Undergraduate and Fifth-Year Research

Kayleigh Watson worked in Nathan Ahlgren’s lab and assisted Emily Dart, a doctoral student in the lab, with studying the microbial communities of Walden Pond in Concord. Kayleigh collected water samples from the pond, filtered the water, and isolated viruses and cyanobacteria from the samples. In the lab, she experimented to determine the types of media that would exhibit the best cyanobacterial growth, and performed DNA extractions.

In addition, Kayleigh traveled with the research team to Cape Cod, to collect and process water samples from 12 kettle ponds.

DNA methylation is an epigenetic DNA modification that usually results in gene silencing and often plays a role in developmental changes in certain eukaryotes. Past studies attempted to elucidate whether D. discoideum, a eukaryotic social amoeba, uses DNA methylation despite only having a homolog of one DNA methyltransferase, DNMT2. Tayla Cormier’s research has found only 11 methylated sites out of a potential 7.5 million. This summer, she worked to confirm the low-level methylation found in the genome by bisulfite sequencing PCR targeting a cluster of methylated sites on chromosome 4 of D. discoideum.

This summer, Alaina Tabani worked  with fruit flies to analyze the genetic basis of obesity. Alaina grew the flies using their regular food, food with 10 percent coconut oil, and food with 10 percent pig fat. The gut microbiome of the first and second generation of flies grown on the different mediums will be compared to see changes in the microbiota between lean and obese flies. Moreover, analyzing the second generation will also allow the team to see if the gut microbiome composition is passed down from parent to offspring. It is hypothesized that the lean and obese flies will have different gut microbiome compositions. If this is true, preventive strategies can be derived to reduce obesity acquired through inheritance in human populations.

Many aggressive human tumors have an overactive enzyme called PLC-gamma. The Thackeray lab is looking for a new drug to inhibit this protein. Using the fruit fly Drosophila, which has the same gene in its genome, Eugenia Cojocaru screened nine small molecules that are potential inhibitors of PLC-gamma. In the genetically modified strain Eugenia used, such inhibition manifests itself in smaller fly wings, and an increased number of a photoreceptor called R7 in the compound eye. One of the drugs showed an effect on wing area, so Eugenia will examine this drug in further analyses.

Isabella Teixeira focused on the role of FGF signaling during neural development of C. teleta. She cloned several neural marker genes and tested their probe using a staining technique called whole mount in situ hybridization (WMISH). This allowed her to record the expression pattern of marker genes during different stages of development. She also completed several drug experiments with SU5402, an inhibitor of Fibroblast Growth Factor Receptors (FGFRs). An immunostaining technique, using Hoechst, Tubulin and 5’HT-lir, as well as WMISH, using eval1, were completed to analyze if blocking FGFR had an impact on the neural development of the animals.

During the summer, Sadie O’Neil worked in the Foster-Baker Lab, with the goal of raising the newest generation of three-spined stickleback fish. In the beginning of the summer, the lab received thousands of fertilized three-spined stickleback eggs from its team in Alaska. For two months, the team hatched the eggs, changed the water surrounding the fry (baby fish) every three days, and fed every single jar thousands of brine shrimp every morning and every night. Over the year, these fish will grow into the next generation of specimens used for evolutionary research in the Foster-Baker Lab.

Rafael Levin interned at the Proteomics Core Unit at the Spanish National Cancer Research Center (CNIO). This large-scale study focuses on the identification, quantification, and functional analysis of the proteome, which is the set of proteins expressed in a cell at a point in time. Rafael  worked on optimizing a protocol that is used for the chemical tagging of amino acids, an essential step in the sample prepping process. This will lead to a more efficient use of expensive reagents, therefore obtaining better quality data.

This summer, Nicole Minghella worked on raising stickleback fry. Once these fish are adults, lab members will use them for behavioral studies, examining schooling patterns. As part of caring for the fry, Nicole examined stickleback eggs under a microscope to monitor their development, feeding them brine shrimp twice a day and changing their water every three days. She also assisted with experiments on adult stickleback, studying their behavior when they were exposed to different predator cues.

During the summer, Slesha Shrestha studied the effects of excess dietary fat and sugar on the gut microbiome and liver fibrosis in LDLR-/- mice. It The project’s main goal was to see Ii there was any relationship between the excess dietary intake of fat and sugar, changes in gut microbiome, dyslipidemia, and systemic inflammation.

During the summer, Noa Petler investigated whether fats or sugars have a more significant effect on dyslipidemia and systemic inflammation in humans. Noa used mice with metabolisms made to simulate human ones, and looked at three different diets with different proportions of fats and sugars in each. Focusing on the cardiac area, Noa conducted ELISAs and colorimetric triglyceride assays to quantify cytokine levels in the cardiac tissue and triglyceride levels in the serum. In addition to this, Noa stained and imaged sections of the aortas with Picro Sirius Red dye and Hematoxylin and Eosin dye in order to investigate plaque buildup and the effects of inflammation.

As part of her summer research, Hannah Cooper studied the seed dispersal patterns of desert ants in Tucson, Ariz. She was responsible for collecting ants in the field and, back in the lab, observing which seeds they preferred back. The study aims to determine whether ants prefer grass seeds or woody plant seeds, and how this preference may alter the ecology of the desert because of where the ants disperse the seeds.

G quadruplex (G4) DNA acts as a roadblock in DNA replication potentially resulting in oncogenes — an overload of G4 DNA could lead to apoptosis of cells. There is an important balance between G4 DNA and normal DNA.  Mariah Torcivia worked with researchers to test the effects of small molecule drugs on the amount of G4 DNA present in the nuclei of cell from a human cell line derived from a lung cancer. The projects aims to bring more effective cancer drugs into clinical trials.

Katie Crowley has been working in the Stickleback lab, studying the evolution of both the fish and the parasite found within them. In the summer, she traveled to Alaska, where she raised the fry to be used for future research.

This summer, Nicolina Braccio worked on identifying which cis-regulatory modules (CRMs) regulate and promote Twin of Eyeless (TOY) expression in Drosophila melanogaster. The TOY gene is responsible for controlling eyesight in Drosophila. Scientists study the gene due to its homologous relationship with the Pax-6 gene, which regulates eyesight in humans. CRMs are DNA sequences that allow transcription factors to bind to and regulate a gene. By understanding which CRMs regulate TOY in Drosophila, scientists could apply this knowledge to the Pax-6 gene in humans.

Kyung Song worked on a project that aims to elucidate the general function of the IAB5 enhancer at the sequence and molecular level. This summer, Kyung tried to discover expression patterns of target genes for analyzation of enhancer elements’ spatiotemporal functions. In addition, Kyung sought to pinpoint the transcription factor landscape of the cell lines. 

This summer, Regan Conrad created an image processing pipeline in Matlab and ImageJ that could be used to quantitatively analyze images of Drosophila melanogaster taken on a microscope. The D. melanogaster embryos were stained during in-situ hybridization for TOY (twin of eyeless) gene expression. The team took images of the embryos, then rotated, resized, and normalized the images as part of data extraction.

Liz Tchantouridze worked to develop a math model that would help her research team better understand regulation of the twin of eyeless (TOY) gene in Drosophila. The gene controls eye development in the fruit fly.