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School established in 2016 with the merger of the Schools of Applied Physiology and Biology
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ItemPredator Induced and Non-Induced Eastern Oyster Shell Hardness Data(Georgia Institute of Technology, 2024-08) Roney, Sarah ; Dickinson, Gary ; Belgrad, Ben ; Weissburg, Marc J.This data is associated with the study "Eastern oysters minimize costs of inducible defenses by changing shell strengthening mechanism with age". Data was collected from eastern oysters, Crassostrea virginica, of two age groups (four-week and eight-week-old) that were induced with chemical cues from blue crabs, Callinectes sapidus, or not induced. Measurements included the Vickers hardness values of foliated and prismatic oyster shell layers, as well as the number and length of cracks resulting from hardness tests.
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ItemPredator Induced and Non-Induced Eastern Oyster Shell Thickness Data(Georgia Institute of Technology, 2024-08) Roney, Sarah ; Dickinson, Gary ; Belgrad, Ben ; Weissburg, Marc J.This data is associated with the study "Eastern oysters minimize costs of inducible defenses by changing shell strengthening mechanism with age". This study tested which mechanism, hardness or thickness, juvenile eastern oysters use to strengthen their shells in response to chemical cues from predators. Data was collected from eastern oysters, Crassostrea virginica, grown in a nursery in Dauphin Island, AL with or without exposure to chemical cues from blue crabs, Callinectes sapidus. Two age groups (four-week and eight-week-old post-settlement) of juveniles were included in this study. Oyster shell thickness overall and within both shell layers was measured.
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ItemFrom microbes to whale sharks: how studying some of the smallest and largest organisms can inform elasmobranch biology and ecology(Georgia Institute of Technology, 2024-07-29) Perry, CameronWhale sharks (Rhincodon typus) are the largest extant fish in the sea; however, there are still large knowledge gaps in their biology and ecology. Information about whale shark reproduction and mating has proven difficult due to logistical constraints of studying a large highly migratory pelagic species. Small oceanic islands can provide insight into these environments and ex-situ field research identified a unique and reliable aggregation of whale sharks in waters surrounding the remote South Atlantic Island of St. Helena. Sharks arrived seasonally in St. Helena waters from December to May each year, peaking in January. Using photo-ID, a total of 277 individual sharks were identified, consisting of a 1.1:1 sex ratio of male and female sharks ranging from 5-12 meters in total length, with 86% of males and 51% of females estimated to be mature. Eyewitness accounts of mating behavior were reported by reliable local observers on two separate occasions, which comprise the first observations of copulation in this species and are consistent with the size and sex demographics of the population. Acoustic telemetry showed that animals use the habitats around the entire island but are focused on the leeward side. Horizontal movements away from the island proved difficult to track, due to deep-diving behavior that either damaged or caused premature detachment of the archival satellite tags, however, some individuals showed large scale movement away from the island towards both Africa and South America. Deployment of CATS camera tags and MiniPAT tags allowed for exploration of the subsurface/diving behaviors and conspecific interactions of whale sharks in St. Helena. Deep dives (>100 meters) in St. Helena were dynamic, characterized by steep pitch angles and activity at depth. However, deep dives were not uniform suggesting that individual context and motivation are important for the function of the dives. Some evidence supports that deep dives may be associated with searching/foraging behaviors due to changes in activity and observed behaviors at depth. However, the cause of these behaviors is unknown and whether they are linked to reproductive behaviors cannot be ruled out. Pre-copulatory and social behaviors were observed on video further supporting that St. Helena is a unique location for whale shark reproductive ecology and conspecific interactions. Due to its likely role in the reproductive ecology of the whale shark, St. Helena represents a critical habitat for this endangered species. Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has begun to explore the role of body-associated microbiomes in shaping elasmobranch health. There have been burgeoning efforts to understand elasmobranch microbiomes, exploring microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. I identified major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. There is a need to prioritize research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions may be critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care. Elasmobranchs are exposed to a plethora of microbes as they move through their aquatic environment in both horizontal and vertical dimensions. Therefore, understanding of environmental microbiomes is important for complete understanding of host-associated microbiomes in both natural and artificial settings. Longitudinal sampling of a large public elasmobranch aquarium exhibit revealed a dynamic and evolving water column microbiome across 18 months. Water column microbial dynamics were driven by a diverse nitrifying community likely linked to the initial seeding of the exhibit and waste products from the inhabitants. Few microbial members were observed across all sampling time points suggesting that there are significant selection processes that alter community composition, such as ozonation and treatment of the water. Addition of sharks and fish into the exhibit had small but measurable effects on community dynamics and composition. A final “stable” state was not reached over the course of sampling suggesting that microbial succession dynamics may still be occurring or that stable final community states may not be a reasonable expectation in managed care environments.
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ItemFrom Cells to Molecules: An Overview on the Dynamics of Accelerated Whole Tooth Regeneration(Georgia Institute of Technology, 2024-07-27) Mubeen, TalhaHealthy teeth play a vital role in our well-being, affecting everything from what we eat to how we interact with the world. Losing teeth, whether from injury, disease, lack of nutrients, or birth defects, can have serious consequences for our physical and social health. Therefore, to advance the development of effective regenerative therapies and improve dental health, a comprehensive understanding of tooth biology is essential. Tooth development (morphogenesis) is a complex process involving interactions between embryonic epithelium and ectomesenchyme, leading to the formation of specialized dental structures through distinct stages. While the basic process of tooth development is conserved across species, the ability to repair and regenerate teeth differs. Humans and many mammals have two sets of teeth with limited reparative capacity, while rodents can continually renew dental tissues lost due to gnawing. On the other end of the spectrum, a wide array of species, including numerous bony fish and reptiles, along with other vertebrates, demonstrate a remarkable ability for lifelong tooth replacement. The current paradigm in dental research largely focuses on models such as mice which lack the ability to replace their dentition. This significantly limits our understanding of tooth replacement mechanisms, making it imperative to broaden our investigative lens to incorporate alternative models. Lake Malawi Cichlids exhibit remarkable ability to continuously replace teeth every ~ sixty days throughout life (polyphyodonty), offer a powerful model to study this fascinating regenerative process. This evolutionary adaptation stems from the persistence of an embryonic dental lamina, a specialized tissue responsible for tooth replacement. However, the cellular and molecular makeup of replacement teeth in polyphyodonts, along with the intricate mechanisms driving their continuous tooth regeneration, remain unknown. To address this gap, we transcriptionally profiled meticulously dissected individual replacement teeth and adjacent oral lamina in Lake Malawi cichlids using single nuclei RNA sequencing (snRNA-seq) to make two main discoveries. First, despite hundreds of millions of years of evolution, we demonstrate conservation of cell type gene expression across vertebrate teeth (fish, mouse, human). Second, we used an approach that combines marker gene expression and developmental potential of dental cells to uncover the transcriptional signature of stem-like cells in regenerating teeth. To further delve into the intricacies of cellular and molecular signatures governing the lifelong tooth replacement in cichlids, we developed a plucking-induced tooth replacement model by combining tooth removal as microinjury with vital staining techniques. An accelerated rate of tooth replacement was observed on the plucked side after two weeks, which was consistent across species with diverse tooth formulas. We next coupled this pluck-control paradigm with snRNA-seq of cichlid dental apparatus to model dental embryonic cell fate specification and provide a temporal account of cellular and molecular events during the first seven days following tooth removal. We demonstrate a cascade of sequential interactions between cell populations which involved not only communication within dental cells but also extension to supporting cells like immune and bone cells. The interaction pattern mimicked the process of tooth formation with intense crosstalk between epithelial and mesenchymal sub-populations, orchestrated by Collagen, Semaphorin, Slit-Robo, Notch, BMP, and MMP signaling pathways. In addition, we shed light on the hierarchy and remarkable plasticity of the dental epithelium. We propose a more nuanced role of supporting non-ameloblast epithelial cells in response to tooth removal mediated by immune and nerve guidance cues. In summary, this work significantly emphasizes the value of a comparative framework in the study of vertebrate oral and regenerative biology. It provides new insights into cellular and molecular interactions that can accelerate tooth replacement thereby laying robust groundwork for understanding tooth eruption syndromes and advancements in regeneration.
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ItemToward Advancing the Definitions of Sequence-Discrete Prokaryotic Species and Intra-Species Units, and Quantifying Their Distribution Patterns in Marine Environments(Georgia Institute of Technology, 2024-07-22) Conrad, Roth EdwardMicrobial communities constitute the majority of Earth's biodiversity and play fundamental roles in ecosystem function, biogeochemical cycling, and human health. Recent advancements in genomic and metagenomic technologies have revolutionized our understanding of microbial diversity, revealing intricate patterns of genetic variation and ecological adaptation within microbial populations. Central to this understanding is the concept of microbial species and intra-species units, defined largely by genomic similarity metrics such as the average nucleotide identity (ANI) and shared gene content. The delineation of microbial species has evolved beyond traditional morphological criteria to encompass genomic coherence and ecological cohesion. Studies have shown that microbial populations often exhibit discrete genomic clusters with high ANI (>95%) within species, while ANI values below 90% typically differentiate between species. These genomic discontinuities not only define species boundaries but also underscore the presence of finer-scale diversity within microbial populations, such as strains and sequence types, crucial for understanding ecological interactions and adaptive responses. In chapter 1, we show that another discontinuity exists between 99.2% and 99.8% (midpoint 99.5%) ANI in most of the 330, best-sampled bacterial species with at least 10 genome representatives each available in the public databases. Similar patterns were observed with long-read metagenomes, suggesting that the results reported in the chapter are not merely the effect of isolation biases. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ~20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity The identification of species-level (previous work by the Konstantinidis Lab) and intra-species units (this thesis, Chapter 1) highlighted the imperative need to answer the question, what drives these sequence-discrete units? Moreover, the mechanisms that maintain genomic coherence within microbial populations, including ecological interactions and horizontal gene transfer mediated by homologous and non-homologous recombination, are pivotal for species stability and adaptive potential. These mechanisms challenge traditional models of microbial speciation based on asexual (clonal) reproduction, emphasizing the synergy between ecological cohesion and genetic exchange in shaping microbial diversity across diverse habitats. In chapter 3, by analyzing closely related isolate genomes from the same or related samples using a novel methodology to identify recent recombination events we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection driven) horizontal gene flow, mediated by homologous recombination, often underlie the species- and intra-species-units. Ecological cohesiveness was inferred based on higher similarity in temporal abundance patterns of genomes of the same vs. different units, while recombination frequency was shown to have two times or more impact on sequence evolution than point (diversifying) mutation. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or selection-driven recombination, but not their synergistic effect, and provide a mechanistic explanation of how members of species- and intra-species units cohere together. Despite elucidation of the mechanisms of species cohesion by the work described in Chapter 3, it is important to realize that microbial species are not constant but undergo substantial gene content gain and loss (or fluidity). For instance, environmental perturbations, such as changes in salinity or light intensity, can drive adaptive shifts within microbial populations, influencing the dynamics of core and accessory genome components. The maintenance of genomic diversity within populations, despite selective pressures, highlights the role of adaptive pangenomes in microbial ecology. Understanding these dynamics is essential for predicting microbial responses to environmental change and for harnessing microbial diversity in biotechnological applications. Toward addressing this knowledge gap, the work under Chapter 2 showed that the pangenome of the Salinibacter ruber, isolated over the course of one month from a single saltern, is open and similar in size to that of randomly sampled Escherichia coli genomes, isolated over many years by various labs across globe [Pangenome is defined as the total non-redundant genes of all members of a species or group of genomes]. While most of the accessory (noncore) genes of Sal. ruber were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions in the salterns changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, these results provide an explanation for how this immense intraspecies gene diversity is maintained, and quantified what fraction of the pangenome may be ecologically important during transitions in environmental conditions. In marine environments, microbial communities exhibit depth-stratified diversity patterns, with distinct genomic adaptations correlating with environmental gradients. Metagenomic analyses of oceanic samples reveal site-specific genomic signatures and functional adaptations, shedding light on the genomic basis of microbial niche specialization and biogeochemical cycling in the marine realm. However, it remains challenging to determine when the populations retrieved from separate samples or locations are identical or not in terms of sequence diversity and gene content based on short-read data. To answer this question, the work described in chapter 5 employed the approaches developed in other chapters of this thesis as well as a new approach to define which reads recruited from a metagenome belong to a target population and define the ANIr concept (average nucleotide identity of mapped reads). By applying this new approach to samples from the Gulf of Mexico (GoM) described in chapter 4, this work showed that most populations showed high ANIr (i.e. were identical) in only one or a few samples of an ocean basin at similar depths, and that the ANIr decreased and gene-content differences increased between samples where a closely related population was detected (e.g., same 95% ANI-based genomospecies), and that also correlated with the distance (horizontal or vertical) between the samples. Accordingly, only a few truly cosmopolitan populations in the World’s oceans were identified. Interestingly, a few of these cosmopolitan populations, identified with closest matches to Alteromonas macleodii (97% AAI), Prochlorococcus marinus (79% AAI) and Desulfuromonas soudanensis (40% AAI), showed high relative abundance between samples from both the surface (0-200m) and the deep (>1000m). These data suggest that ubiquitous marine taxa may show significant endemic adaptation as they disperse, indicative of local population divergence and speciation, and provide a highly needed methodology to identify and track such populations. Finally, the detection and monitoring of target genes such as nitrogen-cycling and antimicrobial resistance genes (ARGs) in microbial populations to assess the relative importance of different functions pose significant challenges due to sequence similarity with non-target genes and assembly artifacts. Novel computational tools, such as ROCker models, enhance the accuracy of ARG (or other target gene) detection from short-read sequences, providing robust frameworks for surveillance and management of antimicrobial resistance in environmental and clinical settings. However, the ROCker tool developed previously by the Konstantinidis lab has a few shortcomings when dealing with the more recent, big data that have become available. Most notably, it employs a couple old bioinformatics libraries that are not supported anymore and is not friendly to the non-expert user. The work under Chapter 6 describes the new version of ROCker that effectively alleviates these shortcomings, and the development of new ROCker models for families of ARGs that were not covered previously by a model. Specifically, novel ROCker models for macrolide resistance genes that target the broad functional classes of mcr, mph, erm, and lnu genes as well as models targeting specific clades containing mcr-1, mphA, ermB, lnuF, lnuB, and lnuG genes were developed and validated with simulated reads spanning a range of common read lengths (100, 150, 250, and 300 base pairs). Subsequently, these simulated reads were used to challenge the filtering efficacy of ROCker vs. common static filtering approaches. ROCker models generally had improved F1 scores [2 x precision x recall/(precision + recall)] and consistently showed lower false-positive rates (FPR) and false-negative rates (FNR) compared to alternative methods such as similarity searches using BLASTx with various e-value thresholds or hidden Markov models. The ROCker models and all related reference material and data are freely available through http://enve-omics.ce.gatech.edu/rocker/models. These new ROCker models further expand the available model collection developed previously for other genes, including β-lactamases, and their application to short-read metagenomes, metatranscriptomes, and PCR amplicon data should facilitate the reliable detection and quantification of antimicrobial resistance genes. Therefore, this thesis integrated genomic and metagenomic approaches to elucidate microbial diversity, adaptation mechanisms, and speciation dynamics across various ecosystems. By exploring these interconnected themes, this thesis advanced our understanding of microbial community ecology, informed on the microbial species definition and surveillance strategies, and contributed to the sustainable management of microbial resources and health implications.
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ItemKinematic improvement differs between transradial versus partial hand prosthesis use following interlimb transfer(Georgia Institute of Technology, 2024-06) Alterman, Bennett ; Ali, Saif ; Keeton, Emily ; Hendrix, William ; Lee, Jade ; Binkley, Kartina ; Johnson, John ; Wang, Shuo ; Kling, James ; Wheaton, Lewis A.Developing empirical approaches to functional rehabilitation during the acute and sub-acute stages following amputation remains an area of need. For persons with unilateral limb loss, interlimb training (ILT) is a potentially attractive approach, as it may allow for prosthesis use learning on the unaffected side while awaiting fitting with the prosthesis on the affected side. Understanding the possible benefits of ILT for functional adaptation with prostheses will be beneficial to our understanding of its utility, particularly across levels of upper-extremity amputation. Persons with sound limbs performed simple and complex reach-to-grasp tasks while wearing either a transradial or partial-hand prosthesis simulator in a 5-day ILT paradigm. We hypothesized that participating in ILT would result in motor improvements, particularly for partial hand device use and during increased task complexity. ILT yielded modest effects for both groups, showing significant increases in reach peak velocity, while only partial-hand users showed decreases in reach duration. Overall, the most notable and consistent effects were seen in partial hand users. These results suggest interlimb training may provide tangible benefit as an indicator of future prosthesis adaptation during early-stage amputation rehabilitation, especially with partial hand loss.
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ItemEvolution of polarity establishment: The long and short story(Georgia Institute of Technology, 2024-05-15) Kaul, SamikshaWhile early developmental traits are nearly invariant across taxa, the underlying genetic architecture can be complex and significantly diverged. Because the functioning of the genes involved in such complex processes is often dependent on interactions with other genes, it can be difficult to investigate how the genes, and more importantly, the overall interacting networks evolve. An example of this is the early embryonic process of polarity establishment, whereby dynamically interacting genes work together to establish asymmetric cell division in the early embryo. The genetic and cellular dynamics of this process are well characterized in the C. elegans embryo but how these genes are evolving across different evolutionary timescales is yet to be understood. This thesis advances what is known regarding the evolution of polarity establishment at the inter- and intraspecific level. By comparing coding sequences as well as variant data, genes involved in polarity establishment were shown to have differed in levels of divergence as they evolved over the Caenorhabditis species phylogeny, and these same genes also exhibited similar patterns of variation within C. elegans, suggesting parallel levels of selection over short and long timescales. A wild isolate of C. elegans was also used to assess how critical polarity establishment genes in a hyperdiverged region vary at the genomic level and the role the genetic background plays in how these genes respond to perturbations. By generating near isogenic lines (NILs) and introducing a genetic perturbation by way of gene knockout in the parents and NILs, it was shown that breaking background interactions can reveal underlying epistasis among genes in the polarity establishment pathway. Furthermore, the importance of using strong quantitative techniques was demonstrated to capture the subtleties of polarity phenotypes in early embryogenesis with the development and implementation of two novel approaches. Natural variation in transcript abundance of critical polarity establishment genes in a hyperdiverged region was revealed by pairing single molecule fluorescence in situ hybridization with a microfluidic chip for high throughput data collection with high spatial and temporal resolution. Also, the effects of a synthetic temperature sensitive mutant of a polarity establishment gene were better characterized by using a temperature control device that provided more precise control of the environment to be able to collect quantitative phenotypic data.
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ItemInvestigating The Mechanisms Underlying Metamorphosis in The Chordate Ciona Robusta(Georgia Institute of Technology, 2024-04-29) Johnson, ChristopherIn 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.
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ItemIntegrating genomic and multiomic data for computational analysis of gene regulation in circulating immune cells(Georgia Institute of Technology, 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.
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ItemChordate-specific gene regulatory network of neuron development in Ciona.(Georgia Institute of Technology, 2023-12-12) Kim, KwantaeIn this research, I investigated the complex gene regulatory networks underlying neurogenesis, taking advantage of the unique neurons of the Ciona model system. I revealed that Fgf signaling is crucial for the neurogenesis of Bipolar Tail Neurons (BTNs) by controlling the expression of Neurogenin, the fate-determining transcription factor in these neurons. Then I also characterized multiple effector genes functioning in the development of BTNs. Additionally, I determined the vital role of the Pax3/7 transcription factor in the neural plate border to induce the neural tube closure. Finally, I demonstrated how the Pax3/7 also orchestrates an intricate gene regulatory network upstream of multiple transcription factors and functional effectors during the neurogenesis of Descending Decussating Neurons (ddNs). I found that the majority of this network’s regulatory branches are shared with other neurons in Ciona or even other organisms including vertebrates. Moreover, I revealed the role of key putative effector genes during the neurogenesis of ddNs. These findings will provide profound insights into developmental mechanisms in the central nervous system of chordates.