Biochemistry Authentic Scientific Inquiry Lab (BASIL), Ursinus College
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https://serc.carleton.edu/curenet/collection/220515.html
The Biochemistry Authentic Scientific Inquiry Lab (BASIL, https://basilbiochem.github.io/basil/) is a modularly-designed CURE aimed at supporting the transition of students to thinking as scientist. The students identify the function of proteins that are available in the Protein Data Bank that have known structures but no known functions. The modular design of BASIL allows instructors to tailor the CURE to their needs.
CURE Development
The idea for BASIL was inspired when we noticed that students in our research lab using a recently developed software were moving beyond our initial research questions to ask and tackle interesting research questions of their own. We thought that this presented a great opportunity to expand this type of research into a broader CURE. We assembled a small team and wrote an NSF proposal, which was not initially successful but provided helpful feedback. We expanded our team from RIT and Dowling College to include colleagues who were part of our personal/professional network and created a poster for ASBMB 2014 in San Diego to recruit additional participants, who contributed to a subsequent successful proposal.
Development of the BASIL curriculum began in summer 2015, with initial contribution and implementation on six very different campuses: St. Mary's University San Antonio (a minority serving institution), Ursinus College, Hope College, Oral Roberts University (three liberal arts PUIs), Cal Poly San Luis Obispo (a large public institution), and the Rochester Institute of Technology (a comprehensive university transitioning to a Carnegie class 2 Ph.D.-granting institution). Throughout this process, we also had the constant presence and influence of a biochemistry education focus spearheaded by Trevor Anderson from Purdue. The development of BASIL was unique because it was a true group effort, only made possible by the diverse expertise available on our multidisciplinary team (e.g., computer scientists, bioinformaticists, biochemists, etc.).
The focus of the BASIL CURE team has shifted greatly over time. At first we were thinking about how to approach moving the concept to a CURE, as well as how to disseminate and assess the program. Now that the main modules are published, we are shifting again to consider sustainability and growth (e.g., expanding modules). We have also increased the number of faculty on the team who are interested in assessment to develop the evaluation of our program further. The research itself remains novel as we continue to explore ways to model and assay new enzyme classes.
Modular design allows for flexible implementation
Through iteration we developed 5 computational modules and 6 wet-lab modules that allow students to predict protein function and then test that prediction in the lab. How the CURE was integrated into curricula varied by institutions. It was built with a modular design from the beginning to facilitate flexible implementation. Most BASIL instructors carried out all of the wet lab modules and the majority of the computational modules within a single course. They commented that some modules were omitted due to time constraints, technical issues, or lack of alignment with course goals. The omitted modules were typically the final computational and wet lab modules involving molecular docking analyses and kinetic analysis. Note that, as with many experimental protocols, some wet lab modules must be carried out sequentially in order to obtain purified protein. At some institutions, earlier steps such as transformation and expression were delegated to teaching assistants or lab preparation personnel, in one case because they have already been covered in earlier courses.
In some instances, only the wet lab or computational modules were implemented. For example, computational modules were used alone for one course aimed at Masters students and senior undergraduates. At Ursinus College, students in a Structural Biology course carried out the computational modules while students enrolled in a Biochemistry course carried out the wet lab modules. Students then came together in cross-course groups to inform each other's projects and to jointly develop posters for a session that was very well-received by the entire Ursinus community.
Barriers to implementation
During the iterations of the curriculum on our campuses, we found that challenges for the BASIL CURE fell into three main categories: technical problems, instructor challenges, and student difficulties. They ranged from short-term minimal issues to long-term impacts. Technical problems included lack of access to equipment, despite the fact that the BASIL modules were devised to employ commonly-available laboratory equipment. Sometimes there was a bottleneck, for example, if only a single spectrophotometer was available. However, flexibility is increased because protein activity assays can be carried out qualitatively if no spectrophotometer is at hand. Many faculty members found that software installation or use (especially with PyRx) was frustrating, especially if institutional IT support was not available.
Some instructors found that the time required to learn a new curriculum was a barrier to implementation. We appreciate that there is a learning curve associated with some of the computational software, and accordingly we have included video tutorials for the computational modules. On some campuses, the lack of Teaching Assistant support or other laboratory preparation personnel increased the time commitment by the faculty member.
The learning curve and technical issues discussed above hold true for the students as well as the instructors. BASIL instructors reported that these challenges can lead to frustration for some students. Some of the students were simply not interested in the challenge of a CURE, preferring a cookbook style lab simply to fulfill a graduation requirement. Others were frustrated by the lack of success at intermediate points during the academic term. In the wet lab portion of the BASIL curriculum, students frequently need to troubleshoot problems with expression levels and protein purification. Several students were challenged by the more advanced computational activities and the different perspective required for bioinformatics work, where they need to think in terms of "possible answers" to the question being asked, rather than a "right answer". Finally, the nature of the BASIL curriculum was problematic for some students, as it did not line up neatly with the co-requisite biochemistry lecture course. Nonetheless, we believe that the frustrations encountered and, oftentimes overcome, provide a framework that may assist in the development of characteristics of a scientist such as resilience and persistence.
Indicators for success
Faculty adopting the curriculum at their institution and engaging with the BASIL team is one measure of success. For students, developing the ability to communicate their findings (e.g., lab notebook, poster presentation, or a research paper) is an indicator that they have gained relevant skills. Some students have even presented their work at a regional/national meetings. Success for students is also that they are learning and growing as scientists and we are in the process of developing assessments for that. BASIL has resulted in scientific publications including those on assessment and the challenges of moving to a CURE. Relevance outside of the classroom comes through the students who graduate and go on to wonderful adventures using the skills that they learned. Many have gone onto graduate programs, medical schools, and one was a Fulbright Scholar.
Resources
Initially, we applied to NSF for funding to support BASIL. After the first proposal was unsuccessful, a second and third were subsequently funded to support development of the modules and design the assessment protocol. To promote sustainability, we designed modules that relied on commonly-available equipment and identified inexpensive options early in the process. We discussed ways to use existing resources to support the CURE that did not add to costs.
We were lucky enough to get a second grant funded and are now writing our third. Sustainability will come from the passion of those involved to keep the BASIL curriculum up-to-date. We also need to consider how to distribute the leadership as the program grows and as folks retire or choose to leave the team. We have some sustainability issues to still consider, especially related to the IT logistics of the program (e.g., server maintenance).
Stakeholder Buy-In
Students: The students participate in BASIL because it is part of their required curriculum for their undergraduate biochemistry (or other) lab course. We describe the project as a novel research experience, which is often all that is needed to get students excited. However, there are some students who do not like the open inquiry design and become frustrated, especially during the computational modules. We help students navigate this frustration by discussing how even the computational modules are part of the research process and that exact answers may not be available.
Faculty: Initial recruiting of faculty was done based on personal relationships. The next phase of recruiting happened as a poster presentation at the 2014 ASBMB meeting, which was an unabashed recruiting poster. Following that, additional faculty adopted the curriculum based on word of mouth, additional presentations at national meetings, and publications. Once the modules were made available on GitHub and the initial paper on the flexibility of implementation of BASIL was published (https://iubmb.onlinelibrary.wiley.com/doi/abs/10.1002/bmb.21287) it has become somewhat easier to attract adopters. The flexibility of the modules facilitates adoption and we support new adopters with written faculty resources, personal conversations, and a discussion board. Moreover, having the assessment data on anticipated learning outcomes supports faculty adoption.
Administrators: In most cases, the administrators warmed up to the fact that the project was funded by NSF. It helps that the estimated cost to run the lab is about the same as a classical biochemistry lab curriculum. Individual faculty have spearheaded a publicity campaign for the BASIL project on their institutional websites and alumni magazines. Increasing the visibility assists in administrator buy-in. Our assessment data can also benefit administrator buy-in.
Sustaining Change
The BASIL CURE has been adopted by 10 faculty at a range of institutions. Sustainability at this point is mostly based on faculty's motivation to continue using the curriculum. A key to success was building a team of faculty with myriad expertise. Whenever problems arose, someone on the team had the expertise needed (e.g., software glitch, a wet lab snafu, publication or grant writing needs, publicity, recruiting, etc.).
A large part of the funding for BASIL focused on assessment by Trevor Anderson and his graduate student Stefan Irby. In truth, the robust character of the assessment was paramount to initial and continued funding opportunities. We assessed not only the students, but also faculty and TA growth. Several BASIL faculty became interested in learning more about discipline-based educational research. These faculty development opportunities, supported through interactions with Trevor, were critical and fortuitous occurrences that will benefit sustainability. Stefan has now transitioned to a postdoc position and, while maintaining his contact with BASIL, has additional projects to consider. Trevor is close to retirement and has been mentoring other faculty in assessment so that these efforts can continue when he leaves. He is actively mentoring other team members to accomplish this transfer of responsibility. For example, Rebecca Roberts took a sabbatical at Purdue to work with and learn from him. With continued mentorship from Trevor, Rebecca Roberts will begin to spearhead the BASIL assessment sub-group. If we had lacked the financial support and interest of faculty in the assessment arena this leadership transition would not be possible.
Having a charismatic group leader has helped defray faculty burnout. Paul has such passion for the project and strong leadership skills that enable him to bring together a diverse group of people that work well together. He encourages open communication and transparency within the group and allowed people to find their place and their voice. He allowed us all to flourish and to take on leadership in various aspects of the project. While this happened organically and fortuitously so far, as the team grows we may need to consider how to support/develop new leaders and engineer in leadership transitions more directly.A barrier is the time commitment required by the core BASIL team; the heavy work-load is creating substantial challenges. BASIL is currently in the process of shifting to a distributed leadership organization to help alleviate these problems by allowing some flux of involvement without disrupting the program operation. This will involve a 3-team structure: assessment, expansion & support of BASIL adoption, and BASIL curriculum expansion.
Advice for Implementation
What do you wish you had known when you started? The importance of getting together with the group face-to-face. While this can be expensive, the biggest leaps forward for the BASIL project occurred when we were all in a room together for a day or two.
Given the focus on assessment from the get go, we have learned that IRB systems vary at different institutions. It's important for all members to respect each IRB and work within those parameters.
What advice would you give others who are just getting started with their CUREs? Find the passionate and talented people and work on effective communication between all. Understand the career goals of everyone on your team and work to support each persons needs. If someone feels appreciated and supported, then they are more likely to continue in the project.