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Charlotte Berkes, Ph.D.

Associate Professor



Ph.D., University of Washington
B.S., Pennsylvania State University


  • Immunology
  • Microbiology
  • Principles of Biology I
  • Cell Biology
  • Genetics lab
  • SEA-PHAGES lab
  • Directed Study/Senior Thesis


I am currently working on several projects related to fungal pathogenesis, antifungal drug discovery and innate immunity in my lab: 

  1. Anti-fungal drug development. The pathogenic fungus Histoplasma capsulatum infects lung macrophages and, in immunocompromised individuals, may develop into histoplasmosis, a life-threatening disease. Few advances have been made in the treatment of histoplasmosis in recent decades, and there is a great need for development of novel therapies for diseases caused by Histoplasma and other pathogenic fungi. My lab has recently discovered that a subset of kinase inhibitors are potent inhibitors of Histoplasma growth in vitro. I am currently expanding on this work by conducting a screen of a large kinase inhibitor set in collaboration with the Structural Genomics Consortium at the University of North Carolina, Chapel Hill. I also collaborate with Jimmy Franco (Chemistry, Merrimack College) and David Toth (Computer Science, University of Mary Washington), using medicinal chemistry and computational approaches to identify antifungal compounds. This work places students at the interface of multiple disciplines including microbiology, cell biology, biochemistry, medicinal chemistry, organic chemistry and computer science, enabling them to contribute to drug discovery by employing an interdisciplinary approach.  
  2. Characterizing Dictyostelium pattern recognition receptors. Work in recent years has uncovered evolutionarily conserved protein families that play an important role in the ability of immune cells to detect the presence of bacteria, viruses, fungi and parasites. However, these proteins (generally referred to as “pattern recognition receptors” are not restricted to vertebrate organisms. The genome of the simple social amoeba Dictyostelium discoidium contains genes whose sequence suggests they may play a role in the ability of the amoeba to sense, eat, and/or destroy microbes. My research in the molecular mechanisms of microbial sensing offers students at Merrimack College the opportunity to immerse themselves in the fields of immunology, cell biology and genetics.  
  3. Cell visualization by image cytometry. Sophisticated algorithms allow both visualization and rapid quantification of cells. While image cytometry is similar to flow cytometry in its ability to quantify cell populations, its visual and highly intuitive nature make it highly accessible to undergraduates. I work with scientists at Nexcelom Bioscience (a partner of the Center for Student Research in the Life Sciences) to develop new ways to use this technology for research and in the classroom.

Recent Publications

Berkes, C. A., Chan, L. L. (2015)  Investigation of macrophage differentiation and cytokine production in an undergraduate immunology laboratory using image cytometry.  Bioscene: Journal of College Biology Teaching 41(2); 3-10.  

Isaac, D. T.†, Berkes, C. A., Hocking-Murray, D., Coady, A., English, B., Lee, Y. N., and Sil, A.  (2015) Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection.  Molecular Microbiology, doi:10.1111/mmi.13168       †These authors contributed equally to this work

Welkin H. Pope, Charles A. Bowman, Daniel A. Russell, Deborah Jacobs-Sera, David J. Asai, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES)*, Phage Hunters Integrating Research and Education (PHIRE) PHIRE4, Mycobacterial Genetics Course (MGC), Steven G. Cresawn, William R. Jacobs Jr., Roger W. Hendrix, Jeffrey G. Lawrence, and Graham F. Hatfull. (2015) *Merrimack College Authors: LeBlanc-Straceski, Janine,  Berkes, Charlotte,  DiVito, Michael, Flaherty, Nicholas, Gagnon, Miranda,  Langone, Allison,  Preston, Anthony,  Vasquez Gwendolyn.  2015.  Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.  eLife;4:e06416. DOI:

Daniels, D.*, Berkes, C. , Nekoie, A.*, and Franco, J.  (2015)  Fighting tuberculosis in an undergraduate laboratory: synthesizing, analyzing and evaluating inhibitors.  J Chem Ed. 92(5):928-931.

Toth, D., Franco, J. and Berkes, C.  (2013)  Attacking HIV, Tuberculosis and Histoplasmosis with XSEDE Resources, Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway Discovery, July 2013. 

Franco J., Blackie, M., Toth, D., Smith, P., Capuano, J.*, Fastnacht, K.*, Berkes, C.  (2013)  A structural comparative approach to identifying novel antimalarial inhibitors.  Comput Biol Chem. 45:42-7.  

Berkes, C. A., Chan, L. L., Wilkinson, A.* and Paradis, B.*  (2013) Use of image cytometry for quantification of pathogenic fungi in association with host cells.  J Vis Exp. Jun 19;(76).  

Berkes, C. A., Chan, L. L., Wilkinson, A.* and Paradis, B.*  (2012)  Rapid quantification of pathogenic fungi by Cellometer image based cytometry.  J Microbiol Methods 91(3):468-76.  

Chan, L. L., Kury, A.*, Wilkinson, A.*, Berkes, C. A. and Pirani, A. (2012) Novel image cytometric method for detection of physiological changes in Saccharomyces cerevisiae.  J Ind Microbiol Biotechnol 39(11):1615-23.

Inglis, D. O., Berkes, C. A., Hocking Murray, D. R. and Sil, A.  (2010) Conidia but not yeast of the fungal pathogen Histoplasma capsulatum trigger a Type I interferon innate immune response in murine macrophages.  Infect Immun. 78(9):3871-3882.




Mendel 352