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- Title
- 2009-2010 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
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Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2009-2010
- PURL
- http://purl.flvc.org/fau/fd/FA00007672
- Format
- Document (PDF)
- Title
- 2010-2011 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2010-2011
- PURL
- http://purl.flvc.org/fau/fd/FA00007679
- Format
- Document (PDF)
- Title
- 2012-2013 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
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Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2012-2013
- PURL
- http://purl.flvc.org/fau/fd/FA00007686
- Format
- Document (PDF)
- Title
- 2013-2014 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2013-2014
- PURL
- http://purl.flvc.org/fau/fd/FA00007693
- Format
- Document (PDF)
- Title
- 2014-2015 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2014-2015
- PURL
- http://purl.flvc.org/fau/fd/FA00007700
- Format
- Document (PDF)
- Title
- 2015-2016 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2015-2016
- PURL
- http://purl.flvc.org/fau/fd/FA00007707
- Format
- Document (PDF)
- Title
- 2016-2017 Program Review Biological Sciences.
- Creator
- Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Florida Atlantic University Departmental Dashboard Indicators. Department program reviews for Charles E. Schmidt College of Science, Florida Atlantic University.
- Date Issued
- 2016-2017
- PURL
- http://purl.flvc.org/fau/fd/FA00007714
- Format
- Document (PDF)
- Title
- 2D AND 3D SHAPE VARIATION AMONG ELASMOBRANCH OLFACTORY ROSETTES.
- Creator
- Clark, Aubrey E., Porter, Marianne E., Meredith, Tricia L., Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
The functional impacts of olfactory rosette variation in elasmobranchs is unresolved. Our goal was to quantify rosette morphology and shape from 14 species using dissections, phylogenetic comparisons, and microCT imaging. We hypothesized that lamellar count and rosette shape (fineness ratio) would not scale with animal size, but internal rosette size variables must scale positively. We found that fineness ratio and lamellar counts varied significantly among species, and were positively...
Show moreThe functional impacts of olfactory rosette variation in elasmobranchs is unresolved. Our goal was to quantify rosette morphology and shape from 14 species using dissections, phylogenetic comparisons, and microCT imaging. We hypothesized that lamellar count and rosette shape (fineness ratio) would not scale with animal size, but internal rosette size variables must scale positively. We found that fineness ratio and lamellar counts varied significantly among species, and were positively correlated. The first two principal components of the pPCA explained 82% of the variation, with fineness ratio and lamellar count contributing the most. There were no significant differences between rosette structure or volume when comparing dissected values to in situ values obtained using diceCT. Based on our results, we hypothesize that variations in rosette shape and morphology will impact hydrodynamics and optimize odorant detection, and these data can be used to create 3D models for future hydrodynamic studies.
Show less - Date Issued
- 2020
- PURL
- http://purl.flvc.org/fau/fd/FA00013591
- Subject Headings
- Elasmobranchs, Olfactory sensors, Morphology
- Format
- Document (PDF)
- Title
- A Comparative Study on the Tensile Properties of Shark Skin.
- Creator
- Creager, Shelby, Porter, Marianne C., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Our goal was to assess regional differences in denticle density and skin tensile properties in four coastal species of shark. We hypothesized that the denticle density, tensile strength (MPa), stiffness (MPa), and toughness of skin (MJ·m^-3) would vary regionally along the body of an individual and among species. An hourglass-shaped punch was used to extract the skin samples at 10 anatomical landmarks and denticle density was quantified. Denticle density varied significantly among both...
Show moreOur goal was to assess regional differences in denticle density and skin tensile properties in four coastal species of shark. We hypothesized that the denticle density, tensile strength (MPa), stiffness (MPa), and toughness of skin (MJ·m^-3) would vary regionally along the body of an individual and among species. An hourglass-shaped punch was used to extract the skin samples at 10 anatomical landmarks and denticle density was quantified. Denticle density varied significantly among both regions and species, and showed a significant species by region interaction. Skin samples were tested in tension at a strain rate of 2 mm-s until failure. We found significant species and region effects for all tensile and denticle density properties. Also, denticle density increases with skin stiffness but decreases with toughness. Shark skin toughness is similar to that of mammalian tendons. These data show shark skin functions as an exotendon, able to conserve energy during swimming.
Show less - Date Issued
- 2016
- PURL
- http://purl.flvc.org/fau/fd/FA00004761, http://purl.flvc.org/fau/fd/FA00004761
- Subject Headings
- Sharks--Anatomy., Sharks--Locomotion., Surfaces (Physics), Biophysics.
- Format
- Document (PDF)
- Title
- A comparison of body proportions in juvenile sea turtles: how shape may optimize survival in a vulnerable life stage.
- Creator
- Pate, Jessica Hope, Salmon, Michael, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Marine turtles produce many offspring which offsets the high mortality experienced by turtles during early development. Juvenile mortality might be reduced by evolving effective behavioral as well as morphological anti-predator defenses. Body proportions of three species (Caretta caretta, Chelonia mydas, Dermochelys coriacea) of turtles were measured in the first fourteen weeks of development to examine how growth may mitigate predation by gape-limited predators. Growth was categorized as...
Show moreMarine turtles produce many offspring which offsets the high mortality experienced by turtles during early development. Juvenile mortality might be reduced by evolving effective behavioral as well as morphological anti-predator defenses. Body proportions of three species (Caretta caretta, Chelonia mydas, Dermochelys coriacea) of turtles were measured in the first fourteen weeks of development to examine how growth may mitigate predation by gape-limited predators. Growth was categorized as isometric if shape did not change during development or allometric if body shape did change. All three species showed allometric growth in carapace width; however it was less pronounced in the larger D. coriacea turtles. Allometric growth in carapace width decreased as all three species grew in size. When high predation occurs in early development, many species will favor rapid growth into a size refuge. Juvenile sea turtles may optimize their survival by growing allometrically when predation risk is the greatest.
Show less - Date Issued
- 2014
- PURL
- http://purl.flvc.org/fau/fd/FA00004223, http://purl.flvc.org/fau/fd/FA00004223
- Subject Headings
- Predation (Biology), Sea turtles -- Growth, Sea turtles -- Mortality, Sea turtles -- Population viability analysis
- Format
- Document (PDF)
- Title
- A DISINHIBITORY MICROCIRCUIT FOR GATED CEREBELLAR LEARNING.
- Creator
- Zhang, Ke, Christie, Jason, Dawson-Scully, Ken, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Performance motor errors trigger animals’ adaptive learning behaviors to improve the accuracy and efficiency of the movement. The cerebellum is one of the key brain centers for encoding motor performance and motor learning. Climbing fibers relay information related to motor errors to the cerebellar cortex, evoking elevation of intracellular Ca2+ signals at Purkinje cell dendrites and inducing plasticity at coactive parallel fiber synapses, ultimately recalibrating sensorimotor associations to...
Show morePerformance motor errors trigger animals’ adaptive learning behaviors to improve the accuracy and efficiency of the movement. The cerebellum is one of the key brain centers for encoding motor performance and motor learning. Climbing fibers relay information related to motor errors to the cerebellar cortex, evoking elevation of intracellular Ca2+ signals at Purkinje cell dendrites and inducing plasticity at coactive parallel fiber synapses, ultimately recalibrating sensorimotor associations to alter behavior. Molecular layer interneurons (MLIs) inhibit Purkinje cells to modulate dendritic excitability and action potential output. How MLIs contribute to the regulation and encoding of climbing fiber-evoked adaptive movements remains poorly understood. In this dissertation, I used genetic tools to manipulate the activity of MLIs while monitoring Purkinje cell dendritic activity during a cerebellum-dependent motor learning task with different contexts to evaluate how MLIs are involved in this process. The results show that by suppressing dendritic Ca2+ signals in Purkinje cells, MLI activity coincident with climbing fiber-mediated excitation prevents the occurrence of learning when adaptation is not necessary. On the other hand, with error signals present, disinhibition onto Purkinje cells, mediated by MLI-MLI microcircuit, unlocked the ability of climbing fibers to induce plasticity and motor learning.
Show less - Date Issued
- 2020
- PURL
- http://purl.flvc.org/fau/fd/FA00013526
- Subject Headings
- Cerebellum, Interneurons, Purkinje cells, Dendrites, Sensorimotor integration, Neuroplasticity
- Format
- Document (PDF)
- Title
- A Framework for Understanding Power Supply and Demand in Presynaptic Nerve Terminals.
- Creator
- Justs, Karlis Anthony, Macleod, Gregory T., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
The molecular mechanisms of synaptic function and development have been studied extensively, but little is known about the energy requirements of synapses, or the mechanisms that coordinate their energy production with their metabolic demands. These are oversights, as synapses with high energy demands are more susceptible to degeneration and degrade in the early stages of diseases such as amyotrophic lateral sclerosis, spinal muscle atrophy and Parkinson’s disease. Here, in a structure...
Show moreThe molecular mechanisms of synaptic function and development have been studied extensively, but little is known about the energy requirements of synapses, or the mechanisms that coordinate their energy production with their metabolic demands. These are oversights, as synapses with high energy demands are more susceptible to degeneration and degrade in the early stages of diseases such as amyotrophic lateral sclerosis, spinal muscle atrophy and Parkinson’s disease. Here, in a structure-function study at Drosophila motor neuron terminals, a neurophysiological model was generated to investigate how power (ATP/s) supply is integrated to satisfy the power demand of presynaptic terminals. Power demands were estimated from six nerve terminals through direct measurements of neurotransmitter release and Ca2+ entry, as well as theoretical estimation of Na+ entry and power demands at rest (cost of housekeeping). The data was leveraged with a computational model that simulated the power demands of the terminals during their physiological activity, revealing high volatility in which power demands can increase 15-fold within milliseconds as neurons transition from rest to activity. Another computational model was generated that simulated ATP production scenarios regarding feedback to the power supply machinery (Oxphos and glycolysis) through changes in nucleotide concentrations, showing that feedback from nucleotides alone fail to stimulate power supply to match the power demands of each terminal. Failure of feedback models invokes the need for feed forward mechanisms (such as Ca2+) to stimulate power supply machinery to match power demands. We also quantified mitochondrial volume, density, number and size in each nerve terminal, revealing all four features positively correlate with the terminals power demands. This suggests the terminals enhance their oxidative capacity by increasing mitochondrial content to satisfy their power demands. And lastly, we demonstrate that abolishing an ATP buffering system (the phosphagen system) does not impair neurotransmission in the nerve terminals, suggesting motor nerve terminals are capable of satisfying their power demands without the ATP buffering system.
Show less - Date Issued
- 2019
- PURL
- http://purl.flvc.org/fau/fd/FA00013323
- Subject Headings
- Presynaptic Terminals, Adenosine triphosphate, Synapses--metabolism, Bioenergetics
- Format
- Document (PDF)
- Title
- A generalized stochastic birth/death population model based on Indian RiverLagoon dolphins.
- Creator
- Stonger, Jon, Noonburg, Erik G., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
For over a decade, researchers at Harbor Branch Oceanographic Institute (HBOI) have conducted surveys of the bottlenose dolphin (Tursiops truncatus) population of Indian River Lagoon (IRL) in Florida. I have constructed a 4-stage population model using the statistical program R. The model is used to conduct a viability analysis by analyzing the relationship between birth, calf and adult survival rates. The power analysis compares survey frequency to expected confidence intervals in estimating...
Show moreFor over a decade, researchers at Harbor Branch Oceanographic Institute (HBOI) have conducted surveys of the bottlenose dolphin (Tursiops truncatus) population of Indian River Lagoon (IRL) in Florida. I have constructed a 4-stage population model using the statistical program R. The model is used to conduct a viability analysis by analyzing the relationship between birth, calf and adult survival rates. The power analysis compares survey frequency to expected confidence intervals in estimating abundance. The sensitivity analysis shows that the population is most sensitive to changes in adult survival, followed by birth rate and calf survival. The model shows a strong chance of viability over a 50 year time span. The population is vulnerable to long periods of decline if birth, calf or adult survival rates fall below certain thresholds. Overall, the model simulates the future impacts of demographic change, providing a tool for conservation efforts.
Show less - Date Issued
- 2014
- PURL
- http://purl.flvc.org/fau/fd/FA00004163, http://purl.flvc.org/fau/fd/FA00004163
- Subject Headings
- Animal populations -- Estimates, Bottlenose dolphin -- Florida -- Indian River Lagoon -- Geographical distribution, Indian River (Fla : Lagoon), Marine mammal populations -- Estimates -- Florida -- Mathematical models, Population biology, Stochastic processes
- Format
- Document (PDF)
- Title
- A habitat suitability model for wading birds in a large subtropical lake: linking hydrologic fluctuations and nesting.
- Creator
- Botta, Richard A., Gawlik, Dale E., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Anthropogenic hydrologic alterations can affect the quality of lake littoral zone habitats for wading birds, such as the great egret (Ardea alba), snowy egret (Egretta thula), and white ibis (Eudocimus albus). One such lake in Florida, Lake Okeechobee, has experienced a marked decline in wading bird nesting since the 1970’s, concomitant with changes in lake level management. It’s hypothesized that a reduction in foraging habitat has led to the nesting decline; however, there is little...
Show moreAnthropogenic hydrologic alterations can affect the quality of lake littoral zone habitats for wading birds, such as the great egret (Ardea alba), snowy egret (Egretta thula), and white ibis (Eudocimus albus). One such lake in Florida, Lake Okeechobee, has experienced a marked decline in wading bird nesting since the 1970’s, concomitant with changes in lake level management. It’s hypothesized that a reduction in foraging habitat has led to the nesting decline; however, there is little quantitative evidence of this link. A habitat suitability model was developed for Lake Okeechobee wading birds that incorporate the spatial and temporal dynamics of environmental factors that affect wading bird foraging and tests whether foraging habitat is linked to numbers of nests.
Show less - Date Issued
- 2014
- PURL
- http://purl.flvc.org/fau/fd/FA00004082
- Subject Headings
- Birds -- Florida -- Lake Okeechobee -- Geographical distribution, Estuarine ecology -- Florida -- Lake Okeechobee, Restoration ecology -- Florida -- Lake Okeechobee, Water birds -- Habitat
- Format
- Document (PDF)
- Title
- A neuronal G protein-coupled receptor mediates the effect of diet on lifespan and development in Caenorhabditis elegans through autophagy.
- Creator
- Parker, Thomas A., Jia, Kailiang, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Animals rely on the integration of a variety of external cues to understand and respond appropriately to their environment. The relative amounts of food and constitutively secreted pheromone detected by the nematode C. elegans determines how it will develop and grow. Starvation conditions cause the animal to enter a protective stage, termed dauer. Dauer animals are non-eating, long-lived and stress resistant. Yet, when these animals are introduced to food replete conditions they will recover...
Show moreAnimals rely on the integration of a variety of external cues to understand and respond appropriately to their environment. The relative amounts of food and constitutively secreted pheromone detected by the nematode C. elegans determines how it will develop and grow. Starvation conditions cause the animal to enter a protective stage, termed dauer. Dauer animals are non-eating, long-lived and stress resistant. Yet, when these animals are introduced to food replete conditions they will recover from dauer and proceed into normal development. Furthermore, food restriction has been demonstrated to extend the lifespan of a wide-range of species including C. elegans. However, the exact mechanism by which food signals are detected and transduced by C. elegans to influence development and longevity remains unknown. Here, we identify a G protein-coupled receptor (GPCR) DCAR-1 that acts in two chemosensory neurons to mediate food signaling in an autophagy-related manner. The DCAR-1 ligand Dihydrocaffeic acid (DHCA) competes with dauer-inducing pheromone to promote growth. DHCA is a key intermediate in the shikimate pathway, which is required to synthesize folate and aromatic amino acids. We report that dcar-1 mutations influence dauer formation and extend wildtype lifespan via a mechanism of dietary restriction. Moreover, we show that the lifespan extension of dcar-1 mutants is completely dependent on autophagy gene atg- 18. Furthermore, our data suggests metabolites derived from shikimate are food signals that control aging and dauer development through GPCR signaling in C. elegans. These studies will contribute to the delineation of mechanisms behind the beneficial effects of dietary restriction in eukaryotic organisms.
Show less - Date Issued
- 2019
- PURL
- http://purl.flvc.org/fau/fd/FA00013338
- Subject Headings
- Caenorhabditis elegans, Autophagy, Receptors, G-Protein-Coupled, Longevity, Diet
- Format
- Document (PDF)
- Title
- A Novel Interaction: The thin stripe hermit Crab, Clibanarius vittatus, kills the Florida crown conch, Melongena corona, for its shell.
- Creator
- Cutter, Jennifer, Devlin, Donna, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
The hermit crab Clibanarius vittatus kills Melongena corona solely to acquire a better fitting shell. This finding is contrary to previous studies, which found that hermit crabs of other species cannot kill gastropods or, in most instances, remove freshly dead gastropods from their shells. This interaction cannot be classified as predation because Melongena tissue was never consumed. Clibanarius killed Melongena only when by doing so they could trade up to a better fitting shell. It cannot be...
Show moreThe hermit crab Clibanarius vittatus kills Melongena corona solely to acquire a better fitting shell. This finding is contrary to previous studies, which found that hermit crabs of other species cannot kill gastropods or, in most instances, remove freshly dead gastropods from their shells. This interaction cannot be classified as predation because Melongena tissue was never consumed. Clibanarius killed Melongena only when by doing so they could trade up to a better fitting shell. It cannot be classified as competition because there is no opportunity for Melongena to gain from the interaction. Therefore the term “lethal eviction” is hereby proposed for this interaction. The ability to kill a gastropod to obtain a superior shell gives Clibanarius vittatus an evolutionary advantage over other hermit crab species. It is not known if the outcome of this interaction is widespread where both species occur or if it is confined to the study area.
Show less - Date Issued
- 2017
- PURL
- http://purl.flvc.org/fau/fd/FA00004925, http://purl.flvc.org/fau/fd/FA00004925
- Subject Headings
- Crabs--Behavior., Crab culture., Predation (Biology), Adaptation (Physiology), Aquatic ecology., Intertidal ecology., Conservation biology.
- Format
- Document (PDF)
- Title
- A Novel Role of the Ankyrin-Binding Motif of L1-Type CAM Neuroglian in Nuclear Import and Transcriptional Regulation of Myc.
- Creator
- Kakad, Priyanka P., Godenschwege, Tanja A., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
L1-type cell adhesion molecule (L1CAM) plays an essential role in the development of nervous system and is also highly relevant for the progression of diseases such as Alzheimer’s disease, stroke and cancers, some of the leading causes of human mortality. In addition to its canonical role as a plasma membrane protein organizing the cytoskeleton, recent in vitro studies have revealed that transmembrane as well as cytosolic fragments of proteolytically cleaved vertebrate L1CAM translocate to...
Show moreL1-type cell adhesion molecule (L1CAM) plays an essential role in the development of nervous system and is also highly relevant for the progression of diseases such as Alzheimer’s disease, stroke and cancers, some of the leading causes of human mortality. In addition to its canonical role as a plasma membrane protein organizing the cytoskeleton, recent in vitro studies have revealed that transmembrane as well as cytosolic fragments of proteolytically cleaved vertebrate L1CAM translocate to the nucleus and regulate expression of genes involved in DNA post-replication repair, cell cycle control, migration and differentiation. However, little is known about the in vivo function of L1CAM in the adult nervous system. This dissertation research focuses on studying in vivo nuclear translocation and function of L1CAM. Using the Drosophila model system, we first show that the sole Drosophila L1CAM homolog, Neuroglian (Nrg), is proteolytically cleaved by Alzheimer’s associated secretases, similar to L1CAM, and is also translocated to the nucleus in the adult nervous system. Subsequently, we have shown that the deletion of highly conserved Ankyrin binding domain or FIGQY motif disrupts nuclear import. Further experiments have revealed that the nuclear translocation of Nrg is in fact regulated by the phosphorylation of the FIGQY motif. Importantly, our studies also show transgenic expression of full-length Nrg or the intracellular domain of Nrg resulted in increased myc expression, which is associated with increased sensitivity to oxidative stress and reduced life span. On the other hand, deletion of the FIGQY motif or mutations preventing its phosphorylation led to decrease in myc expression. In summary, we have identified a novel role for the highly conserved Ankyrin binding domain in nuclear translocation and transcriptional regulation of the Drosophila myc oncogene, which is of high relevance to neurodegenerative diseases and cancer associated with oxidative stress.
Show less - Date Issued
- 2018
- PURL
- http://purl.flvc.org/fau/fd/FA00013076
- Subject Headings
- Cell adhesion molecules., Myc proteins., Transcription, Genetic., Transcription factors, Gene expression., Ankyrins., Translocation, Genetic.
- Format
- Document (PDF)
- Title
- A SHOTGUN METAGENOMIC APPROACH TO THE BIOSYNTHESIS OF MARINE NATURAL PRODUCTS.
- Creator
- Miller-Xavier, René Kathleen, Mincer, Tracy, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
- Abstract/Description
-
Genomics has been revolutionized by improved sequencing technologies, allowing for the detailed exploration of microbial dark matter and complex microscopic ecosystems. The bottleneck in genomic workflows has shifted from high-throughput sequencing to data analysis. This dissertation developed the Florida Center for Coastal and Human Health Shotgun Metagenomics Workflow (FCHsm) that is easy to use and tailor to unique datasets. This work acts as the beta-testing for the workflow, as it...
Show moreGenomics has been revolutionized by improved sequencing technologies, allowing for the detailed exploration of microbial dark matter and complex microscopic ecosystems. The bottleneck in genomic workflows has shifted from high-throughput sequencing to data analysis. This dissertation developed the Florida Center for Coastal and Human Health Shotgun Metagenomics Workflow (FCHsm) that is easy to use and tailor to unique datasets. This work acts as the beta-testing for the workflow, as it analyzes disparate biomes (environmental and host microbiomes) at varying sequencing depths (shallow and deep). FCHsm was used to resolve molecular dynamics and mine trans-kingdom metagenomes for secondary metabolic biosynthetic gene clusters (BGCs) in two marine environments— Indian River Lagoon toxic harmful algal blooms (IRL HABs) and the medicinal Leiodermatium sponge holobiont. First, an in silico mock dataset was analyzed to benchmark the FCHsm workflow. Sourmash, coupled with the Genome Taxonomy Database, outcompeted the other taxonomic profilers by accurately predicting the size of the mock metagenome (450 genomes) and recalling the highest number of species (82 %) and strains (44 %). Nonpareil calculated the sequencing effort needed for 100 % coverage for all the datasets and correctly estimated the 75 Gbp of sequencing needed for almost 100 % coverage of the mock metagenomes (99.5 %). Next, the trans-kingdom metagenomes of the IRL were explored, and potential HAB biomarkers were identified.
Show less - Date Issued
- 2023
- PURL
- http://purl.flvc.org/fau/fd/FA00014186
- Subject Headings
- Marine natural products, Metagenomics
- Format
- Document (PDF)
- Title
- A structural and thermodynamic comparison of substrate interactions and catalysis by family 6 glycosyltransferases from Bacteroides ovatus, Parachlamydia acanthamoebae, and Bos taurus.
- Creator
- Stinson, Brittany, Brew, Keith, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Family 6 Glycosyltransferases (GT6s) are involved in the biosynthesis of complex glycans and can be found in all vertebrates, cyanophages, and some bacteria and unicellular eukaryotes. Understanding variations within family 6 GTs is important because of the roles of their products in cellular recognition, intercellular interactions, pathogenicity, and immunity and is likewise important for understanding the evolution of GTs. PaGT6 (from Parchlamydia acanthamoebae) and α3GT (from Bos taurus)...
Show moreFamily 6 Glycosyltransferases (GT6s) are involved in the biosynthesis of complex glycans and can be found in all vertebrates, cyanophages, and some bacteria and unicellular eukaryotes. Understanding variations within family 6 GTs is important because of the roles of their products in cellular recognition, intercellular interactions, pathogenicity, and immunity and is likewise important for understanding the evolution of GTs. PaGT6 (from Parchlamydia acanthamoebae) and α3GT (from Bos taurus) both require a divalent metal ion for catalysis which binds to a DXD motif. In BoGT6a from Bacteroides ovatus a NXN motif replaces DXD, and activity is metal-independent. However, mutating the NXN motif in BoGT6a to DXD did not introduce metal-dependency, indicating that metal-dependency is linked to additional differences. Calorimetric studies have shown that the presence of a divalent metal ion enhances UDP and donor substrate binding to PaGT6 and causes an increase in the entropy of the interaction. Protein modelling of PaGT6 has revealed that the presence of Mn2+ allows a hydrogen bond to form between Asp 97 and UDP-GalNAc, causing the donor substrate to bend and form hydrogen bonds with His 119, Asn 229, Lys 228, and Arg 234. These interactions do not occur in the absence of Mn2+. Investigation of acceptor substrate binding revealed that the presence of UDP enhances acceptor substrate binding to BoGT6a and PaGT6. Calorimetric titrations of BoGT6a with 2-fucosyllactose in the absence and presence of UDP showed that UDP increases the affinity of 2-fucosyllactose 16-fold with little effect on ΔH. Measurements of ΔCp for 2-fucosyllactose binding indicate that there is not a hydrophobic effect for the binding of 2-fucosyllactose. The preferred acceptor substrate for the bovine and Bacteroides GT6 has a β-1,4 linked galactose, but P. acanthamoebae GT6 prefers an acceptor substrate with a β-1,3 linked galactose. The N-terminus of the catalytic domain of bacterial GT6s is truncated by 47 residues relative to the catalytic domain of bovine α3GT. Removal of this region from α3GT results in an unfolded protein, indicating that although this region is not directly involved in substrate binding, it forms interactions necessary for the stability of the catalytic domain.
Show less - Date Issued
- 2018
- PURL
- http://purl.flvc.org/fau/fd/FA00013047
- Subject Headings
- Glycosyltransferases, Bacteroides, Chlamydiales, Acanthamoeba, Bos taurus, Cattle
- Format
- Document (PDF)
- Title
- A Study on Reversing the Immunosuppressive Phenotype of Tumor Associated Macrophages.
- Creator
- Liddle, Genevieve M., Hartmann, James X., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
- Abstract/Description
-
Extracellular stimuli may influence the M1/M2 phenotypic polarization of macrophages. We examined M1/M2 biomarkers, phagocytic activity, and tumoricidal activity in RAW 264.7 mouse macrophages. Macrophages were treated with conditioned media (CM) from 4T1 breast cancer cells, curcumin, 22-oxacalcitriol, LPS, or a combination of the previously listed. Arginase activity, a M2 phenotypic biomarker, was upregulated by the treatment of macrophages with conditioned media. Curcumin, 22-...
Show moreExtracellular stimuli may influence the M1/M2 phenotypic polarization of macrophages. We examined M1/M2 biomarkers, phagocytic activity, and tumoricidal activity in RAW 264.7 mouse macrophages. Macrophages were treated with conditioned media (CM) from 4T1 breast cancer cells, curcumin, 22-oxacalcitriol, LPS, or a combination of the previously listed. Arginase activity, a M2 phenotypic biomarker, was upregulated by the treatment of macrophages with conditioned media. Curcumin, 22- oxacalcitriol, and LPS partially inhibited RAW 264.7 arginase activity in the presence of 4T1 breast cancer media. 22-oxacalcitriol increased the phagocytic ability of RAW 264.7 macrophages in the presence of M2 polarizing substances produced by the 4T1 breast cancer cells. Also, LPS increased RAW 264.7 phagocytic ability in the presence of 4T1 breast cancer CM. This study looked at the potential substances that would possibly reverse the M2 tumor promoting macrophage phenotype seen in the breast cancer tumor environment.
Show less - Date Issued
- 2017
- PURL
- http://purl.flvc.org/fau/fd/FA00004867
- Subject Headings
- Macrophages., Breast--Cancer--Treatment., Tumors--Immunological aspects., Cancer--Immunological aspects., Biological response modifiers., Cancer--Molecular aspects.
- Format
- Document (PDF)