Expanded emphasis on writing research funding proposals substitutes for hands-on experimentation following the transition to online instruction for an Advanced Cell Biology laboratory course
Under normal circumstances, the Advanced Cell Biology laboratory course at California State University, Sacramento includes a significant CURE component. This course is an upper division capstone-like course for Biology majors that enrolls 20 students. Students first focus on mastering practical laboratory skills and common methods for the culture of mammalian cells. Then, they apply their learning to the development and execution of small group research projects that culminate in the writing of research funding proposals. For these projects, students complete the following: (1) conduct a literature search to identify a putative toxin in the American River with suspected adverse effects on mammalian cells, (2) sample river water and perform mass spectrometry to determine presence of the toxin, (3) design and conduct high-throughput experiments to analyze cell viability and death in response to the toxin, and (4) write a research funding proposal using their results as preliminary data. Due to the mid-semester switch to online instruction during Spring 2020, students were unable to complete the majority of their CURE. At the point of the transition, they had already identified their toxins of interest and submitted pre-proposals; however, they were unable to perform their proposed experiments to gather preliminary data about the cellular effects of their toxins, nor conduct the mass spectrometry analyses. Instead, the CURE was modified to expand the research funding proposal writing component. Additional opportunities were introduced for students to explore new and different assays for incorporation into their funding proposals. Students are usually restricted to three specific assays based on available equipment and funding. For the online CURE, students were instructed about additional assays not normally included in the curriculum. They worked with their group to research these new assays and determine which assays would be appropriate for investigating their hypotheses. Groups then drafted experimental design plans for their new assays and created graphs/figures of their predicted preliminary results for inclusion in their funding proposals. At the conclusion of the course, student feedback about these CURE modifications was gathered informally through class discussions and through a course feedback question on the final exam. Students universally commented they felt their research experience was not as impactful since they could not conduct hands-on experiments in the laboratory. However, on the positive side, many students noted how much they appreciated being able to design projects that incorporated additional relevant assays. They said this approach made writing their funding proposals seem more authentic, because generally, competitive funding proposals involve more extensive experimental plans, proposed assays, and preliminary data than the limited assays they would have been able to accomplish in-person in the laboratory. For future versions of this CURE, either in-person or online, including the opportunity for students to incorporate additional assays into their research proposals merits consideration based on positive feedback from students in Spring 2020. This modification seems to hold irrespective of whether or not students can actually conduct the assays in the laboratory to gather preliminary data. However, this initial attempt at expanding the research proposal writing component of the CURE was largely structured around information about additional assays provided by the instructor. In the future, this could be improved by thoughtful planning that shifts the exploration of new assays to a student-driven approach.
As part of broader efforts by our Biology faculty, we have been developing scaffolded Course-Based Undergraduate Research Experiences (CUREs) across our curriculum to build skills and experiences in the fields of Genomics and Bioinformatics. One of the first such experiences for our students is a Genome Sequencing Lab in our introductory biology course lab series. This lab is focused on introducing students to sequencing data, basic data analysis and bioinformatic tools, concepts in genomics, and discovery science through their participation in a novel
de novo genome sequencing project. While the target species can changes as needed (our focal species thus far has been the live-bearing, hemiclonal fish species
Poeciliopsis monacha), the approach and methods are all targeted towards introducing students to entry-level lab and bioinformatic skills while providing them a unique, discovery-based experience. We use Oxford Nanopore MinION technology to highlight the advanced technology associated with this highly accessible work. Learning Outcomes for this CURE include the following: (1) students will develop an altered DNA isolation protocol to test expectations of their experimental design; (2) students will use multiple lines of evidence to evaluate and select a DNA sample for sequencing; (3) students will use summary statistics to describe sequencing data; (4) students will identify the different components of a genome using a homology-based search tool and reference database. Typically, this lab consists of a three-week process. During Week 1, students isolate DNA from a sample using a simple, non-toxic, “salting out" isolation method. They must read a protocol and propose to “improve" expected outcomes based off of, generally, improving the protocol's sample handling through targeting contaminant removal, thermal stress, or physical stress. After isolation, students evaluate the result and pick one sample from each class to serve as the sample to sequence for their class based on multiple target measures (purity, fragmentation, and yield). In Week 2, students take sequencing data from an organism with virtually no previous genetic sequence data and identify genes (using a BLAST-approach) and repetitive elements (using a Hidden-Markov Model approach) found in their sequencing. Finally, in Week 3, they turn in short reports on their findings. To move this lab “online," we substituted all lab aspects with video demos and instruction, provided additional background information instruction, implemented a cloud-based approach to data analysis, and reduced writing components to hone in on the “Results" and “Discussion" aspects of scientific writing. This removed some of the opportunities for student creativity in experimental design, but retained the overall discovery component of the work. This led to reduced feelings of ownership of the project by students, but still supported their science identity development by allowing them to participate in a novel research inquiry and make discoveries that were previously unknown. Overall, student feedback was positive. Students enjoyed the exploratory nature of the work, however, online materials could be further improved to better engage students (e.g. shortening video resources or building in interactive quizzes) and more support for understanding the parts of genome and their relationship to the results from the bioinformatics analyses.
Virtual CURE in Times of Crisis
Introduction to Environmental Science (ENVS 201) is an entry-level science class of 60-80 students, generally taken by non-science majors to satisfy Life Science and Laboratory Practice general education requirements.
In the original CURE research project, ENVS 201 students conduct a study of a water quality site in Monterey County. Students are responsible for designing a project, understanding and implementing field and lab methods, conducting research on water quality, collecting and analyzing data, creating comprehensible graphs and data tables, writing a scientific quality report, and presenting the study to classmates. The learning goals include developing a project proposal, two questions/hypotheses and designing a competent project that tests hypotheses and answers questions related to water quality parameters (nitrate, phosphate, dissolved oxygen, fecal coliform, turbidity, temperature, and pH). Students visit a stormwater or agricultural runoff waterbody and collect samples to be brought back to lab for testing of the above parameters. This group project requires students to collaborate, learn to work together, communicate effectively, and take responsibility for completing the work in a team setting.
In Spring 2020, ENVS 201 was modified to an online course and specific changes were made to the CURE. Students no longer visited their field location for water sampling. In addition, students did not perform the laboratory tests or contribute to any data collection. Instead, datasets were provided from past semesters of this project. Students had access to 5 years of data for their selected sites and multiple other sites. Students still completed library research, wrote a literature review on water quality, formed questions/hypotheses, performed data analysis, and wrote a scientific style paper about their project.
In the online CURE, students did not have the opportunity to get outside during class time, visit a local waterbody, collect the water samples used in their study, or experience any of the laboratory methods in data collection. In addition, students did not have to spend money on gas to drive to a field site once a week for 4 weeks, and were able to focus their efforts more on improving data analysis skills, researching the topic of water quality, writing a literature review and scientific report. Spring 2020 student course evaluations of ENVS 201 were positive, with 97% of students (45 out of 79 students completed a course evaluation) rating the course as “Outstanding" or “Very Good."
For Fall 2020, I plan to incorporate two new elements to improve engagement with the online CURE. There will be an additional assignment requiring students to visit a local waterbody in their community and complete a Site Assessment, in which students will characterize a waterbody with various criteria including an estimation of flow discharge and turbidity, and observations of weather conditions, trash, wildlife and human presence. This assignment will give students a sense of place where they live, outside time during Environmental Science class, and a visual for how water quality can be influenced by human activities. I also plan to incorporate new datasets from other areas outside of Monterey County, which may be closer to students' homes and thus more interesting and relevant to them.
Unforeseen benefits of the transition to a virtual CURE from the student perspective
Cell biology and genetics lab is an upper-division CURE required for all biology majors at Fresno State. Some of the learning goals include those expected in a CURE: performing fundamental lab techniques, creating a hypothesis, designing an experiment that includes multiple methods for addressing the hypothesis, troubleshooting complications, collecting and interpreting data, and communicating results. After reading background literature, student groups design their own experiments related to crossing genetically diverse populations of a worm species and then performing genetic and phenotypic analyses of hybrid offspring. At the time instruction moved to virtual, students had already practiced the essential techniques, iteratively refined their experimental designs, and just started to collect data. The main modification to the CURE involved asking students to create fake numerical data that comprised data sets they thought would support their hypothesis. After specific research ethics training to indicate that falsifying data is not an acceptable scientific practice, they used their falsified data in subsequent analyses and presentations. This rapid redesign maintained many of the recognized CURE components (Auchincloss et al. 2014 CBE LSE). Students were involved in multiple scientific practices, discovery was at the core of the course design, research was collaborative, and iteration was involved. Student groups developed hypotheses autonomously, and they were assessed as practicing research scientists through their communication. The main negative impact on the CURE design was that the purposeful invention of data eliminated the external importance of their efforts. However, student feedback from IRB-approved human subjects research surveys did not note student perception of this drawback. Instead, feedback indicated some benefits to virtual delivery, including the elimination of resource bottlenecks (e.g. microscope station availability) and reduction in the amount of time outside of class that students had previously needed to invest to complete their projects. At the end of the semester, despite the hasty redesign, students indicated they would recommend the course to friends (75% agree, 20% neutral), that a CURE should be offered earlier in the curriculum (78% agree, 11% neutral), and that the course had a positive impact in their interest in science (80% positive, 15% neutral). Although virtual CUREs are not necessarily always ideal, they have potential benefits. Although this course has been approved to be held in person this coming fall, some virtual/online components will still be integrated. For example, experimental design will focus more on meta-analysis of existing data, more support will be provided to groups to use digital collaboration tools like shared Google Docs and Sheets, and student groups will leverage Zoom to record and present their semester-end oral presentations for peers to watch and evaluate. Students have indicated that purposeful changes to CUREs can maintain and possibly enhance their value, and our present circumstances can be a catalyst for incorporating those changes.
Designing an Oxygenase Enzyme: From Benchtop to Laptop
John Molthen and Dr. Gönül Schara
The goal of this CURE is to expose students to the process of protein engineering to improve the characteristics of an oxygenase enzyme. In the laboratory, students performed saturation mutagenesis approach of protein engineering to generate oxygenase variants via three-step overlap extension polymerase chain reaction (PCR). Each group of students focused on constructing a saturation mutagenesis gene library encoding all possible amino acids at their assigned amino acid position. During the labs, students worked in teams of 2-3 and conducted DNA extractions, PCRs, running gels, and other lab procedures. After switching to online, students carried out computational modeling to generate oxygenase variants using the PyMOL software and screen these oxygenase variants towards selected drugs using the AutoDock Vina docking software. Each student was assigned three different drugs and one amino acid position within the active site region. Students first mutated their assigned position into all possible amino acids using PyMOL and generated nineteen different oxygenase variants in protein data bank format. Students then used AutoDock Vina to predict the binding affinity and docked pose of the drug substrates. Students finally analyzed their docking output and concluded on the best drug choice for the wild-type oxygenase enzyme and the amino acid substitution(s) that gave better results compared to the wild-type enzyme. At the end of the semester, each student individually presented a poster on their work and wrote a report following the American Chemistry Society guidelines. One of my student, John Molthen will be highlighting a specific example of this modification in the submitted video. With this course modification, students were introduced to the programming environments related to protein structure visualization and modification as well as molecular docking used in modern biochemisty research. Student feedback indicates that such modification increased their appreciation for the roles of chemists in the computer-aided protein design and molecular modeling process and their knowledge about, and confidence in using, online databases and computational tools. Teaching sessions worked well, but student interactions could have been improved.
Pivoting to an online Microbial CURE in the time of COVID-19
General Microbiology at Sacramento State is a 4-unit core course taken by most of our Biological Sciences majors within a year of graduation. The course serves over 300 students each year and includes a large lecture class of 70 to 100 students subdivided into laboratory sections of approximately 24 students each. We recently revised the curriculum in this course to provide students with a CURE. Through a paradigm shift, we dramatically modified the typical end-of-semester microbial unknown lab activity where students are given one of a handful of bacteria, and required to identify it to species level. Now, instead of working through a two-week “cook-book" activity, our students experience an eight-week integrated learning/research experience that contributes to the understanding of the microbial ecosystem and health of our nearby American River. During the CURE, prior to COVID-19, microbiology students isolated sediment and water at the river's edge, evaluated water quality, and after running dozens of biochemical tests and reviewing the data, discerned the identity of bacteria in our precious waterway and the relevance of finding it there. June 2019 we presented the details of our CURE at the American Society for Microbiology annual meeting, including our data that found our students had comparable lab-skill self-efficacy to students that participate in an independent Undergraduate Research Experience.
When instruction went online March 2020 we had to pivot our CURE, keeping student safety, well-being, and learning outcomes as highest priorities. Student safety required us to remove the wet-lab portion of the project, as it is not safe to culture microbes outside of a designated BSL-2 lab. Student well-being was met by continuing to meet synchronously to serve as an anchor in the storm of change. Student learning outcomes were met by shifting the CURE to an online format in a way that the students could still experience data evaluation, discernment, and discovery. In quick time, we reviewed previous student data and selected the top 12 organisms our students had previously identified in the river, and then we built an online experience, rolling out experimental results from the selected organisms twice a week over 8 weeks. We engaged our TAs in the development process, several of which provided photos of data they had saved from their own CURE experience. We were purposeful about keeping the revised CURE as realistic as possible by including photos of previously obtained data that were inconclusive, and we allowed students to ask for additional data as needed. As it was done hurriedly, some of the data that was posted was incorrect, which added a shared experience with our students, and required revision on our part as well as humility and humor. As in previous semesters, students interpreted their results and formulated conclusions about their organisms' metabolic processes, identity, and relevance to the American River. To encourage more active learning, we added an additional research component to our virtual CURE, asking the students to delve into the primary literature and identify a unique molecule produced by their organism (e.g. pilus or antibiotic pump, not 16sRNA) that they could amplify with PCR to more accurately classify or characterize their organism. At the end of the semester, numerous students provided unsolicited feedback to faculty on the virtual portion of the course. On the whole, students stated that they were pleased we continued synchronously, and enjoyed the inquiry-driven research. Additionally, students scored similarly, if not better than previous semesters on the assessments that were given during the CURE portion of our course.