Creating a slide of nematodes for colony counting
Author: Kallahan Minor | Major: Biology | Semester: Spring 2024
Hello, my name is Kallahan Minor, and I am a biology major. Over the last 11 months, I have been working under Dr. Fiona Goggin in the Entomology and Plant Pathology Department. The research I assist in focuses on understanding nematode infection in transgenic lines of Arabidopsis thaliana and Glycine max (soybean). Specifically, we are investigating the role of small signaling molecules called Plant Elicitor Peptides (PEPs) in plant defense response to nematode infection, with a goal to provide a new avenue of pest management in large-scale agriculture. My future plans include pursuing molecular biology research in graduate school.
My research project stems from preliminary research showing that GmPEPs from the soybean variety Williams82 significantly reduced infection from two major nematode species. However, when the same GmPEPs were applied to the Magellan soybean variety, differences in susceptibility to nematodes were observed. This led us to hypothesize that GmPEP receptor diversity between these soybean lines might explain this observed variation since these receptors are essential for activating downstream defense responses.
To investigate this, I will analyze the interspecific receptor diversity between Magellan and Williams82 soybean lines. With assistance from Dr. Payal Sanadhya, a former postdoctoral in Dr. Goggins’s lab, we located the GmPEP receptors in Willaims82 by using the BLAST software, to compare its genome to the known PEP receptor sequences from another soybean variety, ZH13 as a reference. This analysis revealed the locations of the three PEP receptor sequences in Williams82.
Next, we focused on identifying Single Nucleotide Polymorphisms (SNPs) in the receptor sequences. Again, using ZH13 as a reference, we conducted multiple sequence alignments (MSA) with the AliView software, which highlighted SNPs found in Willaims82 against ZH13. It was crucial to determine if these SNPs led to amino acid changes that could then affect protein function, so we translated the nucleotide sequences into amino acids and conducted another MSA using a different software called ClustalOmega. The results from this analysis show minimal amino acid changes in Willaims82.
In the next phase of my research, I will analyze PEPR sequences between Williams82 and Magellan. This involves amplifying and cloning Magellan genomic DNA using primers designed from Williams82 PEPR sequences. After sequencing the amplified PEPR sequences from Magellan, I will perform more Multiple Sequence Alignments to identify SNPs and amino acid changes compared to Willaims82. Additionally, I will categorize these amino acid changes for both Williams82 and Magellan into their location in the protein’s functional domains: Leucine-rich-repeat, transmembrane, and kinase domains.
To complement the bioinformatic analysis, I will conduct a nematode infection bioassay. Both Magellan and Williams82 soybeans treated with GmPEPs will be separately infected with the Soybean Cyst Nematode and the Root Knot Nematode. This bioassay will support our hypothesis that Magellan may be more susceptible to nematode infection due to receptor diversity.
My research journey has so far been challenging yet rewarding. The major challenge I faced was understanding and utilizing the bioinformatics tools and techniques that were previously unknown to me. With guidance from Dr. Sanadhya and support from Dr. Goggin, I was able to overcome these hurdles and gain valuable skills in bioinformatic analysis. Dr. Goggin has played a pivotal role in my research by providing constant support and mentorship throughout my project.
Looking ahead, I plan to pursue a career in research, focusing on molecular biology and biochemistry. I will soon be applying for graduate programs that emphasize plant molecular biology in the biotechnology field. This research experience so far has reinforced my passion for biology and provided a solid foundation for my future endeavors. I am grateful for the opportunity to work with my mentors and colleagues, and I look forward to continuing my research project through the end of this year.