Series
Master of Science in Biology
Master of Science in Biology
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Series Type
Degree Series
Description
This series includes theses associated with the Master of Science in Biology and the earlier Master of Science in Applied Biology
Associated Organization(s)
Associated Organization(s)
Organizational Unit
School of Biological Sciences
School established in 2016 with the merger of the Schools of Applied Physiology and Biology
Organizational Unit
School of Biology
School established in 1959; merged with School of Applied Physiology in 2016 to become the School of Biological Sciences
167 results
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ItemCharacterizing signatures of ribonucleoside monophosphate incorporation in topoisomerase I deficient Saccharomyces cerevisiae strains(Georgia Institute of Technology, 2023-07-31) Randhawa, Supreet SinghRibonucleoside monophosphates (rNMPs) are the most common non-canonical nucleotides incorporated into genomic DNA. The 2′-hydroxyl group on the pentose sugar of rNMPs facilitates self-reactivity, increases genotoxic risk of single-strand breaks, and alters the topological and elastic properties of the DNA duplex, all of which drive intracellular metabolic stress. The highly conserved ribonucleotide excision repair (RER) pathway enables error-free removal of rNMPs from genomes across the tree of life. Failures in the RER pathway have been implicated in promoting type I interferonopathies in humans such as Aicardi-Goutières syndrome, a degenerative neurological encephalopathy. Topoisomerase I (Top1), an enzyme traditionally recognized as relieving torsional stress as a result of genome replication or gene transcription, possesses mutagenic ribonuclease activity in the absence of RER. This thesis investigates Top1-cleavage bias towards rNMPs embedded in nuclear and mitochondrial DNA using Saccharomyces cerevisiae as a model organism. Using ribose-seq, we elucidate distinct rNMP incorporation patterns in top1-null mutants suggesting that Top1 may have a cleavage bias towards ribouridine and riboadenosine in nuclear and mitochondrial DNA, respectively. Our analysis reveals no appreciable rNMP removal bias by Top1 when comparing leading and lagging strands, and no distinct dinucleotide rNMP incorporation patterns in mitochondrial DNA regardless of RER or Top1 activity. Taken together, our analysis provides novel insight regarding Top1-cleavage bias towards rNMPs embedded in nuclear DNA, strengthening the idea that Top1 plays a role in preserving genome stability.
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ItemCharacterizing signatures of ribonucleoside monophosphate incorporation in topoisomerase I deficient Saccharomyces cerevisiae strains(Georgia Institute of Technology, 2023-07-31) Randhawa, Supreet SinghRibonucleoside monophosphates (rNMPs) are the most common non-canonical nucleotides incorporated into genomic DNA. The 2′-hydroxyl group on the pentose sugar of rNMPs facilitates self-reactivity, increases genotoxic risk of single-strand breaks, and alters the topological and elastic properties of the DNA duplex, all of which drive intracellular metabolic stress. The highly conserved ribonucleotide excision repair (RER) pathway enables error-free removal of rNMPs from genomes across the tree of life. Failures in the RER pathway have been implicated in promoting type I interferonopathies in humans such as Aicardi-Goutières syndrome, a degenerative neurological encephalopathy. Topoisomerase I (Top1), an enzyme traditionally recognized as relieving torsional stress as a result of genome replication or gene transcription, possesses mutagenic ribonuclease activity in the absence of RER. This thesis investigates Top1-cleavage bias towards rNMPs embedded in nuclear and mitochondrial DNA using Saccharomyces cerevisiae as a model organism. Using ribose-seq, we elucidate distinct rNMP incorporation patterns in top1-null mutants suggesting that Top1 may have a cleavage bias towards ribouridine and riboadenosine in nuclear and mitochondrial DNA, respectively. Our analysis reveals no appreciable rNMP removal bias by Top1 when comparing leading and lagging strands, and no distinct dinucleotide rNMP incorporation patterns in mitochondrial DNA regardless of RER or Top1 activity. Taken together, our analysis provides novel insight regarding Top1-cleavage bias towards rNMPs embedded in nuclear DNA, strengthening the idea that Top1 plays a role in preserving genome stability.
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ItemExperiments to optimize the ribose-seq protocol(Georgia Institute of Technology, 2023-07-31) Bahl, SmritiRibonucleoside monophosphates (rNMPs), the units of RNA, are the most abundant non-standard nucleotides found in genomic DNA. They can be incorporated by DNA polymerases during DNA replication and repair, by hydroxyl radicals during oxidative stress or during incomplete maturation of Okazaki fragments. rNMPs have profound consequences on genome stability, DNA structure, function, and various cellular processes. To better understand these effects, the Storici lab developed the ribose-seq protocol which is a systematic technique for capturing and analyzing rNMPs in genomic DNA. The aim of this study is to optimize the ribose-seq protocol by enhancing the efficiency and accuracy of rNMP detection while minimizing the required amount of starting DNA, thereby enabling easier acquisition also for possible clinical applications. We systematically investigated three key steps of the protocol: (1) adaptor ligation, (2) self-ligation using Arabidopsis thaliana tRNA ligase (AtRNL), and (3) degradation of linear single-stranded DNA (ssDNA) using exonuclease. Through rigorous experimentation and analysis, we observed that modifying the adaptor ligation conditions resulted in approximately a 30% increase in ligation efficiency of the adaptor to the fragmented DNA. The use of AtRNL with an extended incubation period at lower temperature enabled improved circularization of DNA containing the rNMPs, resulting in more abundant ribose-seq library product. Furthermore, novel exonucleases were evaluated as potential replacements for T5 exonuclease in order to effectively eliminate the remaining linear ssDNA following AtRNL self-ligation and protect the circular ssDNA structures containing rNMPs from exonuclease-mediated degradation. To validate the findings of this project, ribose-seq libraries were constructed using Saccharomyces cerevisiae DNA, demonstrating the potential to reduce the starting DNA amount by up to 50%. These findings present a significant advancement in the ribose-seq methodology, enabling researchers to investigate ribonucleotide-mediated genomic processes with enhanced sensitivity and reduced resource requirements.
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ItemImpact of protein sequence on prion strain formation(Georgia Institute of Technology, 2023-07-25) Chen, Mechelle JiaxiYeast amyloid-based prions control heritable traits and typically contain a prion forming domain (PrD) that is required for polymerization and amyloid core formation. Different components of PrD are required for prion formation in different types of cells. For example, Sup35 protein, forming the [PSI^+] prion, contains PrD (Sup35N) rich in Q and N residues (QNR), required for prion formation in yeast, a region of oligopeptide repeats (OPR), involved in prion propagation, and a C-proximal region (CPR) required for prion formation in mammalian cells. We compared in vitro seeding and cross-seeding properties of the Sup35 PrD-containing region (Sup35NM) and its deletion variants, including Sup35NMΔ2-39 (missing QNR), Sup35NMΔ75-123 (missing part of the OPR and the entire CPR), and Sup35NMΔ98-123 (missing only CPR). We determined that all these constructs produce aggregate in vitro, although Sup35NMΔ75-123 is proteolytically unstable and produces aggregates with unusual features. Sup35NM and Sup35NMΔ2-39 cross-seed aggregation of each other, while Sup35NMΔ75-123 cross-seeds Sup35NM and Sup35NMΔ39. Upon transfection into yeast, Sup35NMΔ2-39 produces larger proportion of weaker prion variants with a longer polymer size, compared to Sup35NM, while in cross-seeded combinations, the seed influences the properties of resulting prion variants. Understanding the impact of protein sequences on prion formation and properties improves our understanding of the mechanism of prion formation and serves as a guideline for potential anti-amyloid therapies.
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ItemChanges of community structure of seagrass-associated elasmobranchs and teleosts in Florida’s “Big Bend” ecosystem(Georgia Institute of Technology, 2023-05-02) Rackley, Piper M.Sharks play a significant ecological role as predatory species in the world’s oceans. While they have been around for millions of years, they face many threats today, such as fishing and habitat destruction (via pollution and coastal development), that diminish their populations, and some species are on the verge of extinction. Over the past four decades, ocean water temperatures have risen significantly and have severely altered marine ecosystems. Florida’s “Big Bend” ecosystem is a diverse seagrass ecosystem and is characterized by the gradient of freshwater influence that enters the system from major rivers in its northern region. This study took place from 2009 to 2021 and covered four sections of the “Big Bend” that varied in abiotic factors, such as salinity, water clarity, temperature, etc. We hypothesize that the abundance and distribution of these elasmobranch and large teleost species are associated with differences in abiotic factors between our sampling sites. Specifically, salinities and water temperature will play a significant role in the habitat usage of these organisms, and we expect there to be significant impacts of these factors that indicate habitat preferences amongst these species.
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ItemMechanisms of Coherence and Incoherence Between GWAS and Single-Cell eQTL Effects in Crohn's Disease(Georgia Institute of Technology, 2023-05-02) Collins, Jared BlakeThe integration of expression quantitative trait loci with GWAS data has proven invaluable in the exploration of mechanisms through which genetic variants influence complex traits. However, it has also highlighted instances of incoherence in which the eQTL effects of GWAS risk variants seemingly contradict observed case and control expression. Patterns of incoherence may indicate variants associated with disease via protection, but due to the highly heterogenous nature of varying cell-types, may also indicate cell-type specific associations with disease that are convoluted by bulk RNA sequencing. Here, we conduct exploratory analysis integrating sceQTL and GWAS data associated with Crohn’s Disease to assess patterns of coherence and incoherence, using both bulk RNA-seq and predicted single-cell gene expression for case-control expression. We show that integration of GWAS summary statistics with single-cell eQTL data is a promising approach for uncovering cell type specific patterns of coherence and incoherence, and may suggest functional mechanisms underlying these associations.
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ItemNitrate and Phosphate Loads, but not Light Availability, Impact Freshwater Phytoplankton Diversity via Tradeoffs Between Dominant Species(Georgia Institute of Technology, 2022-12-01) Southard, Michael KeltonEutrophication 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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ItemCharacterization of chromatinized hydrogen peroxide biosensor in cancer cells(Georgia Institute of Technology, 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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ItemTrophic structure in the Western Tropical North Atlantic Ocean using Stable Isotope Abundances (δ15N and δ13C)(Georgia Institute of Technology, 2022-05-06) Salter, Shannon MarieWe 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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ItemPhylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae(Georgia Institute of Technology, 2021-12-14) Lindsey, CharlesThe 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.