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School of Biological Sciences

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College of Sciences

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Center for the Study of Systems Biology

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Publication Search Results

Now showing 1 - 10 of 15

Changes 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.
Decoding Disease Persistence in Pediatric Acute Lymphoblastic Leukemia One Single Cell at a Time

(Georgia Institute of Technology, 2020-12) Imbach, Kathleen Jane

In order to understand the biological and molecular mechanisms underlying disease resistance to therapy in pediatric acute lymphoblastic leukemia (ALL), we performed an investigation utilizing single-cell RNA-sequencing (scRNA-seq) on the 10X Genomics Chromium platform. Bone marrow samples from seven patients were collected, four of whom exhibited measurable residual disease (MRD) after induction therapy, and three patients who did not. Cells from bone marrow tissue were extracted from each patient at the time of diagnosis, prior to treatment efforts. Leukemic cells were separated from peripheral immune cells using flow cytometry and ~1000 single cells were sequenced from each patients’ cell populations. The goal of this study was to discern how the immune and leukemic cell populations and gene expression therein vary at the time of diagnosis between patients who do or do not respond to induction. Our results demonstrate a comparative increase in immune exhaustion signatures in the immune cells of MRD-positive patients, corroborating previous findings that implicate the role of exhaustion in resistant disease. We also show a discrepancy of cell cycle states in the leukemic cell compartment according to disease outcome, with an enrichment of blasts from MRD-negative patients exhibiting genetic signatures of S- and G2/M-phase.
Single Cell Analysis of Patients with Perianal Chron’s Disease

(Georgia Institute of Technology, 2020-05) Ferguson, Katherine Elizabeth

Perianal Chron’s Disease is a debilitating form of Chron’s Disease that often involves rectal tissue in its manifestation in the body. There is a greater need for understanding of the role of the epithelial tissue in the rectum in the pathology of Chron’s Disease. This study aims to determine cellular make-up of rectal-derived organoids grown from Chron’s Disease patients. Through the use of single-cell transcriptomics, this study will determine the cell types present in four rectal-derived organoids and use differential expression to analyze differences in epithelial tissue of Chron’s Disease patients in comparison to a healthy individual.
scRNA-seq dropouts serve as a signal for tissue heterogeneity in autism spectrum disorder

(Georgia Institute of Technology, 2020-05) Spencer, Collin

Analysis of single-cell RNA-sequencing (scRNA-seq) data is plagued by dropouts, zero counts for mRNA transcripts due to low mRNA in individual cells and inefficient mRNA capture. Dropouts are traditionally treated as an error to be corrected through normalization while performing unsupervised clustering of single cells based on highly expressed, variable transcripts. A novel algorithm, co-occurrence clustering, treats dropouts as a signal and binarizes scRNA-seq data for cell clustering, producing the same clusters as Seurat. Previous application of Seurat to single nuclear RNA-sequencing (snRNA-seq) data taken from the prefrontal cortex (PFC) and anterior cingulate cortex (ACC) of patients with autism spectrum disorder (ASD) found no difference in clusters between brain regions. This seems at odds with literature suggesting tissue-specific emergence of co-expression networks and regional specialization in the brain. We applied co-occurrence clustering to ASD samples to parse interregional heterogeneity between the PFC and ACC and identify novel cell clusters.
Time of day predicts the activity budget in the Emerald Tree Boa (Boidae: Corallus batesii) across multiple behaviors

(Georgia Institute of Technology, 2020-05) Berry, Savannah Margaret

Exploring the spatial ecology and behavior of organisms is essential to understand an organism’s niche and how to better accommodate animals that are kept in captivity (Ross et al., 2011; Plowman, 2003). Emerald Tree Boas (Corallus batesii) are commonly kept as pets and are important predators in the Amazon; however, despite their commercial exploitation and ecological importance, little is known about their behavior. This paper attempts to fill this literature gap by quantifying the behavior of a juvenile Corallus batesii. The activity budget of the snake was video recorded over a period of three months and was coded using the event logging software, BORIS (Friard & Gamba, 2016). After conducting individual regression analyses on five behaviors (hunting, moving, resting, other: stationary, and out of view), it was found that time of day significantly predicted the behaviors of hunting (p=0.0178, df=23, t=8.50) and resting (p=0.00337, df=23, t=3.52). Hunting behavior was observed between the hours of 2200 h and 700 h and resting between 800 h and 2100 h.
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.
Population genetics and genomics of eusocial animals

(Georgia Institute of Technology, 2017-11-09) Chau, Linh M.

Major evolutionary transitions have been associated with increases in organismal complexity. One of the latest evolutionary transitions is from solitary life to eusociality. This transition led to a reproductive division of labor in which individuals are divided into castes. Reproductive castes are responsible for reproduction, while nonreproductive castes take part in colony maintenance and brood care. This division of labor represents a challenge to selection and has long been of curiosity to researchers. My dissertation research examined the population genetics and genomics of eusociality in a spectrum of eusocial species. First, I examined the population structure and genetic diversity of Vespula pensylvanica, a wasp native to North America that has invaded the Hawaiian archipelago. I found a lack of population structure in V. pensylvanica’s native range and determined how the population structure of invasive social insects can be shaped by geography. I also examined the population genetics of captive naked mole rats, one of the only known eusocial mammals. I sought to understand how captivity can shape the population structure of a eusocial animal. Interestingly, there was evidence that naked mole rat populations are not as inbred as previously theorized and that sex ratios are equal within captive colonies. Finally, I examined how the phenomenon of gene duplication can affect the evolution of castes in eusocial species. I uncovered a relationship between duplication rate and level of sociality across the bees. Also, I saw that duplicates were differently expressed across phenotypes compared to single copy genes. These studies provide insight on an array of population genetic and genomic questions concerning the evolution of eusociality. Therefore, this research furthers our understanding of the rare distribution of this social system across the tree of life.
Determining how Freshwater Copepods Follow Planar Dextran Trails

(Georgia Institute of Technology, 2017-05) Young, Madison R.

In this study two species of freshwater copepods, Hesperodiaptomus shoshone (H. shoshone), and Hesperodiaptomus arcticus (H. arcticus) will be used to determine how some species of freshwater copepods interact with planar dextran trails. When a copepod swims through water, hydrodynamic disturbances with a variety of structures are created; some are vortical, planar, or laminar. Initial studies show that these copepods avidly follow laminar trails in an upstream fashion [Pender Healy]. However, when copepods execute turns or fast swimming, vortices are created. When copepods execute slow turns, planar wakes are formed. The direction of flow in the wakes and the location of the wakes provide information on the location of the copepod that is generating that wake. The intent of this research is to determine if the signals in the wakes can lead the following copepod to the source of the disturbance. Hence, all analyses focused on events where a copepod responded to the signal. Responses include reorientation or angle of entrance, time spent in trail, preference for a particular trail width and edge following behavior [Strouhal number]. The goal is to understand more about their how they sense and respond to changes in their environment and it is hypothesized that both species will interact more with the wide trail and that H. arcticus will spend more time in the trail and enter at a greater angle. It is also hypothesized that both species adhere to ideal Strouhal values. To test this, two dextran (a polysaccharide) trails will be simultaneously dropped into a tank containing the copepods. One of the trails will be 2mm and the other will be 4mm. It is expected that the copepod will wobble or traverse the trail to contact the edges; edge following enables the copepod to stay on track. Alternatively, the copepod may follow the center of the trail where the flow is the fastest and therefore is relying on flow speed rather than the shear found in the edge of the trail. Analyses of the location of the follower relative to the edge versus the center of the trail can assess whether the copepod is sensing flow shear versus flow speed. A MatLab script will be used to find more detailed information (Figures 11-22). Both species prefer to follow the wider trail (Figure 5 and 6), and H. arcticus spend more time in the trail than H. shoshone. Hesperodiaptomus shoshone followed the 4mm trail eighteen times for an average of 2.14 seconds and the 2mm trail five times for an average of 1.36 seconds. The number of encounters was also determined, which confirms that the proportion of encounters resulting in follows is much higher for the 4mm trial than the 2mm trial in both species (Table 3). This data illustrates statistically significant results (p<0.05) that H. shoshone prefer to follow the wider trail and follow for longer periods of time compared to the smaller one. These results were compared to the results for H. arcticus, which followed the 4mm trail twelve times for an average of 5.08 seconds (Figure 6). This comparison between both species on the 4mm trail confirmed that H. arctius spend more time in the trail than H. shoshone (p<0.05). The average angles of entrance were 29.16° for H. shoshone on the 4mm trail and 21.08° on the 2mm trail, and 39.69° for H. arcticus on the 4mm trail (Table 2). When compared, the results demonstrated that H. arcticus enters the trail at a greater angle than H. shoshone on both the 2mm and 4mm trails (p<0.05). There was not enough of the wobbling behavior shown to find Strouhal Values at this time.
Determining how Freshwater Copepods Follow Planar Dextrain Trails

(Georgia Institute of Technology, 2017-05) Young, Madison Ruth

In this study two species of freshwater copepods, Hesperodiaptomus shoshone (H. shoshone), and Hesperodiaptomus arcticus (H. arcticus) will be used to determine how some species of freshwater copepods interact with planar dextran trails. When a copepod swims through water, hydrodynamic disturbances with a variety of structures are created; some are vortical, planar, or laminar. Initial studies show that these copepods avidly follow laminar trails in an upstream fashion [Pender Healy]. However, when copepods execute turns or fast swimming, vortices are created. When copepods execute slow turns, planar wakes are formed. The direction of flow in the wakes and the location of the wakes provide information on the location of the copepod that is generating that wake. The intent of this research is to determine if the signals in the wakes can lead the following copepod to the source of the disturbance. Hence, all analyses focused on events where a copepod responded to the signal. Responses include reorientation or angle of entrance, time spent in trail, preference for a particular trail width and edge following behavior [Strouhal number]. The goal is to understand more about their how they sense and respond to changes in their environment and it is hypothesized that both species will interact more with the wide trail and that H. arcticus will spend more time in the trail and enter at a greater angle. It is also hypothesized that both species adhere to ideal Strouhal values. To test this, two dextran (a polysaccharide) trails will be simultaneously dropped into a tank containing the copepods. One of the trails will be 2mm and the other will be 4mm. It is expected that the copepod will wobble or traverse the trail to contact the edges; edge following enables the copepod to stay on track. Alternatively, the copepod may follow the center of the trail where the flow is the fastest and therefore is relying on flow speed rather than the shear found in the edge of the trail. Analyses of the location of the follower relative to the edge versus the center of the trail can assess whether the copepod is sensing flow shear versus flow speed. A MatLab script will be used to find more detailed information (Figures 11-22). Both species prefer to follow the wider trail (Figure 5 and 6), and H. arcticus spend more time in the trail than H. shoshone. Hesperodiaptomus shoshone followed the 4mm trail eighteen times for an average of 2.14 seconds and the 2mm trail five times for an average of 1.36 seconds. The number of encounters was also determined, which confirms that the proportion of encounters resulting in follows is much higher for the 4mm trial than the 2mm trial in both species (Table 3). These data illustrates statistically significant results (p<0.05) that H. shoshone prefer to follow the wider trail and follow for longer periods of time compared to the smaller one. These results were compared to the results for H. arcticus, which followed the 4mm trail twelve times for an average of 5.08 seconds (Figure 6). This comparison between both species on the 4mm trail confirmed that H. arctius spend more time in the trail than H. shoshone (p<0.05). The average angles of entrance were 29.16° for H. shoshone on the 4mm trail and 21.08° on the 2mm trail, and 39.69° for H. arcticus on the 4mm trail (Table 2). When compared, the results demonstrated that H. arcticus enters the trail at a greater angle than H. shoshone on both the 2mm and 4mm trails (p<0.05). There was not enough of the wobbling behavior shown to find Strouhal Values at this time.
Aggressive Phenotypes in Malawi Cichlids Associated with V1AR Variant

(Georgia Institute of Technology, 2016-12) Schappaugh, Nicholas A.

The cichlid model provides a great opportunity to explore diversity in behavioral phenotypes. Different groups of Malawi cichlids exhibit distinct patterns of behavior for a variety of scenarios, including aggressive encounters. These cichlids, characterized by the rocky or sandy habitats they occupy, exhibit strong genetic divergence, possessing large numbers of alternatively fixed variants between them. One such variant exists in the gene avpr1a, also known as V1aR, a major receptor for vasopressin in humans. This gene has been linked to behavioral effects across a variety of animal species, with this specific variant likely to have significant structural implications for the receptor product. Here we investigate the aggressive behaviors of a set of rock and sand hybrid fish for their association with the variant observed in V1aR. While specific metrics of aggression showed similar trends in these hybrids compared to those observed in the parental rock and sand species, ultimately these trends were not significant and were inconclusive. However, these results serve as a preliminary investigation of this gene’s involvement in cichlid aggressive behavior. In future work, further examination of the locus will be conducted utilizing more precise and powerful methods in order to draw stronger conclusions.