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School of Biological Sciences

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https://hdl.handle.net/1853/70750

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Organizational Unit

College of Sciences

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Organizational Unit

Center for the Study of Systems Biology

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https://finding-aids.library.gatech.edu/agents/corporate_entities/1131

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Publication Search Results

Now showing 1 - 10 of 60

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

(Georgia Institute of Technology, 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.
Evolutionary benefits of latency in within-host HIV infection dynamics

(Georgia Institute of Technology, 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.
Dominance and exhibit use in captive African elephants (Loxodonta africana)

(Georgia Institute of Technology, 2018-12-06) Iacono, Jennifer

The African elephant (Loxodonta africana) is a highly social species that typically lives in large, matrilineal family groups called herds which contain a linear dominance hierarchy between the adult females. Management plans for African elephants in human care try to replicate their natural social structures by creating small herds of females but these individuals typically are unrelated except in the case of mothers and their offspring. Despite low genetic relatedness, these females still create their own dominance hierarchies within the herds. Although elephants in human care have all of their needs provided for, dominance within herds can lead to preferential access to high-value resources such as food, water, and shade structures. The purpose of this study was to observe how the two female African elephants at Zoo Atlanta, Tara and Kelly, interacted with each other in terms of their usage of their current exhibit space. An incident occurred during data collection that led to a week-long physical separation of the elephants and the results of this study were then separated into two data sets. Anecdotal evidence of Kelly being the dominant individual was confirmed by Kelly initiating all 110 observed social interactions throughout the course of the study. Tara typically showed her submissiveness by walking away from the interaction. After the incident there was a higher mean frequency of social interactions between the two elephants per hour. The amount of neutral and agonistic behaviors rose as well. It appeared that Kelly was re-establishing her dominance over Tara after their separation. Both elephants had non-random patterns of exhibit spatial use when they were together and when they were alone in the exhibit, as well as before and after the incident. Before the incident, Kelly dominated use of the two areas that had direct access to the indoor barn when both females were in the exhibit together while Tara used the remaining two areas more often. These elephants have a complex social history, which includes Kelly dominating use of the barn and resources after a change to their social structure. As the dominant individual, Kelly had preferential access to this putative high-value area. Kelly continued to stay in the areas closest to the barn when separated from Tara. The pattern of spatial use in the exhibit displayed by Tara when separated from Kelly was different from her pattern when they were together; Tara used the area closest to the barn when alone. The patterns after the incident were similar to those from the before results except Tara used the furthest area from the barn with a higher frequency when alone in the exhibit in addition to the closest. This change may have been caused by Tara’s restricted mobility after the incident. Before the incident all social interactions between the elephants, including agonism, occurred randomly throughout the outside portion of the exhibit despite both elephants having specific patterns in how they used the exhibit. After the incident there was a non-random pattern in the location of all social interactions. More occurred in the area closest to the barn than would be randomly expected, which matches Kelly’s dominating use of that area. Although the occurrence of agonistic behaviors by area changed after the incident, the pattern was still not statistically significant.
Investigating ice slurry’s perceived mechanical abrasive quality to increase pathogen reduction on poultry during immersion chilling

(Georgia Institute of Technology, 2018-04-26) Richter, Stephanie

The poultry industry is an integral part of Georgia’s economy, accounting for more than half of the state’s agricultural output. In Georgia, more than 20 million pounds of broiler meat are produced daily. Poultry processing entails many phases, and this thesis focuses upon the immersion chilling step. The chilling phase is critical to reducing pathogen presence and ensuring meat product shelf-life. Immersion chilling consumes intense amounts of water and energy resources, and the industry is trying to discover more efficient approaches for processing. This thesis is based upon a multi-year project investigating ice slurry as an alternative chilling medium for the poultry industry. Ice slurry is composed of small characteristic length ice particles and a salt-brine solution that acts as a freezing point depressant. The salt is an important component in maintaining the ice slurry in a homogenous state (i.e., reduce ice agglomeration and media separation). Ice slurry is hypothesized to provide a disruptive scrubbing/abrasive phenomenon resulting in greater pathogen reduction compared to tradition chilled water medium. Pathogen reduction experiments were conducted to determine the Salmonella pathogen reduction capability of chilled water and ice slurry on whole carcasses and wing-parts. Pathogen reduction experiments combined experimental factors of: peracetic acid (PAA) antimicrobial concentration, media salinity, time of immersion chilling, and air agitation levels. Treatment combinations were compared to discover the optimum relationship between factors resulting in the best reduction from STR concentrations pre- and post-chilling. The project also investigated the salt-uptake tendencies of whole carcasses during immersion chilling. Whole carcasses, without the giblets (WOGs) were chilled by either air chill, chilled water, or 4.5% salinity chilled water. Post-chilling, three sample types were collected per each carcass (breast skin, white meat, and dark meat). Results initially addressed salt-uptake concerns when ice slurry medium is used for immersion chilling. Initial findings indicated that salt concentrations increased in the skin, yet did not affect white or dark meat. The skin acts as a barrier that prevents salt penetration into the white and dark meat, furthering the consideration of ice slurry as a poultry chilling medium.
Applied bioinformatics for exploring diversity patterns in meta-omic data

(Georgia Institute of Technology, 2018-04-25) Ranjan, Piyush

This thesis explores the utility of applied bioinformatic approaches to better understand sequence space and phylogenetic diversity in meta-omic clinical and environmental datasets. In three chapters, the thesis describes how applied bioinformatic techniques can be used to 1) identify and quantify sequence variation in the form of insertions and deletions generated as an effect of off-target activity by CRISPR-Cas9 nuclease using high throughput targeted gene amplicon sequencing; 2) identify and quantify the abundance of elements of the bacterial defense systems, CRISPRs, to explore viral-microbe interaction dynamics in natural microbial communities living in marine oxygen minimum zones using high-throughput metagenome sequencing; and 3) investigate phylogenetic variation in an underexplored phylum of bacteria, Atribacteria, that are found as dominant members of microbial communities in methane hydrate-bearing marine sediments again using high-throughput metagenome sequencing.
Regulation of the type VI secretion system in environmental isolates of vibrio cholerae

(Georgia Institute of Technology, 2017-12-14) Hoffmann, Tobias

Vibrio cholerae is a human pathogen that causes the severe diarrheal disease cholera, but can also inhabit aquatic environments. The type-VI secretion system (T6SS) is a macromolecular contractile machine that injects neighboring cells with cytotoxic effector proteins. Clinical strains of V. cholerae express the T6SS only when exposed to high cell density and starvation conditions in the presence of chitin, a process regulated by the master regulator QstR. The atypical clinical strain V52 expresses its T6SS constitutively, a trait shared by many V. cholerae strains isolated from the environment. Recently it was discovered that the TfoY regulator controls T6SS expression independent of QstR in V52. In examining strains from environmental sources, I found that one constitutive environmental strain is also under TfoY control. However, I also uncovered that T6SS-mediated constitutive killing in four additional environmental strains was unaffected by a tfoY deletion. Furthermore, I demonstrated that other known regulators (TfoX, QstR, OscR) also played no role in T6SS expression in these strains. For example, the environmental strain BGT69 remains capable of T6SS-mediated killing when these four known T6SS regulators were deleted. These results suggest the presence of a novel regulatory pathway(s) for type-VI secretion in this and other environmental strains of V. cholerae.
The interactive effects of environmental warming and habitat fragmentation on the structure of experimental protist communities

(Georgia Institute of Technology, 2016-08-01) Tsai, Meng-Hsiu

Global biodiversity is threatened by substantial and increasing human activity, such as human-induced environmental warming and habitat fragmentation. The effects of warming and fragmentation on biodiversity have been carefully studied, yet their potential interactive effects are less understood. Using freshwater protist communities subject to warming and fragmentation, I present the first experimental evidence of the interactive effects of warming and fragmentation on biodiversity. Somewhat unexpectedly, I found that fragmentation positively affected biodiversity. The magnitude of the effects of fragmentation, however, varied with the warming treatments. In one of our experimental communities (Combination B), fragmentation showed a much stronger positive effect on protist richness when warming was not conducted, but it showed a weaker but significant positive effect under a warming scenario. In other communities (from Combination C), however, fragmentation showed a stronger positive effect on richness when warming was present than when it was absent in experimental treatments. I further show that these long-term effects may be due to the alternation of individual species growth rate affected by warming, fragmentation and their interaction in short-term projections. Moreover, these findings of positive effects of fragmentation and interactions with warming can be useful for understanding conservation strategies, especially in areas where biodiversity is currently threatened or will be in the future.
Effects of competition, disturbance and productivity on the dynamics of inducible trophic polymorphism in tetrahymena vorax

(Georgia Institute of Technology, 2016-08-01) Yin, Yi

Inducible trophic polymorphism enables organisms to alter their trophic level when facing environmental changes, and therefore can ameliorate the intensity of competition. The freshwater ciliated protist Tetrahymena vorax was found to have three distinct phenotypic morphs with two trophic levels. Its carnivorous macrostomes consume intraspecific competitors and its bacterivorous pyriform microstome morph and tailed microstome morph indiscriminately. Cannibalism here indicates an extreme case of niche differentiation and resource utilization via phenotypic plasticity and significantly affects the dynamic equilibrium of T. vorax’s three morphs. By manipulating productivity level, disturbance frequency and the presence or absence of an interspecific competitor species Colpdium striatum, I demonstrated the dynamic transformations of T. vorax’s three morphs and endeavored to explain the underlying mechanisms. In this study, I also tested some classic assumptions about phenotypic tradeoffs in T. vorax and hence clarified some misunderstandings and proposed novel hypotheses.
Sustainable tilapia feed derived from urban food waste

(Georgia Institute of Technology, 2015-12-08) Chaddick, Justin Garrett

Finding an alternative to fishmeal and fish oil in animal feeds has been a topic of increasing interest due to the pressures being put on the ocean’s fisheries and the increasing world demand for animal protein. An often-overlooked source of nutrients is in the form of food waste. One third of all food produced globally ends up in landfills, wasting a huge amount of nutrients and embodied energy that could otherwise be redirected towards productive use. This study investigated the feasibility of feeding Hermetia illucens, the black soldier fly larvae (BSFL), grown on urban food waste, and Lemna minor, a species of duckweed, to tilapia in a recirculating aquaponic system as a compound feed. The study compared the growth of two groups of 58 tilapia over 44 days; one group was fed commercial pellets and the other a compound feed composed of BSFL and duckweed. The group fed the commercial pellets achieved heavier weight gain than the group fed the experimental feed but both groups resulted in steady weight gain and had similar mortality rates. Feeding the experimental feed composed of BSFL and duckweed to tilapia in an aquaponics system is an effective method of diverting food waste from the landfill and further research should be done to optimize this process.
From rivers to natural gas: The influence of allochthonous inputs on marine nitrogen fixation and the carbon cycle

(Georgia Institute of Technology, 2015-12-04) Weber, Sarah C.

The Western Tropical North Atlantic (WTNA) was once thought to be a net source of carbon dioxide (CO₂) to the atmosphere, but recent studies have shown that this Amazon River influenced region may actually act as a net sink for CO₂. During a 2010 research cruise to the WTNA, we characterized the impact of the Amazon River on offshore diazotrophy (N₂-fixation) and the resulting stimulation of biological carbon export from surface waters. Through the delivery of phosphate- and silicate-replete waters to the nitrogen (N) limited surface waters of the WTNA, the aging Amazon River plume promotes the growth of diatom-diazotoph associations (DDAs). Regions supporting large DDA blooms were associated with increased pCO₂ and DIC drawdown in the surface waters, reflecting the net export of carbon from the mixed layer. The existence of this biologically mediated linkage between the C and N cycles in productive surface waters is well known, but we have only recently discovered a stimulatory relationship in deep waters between oil/gas release and N₂-fixation. This association was first observed after the Deepwater Horizon oil spill in 2010 and we again saw evidence for it in the days following the Hercules 265 natural gas blowout. This blowout event was characterized by the release of an unknown quantity of natural gas into the shelf waters of the Northern Gulf of Mexico, but we detected a response from the marine microbial community within days. We observed a significant drawdown of dissolved oxygen and found biogeochemical evidence for the incorporation of methane-carbon into the food web, along with a modest stimulation of N₂-fixation. The episodic nature of anthropogenic blowouts makes them difficult to study, so we use cold seeps in the Gulf of Mexico as natural analogues. Interestingly, we have measured both methane oxidation and N₂-fixation at depth above some of the more active seeps. Using NanoSIMS analyses, we have taken the first steps towards physically characterizing the organisms utilizing these metabolisms. It appears that different organisms are carrying out these processes, with CH₄-assimilation occurring primarily in individual particles or small aggregates, whereas N₂-fixtion was associated with larger, sulfur-containing aggregates. Continued NanoSIMS work in combination with the use of microbial ID techniques will help to further characterize these unique deepwater diazotrophs.