Using NSF's NEON Data in an Undergraduate Ecology CURE on the Ecological Impacts of Global Climate Change part of CUREnet:CURE Collection
We live in a time where we can see a very real need for a basic understanding of ecological terminology, concepts, and methodologies to improve public policy and other ecological problem-solving decisions, especially in light of global climate change. Across the field, there is a major push to incorporate computational thinking and an understanding of human social systems throughout the science curriculum. In ecology and other STEMM fields, basic programming and coding skills have become essential and marketable, as has the ability to mine and analyze large data sets.In this semester-long CURE, students individually develop and answer their own ecological research question using a selection of publicly available datasets from the expansive NSF NEON data repository. Generally, at the beginning of the course the instructor selects several data products from a specific geographic region. After gaining familiarity with the NEON project through videos, a NEON data tutorial, and a case study, students also use these curated NEON data products to begin forming their independent research projects. Most students ultimately incorporate other data products either from NEON or other databases into their final research projects. Students use mostly R to download, wrangle, and analyze their data. The instructor assumes no prior knowledge of R or coding at the beginning of the course. Throughout the semester, students complete mini-assignments and tutorials which introduce them to the necessary coding skills to download, clean, analyze, and visualize their chosen data products. Additionally, students are provided with a wide range of free resources, including videos, tutorials, and the free online textbook Passion Driven Statistics to help them master the skills they need to complete their individual research projects. During weekly in-class one-on-one meetings with the instructor, students work to identify, collect, and analyze data that would address an existing hypothesis/ problem in the field of ecology and global climate change. Ultimately, students present their findings to the larger campus community during the annual undergraduate research day at our institution.

Genome to phenome: DNA-protein interactions involved in butterfly wing colored development part of CUREnet:Institutes:University of Puerto Rico:Examples
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.

Exploring the Structure-Function Relationship in RNA Biochemistry part of CUREnet:Institutes:CU Denver:Examples

Genome Solver: Microbial Comparative Genomics part of CUREnet:CURE Collection
Genome Solver began in 2011 as way to teach Bioinformatics tools to undergraduate faculty. As part of the Genome Solver project as a whole, we developed a Community Science Project (CSP) for faculty and students to join. The CSP explores horizontal gene transfer (HGT) between bacteria and the phages that infect them. Students get involved in this project and develop testable hypotheses about the role HGT between bacteria and phages play in microbial evolution. Our own work has demonstrated that undergraduates can produce publishable data using this approach. We invite faculty and their students to participate in the search for additional evidence of this type of HGT by investigating the vast wealth of phage and bacterial sequences currently in databases. All that is needed is a computer, an Internet connection, and enthusiasm for research. Faculty and students can work on an organism of interest or we can help them pick organisms to explore these phenomena. By pooling all of the information from a variety of small projects under the umbrella of the Genome Solver CSP, we will be able to better understand the role of HGT in bacterial evolution.

CREARE: Coral Response to Environment Authentic Research Experience part of CUREnet:CURE Collection
There is growing body of evidence to support that students who directly experience authentic scientific research are more likely to continue onto advanced degrees and careers in Science, Technology, Engineering and Mathematics (STEM). In an effort to introduce more students to the benefits of scientific research we have drawn on an ongoing research project aimed at understanding how Corals Respond to the Environment (CRE) to develop an interdisciplinary laboratory course based on Authentic Research Experiences (ARE). A small cohort of undergraduate students enrolled in a semester-long course, entitled CREARE, perform biochemical experiments in the laboratory, analyze environmental data by R statistical software and prepared a report modeled after a research manuscript to present their work. The impact of CREARE on student learning gains and attitudes towards science is being measured, as is the impact of CREARE on participants' career choices and retention in STEM. This multidisciplinary research program addresses the impact of climate change on the health of a critically endangered coral species, ultimately leading to a better stewardship of this invaluable resource. Furthermore, CREARE offers a unique experience for students, one that may serve as a model for the development of more research-based courses, leading to improved retention in our STEM departments.

Histology CURE Lab in Breast Cancer part of CUREnet:Institutes:Hampton University:Hampton CURE Examples

Using Artificial Intelligence in Introductory Programming Courses part of CUREnet:CURE Collection
This CURE is part of the introductory programming course in the Computer Science major at our university. When AI gained the ability to generate computer code, it became apparent that this would have major impact on how programming courses were going to be taught. In addition to code generation and auto-completion during manual development, it can be used for bug detection and testing, generating internal and external documentation, translating between different programming languages, refactoring code, and others. Not all these uses are relevant to introductory programming classes, but students can start building their skills using AI in this class.In this CURE, students learn how to evaluate AI engines objectively with regard to their ability to produce simple computer programs appropriate for the level of this course. Students can use the AI engines they themselves select, free or for pay; they can construct their own measurement instruments, simple or complex; and they use simple statistical analysis in Excel to evaluate the results. Finally, students submit their reports in a format used by an academic conference which introduces them to a professional level of research.

Karst Study Using Geophysics at Bracken Bat Cave Preserve​ part of CUREnet:Institutes:Ad-Hoc CURE Institutes:Examples
South Central Texas depends on deep seated aquifers to maintain a water supply for over 5 million people. Much of this water supply is recharged through karst features in the Texas Hill Country. Understanding the features on a property helps determine the appropriate level of development, but geophysical methods have limitations on interpreting feature size. Students in this project built on previous work to examine the error of two common geophysical methods when detecting humanly accessible shallow karst features. They gained skills in site analysis using spatial software and high-resolution GPS collection, field work planning, data collection and analysis.

Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug Design part of CUREnet:CURE Collection
An Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug DesignEach class during the semester has components focused on a) the project and b) foundational concepts of introductory chemistry that they see in the lecture sections. The project features all the standard elements of a CURE, Relevance, Scientific Background, Hypothesis Development, A Proposal, Experiments & Teamwork, Data Collection and Documentation, Analysis and evidence based conclusions, and a formal presentation of the overall project..This CURE is taught in a standard 4 hour lab taught once a week throughout the semester (14 weeks)Each class during the semester has components focused on a) the project and b) foundational concepts of introductory chemistry that they see in the separate lecture sections. The project was designed to satisfy the standard Chemistry Lab Learning Goals that all sections of General Chemistry Lab address. The CURE project, threaded throughout the semester, features all the standard elements of a CURE, Relevance, Scientific Background, Hypothesis Development, A Proposal, Experiments & Teamwork, Data Collection and Reproducibility, Data Analysis and evidence based conclusions, and a formal presentation of the overall project..In this CURE section students gain both technical expertise & research experience through the lens of Antimalarial Drug Design. During the semester they develop and present a research project proposal including relevance, scientific background, and hypothesis development. They design and perform experiments using a variety of classic chemistry techniques (titration, kinetics, spectroscopy, molecular modeling) in the context of experiments to explore structure function relationships of potential antimalarial drugs targeted towards a specific enzyme, Malate Dehydrogenase. Students will develop and test research ideas related to novel approaches to target the parasite but not the human host. Based on appropriate data analysis they select key experiments to repeat to establish reproducibility, allowing them to draw evidence based conclusions. At the end of the semester they present all aspects of their project in a final presentation. Each of the three presentations in the course includes peer review and revision prior to the graded presentations and students are provided with extensive rubrics for each presentation.

Bioinnovation Laboratory part of CUREnet:CURE Collection
This CURE introduces students to lab skills used in the bioengineering field as well as the critical business, legal, and ethical components involved in the biotechnology industry and entrepreneurism. During this course, students participate in a research project involving the evaluation of the mesenchymal stem cell (MSC) secretome when cultured on polydimethylsiloxane (PDMS) engineered scaffolds. The driving force behind this research is to understand secretome composition and the use of MSCs for tailored disease-specific treatments and biomaterial applications. Specific research questions and parameters change with each iteration of the course; however, projects begin with student groups selecting an area of regenerative medicine that could benefit from the optimization of stem cell therapy. Students justify the alteration of environmental parameters (such as substrate stiffness, cell density, protein coating, pH, confinement, etc) based on their area of regenerative medicine. For example, students may create a PDMS gel stiffness that mimics "diseased" versus "healthy" liver tissue and evaluate changes in secretome components as a function of these different scaffolds. For all groups, MSC secretome is collected at various time points and evaluated through enzyme-linked immunosorbent assays (ELISAs) to determine the effects of changed environmental parameters on MSC secretion. Collectively, the data helps to build an understanding of how cell secretome changes as a function of the environment and contributes to our growing understanding on the ability to "tune" cells to secrete desired cytokines of interest for stem cell therapy and manufacturing.