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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. 

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. 

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 these are “orphans,” with high quality structures and pre-cloned expression plasmids available, but no research on their enzymatic function or role in native organisms. The BASIL consortium of undergraduate biochemistry faculty and students seeks to identify functional properties of a subset of these uncharacterized proteins, seeking to unify structure and function relationships. Currently, implementable modules are available for faculty who wish to adopt them, and expected student results will be presented.Support or Funding InformationSupported by NSF IUSE 1709278This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal. 

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 changes in faculty and teaching assistant competence in two areas: effective teaching with structural biology tools and the development of skills in the area of measuring learning gains by students. As we conduct the lab on these different campuses, we will also focus on advantages of our approach and barriers to implementation that exist on each campus, from the level of student acceptance and faculty training, to resources that are needed to changes in the culture at the departmental and institutional levels. As we analyze the feasibility of this approach on other campuses, we will seek input from other potential adopters about their level of interest and the barriers that they anticipate on their campuses. 

Abstract Understanding the molecular evolution of the SARS‐CoV‐2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three‐dimensional structures of SARS‐CoV‐2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID‐19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi‐Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure‐based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.