RONG LI LABORATORY

biosketch

I received my Degree in Industrial Biotechnology from the University of Milano-Bicocca in 2001 and my Ph.D. in Immunology from the University of Rome “Tor Vergata” in 2006. I formerly worked as a graduate student in Prof. Paola Ricciardi-Castagnoli's lab at the Department of Biotechnology and Bioscience of the Milano-Bicocca University. I joined Rong Li’s group as a Postdoctoral Research Associate in May 2006 and currently work in her lab at the Stowers Institute for Medical Research located in Kansas City, Missouri. Here, I also actively collaborate with the Proteomics Center, headed by Michael Washburn.

During my Ph.D. studies, my main research focus was in the application of Functional Genomics approaches to study host-pathogen interactions. I therefore acquired a deep expertise in analyzing microarray data to investigate the transcriptional response of cells of the immune system to invading pathogens. In particular, I contributed in developing algorithms and software for the identification of differentially expressed genes in microarray data and I have analyzed the transcriptional modulation of mouse dendritic cells after encounter of various bacteria and parasites.

current projects

Biological systems are characterized by the ability to adapt to even the most challenging situations. Examples include pathogens and cancer cells that evolve immune escape mechanisms and develop resistances towards a variety of drugs. In an effort to better understand this remarkable ability, we studied how yeast cells deprived of a protein important for cell division (type II myosin) gradually recovered their ability to divide through an adaptive evolution process. In collaboration with Dr. Giulia Rancati, we discovered that among the most important changes in the genome that accounted for the emergence of these evolved mechanisms were changes in the number of chromosomes, known as aneuploidy. We recently started a new research project in which we plan to generalize this finding by testing whether a similar adaptive evolution process can be observed also in response to perturbations in other components of the cell division machinery.

contact

e-mail: nxp {at} stowers {dot} org

publications

Aneuploidy and adaptive evolution:

*Pavelka N, *Rancati G, *Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R: Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature 2010, 468:321. [Abstract|News&Views]

Pavelka N, Rancati G, Li R: Dr Jekyll and Mr Hyde: role of aneuploidy in cellular adaptation and cancer. Curr Opin Cell Biol 2010, 22:809. [Abstract]

*Rancati G, *Pavelka N, Fleharty B, Noll A, Trimble R, Walton K, Perera A, Staehling-Hampton K, Seidel CW, Li R: Aneuploidy Underlies Rapid Adaptive Evolution of Yeast Cells Deprived of a Conserved Cytokinesis Motor. Cell 2008, 135:879. [Abstract|Preview|F1000|PaperClip]

Analysis of microarray and proteomics data:

Fournier ML, Paulson A, Pavelka N, Mosley AL, Zueckert-Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, Seidel C, Florens LA, Washburn MP: Delayed Correlation of mRNA and Protein Expression in Rapamycin Treated Cells and a Role for Ggc1 in Cellular Sensitivity to Rapamycin. Mol Cell Proteomics 2010, 9:271. [Abstract]

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP: Statistical Similarities Between Transcriptomics and Quantitative Shotgun Proteomics Data. Mol Cell Proteomics 2008, 7:631. [Abstract]

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P: The Genopolis Microarray Database. BMC Bioinformatics 2007, 8(Suppl 1):S21. [Abstract|PDF]

Pelizzola M, Pavelka N, Foti M, Ricciardi-Castagnoli P: AMDA: an R package for the automated microarray data analysis. BMC Bioinformatics 2006, 7:335. [Abstract|PDF]

*Pavelka N, *Pelizzola M, *Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P: A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics 2004, 5:203. [Abstract|PDF]

Functional genomics of host-pathogen interactions:

Vizzardelli C, Pavelka N, Luchini A, Zanoni I, Bendickson L, Pelizzola M, Beretta O, Foti M, Granucci F, Nilsen-Hamilton M et al: Effects of dexamethazone on LPS-induced activation and migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis. Eur J Immunol 2006, 36:1504. [Abstract]

Foti M, Granucci F, Pelizzola M, Pavelka N, Beretta O, Vizzardelli C, Urbano M, Zanoni I, Capuano G, Mingozzi F et al: Gene Profiling of Dendritic cells during Host-Pathogen Interactions. In: Handbook of Dendritic Cells: Biology, Diseases and Therapies. Edited by Lutz MB, Romani N, Steinkasserer A, vol. 1, 1 edn. Weinheim, Germany: Wiley-VCH; 2006: 175. [Table of contents]

Foti M, Granucci F, Pelizzola M, Pavelka N, Beretta O, Vizzardelli C, Urbano M, Zanoni I, Capuano G, Mingozzi F et al: Transcriptional profiling of dentritic cells in response to pathogens. In: Immunogenomics and Human Disease. Edited by Falus A, vol. 1, 1 edn. Chichester, England: John Wiley & Sons, Ltd.; 2006: 461. [Abstract]

Aebischer T, Bennett CL, Pelizzola M, Vizzardelli C, Pavelka N, Urbano M, Capozzoli M, Luchini A, Ilg T, Granucci F et al: A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana. Eur J Immunol 2005, 35:476. [Abstract]

*Trottein F, *Pavelka N, Vizzardelli C, Angeli V, Zouain CS, Pelizzola M, Capozzoli M, Urbano M, Capron M, Belardelli F et al: A type I IFN-dependent pathway induced by Schistosoma mansoni eggs in mouse myeloid dendritic cells generates an inflammatory signature. J Immunol 2004, 172:3011. [Abstract|PDF|F1000]

Granucci F, Vizzardelli C, Pavelka N, Feau S, Persico M, Virzi E, Rescigno M, Moro G, Ricciardi-Castagnoli P: Inducible IL-2 production by dendritic cells revealed by global gene expression analysis. Nat Immunol 2001, 2:882. [Abstract|News&Views|F1000]

Immunobiology of dendritic cells:

Granucci F, Zanoni I, Pavelka N, Van Dommelen SL, Andoniou CE, Belardelli F, Degli Esposti MA, Ricciardi-Castagnoli P: A contribution of mouse dendritic cell-derived IL-2 for NK cell activation. J Exp Med 2004, 200:287. [Abstract|PDF]

Granucci F, Feau S, Zanoni I, Pavelka N, Vizzardelli C, Raimondi G, Ricciardi-Castagnoli P: The immune response is initiated by dendritic cells via interaction with microorganisms and interleukin-2 production. J Infect Dis 2003, 187 Suppl 2:S346. [Abstract|PDF]

Other collaborations in functional genomics:

*Mineri R, *Pavelka N, Fernandez-Vizarra E, Ricciardi-Castagnoli P, Zeviani M, Tiranti V: How do human cells react to the absence of mitochondrial DNA? PLoS One 2009, 4(5):e5713. [Full text|PDF].

Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Moller S et al: Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PLoS Genet 2005, 1:e48. [Full Text|PDF]

(*equal contribution)