BioEd Summit 2024 - Team Projects

Team Just - Franklin:  The importance of personalized genomics in breast cancer diagnosis and treatment: A case study involving the androgen receptor gene

In Triple-Negative Breast Cancer (TNBC), the absence of Androgen Receptor (AR) expression, alongside estrogen receptor (ER), progesterone receptor (PR), and HER2, defines the aggressive "quadruple negative" subtype. AR-negative TNBC, particularly prevalent among African American women, is associated with a poorer prognosis due to enriched basal and immune signatures. This case study, designed for high school and undergraduate biology students, highlights the importance of including AR status in breast cancer classification. AR acts as a critical prognostic marker and a potential target for immune-based therapies. Utilizing NCBI tools such as ClinVar, PDB, BLAST, PubMed, iCn3D and GEO databases can help students explore AR’s role in TNBC and guide the development of more personalized and effective treatment strategies.

Team Members:

• Nik Tsotakos, Ph.D. - Penn State Harrisburg (Team Lead)
• Antonio Colom, Ph.D. - Interamerican University of Puerto Rico, Metropolitan Campus
• Morgan D'Ausilio, Ph.D. - The Pingry School
• Pradip Misra, Ed.D. - Bagdad Unified School District
• Deirdre O'Mara, B.A. - The Pingry School
• Nirmal Singh, Ph.D. - MassBay Community College
• Ning Sui, Ph.D. - North Carolina State University
• Shweta Tripathi, Ph.D. - Tuskegee University

Team Dayhoff:  Molecular basis of Insulin Receptor function using NCBI tools

Students that have successfully completed a majors level introductory biology course or equivalent will explore the structure and evolutionary relationships in the insulin receptor while being introduced to the genetic basis of disease. This exercise is intended to be completed as a guided case study completed in a 3 hour lab, distributed across lectures or hybrid between in person and self-directed work. NCBI resources utilized in this activity: iCn3D, ClinVar, dbSNP, BLAST, COBALT, Comparative Genome Viewer, NCBI Gene, Structure, NLM Bookshelf, OMIM. Other resources included: PDB, GeneCards, Reactome

Team Members:

• Kelly Vaughan, Ph.D. - King University (Team Lead)
• Kehinde Idowu, Ph.D. - Texas Southern University
• Jeffrey Robinson, Ph.D. - University of Maryland Baltimore County
• Katie Sandlin, M.S. - Genomics Education Partnership / The University of Alabama

Team Carver | Sublime Dynamite:  Using NCBI Tools for high school genetics investigation

The goal of the curriculum package is to provide a more accessible, authentic experience with actual genetic data for 9th/10th grade and AP biology students in high school. We are developing two different lesson plans:
Lesson 1 (for AP Biology Students): Comparative genetics across species, how those differences in biological sequences affect our view of evolutionary relationships. (This activity can be used instead of "AP Biology Investigative Lab 3: The Blast Lab")
Lesson 2 (for 9th/10th grade Biology Students): Comparative genetics within humans, identifying location of mutations and types of mutations by comparing "wild type" genes with mutated genes
NCBI resources used in these activities: Gene, BLAST, COBALT, TreeViewer

Team Members:

• Richard (Jake) Zimny, B.A., M.Ed - The School District of Philadelphia, Pennsylvania (Team Lead)
• Brandon Boswell, B.S. - Broward County Public Schools, Florida
• Mary Knight, B.S., M.Ed - Arlington Public Schools, Virginia

Team McClintock:  In the Weeds: Genomic analysis of glyphosate resistance in crop fields

We have developed an activity that at its core studies the Central Dogma and protein structure and is designed for high school A&P Biology and college Introductory Biology courses, but can be modified for upper level classes including Environmental Biology. This project compares structural and molecular differences between a Roundup (glyphosate)-resistant and a Roundup (glyphosate)-sensitive weed, using Arabidopsis as a model organism. The students will figure out which protein is targeted, identify DNA and amino acid substitutions between the resistant- and sensitive-varietals, and vizualize and predict the impact of the substitution on the protein structure. Then, the students will suggest an alternative herbicide that uses a different pathway to kill the resistant weed. The following NCBI databases are used: PubMed, PubChem, nucleotide BLAST, protein BLAST, and iCn3D.

Team Members:

• Jennifer Schroeder, Ph.D. - Young Harris College (Team Lead)
• Hattie Dambroski, Ph.D. - Normandale Community College
• Marie Montes-Matias, Ph.D. - Union College of Union County, New Jersey
• Michael Peglar, Ph.D. - Northern Virginia Community College, Annandale Campus
• Cynthia Woosley, M.S. - Virginia Highlands Community College

Team Finlay | Flu Fighters:  The ever-evolving need for new flu vaccines 

The goal of this project is to help students learn how vaccinations in general function and how antigen sequence/structure affects vaccine efficacy. This project is modular, to allow instructors flexibility in choosing the length of the project and the target audience. By choosing to do only 1 module or 2-3 modules, the project can be tailored to either early-stage undergraduate students or late-stage undergraduate students.
In Part 1, students will focus on hemagglutinin subtype H1, the subtype targeted by current influenza vaccines. Students will align the amino acid sequences of H1 hemagglutinin variants to understand the concept of antigenic drift. Students will further look at the 3D protein structure of H1, and note the regions of variability how that might influence vaccine effectiveness.
In Part 2, students will compare compare H1 amino acid sequence with the H5 subtype (a subtype found in an avian influenza virus), and discuss the potential of current flu vaccines against H5.
In Part 3, students will dive deeper into the concept of antigenic drift, extrapolate on the knowledge from Parts 1 and 2 to explore amino acid sequences of several measles hemagglutinin proteins, and make the connection to why we do not require new measles vaccines periodically as we do for the flu.
NCBI resources used in this project:  NCBI Protein database, COBALT, iCn3D

Team Members:

• Heather Patterson, Ph.D. - University of Alabama at Birmingham (Team Lead)
• Gabriel (Gabe) Guzman, Ph.D. - Triton College
• Ferdinand Nanfack-Minkeu, Ph.D. - College of Wooster
• Kari Severson, Ph.D. - Rockford University
• Ifrah Shahi, Ph.D. - University of Pennsylvania / Children's Hospital of Philadelphia

Team Uchida:  A Tale of Two Diabetes

The goal of this activity is for introductory genetics college students to understand that most human phenotypes are controlled by genes at multiple loci. This is also adaptable for more advanced, independent study and for inclusion in related course topics like Physiology, Microbiology, etc.
Students will use NCBI databases to explore gene variants implicated in Type 2 Diabetes and evaluate gene characteristics such as pathogenicity, type of mutation, 3D structures. Although this activity is designed for Type 2 Diabetes, it can easily be adapted to other diseases/phenotypes.

Team Members:

• Natasha (Natalie) Minkovsky, Ph.D. - Community College of Baltimore County (Team Lead)
• Kaitlin Bonner, Ph.D. - St. John Fisher University
• Cathy Dobbs, Ph.D. - Joliet Junior College
• Karla Fuller, Ph.D. - Guttman Community College - CUNY
• Lia Walker, Ph.D. - Chowan University

Team Project Curricular Materials Disclaimer

The curricular materials, accessible on GitHub, are the creation and work-product of each particular team. We welcome you to explore and consider adoption of these curricula for use in your own teaching efforts. However, please be aware that NCBI does not "own" these nor do we provide support for them. We encourage you to contact a member of the team if you have any specific questions.