This summer, Elijah and Frances participated in summer research thanks to our new NSF funding!! We explored the impact of growth conditions on bacterial and fungal metabolism (specifically working on bat-associated bacteria and soil- and cave-derived fungi), expanded our microbial collection by collecting bacteria and fungi from Grand Caverns, ran hundreds of mass spectrometry experiments, worked on a review paper, and put together some exciting results for the final symposium at the end of the summer. The science was great, as usual, but the best part was getting to know Frances and Elijah better.
Elijah’s project was an expansion of an interesting result some students in Instrumental Analysis Laboratory (352L) found last Spring. One of our major research projects is exploring the bat microbiome for antifungal metabolites that may help combat the devastating White Nose Syndrome that is killing bats en masse across the United States. We have several promising bacterial strains that possess antifungal activity against Pseudogymnoascus destructans, the fungus that causes White Nose Syndrome, but the molecules that these strains produce vary each time we grow them (which makes new molecule discovery challenging).
In the Spring, my 352L students evaluated the impact of 12 different growth conditions on metabolite profiles of our most promising bacterial strain, Streptomyces buecherae. Weirdly, treatment of the bacteria with suberoylanilide hydroxamic acid (SAHA for short) had major impacts on the metabolite profiles (look at the image to the left!). SAHA works as a histone deacetylase inhibitor, which prevents enzymes from removing acetyl groups from histones. Histone deacetylation causes DNA to remain transcriptionally inactive, meaning that biosynthetic pathways responsible for producing molecules (like the antifungals we are searching for) are turned “off.” By treating an organism with SAHA, we hoped that we could let the DNA exist in a more transcriptionally active state and induce metabolite formation. The strange part is, S. buecherae doesn’t have histones! But, after some reproducibility challenges, the SAHA worked, and induced formation of several bioactive metabolites that Elijah tentatively identified over the summer. This coming academic year, we will be working to understand how this happened and if any of these induced metabolites may be useful in treating White Nose Syndrome.
In addition to exploring bacterial compounds active against fungi, we also explored fungal compounds that may be useful for medicinal purposes. Just like bacteria, fungi are very sensitive to their environments, and biosynthesize molecules that help them survive when they are provided with a competitive advantage. The majority of these molecules are not produced unless triggered by an external stressor. Frances explored the use of fungal-fungal co-culturing as one such stressor, in which two or more fungal strains are grown on the same media to introduce competition for limited space and resources. We followed a three step process for identifying promising co-cultures. First, cultures from the same environmental location were grown in monoculture and in co-culture on Petri dishes and inspected for visual changes. In the image to the right, you can see a clear visual difference in the gray fungus at the border where it interacts with the white fungus--it clearly has put up some sort of yellow barrier at that border, which could indicate some interesting chemical changes! Then, co-cultures with notable visual changes were grown on rice for chemical extraction and analysis. Finally, any cultures that had notable chemical changes (i.e. new or highly upregulated metabolites in co-culture that were not present in either monoculture), reproducibility was assessed and induced compounds were explored.
Frances grew so many Petri dishes and completed dozens of different extractions with lots of colorful results. We found five co-culture pairs that have promising differences in metabolite profiles that we are continuing to explore this semester. Again, we are struggling with reproducibility in our results (a common theme in natural products chemistry), but we are hopeful that one of our many leads will guide us somewhere exciting and help us discover a new bioactive molecule! In addition to exploring bacterial compounds active against fungi, we also explored fungal compounds that may be useful for medicinal purposes. Just like bacteria, fungi are very sensitive to their environments, and biosynthesize molecules that help them survive when they are provided with a competitive advantage. The majority of these molecules are not produced unless triggered by an external stressor. Frances explored the use of fungal-fungal co-culturing as one such stressor, in which two or more fungal strains are grown on the same media to introduce competition for limited space and resources. We followed a three step process for identifying promising co-cultures. First, cultures from the same environmental location were grown in monoculture and in co-culture on Petri dishes and inspected for visual changes. In the image to the right, you can see a clear visual difference in the gray fungus at the border where it interacts with the white fungus--it clearly has put up some sort of yellow barrier at that border, which could indicate some interesting chemical changes! Then, co-cultures with notable visual changes were grown on rice for chemical extraction and analysis. Finally, any cultures that had notable chemical changes (i.e. new or highly upregulated metabolites in co-culture that were not present in either monoculture), reproducibility was assessed and induced compounds were explored. Frances grew so many Petri dishes and completed dozens of different extractions with lots of colorful results. We found five co-culture pairs that have promising differences in metabolite profiles that we are continuing to explore this semester. Again, we are struggling with reproducibility in our results (a common theme in natural products chemistry), but we are hopeful that one of our many leads will guide us somewhere exciting and help us discover a new bioactive molecule!
In addition to moving forward on the two projects I just talked about, we got to go back to Grand Caverns to expand our culture collection! Like we did last summer, we were guided by the amazing Dr. Ángel Garcia of JMU Geology, but this time, to the “Drapery Room.” Unlike the haunted Dante’s Inferno (which we visited last summer), the Drapery Room is not part of any tours offered by Grand Caverns and is only open to researchers. What a fantastic opportunity! Dr. Garcia noticed a strange filament growing on the walls there which prompted us to check out the location. We took dozens of swabs, collected cave water, and cultured our microbes when we returned to lab. And wow, we got some cool stuff!! Frances and Elijah put in a lot of extra work subculturing these organisms (which grew surprisingly quickly compared to our previous isolates) and now our Grand Caverns Collection has grown close to 50 strains! So excited to learn more about them and what they might be capable of.
The Drapery Room Expedition! Featuring mysterious filaments (left), Elijah collecting cave water, and Frances posing between the drapes.
A glimpse into the microbial life of the Drapery Room. This is just a tiny fraction of what we were able to culture from the Drapery room! To the left is the "filament" that grew on the cavern walls--definitely a fungus! We also got some unexpected filaments (zoomed in in the middle and right hand pictures), as well as some bacteria that grow in classic circular colonies. Particularly interesting is the bacteria on the right, which prevent fungi from growing near them! Future antifungal investigation, perhaps?
As a final adventure before the research symposium, Elijah, Frances, and I headed off to experience “CaveSim” at Grand Caverns! The CaveSim team creates realistic caves that are housed in trailers so that they can move around to schools and public events around the country. They teach people of all ages about the science of caves, the importance of conservation and responsible cave stewardship, the physics behind the rescue equipment used in caving expeditions, and more.
Adventures in CaveSim! Frances crawls through the mobile cave (and Dr. Caesar creepily captures the camera footage of her), Elijah "rescues" Frances using rescue rope (a fun physics lesson), and Elijah attempts to fit through an 8.5 inch squeeze meant to mimic the tight spaces in the caves!
Last but not least was the week of symposium! I loved hearing all about the amazing research that happened in the department (and across the College of Science and Math as a whole), and was so so proud of Frances and Elijah for putting together some pretty dang awesome posters! They did a fantastic job presenting their science to all of their visitors and I think we all grew for the better this summer. Always nice to end the summer with a reminder of why I picked this job to begin with. The students are awesome, and I love watching them grow as scientists, find their confidence, and share their stories with the world. Now, for a new year!
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