Bacterial gene regulation in response to stress

Project Overview: Bacteria respond to stressful changes in their environment by changing their patterns of gene expression. The RpoS protein coordinates E. coli’s general stress response, allowing the cell to survive a variety of stresses, including starvation, pH, osmotic stress, and high and low temperatures. RpoS does this by altering the expression of about ¼ of the genes in the E. coli genome. RpoS is thought to also be important for stress responses in related species, including important pathogens like Salmonella and Klebsiella, but we know much less about it.

Students working in the Stoebel lab will work on one or both of the following topics:

1) The timing of RpoS-dependent gene expression in response to stresses  

Recent work in the lab has shown that RpoS-dependent genes vary in their response to changing levels of RpoS, which likely helps to coordinate responses to different stresses. This project will examine what determines the timing of how RpoS-dependent genes are expressed in response to stress.

Students will use transcriptional fusions to luciferase to monitor gene expression in response to various stresses. Students will be responsible for the analysis of the data using R. This is a good project for students who enjoy a combination of working at the bench and who are interested in the mechanistic details of molecular biology, as well as data analysis with R. Students do not need prior background in all of these areas, but a willingness to learn is essential.

2) The regulation of RpoS in pathogenic relatives of E. coli

While we know a great deal about how RpoS is regulated in one strain of E. coli, we know much less about how it is regulated in other species.

Students working on this project will use western blotting to study how the RpoS protein is regulated in response to a variety of stress conditions. These tests will be guided by our detailed knowledge of this system in E. coli, and by predictions based on genome content of relatives. In addition, students working on this project will study the contribution of RpoS to the survival of these species in the face of stress conditions. Students working on this project should expect to learn microbiological and molecular biology techniques.

To apply for this position:

1) Meet with Prof Stoebel to talk about the project and your experiences.

2) Your essay can be brief, but please describe what interests you about this project and what your background experience, if any, is.

3) Also complete the Biology Department supplemental application form.

All parts of the application should be submitted by Feb 28th for complete consideration.

These are laboratory positions and cannot be done remotely.

Name of research group, project, or lab
Stoebel Lab
Logistics Information:
Project categories
Biomedical Sciences
Student ranks applicable
Student qualifications

Skills/background required for both projects:  Students should have had Bio23 and an interest in laboratory work. Students will be matched to projects based on their background and interests.

Time commitment
Summer - Full Time
Paid Research
Number of openings
Contact Information:
Mentor name
Daniel Stoebel
Mentor email
Mentor position
Name of project director or principal investigator
Dan Stoebel
Email address of project director or principal investigator
5 sp. | 17 appl.
Hours per week
Summer - Full Time
Project categories
Biology (+1)
BiologyBiomedical Sciences