UROP Project
Distinguishing friend from foe: identifying novel genetic pathways for innate immune recognition of beneficial and pathogenic bacteria.
microbiome, microbiology, immunity, immunology, plant
Research Mentor: David Thoms,
Department, College, Affiliation: Biological Science, Arts and Sciences
Contact Email: dt22o@fsu.edu
Research Assistant Supervisor (if different from mentor):
Research Assistant Supervisor Email:
Faculty Collaborators:
Faculty Collaborators Email:
Department, College, Affiliation: Biological Science, Arts and Sciences
Contact Email: dt22o@fsu.edu
Research Assistant Supervisor (if different from mentor):
Research Assistant Supervisor Email:
Faculty Collaborators:
Faculty Collaborators Email:
Looking for Research Assistants: Yes
Number of Research Assistants: 4
Relevant Majors: Open to all majors
Project Location: On FSU Main Campus
Research Assistant Transportation Required: Remote or In-person: In-person
Approximate Weekly Hours: 12 hours per week, During business hours
Roundtable Times and Zoom Link: Wednesday September 6, 1:00p to 1:30p, https://fsu.zoom.us/j/99897721388
Thursday September 7, 3:00p to 3:30p, https://fsu.zoom.us/j/93516080463
Friday September 8, 1:30p to 2:00p, https://fsu.zoom.us/j/96967614499
Number of Research Assistants: 4
Relevant Majors: Open to all majors
Project Location: On FSU Main Campus
Research Assistant Transportation Required: Remote or In-person: In-person
Approximate Weekly Hours: 12 hours per week, During business hours
Roundtable Times and Zoom Link: Wednesday September 6, 1:00p to 1:30p, https://fsu.zoom.us/j/99897721388
Thursday September 7, 3:00p to 3:30p, https://fsu.zoom.us/j/93516080463
Friday September 8, 1:30p to 2:00p, https://fsu.zoom.us/j/96967614499
Project Description
The microbiome, a collection of symbiotic microbes within and on a host, has broad implications, ranging from human health to ecosystem balance and sustainable agriculture. Both plants and animals rely on a healthy microbiome for growth and fitness. Maintaining a healthy microbiome is vital for survival, as an unhealthy microbiome reduces fitness and can even lead to death. Creating a healthy microbiome involves controlling pathogens while nurturing beneficial microbes. Yet, pathogens and beneficial microbes are often very similar and distinguishing between them is challenging, even with advanced techniques. The immune system likely plays a role, but the details are complex and unclear.While mammals employ two immune strategies, plants offer a simpler model to study immune-microbe interactions due to their possession of only one, akin to ours. Contrary to the animal gut, plant roots are externally colonized by microbes, allowing easier live studies on an intact organism. Therefore, the Thoms lab uses plant roots to investigate how immunity discerns pathogenic and beneficial bacteria and shapes bacterial growth based on their lifestyles. To identify how immunity distinguishes between bacterial lifestyles, you will use a model system composing of the plant root, a pathogen, and a beneficial strain. We have found that this pathogen induces a novel potent immune response, while the beneficial does not. Working in teams of two, you will use immune assays to perform a classic forward genetic screen. You will screen through plant mutants to identify candidates that are unable to induce an immune response to the pathogen. The candidate mutants will be full genome sequenced to identify the mutated genes and to discover the novel immune pathways required for distinguishing friend from foe.
Research Tasks: preparing media, autoclaving and cleaning lab supplies and equipment, setting up and running immune assays, plant propagation, collecting seeds without cross-contamination, organizing mutant collections, practicing good aseptic microbiology technique, maintaining a detailed electronic lab notebook, collecting data, maintaining a clean lab environment, reviewing the literature and presenting your results.
Skills that research assistant(s) may need: demonstration of your ability to follow instructions (required), attention to detail (recommended), good organization (recommended), dedication and passion for your role in the lab (required)
Mentoring Philosophy
Our purpose: To do “good” science with integrity. Experiments that are not honest and trustworthy are experiments not worth doing. This includes accurate enough documentation to facilitate repeatability.Our vision: To pioneer understanding of how Nature balances symbiotic relations between multicellular hosts and their microbial communities to improve host health and productivity.
Mentorship meetings are crucial for ensuring trainee learning and practice of effective experimentation. Mentorship meetings should be used to ask questions about the literature and to discuss hypotheses, experimental design, data analysis, and conclusions. I practice an open door policy, and meetings can be held at the bench, in my office, or even in the hallway. Meetings over text or video are discouraged. Trainees are expected to meet with me a minimum of once per week. Mentorship meetings may be scheduled ahead of time with me to ensure sufficient access. However, spontaneous or unscheduled meetings are also encouraged, so long as time is available. These meetings are key to your professional development as a scientist and lab member.
The lab also maintains its own Slack channel (or similar app) for communication. Slack should be used to discuss lab business, schedule celebrations, share papers and protocols, and for peer-to-peer communication concerning the lab. Slack can also be a more effective way than email to contact me.
Overall, I want you to feel comfortable talking with me and other lab members and to provide easy access to mentorship and communication.