Organizational Unit:
School of Biological Sciences

Permanent Link
https://hdl.handle.net/1853/70750
Research Organization Registry ID
Description
Previous Names
Parent Organization
Parent Organization
Organizational Unit
Includes Organization(s)
ArchiveSpace Name Record
https://finding-aids.library.gatech.edu/agents/corporate_entities/1131

Filters

2023 - 2024 5
5
5
5
Reset filters

Settings
Start date: 1999 × search.filters.applied.f.isSeriesOfPublicationTitle: Doctor of Philosophy with a Major in Biology ×

Publication Search Results

Now showing 1 - 5 of 5
Thumbnail Image
Item

Investigating The Mechanisms Underlying Metamorphosis in The Chordate Ciona Robusta

2024-04-29 , Johnson, Christopher

In our study, we investigate the multifaceted roles of papillae in tunicate larvae, pivotal for sensory perception, adhesion, and metamorphosis regulation, particularly in the model organism Ciona. Through molecular marker identification and CRISPR/Cas9-mediated mutagenesis, we delineate the intricate cellular diversity within papillae, elucidating the regulatory networks orchestrated by key transcription factors and signaling pathways. Concurrently, we explore the evolutionary divergence in the expression patterns of Myomaker (Mymk), a fusogenic factor crucial for myoblast fusion and muscle multinucleation, between vertebrates and tunicates. By analyzing cisregulatory sequences of Mymk, we unveil the underlying mechanisms driving the differential spatiotemporal expression patterns in these organisms. Our findings not only deepen our understanding of tunicate development but also provide insights into the evolutionary history of myoblast fusion regulation across chordates.

View
Thumbnail Image
Item

Toward Quantifying the Patterns of Bacteria and Fungi in the Atmosphere and their Functional Role in Cloud Formation Via Ice Nucleation

2023-04-27 , Davila Santiago, Lizbeth

The atmosphere has received little attention for its biological component, especially when compared to its physical and chemical components. The study of bioaerosols and their relationship with the atmosphere has gained particular attention in the last couple decades because accumulating evidence suggests that bioaerosols may interact with the atmosphere, biosphere, weather, and public health. Moreover, the role of airborne cells in cloud formation and precipitation by serving as precursors for ice nucleation or ice nuclei (IN) at warmer temperatures than abiotic particles (e.g. dust) has been recognized. Even though the atmosphere is a hostile environment for living organisms (e.g., stress caused by low temperatures, high UV-radiation, pH changes, oxidative and osmotic stress, amongst others), microorganisms are present and relatively abundant (e.g., 102 -106 cell/m3) in the atmosphere. However, the effects of common atmospheric conditions (some mentioned above) on microbial community patterns and on the ice nucleation activity of IN bacterial species remain poorly understood. Therefore, a major objective of this study was to establish microbial (bacteria and fungi) compositional and diversity patterns between dry-air and rain samples collected in an urban setting (Metro Atlanta) over two consecutive years with culture-independent techniques and amplicon sequencing. The results revealed significant changes in community structure among sample types, including pathogenic and/or allergen fraction of the community, but not strong seasonality. Furthermore, the ice nucleation activity of three different bacterial IN species (Pseudomonas syringae (Gram -), Lysinibacillus parviboronicapiens (Gram +), and Xanthomonas campestris (Gram -) after exposure to a range of acidity, oxidative and UV radiation stressors and a combination of them by immersion freezing testing. Bacterial and fungal communities in dry-air samples do not appear to mirror the same community structure of rain samples, and seasonality is not a strong factor in shaping the microbial community of the atmosphere in a subtropical climate as Metro Atlanta. Pseudomonas syringae, and to a lesser extent the other two species evaluted, retained efficient ice nucleation activity (T50 above -10ºC; T50 represents the temperature that 50% of the water droplets froze as an effect of the present of the cells) even after viability loss due to acidic pH (pH = 2.5). Collectively, this research provides new insights into the public health aspect of bioaerosols as well as their role in weather/climate patterns.

View
Thumbnail Image
Item

Integrating genomic and multiomic data for computational analysis of gene regulation in circulating immune cells

2024-04-26 , Brown, Margaret R.

In the post-GWAS era, genetic associations with pathology have sparked interest in gene regulatory mechanisms since the majority of GWAS variants are located in noncoding regions. This idea fuels the hypothesis that trait associated variants are causal to gene expression variability. The primary question driving this thesis, is whether distinct gene regulatory mechanisms associated with genetics can be identified in circulating immune cells. First, eQTL fine mapping was performed using an all-but-one conditional analysis approach to prioritize putatively causal variants by disentangling the effects of linkage disequilibrium in peripheral blood. Identified eQTL for genes associated with inflammatory bowel disease were observed in immune cell populations, suggesting a functional relationship between genetics and gene expression variability. Next, heterogeneous gene regulatory mechanisms were observed in single nuclear multiomic data of circulating immune cells from individuals with Crohn’s disease and healthy donors. Paralleled heterogeneity was observed in both arms of the adaptative immune system, including an inflammatory signature within a subset of Crohn’s disease donors. Finally, an unprecedented approach to explain gene expression was implemented by training machine learning models on chromatin accessibility data, which demonstrated that ATAC peaks which are important for explaining gene expression are enriched with inflammatory disease GWAS variants. Altogether, this thesis highlights the genetic relevance of gene regulation in circulating immune cells for inflammatory disease and suggests that the interplay of genetics and pathology with respect to gene regulation is complex and heterogeneous among individuals.

View
Thumbnail Image
Item

Salt Marsh Functional Ecology: From Root-Microbe Interactions to Ecosystem Restoration

2023-04-25 , Rolando Betancourt, Jose Luis

Salt marshes are highly productive intertidal wetland ecosystems located along wave-protected coastlines. Although salt marshes provide numerous ecosystem services, they are vulnerable to degradation by climate change, sudden vegetation dieback events, and unsustainable coastal development. To inform the adaptive management of marsh ecosystems, this dissertation addresses gaps in fundamental science related to the resilience and adaptability of salt marshes to environmental stressors, as well as their potential for restoration. In the first section of this thesis, I leveraged in situ biomass gradients of Spartina alterniflora -a foundational plant species that predominates over primary production on US Atlantic and Gulf of Mexico coastlines- as a natural laboratory to investigate the relationship between plant primary productivity, and plant-microbe interactions in the root zone. Multi-omics and biogeochemistry approaches were closely coupled to interrogate plant-microbe interactions and their implications for ecosystem function. My results show that enhanced microbial activity in the rhizosphere replenishes nutrients and terminal electron acceptors in higher biomass stands. Specifically, my research uncovered novel sulfur-oxidizing endosymbionts that benefit S. alterniflora by detoxifying the root-zone, and by fixing C and N that may be transferred to the host plant. I conclude that marine coastal plants rely on the fast recycling of sulfur in their root zone for organic matter breakdown and nutrient cycling, and I show for the first time that the rapid cycling of sulfur supports nitrogen fixation in the roots of a coastal marine plant. A second investigation of my dissertation focused on an impaired salt marsh ecosystem in Charleston, SC that had experienced sudden vegetation dieback (SVD). I investigated the causal effects of dieback, the potential for restoration through grass planting, and the ecosystem's resilience to sea level rise. Dieback was associated with extreme weather events such as droughts and flooding influenced by hurricane Joaquin. I conclude that failure to consider the increasing frequency and intensity of extreme climatic events in ecosystem models underestimates salt marsh vulnerability to climate change and rapid restoration of marsh dieback is crucial to avoid further degradation by marsh erosion. Coastal restoration is a multibillion-dollar global industry and a common restoration strategy in the U.S. involves S. alterniflora grass planting. My dissertation has revealed that the root microbiome of this foundational plant is closely linked to its productivity and plays a key role in the functioning of salt marshes. Further, climate change mitigation actions are urgently needed to preserve coastal marsh ecosystems, and future research is warranted to harness the root microbiome to improve the resilience and restoration of coastal marshes.

View
Thumbnail Image
Item

Probing Bacterial Biofilm Physiology Using Electrochemistry and Mass Spectrometry Techniques

2023-04-27 , Klementiev, Alexander Dmitri

During infection, bacteria form complex, spatially-organized communities that involve physical and chemical interactions. These interactions are key to community function, allowing bacteria to evade host defenses and persist despite an often robust immune response. While imaging technologies have allowed assessment of the spatial organization of these communities, we know little about the chemical environment. In this thesis, I leverage electrochemical and mass spectrometry techniques to study the chemical environment surrounding bacterial biofilms at the micron scale. Using electrochemical methods, including scanning electrochemical microscopy, I discovered that biofilms of the opportunistic pathogen Pseudomonas aeruginosa actively deplete oxygen immediately adjacent to the biofilms, forming stable oxygen gradients that extend over 100 microns from the surface of the biofilm. These oxygen gradients persist even upon exposure to high levels of antibiotics. While electrochemical methods allow for the targeted quantification of specific molecules, untargeted mass spectrometry approaches capture the global chemical profile. Using mass spectrometry, we study the interactions between the oral pathogen Aggregatibacter actinomycetemcomitans and the oral commensal Streptococcus gordonii, which are etiological agents of periodontitis. Among the thousands of molecules detected, we focus on understanding the role of glutathione produced by A. actinomycetemcomitans and the benefit it provides to S. gordonii. Together, these tools provide complementary methods to eavesdrop on the chemical interactions which shape bacterial infections.

View