An official website of the United States government
Students often struggle with visualizing protein structures when working with two-dimensional textbook and lecture materials, so introducing them to 3D visualization software developed by and for structural biologists offers them a unique opportunity to work with authentic data while furthering their spatial reasoning skills and understanding of molecular structure and function. This article presents an active learning virtual laboratory in which students use authentic structural biology data to investigate the effects of both hypothetical and real-world SARS-CoV-2 mutations on the virus’s ability to bind to human ACE2 receptors and infect a host, causing COVID-19. Through this activity, introductory-level college students or advanced high school students gain a better understanding of applied biology, such as how vaccines and treatments are designed, as well as strengthening their understanding of core disciplinary concepts, such as the relationship between protein structure and function and the central dogma of molecular biology. While there were challenges during the pilot phase of activity development due to COVID-19 restrictions, students in the pilot groups came away from the activity with deeper understanding of the relationship between proteins and amino acid sequences and a new appreciation for the ways researchers design treatments for and study viruses.
more »
« less
Virtual Boot Camp: COVID ‐19 evolution and structural biology
COVID‐19‐related campus closures necessitated invention of an intensive online learning experience that introduced students to Structural Bioinformatics. The program engaged 33 students from 11 different institutions ranging from high school to graduate school. The objectives of the intensive, 1‐week Boot Camp focused on helping students build a foundation for studying the SARS‐CoV‐2 Main Protease (Nsp5) to understand how the protein evolved during the first 6 months of the COVID‐19 pandemic by exploring amino acid sequence and 3D atomic‐level structure using various structural bioinformatics tools. Participants analyzed how the protein changed as the virus spread around the world, comparing Nsp5 from the original viral isolate to 161 unique sequence/structure variants.
more »
« less
- PAR ID:
- 10187212
- Date Published:
- Journal Name:
- Biochemistry and Molecular Biology Education
- ISSN:
- 1470-8175
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The COVID‐19 pandemic brought to light the continued issues in access to research opportunities. Many of our undergraduate students at research‐intensive institutes lost their ability to go into labs to gain experience. However, students at most smaller colleges and universities faced these challenges to bring research opportunities to students long before the pandemic. Thus, our lower‐cost community colleges and higher education institutes with diverse students lack equity when it comes to research investments. This highlights the need for bringing research into diverse institutes using novel approaches. Over the past ten years, our team has built a strategy for integrating genomic and molecular bioinformatics tools into undergraduate opportunities. Developing bioinformatics training material, professor training opportunities, summer research opportunities, and organized large scale research projects, our team has developed a distributed research network. Our goal is to bring genomic and bioinformatic literacy to early undergraduate training to increase STEM retention while improving research equity issues. Having students work on characterizing challenging clinical variants, known as Variants of Uncertain Significance (VUS), brings novel research projects to students while filling the growing needs of clinical variant characterizations. At the core training, we focus on bringing tools to professors and instructors, lowering the initiation efforts to performing bioinformatics research. These include the optimization of protein homology modeling, molecular dynamic simulations through analysis with a few mouse clicks (or two lines of code for Linux users), 3D protein printing, deep evolutionary profiling with hundreds of species using user‐friendly tools, assessing expression from the NCBI SRA, and integrating genomic databases (GTEx, Human Protein Atlas, Geno2MP, gnomAD, Comparative Toxicogenomics Database, PharmGKB, Open Targets Genetics). Once in the hands of professors, they have implemented these tools into independent research projects for their students, coursework design such as bioinformatics classes, and research clubs. Over the past ten years, we have thus impacted hundreds of students with these tools. This can best be highlighted by the student's successes integrating the tools into publications on the NMDA receptors (PMID:34726335), CFTR database for cystic fibrosis (PMID: 32734384), NAA10 variant analysis (PMID: 33335012), multiple sclerosis genetics (PMID: 31482761), COVID‐19 immune response (PMID:34335605), the SARS‐CoV‐2 evolution/structural dynamicome (PMID: 32587094), CCR5 role in diverse phenotypes and bioethics (accepted), and SOX gene developmental biology (in review). Thus, the development of tools and strategies and the distribution of research projects can reach students and faculty at any institute, bringing equitable research opportunities to those who traditionally do not have many opportunities.more » « less
-
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.more » « less
-
Flapan, Erica (Ed.)Since 2012 the University of North Carolina at Greensboro (UNCG) has held an annual summer school in computational number theory aimed at first- and second-year graduate students. In 2020 we were in charge of running the school, entitled An Introduction to Ergodic Theory via Continued Fractions. Given the ongoing COVID-19 outbreak, we decided, in mid-March 2020, to run the school entirely online. In this article we will describe how we carefully tried to preserve as many desirable features of an intensive summer school experience as we could online. Since surveys indicated that the participants were uniformly pleased with their experiences, we hope that our account will help others who wish to organize similar online events.more » « less
-
Importance Adverse outcomes of COVID-19 in the pediatric population include disease and hospitalization, leading to school absenteeism. Booster vaccination for eligible individuals across all ages may promote health and school attendance. Objective To assess whether accelerating COVID-19 bivalent booster vaccination uptake across the general population would be associated with reduced pediatric hospitalizations and school absenteeism. Design, Setting, and Participants In this decision analytical model, a simulation model of COVID-19 transmission was fitted to reported incidence data from October 1, 2020, to September 30, 2022, with outcomes simulated from October 1, 2022, to March 31, 2023. The transmission model included the entire age-stratified US population, and the outcome model included children younger than 18 years. Interventions Simulated scenarios of accelerated bivalent COVID-19 booster campaigns to achieve uptake that was either one-half of or similar to the age-specific uptake observed for 2020 to 2021 seasonal influenza vaccination in the eligible population across all age groups. Main Outcomes and Measures The main outcomes were estimated hospitalizations, intensive care unit admissions, and isolation days of symptomatic infection averted among children aged 0 to 17 years and estimated days of school absenteeism averted among children aged 5 to 17 years under the accelerated bivalent booster campaign simulated scenarios. Results Among children aged 5 to 17 years, a COVID-19 bivalent booster campaign achieving age-specific coverage similar to influenza vaccination could have averted an estimated 5 448 694 (95% credible interval [CrI], 4 936 933-5 957 507) days of school absenteeism due to COVID-19 illness. In addition, the booster campaign could have prevented an estimated 10 019 (95% CrI, 8756-11 278) hospitalizations among the pediatric population aged 0 to 17 years, of which 2645 (95% CrI, 2152-3147) were estimated to require intensive care. A less ambitious booster campaign with only 50% of the age-specific uptake of influenza vaccination among eligible individuals could have averted an estimated 2 875 926 (95% CrI, 2 524 351-3 332 783) days of school absenteeism among children aged 5 to 17 years and an estimated 5791 (95% CrI, 4391-6932) hospitalizations among children aged 0 to 17 years, of which 1397 (95% CrI, 846-1948) were estimated to require intensive care. Conclusions and Relevance In this decision analytical model, increased uptake of bivalent booster vaccination among eligible age groups was associated with decreased hospitalizations and school absenteeism in the pediatric population. These findings suggest that although COVID-19 prevention strategies often focus on older populations, the benefits of booster campaigns for children may be substantial.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1002/bmb.21428
