Protein Evolution
Scott Cooper, University of Wisconsin-La Crosse
In this activity students explore the evolution of proteins by comparing 2D and 3D alignments of orthologs and paralogs.

Molecular Techniques in Ecology and Evolution
steven kimble, Towson University
Microbiomes are the huge communities of microbes that live in and on host organisms, and are typically intimately involved with the host in myriad ways, including in immune, metabolic, and behavior functions. As ecosystems, these microbiomes are sensitive to changes in their environments, such as host aging, disease state, or contact with pollutants. They could therefore be used as bioindicators of host health, but the membership and functions of microbiomes are poorly understood in almost all creatures, especially reptiles and amphibians. In this CURE we use modern field, laboratory, and bioinformatic tools to describe and analyze the microbiomes of non-model organisms such as frogs, turtles, and reef fish.

Reconstructing the Evolution of Cauliflower and Broccoli
Sarah Deel, Carleton College; Susan Singer, Carleton College; Debby Walser-Kuntz, Carleton College
This laboratory exercise focuses on the connections between plant genetics and morphology.

Searching Genbank
Jeff Bell, California State University-Chico
An active problem-based assignment that uses the Genbank database to teach the basics of molecular biology and molecular evolution

MCC: Malate Dehydrogenase CUREs Community
Ellis Bell, University of San Diego
The Malate Dehydrogenase CUREs Community (MCC) project is designed to facilitate the adoption of effective, protein‐centric, Course Based Undergraduate Research Experiences (CUREs) into teaching labs at a wide variety of undergraduate serving institutions. (Primarily Undergraduate Institutions, Research Intensive Universities and Community Colleges) MCC coordinates and conducts pedagogical research into two major features of CUREs:1) their duration (whole semester versus 5‐6 week modules incorporated into a lab class), and 2) the impact of scientific collaboration between institutions (a key aspect of much modern research). Using validated assessment tools we seek to establish their effects on student confidence, persistence in STEM, and ability to design research experiments and interprete data. To facilitate faculty adoption of CURE approaches the project provides a number of resources. These focus on a variety of research areas related to Malate Dehydrogenase including mechanisms of catalysis and regulation, adaptation and evolution, cofactor specificity, folding and stability and interactions in metabolons. Resources include biologics, experimental protocols and assessment tools. The project also coordinates interactions between courses at different institutions to allow incorporation of scientific collaboration into CUREs. These collaborations also facilitate the use of more sophisticated experimental approaches and broaden the experimental scope of the CUREs.

Genomics Education Partnership
Laura Reed, The University of Alabama; Katie Sandlin, The University of Alabama
The goal of the Genomics Education Partnership is to provide opportunities for undergraduate students to participate in genomics research. GEP is a collaboration between a growing number of primarily undergraduate institutions, the Biology Dept and Genome Center of Washington University in St. Louis, and the Biology Dept at the University of Alabama. Participating undergraduates learn to take raw sequence data to high quality finished sequence, and to annotate genes and other features, leading to analysis of a question in genomics and research publication. GEP organizes research projects and provides training/collaboration workshops for PUI faculty and teaching assistants.

Molecular Parasitology
Swati Agrawal, University of Mary Washington
In Spring 2021, we piloted a mini-CURE where student groups from University of Mary Washington and Georgia State University collaboratively completed research projects as part of a research-intensive course on Molecular Parasitology. The benefits of this approach were immediately obvious as students interacted across institutions, learned from each other's disciplinary expertise while informing their own research with data collected by their collaborators.

Design2Data
Ashley Vater, University of California-Davis
The D2D program is centered around an undergraduate-friendly protocol workflow that follows the design-build-test-learn engineering framework. This protocol has served as the scaffold for a successful undergraduate training program and has been further developed into courses that range from a 10-week freshman seminar to a year-long, upper-division molecular biology course. The overarching research goal of this CURE probes the current predictive limitations of protein-modeling software by functionally characterizing single amino acid mutants in a robust model system. The most interesting outcomes of this project are dependent on large datasets, and, as such, the project is optimal for multi-institutional collaborations.

Genome to phenome: DNA-protein interactions involved in butterfly wing colored development
Michelle Borrero, University of Puerto Rico
We are interested in understanding the genomic mechanisms underlying morphological differences within species. We will use the wing color pattern of Heliconius erato as a model. We have developed a Course-based undergraduate research experience (CURE) that will engage undergraduate biology majors in the identification and purification of transcription factors in butterfly wing development. Through this experience students will be able to use the knowledge and concepts from the literature to make and defend decisions, explain the role of DNA binding proteins in the genome to phenome relationship and recognize the application and utility of the techniques used in the research for their career development.

Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction
Wade Powell, Kenyon College
This laboratory exercise is a guided discovery of computational methods for comparing protein sequences. Students perform BLAST searches of reported CYP1A sequences and construct phylogenetic trees using CYP1A amino acid sequences from various vertebrate species, especially those with multiple CYP1A paralogs.