demand worldwide.Correct classification of high-yield rice is a key step of breeding.However,manual measurements within breeding programs are time consuming and have high cost and low throughput,which limit the application in large-scale field phenotyping.In this study,we developed an accurate large-scale approach and presented the potential usage of hyperspectral data for rice yield measurement using the XGBoost algorithm to speed up the rice breeding process for many breeders.In total,13 japonica rice lines in regional trials in northern China were divided into different categories according to the manual measurement of yield.Using an Unmanned Aerial Vehicle(UAV)platform equipped with a hyperspectral camera to capture images over multiple time series,a rice yield classification model based on the XGBoost algorithm was proposed.Four comparison experiments were carried out through the intraline test and the interline test considering lodging characteristics at the midmature stage or not.The result revealed that the degree of lodging in the midmature stage was an important feature affecting the classification accuracy of rice.Thus,we developed a low-cost,high-throughput phenotyping and nondestructive method by combining UAV-based hyperspectral measurements and machine learning for estimation of rice yield to improve rice breeding efficiency. | Jian Wang Bizhi Wu Markus VKohnen Daqi Lin Changcai Yang Xiaowei Wang Ailing Qiang Wei Liu Jianbin Kang Hua Li Jing Shen Tianhao Yao Jun Su Bangyu Li Lianfeng Gu | 2021 | Plant Phenomics2021，3，1： | 0 |
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