What'd You Do This Summer? - Featuring Lydia Jordache
Senior majoring in Microbiology
Conducts research in the Weinert Lab under the direction of
Associate Professor of Biochemistry and Molecular Biology
Many students spend their summers as an undergraduate taking time away from the studies and either working a summer job or enjoying the opportunity to spend time with family and friends. Not Lydia. As a recipient of a Summer Undergraduate Research Fellowship (S.U.R.F.) Award she spent the 2020 summer conducting research, specifically using bioinformatics to analyze how globin-coupled sensors influence virulence phenotypes in bacteria.
Antibiotic resistant Microorganisms is an issue the world is quickly having to address. Lydia’s research is contributing towards the understanding of how globin-coupled sensors in bacteria can possible identify alternatives to the world’s currently available antibiotics, and hopefully slow the development of these microorganisms.
Using phylogenetic analysis from a variety of different programs, Lydia identified bacteria that contained globin-coupled sensors (GCS’s) that were related to the GCS’s studied in the Weinert Laboratory. After identifying these protein relatives, she was then able to use TREND and FlaGs servers to parse out clades, commonly known as evolutionarily closely related groups, and the surrounding genes located near the identified GCS’s. She then isolated clades of genome neighborhoods and examined them for potential virulence proteins, particularly motility-related genes. Virulence genes are advantageous to the bacteria, and motility is a virulence factor.
After finding certain motility proteins of interest, Lydia examined their sequences for amino acid residues that were consistently appearing, commonly referred to as "conserved". She then compared these conserved residues to the general conservation sequence of a larger, less-specific, conglomeration of highly similar proteins. Her research found that some residues only indicated as being conserved when also attributed to being near a GCS in the genome.
Lydia mapped these residues on a 3D model of both a GCS and the motility proteins of interest, and then docked them to visualize how they may be potentially interacting within the cell. Her docking models, and collective research, illustrated how globin-coupled sensors might play a role in the some of the virulence pathways within bacteria.
This was not Lydia’s original research plan. As the world shutdown, due to the COVID-19 pandemic, and people were forced to quickly adapt, she worked with her mentor to refocus her research and adapt in kind. Initially her research was going to involve developing her skills in culturing bacteria, as well as gaining new skills in the investigation of these cultured bacteria’s intracellular molecules. She admits that adapting to her new research, which involved bioinformatics, was difficult due her lack of experience in the field. “My classes had never prepared, or educated, me in bioinformatics at this point, and so this was a new skill that I had to develop,” said Lydia. “The change of plans ended up being a great thing, however, because the entire experience was new for me and it has already shown to be useful in my academic and research life.”
"Receiving the SURF award provided me a huge boost of encouragement," Lydia says. "It has allowed me not only to get a more personalized and unique research experience but has also allowed me to believe that I am capable of producing something of value!" After graduation she plans to attend a graduate program in Microbiology, preferably studying bacteria. Although she doesn't yet know where this will take her, or even what subset of microbiology fascinates her the most, she remains excited about what her future holds and extremely motivated to learn all she can.