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| 1 | One-step generation of complete gene knockout mice and monkeys by CRISPR/Cas9-mediated gene editing with multiple sgRNAs显示文摘CRISPR/Cas9 系统是一个有效编辑基因的方法,但是编辑基因的动物的多数显示出 mosaicism,与编辑仅仅在房间的部分发生。这里,我们证明那单个基因或多重基因能被 Cas9 mRNA 和多重邻近的单个指南的 RNA 的 zygotic 注射完全在老鼠和猴子胚胎击倒(spaced 10-200 bp 分开) 指向仅仅一把单个钥匙每基因的 exon。个别地在 Y 染色体上跟随八基因的指向的删除的 F0 老鼠的 Phenotypic 分析在产生猛烈老鼠表明了这条途径的坚韧性。重要地,这条途径在高效率交付完全的基因大美人(Arntl 上的 100% 并且 91% 在 Prrt2 上) 在猴子胚胎。最后,我们能在一个单个步骤产生一只完全的 Prrt2 猛烈猴子,表明在很快建立编辑基因的猴子模型的这条途径的实用性。 | Erwei Zuo Yi-Jun Cai Kui Li Yu Wei Bang-An Wang Yidi Sun Zhen Liu Jiwei Liu Xinde Hu Wei Wei Xiaona Huo Linyu Shi Cheng Tang Dan Liang Yan Wang Yan-Hong Nie Chen-Chen Zhang Xuan Yao Xing Wang Changyang Zhou Wenqin Ying Qifang Wang Ren-Chao Chen Qi Shen Guo-Liang Xu Jinsong Li Qiang Sun Zhi-Qi Xiong Hui Yang | 2017 | Cell Research2017，27，7： | 21 |
| 2 | Highly efficient base editing in human tripronuclear zygotes显示文摘 | Changyang Zhou Meiling Zhang Yu Wei Yidi Sun Yun Sun Hong Pan Ning Yao Wanxia Zhong Yixue Li Weiping Li3 Hui Yang Zi-jiang Chen | 2017 | Protein & Cell2017，8，10： | 6 |
| 3 | Indiscriminate ssDNA cleavage activity of CRISPR-Cas12a induces no detectable off-target effects in mouse embryos显示文摘Dear Editor,Newly discovered characteristics like'collateral effect'or trans-cleavage in CRISPR-Cas13 and CRISPR-Cas12 systems have enabled their usage in nucleic acid detection(Gootenberg et al.2017,2018;Chen et al.2018).The collateral RNA cleavage of Cas13a has been reported to be harmful for cell development(Wang et al.2019;Buchman et al.2020).As a representative gene editor of CRISPR-Cas12 system,CRISPR-Cas12a(Cpf1)holds great potential for therapeutic applications in the future(Zetsche et al.2015;Koo et al.2018;Campa et al.2019). | Yu Wei Yingsi Zhou Yajing Liu Wenqin Ying Ruiming Lv Qimeng Zhao Haibo Zhou Erwei Zuo Yidi Sun Hui Yang Changyang Zhou | 2021 | Protein & Cell2021，12，9： | 2 |
| 4 | Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice显示文摘We here report a genome-editing strategy to correct spinal muscular atrophy(SMA).Rather than directly targeting the pathogenic exonic mutations,our strategy employed Cas9 and guide-sg RNA for the targeted disruption of intronic splicing-regulatory elements.We disrupted intronic splicing silencers(ISSs,including ISS-N1 and ISS+100)of survival motor neuron(SMN)2,a key modifier gene of SMA,to enhance exon 7 inclusion and full-length SMN expression in SMA iPSCs.Survival of splicing-corrected iPSC-derived motor neurons was rescued with SMN restoration.Furthermore,co-injection of Cas9 mRNA from Streptococcus pyogenes(SpCas9)or Cas9 from Staphylococcus aureus(SaCas9)alongside their corresponding sgRNAs targeting ISS-N1 into zygotes rescued 56%and 100%of severe SMA transgenic mice(Smn-/-,SMN2tg/-).The median survival of the resulting mice was extended to>400 days.Collectively,our study provides proof-of-principle for a new strategy to therapeutically intervene in SMA and other RNA-splicing-related diseases. | Jin-Jing Li Xiang Lin Cheng Tang Ying-Qian Lu Xinde Hu Erwei Zuo He Li Wenqin Ying Yidi Sun Lu-Lu Lai Hai-Zhu Chen Xin-Xin Guo Qi-Jie Zhang Shuang Wu Changyang Zhou Xiaowen Shen Qifang Wang Min-Ting Lin Li-Xiang Ma Ning Wang Adrian R.Krainer Linyu Shi Hui Yang Wan-Jin Chen | 2020 | National Science Review2020，7，1： | 1 |
| 5 | Kinase-substrate Edge Biomarkers Provide a More Accurate Prognostic Prediction in ER-negative Breast Cancer显示文摘The estrogen receptor(ER)-negative breast cancer subtype is aggressive with few treatment options available.To identify specific prognostic factors for ER-negative breast cancer,this study included 705,729 and 1034 breast invasive cancer patients from the Surveillance,Epidemiology,and End Results(SEER)and The Cancer Genome Atlas(TCGA)databases,respectively.To identify key differential kinase-substrate node and edge biomarkers between ER-negative and ERpositive breast cancer patients,we adopted a network-based method using correlation coefficients between molecular pairs in the kinase regulatory network.Integrated analysis of the clinical and molecular data revealed the significant prognostic power of kinase-substrate node and edge features for both subtypes of breast cancer.Two promising kinase-substrate edge features,CSNK1A1-NFATC3 and SRC-OCLN,were identified for more accurate prognostic prediction in ERnegative breast cancer patients. | Yidi Sun Chen Li Shichao Pang Qianlan Yao Luonan Chen Yixue Li Rong Zeng | 2020 | Genomics, Proteomics & Bioinformatics2020，18，5： | 1 |
| 6 | Sli2 (Ypkl), a homologue of mammalian protein kinase SGK, is a downstream kinase in the sphingolipid-mediated signaling pathway of yeast 显示文摘 | Yidi Sun Ritsuko T Daisuke T | 2000 | Mal Cell Biol2000，20，12： | 1 |
| 7 | Application of nitrogen loaded biochar in purifying agricultural wastewater and as a nitrogen releaser for rice production显示文摘Herein a new approach to the application of agricultural eutrophic wastewater for rice plant cultivation is described.Biochar was used as a medium for the sorption of ammonia from simulated wastewater and subsequently as a nitrogen(N)releaser in the cultivation of rice plants.The main goals of this approach were to isolate ammonia from simulated wastewater and transfer it into rice cultivation,and or explore how exogenous N promoted the growth of rice.The results demonstrate that according to X-ray diffraction phase analysis,most of the properties of biochar were retained before and after loading NH_(4)^(+)-N.Compared with biochar,the crystal peak of AlOOH in N-loaded biochar(NLB)disappeared and the intensity of the crystal peak of CuCaSe_(2)decreased,which was the important mechanism allowing it to adsorb 30.8%of the N present in simulated low N-concentration agricultural wastewater.The soil N content in NLB treatments was higher than in Non-NLB treatments during the critical tillering and reproductive growth stages.Moreover,the N adsorption-desorption process of NLB matched the N requirements of the rice plant,and thus greatly increased the tiller number by 11.9%and rice yield by 7.5%.These results indicated that the indirect use of ammonia derived from wastewater using biochar as a sorption and releasing medium for rice plant cultivation was promising.This is the first time that biochar was used for possibly indirect reuse of agricultural eutrophic wastewater and enhancement of rice plant growth. | Hongyang Chen Yidi Sun Yang Sun Yanzhi Wang Yanqi Li Qi Wu Daocai Chi | 2023 | International Journal of Agricultural and Biological Engineering2023，16，4： | 0 |
| 8 | Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies显示文摘3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic.In this study,an efficient aerobic skatole-degrading consortium was obtained.Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses.Bioinformatic analyses indicated that the skatole downstream degradation wasmainly via the catechol pathway,and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase.Genome binning and gene analyses indicated that Pseudomonas,Pseudoclavibacter,and Raineyella should cooperate with Rhodococcus for the skatole degradation process.Moreover,a pure strain Rhodococcus sp.DMU1 was successfully obtained which could utilize skatole as the sole carbon source.Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium.Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway.Collectively,our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader,and the degradation mainly proceeded via the catechol pathway. | Qiao Ma Nan Meng Jiancheng Su Yujie Li Jiazheng Gu Yidi Wang Jingwei Wang Yuanyuan Qu Zelong Zhao Yeqing Sun | 2023 | Journal of Environmental Sciences2023，，5： | 0 |
| 9 | Comparative study on Photobiomodulation between 630 nm and 810 nm LED in diabetic wound healing both in vitro and in vivo显示文摘Photobiomodulation(PBM)promoting wound healing has been demonstrated by many studies.Currently,630 nm and 810 nm light-emitting diodes(LEDs),as light sources,are frequently used in the treatment of diabetic foot ulcers(DFUs)in clinics.However,the dose-effect relationship of LED-mediated PBM is not fully understood.Furthermore,among the 630 nm and 810 nm LEDs,which one gets a better effect on accelerating the wound healing of diabetic ulcers is not clear.The aim of this study is to evaluate and compare the effects of 630 nm and 810 nm LED-mediated PBM in wound healing both in vitro and in vivo.Our results showed that both 630 nm and 810 nm LED irradiation significantly promoted the proliferation of mouse fibroblast cells(L929)at different light irradiances(1,5,and 10 mW/cm^(2)).The cell proliferation rate increased with the extension of irradiation time(100,200,and 500 s),but it decreased when the irradiation time was over 500 s.Both 630 nm and 810nm LED irradiation(5 mW/cm^(2))significantly improved the migration capability of L929 cells.No difference between 630 nm and 810 nm LED-mediated PBM in promoting cell proliferation and migration was detected.In vivo results presented that both 630 nm and 810 nm LED irradiation promoted the wound healing and the expression of the vascular endothelial growth factor(VEGF)and transforming growth factor(TGF)in the wounded skin of type 2 diabetic mice.Overall,these results suggested that LED-mediated PBM promotes wound healing of diabetic mice through promoting fibroblast cell proliferation,migration,and the expression of growth factors in the wounded skin.LEDs(630 nm and 810 nm)have a similar outcome in promoting wound healing of type 2 diabetic mice. | Hongyou Zhao Tengda Ji Tianzhen Sun Haolin Liu Yidi Liu Defu Chen Ying Wang Yizhou Tan Jing Zeng Haixia Qiu Ying Gu | 2022 | Journal of Innovative Optical Health Sciences2022，15，2： | 0 |
| 10 | Physical dosimetric reconstruction of a case of large area back skin injury due to overexposure in an interventional procedure显示文摘To estimate the physical dose of skin and key organs in a case of overexposure during a cardiac interventional procedure.Methods The female patient aged 50 suffered from owerexposure during ardiac interventional therapy in a hospital,Xinxiang city,Henan province,China in January 2020.The mesh-type phantom for the patient was constructed based on the adult mesh-type reference computational phantoms(MRCPs)released by the International Comission on Radiological Protection Publication 145 (ICRP145)and phantom deformation technology.Models of exposure scenario were constructed and simulated with particle and heavy ion transport code system(PHTTS)according to exposure conditions.Resuts:The maximum absorbed dose of key organs/tissues under iradiation in posteroanterior(PA)and 30°left anterior oblique directions(LOA)was 632.4 and 305.6 mGy,respectively.The let lung,heart,and left mammary gland received a larger dose under both iradiation conditions.The ratio of the absorbed dose with and without shielding was a lculated,and the relative difference in most organs was<1%between two directions.The iso-dose curve of the back skin revealed the ditribution of the absorbed dose(0.1-5.2 Gy).The dose estimate of key tssues/organs was higher than the conventional level,especially the local skin,up to 5.2 Gy.Concusions The interventional procedure in this ase resulted in a higher dose.Monte Carlo codes combined with the MRCPs can be employed to estimate physical dose to individuals in concrete irradia tion scenarios. | Yuchen Yin Xuan Wang Xianghui Kong Wenyue Zhang Yidi Wang Yuxuan Mao Jianwei Wang Tianhe Jia Yu Tu Bingjie Zhang Liang Sun | 2022 | Radiation Medicine and Protection2022，3，1： | 0 |
| 11 | CRISPR-mediated acceleration of wheat improvement:advances and perspectives显示文摘Common wheat(Triticum aestivum)is one of the most widely cultivated and consumed crops globally.In the face of limited arable land and climate changes,it is a great challenge to maintain current and increase future wheat production.Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition.However,clustered regularly interspaced short palindromic repeat(CRISPR)/CRISPR-associ-ated nuclease(Cas)genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species,thereby opening up new possibilities for biotechnology and breeding.In this review,we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat,emphasizing recent breakthroughs in precise and multiplex genome editing.We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells.Furthermore,we summarize the recent applications and ad-vancements of CRISPR/Cas technologies for wheat improvement.Lastly,we discuss the remaining chal-lenges specific to wheat genome editing and its future prospects. | Ximeng Zhou Yidi Zhao Pei Ni Zhongfu Ni Qixin Sun Yuan Zong | 2023 | Journal of Genetics and Genomics2023，50，11： | 0 |
| 12 | The TaTCP4/10-B1 cascade regulates awn elongation in wheat(Triticum aestivum L.)显示文摘Awns are important morphological markers for wheat and exert a strong physiological effect on wheat yield.The awn elongation suppressor B1 has recently been cloned through association and linkage analysis in wheat.However,the mechanism of awn inhibition centered around B1 remains to be clarified.Here,we identified an allelic variant in the coding region of B1 through analysis of re-sequencing data;this variant causes an amino acid substitution and premature termination,resulting in a long-awn phenotype.Transcriptome analysis indicated that B1 inhibited awn elongation by impeding cytokinin-and auxinpromoted cell division.Moreover,B1 directly repressed the expression of TaRAE2 and TaLks2,whose orthologs have been reported to promote awn development in rice or barley.More importantly,we found that TaTCP4 and TaTCP10 synergistically inhibited the expression of B1,and a G-to-A mutation in the B1 promoter attenuated its inhibition by TaTCP4/10.Taken together,our results reveal novel mechanisms of awn development and provide genetic resources for trait improvement in wheat. | Wensheng Ke Jiewen Xing Zhaoyan Chen Yidi Zhao Weiya Xu Lulu Tian Jinquan Guo Xiaoming Xie Dejie Du Zihao Wang Yufeng Li Jin Xu Mingming Xin Weilong Guo Zhaorong Hu Zhenqi Su Jie Liu Huiru Peng Yingyin Yao Qixin Sun Zhongfu Ni | 2023 | Plant Communications2023，4，4： | 0 |
| 13 | Scientists Map Single-Cell Spatial Distribution Atlas of Macaque Cortex显示文摘A recent study published in Cell successfully mapped the cell-type taxonomy in the macaque cortex and revealed the relationship between cell-type composition and various primate brain regions,by using the self-developed spatial transcriptome sequencing technology Stereo-seq and snRNA-seq technology.These findings provide a molecular and cellular basis for further investigation into neural circuits. | SUN Yidi | 2023 | Bulletin of the Chinese Academy of Sciences2023，37，3： | 0 |
| 14 | Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer显示文摘Mass spectrometry(MS)-based proteomics and phosphoproteomics are powerful methods to study the biological mechanisms,diagnostic biomarkers,prognostic analysis,and drug therapy of tumors.Dataindependent acquisition(DIA)mode is considered to perform better than data-dependent acquisition(DDA)mode in terms of quantitative reproducibility,specificity,accuracy,and identification of lowabundance proteins.Mini patient derived xenograft(MiniPDX)model is an effective model to assess the response to antineoplastic drugs in vivo and is helpful for the precise treatment of cancer patients.Kinases are favorable spots for tumor-targeted drugs,and their functional completion relies on signaling pathways through phosphorylating downstream substrates.Kinase-phosphorylation networks or edge interactions are considered more credible and permanent for characterizing complex diseases.Here,we provide a workflow for personalized drug response assessment in primary and metastatic colorectal cancer(CRC)tumors using DIA proteomic data,DIA phosphoproteomic data,and MiniPDX models.Three kinase inhibitors,afatinib,gefitinib,and regorafenib,are tested pharmacologically.The process mainly includes the following steps:clinical tissue collection,sample preparation,hybrid spectral libraries establishment,MS data acquisition,kinase-substrate network construction,in vivo drug test,and elastic regression modeling.Our protocol gives a more direct data basis for individual drug responses,and will improve the selection of treatment strategies for patients without the druggable mutation. | Xumiao Li Yiming Huang Kuo Zheng Guanyu Yu Qinqin Wang Lei Gu Jingquan Li Hui Wang Wei Zhang Yidi Sun Chen Li | 2023 | Biophysics Reports2023，9，2： | 0 |
| 15 | Base editing technology显示文摘The largest class of known human pathogenic mutations is point mutation,also known as single nucleotide polymorphism(SNP)[1].Precise and efficient editing of these SNPs has been of great interest for the treatment of genetic disorders.Base editing is a genome editing method which can precisely induce point mutations on DNA or RNA at the target loci without generating double strand breaks[2–5]. | Yidi SUN Erwei ZUO Hui YANG | 2020 | Frontiers of Agricultural Science and Engineering2020，7，2： | 0 |
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