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| 1 | MicroRNAs in tomato plants显示文摘MicroRNAs (miRNAs) are a specialized class of small silencing RNAs that regulate gene expression in eukaryotes.In plants,miRNAs negatively regulate target mRNAs containing a highly complementary sequence by either mRNA cleavage or translational repression.As a model plant to study fleshy fruit ripening,miRNA studies in tomato have made great progress recently.MiRNAs were predicted to be involved in nearly all biological processes in tomato,particularly development,differentiation,and biotic and abiotic stress responses.Surprisingly,several miRNAs were verified to be involved in tomato fruit ripening and senescence.Recent studies suggest that miRNAs are related to host-virus interactions,which raises the possibility that miRNAs can be used as diagnostic markers for response to virus infection in tomato plants.In this review,we summarize our current knowledge systematically and advance future directions for miRNA research in tomato. | ZUO JinHua WANG YunXiang LIU HaiPing MA YuanZheng JU Zheng ZHAI BaiQiang FU DaQi ZHU Yi LUO YunBo ZHU BenZhong | 2011 | Science China(Life Sciences)2011，54，7： | 13 |
| 2 | Virus-induced Gene Silencing in Eggplant(Solanum melongena)显示文摘Eggplant(Solanum melongena)is an economically important vegetable requiring investigation into its various genomic functions.The current limitation in the investigation of genomic function in eggplant is the lack of effective tools available for conducting functional assays.Virus-induced gene silencing(VIGS)has played a critical role in the functional genetic analyses.In this paper,TRV-mediated VIGS was successfully elicited in eggplant.We first cloned the CDS sequence of PDS(PHYTOENE DESATURASE) in eggplant and then silenced the PDS gene.Photo-bleaching was shown on the newly-developed leaves four weeks after agroinoculation,indicating that VIGS can be used to silence genes in eggplant.To further illustrate the reliability of VIGS in eggplant,we selected Chl H,Su and CLA1 as reporters to elicit VIGS using the high-pressure spray method.Suppression of Chl H and Su led to yellow leaves,while the depletion of CLA1 resulted in albino.In conclusion,four genes,PDS,Chl H,Su(Sulfur),CLA1,were down-regulated significantly by VIGS,indicating that the VIGS system can be successfully applied in eggplant and is a reliable tool for the study of gene function. | Haiping Liu Daqi Fu Benzhong Zhu Huaxue Yan Xiaoying Shen Jinhua Zuo Yi Zhu Yunbo Luo | 2012 | Journal of Integrative Plant Biology2012，54，6： | 11 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | Underrepresentation of active histone modification marks in evolutionarily young genes显示文摘evolutionarily 新的基因能很快在基本生物过程发展必要角色,这被知道。不过,他们怎么获得他们的新奇 transcriptional 模式的内在的分子的机制少些除了 cis 规章的进化的角色被描绘。Epigenetic 修正提供其他的可能性。这里,我们检验了 histone 修正怎么由更新的新基因数据集的综合分析在果蝇 melanogaster 在不同基因年龄组之中变化了并且出版了 epigenomic 数据。我们越过在哪儿的各种各样的数据集发现了一个柔韧的模式活跃 histone 修正的范围和紧张, histone 3 离氨酸 4 trimethylation 和离氨酸 36 trimethylation,与进化年龄增加了。如此的时间的关联为压抑的 histone 标记否定、弱得多,离氨酸 9 trimethylation,它被期望与 heterochromatin 给它的主要协会。由有附近的旧基因的进一步的比较,新基因的活跃标记的弄空能被本地 epigenetic 上下文仅仅部分解释。所有这些数据与观察一致那更旧的基因忍受相对更高的表示层次并且建议 histone 修正的进化能在基因出生以后在 transcriptional 进化被含有。 | Daqi Yu Wenwen Shi Yong E. Zhang | 2017 | Insect Science2017，24，2： | 2 |
| 10 | 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 |
| 11 | Separating group compositions in naphtha by adsorption and solvent extraction to improve olefin yields of steam cracking process显示文摘 | Liu Jichang Shen Benxian Wang Daqi | 2009 | Journal of Petroleum Science & Engineering2009，66，34： | 1 |
| 12 | The optimal number of hide nodes in multilayed feedforward neural network显示文摘 | Daqi Gan | | 0，，： | 1 |
| 13 | Optimization of the enzymatic pretreatment in oat bran protein extraction by particle swarm optimization algorithms for response surface modeling显示文摘 | LIU Jing GUAN Xiao ZHU Daqi | 2008 | LWT-Food Science and Technology2008，41，10： | 1 |
| 14 | Cache Allocation in CDN: An Evolutionary Game Generalized Particle Model显示文摘 | Feng Xiang Francis C M Lau Gao Daqi | 2009 | Complex Sciences2009，5，1： | 1 |
| 15 | Basic Principles of Pattern Classification Methods Based on Improved RBF Neural Networks显示文摘 | Gao Daqi Yanggenxing | 2001 | Journal of East China University of Science and Technology2001，27，6： | 1 |
| 16 | Allograft versus autograft for anterior cruciate ligament reconstruction: an up-to-date meta-analysis of prospective studies显示文摘 | Jianzhong Hu Jin Qu Daqi Xu Jingyong Zhou Hongbin Lu | 2013 | International Orthopaedics2013，，2： | 1 |
| 17 | :A novel five - connected 3 - D zeolite - like framework with intersecting helical chains in diamondoid net of Cd Ⅱ(mpdc=2,6 -dimethylpyridine - 3,5 - dicarboxylate ) 显示文摘 | Kunlin Huang Yangting He Daqi Wang | 2007 | Journal of Molecular Structure2007，832，13： | 1 |
| 18 | Adaptive RBF networks for pattern classifications 显示文摘 | Gao Daqi Yang Genxing | 2002 | Neural Networks2002，1，： | 1 |
| 19 | networks architecture with teachers 显示文摘 | Daqi Guo Study on the linear primary {unction {orword three layers neural | 1998 | Journal of Computers1998，21，1： | 1 |
| 20 | Clinical outcomes of remnant preserving augmentation in anterior cruciate ligament reconstruction: a systematic review显示文摘 | Jianzhong Hu Jin Qu Daqi Xu Tao Zhang Jingyong Zhou Hongbin Lu | 2014 | Knee Surgery, Sports Traumatology, Arthroscopy2014，，9： | 1 |
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