Research Fellow Simonds

*

SHIYING ZHANG

Cornell University, Ithaca, NY *4853. Phone: 607/227-9638. E-mail: ****@*******.*** Education

Ph.D Cornell University, Ithaca, New York. Major in Biology M.S Shandong Agricultural University, China. Major in Biochemistry B.S Shandong Normal University. Major in Analytical Chemistry Skills

Molecular biology techniques, PCR, RT-PCR, mutagenesis, etc.

Cell culture techniques, including 3-D cell culture, infection, FISH, etc.

Microbiological techniques, in vivo and in vitro functional assays

Microbiome, transcriptome, and metabolomics data analysis

Managerial experience with excellent communication skills

Strong problem solving and attention to details

Experience

2013-present Dept. Clinical Sciences, Vet. College, Cornell University, Ithaca, NY. Senior Research Associate

Antimicrobial compound identification/testing, in vivo and in vitro

Pathogen-host interaction, gene expression and analysis

Metagenome, transcriptome, and microbiome data analysis

Translational research on probiotics and antimicrobial agents

New employee and student training

Laboratory management

Research Associate

IBD-associated E. coli growth and virulence regulation

Colorectal cancer associated E. coli virulence gene regulation

CRISPR-cas9 technology of gene knockout in macrophages

Microbial interaction within micro-community

Mentoring graduate/undergraduate students

2007-2012 Boyce Thompson Institute (BTI), Ithaca, NY. Research Associate.

Developed novel endogenous virus-eradicating method for existing cell lines

Developed multiple virus-free cell lines available for commercialization

Translational research on insect cell application and marketing

Technical support for BTI cell line users

Coordinator for collaborative projects

Postdoctoral Associate

Insect cell line selection and characterization by virus and protein production

Cell line engineering for high protein production

Single cell cloning, established over 200 cell lines from insect eggs

Flow cytometry for cell line screening

2

Mentoring students

2003-07 Senior Scientist, Environmental Associates, Ltd, Ithaca, NY

Managed Molecular Typing laboratory

Established the Molecular Typing program

Oversight daily operation in Bacteriology and Virology section

In charge of QC and lab reports

Wrote and updated SOPs

Trained new employees

1999-2003 Associate Director. Etron, Inc. Ithaca, NY

Oversight of Research and development

Provided technical support for customers

System organization

1996-99 U.S Army Research Fellow. Molecular Medicine, Cornell University, Ithaca, NY

Received research grant from the Breast Cancer Research Program, Department of Defense, U S Army

Studied breast cancer development and metastasizing of the lung 1994-96 National Institutes of Health. NIDDK, Bethesda. MD Postdoctoral Research Fellow

Received 5 year fellowship

Studied the specificities of different G-protein β subunits in signal transduction

Defined the functional domain(s) of β1 in MAP kinase and PLC activation pathways

Trained interns

1988-90 Research Assistant. Biochemistry, Cell and Molecular Biology. Cornell University

Protein purification

Protein kinase activity assays

Laboratory organization and management

Trained new undergraduate students

Publications

1. Shiying Zhang, Jordan Rios, Belgin Dogan and Kenneth W Simpson (2022). Microbial interaction between Klebsiella pneumonia and Escherichia. coli during culturing (In preparation).

2. Shiying Zhang, Qiong Wu, Belgin Dogan, and Kenneth W Simpson (2022). Small Boron- containing molecules regulate the growth and virulence of IBD-associated E. coli in vitro. (In preparation).

3. Ann V. Nguyen, Arash Yahyazadeh Shourabi, Mohammad Yaghoobi, Shiying Zhang, Kenneth W. Simpson, Alireza Abbaspourrad (2022). A high-throughput integrated biofilm- on-a-chip platform for the investigation of combinatory physicochemical responses to chemical and fluid shear stress. ACS Appl. Mater. Interfaces. (Submitted). 3

4. Shiying Zhang, Shan Gao, Zhangjun Fei, Paul Debbie, and Gary Blissard (2022). A novel method to abrogate intracellular RNA virus by co-culturing. (In preparation). 5. Shiying Zhang, Xochitl Morgan, Belgin Dogan, Francois-Pierre Martin, Suzy Strickler, Akihiko Oka, Jeremy Herzog, Bo Liu, Scot E Dowd, Curtis Huttenhower, Matthieu Pichaud, Esra I Dogan, Jack Satsangi, Randy Longman, Rhonda Yantiss, Lukas A Mueller, Ellen Scherl, R. Balfour Sartor, Kenneth W Simpson. (2022) Mucosal metabolites fuel the growth and virulence of E. coli linked to crohn’s disease. JCI Insight (accepted) 6. Davachi, Seyed Mohammad; Dogan, Belgin; Khazdooz, Leila; Zhang, Shiying; Khojastegi, Anahita; Fei, Zhangjun; Sun, Honghe; Meletharayil, Gopinathan; Kapoor, Rohit; Simpson, Kenneth; Abbaspourrad, Alireza (2022). Long-term probiotic bacterial storage at ambient temperature: viability and functional assessments. Agric. Food Chem (under review). 7. Viladomiu M, Khounlotham M, Dogan B, Lima S, Elsaadi A, Herzog J, Schoenborn A, Ellermann M, Liu B, Zhang S, Gulati A. Adherent-invasive E. coli promote ER stress to support il23r-driven agr2-dependent ileocolitis. Gastroenterology. 2022 Feb 1;162(3): S55. 8. Wang J, Bleich RM, Zarmer S, Zhang S, Dogan B, Simpson KW, Arthur JC (2021). Long- read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue. PLoS One. 16(10):e0259141. doi: 10.1371/journal.pone.0259141.

9. Morteza Azizi, Ann V. Nguyen, Belgin Dogan, Shiying Zhang, Kenneth W. Simpson, and Alireza Abbaspourrad (2021). Antimicrobial Susceptibility Testing in a Rapid Single Test via an Egg-like Multivolume Microchamber-Based Microfluidic Platform. ACS Appl. Mater. Interfaces 2021, 13, 17, 19581–19592

10. Azizi M, Davaji B, Nguyen AV, Zhang S, Dogan B, Simpson KW, Abbaspourrad A. (2021). Gradient-Based Microfluidic Platform for One Single Rapid Antimicrobial Susceptibility Testing. ACS Sens. 2021 Apr 23;6(4):1560-1571. doi: 10.1021/acssensors.0c02428. Epub 2021 Apr 14. PMID: 33851833.

11. Nguyen AV, Azizi M, Yaghoobi M, Dogan B, Zhang S, Simpson KW, Abbaspourrad A.

(2021). Diffusion-Convection Hybrid Microfluidic Platform for Rapid Antibiotic Susceptibility Testing. Anal Chem.; 93(14):5789-5796. doi: 10.1021/acs.analchem.0c05248. Epub 2021 Mar 31. PMID: 33788554.

12. Azizi M, Davaji B, Nguyen AV, Mokhtare A, Zhang S, Dogan B, Gibney PA, Simpson KW, Abbaspourrad A (2021). Biological small-molecule assays using gradient-based microfluidics. Biosens Bioelectron. 2021 Apr 15;178:113038. doi: 10.1016/j.bios.2021.113038. E pub 2021 Jan 27. PMID: 33556809. 13. Zhang, S., Dogan, B., Guo, C., Herlekar, D., Stewart, K., Scherl, E. J., & Simpson, K. W.

(2020). Short Chain Fatty Acids Modulate the Growth and Virulence of Pathosymbiont Escherichia coli and Host Response. Antibiotics (Basel, Switzerland), 9(8), 462. https://doi.org/10.3390/antibiotics9080462

14. Dogan B, Zhang S, Kalla SE, Dogan EI, Guo C, Ang CR, Simpson KW. Molecular and Phenotypic Characterization of Escherichia coli Associated with Granulomatous Colitis of Boxer Dogs. Antibiotics (Basel). 2020 Aug 25;9(9):540. doi: 10.3390/antibiotics9090540. PMID: 32854367; PMCID: PMC7559917.

4

15. Zhang, S., Fu, J., Dogan, B. et al. 5-Aminosalicylic acid downregulates the growth and virulence of Escherichia coli associated with IBD and colorectal cancer, and upregulates host anti-inflammatory activity. J Antibiot 71, 950–961 (2018). https://doi.org/10.1038/s41429- 018-0081-8

16. Dogan B, Fu J, Zhang S, Scherl EJ, Simpson KW. Rifaximin decreases virulence of Crohn's disease-associated Escherichia coli and epithelial inflammatory responses. J Antibiot

(Tokyo). 2018 May;71(5):485-494. doi: 10.1038/s41429-017-0022-y. Epub 2018 Feb 6. PMID: 29410518.

17. Morteza Azizi, Meisam Zaferani, Belgin Dogan, Shiying Zhang, Kenneth W. Simpson, and Alireza Abbaspourrad (2018). Nanoliter-Sized Microchamber/Microarray Microfluidic Platform for Rapid Antibiotic Susceptibility Testing. Analytical Chemistry, DOI: 10.1021/acs.analchem.8b03817

18. Seyed Ramin Pajoumshariati, Morteza Azizi, Shiying Zhang, Belgin Dogan, Kenneth W Simpson, and Alireza Abbaspourrad (2018). Microbiome within a Membrane: A Microfluidic Based Model for Spatially Constrained Culture of Intestinal Microbiota. Adv. Funct. Mater. 48. DOI: 10.1002/adfm.201870339

19. Seyed Ramin Pajoumshariati, Morteza Azizi, Shiying Zhang, Belgin Dogan, Kenneth W Simpson, and Alireza Abbaspourrad (2018). A Microfluidic-based Model for Spatially Constrained Culture of Intestinal Microbiota. Adv. Funct. Mater. 1805568. DOI: 10.1002/adfm.201805568.

20. Shiying Zhang, Jing Fu, Belgin Dogan, Ellen J Scherl, and Simpson KW (2018). 5- Aminosalicylic acid downregulates the growth and virulence of Escherichia coli associated with IBD and colorectal cancer, and upregulates host anti-inflammatory activity. J. Antibiot. DOI : 10.1038/s41429-018-0081-8. July 26, 2018.

21. Dogan B, Fu J, Zhang Shiying, Scherl EJ, Simpson KW (2018). Rifaximin decreases virulence of Crohn's disease-associated Escherichia coli and epithelial inflammatory responses. J Antibiot (Tokyo). 71(5):485-494.

22. Chen, Y.-R.; Zhong, S.; Fei, Z.; Gao, S.; Zhang, Shiying.; Li, Z.; Wang, P.; Blissard, G.W.

(2014) Transcriptome Responses of the Host Trichoplusia ni to Infection by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus. J. Virol. 2014, 88, 13781–13797. 23. Chen, Y; Zhong, S; Fei, Z; Hashimoto, Y; Xiang, J; Zhang, Shiying; and Blissard, G (2013). The transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells. J. Virol.. 87, 6391-6405. 24. Shiying Zhang, Yoshi Hashimoto, Sheng Zhang, Yun-Ru Chen and Gary W Blissard (2012). Correction: BTI-Tnao38, a new cell line derived from Trichoplusia ni, is permissive for AcMNPV infection and produces high levels of recombinant proteins. BMC Biotech, 12:12- 18.

25. Shan M, Zhang Shiying, Jiang L, Ma M, Li GX (2011). Susceptibility to AcMNPV and expression of recombinant proteins by a novel cell clone derived from a Trichoplusia ni QAU-BTI-Tn9-4s cell line. Virol Sin. 26(5):297-305. doi: 10.1007/s12250-011-3201-1. 26. Hung-Chi Cheng, Mossaad Abdel-Ghany, Shiying Zhang and Bendicht U. Pauli (1999) Is the Fisher 344/CRJ rat a protein-knock-out model for dipeptidyl peptidase IV-mediated lung metastasis of breast cancer? Clinical &Experimental Metastasis, 17:609-615. 5

27. Susan Pellegrino, Shiying Zhang, Anja Garritsen, and William F. Simonds (1997). The coil- coil region of the G-protein β-subunit: Mutational analysis of Gγ and effector interactions. J. Biol. Chem. 272:253**-*****.

28. Shiying Zhang, Omar A. Coso, Regina Collins, J. Silvio Gutkind and William F. Simonds

(1996) Selective activation of effector pathway by brain-specific G-protein β5. J. Biol. Chem. 271:335**-*****.

29. Shiying Zhang, Omar A. Coso, Regina Collins, J. Silvio Gutkind and William F. Simonds

(1996). A Carboxyl mutant of the G-protein β subunit deficient in the activation of phospholipase C-β. J. Biol. Chem. 271:202**-*****. 30. Shiying Zhang and Andre T. Jagendorf (1995) Some unique characteristics of thylakoid unisite ATPase. J. Biol. Chem. 270:6607-6614.

31. Shiying Zhang, D. D. Letham, and A. T. Jagendorf (1993). Inhibition of thylakoid ATPase by venturicidinas an indicator of CF1-CF0 interaction. Plant physiology, 101, 127-133. DOI: 10.1104/pp.101.1.127.

32. M Abdel-Ghany, K el-Gendy, S Zhang, D Raden, and E Racker (1989) Brain protein kinase C phosphorylating poly(arginine,serine) or lamin B is stimulated by anions and by an activator purified from bovine serum albumin preparations. Proc. Nat. Aca. Sci. USA, 86: 1761-5. PMID 2928301

Contact this candidate