Honors & Awards

  • Postdoctoral Fellow, Stanford Training Program in Aging Research, NIH T32, Stanford University (2016-2017)
  • Bass Instructional Fellowship, Duke University (2014)
  • Jo Rae Wright Fellowship for Outstanding Women in Science, Duke University (2014)
  • Selected Presenter, Gordon Conference on Microbial Toxins & Pathogenicity (2014)
  • Selected Speaker, American Cell Biology / International Federation for Cell Biology Meeting (2014)
  • Best poster presentation, Molecular Genetics and Microbiology Department Retreat, Duke University (2013)
  • Meritorious Research Travel Award, Duke University (2013)
  • Poston Award for Outstanding Oral Presentation, Meeting of the North Carolina Branch of the American Society for Microbiology (2013)
  • Selected Speaker, 6th Biennial Chlamydia Basic Research Science Meeting (2013)
  • Predoctoral Fellowship #11PRE7360030, American Heart Association Mid-Atlantic Affiliate (2011-2013)
  • Preparing Future Faculty Fellow, Duke University (2011-2012)
  • Undergraduate Honors: Biology Award, Lewis & Clark College (2007)
  • Undergraduate Fellowship: Kent Swanson Jr. Memorial Scholarship, Lewis & Clark College (2006)

Professional Education

  • Doctor of Philosophy, Duke University (2015)
  • Bachelor of Arts, Lewis & Clark College (2007)

Stanford Advisors

Current Research and Scholarly Interests

I am compelled to understand the underlying processes that determine cellular form, function, and specificity. In my graduate work, I studied how a human bacterial pathogen Chlamydia manipulates the cell biology of host cells in the lab of Dr. Raphael Valdivia at Duke University. As a postdoc in the Shen Lab, I am now investigating how neurons both initially polarize and outgrow highly distinct processes - the axon and dendrite - in vivo by monitoring a single neuron from its birth in our model organism C. elegans.

All Publications

  • Differential Translocation of Host Cellular Materials into the Chlamydia trachomatis Inclusion Lumen during Chemical Fixation PLOS ONE Kokes, M., Valdivia, R. H. 2015; 10 (10)


    Chlamydia trachomatis manipulates host cellular pathways to ensure its proliferation and survival. Translocation of host materials into the pathogenic vacuole (termed 'inclusion') may facilitate nutrient acquisition and various organelles have been observed within the inclusion, including lipid droplets, peroxisomes, multivesicular body components, and membranes of the endoplasmic reticulum (ER). However, few of these processes have been documented in living cells. Here, we survey the localization of a broad panel of subcellular elements and find ER, mitochondria, and inclusion membranes within the inclusion lumen of fixed cells. However, we see little evidence of intraluminal localization of these organelles in live inclusions. Using time-lapse video microscopy we document ER marker translocation into the inclusion lumen during chemical fixation. These intra-inclusion ER elements resist a variety of post-fixation manipulations and are detectable via immunofluorescence microscopy. We speculate that the localization of a subset of organelles may be exaggerated during fixation. Finally, we find similar structures within the pathogenic vacuole of Coxiella burnetti infected cells, suggesting that fixation-induced translocation of cellular materials may occur into the vacuole of a range of intracellular pathogens.

    View details for DOI 10.1371/journal.pone.0139153

    View details for Web of Science ID 000362177100034

    View details for PubMedID 26426122

  • Integrating Chemical Mutagenesis and Whole-Genome Sequencing as a Platform for Forward and Reverse Genetic Analysis of Chlamydia CELL HOST & MICROBE Kokes, M., Dunn, J. D., Granek, J. A., Nguyen, B. D., Barker, J. R., Valdivia, R. H., Bastidas, R. J. 2015; 17 (5): 716-725


    Gene inactivation by transposon insertion or allelic exchange is a powerful approach to probe gene function. Unfortunately, many microbes, including Chlamydia, are not amenable to routine molecular genetic manipulations. Here we describe an arrayed library of chemically induced mutants of the genetically intransigent pathogen Chlamydia trachomatis, in which all mutations have been identified by whole-genome sequencing, providing a platform for reverse genetic applications. An analysis of possible loss-of-function mutations in the collection uncovered plasticity in the central metabolic properties of this obligate intracellular pathogen. We also describe the use of the library in a forward genetic screen that identified InaC as a bacterial factor that binds host ARF and 14-3-3 proteins and modulates F-actin assembly and Golgi redistribution around the pathogenic vacuole. This work provides a robust platform for reverse and forward genetic approaches in Chlamydia and should serve as a valuable resource to the community.

    View details for DOI 10.1016/j.chom.2015.03.014

    View details for Web of Science ID 000356101500022

    View details for PubMedID 25920978

  • Reassessing the role of the secreted protease CPAF in Chlamydia trachomatis infection through genetic approaches PATHOGENS AND DISEASE Snavely, E. A., Kokes, M., Dunn, J. D., Saka, H. A., Nguyen, B. D., Bastidas, R. J., McCafferty, D. G., Valdivia, R. H. 2014; 71 (3): 336-351


    The secreted Chlamydia protease CPAF cleaves a defined set of mammalian and Chlamydia proteins in vitro. As a result, this protease has been proposed to modulate a range of bacterial and host cellular functions. However, it has recently come into question the extent to which many of its identified substrates constitute bona fide targets of proteolysis in infected host cell rather than artifacts of postlysis degradation. Here, we clarify the role played by CPAF in cellular models of infection by analyzing Chlamydia trachomatis mutants deficient for CPAF activity. Using reverse genetic approaches, we identified two C. trachomatis strains possessing nonsense, loss-of-function mutations in cpa (CT858) and a third strain containing a mutation in type II secretion (T2S) machinery that inhibited CPAF activity by blocking zymogen secretion and subsequent proteolytic maturation into the active hydrolase. HeLa cells infected with T2S(-) or CPAF(-) C. trachomatis mutants lacked detectable in vitro CPAF proteolytic activity and were not defective for cellular traits that have been previously attributed to CPAF activity, including resistance to staurosporine-induced apoptosis, Golgi fragmentation, altered NFκB-dependent gene expression, and resistance to reinfection. However, CPAF-deficient mutants did display impaired generation of infectious elementary bodies (EBs), indicating an important role for this protease in the full replicative potential of C. trachomatis. In addition, we provide compelling evidence in live cells that CPAF-mediated protein processing of at least two host protein targets, vimentin filaments and the nuclear envelope protein lamin-associated protein-1 (LAP1), occurs rapidly after the loss of the inclusion membrane integrity, but before loss of plasma membrane permeability and cell lysis. CPAF-dependent processing of host proteins correlates with a loss of inclusion membrane integrity, and so we propose that CPAF plays a role late in infection, possibly during the stages leading to the dismantling of the infected cell prior to the release of EBs during cell lysis.

    View details for DOI 10.1111/2049-632X.12179

    View details for Web of Science ID 000340392000006

    View details for PubMedID 24838663

  • Cell Biology of the Chlamydial Inclusion Intracellular Pathogens I: Chlamydiales Kokes, M., Valdivia, R. H. edited by Tan, M., Bavoil, P. M. ASM Press. 2012: 170–191
  • glo-3, a Novel Caenorhabditis elegans Gene, Is Required for Lysosome-Related Organelle Biogenesis GENETICS Rabbitts, B. M., Ciotti, M. K., Miller, N. E., Kramer, M., Lawrenson, A. L., Levitte, S., Kremer, S., Kwan, E., Weis, A. M., Hermann, G. J. 2008; 180 (2): 857-871


    Gut granules are specialized lysosome-related organelles that act as sites of fat storage in Caenorhabditis elegans intestinal cells. We identified mutations in a gene, glo-3, that functions in the formation of embryonic gut granules. Some glo-3(-) alleles displayed a complete loss of embryonic gut granules, while other glo-3(-) alleles had reduced numbers of gut granules. A subset of glo-3 alleles led to mislocalization of gut granule contents into the intestinal lumen, consistent with a defect in intracellular trafficking. glo-3(-) embryos lacking gut granules developed into adults containing gut granules, indicating that glo-3(+) function may be differentially required during development. We find that glo-3(+) acts in parallel with or downstream of the AP-3 complex and the PGP-2 ABC transporter in gut granule biogenesis. glo-3 encodes a predicted membrane-associated protein that lacks obvious sequence homologs outside of nematodes. glo-3 expression initiates in embryonic intestinal precursors and persists almost exclusively in intestinal cells through adulthood. GLO-3GFP localizes to the gut granule membrane, suggesting it could play a direct role in the trafficking events at the gut granule. smg-1(-) suppression of glo-3(-) nonsense alleles indicates that the C-terminal half of GLO-3, predicted to be present in the cytoplasm, is not necessary for gut granule formation. Our studies identify GLO-3 as a novel player in the formation of lysosome-related organelles.

    View details for DOI 10.1534/genetics.108.093534

    View details for Web of Science ID 000260284400013

    View details for PubMedID 18780725