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, Bridgewater State 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.

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.

Prooxidant effects on C. elegans
Joshua Gray, United States Coast Guard Academy
Students assess the effect of novel prooxidant or redox cycling compounds on C. elegans. Over the first five laboratory periods, students learned culturing methods for C. elegans and several experimental techniques such as LD50, lifespan, chemotaxis, rigor mortis, and quantitative real-time RT-PCR assays, while developing a novel research hypothesis focused regarding the mechanism of action of their compound. After peer reviewed proposal presentations, students spend subsequent weeks designing and performing experiments, trouble-shooting difficulties they encountered with their peers, researching and applying additional experimental techniques from the literature, and reporting their findings each week at the beginning of each lab period, mimicking a lab meeting format. The final presentation highlights outcomes from the semester and proposed plans for future experiments.

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.

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

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.

Erin Rehrig, Fitchburg State University

The MCC project
Students will construct mutants of the enzyme malate dehydrogenase in order to study structure-function relationships of the enzyme.