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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Persistent Transcriptome Alterations in Zebrafish Embryos After Discontinued Opioid Exposure
(MDPI AG, 2025-05) North, Ryan; Cooper, Gwendolyn; Mears, Lucas; Bothner, Brian; Dlakić, Mensur; Merzdorf, Christa
Much attention has been paid to the public health crisis that has resulted from the opioid epidemic. Given the high number of opioid users that are of childbearing age, the impact of utero exposure is a serious concern. Unfortunately, there is little knowledge regarding the consequences of opioid exposure during early development. While neurobehavioral effects of opioid exposure are well-documented, effects of exposure on embryogenesis remain largely unexplored. To address this gap in knowledge, we investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish (Danio rerio) embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant (oxycodone HCl 10.6 ng/L and fentanyl citrate 0.629 ng/L) and therapeutically relevant doses (oxycodone HCl 35.14 μg/L and fentanyl citrate 3.14 μg/L) from 2 to 24 h post-fertilization (hpf), followed by another 24 h of opioid-free development. mRNA profiling at 48 hpf revealed dose- and drug-specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed transcripts (DETs) than higher doses, potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total, 892 DETs (corresponding to 866 genes) were identified across all conditions suggesting continued differential gene expression well after cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix (ECM) organization, cell adhesion, and visual and nervous system formation. Key pathways include those involved in axon guidance, synapse formation, and ECM biosynthesis/remodeling, all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that very early developmental exposure to opioids induces persistent transcriptomic changes which may have lasting implications for vertebrate cellular functions. Overall, these data provide insights into the molecular mechanisms of opioid-induced alterations during development.
Genetic isolation and metabolic complexity of an Antarctic subglacial microbiome
(Springer Science and Business Media LLC, 2025-08) Kim, Kyung Mo; Hwang, Kyuin; Lee, Hanbyul; Cho, Ahnna; Davis, Christina; Christner, Brent C.; Priscu, John C.; Kim, Ok-Sun
Microbes inhabiting and evolving in aquatic ecosystems beneath polar ice sheets subsist under energy-limited conditions while in relative isolation from surface gene pools and their common ancestral populations of origin. Samples obtained from beneath West Antarctic Ice Sheet (WAIS) allowed us to examine evolutionary relationships of and identify metabolic pathways in microbial genomes recovered from the Mercer Subglacial Lake (SLM) ecosystem. We obtained 1,374 single-cell amplified genomes (SAGs) from individual bacterial and archaeal cells that were isolated from samples of SLM’s water column and sediments. These genomes reveal that a diversity of microorganisms including Patescibacteria exists in SLM. Comparative analyses show that most genomes correspond to new species and taxonomic groups, with phylogenomic and functional evidence supporting their genetic isolation from marine and surface biomes. Genomic data reveal diverse metabolisms in SLM that are capable of oxidizing organic and inorganic compounds via aerobic or anaerobic respiration. Distinct metabolic guild structures are observed for the subglacial populations, where trophic shifts from organotrophy to chemolithotrophy may depend on oxygen availability. Our SAG data suggest versatile metabolic capabilities in the characterized microbial assemblage, reveal key energy-generating strategies in the subglacial aquatic ecosystem, and provide a framework to assess microbial evolution beneath WAIS.
A guide to publishing in Biofilm: how to avoid a desk rejection
(Elsevier BV, 2025-04) Coenye, Tom; Goeres, Darla M.; Kjellerup, Birthe V.; Kovács, Ákos T.
The biofilm field is booming. Metrics produced by PubMed show the first manuscript referencing ‘biofilm’ was published in 1975 in Microbial Ecology [1], and from 2005 onwards the publication numbers have been in the thousands, with 9,486 papers published just in 2024. The field has also widened in scope and currently encompasses most, if not all, subdisciplines of microbiology as well as many in engineering. Large multidisciplinary centers focused on biofilm research have been established worldwide, including the Center for Biofilm Engineering in the US (celebrating its 35th anniversary of biofilm research in 2025) [2], the Singapore Centre for Environmental Life Sciences Engineering (established in 2011), the Costerton Biofilm Center in Copenhagen (Denmark, established in 2015) and the National Biofilms Innovation Centre in the UK (launched in 2018). Biofilm research has become truly global, as is also evidenced by the increasing number of large international biofilm-related conferences taking place in different continents (including Eurobiofilms and the Biofilm 1–11 conference series in Europe, the ASM Biofilm conference in the US, and the Asia-Pacific Biofilm conferences in China). Several international initiatives were taken in recent years to discuss bottlenecks in biofilm research and identify priority questions to guide research and policy making [3,4]. In addition, standardized methods are increasingly being developed and used, showing that the field has been accepted, integrated and matured [[5], [6], [7]]. Collectively these points suggest the biofilm field is thriving.
Protein-primed homopolymer synthesis by an antiviral reverse transcriptas
(Springer Science and Business Media, 2025-05) Tang, Stephen; Žedaveinytė, Rimantė; Burman, Nathaniel; Pandey, Shishir; Mancilla-Ramı́rez, Javier; Kulber, Louie M.; Wiegand, Tanner; Wilkinson, Royce A.; Ma, Yanzhe; Zhang, Dennis J.; Lampe, George D.; Berisa, Mirela; Jovanović, Marko; Wiedenheft, Blake; Sternberg, Samuel H.
Bacteria defend themselves from viral predation using diverse immune systems, many of which target foreign DNA for degradation1. Defence-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by using DNA synthesis instead2,3. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene that encodes the antiviral effector protein Neo4,5. It remains unclear whether similar mechanisms of defence are used by other related DRT families. Here, we show that DRT9 systems defend against phage using DNA homopolymer synthesis. Viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell, driving abortive infection and population-level immunity. Cryo-electron microscopy structures reveal how a non-coding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and poly-dA synthesis. Notably, biochemical and functional experiments identify tyrosine residues within the reverse transcriptase itself that probably prime DNA synthesis, leading to the formation of protein–DNA covalent adducts. Synthesis of poly-dA by DRT9 in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers. Collectively, our study identifies a nucleic-acid-driven defence system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.
Narrative power in the narrative policy framework
(Wiley, 2025-05) Shanahan, Elizabeth A.; DeLeo, Rob A.; Koebele, Elizabeth A.; Taylor, Kristin; Crow, Deserai A.; Blanch-Hartigan, Danielle; Albright, Elizabeth A.; Birkland, Thomas A.; Minkowitz, Honey
The Narrative Policy Framework lacks clear and empirical explanations of power. Yet, the study of narratives is inherently the study of power in shaping policy outputs and decisions. We develop a conceptual model positing that expressions of power (power to, with, and over) may be discovered in narrative constructs (e.g., narrative structure, communication forum). We suggest that the dilemma of measuring the “unobserved” in power may be addressed methodologically using a counterfactual (e.g., experiment, comparative study). Finally, we uphold the use of keystone NPF variables (e.g., policy decisions, attention) as proxy measures of the outcomes of narrative power in the policy process. Taken together, this model advances the operationalization and measurement of narrative power in the policy process.