3 students got their hands dirty with scientific research this summer
Research in biology and chemistry: Fungal populations, DNA protective chromatin and plastic ingredients
This summer, three undergraduates get their hands dirty with scientific research: growing mushrooms, studying yeast DNA, and observing the movements of molecules. Immaculata’s biology and chemistry professors have discussed possible research topics with these three students and offer guidance as the students hypothesize, develop and follow research procedures, and collect data. Students gain experience useful for their resumes and refine their career goals and graduate plans.
What types of mushrooms grow in campus compost?
Research student : Sydnie Panetta ’22, major in biology
The project: During composting, microbes and fungi break down solid organic matter into usable material for plant growth. Factors such as the method of composting and the ingredients that go into the compost cause different types of fungal communities to grow.
Biology professor Sister Susan Cronin, IHM, Ph.D., produces compost by stacking leaves, grass, eggshells and plant waste in bins and stirring periodically to promote decomposition. Sydnie used cotton swabs to take samples from the compost bins. She then stamped plaques indicating the growing organisms and incubated the plaques to see which fungal populations would grow.
Initially, Sydnie used cellulose as a growing medium, but she struggled to grow mushrooms on this material consistently. Cellulose, a hard substance that strengthens plant cell walls, must break down for plant material to break down into compost. Sydnie switched to a more general medium of yeast, peptone and dextrose, which provided an ideal environment for the growth of the fungi.
Sydnie extracted fungal DNA from her samples, then performed polymerase chain reactions (PCR), which amplify a small section of DNA into many copies. She will send the DNA to a company for genetic sequencing and can then match the results to DNA in a database to identify fungal populations.
Why is this important: This large project can be used to answer a variety of questions, Sydnie says, such as how different fungal species interact and whether temperature or location affects the rate of decay or the fungal communities that thrive.
Sydnie kept the dormant mushroom samples in the lab refrigerator so that once she identified them, she could continue testing to see which ones degrade cellulose or to explore other research questions. Future students can continue with the project.
Lessons learned: When the fungus stopped growing on Sydnie’s cellulosic medium, she had to find alternatives. “Research won’t always go as planned, so it was good to say, ‘It’s not working. How can we do it another way? ‘ Sydnie comments. “I was talking to Sister Susan and she was like, ‘This is all part of the research, and you haven’t done anything wrong. It’s just part of the way it goes. Sydnie also enjoyed gaining experience with lab equipment, learning how to perform PCRs, and fabricate the culture medium.
Future goals and interests: “This project also helped me get to know myself better,” Sydnie recalls. “There is nothing more that I enjoy than being in the microbiology lab. She enjoys problem-solving and research, and explores graduate programs in microbiology or public health with an emphasis on infectious disease control.
Does Chromatin Protect DNA From Harmful Chemicals?
Research student : Julianna Rotondo ’22, major in biology
The project: Chromatin packs long DNA molecules into tight coils that can fit into cell nuclei. The structure of chromatin can change from compact to extensive, which affects DNA replication and gene expression.
Condensed chromatin protects DNA, preventing most proteins from accessing it. Julianna and her mentor Dan Ginsburg, Ph.D., associate professor of biology, wondered if the chromatin in a strain of yeast would also protect DNA from harmful agents.
Julianna added different reagents to two samples of a yeast culture to change the yeast chromatin structure. One reagent, a pesticide, disassembled and opened the chromatin, and another reagent protected the chromatin and kept it compact. Julianna then exposed the two samples to two different DNA-damaging carcinogens, placed the cultures on culture medium, and counted the yeast colonies that developed.
She hypothesized that carcinogens would cause more damage to the culture with open chromatin. “These plaques should show less growth,” commented Julianna, “because the chromatin opening reagent should allow the damaging reagent more direct access to DNA (which kills cells).” Conversely, Julianna predicted that plates treated with the Chromatin Protective Reagent would show greater growth of the yeast colonies, as their DNA should have been protected and allowed to multiply. “By putting the data into Excel, we can graph the number of colonies to see if the results match what would be expected,” Julianna said.
Why is this important: So far, the difference in yeast growth suggests that chromatin appears to make DNA less susceptible to damage. The discovery could help pave the way for treatments that keep chromatin in a compact state to protect DNA when a cell is exposed to harmful chemicals.
Lessons learned: In addition to learning the structure of chromatin, Julianna learned new techniques, equipment and laboratory protocols. She also gained experience in collecting and analyzing data using Excel.
Future goals and interests: Julianna will continue her project this year, studying how well chromatin protects DNA against other harmful agents. At first, Julianna thought the research would be intimidating. “I actually really enjoy it, which I hadn’t expected, and I can’t wait to come to the lab to do some research. For the future of my career, I want to be a genetic counselor, and there are options for research positions that I hadn’t considered before.
What materials are the different plastics made of?
Research student : Ilyse Gorman ’22, major in chemistry and secondary education
The project: Ilyse works to identify ingredients in different colors and classifications of plastics by studying how their molecules react to infrared energy. “Molecules have different vibrational states when infrared energy hits them,” Ilyse explained. Their vibrational energy can be represented as peaks on a graph, and each molecule has a distinctive “fingerprint” peak that Ilyse uses to locate materials in plastics.
Jiangyue (Luna) Zhang, Ph.D., professor of chemistry, and Sister Rose Mulligan, IHM, Ph.D., associate professor of chemistry, invited Ilyse to participate in this project and helped her achieve the Clare Prize. Boothe Luce Undergraduate Research Scholar Award, a scholarship for women in science and education.
Ilyse is using two different machines for this project, the Reva Raman spectrometer, a newer instrument in undergraduate labs, and an infrared (IR) spectrometer, both of which use infrared energy to interact with molecules. “Raman spectroscopy and IR spectroscopy complement each other, as each detects areas of identical but also different vibrational energies,” said Sister Rose. Ilyse compares the graphs of the two machines and uses the IR spectrometer, a more commonly used tool, to confirm her guesses about the types of plastic she is scanning.
“I also have some unknown plastics that I run through machines to see if I can figure out what it is,” Ilyse said. She can compare graphs of known plastics with unknowns to see if their peaks match and indicate which molecules might be in unknown plastics.
Why is this important: “The ability to identify plastics quickly, in a non-destructive manner, is useful for recycling and forensic purposes,” Sister Rose commented. Not all plastics have a recycling number, and facilities need to know how to categorize and handle materials. Some plastics are easy to recycle, Ilyse said, while others, like PVC, must undergo a special process to break down components and handle toxic byproducts safely. Forensic pathologists may also benefit from the ability to identify plastics at crime scenes to help them gather evidence.
Lessons learned: Ilyse learned to use a graphics program to batch process large amounts of data into a simplified format for analysis. She also writes a lab procedure for undergraduate forensic science students to learn how to test and classify plastics. Students will use the spectrometers to analyze known and unknown plastics, compare the results, and identify molecules in the unknown material.
Future goals and interests: Ilyse says her research efforts inspired her to get her future high school chemistry students to start doing mini-projects to get their first experience. “I want to get them the idea of doing research before you go to college, so they can start thinking about it sooner,” Ilyse explained. “It makes them more independent in their education.”