Biology and chemistry research: Fungal populations, DNA-protecting chromatin and plastic ingredients
This summer, three undergraduate students are getting their hands dirty with scientific research—growing fungi, studying yeast DNA and watching the movements of molecules. Immaculata’s biology and chemistry professors discussed possible research topics with these three students and are offering guidance as the students make hypotheses, develop and follow research procedures and collect data. The students are gaining useful experience for their resumes and refining their career goals and graduate school plans.
What kinds of fungi grow in campus compost?
Student researcher: Sydnie Panetta ’22, biology major
The project: During composting, microbes and fungi break down solid organic matter into usable material for growing plants. Factors such as the composting method 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 piling leaves, grass, eggshells and vegetable waste into bins and stirring periodically to promote decomposition. Sydnie used cotton swabs to take samples from the compost bins. She then swabbed plates that indicated growing organisms and incubated the plates to see what fungal populations would develop.
Initially, Sydnie used cellulose as her growing medium, but she had difficulty getting fungi to grow on that material consistently. Cellulose, a tough substance that strengthens plant cell walls, has to degrade for plant material to break down into compost. Sydnie shifted to a more general medium of yeast, peptone and dextrose, which provided an ideal environment for fungus growth.
Sydnie extracted fungal DNA from her samples and then ran 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 the fungal populations.
Why it matters: This broad project can be used to answer a variety of questions, Sydnie says, such as how different fungal species interact and whether temperature or location affect the rate of decomposition or the fungal communities that grow.
Sydnie kept the fungi samples dormant in the lab refrigerator so that once she identifies them, she can continue testing to see which ones degrade cellulose or to explore other research questions. Future students may continue the project.
Lessons learned: When fungus stopped growing on Sydnie’s cellulose medium, she had to come up with alternatives. “Research isn’t always going to go as planned, so it was good to say, ‘This isn’t working out. How can we go about this another way?’” Sydnie comments. “I’d talk to Sister Susan, and she’d say, “It’s all part of research, and it’s nothing you did wrong. This is just part of how it goes.” Sydnie also enjoyed gaining experience with lab equipment, learning to conduct PCRs and making the growing medium.
Future goals and interests: “This project also helped me learn about myself,” Sydnie reflects. “There’s nothing more that I enjoy than being in the microbiology lab.” She enjoys problem-solving and conducting research, and she is exploring graduate programs in microbiology or public health with a focus on infectious disease control.
Does chromatin protect DNA from damaging chemicals?
Student researcher: Julianna Rotondo ’22, biology major
The project: Chromatin packages long DNA molecules into tight coils that can fit within cell nuclei. The structure of chromatin can change from compact to expanded, which affects DNA replication and gene expression.
Condensed chromatin protects DNA, blocking most proteins from accessing it. Julianna and her faculty mentor, Dan Ginsburg, Ph.D., associate biology professor, wondered if chromatin within a strain of yeast would also protect DNA from damaging agents.
Julianna added different reagents to two samples of a yeast culture to change the yeast’s chromatin structure. One reagent, a pesticide, disassembled and opened the chromatin, and another reagent protected the chromatin and kept it compact. Julianna then exposed both samples to two different DNA-damaging carcinogens, placed the cultures on a growing medium, and counted the colonies of yeast that grew.
She hypothesized that the carcinogens would do more damage to the culture with the open chromatin. “Those plates should show less growth,” Julianna commented, “because the chromatin-opening reagent should allow the damaging reagent more direct access to the DNA (which kills the cells).” Conversely, Julianna anticipated that the plates treated with the chromatin-protecting reagent would show more yeast colony growth, because their DNA should have been shielded 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 it matters: So far, the difference in yeast growth suggests that chromatin seems to make DNA less sensitive to damage. This finding could help pave the way for treatments that keep chromatin in a compact state to protect DNA during a cell’s exposure to harmful chemicals.
Lessons learned: In addition to learning about chromatin’s structure, Julianna learned new lab techniques, equipment and protocols. She also gained experience collecting and analyzing data using Excel.
Future goals and interests: Julianna will continue her project this year, studying how well chromatin protects DNA from other damaging agents. At first, Julianna thought research would be intimidating. “I actually really enjoy it, which is not something I anticipated, and I really look forward to coming in the lab to do research. Looking forward in my career, I want to be a genetic counselor, and there’s options for research positions that I hadn’t considered before.”
What materials make up different plastics?
Student researcher: Ilyse Gorman ’22, chemistry and secondary education major
The project: Ilyse is working to identify the 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 depicted as peaks on a graph, and each molecule has a distinctive “fingerprint” peak that Ilyse is using to pinpoint the materials in the plastics.
Jiangyue (Luna) Zhang, Ph.D., chemistry professor, and Sister Rose Mulligan, IHM, Ph.D., associate chemistry professor, invited Ilyse to participate in this project and helped her secure the Clare Boothe Luce Undergraduate Research Scholar Award, a grant for women in science and education.
Ilyse is using two different machines for this project, the Reva Raman spectrometer, a newer instrument in undergraduate laboratories, and an infrared (IR) spectrometer, both of which use infrared energy to interact with molecules. “Raman and IR spectroscopy complement each other, because each detects some of the same but also different areas of vibrational energies,” said Sister Rose. Ilyse is comparing graphs from the two machines and using the IR spectrometer, a more commonly used tool, to confirm her guesses about what types of plastic she is analyzing.
“I also have some unknown plastics that I’m running through the machines to see if I can figure out what those are,” Ilyse said. She can compare the graphs of known plastics with unknown to see if their peaks match up and indicate which molecules could be in the unknown plastics.
Why it matters: “The ability to identify plastics quickly, in a non-destructive manner, is useful for recycling purposes and forensic science,” commented Sister Rose. Not every plastic has a recycling number stamped on it, and facilities need to know how to categorize and process the 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 scientists can also benefit from being able to identify plastics at crime scenes to help them gather evidence.
Lessons learned: Ilyse has learned to use a graphing program to batch process large amounts of data it into a streamlined format for analysis. She is also writing a lab procedure for undergraduate forensic science students to learn 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 have inspired her to have her future high school chemistry students start doing mini projects to gain some early experience. “I want to put the idea of doing research in their heads before they get to college, so they can start thinking about it sooner,” Ilyse reflected. “It gets them more independent in their education.”