By: Ashley Bergeron
Staff-Writer
IN LSAMP (Louis Stokes Alliance for Minority Participation) is a program whose goal is to increase participation and advancement of underrepresented students in STEM. Dr. Grace Muna of the chemistry department is the organizer for the IU South Bend chapter of the program.
On Sept. 29, IN LSAMP students and one student who received the Garber Research Fellowship scholarship – an IU South Bend chemistry scholarship given to qualified students for summer research – showed their research to the IU South Bend community. Another student also had his research funded by the National Institute of Health (NIT). The students’ posters were displayed in Wiekamp Hall, and professors and other students could ask questions about their research. Let’s learn about the students and their research.
Hannah Gregor
Hannah Gregor is a Garber Research Fellowship student and a biochemistry major. The title of her research is “Investigation of Fluorescent Hydrogen Sulfide Probes and Synthesis of Enzyme Inhibitors and Protective Molecules”. The professor who helped her with her research was Dr. Kasey Clear. One of the goals of this research was to figure out if ß-cyclodextrin was able to form an inclusion complex with P3, a turn-on fluorescent probe, and increase the selectivity of P3 for selecting hydrogen sulfide (H₂S) over biothiols. It’s important to detect H₂S because diseases have been linked to overproduction and underproduction of the molecule. ß-cyclodextrin was able to form an inclusion complex, but it was not able to increase the fluorescence intensity of P3. The other part of Gregor’s research was the synthesis of STI1 inhibitor. Gregor was able to successfully synthesize and purify the inhibitor.
Abigael Jennifer Ngoumape
Abigael Jennifer Ngoumape is an IN LSAMP scholar and a biochemistry major. The title of her research is “Synthesis and Electrochemical Analysis of 1,4-Naphthoquinone Derivatives and the Effect of Hydrogen Sulfide on Electrochemical Properties”. The professor who helped her with her research was Clear. 1,4-Naphthoquinones (1,4-NQs) are organic molecules that can engage catalytic reactions with H₂S, which leads to the generation of reactive sulfur species (RSS). However, the exact mechanism for this reaction is unknown, and the structure of the 1,4-NQ can affect what specific effects are observed during the reaction. Ngoumape first synthesizes the 1,4-NQs DCNQ and HMNQ. Ngoumape used cyclic voltammetry (CV) to analyze the redox properties of five 1,4-NQ compounds. The experiments were done in aqueous solutions to imitate real life. Hydrogen sulfide was also introduced to the solutions to observe its electrochemical effects on the 1,4-NQs. The CV results showed that the 1,4-NQs molecules can undergo quasireversible redox reactions, meaning that they can be easily redoxed and oxidized. When hydrogen sulfide was added to the CV, some of the molecules initially lost their reduction signal and a new peak appeared at a lower potential. This suggests that hydrogen sulfide causes reduction and subsequent autoxidation, or spontaneous oxidation of a compound in the air, resulting in a redox-active 1,4-NQ to sulfur adduct. An adduct is a product of direct addition of two or more distinct molecules.
Allyce Rogers
Allyce Rogers is an IN LSAMP scholar and a biology major. The title of her research is “Comparing Vegetative and Pollinator Diversity in Restored and Natural Populations Phemeranthus rugospermus (an endangered species)”. Professors Deborah Marr and Andrew Schnabel, as well as fellow biology student Gabby Gabrielson, who has her own research project about the same plant species, were also a part of the research project. Phemeranthus rugospermus (common name: flame flower) is endangered in every state in its range. Remnant or original sites were compared to restored sites that are in nature reserves in terms of population. Phemeranthus rugospermus grows in oak savannas or sand prairies, which are harsh environments that are next to sand dunes. Restored sites had significantly more individuals compared to remnant sites. The remnant sites’ populations have been going down, as there were about 61 individuals in each site during the 1990s. Now, there are only about three. The number of floral visitors and how many times a floral visitor visited a Phemeranthus rugospermus individual were recorded. There were nine species of floral visitors, including hoverflies, ants and sweat bees. Restored sites have more floral visitors visiting compared to remnant sites.
Ashley Rojas-Romero
Ashley Rojas-Romero is an IN LSAMP scholar and a biology major. The title of her research is “Acid Tolerance and Resistance to Oxidative Stress in Oral Bifidobacterium and Streptococcus Species”. She worked with Dr. Yilei Qian for her research. Bifidobacterium is bacteria that is found in the gut, but Bifidobacterium dentium has been found inside the mouth as well as the gut. Rojas-Romero hypothesized that the reason B.dentium was able to survive in the oral cavity was due to its PolyP-producing ability. She compared it to Bifidobacterium longum (intestine-only) and Streptococcus mutans (oral-only). The three bacteria were grown in three different cultures: a control, Pi/S and AMS. B. dentium was able to grow the most out of the three. A H₂O₂ susceptibility test was done which showed that S. mutans was the most resistant to hydrogen peroxide, which was expected, as it is aerotolerant, meaning that it does not require oxygen but can tolerate its presence, while the other two are not. A pH 4 acid tolerance test was performed, which showed that B. dentium was the most acid-resistant out of the three. It is to note that it is hard to replicate the environment of the mouth in the lab, so these results may not be accurate in practice.
Nathaniel Smith
Nathaniel Smith is an IN LSAMP scholar and a biology major. The title of his research is “Cloning and Expression of the Arylphorin Subunit Alpha-like Protein in E. Coli”. Smith did his research with Dr. Shazir Rizk. The goal of this experiment was to clone Arylphorin, an enzyme found in the saliva of wax worms that can break down Polyethylene (PE), a common type of plastic that’s hard to break down. Smith used E. Coli for the initial cloning, expression, and purification of the enzyme. The AI tool AlphaFold2 was used to better understand the structure of Arylphorin and its interaction with PE. The results of this experiment were that the Arylphorin gene can be successfully cloned using the pTac plasmids. The protein band of the cloned gene was at 65 kDa, which was lower than the expected 75 kDa. Smith has future plans for the Arylphorin enzyme, which are expression from additional plasmid types, analysis of sequencing results and testing isolated enzyme on polyethylene.
Erik Vardanian
Erik Vardanian had his research funded by NIT and is a computer science major. The title of his research is “Genome structure database: A web resource for genome structural data using a nearest neighbor model”. Vardanian worked with T. Murlidharan Nair. The goal of this project was to make a website that biologists can use to see the genomic structure of common DNA sequences. The project is currently in an active development phase. The things that have been accomplished so far include crafting node.js scripts that play an important role in harnessing the potential of Web Graphics Library (WebGL), developing a script that is capable of visualizing complex DNA structure data, enhancing the project’s back-end functionality and creating a node.js script that establishes seamless communication with the back-end database, which ensures that the user can access and work with the genomic data efficiently. WebGL is a specialized JavaScript application programming interface (API) tailored for rendering dynamic 3D and 2D graphics directly within web browsers. The future research of the project is the plan to implement a method for annotating structural regions using data source from the ENCODE project. ENCODE stands for Encyclopedia of DNA Elements, and it’s a public research project whose goal is to make an exhaustive list of functional parts of the human genome.
Two students, Zahra Alexander and Joel Rael, have also done research over the summer, but theirs were not presented at the conference. The group is planning on going to a research conference in Chicago on Nov 4.
