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.
Implementing the CURE: Combining Wet-Lab Protein Biochemistry with Computational Analysis to Provide Gains in Student Learning in the Biochemistry Teaching Lab
Most undergraduates studying biochemistry and molecular biology get their broadest exposure to wet-lab techniques in protein and nucleic acid chemistry (and, increasingly, computer/visualization) in their upper-level laboratory courses. These tend to be juniors and seniors with well-defined career goals. Some of these students will have already have a research background in a traditional one-to-one (or one-to-few) research mentoring setting, for example a summer research program. This approach has proved effective at increasing student learning and persistence in the sciences. At the same time, extended full-time PI-directed research is limited in the number of students served, and can even present a barrier. To broaden the impact of teaching through research, many practitioners have adopted a CURE, or Course-based Undergraduate Research Experience, approach.This presentation reports on “BASIL” (Biochemical Authentic Scientific Inquiry Laboratory), a team of faculty who have worked to bring computational and wet-lab protein science to the biochemistry teaching lab. Together, we have developed a protein biochemistry CURE to determine enzymatic function of proteins of unknown activity. This work leverages the results of the Protein Structure Initiative, a fifteen-year NIH-funded effort which concluded in 2015 with the publication and distribution of more than 5000 previously uncharacterized proteins. The great majority of more »
- Award ID(s):
- 1709278
- Publication Date:
- NSF-PAR ID:
- 10071714
- Journal Name:
- The FASEB journal
- Volume:
- 32
- Issue:
- 1
- Page Range or eLocation-ID:
- supplement
- ISSN:
- 0892-6638
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We are seeking to incorporate authentic inquiry into an undergraduate biochemistry lab course. Students on six campuses are combining computational (“in silico”) and wet lab (“in vitro”) techniques as they characterize proteins whose three dimensional structures are known but to which functions have not been previously ascribed. The in silico modules include protein visualization with PyMOL, structural alignment using Dali and ProMOL, sequence exploration with BLAST and Pfam, and ligand docking with PyRX and Autodock Vina. The goal is to predict the function of the protein and to identify the most promising substrates for the active sites. In the wet lab, students express and purify their target proteins, then conduct enzyme kinetics with substrates selected from their docking studies. Their learning as students and their growth as scientists is being assessed in terms of research methods, visualization, biological context, and mechanism of protein function. The lab course is an extension of successful undergraduate research efforts at RIT and Dowling College. The modules that are developed will be disseminated to the scientific community via a web site (promol.org), including both protocols and captioned video instruction in the techniques involved. Over the course of the project, we will also be following changesmore »
-
Responding to the need to teach remotely due to COVID-19, we used readily available computational approaches (and developed associated tutorials (https://mdh-cures-community.squarespace.com/virtual-cures-and-ures)) to teach virtual Course-Based Undergraduate Research Experience (CURE) laboratories that fulfil generally accepted main components of CUREs or Undergraduate Research Experiences (UREs): Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis, Conclusions, and Presentation1. We then developed and taught remotely, in three phases, protein-centric CURE activities that are adaptable to virtually any protein, emphasizing contributions of noncovalent interactions to structure, binding and catalysis (an ASBMB learning framework2 foundational concept). The courses had five learning goals (unchanged in the virtual format),focused on i) use of primary literature and bioinformatics, ii) the roles of non-covalent interactions, iii) keeping accurate laboratory notebooks, iv) hypothesis development and research proposal writing, and, v) presenting the project and drawing evidence based conclusions The first phase, Developing a Research Proposal, contains three modules, and develops hallmarks of a good student-developed hypothesis using available literature (PubMed3) and preliminary observations obtained using bioinformatics, Module 1: Using Primary Literature and Data Bases (Protein Data Base4, Blast5 and Clustal Omega6), Module 2: Molecular Visualization (PyMol7 and Chimera8), culminating in a research proposal (Module 3). Provided rubrics guide student expectations. Inmore »
-
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.
-
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.
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Publisher's Version of Record
- The DOI is not currently available
