Isolation and characterization of antibiotic-producing soil bacteria part of CUREnet:Institutes:NC Central University:Examples
One of the biggest threat in hospitals is the rising cases of people who harbor antibiotic-resistant bacterial strains. Therefore, it is critical to find and characterize novel antibiotics to combat the resistant strains. Most of the antibiotics used in healthcare settings come from anti-biotic producing bacteria and fungi found in the soil. The goal of this CURE will be to isolate antibiotic-producing bacteria and fungi from the soil in the local area, and to determine the chemistry of the antibiotics. An extension of the project will be to determine how the presence of antibiotic-producing microbes affect other organisms resident in the soil, as it is unclear as to why microbes use energy to produce antibiotic factors.

An Arabidopsis Mutant Screen CURE for a Cell and Molecular Biology Laboratory Course part of CUREnet:CURE Collection
This CURE is designed from a crucial component of a chloroplast lipid signaling research project and has been implemented for a cell and molecular biology laboratory course at Michigan State University. The research laboratory generated an engineered plant line producing a lipid-derived plant hormone and mutagenized this line. The research question is "what transporters or receptors are involved in the hormone signaling transduction or perception processes?". Students form research hypotheses based on the research model, design experiments, perform experiments, collect and analyze data, make scientific arguments, and share their findings with the learning community. Specifically, the students culture the mutagenized plant population and select the desired mutant phenotypes, followed by genotyping the mutants and characterizing the mutants by basic biochemical approaches. Mathematics is also integrated into the course design. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they use the core idea of information flow and data they generate in the lab to make claims about their mutant plants and support these claims with evidence and reasoning.

MCC: Malate Dehydrogenase CUREs Community part of CUREnet:CURE Collection
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 part of CUREnet:CURE Collection
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.

Resequencing of Commercial Microorganisms part of CUREnet:Institutes:Community College of Rhode island:Examples
Students choose a probiotic pill or product with labeling that indicates the species and strain of bacteria in the product. Products are chosen so that a high quality reference genome sequence is available on NCBI. After DNA isolation and library preparation, high-quality student samples are pooled for next-gen sequencing on an Illumina MiSeq. The following semester, students in the required bioinformatics course will analyze the FASTQ files from the NGS run with a simple variant call workflow on usegalaxy.org. Then, each student will use a R Shiny app developed for this CURE to convert the VCF output from Galaxy to a FASTA file for an assigned gene in the resequenced genome. Students will complete their research experience by submitting the FASTA file to the NCBI Nucleotide Database.

The Effect of Silver Nanoparticles on Plant Growth and Herbivory part of CUREnet:Institutes:Community College of Rhode island:Examples
In this CURE, students will conduct experiments to determine the effects of silver nanoparticles on plant growth and insect herbivory. Students will synthesize their own nanoparticles and treat Arabididopsis plants with them. After 5 weeks, insects (Pieris rapae, caterpillars) will be placed on plants and insect herbivory will be assessed across treatments. Insects will be weighted before and after feeding assays. Plant growth rates and insect herbivory measurements will be done using digital photography and image analysis using MathLab.

Neurogenetics Laboratory: Mapping a functional circuit for cold nociception in Drosophila part of CUREnet:Institutes:Alabama State University:Examples
Students will work in small groups to identify neural populations that may be involved in the Drosophila larval response to noxious cold. They will use the GAL4/UAS expression system to excite or inhibit neural populations and assess the impact of their manipulation on the larvae's behavioral response to cold. If a relevant neural population is identified, students will then identify (based on current literature) genes that are likely to be involved in neurite development and/or maintenance in that population. They will use mutations and/or RNA interference to disrupt the function of these genes in the population of interest and assess the effect of the disruption on neuronal morphology and larval behavior.

The HICA project part of CUREnet:CURE Collection
In this CURE, inspired by the work of Hoffmann, et al., students prepare mutant Haemophilus influenzae carbonic anhydrase (HICA) proteins. Using PyMOL to visualize the three-dimensional structure of the HICA protein, students choose one or more surface amino acid residues to mutate to histidine residues in order to create a surface histidine cluster that will allow the mutant protein to bind to a nickel affinity column. Using site-directed mutagenesis, recombinant plasmids are constructed and are then used to transform an E. coli expression vector. The mutant HICA protein is overexpressed, cells are lysed, and students load the cell lysate onto Ni-NTA columns and determine the imidazole concentration required to elute the mutant protein. The construction of a library of mutant proteins will allow the development of a general method in which specific surface histidine residues of any protein can be mutated in order to facilitate affinity purification. The Haemophilus influenzae bacterium described herein is a respiratory pathogen that causes meningitis (in its encapsulated form) and mucosal infections such as otitis media, sinusitis and conjunctivitis (in its unencapsulated form). A recent study showed that the carbonic anhydrase enzyme is absolutely required for pathogenesis. Furthermore, expression of the HICA enzyme allows the pathogen to survive in host immune cells (Langereis, et al.). These observations make the study of HICA itself particularly attractive, in addition to the overall goal of contributing to a body of work that will allow the minimal histidine character required for nickel affinity to be ascertained.

Problem Solving for Middle School Teachers part of CUREnet:CURE Collection
The primary goal of this class is for the students to creatively engage in mathematical investigations which provide the opportunity to integrate and apply previously learned mathematical knowledge to non-routine problems. We will examine a variety of strategies and skills that can be used to explore the fascinating world of mathematical problem solving. The course will cultivate students' habits of mind with respect to dissecting challenging mathematical problems for the purpose of solving them, as well as extending them by posing new related problems. Students will be expected to justify their solution methods through both written and oral presentations, demonstrating knowledge of reasoning and proof, mathematical communication, and mathematical connections. Each student will be expected to take an active role in all parts of the class. The assignments and activities are designed to enhance your understanding, appreciation, and practical experience of exploring and solving problems.

Exploring eukaryotic protein structure and post-translational modifications. part of CUREnet:Institutes:Bowie State University:Examples
This CURE will provide opportunity for students to think and act as researchers by using computational, biochemical, and bioanalytical techniques to examine tick antigen proteins. The CURE is designed as a lab for upper-level students who are taking or have taken a one-semester introductory biochemistry course, but two semesters would be even better. It could also be adapted for cell/molecular biology or (bio) analytical chemistry instrumentational analysis labs. It has been taught for classes ranging from 12-24 students. Ticks are notorious vectors of viral, protozoan, and bacterial diseases, including Lyme disease. While an anti-vector vaccine capable of protecting people from diseases transmitted by a particular tick species is an alluring goal, only one such anti-tick vaccine is currently available. This vaccine targets Bm86, a protein from the midgut of Rhipicephalus microplus, a cattle tick. Not only does the vaccine limit parasitism of the cattle by ticks, data suggests that it can also prevent transmission of tick-borne diseases including bovine anaplasmosis and babesiosis. However, similar vaccination approaches have not succeeded thus far against ticks that transmit diseases to humans, and little is known about the antibody response to the antigen, or about the protein itself. Since the protein's structure and function are unknown, the research goal of this CURE is to purify Bm86 using an insect cell/baculovirus expression system and characterize it, including domain structure and post-translational modifications (glycosylation sites). There are homologs to Bm86 in every sequenced tick species examined, and future CUREs will characterize some of the homologs including those in Ixodes scapularis, the tick that is mainly responsible for transmitting Lyme in the eastern US, and Haemaphysalis longicornis, the Asian longhorned tick, a newly-discovered invasive species in the area that also has significant disease-transmitting potential. By understanding the structure and post-translational modifications of this protein, we hope to gain a better understanding of how to make effective anti-tick vaccines, including those for humans, that may prevent transmission of Lyme disease. Importantly, the basic parameters of this CURE can be used to examine other proteins besides tick antigens. For example, during the pandemic, the CURE pivoted from the tick antigen to the SARS-CoV-2 nucleocapsid protein, which was also expressed in an insect cell system. Instead of characterizing glycosylation sites, we characterized phosphorylation sites. It's therefore possible to use this same framework for many different eukaryotic proteins that may be of research interest.