Mandy Lin ’23
Creating nirK and nosZ Microarrays to Study Denitrification
I worked on building microarrays for nirK and nosZ — two genes in the denitrification pathway — in order to study denitrification and nitrogen loss in the ocean. Both genes are important because nitrous oxide, a potent greenhouse gas, is produced during the pathway. The microarrays will be used to determine the organisms in my mentor’s ocean samples that use these two genes. My project involved narrowing down all the nirK and nosZ gene sequences from the National Center for Biotechnology Information database and identifying the best 70 base-pair regions to be the probes on the microarray. I used various programs including CD-HIT, MAFFT, EMBOSS and RAxML-NG to make clusters, alignments, consensus sequences and phylogenetic trees to organize and analyze the genes. I also was able to learn and improve my programming skills by writing shell scripts, SLURM scripts and a MATLAB program. In addition, I used Excel to create a database of the sequences to aid in sequence analyses. Although this internship was not directly related to my career path, I learned valuable data analysis and coding skills, and I gained a better understanding of oceanographic research.
* This internship is connected to the HMEI Water and the Environment Grand Challenges project, “Fate of Nitrite Determines Nitrogen Removal in Coastal Waters.”
Climate and Environmental Science
Ward Lab, Department of Geosciences, Princeton University
Bess Ward, William J. Sinclair Professor of Geosciences and the High Meadows Environmental Institute; Naomi Intrator, Ph.D. candidate, Geosciences