Project Title:

IDBR: EcoChip: A Micro-structured Microbial Habitat Array

Primary Investigators:

Leslie Shor

Brief Description of Project:

The objective of the “EcoChip” project is to develop instrumentation to study complex microbial systems on a single microscope slide. The rationale is that conventional technologies to culture and observe microbes cannot reproduce micro-scale physichemical structure intrinsic to microbial habitats, and that shape microbial communities. Lab-on-a-chip approaches will also enhance productivity by reducing culturing time, promoting assay comparisons, and allowing high-throughput, automated analysis of multiple data streams. Future applications for the research extend to diverse areas including healthcare, especially prevention and treatment of human microbial infections, and environmental science and engineering, including improved wastewater treatment systems, restoring polluted marine and terrestrial environments, and better understanding  the role of microbial feedback cycles in global climate change.

Specific student projects will be defined in consultation this spring between prospective students and the PI, based on student interest and experience. Project options include:

(i)                  Measuring and modeling the multiphase partitioning, mass transport, and availability of biologically-relevant compounds through the silicon rubber EcoChip material as a function of material physical properties;

(ii)                Optimization of ImajeJ and MatLab routines for enhanced automated image processing of optical data streams including oxygen concentration and microbial populations on a micron-scale resolution;

(iii)               Consulting with research team members to adapt prototype instrumentation for new education modules for use as Vanderbilt Student Volunteers for Science (VSVS) demonstrations and/or developing a project web page

Nature of Supervision:

Undergraduate researchers working on this project will join an existing team of researchers of all academic ranks who are committed to working together as colleagues. Collaboration, team-work, and partnerships across academic disciplines and ranks are encouraged, and creativity and communication is emphasized. The student will work under the direct supervision of Leslie Shor and in close partnership with other undergraduates, post-docs, and technicians primarily at the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE). Dr. Shor will lead weekly research progress and planning meetings with all project personnel, and will train and work side-by-side with students in the lab. Meetings and conference calls with other faculty from Vanderbilt University and other universities will take place periodically throughout the summer.

A Brief Research Plan (period is for 10 weeks):

Week 1-2: Learn basics of microbial culturing, microscopy, and automated image processing; formulation of research objectives, and formalization of research plan.

Weeks 3-8: Collection of initial research data, data analysis, and iterative device testing and optimization.

Week 9-10: Prepare final report, research poster and presentation of results. If progress warrants, participate in manuscript planning and drafting.

Number of Open Slots:

2 or 3, depending on applications received

Contact Information:

Leslie M. Shor, Ph.D.
Research Assistant Professor
Dept. of Civil and Environmental Engineering
Jacobs Hall, Room 286
Telephone: 615-343-3388
Email: L.Shor@vanderbilt.edu