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End date: 2022 × search.filters.applied.f.isOrgUnitOfPublicationTitle: School of Biological Sciences × search.filters.applied.f.resourcesubtype: Thesis ×

Publication Search Results

Now showing 1 - 10 of 164
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Nitrate and Phosphate Loads, but not Light Availability, Impact Freshwater Phytoplankton Diversity via Tradeoffs Between Dominant Species

2022-12-01 , Southard, Michael Kelton

Eutrophication of freshwater ecosystems, mainly caused by nitrogen (N) and phosphorus (P) pollution, causes significant economic damages every year in the U.S. Excess N and P deposition in lakes can result in harmful algal blooms, reduced biodiversity, and increased greenhouse gas production, but we still do not fully understand how and why phytoplankton communities react to nutrient enrichment under varying conditions. Several theories – including the niche dimension hypothesis, biomass-driven competition hypothesis, nitrogen detriment hypothesis, and benthic model – are currently being explored in both terrestrial and aquatic producer communities in attempt to better understand the biological mechanisms effecting these systems, and the goal of this study was to determine which models are most applicable to freshwater phytoplankton. Using five-species microcosms of green algae, we found that N and P enrichment significantly reduced diversity (independent of light availability), which was likely mediated through nutrient tradeoffs between the two dominant species, Ankistrodesmus falcatus and Selenastrum capricornutum. Additionally, we observed a significant decrease in monoculture carrying capacity across all species with high N addition in low P concentrations, indicating that high N:P ratios may be physiologically harmful to green algae. These findings suggest that the niche dimension and nitrogen detriment hypotheses may be the most applicable to freshwater phytoplankton communities and could be useful for protecting and mitigating economic losses from these systems.

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Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

2021-12-14 , Lindsey, Charles

The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.

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The Role of Cu, Zn Superoxide Dismutase (SOD1) in Muscle Stem Cell Function

2021-05-04 , Ergun, Utku

Age-related loss of muscle mass and function often referred to as sarcopenia, dramatically affects the quality of life in the elderly population and predisposes them to an increased risk of morbidity, disability, and mortality. The etiology of sarcopenia is a multi-factorial process that involves both intrinsic and extrinsic factors. However, mounting evidence from both animal and human studies suggests that uncontrolled production of reactive oxygen species (ROS) and subsequent oxidative stress and oxidative modifications to key macromolecules such as DNA, RNA, proteins, and lipids are key underlying mechanisms that exacerbate sarcopenia. Cu, Zn superoxide dismutase (SOD1) is one of the essential antioxidant enzymes that are indispensable for redox homeostasis and prevention of oxidative damage. To maintain skeletal muscle homeostasis and repair damaged muscle, a population of dedicated muscle stem cells (MuSC), called satellite cells, activate, express myogenic transcription factors, migrate, proliferate, and fuse with existing myofibers or form de novo myofibers to complete regeneration. However, increased oxidative stress in muscle stem cells may harm the muscle regeneration process by impairing the interactions between existing myofibers with newly regenerated myoblasts and muscle stem cells. Previous studies showed that the whole body-deletion of Sod1 increases the age‐associated sarcopenia in mice; however, effects of deletion of Sod1 specifically in muscle stem cells and how it affects the muscle regeneration processes are still not known. We aimed to fill this gap by investigating the change in myogenesis and muscle regeneration of muscle stem cell-specific Sod1 knock-out (MuSC-Sod1KO) mice. Our in-vivo results revealed that the muscle regeneration and MuSC function are severely compromised in the MuSC-Sod1KO mice. Furthermore, our in-vitro studies show that the proliferation, differentiation, and fusion were impaired in the Sod1KO due to the increased number of apoptotic death in the myogenic progenies. In summary, we provide direct evidence that oxidative stress in muscle stem cells deteriorates and impairs muscle stem cell function by increasing the apoptotic response in muscle stem cells. We hope our study will open the path for better understanding the redox regulation in stem cells and aid in developing strategies to enhance stem cell-based therapies against muscle-wasting conditions, such as sarcopenia.

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Evolutionary benefits of latency in within-host HIV infection dynamics

2019-04-30 , An, Qi

HIV is a retrovirus that infects helper T cells (CD4 + T cells) in the human immune system. At the cellular scale, HIV generates both actively and latently infected cells. Ac- tively infected cells produce mature virions and are often the primary target of antiretroviral therapies. In contrast, latently infected T cells can do not produce virus particles, are hard to detect and treat, and can be reactivated to produce new virions. Understanding the dynamics of latent infections is critical to the development of strategies to treat and control the spread of HIV. In this thesis, we study a variant of within-host models of HIV infection dynamics including proliferation of both susceptible and latently infected CD4+ cells. In this model, HIV infection of susceptible cells can result in acute or latent infections. The key innova- tion here is to identify the relative contributions of the active and latent pathways towards viral fitness, both in the initial and later stages of the within-host dynamics. We do so by leveraging a new approach to decomposing viral fitness developed in the context of phage- bacteria interactions. Our work highlights how variation in susceptible cell densities, viral life history traits, and retroviral therapies jointly influence dynamic selection pressures for active and latent infections.

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Characterization of chromatinized hydrogen peroxide biosensor in cancer cells

2022-06-02 , Pfliger, Jessica M.

Hydrogen Peroxide (H2O2) is an important eukaryotic signaling molecule regulating cellular processes. As one of the most abundant reactive oxidative species (ROS), H2O2 can cause oxidative stress and cytotoxicity at elevated concentrations leading to DNA damage and programmed cell death. Despite the recent advancements in modulating ROS responses for potential cancer therapies, little is known about nuclear ROS temporal emergence and dynamics. To investigate the role of nuclear ROS and H2O2 in chromatin, we established a genetically engineered chromatin-targeted biosensor for H2O2, H2B-HyPer, by fusion of HyPer, a specific H2O2 biosensor, with core histone H2B. In this thesis, I utilized fluorescent microscopy and fluorescent recovery after photobleaching (FRAP) to study the H2O2 dynamics within the chromatin of HCT116 colon cancer cells containing genetically integrated H2B-HyPer. I demonstrate that H2B-HyPer is localized in the nucleus of HCT116/H2B-HyPer cells with an average residence time and mobile fraction of 9.14 minutes and 20.59%, respectively, comparable to the core histones in chromatin. I then show that H2B-HyPer is sensitive to changes in H2O2 levels post addition of H2O2 or DTT in culture medium. Further analysis of H2B-HyPer kinetics revealed a rapid increase and recovery of H2B-HyPer signal intensity in HCT116/H2B-HyPer cells upon treatment with and the removal of H2O2. Altogether, these studies establish H2B-HyPer as an effective biosensor for real-time spatio-temporal tracking of chromatin-proximal H2O2 dynamics.

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The impact of copper oxide nanoparticles on bacterial community assembly

2021-11-22 , Wang, Jiong

A growing amount of copper oxide nanoparticles (CuO NPs) has been released into the environment. CuO NPs are known to be toxic to various organisms, but their impacts on the assembly of ecological communities are poorly understood. We examined the role of CuO NPs in influencing the assembly of laboratory bacterial assemblages consisting of three bacterial species. CuO NPs had significant negative effects on the growth rate and carrying capacity of all three species. Alpha diversity was significantly reduced by CuO NPs, regardless of assembly history. CuO NPs enhanced the inhibitive priority effects of early arriving species on later arriving species during community assembly. By so doing, CuO NPs promoted the importance of assembly history in shaping bacterial community structure, resulting in greater beta diversity between communities subjected to different histories. Moreover, communities in the copper ion treatment tended to have similar alpha and beta diversity as those in the controls, suggesting that copper ions may not be responsible for the effect of CuO NPs on community assembly. Our results indicate that CuO NPs could modify bacterial community structure by changing the importance of community assembly history and thus the strength of priority effects.

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Analysis of the impact of a p53 mutation in a homogeneous genetic background

2020-04-21 , Karunakaran, Kirti A.

In more than 50% of cancers, p53, a tumor suppressor gene involved cell cycle arrest and apoptosis, has been seen to be heavily mutated making it an important gene to study. There are several studies on p53 and its role in cancer, but they ignore the impact of genetic background. Past studies have shown that genetic background can have a significant effect on the phenotypic consequences of cancer driver mutations, however, all these studies are carried out in a heterogeneous environment. The goal of my study was to utilize the CRISPR Cas 9 system to create a loss of function mutation in the p53 gene in a well characterized human cell line (HEYA8F8) and to evaluate the impact of this mutation on cell growth and apoptotic function in identical genetic backgrounds. The resulting mutation was a deletion in codons 33-36 of exon 4 which decreased the length of the protein from 393 to 389 amino acids. Using the cell lines with the specified deletion, growth rates over 96 hours were compared, which resulted in higher cell counts for the mutant in comparison to the wildtype. Assay for drug sensitivity using cisplatin, the standard of care for many cancers, showed that mutant cell lines had decreased apoptotic function (higher cell viability) in comparison to the wild type. The overall results demonstrated that mutations in p53 increase cell viability when treated with chemotherapy and an increase in cell proliferation. We believe that the cell lines with the loss of function mutations in p53 generated will provide an ideal experimental set up to study how the genetic background can evolve to enhance cancer in future studies.

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Trophic structure in the Western Tropical North Atlantic Ocean using Stable Isotope Abundances (δ15N and δ13C)

2022-05-06 , Salter, Shannon Marie

We investigated the biomass concentration and natural abundance of nitrogen and carbon stable isotopes (δ15N and δ13C) of size-fractionated zooplankton collected on two cruises to the Amazon River Plume (ARP) region. Mean animal biomass concentration was 3.34 mg/m2 during the day and 2.68 mg/m2 on Cruise EN614. The mean biomass on Cruise EN640 was 7.22 mg/m2 during the day and 9.60 mg/m2 at night. . Sampling stations were classified into habitat types based on biologically relevant physical and chemical parameters: the young plume core (YPC), old plume core (OPC), outer plume margin (OPM), western plume margin (WPM), and oceanic seawater (OSW). In general, zooplankton δ15N varied markedly and significantly among habitats for both cruises, with generally higher values in the YPC, OPC, WPM, and OSW habitats relative to the OPM habitat. Zooplankton δ15N values reflect the sources of nitrogen supporting biological production, and trophic processing within the food web. Suspended particles collected from these habitats showed lower δ15N values than the zooplankton, but we did not find a consistent increase in animal δ15N with size. Vertical migration led to diel shifts in zooplankton δ15N at the surface, with generally higher δ15N values at night than during the day during both cruises. Zooplankton δ13C values varied less than their δ15N, with no significant differences among habitats or with animal size.

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Assay development for and evaluation of sphingomyelinase D and associated activities in venoms from Loxosceles reclusa and Kukulcania hibernalis and in isolated soil bacteria

2021-08-02 , Lachmayr, Hannah L.

Since a sphingomyelinase D (SMase D) enzyme is presumably the major agent in the necrosis and toxicity of the brown recluse spider venom by cleaving sphingomyelin (SM) to ceramide 1,3-cyclic phosphate (Cer(1,3)P), a rigorous but simple assay would aid in detecting the presence of this sphingomyelinase activity. Several Sicariidae spiders, such as the brown recluse spider Loxosceles reclusa, and some pathogenic bacteria contain phospholipase D (PLase D) enzymes that act on phospholipid substrates. PLases D that cleave SM to release the headgroup choline are also called SMases D. Although the lipid product of the L. reclusa SMase D was initially thought to be ceramide 1-phosphate (Cer1P), a transphosphatidylation mechanism by L. reclusa SMase D has been shown to produce Cer(1,3)P. For this thesis, fluorescent nitrobenzoxadiazole (NBD) analogs of products that are known to be made by various types of SMases (i.e., ceramide, Cer1P and Cer(1,3)P) were synthesized and an elution solvent system was identified that fully resolves these compounds as well as the substrate NBD-SM using silica gel thin-layer chromatography plates. When venom from L. reclusa was assayed, the product was the expected NBD-labeled Cer(1,3)P. Venom from Kukulcania hibernalis, a spider that has been suggested to have SMase D but whose products have not yet been determined, was assayed as well and NBD-Cer(1,3)P was found to be produced. To explore additional biomedically relevant applications of these methodologies, such as to discover bacterial enzymes that can degrade sphingolipids, we attempted to isolate bacteria from the soil with enzymatic activity to degrade SM and/or cyclic Cer(1,3)P. Single isolates of soil microorganisms were selected based on their ability to grow on the restrictive carbon sources SM or Cer(1,3)P and then examined for their cleavage of NBD-SM and/or NBD-Cer(1,3)P. Of four candidate isolates, genome sequencing of two isolates was taxonomically assigned to Klebsiella variicola, a gram-negative bacterium and opportunistic human pathogen. Unfortunately, in the timeframe of this thesis, the conditions to assay the degradatory enzymes were not found. In summary, this work has developed a facile assay for SMase D, characterized for the first time Cer(1,3)P as a breakdown product of the action of K. hibernalis venom on SM, and expanded the methodologies that are available for analysis of activities that produce and degrade Cer(1,3)P.

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Microbiome variation in wild versus captive spotted eagle ryas (Aetobatus narinari)

2019-07-30 , McWhirt, Mary E.

The microbial communities (microbiomes) associated with elasmobranchs are currently not well-understood. The spotted eagle ray (Aetobatus narinari) is a slow-maturing ray that is globally distributed in tropical and warm-temperate waters, and is listed as near-threatened by the IUCN Red List. To evaluate how the environment shapes the spotted eagle ray microbiome, we used 16S rRNA Illumina sequencing to compare the microbiomes of the dorsal skin, gill, and cloaca from a ray population sampled in Sarasota Bay, FL to those from a captive population in the Ocean Voyager exhibit at Georgia Aquarium. Cloaca microbiomes of both populations had the lowest alpha diversity and highest beta diversity. The composition of the gill and skin microbiomes differed between captive and wild populations and are similar to, but distinct from, the water column communities while cloaca microbiomes are more divergent from that of the water. This pattern is consistent with that seen in teleost fishes and marine mammals. These results indicate a dual role for body niche and environmental conditions in shaping ray microbiomes and identify key taxa that may be important to the health of the rays.

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