Building Wet and Dry Lab Skills

Summer 2025 marked the second year of Alabama A&M University students coming to the DOE Joint Genome Institute for research and training experience funded by a DOE training grant. 

Building off the previous year’s project, undergraduate interns Tamyra Long and Zyiah Mikes worked with mentors Yi Zhai and John Vogel from the Plant Functional Genomics Group to study the effects of Brachypodium distachyon plant root exudates on the plant microbiome. This year, however, there was a new aspect to the project - they also worked with Sharon Greenblum from the User Support Analysis team to analyze plant microbiome data via programming languages like Python. The more specific goal of the project is to determine how mutations in plant transporter genes affect microbiome composition and plant growth. Under the supervision of their mentors, they were responsible for all steps of the experiment from growing and inoculating the plants to harvesting the plants and extracting DNA. They also analyzed 16s amplicon data to determine microbiome composition. This gave them an opportunity to learn all steps including both wet lab and computational analysis. They also learned how to log on to Dori – a computer cluster owned and operated by the JGI and Berkeley Lab – to launch a jupyter notebook running R so they could do their data analyses. 

When they weren’t in the lab, they were either exploring Berkeley and acclimating to the weather or practicing soccer with local Bay Area soccer teams – Zyiah plays on the AAMU women’s team and got a chance to train with the Oakland soccer club this summer. 

Want to learn more about their experience? Watch the short video below: 

Video Transcript:

Zyiah Mikes: Hi. My name is Zyiah Mikes. I'm a rising senior majoring in Biology at Alabama A&M. And I'm a summer intern for Sharon and Yi.

Tamyra Long: Hello, everyone. My name is Tamyra Long. I'm a senior at Alabama A&M majoring in Biology, and I'm also an intern at JGI with Yi and Sharon.

Yi Zhai: Hi, everyone. My name is Yi Zhai. I'm a project scientist at Joint Genome Institute. And, also the mentor, for Zyiah and Tamyra.

Sharon Greenblum: Hi. My name is Sharon Greenblum. And, I'm a computational biologist. So I have been working with Zyiah and Tamyra this summer and teaching them more about how to analyze data.

Zyiah Mikes: Dr. Yi Zhai is our mentor for our experimental work or our wet lab stuff. Our current project is how root transporters and root exudates regulate the plant Brachypodium distachyon’s microbiome. And that's what we've been working on this past summer. We used a lot of different experiments in the wet lab, which included PCR, which we're both very comfortable with. We collected seeds. We also use CRISPR-Cas9. And right now we have over 300 plants that we’re trying to figure out the biome of.

Tamyra Long: The other side is what we call the dry lab. We've been focused on analyzing plant microbiome data using different programming languages such as Python, Bash, and RStudio. We also learned how to run Dori, which is a compute cluster owned by JGI, and used Jupyter notebook for a programming environment used to work inside of a programming language. For example, we worked Python inside of Jupyter notebook.

Yi Zhai: And they have learned a lot I think. And they can do like independent work right now. Yeah. Yeah. They're amazing.

Tamyra Long: JGI helped me see what working in this environment would feel like and look like. Watching you all do your work and help us do another project was very inspiring, very inspiring. And the best part was the people at JGI. Everybody was so welcoming. Everybody made me feel comfortable here.

Zyiah Mikes: You guys are both intelligent and confident in your work, and that's something that I have so much respect for. And I've gained so much knowledge from being an intern for you guys.

Yi Zhai: It’s, it’s nice to hear. At least that we are doing something.

Sharon Greenblum: And it’s been fun. I mean. It’s been really fun working with the both of you. I have been so impressed at the questions that you have. Because asking questions is a whole skillset, and both of you are really really good at it.

Tamyra Long: I feel like I opened a new level of confidence because coming here in the beginning, like I said before, I was, I felt like I was down here. And now I feel like I'm up here. I can explain what we're doing. I understand what we're doing, and it was just a great experience overall. So I feel like I'm leaving here with opening a new level of confidence.

Zyiah Mikes: Like Tamyra said, confidence. I am very confident In wet lab. In dry lab, I'm kind of gaining confidence as we finish up and wrap up. The data set that I was working on was very difficult. I had a lot of errors, but I'm still working through those. And it's the confidence that comes with it I think.

Yi Zhai: “De-bugging,”

Zyiah Mikes: Debugging. Exactly.