Increased mitochondrial oxidative stress causes fatigue and metabolic dysfunction in muscle tissue. It is unclear whether the oxidative stress is due to elevated production or impaired consumption of reactive oxygen species (ROS). The purpose of this study is to test whether the capacity of the antioxidant defense system is impaired or the mitochondrial ROS production rate is elevated in response to chronic changes in mitochondrial oxidative stress. To experimentally manipulate mitochondrial oxidative stress, we use an inducible mouse model to knockdown superoxide dismutase 2 (SOD2) in skeletal muscle and heart to increase oxidative stress, and exercise training to decrease oxidative stress. Knockdowns (KD) or littermate controls (CON) performed a six-week voluntary wheel running (EX) or sedentary control intervention (SED). Following completion of the intervention, I isolated heart and skeletal muscle mitochondria using differential centrifugation. I measured mitochondrial hydrogen peroxide (H₂O₂) production rate and tested the antioxidant capacity by treating isolated mitochondria with Auranofin (AFN) or 1-chloro-2,4-dintrobenzene (CDNB), which inhibit the thioredoxin and glutathione S-transferase components of the mitochondrial antioxidant defense system, respectively. KD heart and skeletal muscle had similar absolute H₂O₂ production rates compared to CON, but normalized to oxygen consumption the KD had significantly higher H₂O₂ production. Since absolute H₂O₂ production under vehicle conditions was not different, this suggests that the antioxidant capacity adapts to meet the changes in mitochondrial H₂O₂ production. We will collect data from the exercise-trained cohort next month. I expect to see an increase in H₂O₂ production rate and antioxidant capacity in both groups due to the increased mitochondrial biogenesis from exercise training. These results demonstrate that chronic increases in mitochondrial oxidative stress decrease mitochondrial H₂O₂ production capacity from skeletal muscle.

Understanding the ecology of vegetation systems in Earth’s past in response to past warming events helps contextualize how they might respond to current climate events. Ecological succession is an ecosystem dynamic in which plant species with different life strategies replace each other as plants colonize a disturbed habitat. Reconstructing which successional stage a fossil plant represents is an important step in reconstructing this process in the past. However, fossil plants preserve a limited number of traits. Leaf vein density (LVD) is a trait that relates to maximum photosynthetic rates and can be measured from fossil leaves, but there is limited empirical evidence for how it varies across succession in temperate deciduous forests. To address this knowledge gap, our study measures LVD of modern plant communities across a successional gradient in western North Carolina. We hypothesize that plants in younger forests have greater access to sunlight due to a less established canopy and will therefore have higher LVD to support a higher photosynthetic rate. As succession progresses and the canopy closes, we hypothesize that LVD will decrease with reduced light availability. Samples were taken from five sites in western North Carolina that vary in how long forest re-growth occurred following clear-cut timber harvesting, 4, 21, 44, 94, and roughly 200 years. At each site, leaves were collected and sampled at a community scale and were chemically treated to create images that highlight the veins. We then used ImageJ to measure LVD. The community mean and variance of LVD across succession will be analyzed, using both unweighted and weighted approaches, to test our proposed hypothesis of decreasing LVD through succession. Preliminary results suggest a potential LVD decrease as hypothesized but driven more by understory species rather than dominant tree species. Future work will refine interpretations and consider implications for the fossil record.

The Miocene Climatic Optimum (MCO) (17-14 Ma) represents the most recent significant global warming event and provides valuable insights into the future of our planet with higher CO2 levels and warmer temperatures. The Mascall Formation in central Oregon contains a fossil plant assemblage that reflects the vegetation present during the height of the MCO. Despite over 50 years of research in this formation, there is still much to learn about the ancient plant community. For instance, a fossil specimen, consisting of several leaves, that was collected recently exhibits similar trait to bamboo, which represents a new fossil finding in this formation. This project seeks to confidently assign this specimen to the bamboo subfamily Bambusoideae. By analyzing morphological and vein architectural features of the leaves using various microscopic techniques and digital photography. In addition to studying the specimen itself we explore the fossil plant silica bodies (phytoliths) also present in the surrounding substrate to provide independent evidence that bamboo was present in the region. The phytoliths can then be compared to those of current Native American bamboo to find evidence for relatedness or if it was part of some other lineage of bamboo, whether extinct or still present in South America or Eastern Asia. If the specimen turns out to be bamboo, it would have implications for the climate and ecology of eastern Oregon during the MCO as bamboo was not assumed to have previously been present.  

Grasses (family Poaceae) are highly diverse (~11,800 species), cover nearly 40% of Earth’s ice-free land surface, and play critical ecological and economic roles. Grasses have evolved a variety of unique traits, including an exceptionally high accumulation of silicon in the form of biological silica bodies (phytoliths) in some lineages. Silicon accumulation confers resistance to both abiotic and biotic stresses, including drought and salinity resistance, herbivore defense, and structural support. Despite the role of silicon in the enormous success of grasses, a clear picture of the exact drivers of silicon accumulation in grasses across species and environments has not yet emerged. I hypothesize that elevated silicon concentrations are primarily driven by environmental stress, most notably high temperatures and low precipitation. To test this hypothesis, I used X-ray fluorescence to analyze the leaf silicon concentration of 482 grass leaf samples, encompassing approximately 200 species across all 12 grass subfamilies. Using occurrence records from online databases, I identified the realized climate niche and its environmental conditions (e.g., temperature, precipitation) for each sampled species. The next step is to collect geolocation data from each individual sample, which will be combined with the climate niche data of its species. By comparing the relationship between a plant’s climate niche, its individual growing conditions, and its silicon concentration, a better understanding of environmental drivers of silicon will begin to emerge. Preliminary results taking into account only climate niche and silicon concentration showed no relevant correlations, illustrating the need for individual growing condition data. Because many of the stresses that silicon helps to alleviate are also those that will worsen under climate change (high temperature, drought, insect herbivory), an improved understanding of the environmental drivers of silicon accumulation will allow us to better prepare for the impacts of climate change on our agricultural and ecological systems.

Nanoparticles are drug delivery carriers on the nanometer-length scale, and are promising targeted drug delivery solutions due to their small size and tailorability. However, current materials used to produce nanoparticles are synthetic and typically lead to large amounts of chemical waste and high costs. To explore more sustainable technologies, the Nance and Roumeli labs established a novel bacterial cellulose nanoparticle (BCNP) platform. BCNPs are formulated with a bacteria that produces cellulose and no byproducts when cultured, allowing for less reagents required and non-toxic biodegradable wastes. To be comparable to synthetic nanoparticles as a drug delivery platform, BCNPs must load and release drugs and be biocompatible with mammalian cells. In this project, I explored the tunability of BCNPs through size modification, performed cytotoxicity studies on a microglial cell line, and carried out drug loading studies. I found that higher mixing speeds during BC culturing led to a smaller BCNP size and variable particle concentration. Through cytotoxicity analysis in cell culture, I showed BCNPs were not toxic. Ongoing studies are assessing BCNP cytotoxicity as a function of BCNP dose. To demonstrate drug loading, I am incorporating catalase, an enzyme with the ability to mitigate oxidative stress markers, into BCNPs to analyze their efficacy in an in vitro model of oxidative injury. These results show BCNPs have the potential to become a sustainable nanomedicine platform and provide an important step towards reducing the environmental impact of synthetic nanoparticles.

While flocculation is a desirable trait for brewing yeast because it eases the removal of cells from beer after fermentation, other modes of cell-to-cell adhesion can be detrimental to the brewing process. Mother-daughter separation defects cause cells to form large aggregated clusters which use more oxygen, produce a lower fermentative yield, and require more head space during fermentation. These defects can be caused by mutations to a number of genes, which makes a targeted genetic approach challenging. In this work, we used experimental evolution to eliminate mother-daughter separation defects present in a widely used brewing strain. Cells with this defect are less buoyant and settle faster than non-adhering cells. We used this property to select against cells with this defect by letting the cultures settle and propagating only cells present in the top layer of the media. We propagated top-layer cells for approximately 300 generations (about two months), collected daily optical density measurements, and conducted settling assays. Over time, we found that large, branched cell clusters decreased in frequency in our top-layer samples while the amount of single cells increased, which we confirmed through microscopy and optical density measurements. We characterized the mutations that drive this strain’s separation defect using whole genome sequencing of the evolved and ancestral populations. This project demonstrates how experimental evolution can be used to select against less desirable traits in commercially important yeast strains. Future research could implement similar or reciprocal methods to evolve for decreased or increased flocculation respectively.

Methane is one of the most attractive targets for controlling near-term climate change due to its short lifespan and high potency (34 times that of CO₂). Methanotrophs are bacteria that can consume methane and convert it into CO₂ and biomass. There is growing interest in using these bacteria to mitigate greenhouse gas emissions from sources such as landfills, agricultural feedlots, and abandoned coal mines. However, a key challenge is that to achieve large scale methane sequestration, as well as economic viability of deploying these in the field, we have to significantly improve the growth of methanotrophs at low concentrations of methane. Regulatory genes play an important role in determining how bacteria allocate energy. By deleting specific regulatory genes and measuring the growth rate of these mutants under low methane conditions, we can assess their importance in helping the bacteria survive and thrive in nutrient-limited environments. Using this approach, we can also replicate mutations that have naturally emerged in strains cultivated for over a year under low methane conditions. This allows us to confirm whether these mutations provide a growth advantage. By identifying and testing key genes involved in low-methane growth, we are guiding efforts to engineer a more efficient and resilient strain for real-world applications.

The obsolescence of U.S. Navy parts pose significant challenges in managing diminishing manufacturing sources and material shortages (DMSMS). This research focuses on predicting and mitigating part shortages by analyzing case resolution times, leveraging machine learning and natural language processing (NLP) techniques, and developing data-driven methodologies. In collaboration with the Naval Undersea Warfare Center (NUWC) Keyport division, data is sourced from Navy systems that track part availability and supplier management, providing critical insights into supply chain vulnerabilities. To address these challenges, multiple predictive models were developed, incorporating classification, regression, and clustering techniques. Initial model development utilized publicly available datasets to refine methodologies and test various approaches. Extensive exploratory data analysis (EDA) was conducted to identify patterns in supply chain issues, with a focus on text-based insights and categorical variables with a company response factor. Sentiment analysis and machine learning techniques, including logistic regression, support vector machines (SVM), gradient boosting, and word embedding models, were explored to enhance predictive capabilities. Our work focused on refining these models using real-world Navy data, optimizing classification strategies, and expanding NLP applications for more proactive supply chain management. These advancements aim to improve operations and minimize delays by reducing the time required to resolve cases associated with obsolescent parts.

Learner experiences are under-examined in environmental learning research. Our research consists of studies of experiential aspects of environmental learning by undergraduate researchers, conducted over three years, culminating in a focus on how community-engaged learning (CEL) fosters connections between social justice, ecological consciousness, and student well-being. Research questions we came to consider were: What connections are students drawing between social justice and ecological consciousness? How does engaging in community-based environmental learning affect students’ well-being? Methods such as coding, memoing, reflecting through learning diaries, whole-part-whole analysis, and group collaboration all contributed to establishing an adaptable infrastructure of undergraduate research (UGR) in experiential aspects of the course. Our findings on students’ connections between social justice and ecological consciousness revealed their thoughts about becoming advocates, or “leaning toward justice”, though they had diverse prior knowledge and experiences. Findings on the CEL experience within the large course with regard to well-being showed how students integrate environmental education with community engagement, particularly in addressing issues such as food insecurity, environmental justice, and language barriers for immigrant communities. Some key themes found were that CEL promoted personal growth through unexpected learning, connection to nature & emotional relief, and a sense of belonging in research participants’ experiences. The significance of this research has been to establish a way for undergraduate researchers to drive experiential learning research, and to find research outcomes about how learning experiences foster awareness of social and ecological justice, encouraging students to see themselves as advocates for change. 

The Lidstrom Lab aims to better understand methane-consuming microbes (also called methanotrophs) so that we can develop technologies to remove anthropogenic methane emissions, which will reduce the severity of global warming. Our research explores how the methanotroph Methylotuvimicrobium buryatense 5GB1C can be bioengineered to grow well at the low methane concentrations found in human-made emission sites, while providing value-added products like biomass from dead bacteria that can be used as animal feed. Understanding bacterial methane utilization will allow us to create effective biocatalysts at a far lower monetary and environmental cost. My research project involves deleting cytochrome genes that may be important for the 5GB1C strain to grow in low methane conditions. Manipulating these genes may allow for further improvement of growth at low methane. My targets are three genes that encode cytochromes, which are electron carriers that take electrons from particular reactions and supply them to other reactions that are otherwise energetically unfavorable. My hypothesis is that these cytochromes are involved directly in supplying 5GB1C with electrons needed for the oxidation of methane into methanol. If these cytochromes supply electrons required for methane consumption at low methane, then deleting them would generate a mutant that would grow poorly on methane because it lacks the electron carrier(s). I have generated two possible cytochrome deletion mutants and continue to work on a third cytochrome. Once the mutants that can be generated are sequenced to verify the deletions, cultures will be grown under low methane and methanol conditions to determine how their ability to grow has been affected by the knockout mutations. In this manner, our lab is building a valuable knowledgebase of genes that are suitable for manipulation to improve growth in low methane for the technologies that one day will help curtail the worsening of global warming.

Methane is an extremely potent greenhouse gas, with a warming potential 86 times greater than that of CO2 on a 20-year timescale, and is therefore a top priority for mitigation efforts to combat climate change. Methanotrophic bacteria, such as M. buryatense 5GB1C, metabolize methane as their main source of carbon and chemical energy, a trait that could help slow climate change by reducing emissions. A major obstacle is the rate at which methane consumption occurs at low methane concentrations, which tends to be too low to be appreciable. This project seeks to answer whether currently unknown genes involved in the growth of M. buryatense 5GB1C on low methane could be discovered by comparing its genome with that of a closely related methanotroph, M. alcaliphilum 20Z. While the two have very similar genomes and metabolisms, M. alcaliphilum is not able to grow at low methane concentrations (500 parts per million), while M. buryatense is. I analyzed the two genomes and isolated all genes present in M. buryatense without homologs in M. alcaliphilum. Because they are unique to M. buryatense, they may be involved in the observed growth difference. I systematically performed targeted deletion mutations on many of these candidate genes, and then tested them for growth on low methane compared to the wild type strain, looking for any defect that would suggest a gene directly essential to growth at 500ppm. I confirmed several genes to have no impact on growth at low methane, as well as one that appears to be essential to growth in any conditions, and anticipate reaching conclusions on several more mutants. These findings will help to develop microbial methane mitigation technologies that can be utilized in a great range situations and at a larger scale, essential characteristics for a global impact.

Stress resilience, the ability of cells and tissues to adapt to stimuli, declines with age. Skeletal muscle contraction is a physiological stressor when repeated through exercise training enhances stress resilience and mitigates age-related comorbidities. However, as the body's capacity to mount adaptive responses diminishes with age, the extent to which this decline affects physiological adaptation to stress remains unclear. This would guide future therapeutic strategies surrounding muscular degeneration over the lifespan. The goal of this study is to assess the magnitude of stress response activation across metabolic, oxidative, proteostatic, and heat shock stress response pathways. We use gene expression analysis to evaluate the transcriptional response to controlled in vivo muscle stimulation, providing insight into age-related differences in stress resilience. Young (6mo) and old (23-24mo) male and female mice (C57Bl/6JNia) underwent an in vivo fatiguing muscle stimulation (Stim) or served as an unstimulated control (Unstim). Three hours following the stimulation both right and left limb muscles were collected and processed for gene expression analysis. Following stimulation and collection, I performed tissue processing, RNA extractions, and RT-qPCR assays on muscle tissue. There was a significant increase in PGC1a, HMOX1, TRIM63, and HSPa1a genes in response to muscle stimulation when compared to the unstimulated limb within the same animal. The magnitude of these changes in response to stimulation were not different across age or sex. Analysis of basal changes in unstimulated groups across age and sex is planned for next month. These preliminary results suggest no significant age or sex differences across multiple pathways of stress resilience in skeletal muscle. A strength of this study design is that we use a combined within- and between-animal analysis of both stimulated and unstimulated conditions to control for any potential variations associated with each age, sex, and stimulation condition, increasing confidence in our results.

Climate change and anthropogenic pollution have led to a rise in coral bleaching events. These bleaching events cause the loss of corals’ symbiotic algae cells, depleting coral colonies’ energy and leaving them vulnerable to starvation and death. This study aimed to understand whether the sex of gonochoric corals (in which colonies are either male or female) has any correlation to corals’ growth and development, with implications for corals’ response to bleaching events. For the gonochoric species Porites compressa, preliminary results indicate that female colonies develop their gametes earlier in the year compared to males. Energy conserved to produce these lipid-rich eggs may limit the overall growth of female colonies. However, unlike male colonies, females might be able to resorb their eggs to better recover from bleaching events. In summer 2023, twenty-four P. compressa colonies from Kāne‘ohe Bay, HI were stained with an alizarin dye, sexed as male or female based on sperm/egg histology, and returned to the reef to measure one year of skeletal growth. Following their collection in the summer of 2024, eighteen surviving colonies were scanned using an Artec Spyder to produce 3D models revealing colony surface areas and volumes. We then cut cross-sections of each colony to reveal their alizarin growth bands from 2023, allowing us to determine the amount of growth from 2023-24. We anticipate that differences in growth rates will show that female colonies are saving energy by limiting their growth, leaving them less susceptible to bleaching compared to male colonies.