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澳门威利斯人v9579网:季泉江

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季泉江课题组介绍


Principal Investigator


Quanjiang Ji (季泉江)

Associate Professor (tenured), PI

Address: 393 Huaxia Middle Road, Pudong, Shanghai, China, 200120

Email: quanjiangji@shanghaitech.edu.cn


Associate ProfessorShanghaiTech University, 2021-current;

Assistant Professor, ShanghaiTech University, 2016-2020;

Postdoc., University of California, Berkeley (Advisor: Prof. Michelle Chang), 2014-2016;

Ph.D., University of Chicago (Advisor: Prof. Chuan He), 2009-2014;

B.S., Nanjing University, 2005-2009.


Awards:

NSFC Excellent Young Scholar,2019;

Shanghai Science and Technology Committee Rising-Star Program,2019;

Young Overseas High-Level Talents Introduction Plan, 2016;

Camille and Henry Dreyfus Postdoctoral Fellowship, 2015; 

Chinese Government Award for Outstanding Self-Financed Students Abroad, 2013; 

The Everett E Gilbert Memorial Prize, 2012.


Research


 Advances in the understanding and development of CRISPR-Cas systems have revolutionized the gene editing methods in biology and medicine. However, the imperfect properties of current CRISPR-Cas technology, such as a high off-target rate, a strict PAM requirement, high cell toxicity, and large gene size, restrict its diverse applications. We aim to discover, characterize, and engineer new CRISPR-Cas systems with superior properties compared with current CRISPR-Cas systems. In addition, we leverage different CRISPR-Cas systems to develop rapid and efficient gene editing tools in major human pathogens to facilitate fundamental understanding of infection and drug-resistance mechanisms. Finally, we aim to develop CRISPR-based antimicrobial strategies to counter infections caused by drug-resistant human pathogens. 

CRISPR-Cas characterization and engineering: One potential way to overcome the limitation of current CRISPR-Cas technologies is to discover, characterize, and engineer new CRISPR-Cas systems from other bacteria that may possess rich and distinct biochemical properties for gene editing. We explore and study new CRISPR-Cas systems using multiple approaches, including bioinformatics, biochemical, structural biology, and molecular evolution methods. In addition, we study the fundamental molecular mechanism of current CRISPR-Cas9 systems to evolve PAM-expanded and high-fidelity versions of these enzymes (PLoS Biol, 2019; Nat Catal, 2020; Nat Chem Biol, 2021). Ultimately, we aim to develop compact CRISPR-Cas systems with low off-target rate and expanded targeting sites.

Gene editing in major human pathogens: The rapid emergence of drug-resistant human pathogens has posed a severe public health crisis worldwide, emphasizing the desperate need to identify new drug targets and develop new therapeutic strategies. Genetics is the key means to study bacterial physiology. However, traditional genetic manipulation methods in major human pathogens remain as time-consuming and laborious endeavors. We have created rapid and highly efficient genetic manipulation tools in multiple major human pathogens, including Staphylococcus aureus (JACS, 2017; Chem Sci, 2018; Chem Sci, 2020), Pseudomonas aeruginosa (iScience, 2018), Klebsiella pneumoniae (Appl Environ Microbiol, 2018; Antimicrob Agents Chemother, 2019), and Acinetobacter baumannii (Cell Chem Biol, 2019; STAR Protocols, 2020) by engineering the powerful CRISPR/Cas9 genome editing technology and deaminase-mediated base editing systems. These tools have been requested and utilized by numerous research groups worldwide and are available in Addgene (http://www.addgene.org/Quanjiang_Ji/). We utilize protein engineering and synthetic biology approaches to develop genome-wide screening tools in multiple human pathogens (Cell Reports, 2021). The development of these tools will advance fundamental physiology studies as well as novel drug-target exploration (PNAS, 2018; Mol Microbiol, 2018).

CRISPR-based antimicrobial therapy: We aim to develop CRISPR engineered bacteriophages to counter infections caused by drug-resistant bacterial pathogens using the CRISPR systems developed by ourselves. The engineered bacteriophages are not only able to species-specifically kill target bacterial cells, but also capable of sequence-specifically eliminating certain genes. Therefore, both resistance attenuation and bacterial killing can possibly be achieved using the engineered phages.


Publications


Book Chapters

1. Chen, W. & Ji, Q. (2020) Genetic manipulation of MRSA using CRISPR/Cas9 technology. Methods in Molecular Biology 2069:113-124.


Research Articles and Reviews

2021

20. Wu, Z., Zhang, Y., Yu, H., Pan, D., Wang, Yuj., Wang, Ya., Li, F., Liu, C., Nan, H., Chen, W., Ji, Q.* (2021) Programmed genome editing by a miniature CRISPR-Cas12f nuclease. Nature Chemical Biology 17: 1132-1138.


19. Chen, W.#, Ren, Z.#, Tang, N., Chai, G., Zhang, H., Zhang, Y., Ma, J., Wu, Z., Shen, X., Huang, X., Luo, G.Z.*Ji, Q.* (2021) Targeted genetic screening in bacteria with a Cas12k-guided transposase. Cell Reports 36: 109635.


2020

18. Zhang, Y., Zhang, H., Xu, X., Wang, Yuj, Chen, W., Wang, Ya., Wu, Z., Tang, N., Wang, Yu, Zhao, S., Gan, J.*, Ji, Q.* (2020) Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nature Catalysis 3: 813-823.


17. Yu, H.#, Wu, Z.#, Chen, X., Ji, Q.*, Tao, S.* (2020) CRISPR-CBEI: a designing and analyzing tool kit for cytosine base editor-mediated gene inactivation. mSystems 5: e00350-20.


16. Wang, Y.*, Wang, Z., Ji, Q.* (2020) CRISPR-Cas9-based genome editing and cytidine base editing in Acinetobacter baumanniiSTAR Protocols DOI: 10.1016/j.xpro.2020.100025.


15. Pi, Y., Chen, W., Ji, Q.* (2020) Structural basis of Staphylococcus aureus surface protein SdrC. Biochemistry 59: 1465-1469.


14. Zhang, Y., Zhang, H., Wang, Z., Wu, Z., Wang, Y., Tang, N., Xu, X., Zhao, S., Chen, W.*, Ji, Q.* (2020) Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion. Chemical Science 11: 1657-1664.


13. Wu, Z., Wang, Y., Zhang, Y., Chen, W., Wang, Y., Ji, Q.* (2020) Strategies for developing CRISPR-based gene editing methods in bacteria. Small Methods 4: 1900560.


2019

12. Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J.*, Ji, Q.* (2019) Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. PLoS Biology 17: e3000496.


11. Wang, Y., Wang, Z., Chen, Y., Hua, X., Yu, Y., Ji, Q.* (2019) A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii toward the understanding of H2O2-sensing mechanism of OxyR. Cell Chemical Biology 26: 1732-42. 


10. Zhang, Y., Sun, X., Qian, Y., Yi, H., Song, K., Zhu, H., Zonta, F., Chen, W., Ji, Q., Miersch, S, Sidhu, S.S.*, Wu, D.* (2019) A potent anti-SpuE antibodyallosterically inhibits type III secretion system and attenuates virulence of Pseudomonas aeruginosa. Journal of Molecular Biology 431:4882-4896.


9. Fu, T., Liu, L., Yang, Q.L., Wang, Y., Xu, P., Zhang, L., Liu, S., Dai, Q., Ji, Q., Xu, G.L., He, C., Luo, C.*, Zhang, L.* (2019) Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine. Chemical Science 10: 7407-17.


8. He, T., Wang, R., Liu, D., Walsh, T.R., Zhang, R., Lv, Y., Ke, Y., Ji, Q., Wei, R., Liu, Z., Shen, Y., Wang, G., Sun, L., Lei, L., Lv, Z., Li, Y., Pang, M., Wang, L., Sun, Q., Fu, Y., Song, H., Hao, Y., Shen, Z., Wang, S., Chen, G., Wu, C., Shen, J., Wang, Y. (2019) Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nature Microbiology 4: 1450-6.


7. Sun, Q.#, Wang, Y.#, Dong, N., Shen, L., Zhou, H., Hu, Y., Gu, D., Chen, S., Zhang, R.*, Ji, Q.* (2019) Application of CRISPR/Cas9-based genome editing in studying the mechanism of pandrug resistance in Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy 63: e00113-19.


2018

6. Wang, Y., Wang, S., Chen, W., Song, L., Shen, Z., Yu, F., Li, M., Ji, Q.*(2018) Precise and efficient genome editing in Klebsiella pneumoniae using CRISPR-Cas9 and CRISPR-assisted cytidine deaminase. Applied and Environmental Microbiology 84: e01834-18.


5. Chen, W., Zhang, Y., Zhang, Y., Pi, Y., Gu, T., Song, L., Wang, Y., Ji, Q.* (2018) CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species. iScience 6: 222-31.


4. Wei, W.#, Zhang, Y.#, Gao, R., Li, J., Xu, Y., Wang, S., Ji, Q.*, Feng, Y.* (2018) Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis. Molecular Microbiology 109: 642-62.


3. Song, L., Zhang, Y., Chen, W., Gu, T., Zhang, S.Y., Ji, Q.* (2018) Mechanistic insights into staphylopine-mediated metal acquisition.  PNAS 115: 3942-7.


2. Gu, T.#, Zhao, S.#, Pi, Y., Chen, W., Chen, C., Liu, Q., Li, M., Han, D.*, Ji, Q.* (2018) Highly efficient base editing in Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase. Chemical Science 9: 3248-53.


2017

1. Chen, W., Zhang, Y., Yeo, W.S., Bae, T., Ji, Q.* (2017) Rapid and efficient genome editing in Staphylococcus aureus by using an engineered CRISPR/Cas9 system. JACS 139: 3790-5.


Patents


8. 季泉江、王宇。一种用于鲍曼不动杆菌胞嘧啶碱基编辑质粒及其应用。申请号:201910644444.1
7. 季泉江、王宇。双质粒系统及其应用。申请号:201910644324.1
6. 季泉江、王宇。一种用于肺炎克雷伯菌基因编辑的双质粒系统。申请号:201811039504.9
5. 季泉江、王宇。一种肺炎克雷伯菌基因编辑的表达载体。申请号:201811039489.8
4. 季泉江、陈未中。一种pnCasPA-BEC质粒及其应用。申请号:201810767194.6
3. 季泉江、陈未中。一种pCasPA/pACRISPR双质粒系统及其应用。申请号:201810766759.9
2. 季泉江、顾桐年。一种pnCasSA-BEC质粒及其应用。申请号:201810169946.9
1. 季泉江、陈未中。一种pCasSA质粒及其应用。授权号:ZL201611255504.3


Group Activities



Current Group Members


Weizhong Chen(陈未中)

Associate Research Fellow

Associate Research Fellow, ShanghaiTech University,2020-Current;

Assistant Research Fellow, ShanghaiTech University,2018-2020;

Postdoc., ShanghaiTech University, 2016-2018;

Ph.D., University of Science and Technology of China, 2009-2015

Email: chenwzh@shanghaitech.edu.cn

Zhaowei Wu(吴兆韡)

Assistant Research Fellow

Assistant Research Fellow, ShanghaiTech University,2021-Current;

Postdoc., ShanghaiTech University, 2018-2021;

Ph.D., Northwest A&F University, 2014-2018;

B.S., Northwest A&F University, 2010-2014.

Email: wuzw1@shanghaitech.edu.cn

Fan Li(李帆)

Postdoc

Postdoc., ShanghaiTech University, 2020-Current;

Ph.D., Northwest A&F University, 2015-2020;

B.S., Northwest A&F University, 2011-2015.

Email: lifan@shanghaitech.edu.cn

Yifei Zhang(张翼飞)

Graduate student

Graduate student, ShanghaiTech University, 2016-Current;

B.S., Zhengzhou University, 2012-2016.

Email: zhangyf1@shanghaitech.edu.cn

Ya Zhang(张雅)

Graduate student

Graduate student, ShanghaiTech University, 2017-Current;

B.S., Southwest University, 2013-2017.

Email: zhangya@shanghaitech.edu.cn

Zhipeng Wang(王志鹏

Graduate student

Graduate student, ShanghaiTech University, 2018-Current;

B.S., Zhengzhou University, 2014-2018.

Email: wangzhp@shanghaitech.edu.cn

Yujue Wang(王玉珏

Graduate student

Graduate student, ShanghaiTech University, 2018-Current;

B.S., Shandong University, 2014-2018.

Email: wangyj6@shanghaitech.edu.cn

Hongyuan Zhang(张洪源

Graduate student

Graduate student, ShanghaiTech University, 2018-Current;

B.S., Shandong University, 2014-2018.

Email: zhanghy2@shanghaitech.edu.cn

Na Tang(汤娜

Graduate student

Graduate student, ShanghaiTech University, 2019-Current;

B.S., China Pharmaceutical University, 2015-2019.

Email: tangna@shanghaitech.edu.cn

Yannan Wang(王艳男

Graduate student

Graduate student, ShanghaiTech University, 2019-Current;

B.S., Wuhan University of Technology, 2015-2019.

Email: wangyn5@shanghaitech.edu.cn

Deng Pan(潘登

Graduate student

Graduate student, ShanghaiTech University, 2020-Current;

B.S., Zhengzhou University, 2016-2020.

Email: pandeng@shanghaitech.edu.cn

Jiacheng Ma(马佳诚

Graduate student

Graduate student, ShanghaiTech University, 2020-Current;

B.S., Northwest University, 2016-2020.

Email: majch@shanghaitech.edu.cn

Runze Peng(彭润泽

Graduate student

Graduate student, ShanghaiTech University, 2020-Current;

B.S., Zhengzhou University, 2013-2017.

Email: pengrz@shanghaitech.com










Jin Shi (史进)

Graduate student

Graduate student, ShanghaiTech University, 2021-Current;

B.S., China Pharmaceutical University, 2017-2021.

Email: shijin@shanghaitech.edu.cn


Mengjiao Su苏梦娇

Graduate student

Graduate student, ShanghaiTech University, 2021-Current;

B.S., Chengdu Medical College, 2017-2021.

Email: sumj@shanghaitech.edu.cn


Wenhan Fu傅文翰

Graduate student  

Graduate student, ShanghaiTech University, 2021-Current;

B.S., ShanghaiTech University, 2017-2021.

Email: fuwh@shanghaitech.edu.cn

 











  Alumni

 

 

Liqiang Song(宋立强)

Postdoc   2016-2018

Current: UT Health Science Center (Postdoc)

Yu Wang(王宇)

Postdoc   2017-2019

Current: Jiangxi Agricultural University (Associate Professor)

Yani Zhao(赵雅妮)

B.S.   2015-2019

Current: UNC at Chapel Hill (Ph.D. candidate)

Tongnian Gu (顾桐年)

Ph.D.   2015-2020
 Current: Institute of Biophysics, CAS (Postdoc)

Yishuang Pi (皮义双)

M.S.   2017-2020
 Current: Viva Biotech (Research Scientist)

Chang Liu (刘畅)

B.S.   2017-2021
 Current: University of California, Berkeley (Ph.D. candidate)


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