Amy K. Schmid, Associate Professor  

Amy K. Schmid

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

Office Location: 125 Science Dr, French Family Science Center 4105, Durham, NC 27708
Office Phone: (919) 613-4464
Email Address: amy.schmid@duke.edu
Web Page: http://www.biology.duke.edu/schmidlab
Additional Web Page: http://www.biology.duke.edu/schmidlab

Specialties:
Genomics
Cell and Molecular Biology

Research Categories: Systems biology of archaea: understanding regulatory network responses to environmental extremes

Research Description: Although life science research has entered the post-genomic era, we still understand little about the diversity of microbial life on earth. Information is particularly lacking on microbial extremophiles, which thrive at the limits of life. Extremophiles can be found in deep-sea hydrothermal vents under high pressure and temperature, saturated salt lakes, and polar icecaps. Many of these organisms are members of the third domain of life, the archaea. How do these microorganisms cope with an extreme and changing environment? How do they alter their genetic programs and metabolic pathways to adapt and survive changes in their unique habitats on earth? Central to this process are gene regulatory networks (GRNs) composed of groups of regulatory proteins that switch genes on and off in response to environmental stimuli. Upon sensing a change in the environment, the GRN increases the production of genes encoding proteins that repair damage, restore the cell to a healthy state and prepare for future stress. The organism studied in the current research, called Halobacterium salinarum, thrives in high salt environments. The long-term aim of our work is to determine the underlying mechanisms by which regulatory factors interact in the GRN of H. salinarum enable survival during environmental perturbations. We are using a systems biology approach, which combines cutting-edge high throughput experimental techniques with computational or statistical modeling. Research toward these goals will lay the foundation for rational re-engineering of cellular physiology for desired outcomes such as targeted industrial, environmental and medical purposes.

Recent Publications   (More Publications)   (search)

  1. Tonner, PD; Darnell, CL; Bushell, FML; Lund, PA; Schmid, AK; Schmidler, SC, A Bayesian non-parametric mixed-effects model of microbial growth curves., Plos Computational Biology, vol. 16 no. 10 (October, 2020), pp. e1008366 [doi]  [abs].
  2. Darnell, CL; Zheng, J; Wilson, S; Bertoli, RM; Bisson-Filho, AW; Garner, EC; Schmid, AK, The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea., Mbio, vol. 11 no. 4 (August, 2020) [doi]  [abs].
  3. Hwang, S; Chavarria, NE; Hackley, RK; Schmid, AK; Maupin-Furlow, JA, Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen., International Journal of Molecular Sciences, vol. 20 no. 19 (September, 2019) [doi]  [abs].
  4. Hackley, RK; Schmid, AK, Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response., Journal of Molecular Biology, vol. 431 no. 20 (September, 2019), pp. 4147-4166 [doi]  [abs].
  5. Zaretsky, M; Darnell, CL; Schmid, AK; Eichler, J, N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility., Frontiers in Microbiology, vol. 10 (January, 2019), pp. 1367 [doi]  [abs].

Curriculum Vitae