Amy K. Schmid

Associate Professor of Biology

Office: 
125 Science Dr, French Family Science Center 4105, Durham, NC 27708
Campus Box: 
Box 90338, Durham, NC 27708-0338
Phone: 
(919) 613-4464
Research in my lab seeks to elucidate how cells make decisions in response to environmental cues. My particular focus is on how networks of molecules interact within free-living microbial cells. These networks govern the decision to grow when conditions are optimal or deploy damage repair systems when faced with stress. I study microbial stress responses in extremophiles of the domainArchaea, which represent extreme examples of microbes surviving damage by multiple stressors. These organisms remain viable on the extreme end of the gradient of environmental stress (e.g. high temperature, saturated salt, nutrient starvation). However, extremophiles also adapt during wide variations in conditions and nutrients and therefore provide a study system for both constant and dynamic stress resistance mechanisms. Because archaea resemble life’s earliest ancestors, they can teach us about the origins of stress response features shared amongst all life. In my recent and future work, I compare across species how networks function to regulate important aspects of cell physiology such as growth and division during stress. Ultimately, I seek to uncover how environmental conditions shape the regulatory network over evolutionary time. I use a combination of quantitative and experimental biology approaches, including computational modeling, functional genomics and molecular microbiology. I work across the disciplines of systems biology, microbial stress response, and archaeal molecular biology. My lab group and I are also actively involved in developing microbiology and bioinformatics workshops for various communities (K-12, teachers, researchers).

Education

  • Ph.D., University of Washington 2004

  • B.S., Marquette University 1997

Schmid, A. K., and N. S. Baliga. “Prokaryotic Systems Biology.” In Systems Biology, edited by M. Al-Rubeai and M. Fussenegger, 5:395–423. Springer, 2006.

Hwang, Sungmin, Nikita E. Chavarria, Rylee K. Hackley, Amy K. Schmid, and Julie A. Maupin-Furlow. “Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen..” International Journal of Molecular Sciences 20, no. 19 (September 26, 2019). https://doi.org/10.3390/ijms20194784. Full Text

Hackley, Rylee K., and Amy K. Schmid. “Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response..” Journal of Molecular Biology 431, no. 20 (September 2019): 4147–66. https://doi.org/10.1016/j.jmb.2019.07.029. Full Text

Zaretsky, Marianna, Cynthia L. Darnell, Amy K. Schmid, and Jerry Eichler. “N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility..” Frontiers in Microbiology 10 (January 2019). https://doi.org/10.3389/fmicb.2019.01367. Full Text

Martin, Jonathan H., Katherine Sherwood Rawls, Jou Chin Chan, Sungmin Hwang, Mar Martinez-Pastor, Lana J. McMillan, Laurence Prunetti, Amy K. Schmid, and Julie A. Maupin-Furlow. “GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii..” Journal of Bacteriology 200, no. 17 (September 2018). https://doi.org/10.1128/JB.00244-18. Full Text

Dulmage, Keely A., Cynthia L. Darnell, Angie Vreugdenhil, and Amy K. Schmid. “Copy number variation is associated with gene expression change in archaea..” Microbial Genomics 4, no. 9 (September 2018). https://doi.org/10.1099/mgen.0.000210. Full Text

Eun, Ye-Jin, Po-Yi Ho, Minjeong Kim, Salvatore LaRussa, Lydia Robert, Lars D. Renner, Amy Schmid, Ethan Garner, and Ariel Amir. “Archaeal cells share common size control with bacteria despite noisier growth and division..” Nature Microbiology 3, no. 2 (February 2018): 148–54. https://doi.org/10.1038/s41564-017-0082-6. Full Text

McDowell, Ian C., Dinesh Manandhar, Christopher M. Vockley, Amy K. Schmid, Timothy E. Reddy, and Barbara E. Engelhardt. “Clustering gene expression time series data using an infinite Gaussian process mixture model..” Plos Comput Biol 14, no. 1 (January 2018). https://doi.org/10.1371/journal.pcbi.1005896. Full Text

Bushell, Francesca M. L., Peter D. Tonner, Sara Jabbari, Amy K. Schmid, and Peter A. Lund. “Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth..” Frontiers in Microbiology 9 (January 2018). https://doi.org/10.3389/fmicb.2018.03196. Full Text

Martinez-Pastor, Mar, Peter D. Tonner, Cynthia L. Darnell, and Amy K. Schmid. “Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks..” Annual Review of Genetics 51 (November 2017): 143–70. https://doi.org/10.1146/annurev-genet-120116-023413. Full Text

Darnell, Cynthia L., Peter D. Tonner, Jordan G. Gulli, Scott C. Schmidler, and Amy K. Schmid. “Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis..” Msystems 2, no. 5 (September 19, 2017). https://doi.org/10.1128/mSystems.00032-17. Full Text

Pages

Schmid, Amy, Keely A. Dulmage, Cynthia L. Darnell, and A. Vreugdenhil. “Data and scripts from: Copy number variation is associated with gene expression change in archaea,” May 4, 2018. https://doi.org/10.7924/r4pz54w7h. Full Text

Selected Grants

Causes and consequences of regulatory network rewiring under extreme environmental selection awarded by National Science Foundation (Principal Investigator). 2019 to 2023

CAREER: Elucidating cell cycle regulatory networks across the tree of life awarded by National Science Foundation (Principal Investigator). 2017 to 2022

CAREER: Elucidating cell cycle regulatory networks across the tree of life awarded by National Science Foundation (Principal Investigator). 2017 to 2022

CAREER: Elucidating cell cycle regulatory networks across the tree of life awarded by National Science Foundation (Principal Investigator). 2017 to 2022

Modeling the function and evolution of metabolic networks across hypersaline-adapted archaea awarded by National Science Foundation (Principal Investigator). 2016 to 2020

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2020

Genetics Training Grant awarded by National Institutes of Health (Mentor). 1979 to 2020

Genetics Training Grant awarded by National Institutes of Health (Mentor). 1979 to 2020

Organization and Function of Cellular Structure awarded by National Institutes of Health (Mentor). 1975 to 2020

Pages