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1. Using Protein Function Prediction to Promote Hypothesis-Driven Thinking in Undergraduate Biochemistry Education

   Craig, Paul A; Anderson, Trevor; Herbert J. Bernstein, Herbert J; Daubner, Colette; Goodman, Anya; Irby, Stefan M; Koeppe, Julia; Mills, Jeffrey L; Pikaart, Mike; Ringer McDonald, Ashley; et al (May 2018, The chemist)

   Students at the Rochester Institute of Technology and Dowling College used bioinformatics software, which they had helped develop, to predict the function of protein structures whose functions had not been assigned or confirmed. Over the course of time, they incorporated other bioinformatics tools and moved the project to the wet lab, where they sought to confirm their in silico predictions with in vitro assays. In this process, we saw so much personal and professional growth among our students that we chose to implement their approach in an undergraduate biochemistry teaching lab, which we call BASIL, for Biochemistry Authentic Scientific Inquiry Lab. This curriculum has now been implemented by thirteen faculty members on eight campuses, and we look forward to a long-range exploration of BASIL’s impact on the students who enroll in courses that use the BASIL curriculum. 

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2. Responses to the COVID-19 Pandemic by the Biochemistry Authentic Scientific Inquiry Lab (BASIL) CURE Consortium: Reflections and a Case Study on the Switch to Remote Learning

   https://doi.org/10.1021/acs.jchemed.0c00729  

   Sikora, Arthur; Irby, Stefan M.; Hall, Bonnie L.; Mills, Stephen A.; Koeppe, Julia R.; Pikaart, Michael J.; Wilner, Samantha E.; Craig, Paul A.; Roberts, Rebecca (August 2020, Journal of Chemical Education)

   Campus shutdowns during the SARS-CoV2 pandemic posed unique challenges to faculty and students engaged in laboratory courses. Formerly hands-on experiments had to be quickly pivoted to emergency remote learning. While some resources existed prior to this period, many currently available online modules and/or simulations focus on a single technique. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) curriculum has, for several years, provided a robust, linked, holistic inquiry experience that allows students to make connections between multiple techniques, both computational in nature as well as wet-lab based. As a Course-based Undergraduate Research Experience (CURE), this flexible, module-based curriculum allows students to generate original hypotheses based on analysis of proteins of unknown function. We have taught this curriculum as the upper-level laboratory course on our campuses and were obliged to transition to remote instruction at various points in the course sequence. We report on the experiences of faculty and students over the transition period in this course. Additionally, we report as a case study results of one of our campus’ ongoing discipline-based education research (DBER) on the BASIL curriculum prior to and during remote delivery. 

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3. The BASIL CURE Initiative: Transforming How Students Learn Biochemistry Through Real Research

   https://doi.org/10.33548/SCIENTIA1168  

   Craig, Paul A; Hall, Bonnie L; Koeppe, Julia R; Roberts, Rebecca (January 2025, Scientia)

   Teaching students how to think like scientists is a critical but challenging goal in biochemistry education. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) initiative was conceived by Dr Paul Craig from the Rochester Institute of Technology and is led by colleagues across multiple institutions. They have developed an innovative curriculum that transforms traditional cookbook-style laboratory courses into authentic research experiences, also known as a Course-based Undergraduate Research Experience (CURE). By investigating real proteins with unknown functions, students learn essential scientific skills while expanding our knowledge of protein biochemistry. 

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4. Expanding the BASIL CURE

   https://doi.org/10.35459/tbp.2024.000273  

   Koeppe, Julia R; Dattelbaum, Jonathan D; Hall, Bonnie L; Mills, Stephen A; Offerdahl, Erika G; Pikaart, Michael J; Roberts, Rebecca; Sikora, Arthur; Craig, Paul A (January 2025, The Biophysicist)

   In the Biochemistry Authentic Scientific Inquiry Lab (BASIL) course-based undergraduate research experience, students use a series of computational (sequence and structure comparison, docking) and wet lab (protein expression, purification, and concentration; sodium dodecyl sulfate-polyacrylamide gel electrophoresis [SDS-PAGE]; enzyme activity and kinetics) modules to predict and test the function of protein structures of unknown function found in the Protein Data Bank and UniProt. BASIL was established in 2015 with a core of 10 faculty members on six campuses, with the support of an educational researcher and doctoral student on a seventh campus. Since that time, the number of participating faculty members and campuses has grown, and we have adapted our curriculum to improve access for all who are interested. We have also expanded our curriculum to include new developments that are appearing in computational approaches to life science research. In this article, we provide a history of BASIL, explain our current approach, describe how we have addressed challenges that have appeared, and describe our curriculum development pipeline and our plans for moving forward in a sustainable and equitable fashion. 

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5. Flexible Implementation of the BASIL CURE

   https://doi.org/10.1002/bmb.21287  

   Roberts, Rebecca; Hall, Bonnie; Daubner, Colette; Goodman, Anya; Pikaart, Michael; Sikora, Arthur; Craig, Paul (August 2019, Biochemistry and Molecular Biology Education)

   Abstract Course‐based Undergraduate Research Experiences (CUREs) can be a very effective means to introduce a large number of students to research. CUREs are often an extension of the instructor's research, which may make them difficult to replicate in other settings because of differences in expertise or facilities. The BASIL (Biochemistry Authentic Scientific Inquiry Lab) CURE has evolved over the past 4 years as faculty members with different backgrounds, facilities, and campus cultures have all contributed to a robust curriculum focusing on enzyme function prediction that is suitable for implementation in a wide variety of academic settings. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):498–505, 2019. 

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