A survey on faculty perspectives on the transition to a biochemistry course‐based undergraduate research experience laboratory

Abstract

It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for in silico prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins "of unknown function" in the Protein Data Bank, many of which resulted from the Protein Structure Initiative. Students have used the ProMOL plugin to the PyMOL molecular graphics environment along with BLAST, Pfam, and Dali to predict protein functions. As young scientists, these undergraduate research students wanted to see if their predictions were correct and so they developed an approach for in vitro testing of predicted enzyme function that included literature exploration, selection of a suitable assay and the search for commercially available substrates. Over the past two years, a team of faculty members from seven different campuses (California Polytechnic San Luis Obispo, Hope College, Oral Roberts University, Rochester Institute of Technology, St. Mary's University, Ursinus College, and Purdue University) have transferred this approach to the undergraduate biochemistry teaching laboratory as a Course-based Undergraduate Research Experience. A series of ten course modules and eight instructional videos have been created (www.promol.org/home/basil-modules-1) and the group is now expanding these resources, creating assessments and evaluating how this approach helps student to grow as scientists. The focus of this manuscript will be the logistical implications of this transition on campuses that have different cultures, expectations, schedules, and student populations. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):426-436, 2017.

Anticipated learning outcomes for a biochemistry course‐based undergraduate research experience aimed at predicting protein function from structure: Implications for assessment design

“…This study focuses on a novel biochemistry CURE, developed as part of the BASIL project and implemented at multiple institutions. The BASIL CURE consists of 10 protocols (listed in Table , Column 1 and described in detail in references ) which involve a combination of computational and wet lab biochemical techniques to elucidate the function of proteins whose structures have been solved but their functions have not been confirmed. The CURE was modeled after the work done by researchers in the field to elucidate the function of proteins deposited in the Protein Data Bank [e.g.…”

“…CURE activities have demonstrated positive impacts on many different factors, across academic levels and scientific disciplines, ultimately leading to student persistence in science . Some recently published protein biochemistry CURE examples include: studying protein mutations in tumor and cancer‐related proteins , investigating the effect of mutating non‐conserved protein regions , and characterizing proteins of known structure but unknown function . Some CUREs have been purposely designed in a modular fashion to allow for different implementation strategies .…”

“…Some recently published protein biochemistry CURE examples include: studying protein mutations in tumor and cancer‐related proteins , investigating the effect of mutating non‐conserved protein regions , and characterizing proteins of known structure but unknown function . Some CUREs have been purposely designed in a modular fashion to allow for different implementation strategies . One such example is the biochemistry CURE developed by the Biochemistry Authentic Scientific Inquiry Laboratory (BASIL) as a multi‐institutional collaborative project, described by Craig et al .…”

“…One such example is the biochemistry CURE developed by the Biochemistry Authentic Scientific Inquiry Laboratory (BASIL) as a multi‐institutional collaborative project, described by Craig et al . . The BASIL CURE is a modular CURE focused on assigning function to proteins of known structure but unknown function.…”

Lessons from my undergraduate research students

“…Trevor Anderson and Stefan Irby from Purdue University helped me prepare some questions that focused on the logistics of the project. The results are summarized here, and the full details have been published (15).…”