CREARE: Coral Response to Environment Authentic Research Experience

Juan Ramirez Lugo, University of Puerto Rico-Rio Piedras Campus
Claudia P. Ruiz-Diaz, Department of Environmental Sciences, Universidad de Puerto Rico, Río Piedras
Carlos Toledo-Hernández, Department of Biology, Universidad de Puerto Rico, Bayamón
Location: Puerto Rico

Abstract

There is growing body of evidence to support that students who directly experience authentic scientific research are more likely to continue on to advanced degrees and careers in Science, Technology, Engineering and Mathematics (STEM). In an effort to introduce more students to the benefits of scientific research, we have drawn on an ongoing research project aimed at understanding how Corals Respond to the Environment (CRE) to develop an interdisciplinary laboratory course based on Authentic Research Experiences (ARE). A small cohort of undergraduate students enrolled in a semester-long course, entitled CREARE, perform biochemical experiments in the laboratory, analyze environmental data using R statistical software and prepare a report modeled after a research manuscript to present their work. The impact of CREARE on student learning gains and attitudes towards science is being measured, as is the impact of CREARE on participants' career choices and retention in STEM. This multidisciplinary research program addresses the impact of climate change on the health of a critically endangered coral species, ultimately leading to a better stewardship of this invaluable resource. Furthermore, CREARE offers a unique experience for students, one that may serve as a model for the development of more research-based courses, leading to improved retention in our STEM departments.

Student Goals

  1. Develop skills and competencies to successfully perform scientific research.
  2. Acquire competence and experience in the use of statistical analysis, including large-scale data sets.
  3. Effectively communicate the results of research to peers, members of the scientific community, and the general public.

Research Goals

  1. Determine the seasonal variation in the concentration of the photo-protective peptide polymers melanin and fluorescent proteins in corals inhabiting at 3, 8 and 12 meters of depth.
  2. Monitor fluctuations in sea surface temperature (SST) and solar radiation (SR) throughout a two-year period in nurseries of Acropora cervicornis established in Eastern Puerto Rico at 3, 8, and 12 meters of depth.

Context

This semester-long CURE is intended to be offered to 12–16 students who have completed two introductory courses in Biology, two introductory courses in Chemistry, and one introductory course in Statistics, generally sophomores and juniors. In addition to the 3 hours a week of contact hours with students, instructors are expected to devote at least an additional 3 hours for sample collection, laboratory preparation, additional time for students to perform experiments, answer students questions, reading and providing feedback to students on writing assignments and preparing and analyzing data from student assessment.

Target Audience:Major, Non-major
CURE Duration:A full term

CURE Design

Students will actively participate in a course where the theoretical basis of research will be discussed through targeted analysis of technical and popular scientific literature and through thematic modules in biology, statistics, writing and scientific communication. Students will (1) read and evaluate scientific literature to be able to select and design appropriate experimental methods for the research question, (2) have practical field and laboratory experiences where they will employ effective strategies to obtain scientifically relevant novel data, (3) analyze the results of their experiments, including aspects of statistical analysis for large-scale data management, (4) gain experience working collaboratively with peers and teachers, and finally, (5) communicate the results obtained to stakeholders outside of the classroom. These stakeholders are local coral reef researchers and members of community-based coral conservation and restoration groups. The work is shared with stakeholders through oral or poster presentations at local coral reef symposia (if they coincide with course schedule) or through the coordinating a poster session and inviting stakeholders.

Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Using mathematics and computational thinking
Nature of Research:Field Research, Wet Lab/Bench Research

Tasks that Align Student and Research Goals

Research Goals → 
Student Goals ↓
Research Goal 1: Determine the seasonal variation in the concentration of the photo-protective peptide polymers melanin and fluorescent proteins in corals inhabiting at 3, 8, and 12 meters of depth.
Research Goal 2: Monitor fluctuations in sea surface temperature (SST) and solar radiation (SR) throughout a two-year period in nurseries of Acropora cervicornisestablished in Eastern Puerto Rico at 3, 8 and 12 meters of depth.


Student Goal 1: Develop skills and competencies to successfully perform scientific research.

-Extract tissue from coral samples collected from nurseries at 3, 8, and 12 m of depth

-Perform a phenoloxidase assay to estimate melanin concentration.

-Perform spectrophotometry based estimation of fluorescent proteins.

Extract data from sensors that are collecting environmental conditions at research site.



Student Goal 2: Acquire competence and experience in the use of statistical analysis, including large-scale data sets.

Sensors at the research site are recording SST and SR every 15 minutes. Members of research team collect sensors every month and students will

- Receive monthly data set which typically include 1,000–3,000 usable data points per site per month.

- Handle these data sets and perform statistical analyses to determine significant differences in SST and SR between depths and between months.



Effectively communicate the results of research to peers, members of the scientific community and the general public.

The results obtained from experiments will be included in a final report and also in an oral or poster presentation at the end of the semester.

The results obtained from these analyses will be included in final report and also in an oral or poster presentation at the end of the semester.


Instructional Materials

JMBE Article describing this CURE: https://journals.asm.org/doi/10.1128/jmbe.v22i1.2253C?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Assessment

Instructional Staffing


Juan Ramirez Lugo, University of Puerto Rico-Rio Piedras Campus

There is ample evidence to support that undergraduate students who directly experience scientific research are more likely to continue on to advanced degrees and careers in STEM. Research experiences have been shown to particularly boost retention rates and increase the participation of underrepresented minorities in the research enterprise. In our Department, at a minority serving institution, the medium through which most students get the opportunity to experience scientific inquiry and exploration is through laboratory-based courses. Therefore, I consider of paramount importance to develop and implement course-based research experiences (CUREs) to broaden the benefits of research as a means of improving retention, STEM literacy and STEM-competency to the largest possible portion of our students.

Advice for Implementation

The main crux of this CURE is getting students to become competent at performing statistical analyses using R. Even if students have been introduced to R in the Statistics course, they struggle to apply it to real world circumstances and large data sets. We are spending more time (2 modules vs. 1) in introducing students to R and also starting with a small data set for them to work with before handling the real data. Keeping students engaged after setbacks in experiments is always a challenge and, on occasion, we have students switch tasks (reading, writing) if they become frustrated. Also, having specific periods set aside for answering questions, repeating experiments and giving feedback on writing assignments is very important for time management from the instructors perspective. Otherwise students will consume every single waking minute of your life (which means they are involved, but then again, time is finite).

Using CURE Data

All data produced by students is deposited in a Dropbox folder managed by the instructor. The experimental setup requires that all samples are run in triplicate and tissue slurries tired in -80°C for future analysis (that works in most cases, except if you get hit by a Category 5 hurricane and power goes out for weeks). At the moment, most course participants have only contributed marginally to the data set as they focus on only a small fraction of the data produced, yet some students have become more involved in the project and contributed more substantially. The latter will be included as authors in any eventual publication.

Resources

1. Alon U. 2009. How to Choose a Good Scientific Problem. Molecular Cell 35: 726–728. | doi:10.1016/j.molcel.2009.09.013

2. An Introduction to R. Version 3.3.2 (2016-10-31). R Core Team. https://cran.r-project.org/doc/manuals/R-intro.html

3. Corwin, L. A., Graham, M. J., & Dolan, E. L. (2015). Modeling course-based undergraduate research experiences: An agenda for future research and evaluation. CBE Life Sciences Education, 14(1), 1–13. https://doi.org/10.1187/cbe.14-10-0167

4. Hoegh-Guldberg, O., et al. 2007. Coral reefs under rapid climate change and ocean acidification. Science. 318:1737–1742.

5. Palmer, C.V., et al. 2010. Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals. FASEB J. 24:1935-1946.

6. Palmer, C.V., et al. 2011. A comparative study of phenoloxidase activity in diseased and bleached colonies of the coral Acropora millepora. Deva. Com. Immunol. 35:1098–1101.

7. Perry J. et al. "Science Writing and Communication" in Laboratory Manual for General Biology. Brooks Cole 5th Edition, 2006 pp. 755–765

8. Ruiz-Diaz et al. 2016. The role of coral colony health stat in the recovery of lesions. Peer J. DOI 10.7717/peerj.1531.

9. Strunk W. (2012) The Elements of Style. The Original Edition. Mineola, NY: Dover Publications Inc.

10. van de Water, J. A. et al. 2016. Temporal patterns in innate immunity parameters in reef- building corals and linkages with local climatic conditions. Ecosphere 7(11): e01505. 10.1002/ecs2.1505