Accessing Research through CUREs
C-CoMP is working to broaden access to research by partnering with scientists and educators to design and implement Course-based Undergraduate Research Experiences, or CUREs. CUREs involve all undergraduate students who enroll in a course as collaborators in cutting-edge research by embedding real research projects into the course itself rather than expecting students to do research outside of class or through a separate internship. CUREs are designed to achieve both research and learning goals, which makes them work for students, instructors, and scientists. By engaging in CUREs, students develop knowledge, skills, and abilities related to science and clarify whether they are interested in pursuing research as an educational or career path. Plus, CURE students have the potential to make discoveries that matter to stakeholders outside the classroom.
Disciplines
- Biology
- Environmental science
- Marine biology
- Biological oceanography
- Ecology
Target Course(s)
- Introductory biology
- Microbiology
- Marine Biology
(Majors and non-Majors)
Target Student Population
- Introductory or mid-level undergraduate students
Research Type
- Wet lab
Duration
- One semester (~13 weeks)
Keywords
Mutant, screen, transporter, bacteria, substrate, growth assay, carbon
Disciplines
- Biology
- Genetics
- Microbiology
- Marine Biology
- Biological Oceanography
Target Course(s)
- Genetics
- Microbiology
(Majors and non-Majors)
Target Student Population
- Mid-level Undergraduate students
Research Type
- Wet lab
- Data analysis
- Informatics
Duration
- One semester (~13 weeks)
Keywords
Genetics, Bioinformatics, Microbial metabolism, Bacterial diversity, Marine chemistry, Phytoplankton metabolites
Disciplines
- Biology
- Environmental Science
- Ocean Science
- Biochemistry
Target Course(s)
- Biochemistry
- Oceanography
- Bioinformatics
(Majors and non-Majors)
Target Student Population
- Upper-level Undergraduate students
- Introductory graduate students
Research Type
- Data analysis
- Bioinformatics
Duration
- 15-30 hours of one semester
Keywords
Bioinformatics, Protein, Proteomics
Ocean Genes CURE
Team members
University of Georgia: Erin Dolan, Dillion Doomstorm, Taylor English, Julia Jacob, Mary Ann Moran, McKenzie Powers, William Schroer, Madeline Shepard, Jeremy Shreier
Auburn University: Min Zhong
Auburn University Montgomery: Flor Breitman
Elizabeth City State University: Jade LaDow
Minnesota State University Moorhead: Sara Anderson, Michelle Tigges
Woods Hole Oceanographic Institution: Victoria Centurino
Abstract
Each day in the surface ocean, marine phytoplankton release a substantial portion of their recently fixed carbon into seawater through the processes of exudation, zooplankton feeding, and viral infection. Within minutes, the released metabolites are efficiently scavenged by marine bacteria, who use these organic compounds to grow more biomass (potentially participating in ocean carbon sequestration) or to respire (regenerating the CO2 that was recently fixed). A major barrier to identifying these rapidly cycling molecules and the microbes that use them is lack of knowledge of bacterial transporter function. Transporter proteins are embedded in bacterial membranes, where
they identify specific molecules in seawater and move them into the cell. Yet only a very few marine bacterial transporters can be matched the substrate they take up. This CURE engages undergraduate classes in the discovery of these unknown substrates by screening bacterial transporter mutants to determine the compound that can no longer be taken up. A mutant library of marine bacterium Ruegeria pomeroyi provides us with >100 transporter mutants whose substrates have yet to be identified. The Ocean Genes CURE is designed to address a major gap in ocean knowledge by identifying the substrates marine bacterial transporters bring into the cell, improving understanding of the ocean carbon cycle.
Research goals
- Assess the growth of transporter mutants of the marine bacterium R. pomeroyi on a variety of possible substrates
- Use mutants unable to grow on a given substrate to assign a function to the mutated transporter
Student goals
- Develop skills related to reading scientific literature
- Evaluate claims in scientific papers using evidence-based reasoning
- Formulate testable hypotheses and state their predictions
- Execute protocols accurately
- Make and record measurements and observations
- Identify methodological problems and suggest how to troubleshoot them
- Use appropriate quantitative methods to evaluate results
- Create and interpret informative data visualizations
- Present research findings
- Write results, interpretations, and conclusions
- Make evidence-based arguments using own and others’ findings and draw appropriate conclusions
- Relate conclusions to original hypothesis, consider alternative hypotheses, and suggest future research directions based on findings
- Develop skills in wet-lab work and sterile technique
- Gain knowledge about ocean microorganisms and their role in global biogeochemical cycles
References
Buchan, A., LeCleir, G. R., Gulvik, C. A., & González, J. M. (2014). Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nature Reviews Microbiology, 12(10), 686-698. https://doi.org/10.1038/nrmicro3326.
Cavicchiol, R., Ripple, W. J., Timmis, K. N., Azam, F., Bakken, L. R., Baylis, M., Behrenfeld, M. J., Boetius, A., Boyd, P. W., Classen, A. T., Crowther, T. W., Danovaro, R., Foreman, C. M., Huisman, J., Hutchins, D. A., Jansson, J. K., Karl, D. M., Koskella, B., Welch, D. B. M., ... Webster, N. S. (2019). Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology 17(9): 569-586. https://doi.org/10.1038/s41579-019-0222-5.
Moran, M. A., Ferrer-González, F. X., Fu, H., Nowinski, B., Olofsson, M., Powers, M. A., Schreier, J. E., Schroer, W. F., Smith, C. B., & Uchimiya, M. (2022). The ocean's labile DOC supply chain. Limnology and Oceanography, 67(5), 1007-1021. https://doi.org/10.1002/lno.12053.
Moran, M. A., Kujawinski, E. B., Schroer, W. F., Amin, S. A., Bates, N. R., Bertrand, E. M., Braakman, R., Brown, C. T., Covert, M. W., Doney, S. C., Dyhrman, S. T., Edison, A. S., Eren, A. M., Levine, N. M., Li, L., Ross, A. C., Saito, M. A., Santoro, A. E., Segrè, D., Shade, A., Sullivan, M. B., & Vardi, A. (2022). Microbial metabolites in the marine carbon cycle. Nature microbiology, 7(4), 508-523. https://doi.org/10.1038/s41564-022-01090-3.
Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME communications, 3(1), 37. https://doi.org/10.1038/s43705-023-00244-6.
Seymour, J. R., Amin, S. A., Raina, J. B., & Stocker, R. (2017). Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nature microbiology, 2(7), 1-12. https://doi.org/10.1038/nmicrobiol.2017.65.
Stubbins, A., Moran, M. A., Kujawinski, E. B., & Fatland, R. (2017, July). How do tiny ocean critters affect the global carbon cycle?. Science Journal for Kids and Teens. https://www.sciencejournalforkids.org/articles/how-do-tiny-ocean-critters-affect-the-global-carbon-cycle/.
Connecting Ocean Microbial Genomes to Carbon and Nitrogen Metabolism
Team Members
University of Puget Sound: Oscar A. Sosa (CURE lead instructor)
University of Washington: Zinka Bartolek, Frank X. Ferrer-González (C-CoMP Postdoctoral Fellow), Anitra E. Ingalls, E. Virginia Armbrust
Abstract
This course-based research project introduces undergraduates to foundational genetic concepts, data analysis skills, and genome sequencing to explore the biology of marine microorganisms. Guided by questions, students begin by reading research articles that describe the types of gene functions marine bacteria require to consume phytoplankton metabolites. Students learn basic wet lab microbiology and molecular biology techniques, R programming, and statistics to conduct a high-throughput screen of a diverse collection of marine bacteria using common phytoplankton metabolites as growth substrates. Students examine their data collectively to select bacterial isolates for genome sequencing and learn basic bioinformatics skills to analyze the genomes. The project culminates with an independent inquiry assignment in which students use genome evidence and scientific literature to reconstruct a genetic and biochemical pathway that could support the growth results of their bacterium on marine metabolites. The project incorporates assessments related to group discussions of peer-reviewed research articles, completion of questions based on the articles and lab protocols, weekly lab reports, and a final lab report and research lightning talk. The project highlights the utility of real-world genomic data to solve problems beyond biology.
Research Goals
- Screening a library of novel marine heterotrophic bacteria using high-throughput methods to characterize catabolic phenotypes
- Sequence bacterial genomes of isolates
Student goals:
- Understand, interconnect, and apply core genetic concepts to solve biological problems and continue independent learning in the discipline
- Learn about the types of biological information and insights genomes provide
- Learn how to do high-throughput experimental analysis
- Gain knowledge of genetic pathways through the exploration of microbial metabolism
- Participate effectively in team-oriented research activities and contribute to collaborative learning in the classroom
- Navigate the world of digital information to access, retrieve, analyze, and evaluate primary and secondary scientific literature.
- Recognize and evaluate methods that lead to scientific knowledge
- Formulate research questions and design experiments to address hypotheses and conduct the planned research independently
- Organize, analyze, interpret data collected to present a scientific argument
- Draw independent conclusions
- Critically appraise the work and conclusions of others
- Synthesize and disseminate scientific findings and ideas effectively through spoken and digital means
References
Boysen, A. K., Durham, B. P., Kumler, W., Key, R. S., Heal, K. R., Carlson, L. T., Groussman, R.D., Armbrust, E.V., Ingalls, A. E. (2022). Glycine betaine uptake and metabolism in marine microbial communities. Microbiol., 24(5), 2380-2403. https://doi.org/10.1111/1462-2920.16020.
Karkman, A., Johnson, T. A., Lyra, C., Stedtfeld, R. D., Tamminen, M., Tiedje, J. M., & Virta, M. (2016). High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol., 92(3), fiw014. https://doi.org/10.1093/femsec/fiw014.
Kim, S. Y., Ju, K. S., Metcalf, W. W., Evans, B. S., Kuzuyama, T., Van Der Donk, W. A. (2012). Different biosynthetic pathways to fosfomycin in Pseudomonas syringae and Streptomyces species. Agents Chemother., 56(8), 4175-4183. https://doi.org/10.1128/aac.06478-11.
Moran, M. A., Kujawinski, E. B., Schroer, W. F., Amin, S. A., Bates, N. R., Bertrand, E. M., Braakman, R.C., Brown, T., Covert M.W., Doney, S.C., Dyhrman, S.T., Edison, A.S., Eren., A.M., Levine, N.M., Ross, A.C., Saito, M.A., Santoro, A.E., Segrè, D., Shade, A., Sullivan, M.B., Vardi, A. (2022). Microbial metabolites in the marine carbon cycle. Nat. Microbiol., 7(4), 508-523. https://doi.org/10.1038/s41564-022-01090-3.
Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME Commun., 3(1), 37. https://doi.org/10.1038/s43705-023-00244-6.
Seymour, J. R., Amin, S. A., Raina, J. B., & Stocker, R. (2017). Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat. Microbiol., 2(7), 1-12. https://doi.org/10.1038/nmicrobiol.2017.65.
Velho-Pereira, S., & Kamat, N. M. (2011). Antimicrobial screening of actinobacteria using a modified cross-streak method. Indian J of Pharm. Sci., 73(2), 223. https://doi.org/10.4103/0250-474x.91566.
Funding Sources
This CURE was developed with support from NSF award IDs 2124712 to O.A.S. and 125886 to A.E.I., the University of Puget Sound, Department of Biology (Tacoma, Washington), the Simons Foundation (SCOPE award IDs 426570 and 329108 to A.E.I. and 721244 to E.V.A.) and the Center for Chemical Currencies of a Microbial Planet (C-CoMP; award ID 2019589 to F.X.F-G).
Ocean Protein CURE
Team Members
Woods Hole Oceanographic Institution: Logan Tegler, Mak Saito
University of Georgia: Erin Dolan
Abstract
One way to understand living systems is by characterizing the proteins found in the system. With this in mind, scientists have accumulated a tremendous amount of data on the proteins synthesized by marine life and publicly shared these data through the Ocean Protein Portal. Currently, there are over 100,000 proteins in the Portal; most have not been examined in terms of their ecological and biogeochemical roles. This course-based research project engages students in using a series of freely available ‘omics tools to systematically explore ocean protein data to address research questions of their choice. Students start by exploring the Portal and its functionalities and then choose a protein on which to focus. Students then use the Portal to gather baseline information about their protein of interest (e.g., who makes it, what its function is, how it is distributed) and then conduct a series of tasks to identify the protein’s taxonomic origin, characterize its function, and model its 3D structure. During the first offering of this course, a student made a discovery that resulted in a publication.
Research Goals
Research goals depend on students’ choices and can include the following:
- Explain protein distributions in oceanographic, biochemical, and taxonomic contexts
- Develop hypotheses about the function, distribution, and taxonomic source of various proteins within the ocean
- Characterize the diversity of a specific type of protein (e.g., putative enzyme, transporter) and how its distribution changes across biogeochemical and physical provinces
- Identify interesting and important components of proteins and their biogeochemical functionality across ocean regions and depths
Student Goals
- Learn how to work with and manipulate big 'omics datasets
- Understand how to integrate and interpret data from multiple sources using freely available ‘omics software tools
- Employ an ‘omics workflow to characterize a protein of interest
- Leverage bioinformatics tools to examine the protein structure and function of proteins in marine environments
- Use the output from Protein Data Bank and Alphafold to create and interpret protein structures
- Interpret protein distribution within oceanographic context
- Refine concise writing and speaking skills
References
Saito, M. A., Bertrand, E. M., Duffy, M. E., Gaylord, D. A., Held, N. A., Hervey IV, W. J., ... & Walsh, D. A. (2019). Progress and challenges in ocean metaproteomics and proposed best practices for data sharing. Journal of proteome research, 18(4), 1461-1476. https://doi.org/10.1021/acs.jproteome.8b00761.
Saito, M. A., Saunders, J. K., Chagnon, M., Gaylord, D. A., Shepherd, A., Held, N. A., ... & Kinkade, D. B. (2020). Development of an ocean protein portal for interactive discovery and education. Journal of proteome research, 20(1), 326-336. https://doi.org/10.1021/acs.jproteome.0c00382.