CMOP Undergraduate Intern Mentoring Opportunity
Deadline: March 26, 2010
Selections Announced: April 2, 2010
Name/Title/Institution(s) of senior mentor(s): Brad Tebo/ Division Head/OGI
Name/Title/Institution(s) of frontline mentor(s): Wendy F. Smythe, Graduate Student Research Assistant/ OGI
Project Title: Investigations of natural substrates for deep-sea biofilm formation.
Context for Project:
A variety of natural substrates were deployed at four different sites in the Pacific Ocean off the coast of Hawaii, allowing microbial colonization. Substrates were collected after 6 years deployment, upon which specimens were preserved for analytical and molecular analysis of biofilms formed. Characterization of biofilms from each environment allows for a better understanding for microbe-mineral interactions, and biofilm dynamics in the ocean.
Brief Description. Please address the scope of research and its relevance to the CMOP mission, intellectual environment and research roadmap. Please note any ties to CMOP diversity and knowledge transfer goals. Please see the Research Roadmap and Strategic Implementation Plan at for any guidance. If project is non-CMOP/EBS, please describe project as it relates to research goals of the laboratory group.
Back in the laboratory, the student will be involved in hands-on training with instruments and techniques needed to characterize the samples. Instrumentation for characterization includes stereo and optical microscopy, nanodrop, centrifuge, and other laboratory equipment necessary for analysis. Molecular characterization of the samples will include DNA extraction, and PCR amplification, for T-RFLP analysis and sequencing as a means to better observe community diversity from this environment, and possibly the generation of clone libraries.
A few examples of some key topics covered will include: Geology: how the subsurface geology affects biofilm formation, preferential colonization,, and ways in which the microbes affect the mineralogy of the substrate. Microbiology: diversity of cellular life within the biofilm and the implications for microbial impacts on the environment.
Proposed Outcomes/Broader Impact:
In alignment with the CMOP mission, this project will serve to work with a student population. This project will further facilitate the transfer of knowledge not only between the mentor and intern, but also engage the student in interactions with other scientists, oceanographers, microbiologist and environmental scientists.
Proposed timeline (within a 10 week span):
10 weeks: weekly report, weekly ppt input.
- thin sections ordered 3 day turnaround, SEM preparation, DNA extraction
- mail out thin sections, SEM prep., stereoscope of samples.
- DNA extractions & nanodrop: 8 samples
- PCR of ballast biofilm, gel, if all goes well take to primate center
- T-RFLP PCR
- T-RFLP PCR/CMOP day.
- Finish molecular work if needed, begin SEM analysis & thin section analysis.
- Finish molecular work, continue SEM & petragraphic work.
- Petrographic analysis of deployed thin sections, email report & ppt file.
- Petrographic analysis of deployed thin sections, email report & ppt file.
- Sequence analysis PCR & T-RFLP.
- Continue w/T-RFLP data analysis, finish loose ends for microscopy, email report & ppt file
- T-RFLP data analysis
- Finish loose ends
- Compile data for presentation.
Intern academic experience and skill set should include: Please list majors you would consider, preferred course background, any other needed skills. Please note if you are willing to work with a less experienced intern (freshmen or sophomore) or require a more experienced candidate (junior or senior).
This project is best suited for a more experienced intern (junior/senior with prior lab experience), but can be adjusted to accommodate a less advanced student (freshman/sophomore or little lab experience).