Resequencing of Commercial Microorganisms
Jessica Kaufman, Endicott College
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.

Characterizing the Aging Process Using Caenorhabditis elegans and Reverse Genetics
Joslyn Mills, Brown University
Using gene silencing (RNAi) in the nemotode C. elegans, students will identify genetic modifiers of proteins with roles in aging by reverse genetics. Specifically, students will analyze the effect of knocking down genes on the level of aging-related proteins tagged with fluorophores (GFP, RFP, etc.). Each group of students will use function-specific RNAi libraries (transcription factors, kinases, etc) already established in our lab. Furthermore, students will evaluate the effect of genetic modifiers on proteostasis and lifespan. In addition to becoming familiar with C. elegans work and appreciating the use of model organisms, the students will master microscopy, genetic crosses, gene silencing, and molecular and biochemical readout assays such as qPCR and immunoblotting.

The Effect of Silver Nanoparticles on Plant Growth and Herbivory
Erin Rehrig, Fitchburg State University
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.

Dental and Retinal Physiology in Rana pipiens
Eddie Hernandez, The University of Texas at San Antonio
There is a paucity of literature regarding the characterization of Rana pipiens (leopard frog) dentition and the visual transduction pathway. The literature shows that both the Maxillary and Vomerine teeth are primarily used for simply griping their prey, suggesting they swallow their prey whole without a defined mastication process. Considering there are different teeth morphologies in the frog dentition, this might suggest a more expansive contribution to the mastication process and more broadly to frog alimentation. Another aspect of R. pipiens with scant literature is retinal organization and visual transduction pathways. Although there are some anatomical and physiological similarities between the eye tunicas of the frog and the human, there are significant differences that might help us understand the neurophysiology of how frogs perceive their environment. This CURE will elucidate new information about frog dental and retinal physiology to reveal more specific contributions of the frog dentition that may facilitate alimentation. Furthermore, the neuroretina may also have a specific cellular organization that might help the frogs perceive their environment in a way not previously known. Comparisons can be made with human dental and visual physiology. Biochemistry analysis might provide further information about the digestive and sensory processes. Characterization of frog dentition morphologies and biochemistry analysis of both the teeth and eye tunicas, will allow for more updated physiology of frog dentition and retinal visual transduction pathways. Retinal physiology research, specifically, may elucidate novel information about the frogs' visual sensory perception for predation and survival.

Population Biology of the Gulls of Appledore
Sarah Courchesne, Northern Essex Community College
For more than 10 years, data has been collected on the breeding population of herring and great black-backed gulls on Appledore Island in Maine. The resulting dataset is massive, including morphometrics, family histories, breeding success, total population, and many other parameters. While a small number of students are able to visit the island each year to assist in data collection and sampling, this CURE democratizes biology research, and invites an entire classroom of students to investigate their own questions. Students will process the most recent set of samples collected the previous summer, performing DNA sexing and blood smear analysis, and will additionally pursue their own research questions regarding either the existing data, the samples, or both.

Cell Biology of Tetrahymena thermophila Mutants
Carolyn Wetzel, Holyoke Community College
Tetrahymena thermophila is a widely used model system for studying eukaryotic cell biology. In collaboration with a lead researcher at a different institution, students in this CURE will characterize mutants of Tetrahymena to screen for possible effects of different mutations on basic cell functions such as cell morphology, cilia action, phagocytosis, growth and development, energetics, and response to different stimuli. Student results will be sent to the lead researcher to be incorporated into their larger project and it is expected that any significant student contribution will lead to authorship or acknowledgement in a publication.

Biochemistry of Crithidia fasciculata
Amy Greene, Albright College
Students in my second-semester biochemistry lab will study the biochemistry of the flagellated parasite Crithidia fasciculata. Students in Paul Ulrich's CURE at Georgia State generate C. fasciculata cell lines overexpressing putatively mitochondrial proteins with GFP tags. The goal of my CURE is for students to design experiments study the biochemistry of these cell lines, giving us more information about the structure and function of mitochondrial proteins in this poorly-studied parasite.

Squirrels in the City: Urbanization in a Changing World
Christopher Thawley, University of Rhode Island
Our planet is undergoing a variety of changes due to human activity, including the expansion of cities across landscapes. However, urban environments are not wastelands but functioning ecosystems where organisms encounter a variety new conditions and potential challenges. One way that animals can respond to living in cities is by changing their behaviors. In this course, we will conduct an original research project exploring whether squirrels that live in urban habitats have changed their behaviors in predictable ways.

Spicing things up: Implementation of a CURE to investigate the antimicrobial properties of spices on six bacterial species
Heather Townsend, Community College of Rhode Island
I issue students six bacterial species for use. I have students start the semester understanding primary literature and how to find sources, plagiarism, and how to use citations. They must then pick a spice (one per group) using literature, meaning they have to research that a particular spice has been shown to have antimicrobial properties. Once selected they do a series of dilutions and finally test the dilutions on the six bacterial species. All groups must use the entire class data in their discussion along with the historical data from previous semesters. They end in designing a poster which they finally present at a poster presentation open to the college.

Using Polymerase Chain Reaction to Investigate Food
Frances Turner, Howard Community College