Miranda Mudge

PhD Candidate
Molecular and Cellular Biology Department
University of Washington
​[email protected]
​​Miranda is a PhD candidate in the Molecular and Cellular Biology Department working jointly in the MacCoss and Nunn labs. ​She is broadly interested in using proteomics to better understand how microbiomes influence their environment, specifically by adapting DIA methods for metaproteomics. Her project involves using marine microbiome peptides as biomarkers to forecast the formation of harmful algal blooms. Within the lab, Miranda has also studied how environmentally-relevant cold active bacteria maintain cellular activity after long-term exposure to extreme conditions, as well as how microbiome controls on eukaryotes inhibit viral infections.

​Prior to joining the lab, Miranda studied DNA damage repair at Washington University in St. Louis, as well as developed a mouse melanoma therapeutic model at Missouri State University, where she graduated with a M.S. in Cellular and Molecular Biology.

Research Experience

2018 - present      Molecular and Cellular Biology Ph.D. program, University of Washington,  MacCoss and Nunn Labs
2015 - 2018            Laboratory technician/manager, Washington University in St. Louis, Mosammaparast Lab
2014 - 2015            Graduate assistant, Laboratory instructor - Biomolecular Interactions, Missouri State University
2013 - 2015            Graduate assistant, Laboratory instructor - Introduction to Biomedical Sciences, Missouri State University
2013 - 2014            Cellular and Molecular Biology M.S. program, Missouri State University, DeLong Lab
2009 - 2013            Cellular and Molecular Biology B.S. program, Missouri State University

Publications

  1. Mudge, M.C., Riffle, M., Chebli, G., Plubell, D., Rynearson, T., Noble, W.S., Timmins-Schiffman, E., Kubanek, J., and Nunn., B.L. (2024) Harmful algal blooms preceded by a predictable and quantifiable shift in the oceanic microbiome. Nat. Commun. (in review). 
  2. Nunn., B.L., Timmins-Schiffman, E., Mudge., M.C., et. al. (2024) Microbial metagenomes across a complete phytoplankton bloom cycle: high resolution sampling every 4 hours over 22 days. Scientific Data. (in review).
  3. Nunn, B.L., Brown, T., Timmins-Schiffman, E., Mudge, M., Riffle, M., Axworthy, J.B., and Dilwort, J. (2024) Resilience in a time of stress: revealing the molecular underpinnings of coral survival following bleaching events. bioRxiv. https://doi.org/10.1101/2024.02.587798.
  4. Mudge, M.C., Nunn, B.L., Firth, E., Ewert, M., Hales, K., Fondrie, W.E., Noble, W.S., Toner, J., Light, B., and Junge, K.A. (2021) Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environmental Microbiology 23, 3840-3866. 
  5. Pollara, S.B., Becker, J.W., Nunn, B.L., Boiteau, R., Repeta, D., Mudge, M.C., Downing, G., Chase, D., Harvey, E.L., and Whalen, K.E. (2021) Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality. mSphere 6, e00009-21. 
  6. Byrum, A.K., Carvajal-Maldonado, D., Mudge, M.C., Valle-Garcia, D., Majid, M.C., Patel, R., Sowa, M.E., Gygi, S.P., Harper, J.W., Shi, Y., et al. (2019). Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function. J Cell Biol 218, 422–432.
  7. Soll, J.M., Brickner, J.R., Mudge, M.C., and Mosammaparast, N. (2018). RNA ligase-like domain in activating signal cointegrator 1 complex subunit 1 (ASCC1) regulates ASCC complex function during alkylation damage. J Biol Chem 293, 13524–13533.
  8. Zhao, Y., Mudge, M.C., Soll, J.M., Rodrigues, R.B., Byrum, A.K., Schwarzkopf, E.A., Bradstreet, T.R., Gygi, S.P., Edelson, B.T., and Mosammaparast, N. (2018). OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling. Mol Cell 69, 505-516.e5.
  9. Brickner, J.R., Soll, J.M., Lombardi, P.M., Vågbø, C.B., Mudge, M.C., Oyeniran, C., Rabe, R., Jackson, J., Sullender, M.E., Blazosky, E., et al. (2017). A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair. Nature 551, 389–393.
  10. DeLong, R.K., Mitchell, J.A., Morris, R.T., Comer, J., Hurst, M.N., Ghosh, K., Wanekaya, A., Mudge, M., Schaeffer, A., Washington, L.L., et al. (2017). Enzyme and Cancer Cell Selectivity of Nanoparticles: Inhibition of 3D Metastatic Phenotype and Experimental Melanoma by Zinc Oxide. J Biomed Nanotechnol 13, 221–231.
  11. Ramani, M.*, Mudge, M.C.*, Morris, R.T., Zhang, Y., Warcholek, S.A., Hurst, M.N., Riviere, J.E., and DeLong, R.K. (2017). Zinc Oxide Nanoparticle-Poly I:C RNA Complexes: Implication as Therapeutics against Experimental Melanoma. Mol Pharm 14, 614–625.

Conferences

Oral Presentations
  • "Predicting harmful algal blooms through high-resolution metaproteomics of a bacterial microbiome." Mudge, MC, Timmins-Schiffman, E, Riffle, M, Chebli, G, Kubanek, J, Noble, WS, and Nunn., BL. SICB. Seattle, WA. January 2024. Oral presentation. 
  • "Predicting harmful algal blooms through high-resolution metaproteomics of a bacterial microbiome." Mudge, MC, Min, A, Timmins-Schiffman, E,  Chebli, G, Kubanek, J, Riffle, M, Noble, WS, and Nunn., BL. Cascadia Proteomics Symposium. Seattle, WA. July 2023. Oral presentation. 
  • "Predicting harmful algal blooms through high-resolution metaproteomics of a bacterial microbiome." Mudge, MC, Min, A, Timmins-Schiffman, E,  Chebli, G, Kubanek, J, Riffle, M, Noble, WS, and Nunn., BL. ASLO Aquatic Sciences Meeting 2023: Resilence and Recovery in Aquatic Systems. Palma de Mallorca, Spain. June 2023. Oral presentation. 
  • "Communicating science to science skeptics." Mudge, MC*, Jani, S*, Bishop, K*, Mastick, N*. SciTalk. Portland, OR. April 2023. Oral presentation - Workshop. 

​Poster Presentations
  • “Extreme colds and high salinities provoke proteome remodeling: A hunt for temperature and salinity-specific biomarkers with unique polypeptide structures.” Mudge MC, Hales K, Ewert M, Carpenter SD, Light B, Toner JD, Junge K, Nunn B. Ocean Sciences Meeting. San Diego, CA. February 2020. Poster presentation. 
  • ​“Effects of Nanomaterials on Nucleic Acids and the Structure-Activity of Proteins.” M Abdelhakiem, J Mitchell, MC Mudge, R Carter, B Jones, R DeLong. 2nd International Conference of RNA Nanotechnology and Therapeutics. Lexington, KY. April 2013. Poster Presentations. 
  • ​“Anti-cancer splice-switching oligonucleotide nanoconjugates.” J Dean, H Gann, E Myers, C Simms, MC Mudge, R DeLong. 2nd International Conference of RNA Nanotechnology and Therapeutics. Lexington, KY. April 2013. Poster Presentations. 
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Mudge et al, 2020 - Ocean Sciences Meeting
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Mudge et al, 2020 - Genome Sciences Annual Retreat
Astrobiology Field Workshop 2019 – Friday Harbor
Fun times outside the lab, featuring my dog Brody