Community Highlight: Alison Cupples
Alison Cupples is a professor in the Department of Civil and Environmental Engineering at Michigan State University (MSU). Alison completed her PhD at Stanford University and was a postdoctoral researcher with the USDA at the University of Illinois. She has been a faculty member at MSU for nineteen years with a research focus on the biodegradation of organic contaminants.
How has working with KBase supported your research?
(AC) I have published two papers in the past year that relied heavily on KBase (1,2). The research focused on identifying the genes responsible for contaminant biodegradation in soil, sediments and groundwater. Additionally, I received two NSF grants involving the analysis of environmental samples using KBase (3,4). I am working on additional proposals that include KBase for investigating PFAS biodegradation in enrichment cultures.
Do you have a favorite part about KBase?
(AC) KBase is also very user friendly, making it an ideal for undergraduate and graduate training. This training pertains to the analysis of environmental samples through two projects funded by NSF. For one NSF grant, I am working with two undergraduates to identify methane monooxygenases and propane monooxygenases in groundwater samples. An undergraduate was a co-author on a recent paper that used KBase (2).
Alison (right) and graduate students Mohsen (left) and Zoe (middle) are working with KBase to identify genes involved in the biodegradation of groundwater contaminants.
What role do you see KBase having in open science principles?
(AC) Sharing Narratives is extremely useful when working with students and collaborators. Also, making Narratives available to the public is an excellent technology transfer tool.
Graduate students, Mohsen (right) and Zoe (left), preparing soil samples for DNA extraction and sequencing.
Any tips for using KBase?
(AC) There are so many outstanding features of KBase. Some of my favorites include:
- Online tutorials are extremely helpful.
- Ability to use different apps for assembly and annotation provides great flexibility.
- Ability to download the generated files.
- The jobs tab that indicates the status of each app.
- KBase handles very large files easily with no limitations on size or the number of files uploaded or narratives generated.
References & Links
- Cupples, A. M. 2024. Propane monooxygenases in soil associated metagenomes align most closely to those in the genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia. Current Microbiology. 81:314
- Cupples, A. M., Dang, H., Foss, K., Bernstein, A. and J.R.Thelusmond. 2024. An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase. Archives of Microbiology, 206:363, 1-19.
- NSF Grant: Data mining of contaminant degrading genes in groundwater & sediment metagenomes.
- NSF-BSF Collaborative Research: Developing sustainable approaches for cometabolic degradation of TCE and cDCE in groundwater through stable isotope techniques.
