ScholarWorks

ScholarWorks is an open access repository for the capture of the intellectual work of Montana State University (MSU) in support of its teaching, research and service missions. MSU ScholarWorks is a central point of discovery for accessing, collecting, sharing, preserving, and distributing knowledge to the Montana State University community and the world.

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Scholarship & Research

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Hemolysis of Human Erythrocytes by Methicillin-Resistant Staphylococcus aureus Is Primarily Caused by PSMα Peptides
(MDPI AG, 2025-10)
Nygaard, Tyler K.
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Gao, Annika
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LaTray, Eliot
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Voyich, Jovanka M.
Staphylococcus aureus (S. aureus) is a major cause of human morbidity and mortality worldwide. Hemolysis caused by S. aureus cytotoxins is important for the acquisition of iron and subsequent bacterial survival during infection. S. aureus can express numerous hemolysins that have been shown to target human erythrocytes. However, the relative importance of each of these for causing hemolysis during pathogenesis in humans is not clear. In this study, we have examined the hemolytic capacity of different methicillin-resistant S. aureus (MRSA) deletion mutants against human erythrocytes in suspension using two separate assays. The first assay measured hemolysis caused by extracellular factors produced by MRSA, while the second measured hemolysis following co-culture of MRSA with human erythrocytes. Results from both assays demonstrated that phenol-soluble modulin-α peptides (PSMα) play a dominant role in causing hemolysis of human erythrocytes, highlighting a prominent target for novel therapeutic strategies designed to limit S. aureus iron acquisition and survival during human disease.
Minimum flow decomposition in graphs with cycles using integer linear programming
(Springer Science and Business Media LLC, 2025-11)
Dias, Fernando H. C.
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Williams, Lucia
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Mumey, Brendan
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Tomescu, Alexandru I.
Minimum flow decomposition (MFD) — the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow — is a classical problem in Computer Science, and variants of it are powerful models in a different fields such as Bioinformatics and Transportation. Even on acyclic graphs, the problem is NP-hard, and most practical solutions have been via heuristics or approximations. While there is an extensive body of research on acyclic graphs, currently there is no exact solution on graphs with cycles. In this paper we present the first ILP formulation for three natural variants of the MFD problem in graphs with cycles, asking for a decomposition consisting only of weighted source-to-sink paths or cycles, trails, and walks, respectively. On three datasets of increasing levels of complexity from both Bioinformatics and Transportation, our approaches solve any instance in under 12 minutes. Our implementations are freely available at https://github.com/algbio/MFD-ILP.
Quantitative Comparison of Ad-Valorem Equivalents for Non-Tariff Trade Measures: WTO Versus TRAINS
(Wiley, 2025-11)
Ikeme, Sionegael
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Countryman, Amanda M.
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Manning, Dale T.
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Charlton, Diane
Non-tariff measures (NTMs) play a growing role in trade policy. Economists quantify NTMs by calculating their Ad Valorem Equivalents (AVE), typically employing one of two global NTM datasets: TRAINS from UNCTAD or WTO notifications. While TRAINS data better measure NTMs, their limited coverage over countries and time is inadequate for many types of analyses, and thus researchers often resort to using WTO data, which is not as accurate as the TRAINS but has better coverage. We compare the two datasets to assess whether AVEs from WTO notifications align with those from TRAINS, given similar country and time coverage. We find significant AVE discrepancies between datasets, sometimes reversing signs, warranting caution when using WTO notifications in the absence of TRAINS data to construct NTMs.
The entanglement of individuation and explanation in the discovery of xenogastrulation
(Springer Science and Business Media LLC, 2025-11)
Bollhagen, Andrew
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Mayne, Zachary J.
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Merzdorf, Christa
This paper analyzes an episode of scientific work that was prompted by observations of a novel defect in early embryonic development, which was unexpectedly induced in an experimental context and has tentatively been dubbed “xenogastrulation.” The researchers worked to individuate this as a novel phenomenon—both by distinguishing it from what it is not (e.g., exogastrulation) and by forming a positive conception of what it is—in order to facilitate further inquiry. Our analysis provides new insights into the role of explanatory reasoning in nascent experimental research programs. We argue that the researchers’ efforts to individuate the novel phenomenon were entangled with their efforts to explain it. By this, we mean that tentative answers to the individuative question, “what is it?” also served as tentative answers to the explanatory question, “by what means does it occur?” This case study therefore demonstrates that explanation need not wait until an explanandum has been clearly individuated but instead can be deeply entangled with the process of individuating the explanandum in the first place.
Seismic shifts in the geochemical and microbial composition of a Yellowstone aquifer
(Oxford University Press, 2025-10)
Boyd, Eric S.
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Colman, Daniel R.
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Menchaca, Ana
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Spietz, Rachel L.
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Shoemaker, Anna
Seismic energy, like that released by earthquakes, can fracture rock and thereby alter subsurface fluid flow paths, release substrates from inclusions, and expose fresh mineral surfaces capable of reacting with water. However, it is unclear how such seismic-induced changes influence microbial communities. Volcanically active areas experience frequent seismic activity and thus represent ideal locations to examine the influence of seismic-induced geochemical change on subsurface microbial communities. Here, we demonstrate that energy released in an earthquake swarm in 2021 correlated with extensive temporal change in the geochemical and microbial composition of aquifer fluids sampled from ∼100 m depth in a borehole in Yellowstone National Park. Increased energy absorbed at the borehole over time was correlated with increased concentrations of hydrogen, dissolved organic carbon, and sulfide and was associated with depletion of δ13C in dissolved organic carbon, increased concentrations of cells, and increased abundances of chemolithotrophic, putative hydrogen-oxidizing Dethiobacteraceae and Desulfotomaculum bacteria. Dissipation of the earthquake swarm was associated with decreased concentrations of hydrogen, sulfide, and cells. These results suggest the subsurface biosphere dynamically responds to seismic-induced geochemical change at the level of activity and growth. Laboratory mechanical comminution of rhyolite, the primary bedrock in Yellowstone, released organic carbon and hydrogen and generated hydrogen when exposed to water. This indicates the presence of a large subsurface reservoir of organic carbon and hydrogen that can be released or generated by seismic induced bedrock fracturing. Taken together, these data indicate seismic-induced generation of chemical disequilibria can support the persistence of complex subsurface microbiomes.