Latest content added for UNT Digital Library Partner: UNT Librarieshttps://digital.library.unt.edu/explore/partners/UNT/browse/?fq=str_degree_department:Department+of+Biological+Sciences&start=20&sort=added_d2023-07-08T22:24:53-05:00UNT LibrariesThis is a custom feed for browsing UNT Digital Library Partner: UNT LibrariesThe Impact of Invasive Salmonids on Ecosystem Functioning in South America's Sub-Antarctic Inland and Marine Waters2023-07-08T22:24:53-05:00https://digital.library.unt.edu/ark:/67531/metadc2137564/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2137564/"><img alt="The Impact of Invasive Salmonids on Ecosystem Functioning in South America's Sub-Antarctic Inland and Marine Waters" title="The Impact of Invasive Salmonids on Ecosystem Functioning in South America's Sub-Antarctic Inland and Marine Waters" src="https://digital.library.unt.edu/ark:/67531/metadc2137564/small/"/></a></p><p>Invasions from coho salmon were first reported in the Cape Horn Biosphere Reserve (CHBR) in 2019 which is the most southern distribution registered to date. The CHBR is known for its high number of endemic species and unique biodiversity, such as the native fishes Galaxias maculatus and Aplochiton taeniatus. There are now three invasive salmonid species in the rivers of CHBR and are a potential threat to the native fish taxa. Stable isotope and gut content analysis were used to understand resource utilization by both native galaxiid and invasive salmonid taxa, as well as aquatic macroinvertebrates and riparian spiders. The natural laboratory study approach applied to this research, allowed for comparisons of differences within streams that contain conditions in which fish do not occur naturally, to sites in which high densities of invasive salmonid exist. Analysis of the trophic niche and diet in this study showed the importance of marine resource use by the native galaxiid and coho salmon juveniles supported with elevated δ15N and δ34S ratios. Diet analysis also confirmed there was the highest similarity between the coho salmon juveniles and the native fish. Altered behavior and habitat use was shown through the isotope and diet analysis for the galaxiid in snow melt streams which could be due to the high density of invasive salmonids in these streams. The invasive salmonids were found to impact aquatic macroinvertebrate populations, specifically larger bodied Trichoptera abundance. Aquatic insect emergence was negatively correlated to salmonid densities. The aquatic insect emergence revealed alterations with significantly higher biomass of aquatic insect emergence in upstream sites without invasive fish. Lastly, aquatic insect predator (Hydrobiosidae: Rheochorema sp.) exhibited a suppressed trophic position in rivers with invasive salmonids. An unexpected finding from the study was the refugium stream habitat conditions that has been shown to be important for conserving the native fish in the CHBR. We conclude that the impacts from invasive species are significant enough to disrupt lower trophic levels especially aquatic insects. The altered aquatic emergence and insect behavior have the potential to disrupt food webs and ecosystem functioning in the southernmost protected ecoregion in the world.</p>Role of MicroRNAs and Their Downstream Targets in Zebrafish Thrombopoiesis2023-07-08T22:17:50-05:00https://digital.library.unt.edu/ark:/67531/metadc2137555/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2137555/"><img alt="Role of MicroRNAs and Their Downstream Targets in Zebrafish Thrombopoiesis" title="Role of MicroRNAs and Their Downstream Targets in Zebrafish Thrombopoiesis" src="https://digital.library.unt.edu/ark:/67531/metadc2137555/small/"/></a></p><p>Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, there is limited information on microRNAs' role in zebrafish thrombopoiesis. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, I identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. Knockdown of three microRNAs, mir-7148, let-7b, and mir-223, by the piggyback method in zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. I then verified these findings in zebrafish larvae after the knockdown of the above microRNAs followed by an arterial laser thrombosis assay. I concluded mir-7148, let-7b, and mir-223 are repressors for thrombocyte production. Furthermore, I explored let-7b downstream genes in thrombocytes detected by RNA-seq analysis and chose 14 targets based on their role in cell differentiation (rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8, and lbx1b) that are transcriptional regulators. The qRT-PCR analysis of expression levels the above genes following let-7b knockdown showed significant changes in the expression of 13 targets. I then studied the effect of the 14 targets on thrombocytes production and identified 5 genes (irf5, tgif1, irf8, cebpa, and rorca) that showed thrombocytosis and one gene ikzf1 that showed thrombocytopenia. Furthermore, I tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223. I also identified that tgif1, cebpa, ikzf1, irf5, irf8, and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a opposite expression profiles following let-7b and mir-223 knockdowns (decreased and increased expression, respectively) and knockdown of ikzf1 resulted in thrombocytopenia I confirmed a definitive role for ikzf1 using an ikzf1 mutant obtained from the Zebrafish International Resource Center (ZIRC). The arterial laser thrombosis assay of ikzf1 mutant progeny confirmed our piggyback hybrid knockdown results. Taken together, these studies shed light on understanding the role and the regulatory effects of zebrafish microRNA on thrombopoiesis and identified novel downstream target transcription factors for let-7b and mir-223.</p>Conservation, Connectivity, and Coexistence: Understanding Corridor Efficacy in Fragmented Landscapes2023-07-08T22:07:09-05:00https://digital.library.unt.edu/ark:/67531/metadc2137543/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2137543/"><img alt="Conservation, Connectivity, and Coexistence: Understanding Corridor Efficacy in Fragmented Landscapes" title="Conservation, Connectivity, and Coexistence: Understanding Corridor Efficacy in Fragmented Landscapes" src="https://digital.library.unt.edu/ark:/67531/metadc2137543/small/"/></a></p><p>Conservation corridors, areas of land connecting patches of natural land cover, are frequently cited and implemented as a restorative strategy to counteract fragmentation. Current corridor ecology focuses on experimental corridor systems or designed and built conservation corridors to assess functionality. Such systems and designs are typically short, straight swaths of homogenous land cover with unambiguous transitions between patches. Quantifying the degree to which amorphous landscape configurations, tortuosity, and heterogeneity of land cover and land uses within the corridor has on functional connectedness is a crucial yet overlooked component of corridor efficacy studies. Corridor literature lacks a robust and repeatable methodology for delineating existing landscape elements, recognizing arbitrary edges, and identifying the start and end of ambiguous transitions between the patches and corridor. Using a set of landscapes being studied as part of a global assessment of corridor efficacy, I designed a workflow that standardizes the boundary of corridor-patch interfaces. The proposed method is a quantitative and repeatable approach that minimizes the subjectivity in corridor delineations. This research investigates the degree to which the existence of a corridor modifies the structural and functional connectivity between patches connected by a corridor compared to an intact reference area.</p>Combined Effects of Polycyclic Aromatic Hydrocarbons and Ultraviolet Light on Benthic and Pelagic Macroinvertebrates2023-07-08T21:57:51-05:00https://digital.library.unt.edu/ark:/67531/metadc2137527/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2137527/"><img alt="Combined Effects of Polycyclic Aromatic Hydrocarbons and Ultraviolet Light on Benthic and Pelagic Macroinvertebrates" title="Combined Effects of Polycyclic Aromatic Hydrocarbons and Ultraviolet Light on Benthic and Pelagic Macroinvertebrates" src="https://digital.library.unt.edu/ark:/67531/metadc2137527/small/"/></a></p><p>Crude oil commonly enters freshwater aquatic ecosystems as thin sheens forming on the water surface. Oil contains mixtures of toxic compounds called polycyclic aromatic hydrocarbons (PAHs), some of which are known to be photodynamic, increasing toxicity when combined with ultraviolet radiation. Benthic macroinvertebrate communities are commonly utilized as bioindicators, and as such rely on abundant data in literature concerning benthic macroinvertebrates' relative tolerances to a wide range of pollutants. A series of 10 plastic traps, half of which were filtered from UV radiation, were deployed in an urban pond for 27 days to determine colonization preferences of benthic macroinvertebrates to UV exposure. Results of this in situ experiment indicated that the majority of aquatic insects collected from traps inhabited the UV exposed treatment group, particularly the nonbiting midge, Chironomidae. A series of bioassays were then completed to investigate the sensitivities of a Chironomidae species to thin sheens of crude oil in the presence and absence of UV radiation. All bioassays were conducted using 10 day old Chironomus dilutus larvae cultured in the lab. The series of C. dilutus bioassays were all conducted under the same water quality parameters, temperatures, and oil sheen dosing methods, under a 16:8 photoperiod and exposed to 16 h UV per day. Five replicates (n = 20) were loaded into 350 mL glass crystallizing dishes and exposed to four treatments for 96 hours: no UV/with sheen, with UV/no sheen, both UV and oil sheen, and a control. Three assays with 175 mL water volume were completed, one with no sediment, one with silica sand, and one with fine sand. Sediment type had a significant effect on mortality (p < 0.0001), but significant effects of UV or PAHs were not found. Two more C. dilutus assays were completed with identical parameters as the latter two with sediment, except a decreased water volume of 90 mL was used to bring the sheen closer to sediment. There was a significant effect of PAHs on mortality (p = 0.0003), however, no clear trend showing PAHs driving mortality. Results showed no significant effects of UV, sediment type, or relationship between UV and PAHs. A final bioassay was completed to compare phototoxic effects of PAHs on pelagic organisms with benthic organisms. This bioassay used test species Daphnia magna, for a 48 h exposure period with five replicates (n = 10), 8 h UV exposure and 16:8 photoperiod. All individuals in the control group and UV only group exhibited 0% mortality, and with sheen/with UV treatment group resulted in 100% mortality following the 48 h exposure. The results of the D. magna exposure showed significant effects of PAHs (p < 0.0001), UV (p = 0.037), and photoinduced toxicity (p = 0.024), and were consistent with similar bioassays in the literature. This study suggests that C. dilutus are at low risk to photo-induced oil sheen toxicity.</p>Greater, Lesser, Guessers: A Look into the Hybridization of Greater and Lesser Prairie-Chickens2023-07-08T21:57:42-05:00https://digital.library.unt.edu/ark:/67531/metadc2137526/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2137526/"><img alt="Greater, Lesser, Guessers: A Look into the Hybridization of Greater and Lesser Prairie-Chickens" title="Greater, Lesser, Guessers: A Look into the Hybridization of Greater and Lesser Prairie-Chickens" src="https://digital.library.unt.edu/ark:/67531/metadc2137526/small/"/></a></p><p>My thesis focuses on the conservation consequences of the hybridization of Lesser Prairie-Chickens in Kansas. Specifically, examining how past land management practices altering the species ranges impact the distinctiveness of Lesser Prairie-Chickens. Each chapter is an individual publication that addresses if the Greater and Lesser Prairie-Chicken are distinct when applying the morphological and biological species concepts. Chapter 2 compares the evolutionary history and morphological construct of Lesser Prairie-Chickens and other Galliformes using morphometric analysis. Chapter 3 uses low-resolution microsatellite data to reflect recent changes at the population level. This study aims to observe the Greater and Lesser Prairie-Chicken using the morphological and biological species concepts, two of the many species concepts, to determine the distinctiveness and rate of hybridization for these closely related species.</p>Identification and Characterization of Two Putative Sulfate Transporters Essential for Symbiotic Nitrogen Fixation in Medicago truncatula2023-02-09T17:50:25-06:00https://digital.library.unt.edu/ark:/67531/metadc2048706/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048706/"><img alt="Identification and Characterization of Two Putative Sulfate Transporters Essential for Symbiotic Nitrogen Fixation in Medicago truncatula" title="Identification and Characterization of Two Putative Sulfate Transporters Essential for Symbiotic Nitrogen Fixation in Medicago truncatula" src="https://digital.library.unt.edu/ark:/67531/metadc2048706/small/"/></a></p><p>The process of symbiotic nitrogen fixation (SNF) in legume root nodules requires the channeling and exchange of nutrients within and between the host plant cells and between the plant cells and their resident rhizobia. Using a forward genetics approach in the Medicago truncatula Tnt1 mutant population followed by whole genome sequencing, two putative sulfate transporter genes, MtSULTR3;5 and MtSULTR3;4b, were identified. To support the hypothesis that the defective putative sulfate transporter genes were the causative mutation for the mutants' phenotypes, the M. truncatula Tnt1 population was successfully reverse screened to find other mutant alleles of the genes. The F2 progeny of mutants backcrossed with wildtype R108 demonstrated co-segregation of mutant phenotypes with the mutant alleles confirming that the mutated mtsultr3;5 and mtsultr3;4b genes were the cause of defective SNF in the mutant lines mutated in the respective genes. This finding was further established for mtsultr3;4b by successful functional complementation of a mutant line defective in the gene with the wildtype copy of MtSULTR3;4b. A MtSULTR3;4b promoter-GUS expression experiment indicated MtSULTR3;4b expression in the vasculature and infected and uninfected plant cells of root nodules. MtSULTR3;4b was found to localize to the autophagosome membrane when expressed in Nicotiana benthamiana. A transcriptomics study on the mutant nodules revealed the probable impact of mutated mtsultr3;5 and mtsultr3;4b on expression of genes involved in N fixation and on other biological processes, including possible effects of the mutated genes on the transcriptional regulation of sulfate assimilation pathway in the respective mutants' nodules. The RNAseq study also demonstrated the mis-regulation of nodule zone-specific genes in mtsultr3;5 and mtsultr3;4b mutants. A PCR-based approach was used to study the transcription of MtSULTR3;5 and MtSULTR3;4b in the respective mutant lines. The study demonstrated formation of readthrough chimeric gene-Tnt1 transcripts in mtsultr3;5 mutant alleles and truncated chimeric gene-Tnt1 transcripts and aberrantly spliced transcripts or no transcripts in mtsultr3;4b mutant alleles. Gene expression analysis of all MtSULTR genes using qRT-PCR was carried out in wildtype M. truncatula R108 nodules at a time course to evaluate the MtSULTR genes for their potential involvement in the SNF process.</p>Developing Informatics Tools and Methods Utilizing Whole Genome Sequencing and Transcription Data to Aid Gene Discovery in Medicago truncatula2023-02-09T17:46:32-06:00https://digital.library.unt.edu/ark:/67531/metadc2048698/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048698/"><img alt="Developing Informatics Tools and Methods Utilizing Whole Genome Sequencing and Transcription Data to Aid Gene Discovery in Medicago truncatula" title="Developing Informatics Tools and Methods Utilizing Whole Genome Sequencing and Transcription Data to Aid Gene Discovery in Medicago truncatula" src="https://digital.library.unt.edu/ark:/67531/metadc2048698/small/"/></a></p><p>Research into the mechanism of symbiotic nitrogen fixation between legumes and rhizobia involves a complex interaction between the organisms, and many genes involved in this remain either uncharacterized or undiscovered. Using forward genetics, mutant plant lines are screened to find new genes without reliance on software-based gene prediction. A large population of Tnt1-mutagenized Medicago truncatula lines is used for this purpose.
Herein, the aid of tools like whole genome sequencing (WGS) in this process is explored so that new methods and tools are elucidated. The use of WGS data allows for rapid prediction of all insertions in the genome and has been shown to predict insertion locations that were missed by the TAIL-PCR-based Tnt1 mutant database already in existence. This WGS strategy has been successfully used to find the causal mutations in multiple plant lines. Two WGS strategies are used to analyze insertions in nine sequenced lines and compared with each other and the existing Tnt1 mutant database. It appears that using either WGS method will yield similar results, but the TAIL-PCR-based predictions have much less overlap. The use of the latest R108 genome appears to decrease the degree of disagreement between the methods, while the correlation in the A17 genome update is less clear.
There is also a demonstration of the use of other tools in addition to the WGS prediction output. Combining transcription data from previous experiments with the predicted insertions allowed for the creation of more holistic tables, which could better assist in screening the predictions made for the most likely candidate by highlighting those with expression profiles consistent with the observed mutation phenotype.
Each of these tools and methods has been shown to be effective in screening Tnt1-mutagenized M. truncatula lines to find novel genes. Without further experimental data, determining the most accurate method is not possible. The best practice may be to use multiple methods and align them in comparison tables, leveraging all the predictive power of each of the methods into a single table.</p>Investigating the Spatial Relationship between Suicide and Race/Ethnicity: The Case for Alternate Rate Adjustment Techniques in Medical Geography2023-02-09T17:41:13-06:00https://digital.library.unt.edu/ark:/67531/metadc2048689/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048689/"><img alt="Investigating the Spatial Relationship between Suicide and Race/Ethnicity: The Case for Alternate Rate Adjustment Techniques in Medical Geography" title="Investigating the Spatial Relationship between Suicide and Race/Ethnicity: The Case for Alternate Rate Adjustment Techniques in Medical Geography" src="https://digital.library.unt.edu/ark:/67531/metadc2048689/small/"/></a></p><p>This work explores potential distortions created by race and ethnicity on the visualization, interpretation, and understanding of the spatial distribution of suicide in the United States. Due to radically different suicide rates among racial/ethnic groups, traditional crude or age-adjusted rates may introduce statistical confounding in both linear and spatial models. Using correlation, choropleth mapping, hot spot analysis, and location-allocation modeling, this work shows how traditional methods of health system planning may unintentionally overlook elevated risk in minority-dominated areas like inner cities, the Texas/Mexico border region, and the Deep South. The final chapter introduces a simulation protocol for examining potential distortions in datasets to identify spatial and non-spatial distortions created by the underlying population composition. Methodologically, this dissertation contributes to the discourse on place context versus population composition. More generally, this research points to potential hazards to creating a more inclusive and equitable healthcare system.</p>Developing a Generalizable Two-Input Genetic AND Logic Gate in Arabidopsis thaliana for Multi-Signal Processing2023-02-09T17:34:29-06:00https://digital.library.unt.edu/ark:/67531/metadc2048678/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048678/"><img alt="Developing a Generalizable Two-Input Genetic AND Logic Gate in Arabidopsis thaliana for Multi-Signal Processing" title="Developing a Generalizable Two-Input Genetic AND Logic Gate in Arabidopsis thaliana for Multi-Signal Processing" src="https://digital.library.unt.edu/ark:/67531/metadc2048678/small/"/></a></p><p>With effective engineering using synthetic biology approaches, plant-based platforms could conceivably be designed to minimize the production costs and wastes of high-value products such as medicines, biofuels, and chemical feedstocks that would otherwise be uneconomical. Additionally, modern agricultural crops could be engineered to be more productive, resilient, or restorative in different or rapidly changing environments and climates. To achieve these complex goals, information-processing genetic devices and circuits containing multiple interacting parts that behave predictably must be developed. A genetic Boolean AND logic gate is a device that computes the presence or absence of two inputs (signals, stimuli) and produces an output (response) only if both inputs are present. Here, we optimized individual genetic components and used synthetic protein heterodimerizing domains to rationally assemble genetic AND logic gates that integrate two hormonal inputs in whole plants. These AND gates produce an output only in the presence of both abscisic acid and auxin, but not when either or neither hormone is present. Furthermore, we demonstrate the AND gate can also integrate two plant stresses, cold temperature and bacterial infection, to produce a specific response. The design principles used here are generalizable, and therefore multiple orthogonal AND gates could be assembled and rationally layered to process complex genetic information in plants. In addition to bioproduction, these layered logic gates may also be used in circuits to probe fundamental questions in plant biology such as hormonal crosstalk.</p>Data Mining Using Direct Injection Triple Quadrupole Mass Spectrometry, Infrared Spectroscopy, Inductively Coupled Plasma Optical Emission Spectroscopy, and Polymerase Chain Reaction for the Rapid Identification of Nutraceuticals and Contaminants2023-02-09T17:31:34-06:00https://digital.library.unt.edu/ark:/67531/metadc2048673/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048673/"><img alt="Data Mining Using Direct Injection Triple Quadrupole Mass Spectrometry, Infrared Spectroscopy, Inductively Coupled Plasma Optical Emission Spectroscopy, and Polymerase Chain Reaction for the Rapid Identification of Nutraceuticals and Contaminants" title="Data Mining Using Direct Injection Triple Quadrupole Mass Spectrometry, Infrared Spectroscopy, Inductively Coupled Plasma Optical Emission Spectroscopy, and Polymerase Chain Reaction for the Rapid Identification of Nutraceuticals and Contaminants" src="https://digital.library.unt.edu/ark:/67531/metadc2048673/small/"/></a></p><p>There has been a rapid surge toward "organic" products devoid of GMOs, MSGs, and other common compounds found in processed foods that continue to indicate an association with an increased risk for disease. These consumers seek nutrients and vitamins that are lacking in their diet and lifestyle in the form of nutraceuticals for disease prevention and treatment as well as overall lifestyle enhancement. However, these products generally lack clinical evidence as well as legal definition. Due to this ambiguity, nutraceuticals are neither considered a food product nor a pharmaceutical product. Furthermore, due to their alleged natural properties allowing for safe, therapeutic effects, nutraceuticals are being eagerly sought after by consumers in the place of pharmaceuticals. Additionally, since nutraceutical substances are "naturally" derived, there is a general lack of regulation regarding the manufacturing and distribution process. This mismanagement leads to lack of quality assurance (QA) and quality control (QC) protocols strictly implemented to define appropriate production and storage parameters. Without these critical measures, consumers are subjected to contamination of their products resulting from improper storage conditions and unmanaged production. These contaminants often include heavy metal impurities, pesticides, bacterial activity, and may also be adulterated with illicit drugs, all leading to detrimental health and environmental effects.</p>Migration Tracking, Survival, and Pairing Behavior of American Kestrels Wintering in North Central Texas2023-02-09T17:08:47-06:00https://digital.library.unt.edu/ark:/67531/metadc2048640/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048640/"><img alt="Migration Tracking, Survival, and Pairing Behavior of American Kestrels Wintering in North Central Texas" title="Migration Tracking, Survival, and Pairing Behavior of American Kestrels Wintering in North Central Texas" src="https://digital.library.unt.edu/ark:/67531/metadc2048640/small/"/></a></p><p>The American Kestrel (Falco sparverius) is the smallest and most abundant falcon in North America with a wide geographic range. Unfortunately, surveys have suggested that some kestrel populations have been in decline since the 1950s, though the nominal causes of this decline are unknown. Migratory movement patterns and connectivity have yet to be established for any population of migratory kestrels. In Chapter 2, I investigated methods for attaching migration trackers to kestrels. Specifically, I showed that leg-loop style harnesses may have negatively affected return rates whereas backpack harnesses did not. Based on these results, I recommend that backpack-style Teflon harnesses is the safest and most effective method for attaching tracking devices to small raptors. In Chapter 3, I quantified survivorship for kestrels wintering in north Texas to identify the timing of kestrel mortality. Notably, I found that juvenile kestrels had similar annual survival rates as adults (81.6% versus 79.5%). High overwintering survival in north Texas indicated that once kestrels arrived on their wintering grounds, they were highly likely to survive to spring migration. In Chapter 4, I investigated pairing behaviors previously undocumented in wintering kestrels. I found that winter pairing was relatively common, but more prevalent in urban environments than rural. My data suggested that pairing during the winter could be a coping mechanism to increase kestrel survival in stressful anthropic landscapes. Altogether, this research highlights that the documentation of migratory connectivity is essential to understanding how many processes affect kestrel population dynamics, as I found evidence of potential seasonal carryover effects.</p>Alterations in the Expression of Proteins Associated with Non-Alcoholic Fatty Liver Disease Observed in the Liver of the C57Bl/6 Wild-Type Male Mouse in Response to Exposure of Mixed Vehicle Emissions and/or High Fat Diet Consumption2023-02-09T17:04:29-06:00https://digital.library.unt.edu/ark:/67531/metadc2048632/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048632/"><img alt="Alterations in the Expression of Proteins Associated with Non-Alcoholic Fatty Liver Disease Observed in the Liver of the C57Bl/6 Wild-Type Male Mouse in Response to Exposure of Mixed Vehicle Emissions and/or High Fat Diet Consumption" title="Alterations in the Expression of Proteins Associated with Non-Alcoholic Fatty Liver Disease Observed in the Liver of the C57Bl/6 Wild-Type Male Mouse in Response to Exposure of Mixed Vehicle Emissions and/or High Fat Diet Consumption" src="https://digital.library.unt.edu/ark:/67531/metadc2048632/small/"/></a></p><p>Recent epidemiological studies have demonstrated a correlation between the manifestation of non-alcoholic fatty liver disease (NAFLD) and ambient air pollution levels, which is exacerbated by the presence of other risk factors, such as diabetes, dyslipidemia, obesity, and hypertension. We investigated the hypothesis that exposure to a mixture of gasoline and diesel engine emissions (MVE) coupled with the concurrent consumption of a high-fat (HF) diet promotes the development of a NAFLD phenotype within the liver. Three-month-old male C57Bl/6 mice were placed on either a low fat or HF diet and exposed via whole-body inhalation to either filtered (FA) air or MVE (30 µg PM/m3 gasoline engine emissions + 70 µg PM/m3 diesel engine emissions) 6 hr/day for 30 days. Histology revealed mild microvesicular steatosis and hepatocyte hypertrophy in response to MVE exposure alone, compared to FA controls, yielding a classification of "borderline NASH" under the criteria of the modified NAFLD active score (NAS) system. As anticipated, animals on a HF diet exhibited moderate steatosis; however, we also observed inflammatory infiltrates, hepatocyte hypertrophy, and increased lipid accumulation, with the combined effect of HF diet and MVE exposure. Immunofluorescence staining and RT-qPCR of the liver revealed the presence of lipid peroxidation, altered expression of inflammatory markers, induction of hepatic stellate cell activation biomarkers, and conversion to pyroptosis in response to MVE exposure and/or consumption of a HF diet. Our results indicate that inhalation exposure to traffic-generated air pollution initiates hepatocyte injury within the liver, exacerbates lipid accumulation and hepatocyte injury induced by the consumption of a HF diet, and alters molecular pathways associated with inflammation, fibrogenesis, and cell death, thereby contributing to the progression of NAFLD-related pathologies.</p>Space Use, Microhabitat and Macrohabitat Use of the Three-Toed Box Turtle (Terrapene carolina) in North Texas2023-02-09T17:03:12-06:00https://digital.library.unt.edu/ark:/67531/metadc2048629/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048629/"><img alt="Space Use, Microhabitat and Macrohabitat Use of the Three-Toed Box Turtle (Terrapene carolina) in North Texas" title="Space Use, Microhabitat and Macrohabitat Use of the Three-Toed Box Turtle (Terrapene carolina) in North Texas" src="https://digital.library.unt.edu/ark:/67531/metadc2048629/small/"/></a></p><p>Box turtle (Terrapene carolina) populations are steadily declining due their unique natural history, effects of climate change, and anthropogenic land use change. There is a need for updated information on box turtle space and micro and macro-habitat use to inform conservation efforts. This study used VHF radiotelemetry and GPS data loggers to examine box turtle space and habitat use in North Texas. Box turtle home range sizes averaged 6.6ha (range = 0.79 - 18.08, n = 23), and males (n = 9) had larger home ranges than females (n = 14; W = 31.5, P = 0.05). Home range size was best explained by a combination of variables including sex and body size, but overall, home ranges that consisted of higher percentages of suitable box turtle habitat were smaller. Box turtles used deciduous forest more than expected and wetlands less than expected by chance (Fisher's exact test, P < 0.0001). The most informative variable for box turtle macrohabitat selection was NDVI. Box turtles selected microhabitats with a higher percent litter (t = -2.16, P < 0.05) and understory cover (t = -5.03, P < 0.05). The results of CART analysis showed the nested importance of macro- and microhabitat and identified NDVI as the most important variable for predicting suitable box turtle habitat. Given these results, we postulate that NDVI can be used to identify suitable box turtle habitat at landscape scales to aid in management and conservation efforts. We found that three-toed box turtles are using habitat differently than what has been reported in eastern box turtles, providing support for the theory that three-toed box turtles should be classified as a separate species.</p>Medicago truncatula NPF1.7: Structure-Function Assessment and Potential as a Phytohormone Transporter2023-02-09T16:53:19-06:00https://digital.library.unt.edu/ark:/67531/metadc2048610/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048610/"><img alt="Medicago truncatula NPF1.7: Structure-Function Assessment and Potential as a Phytohormone Transporter" title="Medicago truncatula NPF1.7: Structure-Function Assessment and Potential as a Phytohormone Transporter" src="https://digital.library.unt.edu/ark:/67531/metadc2048610/small/"/></a></p><p>In Medicago truncatula, the MtNPF1.7 transporter has been shown to be essential for root morphology and nodulation development. The allelic MtNPF1.7 mutants, Mtnip-1 (A497V), Mtnip-3 (E171K), and Mtlatd (W341STOP), show altered lateral root growth and compromised legume-rhizobium symbiosis. To assess the role of a series of distinct amino acids in the transporter's function, in silico structural predictions were combined with in planta complementation of the severely defective Mtnip-1 mutant plants. The findings support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. The results also question the existence of a putative TMH4-TMH10 salt bridge, which may not form in MtNPF1.7. Results reveal that a motif conserved among MFS proteins, Motif A, is essential for function. Hypothetically, the Motif A participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. The mutated valine (A497V) in Mtnip-1 may interfere with the lateral helix. Mutating a residue (L253) on the lateral helix with reduced side chain restored Mtnip-1 function. The predicted residue (Q351) for substrate binding is not essential for protein function. To probe the possibility that MtNPF1.7 transports auxin, two heterologous assay systems were attempted. The first was a Xenopus laevis oocyte assay. However, MtNPF1.7 expressed in oocytes failed to show substrate transport, which may due to low expression levels of proteins on the membrane or may be caused by other factors. Second, yeast (Saccharomyces cerevisiae) strains expressing MtNPF1.7 were constructed. They showed an increased flux of radiolabeled IAA and differential susceptibility to 5-fluoroindole-3-acetic acid (F-IAA), a toxic IAA-like compound. These results suggested that MtNPF1.7 may function as an auxin transporter in yeast. Unexpectedly, the Mtnip-1 (A497V) and Mtnip-3 (E171K) proteins when expressed in yeast also showed influx of F-IAA transport in yeast, suggesting the auxin transport remains functional in the mutants, potentially contradicting other results suggesting Mtnip-1 is non-functional. To address the possible role of MtNPF1.7 in auxin responses, the auxin reporter DR5-GUS was used and mutant plants were subjected to gravitropism tests. The auxin reporter DR5::GUS displayed different expression in Mtnip-1 mutant in comparison with DR5::GUS expression in wild-type. In addition, the spatial expression of pMtNPF1.7-GUS partly co-localized with the expression of DR5:GUS in roots and nodules. The Mtnip-1 plants showed altered gravitropic responses to gravistimulus compared to wild-type and Mtnip-3 plants. The results suggest that MtNPF1.7, recognized as a nitrate transporter, may be able to transport auxin and may participate in auxin distribution during M. truncatula root and nodule development. These research findings helps elucidate the complex function of plant NPF transporters.</p>Seeing in the Light: Using Expansion Microscopy to Achieve Super-Resolution in Transmitted Light2023-02-09T16:50:25-06:00https://digital.library.unt.edu/ark:/67531/metadc2048604/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc2048604/"><img alt="Seeing in the Light: Using Expansion Microscopy to Achieve Super-Resolution in Transmitted Light" title="Seeing in the Light: Using Expansion Microscopy to Achieve Super-Resolution in Transmitted Light" src="https://digital.library.unt.edu/ark:/67531/metadc2048604/small/"/></a></p><p>Light microscopy is inherently limited in resolution by properties of light such as diffraction and interference to 170-250 nm. Expansion microscopy is a quickly-developing method which achieves super-resolution by using a swellable hydrogel to physically expand biological samples themselves, rather than depending on the properties of fluorophores. This thesis demonstrates that expansion microscopy is a feasible means for achieving super-resolution in transmitted light microscopy modes. Though it has only been used for fluorescence imaging in the past, here I show that samples prepared for expansion microscopy—including liver tissue slices and myofibrillar bundles—are observable using transmitted light. While the majority of the original sample material is removed in the expansion process, the hydrogel retains visible evidence of these samples. These demonstrate increased detail under brightfield microscopy that is useful for characterization. Sarcomeric regions are identifiable by this method and are confirmed by fluorescence imaging. Thus, expansion microscopy is a means to bring super-resolution to transmitted light imaging and is entirely compatible with fluorescence for the localization of proteins of interest.</p>Multi-Level Effects of Oxygen Exposure in Endothermic Insects2022-09-03T11:07:59-05:00https://digital.library.unt.edu/ark:/67531/metadc1986787/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1986787/"><img alt="Multi-Level Effects of Oxygen Exposure in Endothermic Insects" title="Multi-Level Effects of Oxygen Exposure in Endothermic Insects" src="https://digital.library.unt.edu/ark:/67531/metadc1986787/small/"/></a></p><p>This dissertation examined the phenotypic plasticity of endothermic, flight and respiratory physiology in response to developmental oxygen exposure in the moth Manduca sexta. Development in both 10% O2 hypoxia and 30% O2 hyperoxia treatments were used to look at the physiological consequence on both ends of the oxygen spectrum. Hypoxic insects reached smaller sizes as adults and had longer pupation lengths than controls. Hyperoxic insects were larger at the end of the larval stage, had increased larval growth rates, but also had longer developmental larval developmental times and pupation lengths than controls. There was a decrease in both metabolic rate and thorax temperatures of hypoxic reared insects at normoxic levels. In flight trials hypoxic insects had the lowest critical flight PO2, and the hyperoxic insects had the highest PO2. There was an increase in hypoxic insect flight muscle mitochondria oxygen consumption in permeabilized fibers, but this did not translate to the isolated flight muscle mitochondria metabolic rates. Rearing oxygen level did not significantly affect mitochondrial density and size; myofibril density and size, or tracheal density and size in flight muscle. Overall, I found that higher levels of organization were more susceptible to the effects of chronic oxygen exposure and found more effects of hypoxia than hyperoxia.</p>Inferring a Network of Horizontal Gene Flow among Prokaryotes Using Complementary Approaches2022-09-03T10:53:38-05:00https://digital.library.unt.edu/ark:/67531/metadc1986405/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1986405/"><img alt="Inferring a Network of Horizontal Gene Flow among Prokaryotes Using Complementary Approaches" title="Inferring a Network of Horizontal Gene Flow among Prokaryotes Using Complementary Approaches" src="https://digital.library.unt.edu/ark:/67531/metadc1986405/small/"/></a></p><p>Horizontal gene transfer (HGT), a mechanism that facilitates exchange of genetic material between organisms from different lineages, has a profound impact on prokaryotic evolution. To infer HGT, we first developed a comparative genomics-based tool, APP, which can perform phyletic pattern analysis using completely sequenced genomes to identify genes are unique to a genome or have sporadic distribution in its close relatives. Performance assessment against currently available tools on a manually created 18-genome dataset and 2 benchmarking datasets revealed the superior accuracy of APP over other methods. We then utilized a parametric method to construct a gene exchange network. The composition-based method, Jenson-Shannon Codon Bias (JS-CB), groups genes into clusters based on similar codon usage bias. These clusters were analyzed using APP and examined for the enrichment HGT associated marker genes, then annotated as of native or alien origin based on these multiple lines of evidence. Intergenome clustering enabled identification of genes mobilized across alien components of the genomes (alien-alien transfer) and from native components of donor genomes to the recipient genomes (native-alien transfer). Functional classification of alien gene clusters revealed that metabolism associated genes are most frequently mobilized, in concurrence with previous reports, and additionally, a large number of genes with yet unknown functions were found to have been horizontally transferred, a important finding that needs to be further investigated.</p>Acute Toxicity of Crude Oil Exposures to Early Life Stage Teleosts: Contribution of Impaired Renal Function and Select Environmental Factors2022-09-03T10:29:01-05:00https://digital.library.unt.edu/ark:/67531/metadc1985773/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1985773/"><img alt="Acute Toxicity of Crude Oil Exposures to Early Life Stage Teleosts: Contribution of Impaired Renal Function and Select Environmental Factors" title="Acute Toxicity of Crude Oil Exposures to Early Life Stage Teleosts: Contribution of Impaired Renal Function and Select Environmental Factors" src="https://digital.library.unt.edu/ark:/67531/metadc1985773/small/"/></a></p><p>Oil spills are well-known adverse anthropogenic events, as they can induce severe impacts on the environment and negative economic consequences. Still, much remains to be learned regarding the effects of crude oil exposure to aquatic organisms. The objectives of this dissertation were to fill some of those knowledge gaps by examining the effects of Deepwater Horizon (DWH) crude oil exposure on teleost kidney development and function. To this end, I analyzed how these effects translate into potential osmoregulatory impairments and investigated the interactive effects of ubiquitous natural factors, such as dissolved organic carbon (DOC) and ultraviolet (UV) light, on acute crude oil toxicity. Results demonstrated that acute early life stage (ELS) crude oil exposure induces developmental defects to the primordial kidney in teleost fish (i.e., the pronephros) as evident by alterations in: (1) transcriptional responses of key genes involved in pronephros development and function and (2) alterations in pronephros morphology. Crude oil-exposed zebrafish (Danio rerio) larvae presented defective pronephric function characterized by reduced renal clearance capacity and altered filtration selectivity, factors that likely contributed to the formation of edema. Latent osmoregulatory implications of crude oil exposure during ELS were observed in red drum (Sciaenops ocellatus) larvae, which manifested reduced survival in hypoosmotic waters, likely due to defective pronephros development and function. Finally, DOC-UV co-exposure slightly reduced acute crude oil photo-enhanced toxicity in red drum larvae. This dissertation provided novel information regarding crude oil toxicity that can be incorporated into environmental risk assessment and management for future oil spills.</p>A Sensitive and Robust Machine Learning-Based Framework for Deciphering Antimicrobial Resistance2022-09-03T10:18:01-05:00https://digital.library.unt.edu/ark:/67531/metadc1985530/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1985530/"><img alt="A Sensitive and Robust Machine Learning-Based Framework for Deciphering Antimicrobial Resistance" title="A Sensitive and Robust Machine Learning-Based Framework for Deciphering Antimicrobial Resistance" src="https://digital.library.unt.edu/ark:/67531/metadc1985530/small/"/></a></p><p>Antibiotics have transformed modern medicine in manifold ways. However, the misuse and over-consumption of antibiotics or antimicrobials have led to the rise in antimicrobial resistance (AMR). Unfortunately, robust tools or techniques for the detection of potential loci responsible for AMR before it happens are lacking. The emergence of resistance even when a strain lacks known AMR genes has puzzled researchers for a long time. Clearly, there is a critical need for the development of novel approaches for uncovering yet unknown resistance elements in pathogens and advancing our understanding of emerging resistance mechanisms. To aid in the development of new tools for deciphering AMR, here we propose a machine learning (ML) based framework that provides ML models trained and tested on (1) genotypic AMR and phenotypic antimicrobial susceptibility testing (AST) data, which can predict novel resistance factors in bacterial strains that lack already implicated resistance genes; and (2) complete gene set and AST phenotypic data, which can predict the most important genetic loci involved in resistance to specific antibiotics in bacterial strains. The validation of resistance loci prioritized by our ML pipeline was performed using homology modeling and in silico molecular docking.</p>Regulation of Receptors in Neuronal Cilia with Development, Seizures, and Knockouts: Implications for Excitability2022-09-03T10:11:49-05:00https://digital.library.unt.edu/ark:/67531/metadc1985379/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1985379/"><img alt="Regulation of Receptors in Neuronal Cilia with Development, Seizures, and Knockouts: Implications for Excitability" title="Regulation of Receptors in Neuronal Cilia with Development, Seizures, and Knockouts: Implications for Excitability" src="https://digital.library.unt.edu/ark:/67531/metadc1985379/small/"/></a></p><p>Neurons commonly have a primary cilium, which is a non-motile organelle extending from the centrosome into the extracellular space. In most brain regions, neuronal cilia are enriched in either somatostatin receptor type 3 (SstR3) or melanin concentrating hormone receptor type 1 (MCHR1), or both. The present immunohistochemical study provides novel evidence that primary cilia regulate neuronal excitability via G-protein coupled receptors (GPCRs), and that their identity is governed by brain region and by competition, both in adulthood and in postnatal development. The hippocampus, which is particularly vulnerable to seizures, has opposing gradients of SstR3(+) and MCHR1(+) ciliary GPCRs. We hypothesized that there is a competition between these two ciliary GPCRs, which might take place on any level from gene expression to presence in the cilium. We examined whether receptor colocalization occurs transiently in development before ciliary GPCR dominance is established in neurons in the CNS. In postnatal CA1 and CA3, the first GPCR to appear in cilia was the one that will dominate in adults: MCHR1 in CA1 and SstR3 in CA3. Some days later, the second GPCR was expressed along with the first; dual-receptor cilia were the exclusive type until single-receptor cilia emerged again around P14. Single-receptor cilia then increased in numbers through adulthood. By identifying ciliary receptors that modulate seizure activity in mice, the present study lays a foundation for therapeutic approaches to reduce neuronal excitotoxicity underlying cell death in epilepsy, CNS injury, and neurodegenerative diseases.</p>Assessing Student Perceptions in Short Research Experiences and Course Research Experiences in Undergraduate Biology Laboratories2022-09-03T10:11:38-05:00https://digital.library.unt.edu/ark:/67531/metadc1985376/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1985376/"><img alt="Assessing Student Perceptions in Short Research Experiences and Course Research Experiences in Undergraduate Biology Laboratories" title="Assessing Student Perceptions in Short Research Experiences and Course Research Experiences in Undergraduate Biology Laboratories" src="https://digital.library.unt.edu/ark:/67531/metadc1985376/small/"/></a></p><p>This study examined students' perception between short research experiences (SRE) courses and full-semester course research experiences (CRE) using the Persistence in the Sciences (PITS) survey and the interview questionnaire. The study also aimed to correlate the influence of student's demographic as a predictive indicator for Project Ownership Scores (POS) and Quantitative Literacy (QL) score means. The three courses studied at the University of North Texas were Biology for Science Majors Laboratory (BIOL 1760 SRE), Microbiology with Tiny Earth (BIOL 2042 Tiny Earth SRE), and Introductory Biology Research Laboratory I (BIOL 1750 SEA-PHAGES CRE). The mean scores for the PITS categories leaned favorably towards the research component of each laboratory course assessed in this study. The interview questionnaire showed 66% of the students in the SRE courses and 90% of the students in the CRE course preferred the research component of the lab. Paired survey demographic analysis for BIOL 1760 SRE showed significance for the Science Community Values with associate/bachelor's degree. BIOL 1750 SEA-PHAGES CRE showed significance in three of the six categories when comparing means for Project Ownership Emotion, Self-Efficacy, and Science Identity with Gender. Binary logistics was used to build a regression model to predict demographics with approximately 65% to 75% accuracy for each course. When analyzing students' QL score, the demographic category "Ethnicity" showed significance for BIOL 2042 Tiny Earth SRE. Categorizing the correct response into two categories for the QL test scores, the SRE and CRE courses, and analyzing the PITS scores for paired data sets showed that there was significance in the Networking category for the question "I have discussed my research in this course with professors other than my course instructor." The validated PITS, POS, and interview questionnaire could be a tool for use to analyze laboratories at UNT that offer a SRE or CRE component and to understand students' perceptions on the effectiveness of the laboratory.</p>Temperature Change and Its Consequences for the Physiology of the Eurythermic Sheepshead Minnow (Cyprinodon variegatus)2022-09-03T10:03:52-05:00https://digital.library.unt.edu/ark:/67531/metadc1985323/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1985323/"><img alt="Temperature Change and Its Consequences for the Physiology of the Eurythermic Sheepshead Minnow (Cyprinodon variegatus)" title="Temperature Change and Its Consequences for the Physiology of the Eurythermic Sheepshead Minnow (Cyprinodon variegatus)" src="https://digital.library.unt.edu/ark:/67531/metadc1985323/small/"/></a></p><p>The estuarine sheepshead minnow (Cyprinodon variegatus) is the most eurythermic fish species, with a thermal tolerance window between 0.6°C and 45.1°C. However, little is known about the physiological mechanisms that allow this species to survive this temperature range. In order to understand how sheepshead minnow physiology is affected by temperature acclimation and acute changes in temperature, I conducted research on this species using a multi-level approach. I began at the organismal level, and examined the effects of these temperature changes on the sheepshead minnow's metabolic rate and swimming performance. The next chapter investigated the effects of changing temperatures on cardiac function (i.e., tissue/organ specific effects). In the final chapter, I conducted research at the sub-cellular level, and determined how mitochondrial bioenergetics / function is impacted by changing temperatures. This research shows that while sheepshead minnows are able to sustain heart function and mitochondrial respiration over a broad range of temperatures; they also display a plastic temperature response which is associated with the downregulation of standard metabolic rate and cardiac remodeling to maintain force generation. Collectively, these physiological responses may contribute to the sheepshead minnow's ability to maintain physiological and organismal function across a large temperature range.</p>Investigation of Gene Functions in the Cyanotrophic Bacterium Pseudomonas fluorescens NCIMB 117642022-06-16T11:16:30-05:00https://digital.library.unt.edu/ark:/67531/metadc1944375/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1944375/"><img alt="Investigation of Gene Functions in the Cyanotrophic Bacterium Pseudomonas fluorescens NCIMB 11764" title="Investigation of Gene Functions in the Cyanotrophic Bacterium Pseudomonas fluorescens NCIMB 11764" src="https://digital.library.unt.edu/ark:/67531/metadc1944375/small/"/></a></p><p>Pseudomonas fluorescens NCIMB 11764 (Pf11764) is one of a group of bacteria known as cyanotrophs that exhibit the unique ability to grow on toxic cyanide as the sole nitrogen source. This ability has previously been genetically linked to a conserved cluster of seven genes (Nit1C), the signature gene (nitC) coding for a nitrilase enzyme. Nitrilases convert nitriles to ammonia and a carboxylic acid. Still, for the Pf11764 NitC enzyme (Nit11764), no in vivo substrate has been identified, and the basis of the enzyme's requirement for cyanide growth has remained unclear. Therefore, the gene was cloned and the enzyme was characterized with respect to its structure and function. These efforts resulted in the unique discovery that, aside from its nitrilase activity, Nit11764 exhibits nuclease activity towards both DNA and RNA. This ability is consistent with computer analysis of the protein providing evidence of a preponderance of amino acids with a high probability for RNA binding. A Nit11764 knock-out mutant was shown to exhibit a higher sensitivity to both cyanide (KCN) and mitomycin C, both known to induce chromosomal damage. Thus, the overall conclusion is that Nit11764, and likely the entire Nit1C gene cluster, functions as a possible repair mechanism for overcoming the damage inflicted on Pf11764 nucleic acids by toxic cyanide. Towards a further investigation of the Nit1C gene cluster in Pf11764, a second gene (nitH) annotated as a monooxygenase was also investigated. Interestingly, computer-based analysis shows that NitH also harbors a preponderance of RNA-binding amino acids. The nitH gene was cloned into an expression vector with the long-range goal of defining its role in CN utilization.</p>Metacommunity Dynamics of Medium- and Large-Bodied Mammals in the LBJ National Grasslands2022-06-16T10:59:05-05:00https://digital.library.unt.edu/ark:/67531/metadc1944350/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1944350/"><img alt="Metacommunity Dynamics of Medium- and Large-Bodied Mammals in the LBJ National Grasslands" title="Metacommunity Dynamics of Medium- and Large-Bodied Mammals in the LBJ National Grasslands" src="https://digital.library.unt.edu/ark:/67531/metadc1944350/small/"/></a></p><p>Using metacommunity theory, I investigated the mechanisms of meta-assemblage structure and assembly among medium- to large-bodied mammals in North Texas. Mammals were surveyed with camera-traps in thirty property units of the LBJ National Grasslands (LBJNG). In Chapter II the dispersal and environmental-control based processes in community assembly were quantified within a metacommunity context and the best-fit metacommunity structure identified. A hypothesis-driven modelling approach was used in Chapter III to determine if the patterns of species composition and site use could be explained by island biogeography theory (IBT) or the habitat amount hypothesis (HAH). Islands were defined as the LBJNG property unit or the forest patch bounded by the property unit. Forest cover was selected as the focal habitat for the HAH. Seasonal dynamics were explored in both chapters. Metacommunity structure changed with each season, resulting in quasi-nested and both quasi and idealized Gleasonian and Clementsian structures. Results indicated that the anthropogenic development is, overall, not disadvantageous for this assemblage, that community assembly receives equal contributions from spatial and environmental factors, and that the metacommunity appears to operate under the mass effects paradigm. The patterns of species composition and site use were not explained by either IBT or HAH. Likely because this assemblage of generalist, dispersal-capable mammals are utilizing multiple habitat types both in the protected land and in the private land. This research highlights the versatility of these species and the potential value of rural countryside landscapes for wildlife conservation.</p>Ecosystem Services and Sustainability: A Framework for Improving Decision-Making in Urban Areas2022-06-16T10:55:53-05:00https://digital.library.unt.edu/ark:/67531/metadc1944341/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1944341/"><img alt="Ecosystem Services and Sustainability: A Framework for Improving Decision-Making in Urban Areas" title="Ecosystem Services and Sustainability: A Framework for Improving Decision-Making in Urban Areas" src="https://digital.library.unt.edu/ark:/67531/metadc1944341/small/"/></a></p><p>Ecosystem services are the varied goods and benefits provided by ecosystems that make human life possible. This concept has fostered scientific explorations of the services that nature provides to people with the goal of sustaining those services for future generations. As the world becomes increasingly urban, ecosystems are reshaped, and services are degraded. Provisioning and regulating ecosystem services, landscape planning, decision making, and agricultural systems and technologies play a distinctive role in feeding and sustaining the expanding urban population. Hence, the integrated assessment of these coupled components is necessary to understand food security and sustainable development. Nevertheless, frameworks that incorporate ecosystem services, urbanization, and human wellbeing are still scarce due to several conceptual and methodological gaps that challenge this assessment. As a consequence, these frameworks are not operationalized, and ecosystem services rarely receive proper attention in decision making. This dissertation seeks to improve our understanding of the role of ecosystem services at the landscape level and provides an approach for operationalizing decisions that affect sustainable practices and human wellbeing.</p>Correlation of Watershed NDVI Values to Benthic Macroinvertebrate Biodiversity in Eight North American Wadeable Streams2022-06-16T09:46:05-05:00https://digital.library.unt.edu/ark:/67531/metadc1944222/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1944222/"><img alt="Correlation of Watershed NDVI Values to Benthic Macroinvertebrate Biodiversity in Eight North American Wadeable Streams" title="Correlation of Watershed NDVI Values to Benthic Macroinvertebrate Biodiversity in Eight North American Wadeable Streams" src="https://digital.library.unt.edu/ark:/67531/metadc1944222/small/"/></a></p><p>Water quality of a stream or river is influenced by the surrounding landscape and vegetation. The Normalized Difference Vegetation Index (NDVI) is commonly used to characterize landcover and vegetation density. Benthic macroinvertebrates are ubiquitous in freshwater streams and are excellent indicators of the quality of freshwater habitats. Data from one NDVI remote sensing flight and one macroinvertebrate sampling event for eight wadeable stream study sites in the National Ecological Observatory Network (NEON) were acquired. Proportions of high, moderate, and sparse vegetation were calculated for each stream watershed using ArcGIS. Functional feeding groups and tolerance values were assigned to macroinvertebrate taxa. The Fourth-corner and RLQ methods of analysis, available in the ade4 package for R software, were used to evaluate the relationships of macroinvertebrate traits with environmental variables. Hypothesis testing using Model 6 in the ade4 package resulted in p-values of 0.066 and 0.057 for global (overall) significance. Mean NDVI values of moderately vegetated areas and proportion of sparse vegetation were found to be significant to percent shredders at alpha ≤ 0.05. Results of these methods of analysis, when combined with traditional macroinvertebrate sampling metrics, show that NDVI can be a useful, additional tool to characterize a watershed and its effects on macroinvertebrate community composition and structure.</p>Role of DEFECTIVE IN SYSTEMIC DEFENSE INDUCED BY ABIETANE DITERPENOID 1 (DSA1), a Putative O-Fucosyltransferase, in Plant Systemic Acquired Resistance (SAR)2022-06-16T09:44:28-05:00https://digital.library.unt.edu/ark:/67531/metadc1944217/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1944217/"><img alt="Role of DEFECTIVE IN SYSTEMIC DEFENSE INDUCED BY ABIETANE DITERPENOID 1 (DSA1), a Putative O-Fucosyltransferase, in Plant Systemic Acquired Resistance (SAR)" title="Role of DEFECTIVE IN SYSTEMIC DEFENSE INDUCED BY ABIETANE DITERPENOID 1 (DSA1), a Putative O-Fucosyltransferase, in Plant Systemic Acquired Resistance (SAR)" src="https://digital.library.unt.edu/ark:/67531/metadc1944217/small/"/></a></p><p>Dehydroabietinal (DA), an abietane diterpenoid, was previously demonstrated to be a potent activator of systemic acquired resistance (SAR). DA also promotes flowering time in Arabidopsis thaliana by repressing expression of the flowering repressor FLOWERING LOCUS C (FLC) while simultaneously upregulating expression of FLOWERING LOCUS D (FLD), FLOWERING LOCUS VE (FVE) and RELATIVE OF EARLY FLOWERING 6 (REF6), a set of flowering time promoters. To further understand the mechanism underlying signaling by abietane diterpenoids, Arabidopsis mutants exhibiting reduced responsiveness to abietane diterpenoids were identified. One such mutant plant, ems2/7, exhibited SAR-deficiency and delayed flowering, which were found to be associated with two independent, but linked loci. The gene responsible for the SAR defect in ems2/7 was identified as DEFECTIVE IN SYSTEMIC DEFENSE INDUCED BY ABIETANE DITERPENOID 1 (DSA1). Similar to the missense mutant dsa1-1 identified in the mutant screen, the T-DNA insertion bearing null allele dsa1-2 exhibited SAR deficiency that could be complemented by a genomic copy of DSA1. The gene responsible for the delayed flowering phenotype of ems2/7 remains to be identified. DSA1 encodes a protein that is homologous to human protein O-fucosyltransferase 2. DSA1 is required for long-distance transport of the SAR signal. It is hypothesized that DSA1 is involved in the O-fucosylation-facilitated channeling through the ER/Golgi network of a protein involved in long distance SAR signaling. In a yeast two-hybrid screen, all the DSA1-interacting proteins identified are chloroplast-localized proteins, thus raising the interesting possibility of ER interaction with chloroplast and its potential role in SAR signaling.</p>Influence of Hypoxia on Acute Lead Toxicity and Calcium Homeostasis in Early Life Stage Zebrafish (Danio rerio)2022-01-08T16:07:54-06:00https://digital.library.unt.edu/ark:/67531/metadc1873844/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873844/"><img alt="Influence of Hypoxia on Acute Lead Toxicity and Calcium Homeostasis in Early Life Stage Zebrafish (Danio rerio)" title="Influence of Hypoxia on Acute Lead Toxicity and Calcium Homeostasis in Early Life Stage Zebrafish (Danio rerio)" src="https://digital.library.unt.edu/ark:/67531/metadc1873844/small/"/></a></p><p>The purpose of this study was to investigate the effects of Pb and hypoxia co-exposure on Pb toxicity and Ca homeostasis in early life stage (ELS) zebrafish (Danio rerio). Previous evidence indicates that exposure of ELS zebrafish to hypoxia (~20% air saturation) reduces Ca uptake, likely through down-regulation of the apical epithelial Ca channel (ECaC). Considering that Pb and Ca are known antagonists and compete for uptake pathways, it was hypothesized that co-exposure of Pb with hypoxia would decrease Pb toxicity by reducing Pb uptake (likely mediated through a reduced number of ECaCs). However, it was shown that at 96 hpf, whole body accumulation of both Pb and Ca was lower at 40% air saturation compared to 100% and 20% air saturation. This result closely aligned with the 96h LC50 results which showed the highest mortality of zebrafish at 40% compared to the other air saturation levels. This suggests that toxicity is likely the result of exacerbated hypocalcemia at 40% air saturation due to both Pb competition for Ca binding to Ca uptake channels/transporters, such as ECaC, and potentially reduced expression of such channels/transporters in response to this level of hypoxia. Overall, it appears that ELS zebrafish respond differentially to the 40% and 20% hypoxia levels when co-exposed with Pb. Further investigation is needed to illustrate the physiological and molecular mechanisms underlying this response.</p>Production and Optimization of Para-Hydroxybenzoic Acid (pHBA) in Algae Using Metabolic Engineering and Genomics Approaches2022-01-08T16:04:59-06:00https://digital.library.unt.edu/ark:/67531/metadc1873837/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873837/"><img alt="Production and Optimization of Para-Hydroxybenzoic Acid (pHBA) in Algae Using Metabolic Engineering and Genomics Approaches" title="Production and Optimization of Para-Hydroxybenzoic Acid (pHBA) in Algae Using Metabolic Engineering and Genomics Approaches" src="https://digital.library.unt.edu/ark:/67531/metadc1873837/small/"/></a></p><p>Microalgae being photosynthetic and having quick growth cycles can prove to be excellent candidates as biofactories for the production of aromatic compounds like para-hydroxybenzoic acid (pHBA) that act as a monomer in liquid crystal polymers. We developed transgenic lines of the model alga Chlamydomonas reinhardtii by performing nuclear transformation using electroporation. The transgenic cell lines expressed the ubiC gene that utilized chorismate from the shikimate pathway as a substrate to produce pHBA. The maximum yield of pHBA measured in these lines was 80 mg/L.
Accruing pHBA can be toxic to the cells and the mechanism by which C. reinhardtii could detoxify pHBA is not known. C. reinhardtii genome was thus scanned for sequences similar to UDP-glucosyltransferase (UGT) that can transfer the glucose moiety to pHBA, rendering it non-toxic to the cell lines. Our analysis suggested the absence of any potential UGTs that could glycosylate pHBA and detoxify it. We further performed feeding experiments to test the ability of wt-type C. reinhardtii cells to detoxify pHBA and understand its fate. C. reinhardtii cells were fed with varying concentrations of pHBA and harvested at different time intervals. The HPLC chromatograms indicated a majority of the pHBA was catabolized. Based on these results, literature was reviewed to find a suitable UGT candidate to enable the engineering of the glycosylation mechanism in the alga. A transgenic algal line with gene encoding UGT89B1 was created and fed with varying concentrations of pHBA. HPLC chromatograms from the extracts revealed the presence of phenolic glucoside. Following this, C. reinhardtii was co-transformed with ubiC and gene encoding UGT89B1; this led to the production of pHBA and further glycosylation to pHBA glucoside (phenolic glucoside). The maximum yield of pHBA yields in these cell lines was 180 mg/L. Growing C. reinhardtii lines producing pHBA on a large scale can lead to problems like contamination with bacteria and other algal species, a decline in pH, and a rise in temperature. To circumvent these problems, we explored the plausibility of using other algal strains. We analyzed the genome of Galdieria sulphuraria, a photosynthetic thermophile, that can use more than fifty different carbon sources for its growth and metabolism. We hypothesized several of these traits to have arisen by acquiring genes through horizontal gene transfer. We used a segmentation and clustering algorithm to identify regions of the genome that have atypical nucleotide composition. The atypical segments identified by the method were further analyzed using phylogenetic methods to further support claims of their alien origin. Our method identified 69 genes that were not previously reported as alien genes, some of which could be implicated in imparting resistance to environmental stress factors. Our experiments also revealed G. sulphuraria has a greater extent of alien genes compared to C. reinhardtii.</p>Reduced Visceral Fat and Biological Indices of Inflammation Following Combined Prebiotic/Probiotic Supplementation in Free Living Adults2022-01-08T15:59:18-06:00https://digital.library.unt.edu/ark:/67531/metadc1873827/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873827/"><img alt="Reduced Visceral Fat and Biological Indices of Inflammation Following Combined Prebiotic/Probiotic Supplementation in Free Living Adults" title="Reduced Visceral Fat and Biological Indices of Inflammation Following Combined Prebiotic/Probiotic Supplementation in Free Living Adults" src="https://digital.library.unt.edu/ark:/67531/metadc1873827/small/"/></a></p><p>Probiotics/prebiotic supplementation represents a viable option for addressing systemic inflammation and chronic disease risk resulting from excessive body weight. The purpose of this feasibility study was to determine if 90-d of supplementation with prebiotic and probiotic could alter mRNA responsible for inflammation and subsequently metabolic health in weight stable overweight adults. Participants were advised to not change their diet or exercise habits during the study. All protocols were approved by the University IRB and participants gave written informed consent. Participants were randomly assigned to either placebo (N=7; rice flour) or combined (N=8) prebiotic (PreticX® Xylooligosaccharide; 0.8 g/d; ADIP) and probiotic (MegaDuo® Bacillus subtilis HU58 and Bacillus coagulans SC-208; 3 Billion CFU/d) and measurements were made at baseline, 30, 60, and 90-d. Whole body DXA scans (GE iDXA®) and blood 574-plex mRNA analysis (Nanostring®) were used to generate primary outcomes. Compared to placebo, supplementation was associated with a 36% reduction in visceral adipose tissue (p = 0.001). Supplement resulted in significant, differential expression of 15 mRNA associated with adipose tissue inflammation, systemic inflammation, and/or chronic disease risk. The key findings support that 90-d prebiotic/probiotic supplementation may be associated with an improved metabolic health, reduced adipose tissue inflammation, reduced systemic inflammation, and reduced chronic disease risk. Collectively these findings demonstrate the potential of a prebiotic/probiotic supplement to impact metabolic health risk independent of weight loss in free-living individuals.</p>CO2 Transport and Acid-Base Status during Fluctuations in Metabolic Status in Reptiles2022-01-08T15:52:39-06:00https://digital.library.unt.edu/ark:/67531/metadc1873816/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873816/"><img alt="CO2 Transport and Acid-Base Status during Fluctuations in Metabolic Status in Reptiles" title="CO2 Transport and Acid-Base Status during Fluctuations in Metabolic Status in Reptiles" src="https://digital.library.unt.edu/ark:/67531/metadc1873816/small/"/></a></p><p>Reptiles can often experience perturbations that greatly influence their metabolic status (e.g., temperature, exercise, digestion, and ontogeny). The most common cause of fluctuations in metabolic status in post-embryonic reptiles is arguably digestion and physical activity (which will be further referred to as exercise). The objective of this thesis is to determine the mechanisms involved in CO2 transport during digestion, determine the mechanisms that allow for the maintenance of acid-base homeostasis during digestion, and observing the effect of an understudied form of exercise in semi-aquatic reptiles on the regulation of metabolic acidosis and base deficit. This dissertation provided evidence for potentially novel and under investigated mechanisms for acid-base homeostasis (e.g., small intestine and tissue buffering capacity; Chapters 3 & 4), while also debunking a proposed hypothesis for the function of an anatomical feature that still remains a mystery to comparative physiologist (Chapter 2). This thesis is far from systematic and exhaustive in its approach, however, the work accomplished in this dissertation has become the foundation for multiple distinct paths for ecologically relevant investigations of the regulation of metabolic acidosis/alkalosis in reptiles.</p>Investigating the Effects of Inhaled Diesel Exhaust Particles on Gut Microbiome, Intestinal Integrity, Systemic Inflammation, and Biomarkers of Cardiovascular Disease in Wildtype Mice2022-01-08T15:41:21-06:00https://digital.library.unt.edu/ark:/67531/metadc1873801/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873801/"><img alt="Investigating the Effects of Inhaled Diesel Exhaust Particles on Gut Microbiome, Intestinal Integrity, Systemic Inflammation, and Biomarkers of Cardiovascular Disease in Wildtype Mice" title="Investigating the Effects of Inhaled Diesel Exhaust Particles on Gut Microbiome, Intestinal Integrity, Systemic Inflammation, and Biomarkers of Cardiovascular Disease in Wildtype Mice" src="https://digital.library.unt.edu/ark:/67531/metadc1873801/small/"/></a></p><p>We investigated the hypothesis that exposure to inhaled diesel exhaust PM can alter the gut microbiome and intestinal integrity, thereby promoting systemic inflammatory response and early CVD risk, which are exacerbated by HF diet. Furthermore, we investigated whether the observed exposure and diet-mediated outcomes could be mitigated through probiotic treatment. We performed an exposure study on C57Bl/6 male mice, placed on either a low fat (LF) diet or a high-fat (HF) diet, and exposed via oropharyngeal aspiration to 35 μg diesel exhaust particles (DEP) suspended in 35 μl of sterile saline or sterile saline controls (CON) twice a week for four weeks. A subset of mice on HF diet were dosed with 0.3 g/day (PRO, ~7.5x108 CFU/day) of probiotic Ecologic® Barrier 849 (Winclove Probiotics) in drinking water during the course of the study. For our first aim, we investigated the alterations in the gut microbiome, measured circulating cytokines and lipopolysaccharide (LPS), and measured CVD biomarkers in the heart. Our results revealed that exposure to inhaled DEP results in gut dysbiosis characterized by expansion of the phyla Verrucomicrobia and Proteobacteria and reduction in Actinobacteria, which was exacerbated by HF diet. Probiotics mitigated the DEP-mediated expansion of Proteobacteria and re-established Actinobacteria in the intestine of HF animals. Furthermore, we determined that exposure to inhaled DEP increases systemic LPS and inflammatory markers IL-1α, IL-3, G-CSF, and TNF-α. Furthermore, we found that inhaled DEP exposure results in increased CVD biomarkers sICAM-1, sP-selectin, and thrombomodulin in the heart. Probiotic treatment was effective in attenuating LPS, inflammatory responses, and CVD biomarkers in HF animals, validating the involvement of the microbiome in mediating inhaled DEP-mediated responses. Considering the effects we observed in the microbiota and systemically of the HF and probiotic treatment animals, we investigated the effects of inhaled DEP on intestinal integrity and inflammation in HF ± PRO animals. Our results showed that inhaled DEP in conjunction with HF diet promotes increased goblet cell and mucin 2 expression, tight junction (TJ) proteins (claudin-3, occludin, and zonula occludens (ZO)-1) expression, matrix metalloproteinase (MMP)-9, toll-like receptor (TLR)-4, and decreased TNF-α and IL-10. Moreover, we found that probiotics promoted intestinal immune response following inhaled DEP exposure characterized by an increase in TNF-α and IL-10 and showed variable expression of TJs in the intestine. In conclusion, we found that inhaled DEP exposure results in changes in gut microbial profiles, altered intestinal integrity, systemic inflammation, and increased CVD biomarkers, which are exacerbated by HF diet. The use of probiotics in this study proved to be pivotal in understanding the microbiome's influences on the regulation of intestinal integrity, intestinal inflammation, systemic inflammation, and cardiovascular system following inhaled DEP exposure with HF diet.</p>Quantifying the Effects of Single Nucleotide Changes in the TATA Box of the Cauliflower Mosaic Virus 35S Promoter on Gene Expression in Arabidopsis thaliana2022-01-08T15:24:02-06:00https://digital.library.unt.edu/ark:/67531/metadc1873554/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873554/"><img alt="Quantifying the Effects of Single Nucleotide Changes in the TATA Box of the Cauliflower Mosaic Virus 35S Promoter on Gene Expression in Arabidopsis thaliana" title="Quantifying the Effects of Single Nucleotide Changes in the TATA Box of the Cauliflower Mosaic Virus 35S Promoter on Gene Expression in Arabidopsis thaliana" src="https://digital.library.unt.edu/ark:/67531/metadc1873554/small/"/></a></p><p>Synthetic biology is a rapidly growing field that aims to treat cellular biological networks in an analogous way to electrical circuits. However, the field of plant synthetic biology has not grown at the same pace as bacterial and yeast synthetic biology, leaving a dearth of characterized tools for the community. Due to the need for tools for the synthetic plant biologist, I have endeavored to create a library of well-characterized TATA box variants in the cauliflower mosaic virus (CaMV) 35S promoter using the standardized assembly method Golden Braid 2.0. I introduced single nucleotide changes in the TATA box of the CaMV 35S promoter, a genetic part widely used in plant gene expression studies and agricultural biotechnology. Using a dual-luciferase reporter system, I quantified the transcriptional strength of the altered TATA box sequences and compared to the wild-type sequence, both in transient protoplast assays and stable transgenic Arabidopsis thaliana plants. The library of TATA-box modified CaMV 35S promoters with varying transcriptional strengths created here can provide the plant synthetic biology community with a series of modular Golden Braid-adapted genetic parts that can be used dependably and reproducibly by researchers to fine-tune gene expression levels in complex, yet predictable, synthetic genetic circuits.</p>Manipulation of Lipid Droplet Biogenesis for Enhanced Lipid Storage in Arabidopsis thaliana and Nicotiana benthamiana2022-01-08T15:23:17-06:00https://digital.library.unt.edu/ark:/67531/metadc1873553/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873553/"><img alt="Manipulation of Lipid Droplet Biogenesis for Enhanced Lipid Storage in Arabidopsis thaliana and Nicotiana benthamiana" title="Manipulation of Lipid Droplet Biogenesis for Enhanced Lipid Storage in Arabidopsis thaliana and Nicotiana benthamiana" src="https://digital.library.unt.edu/ark:/67531/metadc1873553/small/"/></a></p><p>In this study, I examined the use of mouse (Mus musculus) Fat Specific Protein 27 (FSP27) ectopically expressed in Arabidopsis thaliana and Nicotiana benthamiana as a means to increase lipid droplet (LD) presence in plant tissues. In mammalian cells, this protein induces cytoplasmic LD clustering and fusion and helps prevent breakdown of LDs contributing to the large, single LD that dominates adipocytes. When expressed in Arabidopsis thaliana and Nicotiana benthamiana, FSP27 retained its functionality and supported the accumulation of numerous and large cytoplasmic LDs, although it failed to produce the large, single LD that typifies adipose cells.
FSP27 has no obvious homologs in plants, but a search for possible distant homologs in Arabidopsis returned a Tudor/PWWP/MBT protein coded for by the gene AT1G80810 which for the purposes of this study, we have called LIPID REGULATORY TUDOR DOMAIN CONTAINING GENE 1 (LRT1). As a possible homolog of FSP27, LRT1 was expected to have a positive regulatory effect on LDs in cells. Instead, a negative regulatory effect was observed in which disruption of the gene induced an accumulation of cytoplasmic LDs in non-seed tissue. A study of lrt1 mutants demonstrated that disruption this gene is the causal factor of the cytoplasmic LD accumulation observed in the mutants, that this phenotype occurs in above ground tissues and is present throughout the early growth stages of the plant. Further examination of lrt1 mutant plants has allowed a preliminary understanding of the role LRT1 may play in LD regulation. Taken together, the results of this study point towards some promising strategies to increase LD content in plant tissues.</p>Multiple Dimensions of Fish Functional Traits, Trait Relationships, and Associations with Community Structure and Dynamics2022-01-08T15:18:03-06:00https://digital.library.unt.edu/ark:/67531/metadc1873545/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1873545/"><img alt="Multiple Dimensions of Fish Functional Traits, Trait Relationships, and Associations with Community Structure and Dynamics" title="Multiple Dimensions of Fish Functional Traits, Trait Relationships, and Associations with Community Structure and Dynamics" src="https://digital.library.unt.edu/ark:/67531/metadc1873545/small/"/></a></p><p>Trait-based approaches are useful in ecological research because of their potential ability to predict species responses from patterns present in the community and to infer mechanisms driving community assembly. Current approaches for fishes are lacking traits across all five fundamental niche dimensions (i.e. habitat, life history, trophic, metabolic and defense). This study quantified a broad range of fish functional traits across all five niche dimensions (commonly used traits and novel traits), quantified intra- and interspecific variation for each trait, tested for relationships among traits within and among niche dimensions, tested for phylogenetic conservatism of traits and assessed trait-environment relationships for a subset of these traits under two different contexts. Approximately one third of the quantified traits exhibited greater intraspecific variation than interspecific variation and were not included in subsequent analyses. There were similarities between phylogeny and trait dendrograms for all traits, and habitat, metabolic and defense traits. The traits identified in chapter 2 were able to explain species responses during different flow periods in two intermittent streams as well as species-specific differences in host microbiome at the onset of drought in one intermittent stream. The novel traits identified in chapter 2 did contribute to our understanding of the community assembly dynamics in chapter 3.</p>Flow-Recruitment Relationships of Smallmouth Buffalo (Ictiobus bubalus) in Three Texas River Basins2021-08-26T21:27:52-05:00https://digital.library.unt.edu/ark:/67531/metadc1833577/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833577/"><img alt="Flow-Recruitment Relationships of Smallmouth Buffalo (Ictiobus bubalus) in Three Texas River Basins" title="Flow-Recruitment Relationships of Smallmouth Buffalo (Ictiobus bubalus) in Three Texas River Basins" src="https://digital.library.unt.edu/ark:/67531/metadc1833577/small/"/></a></p><p>This project focused on the relationship between instream flows and smallmouth buffalo (Ictiobus bubalus) recruitment in the Gulf Coastal Plain of Texas. The flow regime is the dominant factor in lotic systems and, consequently, the relationship between instream flows, including impacts to natural flow regimes, and life-history is a subject of growing interest. Smallmouth buffalo is a good model to investigate the relationship between river flows and variable interannual recruitment success of periodic life-history strategist fish species. Smallmouth buffalo were collected from the Brazos, Colorado, and Guadalupe Rivers of Texas, U.S.A., and otoliths were extracted from individuals in the field and sectioned and photographed in the lab. Photographs of sectioned otoliths were used to estimate age and thus the year in which the individual was spawned by counting back from the time of capture. Population age structure (i.e. a ‘state' or condition at a point in time) was used to infer effects of flow variation on a rates-based process (i.e. recruitment). After controlling for mortality using recruitment index values, interannual variation in recruitment was modeled using multiple components of the flow regime quantified as indicators of hydrologic alteration (IHA) variables based on daily discharge data from USGS gaging stations in each river system. Model selection followed a two-tier approach, first fitting models using only flow attributes associated with the spawning season then adding additional informative parameters from the pre-spawn and post-spawn periods. The primary finding from model selection was that duration of high flow pulses during the spawning season is a critical component of the flow regime associated with successful Smallmouth Buffalo recruitment. These findings have implications for river management and conservation of ecological integrity, in particular populations of periodic life-history strategist species.</p>Studies on the Fibrinolytic Pathway in Zebrafish2021-08-26T21:23:06-05:00https://digital.library.unt.edu/ark:/67531/metadc1833569/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833569/"><img alt="Studies on the Fibrinolytic Pathway in Zebrafish" title="Studies on the Fibrinolytic Pathway in Zebrafish" src="https://digital.library.unt.edu/ark:/67531/metadc1833569/small/"/></a></p><p>Fibrinolysis pathway is an important mechanism for dissolution of fibrin clot by the action of plasmin which is formed from plasminogen, a zymogen via the action of plasminogen activators, i.e. tissue plasminogen activator and urinary plasminogen activator. The regulation of fibrinolysis system in vivo is maintained by plasminogen activators and natural inhibitors i.e. α2-antiplasmin, α2-macroglobulin, Thrombin-activatable fibrinolysis inhibitor (TAFI) and plasminogen activator inhibitor 1 and 2 (PAI-1and PAI-2). There are several fibrinolytic assays developed for human plasma but there are no reports describing fibrinolytic assay using zebrafish plasma. In this study, a fibrinolytic assay via using small amount of zebrafish plasma was developed. This assay was performed under different conditions; one by the addition of exogenous tissue plasminogen activator alone to the pooled zebrafish plasma along with calcium chloride and thromboplastin, second Dade ACTIN was used instead of tissue plasminogen activator and third Dade ACTIN along with thromboplastin was used. Epsilon amino caproic acid (EACA), a synthetic antifibrinolytic agent was used at different concentrations to inhibit fibrinolysis successfully. Similar experiments were performed on human plasma as well to check the applicability of the assay to humans and positive results were obtained. Furthermore, knockdown of tissue plasminogen activator and plasminogen genes was performed and the prolongation of peak time, the time taken for the maximal formation of fibrin was observed, similar to the EACA inhibition. In conclusion, a fibrinolysis assay using miniscule amount of plasma was developed and applied to study knockdown of fibrinolytic pathway genes. The assay developed here may have clinical utility.</p>Analysis of the Accumulation, Toxic Effects, and Risk of Persistent Organic Pollutants in Pinnipeds2021-08-26T21:07:18-05:00https://digital.library.unt.edu/ark:/67531/metadc1833546/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833546/"><img alt="Analysis of the Accumulation, Toxic Effects, and Risk of Persistent Organic Pollutants in Pinnipeds" title="Analysis of the Accumulation, Toxic Effects, and Risk of Persistent Organic Pollutants in Pinnipeds" src="https://digital.library.unt.edu/ark:/67531/metadc1833546/small/"/></a></p><p>The present studies determine the accumulation of persistent organic pollutants (POPs) in three pinniped species, evaluate the relationship with relevant biomarkers of exposure, and calculate toxic effect thresholds. Stranded harp and hooded seals were found to be accumulating PBDEs at levels which could pose a based on threshold levels determined in this study. Northern fur seals are accumulating all three classes of POPs (PCBs, PBDEs, and OCPs) with significant relationships being seen with blubber percent lipid. Correlations between contaminant concentrations and expression levels of relevant biomarkers were seen potentially indicating an effect on multiple pathways. Overall risk can be hard to determine due to factors such as sex and age. Broad threshold response values and hazard quotients were calculated for toxic effect endpoints in pinnipeds. Overall these results suggest that certain populations of pinnipeds are at high risk of experiencing toxic effects due to POP exposure, but it is important to understand effects even at lower concentrations. The relationship between exposure, toxic effects, and other stressors, both environmental and physiological, can impact the overall fitness and survival of pinnipeds.</p>Analysis of Multipartite Bacterial Genomes Using Alignment-Free and Alignment-Based Pipelines2021-08-26T20:46:07-05:00https://digital.library.unt.edu/ark:/67531/metadc1833506/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833506/"><img alt="Analysis of Multipartite Bacterial Genomes Using Alignment-Free and Alignment-Based Pipelines" title="Analysis of Multipartite Bacterial Genomes Using Alignment-Free and Alignment-Based Pipelines" src="https://digital.library.unt.edu/ark:/67531/metadc1833506/small/"/></a></p><p>In this work, we have performed comparative evolutionary analysis, functional genomics analysis, and machine learning analysis to identify the molecular factors that discriminate between multipartite and unipartite bacteria, with the goal to decipher taxon-specific factors and those that are prevalent across the taxa underlying the these traits. We assessed the roles of evolutionary mechanisms, namely, horizontal gene transfer and gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical protein DR_A0179 and hypothetical protein DR_A0109 in Deinococcus radiodurans R1, and Putative phage phi-C31 gp36 major capsid-like protein and hypothetical protein RSP_3729 in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in both bacteria and were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. These genes emphasize the important potential roles of the secondary chromosomes in helping multipartite bacteria to adapt to specialized environments or conditions. In addition, we applied machine learning algorithms to predict multipartite genomes based on gene content of multipartite genomes and their unipartite relatives, and leveraged this to identify genes that are deemed important by machine learning in discriminating between multipartite and unipartite genomes. This approach led to the identification of marker genes that could be used in discriminating between bacteria with multipartite genomes and. bacteria with single chromosome genomes
Furthermore, we examined modules in gene co-expression networks of multipartite Rhodobacter sphaeroides 2.4.1 and its close unipartite relative Rhodobacter capsulatus SB 1003 that were enriched in genes differentially expressing under stressful conditions representing different experiments. This led to the identification of 6 modules in the Rhodobacter sphaeroides 2.4.1 network and 3 modules in the Rhodobacter capsulatus SB 1003 network, which were significantly enriched (2-fold or more) in differentially expressing genes, revealing the vital roles of these gene modules representing different pathways or networks of pathways (known or unknown) in enabling the bacteria to adapt to stressful conditions. Overall, our study highlights genetic factors that may be driving the evolution of multipartite bacterial genomes; future studies may focus on unraveling the specific roles of these genes in the adaptation and maintenance of multipartite genomes.</p>Sociality in Harris's Hawks Revisited: Patterns of Reproductive Output and Delayed Dispersal2021-08-26T20:44:52-05:00https://digital.library.unt.edu/ark:/67531/metadc1833503/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833503/"><img alt="Sociality in Harris's Hawks Revisited: Patterns of Reproductive Output and Delayed Dispersal" title="Sociality in Harris's Hawks Revisited: Patterns of Reproductive Output and Delayed Dispersal" src="https://digital.library.unt.edu/ark:/67531/metadc1833503/small/"/></a></p><p>In the lower Rio Grande Valley of south Texas, more than half the nesting groups of Harris's hawks (Parabuteo unicinctus) include at least one auxiliary group member in addition to a breeding pair. To provide further insight into cooperatively breeding raptors, I evaluated sociality in Harris's hawks through the dual benefits framework. I explored the formation, structure, and stability of cooperative group formation across a spatially variable study area, which includes high levels of urbanization and development as well as remote, undisturbed native habitats with low anthropogenic impact. I used color banding, regular censuses of active territories, and a microsatellite relatedness analysis to examine patterns of sociality, including delayed dispersal, the effect of auxiliary group members on reproductive output, parentage of broods, and the relatedness of auxiliaries compared to the nestlings in their territories. I confirmed cooperative polygamy with genetic techniques for the first time in Harris's hawks and found 58% of juvenile hawks delayed dispersal for at least 6 mo. Using the dual benefits framework, I found social associations that formed through delayed dispersal followed predictions for resource-defense benefits, but sociality among mature non-related hawks more closely followed predictions associated with collective action benefits, specifically reproductive output was significantly reduced in undeveloped habitats, presumably due to a less predictable prey-base.</p>Exploring Flavonoid Glycosylation in Kudzu (Pueraria lobata)2021-08-26T20:34:45-05:00https://digital.library.unt.edu/ark:/67531/metadc1833483/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833483/"><img alt="Exploring Flavonoid Glycosylation in Kudzu (Pueraria lobata)" title="Exploring Flavonoid Glycosylation in Kudzu (Pueraria lobata)" src="https://digital.library.unt.edu/ark:/67531/metadc1833483/small/"/></a></p><p>The isoflavones in kudzu roots, especially the C-glycosylated isoflavone puerarin, have been linked to many health benefits. Puerarin contains a carbon-carbon glycosidic bond that can withstand hydrolysis. The C-glycosylation reaction in the biosynthesis of puerarin has not been thoroughly investigated, with conflicting reports suggesting that it could take place on daidzein, isoliquiritigenin, or 2,7,4ʹ-trihydroxyisoflavanone. Kudzu species were identified for use in comparative transcriptomics. A non-puerarin producing kudzu was identified as Pueraria phaseoloides and a puerarin producing kudzu was identified as Pueraria montana lobata. Through the use of the plant secondary product glycosyltransferase (PSPG) motif, glycosyltransferases (UGTs) were identified from the transcriptomes. The UGTs that had higher digital expression in P. m. lobata were examined further using additional tools to home in on the UGT that could be responsible for puerarin biosynthesis. One of the UGTs identified, UGT71T5, had previously been characterized from kudzu as a C-glycosyltransferase involved in puerarin biosynthesis through in vitro enzyme activity (with daidzein) and a gain of function approach in soybean hairy roots. Previous studies have not supported the end-product of a pathway such as daidzein as the target for C-glycosylation, and no genetic analysis of UGT function had been conducted in kudzu. The activity of recombinant UGT71T5 with daidzein was confirmed in the present work. Following the development of a kudzu hairy root system, UGT71T5 expression was then knocked down by RNA interference (RNAi). When compared to control hairy roots there was a large reduction in puerarin content in the UGT71T5-RNAi roots, confirming the role of this enzyme in puerarin biosynthesis. Isotopic labeling of kudzu plants revealed that labeled daidzein could be directly incorporated into puerarin; however, the percent incorporation of daidzein was substantially lower than that of L-phenylalanine, a compound at the start of the pathway to isoflavone synthesis. The knockdown of 2-hydroxisoflavanone synthase (2-HIS) in kudzu hairy roots blocked formation of puerarin and daidzin (7-O-glycosyldaidzein), and was accompanied by accumulation of C-glycosylated isoliquiritigenin and C-glycosylated liquiritigenin. These compounds were found in low amounts in control hairy roots, but were virtually absent in UGT71T5 knockdown hairy roots. The knockdown of 2-hydroxyisoflavanone dehydratase (2-HID) in kudzu hairy roots resulted in a slight reduction in puerarin but no change to daidzin levels, suggesting that C-glycosylation might stabilize the substrate for 2-HID which can otherwise spontaneously dehydrate. Taken together these results reveal that UGT71T5 is likely the major C-glycosyltransferase involved in puerarin biosynthesis in kudzu. They also provide evidence for an alternative pathway to puerarin biosynthesis through the C-glycosylation of isoliquiritigenin or its immediate precursor. In one pathway, UGT71T5 acts as an operationally soluble enzyme that can directly C-glycosylate daidzein, and in the other pathway UGT71T5 acts as part of a metabolic channel for conversion of a C-glycosylated earlier precursor to puerarin. Other UGT enzymes identified in this work did not show C-glycosyltransferase activity; however, three enzymes showed activity in vitro that could be useful for introducing novel regiospecificity in biochemical synthesis of flavonoid glycosides.</p>Ecological Responses to Severe Flooding in Coastal Ecosystems: Determining the Vegetation Response to Hurricane Harvey within a Texas Coast Salt Marsh2021-08-26T20:33:20-05:00https://digital.library.unt.edu/ark:/67531/metadc1833477/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833477/"><img alt="Ecological Responses to Severe Flooding in Coastal Ecosystems: Determining the Vegetation Response to Hurricane Harvey within a Texas Coast Salt Marsh" title="Ecological Responses to Severe Flooding in Coastal Ecosystems: Determining the Vegetation Response to Hurricane Harvey within a Texas Coast Salt Marsh" src="https://digital.library.unt.edu/ark:/67531/metadc1833477/small/"/></a></p><p>Vegetative health was measured both before and after Hurricane Harvey using remotely sensed vegetation indices on the coastal marshland surrounding Galveston Island's West Bay. Data were recorded on a monthly basis following the hurricane from September of 2005 until September of 2019 in order to document the vegetation response to this significant disturbance event. Both initial impact and recovery were found to be dependent on a variety of factors, including elevation zone, spatial proximity to the bay, the season during which recovery took place, as well as the amount of time since the hurricane. Slope was also tested as a potential variable using a LiDAR-derived slope raster, and while unable to significantly explain variations in vegetative health immediately following the hurricane, it was able to explain some degree of variability among spatially close data points. Among environmental factors, elevation zone appeared to be the most key in determining the degree of vegetation impact, suggesting that the different plant assemblages that make up different portions of the marsh react differently to the severe flooding that took place during Harvey.</p>Effect of Phosphorus Starvation on Metabolism and Spatial Distribution of Phosphatidylcholine in Medicago truncatula Wild-Type and PDIL3 Genotypes2021-08-26T20:33:12-05:00https://digital.library.unt.edu/ark:/67531/metadc1833476/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833476/"><img alt="Effect of Phosphorus Starvation on Metabolism and Spatial Distribution of Phosphatidylcholine in Medicago truncatula Wild-Type and PDIL3 Genotypes" title="Effect of Phosphorus Starvation on Metabolism and Spatial Distribution of Phosphatidylcholine in Medicago truncatula Wild-Type and PDIL3 Genotypes" src="https://digital.library.unt.edu/ark:/67531/metadc1833476/small/"/></a></p><p>Symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. Within nodule cells, N-fixing rhizobia are surrounded by plant-derived symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. First, I investigated the impact of P deprivation on wild-type Medicago truncatula plants. My observations that plants had impaired SNF activity, reduced growth, and accumulated less phosphate in P-deficient tissues (leaves, roots and nodules) is consistent with those of similar previous studies. Galactolipids decreased with increase in phospholipids in all P-starved organs. Matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI-MSI) of phosphatidylcholine (PC) species in nodules showed that under low P environments distributions of some PC species changed, indicating that membrane lipid remodeling during P stress is not uniform across the nodule. Secondly, a metabolomics study was carried out to test the alterations in the metabolic profile of the nodules in P-stress. GC-MS based untargeted metabolomics showed increased levels of amino acids and sugars and decline in amounts of organic acids in P deprived nodules. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in whole plant. My findings showed strong drop in levels of organic acids and phosphorylated compounds in P deprived leaves with moderate reduction in P deprived roots and nodules. Moreover, sugars and amino acids were elevated in whole plant under P deprivation.
Finally, the last project of my thesis involved studying the response of PDIL3 (Phosphate Deficiency-Induced LncRNA-3) a long non-coding RNA (lncRNA) mutant under severe P stress. PDIL3 is known to regulate Pi-deficiency signaling and transport in M. truncatula (Wang et al., 2017). My results confirmed that in P starvation, pdil3 plants showed better shoot growth, accumulated more phosphate in shoots, had impaired SNF and less rhizobial occupancy in nodules than WT. Subsequently, MALDI–MS imaging was used to spatially map and compare the distribution of phosphatidylcholine (PC) species in nodules of pdil3 and WT in P-replete and P-depleted conditions. Several PC species showed changes in distributions in pdil3 nodules compared to WT in both P sufficient and P deprived conditions. These data suggest that PDIL3's role is not just suppression of the Pi transporter, but it may also influence P partitioning between shoots and nodulated roots, meriting further investigation.</p>Studies on Intrinsic Coagulation Pathway of Zebrafish2021-08-26T20:09:07-05:00https://digital.library.unt.edu/ark:/67531/metadc1833433/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833433/"><img alt="Studies on Intrinsic Coagulation Pathway of Zebrafish" title="Studies on Intrinsic Coagulation Pathway of Zebrafish" src="https://digital.library.unt.edu/ark:/67531/metadc1833433/small/"/></a></p><p>In the past couple of decades, the zebrafish has been widely used to study hemostatic disorders. In this study, we generated a CRISPR/Cas9 mediated zebrafish mutant that contains a 55-nucleotide insertion in exon 29 of the von Willebrand factor (vwf) gene. The mutants had impaired ristocetin-mediated agglutination of whole blood, prolonged PTT and more bleeding in the lateral incision compared to wild-type fish. The bleeding phenotype observed here is similar to the phenotype observed in vwf knockout mice and patients with von Willebrand disease (VWD). The mutant model developed here can thus be used for exploring the role of Vwf in angiogenesis and for developing gene therapy. The deficiency of VWF causes VWD and the etiology remains unknown in 30% of Type 1 VWD cases. Previous studies have identified that the ABO blood group and ST3GAL4 (glycosyltransferases) are involved in the regulation of VWF levels. Since VWF is heavily glycosylated, we hypothesized that other glycosyltransferases may also be involved in regulating VWF. We performed a knockdown screen of 234 glycosyltransferase genes and identified 14 genes that altered Vwf levels. The sequencing of these genes in Type 1 VWD patients could help identify novel mutations to decipher the molecular basis for the unknown etiologies in Type 1 VWD. Moreover, therapeutic interventions could be designed in the future by modulation of these gene products to control bleeding or thrombosis.Zebrafish has three f9 genes, f9a, f9b, and f9l and the ortholog to human F9 is unknown. RNA analysis showed an age-dependent increase in expression of all three genes from larval stages to adults, comparable to those observed in mice and humans while mass spectrometry and immunohistochemistry confirmed the presence of all three proteins in the fish. Based on coagulation assays performed after individual gene knockdown and immunodepletion, we identified that zebrafish f9a has functional activity similar to human F9 and Fixl is functionally similar to Fx. Thus, the zebrafish could be used to identify factors controlling f9 gene expression with age and for modeling Hemophilia B in the quest to develop gene therapy protocols.
In zebrafish, dilute plasma with exogenously added human fibrinogen was used for kinetic coagulation assays. Here, we developed a microkinetic assay using 25% zebrafish or 30% human plasma followed by the addition of coagulation activators and CaCl2. Our results showed both zebrafish and human plasmas yielded kinetic PT, kinetic PTT, and kinetic Russel's viper venom time curves similar to previously established human kinetic curves. Moreover, clotting times derived from these kinetic curves were identical to human PT, PTT, and Russel's viper venom time. Thus, the microkinetic assay developed here could measure blood coagulation activity in small animal models like zebrafish and human blood samples obtained from a finger prick in adults or heel prick in infants.</p>Ozone Pollution Monitoring and Population Vulnerability in Dallas-Ft. Worth: A Decision Support Approach2021-08-26T20:07:23-05:00https://digital.library.unt.edu/ark:/67531/metadc1833430/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833430/"><img alt="Ozone Pollution Monitoring and Population Vulnerability in Dallas-Ft. Worth: A Decision Support Approach" title="Ozone Pollution Monitoring and Population Vulnerability in Dallas-Ft. Worth: A Decision Support Approach" src="https://digital.library.unt.edu/ark:/67531/metadc1833430/small/"/></a></p><p>In urban environments, ozone air pollution, poses significant risks to respiratory health. Fixed site monitoring is the primary method of measuring ozone concentrations for health advisories and pollutant reduction, but the spatial scale may not reflect the current population distribution or its future growth. Moreover, formal methods for the placement of ozone monitoring sites within populations potentially omit important spatial criteria, producing monitoring locations that could unintentionally underestimate the exposure burden. Although air pollution affects all people, the combination of underlying health, socioeconomic and demographic factors exacerbate the impact for socially vulnerable population groups. A need exists for assessing the spatial representativeness and data gaps of existing pollution sensor networks and to evaluate future placement strategies of additional sensors. This research also seeks to understand how air pollution monitor placement strategies may neglect social vulnerabilities and therefore, potentially underestimate exposure burdens in vulnerable populations.</p>Biomonitoring at Dallas-Fort Worth International Airport: Relating Watershed Land Use with Aquatic Life Use2021-08-26T20:06:29-05:00https://digital.library.unt.edu/ark:/67531/metadc1833427/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1833427/"><img alt="Biomonitoring at Dallas-Fort Worth International Airport: Relating Watershed Land Use with Aquatic Life Use" title="Biomonitoring at Dallas-Fort Worth International Airport: Relating Watershed Land Use with Aquatic Life Use" src="https://digital.library.unt.edu/ark:/67531/metadc1833427/small/"/></a></p><p>The Dallas-Fort Worth International (DFW) Airport is located in a densely urbanized area with one of the fastest-growing populations in the U.S.A. The airport property includes a large tract of "protected" riparian forest that is unique to the urban surroundings. This dissertation explores variables that influence the benthic macroinvertebrate community structure found in urbanized prairie streams that were initially assessed by the University of North Texas (UNT) Benthic Ecology Lab during four, non-consecutive biomonitoring studies (2004, 2005, 2008, and 2014) funded by the DFW Airport. Additionally, land use analysis was performed using 5-meter resolution satellite imagery and eCognition to characterize the imperviousness of the study area watersheds at multiple scales. Overall, flow conditions and imperviousness at the watershed scale explained the most variability in the benthic stream community. Chironomidae taxa made up 20-50% of stream communities and outperformed all other taxa groups in discriminating between sites of similar flows and urban impairments. This finding highlights the need for genus level identifications of the chironomid family, especially as the dominant taxa in urban prairie streams. Over the course of these biomonitoring survey events, normal flow conditions and flows associated with supra-seasonal drought were experienced. Prevailing drought conditions of 2014 did not negatively influence stream communities, allowing this study to capture the long-term natural (temporal) variability of urban prairie stream communities. Such long-term studies are imperative for discerning between stream impairment versus natural variation, especially as droughts become more frequent and severe.</p>Benefits of Probiotics on Mortality, Growth Performance, Physiological Condition and Gut Histomophology of Juvenile Red Drum (Sciaenops ocellatus)2021-05-26T22:00:32-05:00https://digital.library.unt.edu/ark:/67531/metadc1808465/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1808465/"><img alt="Benefits of Probiotics on Mortality, Growth Performance, Physiological Condition and Gut Histomophology of Juvenile Red Drum (Sciaenops ocellatus)" title="Benefits of Probiotics on Mortality, Growth Performance, Physiological Condition and Gut Histomophology of Juvenile Red Drum (Sciaenops ocellatus)" src="https://digital.library.unt.edu/ark:/67531/metadc1808465/small/"/></a></p><p>Results from the present study found for the first time that the use of bacterial strains of Lactobacillus acidophilus, Lactobacillus casei, Bifidobacterium thermophilum, and Enterococcus faecium from the commercial product PrimaLac® had the potential to act as a possible probiotic for juvenile red drum. The addition of PrimaLac® probiotics [whether as a water-soluble probiotic (WSP) or in a probiotic enhanced starter feed (PESF)] reduced mortality (%M), enhanced growth rates (MW, LT, SGR, and DGR), improved feed conversion efficiencies (FCEs), and physical condition factors in the juvenile red drum. Improvement was quantified using external morphological condition indices (MCIs) and blood physiological condition indices (PCIs). Results showed a strong positive relationship between MCIs and PCIs, which suggested that probiotics treated fish were in better health (lower MCIs) with lower fasting blood glucose and lactate levels than control fish. Addition of probiotics also resulted in improved water quality (lower nitrate, nitrite, and ammonia) in the treatment tanks compared to controls. Application of PrimaLac® probiotics on the morphology and histology of three different regions of the intestine (proximal, mid-and distal) improved intestinal length (Li), mass (Mi), and digesta mass (Md). In 5μm histological sections examined for differences among treatments (probiotics vs. controls), five variables within each intestinal region were also quantified: (i) perimeter ratio (PR) between the internal perimeter (IP) of the intestinal lumen and the external perimeter (EP) of the intestine where, PR = IP/EP; (ii) width of lamina propria (wLP); (iii) thickness of the muscle layer (tM); (iv) the number of goblet cells per segments (GC); and (v) height of enterocytes (hE). Overall, Li and Mi significantly increased by 13.4 ± 1.2% and 11.8 ± 0.9%, respectively, and Md decreased by 33.2 ± 1.21% compared to controls. Significant increases in microvilli heights, PR (by 21.3 ± 1.2%), tM (by 18.4 ± 0.9%), and increased numbers of GC (by 35.1 ± 2.8%) provided evidence that bacteria species from PrimaLac® (whether in WSP or PESF) affected the intestinal histomorphology of juvenile red drum. Collectively, these changes were partially responsible for increased feed assimilation (supported by reduced digesta) and improved overall juvenile red drum growth and condition. These results will add significantly to the limited database on how probiotics, as possible standard practice at the fish farm, may offer significant benefits for fish production and fish health. Addition of probiotics will also be of benefit to most aquaculture species and not only for red drum, but also for other high-value carnivorous species, such as Atlantic salmon, without threat to natural populations or damaging fisheries-based ecosystems that are already on the edge of collapse from over fishing and pollution.</p>Breeding Ecology and Migratory Connectivity of Passerines in the World's Southernmost Forests2021-05-26T21:42:36-05:00https://digital.library.unt.edu/ark:/67531/metadc1808431/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1808431/"><img alt="Breeding Ecology and Migratory Connectivity of Passerines in the World's Southernmost Forests" title="Breeding Ecology and Migratory Connectivity of Passerines in the World's Southernmost Forests" src="https://digital.library.unt.edu/ark:/67531/metadc1808431/small/"/></a></p><p>In the extensive and remote sub-Antarctic forests of South America, birds are the dominant terrestrial vertebrates. Despite considerable efforts to understand the ecology of birds breeding in these forests, our current knowledge for many species is still incomplete. During three breeding seasons (2014 – 2017), I studied the breeding ecology of the five most abundant open-cup forest-dwelling passerines in the sub-Antarctic forest of Navarino Island, Chile (55°04′S, 67°40′W). There were differences in some of the breeding strategies used by birds breeding on Navarino Island versus conspecific populations breeding at lower latitudes. Milvago chimango was the main nest predator of open-cup nesting forest passerines, and the main cause of nest failure. In addition, I found that species built their nests in sites with higher density and taller understory; however, these two factors decreased their nest survival. This mismatch could be due to a change in depredation risk on Navarino Island, and thus, passerines breeding there may be in an ecological trap. In addition, using light-level geolocators, I determined that the migratory connectivity of Elaenia albiceps is weak as a result of the large spatial spread of individuals on the wintering ground, and that the distances among individuals on the breeding grounds are not maintained in the wintering grounds. My study opens further questions about the mechanisms driving differences in breeding strategies among populations. In addition, further research is needed to assess hypotheses that could explain the mismatch between nest-site selection and nest survival and to understand what drives elaenias' movements, not only during winter but throughout their annual cycle.</p>The Development of Potential Therapeutic Anti-Myosin S2 Peptides that Modulate Contraction and Append to the Heart Homing Adduct Tannic Acid without Noticeable Effect on Their Functions2021-05-26T21:38:21-05:00https://digital.library.unt.edu/ark:/67531/metadc1808423/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1808423/"><img alt="The Development of Potential Therapeutic Anti-Myosin S2 Peptides that Modulate Contraction and Append to the Heart Homing Adduct Tannic Acid without Noticeable Effect on Their Functions" title="The Development of Potential Therapeutic Anti-Myosin S2 Peptides that Modulate Contraction and Append to the Heart Homing Adduct Tannic Acid without Noticeable Effect on Their Functions" src="https://digital.library.unt.edu/ark:/67531/metadc1808423/small/"/></a></p><p>This dissertation aimed to explore the S2 region with an attempt to modulate its elasticity in order to tune the contraction output. Two peptides, the stabilizer and destabilizer, showed high potential in modifying the S2 region at the cellular level, thus they were prepared for animal model testing. In this research, (i) S2 elasticity was studied, and the stabilizer and destabilizer peptides were built to tune contraction output through modulating S2 flexibility; (ii) the peptides were attached to heart homing adducts and the bond between them was confirmed; and (iii) it was shown that minor changes were imposed on the modulating peptides' functionality upon attaching to the heart homing adducts. S2 flexibility was confirmed through comparing it to other parts of myosin using simulated force spectroscopy. Modulatory peptides were built and computationally tested for their efficacy through interaction energy measurement, simulated force spectroscopy and molecular dynamics; these were attached to heart homing adducts for heart delivery. Interaction energy tests determined that tannic acid (TA) served well for this purpose. The stoichiometry of the bond between the TA and the modulating peptides was confirmed using mass spectroscopy. The functionality of the modulating peptides was shown to be unaltered through expansion microscopy where they located to the same position on the sarcomere with and without TA. They were also shown to cause the sarcomeres to contract similarly with and without the TA in contractility assay. Taken together, this work prepared the modulating peptides for animal model tests by attaching them to tannic acid.</p>Probabilistic Modeling for Whole Metagenome Profiling2021-05-26T21:18:08-05:00https://digital.library.unt.edu/ark:/67531/metadc1808381/<p><a href="https://digital.library.unt.edu/ark:/67531/metadc1808381/"><img alt="Probabilistic Modeling for Whole Metagenome Profiling" title="Probabilistic Modeling for Whole Metagenome Profiling" src="https://digital.library.unt.edu/ark:/67531/metadc1808381/small/"/></a></p><p>To address the shortcomings in existing Markov model implementations in handling large amount of metagenomic data with comparable or better accuracy in classification, we developed a new algorithm based on pseudo-count supplemented standard Markov model (SMM), which leverages the power of higher order models to more robustly classify reads at different taxonomic levels. Assessment on simulated metagenomic datasets demonstrated that overall SMM was more accurate in classifying reads to their respective taxa at all ranks compared to the interpolated methods. Higher order SMMs (9th order or greater) also outperformed BLAST alignments in assigning taxonomic labels to metagenomic reads at different taxonomic ranks (genus and higher) on tests that masked the read originating species (genome models) in the database. Similar results were obtained by masking at other taxonomic ranks in order to simulate the plausible scenarios of non-representation of the source of a read at different taxonomic levels in the genome database. The performance gap became more pronounced with higher taxonomic levels. To eliminate contaminations in datasets and to further improve our alignment-free approach, we developed a new framework based on a genome segmentation and clustering algorithm. This framework allowed removal of adapter sequences and contaminant DNA, as well as generation of clusters of similar segments, which were then used to sample representative read fragments to constitute training datasets. The parameters of a logistic regression model were learnt from these training datasets using a Bayesian optimization procedure. This allowed us to establish thresholds for classifying metagenomic reads by SMM. This led to the development of a Python-based frontend that combines our SMM algorithm with the logistic regression optimization, named POSMM (Python Optimized Standard Markov Model). POSMM provides a much-needed alternative to metagenome profiling programs. Our algorithm that builds the genome models on the fly, and thus obviates the need to build a database, complements alignment-based classification and can thus be used in concert with alignment-based classifiers to raise the bar in metagenome profiling.</p>