Dr. Yi Xu

***** **** ***** **** *****: acs9m1@r.postjobfree.com

Houston, TX 77062 Tel: 832-***-**** (cell)

OFFICIAL ADDRESS

Department of Medicine/Pulmonary section

Baylor College of Medicine

One Baylor Plaza

Houston, TX 77030

Tel: 832-***-****

E-mail: acs9m1@r.postjobfree.com

EDUCATION

Degree-granting education

Ph. D. Biochemistry, Chinese Academy of Sciences, Beijing, CHINA

M. Sc. Microbiology, Shandong University, CHINA

B. Sc. Biology, Shandong University, CHINA

Postgraduate training

Postdoctoral Associate Biochemistry, University of Houston, USA (1999-2003)

Postdoctoral Fellow Cell Biology, Baylor College of Medicine, USA (2004-2007)

EXPERIENCE/SERVICES

2013 – 2015: Research Associate, Baylor College of Medicine/Infectious diseases section, Houston, TX

The stimulatory and regulatory effects of pneumococcal vaccines (23F, T4) on B cell differentiation and antibody production through Dendritic cells from normal human blood and HIV patients’ blood.

2003 – 2013: Instructor, Baylor College of Medicine/Pulmonary section, Houston, TX

LPS-induced lysosomal/mTOR perinuclear positioning promotes autophagy in mouse macrophages

The effects of mTOR inhibitors, rapamycin, pp242, WYE-354, Ku-0063794 on mTOR signaling, mTOR activity and autophagy.

Selected some proteasome inhibitors to reduce zz-mutant a1-antitrypsin biosynthesis in human primary hepatocytes and hepatocyte cell lines. These findings set up a therapeutic strategy for reduction of liver disease caused by zz-mutant a1-antitrypsin.

Recognized the induction of autophagy by lipopolysaccharide (LPS) through Toll-like receptor 4 signaling pathways in primary human macrophages and mouse macrophage.

Defined a new signaling pathway in which LPS-induced autophagy is regulated through a TRIF-dependent MyD88-independent TLR4 signaling.

Established the relationship between the autophagy and innate immunity against pathogens such as Mycobacterium tuberculosis, Pseudomonas aeruginosa and Klebsiella through a shared signaling pathway that links these two ancient processes.

1999 – 2003: Postdoctoral Associate, University of Houston/Biochemistry Department, Houston, TX

Studied the interaction of Bicyclomycin with Rho, a transcription termination protein in E. coli.

Studied the structure & kinetically function of Rho protein through a series of site-directed mutation.

1993 – 1995: Visiting Scientist, Riken Institute, Japan

Studied of chaperonin (groEL) from an alkaliphilic Bacillus C125 and other heat-shock proteins from Thermococcus profundus DT5432

Grant application experiences:

NIH Kirschstein National Research Service Award (2004 to 2007)

Application for research award from 2008 American Heart Association

Application for funding for pilot/feasibility projects from Texas medical center digestive diseases center (2009).

Application for pilot/feasibility funding from Alpha 1 foundation (2011).

EXPERIENCES for training and mentoring students:

2 summer students, 5 rotation students, 2 Ph.D students, and several visiting postdoctoral fellows.

Responsibilities:

Help student establish their research projects

Help students master research techniques and instruct them during experiments

Help students review relevant materials and prepare for each laboratory meeting.

AWARDS AND HONORS

The Second-rate Invention Award on Excellent Contribution in Development and Application of belta-mannanase (Chinese Academy of Sciences, Beijing, 2000)

NIH Kirschstein National Research Service Award (1F32 HL078520-01, 2004-2007)

SKILL SET

Gene cloning/recombination, site-directed mutagenesis, plasmid construction.

Gene expression in prokaryotic and eukaryotic cells, bacterium incubation & cell culture.

Sequencing, RealTime-PCR technique, DNA and RNA preparation, Genomic analysis.

Design and construct recombinant Lentiviruses for over-expression of target proteins or siRNA-mediated knocking-down gene expression.

Basic animal work.

Bacterial & mammalian genetics, basic techniques for microbiology and biochemistry.

Protein-protein interaction (Immunoprecipitation), Chromatin-protein interaction (ChIP).

Various Hybridizations (Southern, Northern, Western, In-situ etc.).

Protein isolation and purification, kinetic analysis of protein function.

Thin layer chromatography, Ion-exchange, affinity and reserved-phase chromatography.

Gel filtration, ELISA, Immunoassay, immunology and electrophoresis techniques.

Autoradiography. Live cell imaging.

Flow-cytometry, Luminex, Immunohistochemistry, Immunofluorescence, mass spectrometer and Electron Microscopy techniques.

Various biology softwares: Flow-Jo, DNAMAN, Chromas, DNA Master, Plasmid Processor, Fast PCR, ClustalX, SigmaPlot, Treecon, PHYLIP, and so on.

Main publications

1.Yi Xu, E.A. Fattah, Xian-De Liu, C. Jagannath, and Tony Eissa. Harnessing of TLR-mediated autophagy to combat mycobacteria in macrophages

Tuberculosis, 93 S1: S33-S37, 2013.

2. Diana L Bonilla, Abhisek Bhattacharya, Youbao Sha, Yi Xu, Qian Xiang, Arshad Kan, Chinnaswamy Jagannath, Masaaki Komatsu, N Tony Eissa. Autophagy Regulates Phagocytosis by Modulating the Expression of Scavenger Receptors,

Immunity 2013.

3. Liu XD, Ko S, Xu Y, Abdel Fattah E, Xiang Q, Jagannath C, Ishii T, Komatsu M, Eissa NT. Transient aggregation of Ubiquitinated proteins is a cytosolic unfolded protein response to inflammation and ER stress. Journal of Biological Chemistry, 2012, April 19, [Epub ahead of print].

4. Yi Xu, Xiande Liu and T.N. Eissa. Harnessing Of TLR-mediated Autophagy to Eliminate Mycobacterium Tuberculosis from Macrophages,

American Journal of Respiratory and Critical Care Medicine 181: A3219, 2010.

5. Xiande Liu, Yi Xu, C. Fung, Z. Dalu, Q. Xiang, C. Jagannath, T. N. Eissa. BCG Infection Induces P62-Dependent Autophagy-Independent Formation Of Dendritic Cell Aggresome-Like Structures,

American Journal of Respiratory and Critical Care Medicine 181: A3222, 2010.

6. Yi Xu and N. Tony Eissa. Autophagy in innate and adaptive immunity,

Proceedings of the American Thoracic Society 7: 22-28, 2010.

7. Xian-de Liu, Tuhina Mazumdar, Yi Xu, Elizabeth D. Getzoff, and N. Tony Eissa. Identification of a Flavin Mononucleotide Module Residue Critical for Activity of Inducible Nitrite Oxide Synthase

Journal of Immunology, 183: 5977 – 5982, 2009.

8. Chinnaswamy Jagannath, Devin R. Lindsey, Subramanian Dhandayuthapani, Yi Xu, Rbert L. Hunter Jr. & N. Tony Eissa. Autophagy enhances the efficacy of BCG vaccine by increasing peptide presentation in mouse dendritic cells,

Nature Medicine, 15(3): 267-276, 2009.

9. Yi Xu, Xian-De Liu, Xing Gong and N. Tony Eissa. Signaling pathway of autophagy associated with innate immunity.

Autophagy, 4(1): 110-112, 2008.

10. Yi Xu, Chinnaswamy Jagannath, Xian-De Liu, Amir Sharafkhaneh, Katarzyna E. Kolodziejska, and N. Tony Eissa. Toll-like receptor 4 is a sensor for autophagy associated with innate immunity,

Immunity 27: 135-144, 2007.

11. Yi Xu, Jerry Johnson, Harold Kohn, and William R. Widger, ATP binding to Rho transcription termination factor: Mutant F355W ATP-induced fluorescence quenching reveals dynamic ATP binding.

Journal of Biological Chemistry, 278:137**-*****, April 18, 2003.

12. Yi Xu, Harold Kohn, and William R. Widger, Mutations in the rho transcription termination factor that affect RNA tracking.

Journal of Biological Chemistry, 277(33): 300**-*****, August 16, 2002.

13. Bao Q, Tian Y., Li W, Xu Z, Hu S, Dong W, Xue Y, Xu Yi, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H*, Chen R*, Wang J, Yu J, Yang H. A complete sequence of the T. tengcongensis genome.

Genome Research, 12: 689-700, 2002.

14. Wang zhenxiong, Xu Yi and Peijin Zhou, the properties of a cold-shock protein (CspA-like protein) of a Thermus species,

Acta Microbiologica Sinica, 40:13-16, 2000.

15. Yin Jin, Xu Yi, Li Hongqi, Zhou Peijin and Shen Zhongyao, Overexpression of Lambda phage lysis genes and biosynthetic genes of poly-b-hydroxybutyrate in recombinant E.coli,

Tsinghua Science and Technology, 4(2): 1472-1476, 1999.

16. Xu Yi et al., Molecular Cloning and Nucleotide Sequence of the groEL gene from an alkalophilic Bacillus sp. C-125, and The reactivation of thermally-inactivated a-glucosidase by recombinant GroEL,

Biosci. Biotech. Biochem., 60(10): 1633-1636, 1996.

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