Browsing by Subject "Biology"

Now showing 1 - 20 of 48
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    The Anatomy of Flacobdella Pediculata
    (1908-08) Hemingway, Ernest E.
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    Application of Systems Biology Analysis to Hepatic Injury Following Hemorrhagic Shock
    (2014-05) Determan, Charles Edward Jr
    Introduction: This dissertation is focused on the metabolomic and transcriptomic changes that occur as a result of carbohydrate prefeeding during hemorrhagic shock and trauma within the liver of a porcine model. The risk of trauma and hemorrhagic shock continues to be an important issue in both military and civilian sectors. As such, we explored the impact of a prior fed state upon the overall response to hemorrhagic shock and resuscitation. The primary hypotheses were that changes in metabolism at the metabolomic and transcriptomic levels would be dependent upon the fed state. In addition, this thesis explores a more comprehensive analysis of metabolomics datasets to standardize analysis and improve overall consistency.Materials and Methods: Algorithm comparison was accomplished using six commonly applied methods to three synthetic datasets, of different sample sizes, and three openly accessible published datasets. This comparison also incorporated metrics to measure consistency of identified features (i.e. stability) to provide further confidence in results. Metabolomics analysis was accomplished with nuclear magnetic resonance spectroscopy (NMR) and Chenomx software to profile and quantify metabolites in liver extracts. The metabolome was subsequently analyzed with partial least squares discriminant analysis (PLS-DA). Transcriptomics analysis was conducted using next-generation sequencing (NGS) technology to employ RNA-sequencing (RNA-seq) on mRNA extracts from liver biopsies. The RNA-seq data was analyzed using typical processing techniques to generate a count matrix and subsequently analyzed with the Bioconductor package EdgeR. Results: The comparison of algorithms showed that the best algorithm is associated with differently structured datasets (e.g. number of features, number of groups, sample size, etc.). Analysis of the liver metabolome revealed changes in carbon energy sources, amino acid metabolism, oxidative stress, and membrane maintenance. Transcriptomic analysis revealed changes in carbohydrate metabolism, cytokine inflammation, cholesterol synthesis and apoptosis. In addition, there is evidence of increased cytoskeleton reorganization which may correspond to a shrunken, catabolic state which provides and anti-inflammatory condition to mitigate cellular damage.Conclusion: The response to hemorrhagic shock and resuscitation is altered with respect to a fasted or carbohydrate prefed state. Metabolomics and transcriptomic analyses suggest altered metabolic pathways as a result of fed state. Altered carbohydrate metabolism was readily identified thereby confirming both methods were successful. Additionally, indications of membrane maintenance that follow cytoskeletal remodeling and cellular shrinkage are potentially reflected by 3-Hydroxyisovalerate and sn-Glycero-3-phosphocholine. These results provide further evidence for pre-conditioning (e.g. altered diet) and hypertonic resuscitation methods to possibly improve patient outcome. Further research is required in alternative prefeeding substrates (e.g. protein, lipid, etc.) as well as improving the integration of different systems level datasets to understand more thoroughly the systemic effects of hemorrhagic shock and resuscitation.
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    Chloroplast capture between Clarkia xantiana xantiana and Clarkia xantiana parviflora
    (2022) Suri, Amal M.
    Introgression occurs when genetic material from one gene pool gets incorporated into another gene pool. Introgression of chloroplast genomes is when one species inherits the chloroplast genome of another species, termed chloroplast capture. Understanding introgression can provide invaluable insight into reproductive barriers and speciation. Clarkia xantiana xantiana and Clarkia xantiana parviflora are subspecies that diverged about 65,000 years ago. Subspecies xantiana is an outcrossing species, while ssp. parviflora is a selfing species. We hypothesized that chloroplast capture is likely occurring between the two subspecies in sympatric areas, where they co-occur. In this study, we performed a phylogenetic analysis with about 200 complete chloroplast genomes of the subspecies from 6 different hybrid zones and 16 allopatric sites to determine whether chloroplast capture occurred. Additionally, we sampled more vigorously from 4 sympatric sites, where we then performed Polymerase Chain Reaction on those individuals to determine chloroplast genotype. In accordance with current theory, we found that chloroplast capture was asymmetric such that, chloroplasts flowed mainly from the selfing species, ssp. parviflora, into the outcrossing species, ssp. xantiana. There was, however, notable variation in asymmetry among sympatric populations.
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    Comparison of Carbonyl Levels in Young and Old Rats
    (2009-04-08) Brancel, Kiara
    Reactive oxygen species (ROS) are a natural by-product of aerobic cellular metabolism. They are highly reactive molecules which cause oxidative damage, such as carbonylation, to proteins, lipids and DNA. Because of the high metabolism and energy demand of skeletal muscle, it is especially susceptible to carbonylation. Thus the level of carbonylation can be used as a surrogate of the amount of oxidative damage to the tissue. This research uses fluorescent immuno-labeling to visualize the carbonyls within skeletal muscle cross sections in order to compare the carbonyl levels in young and old skeletal muscles. The comparative carbonyl levels are determined by the relative fluorescent intensity of the tissue. In addition, the carbonyl levels in mitochondria and the rest of the subcellular regions can be determined by observing the carbon-associated fluorescence in regions identified by labeling mitochondria with a separate probe. At the beginning of the project, we found one complication was that rat skeletal muscle tissue have high levels of native fluorescence that interfere with carbonyl detection. In order to eliminate this complication, a method was developed to photo-bleach the native fluorescence prior to labeling the carbonyls. Our preliminary results suggest that there was a difference in the levels of oxidative damage in specific areas of the cell. Preliminary results also indicate that older muscle tissue has accumulated a higher level of carbonylation and therefore more oxidative damage. Since with muscle aging the ability to produce force and muscle mass both decrease, these results suggest a correlation of oxidative damage with muscle changes attributed to the aging process. Greater understanding of aging mechanisms will hopefully give rise to the future development of interventional techniques.
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    Comparison of Carbonylation in Young and Old Rat Skeletal Muscle
    (2010-04-21) Brancel, Kiara
    Reactive oxygen species (ROS) are a natural byproduct of aerobic cellular metabolism. They are highly reactive molecules which cause oxidative damage, such as carbonylation, to proteins, lipids and DNA. Because of the high metabolism and energy demand of skeletal muscle, it is especially susceptible to the carbonylation. Thus, the level of carbonylation can be used as a quantitative estimate of the amount of oxidative damage to the tissue.
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    Death Receptors 4 and 5 and Idiopathic Pulmonary Fibrosis
    (2016) Miller, Scott;
    Idiopathic pulmonary fibrosis (IPF) is an irreversible lethal interstitial lung disease with an unknown cause, killing about 40,000 people per year. In IPF, lung fibroblasts become abnormally activated during tissue repair process, creating excessive scar tissue and avoiding cell death. The results from this research study suggest that the apoptotic pathway mediated by TRAIL (tumor necrosis factor-related apoptotic-inducing ligand) receptors, death receptors 4 and 5 (DR4 and DR5), is aberrant in IPF in the presence of a polymerized collagen matrix. Compared to control fibroblasts, IPF fibroblasts express lower levels of DR4 and DR5, making them more resistant to TRAIL-mediated apoptosis. Furthermore, our study suggests that DR4 may be regulated by the transcription factor FoxO3a. Previous research has shown FoxO3a to be important in conferring an apoptosis-resistant IPF fibroblast phenotype, and these results further support this idea.
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    Dopamine binds a D1-D2 heteromer coupled to Gq to activate a phospholipase C dependent mechanism to increase dendritic branching in the developing Medium Spiny Neuron
    (2018-05-04) Pelkey, Lauren, J
    The Medium Spiny Neuron (MSN) composes approximately 95% of the neurons in the striatum in the brain. MSNs are GABAergic neurons that modulate the movement and reward pathways. Cortical and substantia nigra pars compacta neurons release glutamate and dopamine on MSNs, respectively. These inputs are required for the MSN to grow into its typical highly branched, spiny morphology. The Lanier lab found that dopamine increases dendritic branching in the developing MSN. The goal of the current study is to find the mechanism by which dopamine enhances MSN dendritic arborization. The hypothesis is that dopamine increases dendritic branching by binding a D1-D2 heteromer coupled to Gq, which activates phospholipase C (PLC). A striatal-cortical co-culture prepared from day 16 mouse embryos was used to grow MSNs with their afferent cortical neurons. The experimental treatments were: 1) D1 receptor agonist SKF81297, D2 receptor agonist quinpirole, and both SKF81297 & quinpirole, 2) chemogenetic activation of Gq, and 3) PLC antagonist U73122. Treatments were administered in vitro at day 4, and regularly administered until fixation at day 19. It was found that SKF81297 and quinpirole, together and in isolation, were not able to replicate dopamine’s increased branching effect. In addition, it was found that Gq activation, using a chemogenetic approach, resulted in increased branching almost to the same extent as dopamine addition caused. Further, U73122 had no effect on branching on its own, but U73122 significantly attenuated dopamine’s branching effects. Taken together, this data support the hypothesis that dopamine enhances branching by binding a D1-D2 heteromer coupled to Gq, to activate phospholipase C.
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    The Effects of Radiation on Marrow Cell Differentiation
    (2009-04-08) Coghill, Kathleen
    With improved patient survival, cancer treatment induced bone loss (CTIBL) has become and increasingly serious complication of therapy. This study will be looking at the effect of radiation on a marrow cell line's potential to differentiate into osteoblastic, adipocytic, or fibroblastic cells. Alterations in cell differentiation may play a role in CITBL. Marrow stromal cells harvested from p53 knock out transgenic mice were plated into culture flasks. Twelve hours after plating the flasks were irradiated at different clinically relevant radiation doses. The flasks were fixed and stained following two weeks, four weeks, and six weeks of culture and separated into three different analytical groups looking at: Mineralization, Adiposity, and Gene Expression between the different sets of radiation doses. We are investigating the effects of radiation, time dependent cellular differentiation, and reductions in mineralization and adiposity. Preliminary data suggests an inverse relationship between osteoblastic and adipogenic differentiation by marrow cells in vitro following increasing doses of gamma irradiation. This may aid in understanding some fundamental mechanisms of Cancer-Treatment Induced Bone Loss.
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    Exosome-Mediated Protection Against Oxidative Stress: A Connection Between NRF2 And Exosomes
    (2016-12) Rust, Brittney
    The nuclear factor erythroid 2 (NF-E2)-related factor 2 (NRF2) transcription factor has been widely studied for its role as the master regulator of the response to oxidative stress. NRF2 has many mechanisms for protection including upregulation of antioxidant genes, metabolism genes, and proteolysis genes. Furthermore, it was found that a deeply conserved set of NRF2 target genes encode for proteins loaded into exosomes [1]. Exosomes are extracellular microvesicles that are secreted by cells in response to a variety of stimuli, including many stressors. Exosomes serve as a transport mechanism for proteins, RNA, DNA, and other molecules. Therefore, we hypothesized that exosome loading and release is a mechanism used by NRF2 to protect neighboring cells from stress in a non-autonomous manner. In an effort to validate that NRF2 regulates exosomes, I explored the following: (1) exosome release before and after NRF2 activation, (2) the RNA and protein content of NRF2-induced exosomes, and (3) the cytoprotective potential of NRF2-induced exosomes. Overall, based on these studies, we concluded that NRF2 activation induces exosome release, and exosomes are generally enriched for cytoprotective protein SQSTM1. However, although NRF2-induced exosomes were cytoprotective in some assays, this response was not robust enough for me to conclude that NRF2-induced exosomes can protect naïve cells from oxidative stress. Thus, exosomes provide a potential mechanism for NRF2 to provide nearby cells with resources to combat oxidative stress, but further research is necessary to determine whether this mechanism is used in vivo.
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    Exploring Undergraduate Students' Experiences of the Culture of Scientific Research in a Course-based Undergraduate Research Experience
    (2021-09) Dewey, Jessica
    Scientific research has its own culture that can be difficult to enter. Students often learn about and interact with the scientific research culture for the first time as undergraduates when they participate in research experiences such as Course-based Undergraduate Research Experiences (CURE). However, the lack of a single framework that describes the culture of scientific research has resulted in little work specifically exploring students’ experiences and perceptions of this culture, especially in the context of CUREs. This three-paper dissertation fills this gap in the literature by establishing the Culture of Scientific Research (CSR) Framework and using the framework to explore undergraduate students’ experiences and perceptions of the culture of scientific research in the context of a CURE. In the first study, a systematic literature review was performed to identify cultural aspects of scientific research described in prior work. Specifically, the Practices, Norms/Expectations, and Values/Beliefs of scientific research were identified and organized into the CSR Framework. This framework was also validated for biology with practicing biological researchers. The second study presents the first application of the CSR Framework in the context of a biology CURE. Students were interviewed about their feelings of participating in the CURE. The cultural aspects of scientific research that students mentioned in these interviews, as well as their perceptions of those aspects, were investigated. Students’ responses were also compared across the type of project students performed (bench-based vs. computational). Students mentioned nearly all of the aspects in the CSR Framework, but a small number of aspects were the most salient to students. Additionally, bench-based and computational students found different Practices to be salient and held different perceptions of the same cultural aspects. The third study compared the experiences and perceptions of women and men participating in the same CURE course that was the context for the second study. The results found that women and men mentioned many of the same cultural aspects of scientific research and perceived them in similar ways. However, there were subtle differences in how women and men talked about certain aspects. Altogether, these studies provide insight into undergraduates’ experiences and perceptions of the culture of scientific research. More specifically, this work broadens the current understanding of students’ experiences in CUREs and provides a model for how subtle but important differences between students’ experiences can be identified. Understanding students’ experiences of the scientific research culture will allow for future work that drives changes to the culture of scientific research to enable equitable access for all students.
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    Finding Mercie In A College Biology Course For Nonmajors
    (2023-05) Andicoechea, Jonathan
    This dissertation investigates how the numerical representation of women in small collaborative groups influences their learning in a college biology class for non-majors focused on sex, gender, and society. Prior to the start of the semester, the researchers divided students into all-male, all-female, or mixed-gender groups of varying sex ratios. The investigators then addressed how the identity-driven local ecology of these groups shaped student engagement and the emergence of scientific reasoning. Results from two separate but related studies demonstrated that all-female groups outperformed mixed-gender and all-male groups across a range of behavioral, affective, and performance metrics. Yet, a narrower focus on the emergence of scientific reasoning roles and behaviors in all-female groups revealed striking variation among these groups. One all-female group routinely used higher-order science reasoning moves (e.g., providing evidence and reasoning for scientific claims), while another failed to perform academically, because students in this group struggled interpersonally. Data from semi-structured interviews suggest that all-female grouping does increase a sense of belonging in female-identified students—especially if they previously experienced invidious discrimination in science spaces and are thus vulnerable to social identity threat. However, the results also suggest that this type of grouping does not function as a panacea, and that additional social identities and lived experiences modulate whether single-sex grouping results in learning gains or deficits. Further, the second study also suggests that the development of discipline-specific skills depends heavily on the interpersonal knowledge and emotional maturity of students in the group.
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    Functional Magnetic Resonance Imaging and Spectroscopy of Ovarian Cancer
    (2013-09-23) Rattigan, Deviney;
    The goal of this study was to determine the feasibility and clinical utility of acquiring quantitative, multi-parametric, high-field Magnetic Resonance Imaging/Magnetic Resonance Spectroscopy for presurgical characterization of normal ovaries, benign and malignant ovarian tumors as well as to assess the response to chemotherapy.
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    How Global Change Shapes Our World: Nitrogen and Salt Addition Affect Phytoplankton Morphology in a Small Freshwater Lake
    (2024) Rodgers, Amanda;
    Global environmental change has accelerated the deposition of nitrogen and salt into freshwaters. These changes affect the morphology of freshwater microbes, especially phytoplankton, which serve as primary producers for these ecosystems. Morphology reflects a microbe’s response to energy demands, selection, and environmental disturbance. In this pilot experiment, a handmade suspension device held samples from Cedar Bog Lake (East Bethel, MN) in three nitrogen conditions (17.6 mM NaNO3, 9 mM NaNO3, 0 mM NaNO3) crossed with two salt conditions (10 mM of NaCl or 0 mM of NaCl) plus a DI water control for BG11 media in triplicate on the surface of the lake for three weeks. I used flow cytometry to quantify community-level within-sample morphology using circle fit, area-based diameter (ABD) volume, aspect ratio, elongation, ABD area, compactness, particles/mL, and perimeter. A principal components analysis (PCA) revealed trait correlations between ABD area and ABD volume, and between circle fit, elongation, and compactness. A two-way analysis of variance (ANOVA) on the first three principal components (highly significant, accounting for 94.89% of the total variance) revealed a significant effect of nitrogen and a marginally significant effect of salt on principal component three, but no effect of treatment on the first two principal components. Nitrogen had a significant effect on particles/mL but treatment did not affect any of the other morphological traits individually. These results indicate that climate change has a complicated effect on freshwater microbial morphology at the community level. Future studies should focus on long-term changes in morphology in the field, focusing on the effects of nitrogen.
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    Identifying the Role of Transcription Factor 12 in Colorectal Cancer
    (2012-04-18) Schaleben- Boateng, Dane
    Colorectal cancers (CRCs) are caused by genetic mutations in one intestinal cell that cause it to multiply uncontrollably. This abnormal proliferation forms a tumor that can continue to progress from a benign state to malignancy due to more genetic mutations. In a previous study our lab noted that the gene Transcription factor 12 (Tcf12) was frequently mutated in CRC tumors. To determine whether mutation of Tcf12 suppresses or enhances tumor formation, we are analyzing normal mice and mice already prone to develop CRC that were engineered to lackTcf12 function. Preliminary data suggests that these mice have more tumors due to the lack of Tcf12 expression. These results suggest that Tcf12 is a tumor suppressor gene, which normally inhibits tumor formation unless it is silenced due to mutation. We expect that by identifying the exact role of Tcf12 in CRC this will provide a new target for research and development of CRC treatments or biomarkers.
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    The importance of the N13 residue to the activity of the metabolite repair enzyme 2-succino lyase (2SL)
    (2022) Park, Sophia;
    A wide variety of metabolite damage reactions exist alongside long-established biochemical pathways. Succination is a spontaneous damage reaction that can occur between fumarate, an intermediate in the citric acid cycle, and cysteinyl residues of proteins. Succination of cysteinyl residues produces the toxic protein modification S-(2-succino) cysteine (2SC). High cellular levels of 2SC are found in association with mitochondrial stress, diabetes, and cancer, directly contributing to the pathogenesis of human diseases through their various deleterious effects on important metabolic proteins. Recently, a catabolic pathway to repair 2SC damage has been identified in the bacterial species Enterococcus italicus and Dickeya dadantii. The breakdown step in this pathway is performed by 2-succino lyase (2SL), a member of the lyase I-like superfamily of enzymes. The metabolite repair function of 2SL is clear. However, the key active site residues that enable 2SL activity, as opposed to the many other diverse functions of lyase Ilike superfamily enzymes, are unknown. Here we explore the significance of one candidate residue, N13, to 2SL activity by introducing a point mutation (N13I) and comparing the mutant 2SL activity to the wildtype 2SL (WT). A spectrophotometric coupled enzyme assay was performed to determine the kinetic parameters of both the N13I and WT. N13I had a significantly lower Vmax and a significantly higher Km. However, this extreme difference in parameters contradicts the preliminary HPLC data we collected which indicated a much smaller activity difference between the WT and N13I enzymes. We anticipate that the continuation of this research will contribute to the efforts to functionally characterize other lyase I-like superfamily members as 2SC lyases. More broadly, we hope that the characterization of 2SC lyases will uncover their associated—and potentially clinically significant—metabolite repair pathways.
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