Community Highlight: Lauren Cole-Osborn

Dr. Lauren Cole-Osborn (LCO) is a postdoc at Northeastern University and first used KBase as a PhD student. Lauren’s research focuses on understanding the regulation of terpenoid indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus, commonly known as Madagascar periwinkle or Vinca rosea, used to treat cancer. 

How has using KBase supported your research?

(LCO) I was characterizing new transcription factors in C. roseus and wanted to know what tissue types they were most expressed in. A previous paper (Góngora-Castillo et al. 2012) had performed RNA-seq in various tissues of C. roseus so I knew this data existed. However, this was performed before a genome had been sequenced. They had created de novo transcripts, but the gene that I was interested in wasn’t identified properly in this transcriptome. Rather, the gene was correctly predicted from transcripts mapped to a newly sequenced genome (Franke et al. 2019) and with this available data, I just needed to get tissue specific expression values for the new gene models. 

I was pretty sure I had all of the data I needed for this analysis, but I wasn’t sure how to turn it into what I needed. I attended the yearly American Society of Plant Biologists meeting in 2021 and participated in a workshop on how to use KBase, which described exactly how to do what I needed to! The workshop directed us to an example KBase Narrative (Arabidopsis RNA-seq Analysis Tutorial). I used this tutorial as a starting point for my analysis. I followed the example Narrative, substituting in my data, and the analysis went smoothly, leaving me with all the information I needed!

The medicinal plant, Catharanthus roseus or Madagascar periwinkle. Photo credit: Lauren Cole-Osborn

How have you benefited from working with KBase?

(LCO) KBase helped me to quickly answer a question that would be easy for a skilled bioinformatician to answer, but difficult for an experimental biologist like me. The clear user interface and availability of tutorials and example datasets made this process very easy, satisfying, and even fun.

In addition to answering my immediate question, KBase was a great learning tool. I was introduced to the theory behind bioinformatic analyses without getting bogged down by the technical issues that might have come up if I tried to code it. Now that I’ve done this analysis in KBase and understand the theory behind it, I feel more comfortable trying this analysis in other programs, like R.

Finally, KBase was helpful for training others. Recently, a new graduate student came to me with a question similar to the one I previously had – it seemed like she had all of the data but wasn’t sure how to put it all together to answer a specific question. I recognized this as a job that KBase could help with. I showed her how to use KBase and answer her question in less than an hour – a testament to how intuitive KBase is. 

What is your favorite part about using KBase?

(LCO) I think KBase’s user interface is very intuitive. It takes concepts that can seem confusing and difficult and makes them far more approachable for the non-expert. I also love that it is free.

Lauren Cole-Osborn waters medicinal plants used for chemotherapy research in Carolyn Lee-Parsons’s lab in the Mugar Life Sciences Building on Feb. 10, 2021. Photo by Ruby Wallau/Northeastern University

What role do you see KBase having in open science principles ? 

(LCO) Overall, KBase makes bioinformatic analyses less of a black box, which empowers non-experts to expand their toolbox, and facilitates discussion between scientists. For example, when scientists read my work, I hope that young researchers that want to do a similar analysis can quickly find and apply this useful tool. Meanwhile, reviewers and other scientists with more bioinformatics expertise can double check my work and can identify potential errors, facilitating the system of checks and balances that is important for scientific knowledge generation.

Any tips on running RNA-seq in KBase?

(LCO) I was surprised at how long it took to import each of the 500 MB RNA-seq samples (about a half hour per sample). When I first tried running this, I made an error in how I imported them, so I waited for hours and then had to start over. If you are new to KBase, I would recommend trying some of the apps out with only a few samples before trying a large project. 

Links

L.F. Cole-Osborn, S.A. McCallan, O. Prifti, R. Abu, V. Sjoelund, C.W.T. Lee-Parsons. (2024). “The role of the Golden2-like (GLK) transcription factor in regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus.” Plant Cell Reports, 43:141. https://doi.org/10.1007/s00299-024-03208-9

• FAIR Narrative: https://doi.org/10.25982/95510.53/2310383 

KBase RNA-seq Tutorial: Arabidopsis RNA-seq Analysis Tutorial

References:
E. Góngora-Castillo, K.L. Childs, G. Fedewa, J.P. Hamilton, D.K. Liscombe, M. Magallanes-Lundback, K.K. Mandadi, E. Nims, W. Runguphan, B. Vaillancourt, M. Varbanova-Herde, D. Dellapenna, T.D. McKnight, S. O’Connor, C.R. Buell. (2012). Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PloS ONE, 7(12), e52506. https://doi.org/10.1371/journal.pone.0052506

J. Franke, J. Kim, J.P. Hamilton, D. Zhao, G.M. Pham, K. Wiegert-Rininger, E. Crisovan,L. Newton, B. Vaillancourt, E. Tatsis, C.R. Buell, S.E. O’Connor, S. E. (2019). Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis. Chembiochem, 20(1), 83–87. https://doi.org/10.1002/cbic.201800592