Integrative Biology Commons^™

Are Immune Modulating Single Nucleotide Polymorphisms Associated With Necrotizing Enterocolitis?, Ashanti L Franklin, Mariam Said, Clint D Cappiello, Heather Gordish-Dressman, Zohreh Tatari-Calderone, Stanislav Vukmanovic, Khodayar Rais-Bahrami, Naomi L C Luban, Joseph M Devaney, Anthony D Sandler

Genomics and Precision Medicine Faculty Publications

Necrotizing enterocolitis (NEC) is a devastating gastrointestinal emergency. The purpose of this study is to determine if functional single nucleotide polymorphisms (SNPs) in immune-modulating genes pre-dispose infants to NEC. After Institutional Review Board approval and parental consent, buccal swabs were collected for DNA extraction. TaqMan allelic discrimination assays and BglII endonuclease digestion were used to genotype specific inflammatory cytokines and TRIM21. Statistical analysis was completed using logistic regression. 184 neonates were analyzed in the study. Caucasian neonates with IL-6 (rs1800795) were over 6 times more likely to have NEC (p = 0.013; OR = 6.61, 95% CI 1.48-29.39), and over …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

Effect Of Genetic Background On The Dystrophic Phenotype In Mdx Mice., William D Coley, Laurent Bogdanik, Maria Candida Vila, Qing Yu, Terence A Partridge, Kanneboyina Nagaraju, +12 Additional Authors

Genomics and Precision Medicine Faculty Publications

Genetic background significantly affects phenotype in multiple mouse models of human diseases, including muscular dystrophy. This phenotypic variability is partly attributed to genetic modifiers that regulate the disease process. Studies have demonstrated that introduction of the γ-sarcoglycan null allele onto the DBA/2J background confers a more severe muscular dystrophy phenotype than the original strain, demonstrating the presence of genetic modifier loci in the DBA/2J background. To characterize the phenotype of dystrophin deficiency on the DBA/2J background, we created and phenotyped DBA/2J-congenic Dmdmdx mice (D2-mdx) and compared them to the original, C57BL/10ScSn-Dmdmdx (B10-mdx) model. These strains were compared to their respective …

Age-Associated Methylation Suppresses Spry1, Leading To A Failure Of Re-Quiescence And Loss Of The Reserve Stem Cell Pool In Elderly Muscle., Anne Bigot, William J Duddy, Zamalou G Ouandaogo, Elisa Negroni, Virginie Mariot, Svetlana Ghimbovschi, Brennan Harmon, Aurore Wielgosik, Camille Loiseau, Joseph Devaney, Julie Dumonceaux, Gillian Butler-Browne, Vincent Mouly, Stéphanie Duguez

Genomics and Precision Medicine Faculty Publications

The molecular mechanisms by which aging affects stem cell number and function are poorly understood. Murine data have implicated cellular senescence in the loss of muscle stem cells with aging. Here, using human cells and by carrying out experiments within a strictly pre-senescent division count, we demonstrate an impaired capacity for stem cell self-renewal in elderly muscle. We link aging to an increased methylation of the SPRY1 gene, a known regulator of muscle stem cell quiescence. Replenishment of the reserve cell pool was modulated experimentally by demethylation or siRNA knockdown of SPRY1. We propose that suppression of SPRY1 by age-associated …

Effects Of Prenatal Environment Are Revealed By Post-Natal Challenges: Embryonic Hormone Exposure, Adrenocortical Function And Food In Seabird Chicks, Z. Morgan Benowitz-Fredericks, Jannik Schultner, Alexander S. Kitaysky

Faculty Journal Articles

The interaction between prenatal environments and postnatal environments is an important source of phenotypic variability. We examined the ability of prenatal steroid exposure and postnatal energy restriction to explain adrenocortical function and fledging age in captive seabird chicks. We proposed and tested two hypotheses: (1) the strength of prenatal effects is attenuated by challenging postnatal environments (postnatal override) and (2) the strength of prenatal effects increases with the severity of postnatal challenges (postnatal reveal). We reared common murre (Uria aalge) chicks and measured prenatal exposure to corticosterone (CORT) and testosterone (T) from allantoic waste. Adrenocortical function was assessed after 10 …

Multi-Stress Proteomics: The Global Protein Response To Multiple Environmental Stressors In The Porcelain Crab Petrolisthes Cinctipes, Michael A. Garland

Master's Theses

Global climate change is increasing the number of hot days along the California coast as well as increasing the incidence of off-shore upwelling events that lower the pH of intertidal seawater; thus, intertidal organisms are experiencing an increase in more than one stress simultaneously. This study seeks to characterize the global protein response of the eurythermal porcelain crab Petrolisthes cinctipes to changes in thermal, pH, and tidal regime treatments, either combined or individually. The first experiment examined temperature stress alone and sought to determine the effect of chronic temperature acclimation on the acute heat shock response. We compared the proteomic …

Role Of Ime4 Protein In Pho Regulon Of S.Cerevisiae., Jenisha Ghimire

LSU New Orleans Theses and Dissertations

In the yeast Saccharomyces cerevisiae, the IME4 methyltransferase, interacts genetically with methyl binding protein, Pho92, to affect the expression of PHO regulon target genes. Cells mutant in IME4 or PHO92 show increases in the RNA abundance of PHO regulon target genes. The increase in the RNA abundance of the PHO regulon target genes is not additive in the cells double mutant in IME4 and PHO92. Hence, Ime4 and Pho92 interact in a single pathway in PHO regulon. Surprisingly, cells overexpressing IME4 and MUM2 shows increase in some PHO regulon target genes, indicating that IME4 affects the PHO regulon target …

Characterization Of Putative Wnt3a-Inducible Enhancers, Katelynn C. Lee, Nicholas Hum, Aimy Sebastian, Gabriela Loots

STAR Program Research Presentations

The Wnt signaling pathway has been previously shown to play a major role in regulating bone metabolism and it is emerging as a target for the therapeutic intervention of bone thinning disorders such as osteoporosis. Several Wnt proteins have been shown to be expressed in bone and mutations in Wnt pathway members such as Wnt co-receptor Lrp5 and Wnt inhibitor Sost have been shown to be associated with low or high bone mass disorders, however, very little is known about specific roles played by different Wnt ligands in bone development, repair and remodeling. To identify downstream targets of Wnt signaling …

Bioregulatory Systems Medicine: An Innovative Approach To Integrating The Science Of Molecular Networks, Inflammation, And Systems Biology With The Patient's Autoregulatory Capacity?, Alyssa W Goldman, Yvonne Burmeister, Konstantin Cesnulevicius, Martha Herbert, Mary Kane, David Lescheid, Timothy Mccaffrey, Myron Schultz, Bernd Seilheimer, Alta Smit, Georges St Laurent, Brian Berman

Medicine Faculty Publications

Bioregulatory systems medicine (BrSM) is a paradigm that aims to advance current medical practices. The basic scientific and clinical tenets of this approach embrace an interconnected picture of human health, supported largely by recent advances in systems biology and genomics, and focus on the implications of multi-scale interconnectivity for improving therapeutic approaches to disease. This article introduces the formal incorporation of these scientific and clinical elements into a cohesive theoretical model of the BrSM approach. The authors review this integrated body of knowledge and discuss how the emergent conceptual model offers the medical field a new avenue for extending the …

An Investigation Of The Effect Of Malathion On Adaptive Plasticity Of Pseudacris Sierra, Michael Jonathan Maples

Master's Theses

This thesis is composed of two chapters. Chapter one reviews what is known about adaptive plasticity in response to predators, describes the physiological systems involved in such plasticity, and outlines the evolutionary consequences of adaptive plasticity. Chapter two describes a scientific experiment that investigates how malathion may impact adaptive plasticity in the Sierran Treefrog, Pseudacris sierra. Anuran tadpoles suffer high mortality rates due to predation. In response to strong selective forces relating to these high predation rates, tadpoles evolved the ability to adaptively respond to predators through morphological and behavioral plasticity. The morphological and behavioral responses are varied and depend …

Ecology And Morphology Of The Late Miocene Musk Deer, Longirostromeryx Wellsi (Artiodactyla: Moschidae: Blastomerycinae), Katheryn Y. C. Chen

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

Longirostromeryx wellsi, one of the latest surviving members of the extinct clade Blastomerycinae (Artiodactyla: Moschidae), possesses highly derived craniodental morphology that deviates from typical musk deer form. Previous work suggests that the unique anatomy of L. wellsi represents adaptations for occupying open savannas. To test this hypothesis I conduct principal components analysis on five postcranial bones of L. wellsi, comparing them to that of several extant ruminant artiodactyls, which are divided among seven habitat categories. These elements are also compared with the postcrania of other blastomerycines. These analyses indicate that L. wellsi anatomy is most similar to that of other …

Gating Mechanisms Of The Canonical Trp Channel Isoform Trpc4, Dhananjay P. Thakur

Dissertations and Theses (Open Access)

Non-selective cation channels formed by Transient Receptor Potential Canonical (TRPC) proteins play important roles in regulatory and pathophysiological processes. These channels are known to be activated downstream from phospholipase C (PLC) signaling. However, the mechanism by which the PLC pathway activates TRPC4/C5 remains unclear. Uniquely, TRPC4 is maximally activated only when two separate G protein pathways, G_q/11 and G_i/o, are co-stimulated, making it a coincidence detector of G_q/11- and G_i/o -coupled receptor activation. Using HEK293 cells co-expressing mouse TRPC4β and selected G protein-coupled receptors, I observed that coincident stimulation of G_i/o proteins and …

An Empirical And Theoretical Comparison Of The Socio-Ecological Behaviors Of Captive Chimpanzees (Pan Troglodytes), Bonobos (Pan Paniscus), And Western Lowland Gorillas (Gorilla Gorilla): Social Tolerance And Behavioral Responses To Changes In Food Quality And Distribution, Scott C. Milne

Master of Science in Integrative Biology Theses

Chimpanzees and gorillas are sympatric in most of their range in Central Africa, however, bonobos do not overlap with either of the other two species. This difference has been hypothesized to be the main factor leading to the socio-ecological traits of each species. Access to, and competition for, terrestrial herbaceous vegetation (THV) in each of the three species in thought to be linked to the social relationships and female-female bonds of each species. This study sought to provide a direct comparison of the social relationships of each of the three African Great Apes in captivity in order to elucidate similarities …

Assessing Feeding Preferences And Spatial Patterns Of Lagodon Rhomboides Linnaeus, Alexandria V. Lamle

Master of Science in Integrative Biology Theses

Mesograzers have the ability to greatly mitigate the effects of eutrophication in seagrass systems. In this study we look at pinfish (Lagodon rhomboides Linnaeus) as a potential epiphytic grazer and assess feeding preferences during a transitional stage in the ontogenetic diet shift exhibited by these fish. Since pinfish are abundant in seagrass meadows in the northern Gulf of Mexico, their dietary preferences have the potential to greatly impact seagrasses in this system. Twenty-four hour feeding trials were conducted to determine pinfish preference between seagrass (Thalassia testudinum) and algal epiphytes. St. Joseph Bay, FL was also surveyed to …

Akirin-Mediated Gene Regulation During Cardiac Development, Austin M. Howard

Master of Science in Integrative Biology Theses

The highly conserved nuclear protein Akirin was previously identified as a cofactor that modulates Twist transcription factor activity during muscle development in Drosophila melanogaster. Akirin mediates an interaction between the Twist transcription factor and the multisubunit Brahma SWI/SNF-class chromatin remodeling complex at control elements of the Dmef2 locus to maintain optimal myogenic gene expression levels. Therefore, Akirin represents a class of novel secondary cofactors that work with transcription machinery to link transcription factor output with chromatin remodeling machinery to facilitate gene expression. Previous work establishes that Twist and Akirin also interact at Twist-responsive control elements of the tinman gene, …

Delineation Of Aeromonas Hydrophila Pathotypes By Dectection Of Putative Virulence Factors Using Polymerase Chain Reaction And Nematode Challenge Assay, John Metz

Master of Science in Integrative Biology Theses

Aeromonas hydrophila is a Gram-negative, bacterial pathogen of humans and other vertebrates. To delineate pathotypes, the genomes of twenty-eight Aeromonas isolates were screened by PCR to determine the presence of virulence factors including: aerolysin (aerA), cytotoxic enterotoxin (act), hemolysin (ahh1), elastase (ahyB), enolase (eno), S-layer protein (ahsA), serine protease (ser), Type IV Aeromonas pilus (tapA), lipase (lip), and Type Three Secretion System (T3SS) components (aopB, ascV). Genes for ahh1, lip, ser, and ahyB …

Eph-Ephrin Signaling And The Role Of Efn-4 In Caenorhabditis Elegans Nervous Systems Development, Alicia Schwieterman

Master of Science in Integrative Biology Theses

Eph receptor tyrosine kinases and their ephrin ligands are required for multiple aspects of nervous system development including axon outgrowth, synaptic plasticity, and the formation of topographic maps in the visual system. The Caenorhabditis elegans ephrin-A, efn-4, has a defined role in hypodermal patterning but its role in nervous system development is not well understood. We find that loss-of-function mutations in efn-4 lead to suppression of axon branching in C. elegans model of X-linked Kallmann syndrome, a human genetic disorder that presents with loss of sense of smell and failure to undergo spontaneous puberty. In addition, efn-4 mutants have …

Seasonal Dynamics And Micro-Climatic Preference Of Two Alpine Endemic Hypogean Beetles, Stefano Mammola, Elena Piano, Pier Mauro Giachino, Marco Isaia

International Journal of Speleology

Hypogean beetles generally live in stable environments, characterized by constant temperature and high relative humidity. Changes in the underground microclimatic conditions generally induce local migrations of the beetles through the hypogean environment in search of suitable microhabitats. We studied the seasonal dynamics and the micro-climatic preference of two Alpine endemic hypogean beetles - Sphodropsis ghilianii (Coleoptera, Carabidae) and Dellabeffaella roccae (Coleoptera, Cholevidae) - in the hypogean complex of Pugnetto (Graian Alps, Italy). We surveyed the two species for one year, using baited pitfall traps and measuring temperature and humidity along the two main caves. We used logistic regression mixed models …

Comparative Analysis Of Anti-Bd Bacteria From Six Malagasy Frog Species Of Ranomafana National Park, Kelsey Savage

Senior Honors Projects, 2010-2019

As Malagasy amphibians are facing an impending extinction crisis from the lethal skin fungus Batrachochytrium dendrobatidis (Bd), it has become imperative to proactively mitigate the threat. Bd sporangia develop in the skin of infected amphibians and cause the skin to thicken, leading to ionic imbalance and eventual heart failure. It has been shown that certain bacterial species are able to inhibit Bd growth on amphibians by producing antifungal metabolites. Community-based probiotics are one approach used to combat chytridomycosis by inoculating an environment with Bd-inhibitory bacteria so that many amphibian species are treated at once. With this method, it is important …

Fishing For A Sustainable Future: Aquaponics As A Method Of Food Production, Richard Ramsundar

Student Theses 2015-Present

This thesis compares and explains the advantages aquaponics farming has over modern industrial intensive farming. Through a comparison natural capital usage, conservation, recycling and cost, the thesis advocates for the expansion of aquaponics usage in urban settings. The thesis also explains the history of intensive farming and aquaponics in America, the science of how aquaponics operates, the economic and environmental costs of modern intensive farming versus aquaponics farming, and the social implications of aquaponics. Lastly, I propose a policy that reallocates farm subsidies by modifying the Farm Bill. Then I propose policies that support creating a new standard of farm …

Stressed Induced Changes In Karenia Brevis Ribosomal Rna, David Scott Jayroe

Master's Theses

Karenia brevis is a toxic marine dinoflagellate that causes harmful algal blooms (HABs), also known as red tides, in the Gulf of Mexico. These blooms are responsible for massive fish kills, shellfish bed contaminations, adverse human health effects, and vast economic loss. For these reasons, extensive research has gone into understanding the mechanisms and dynamics of bloom behavior by studying K. brevis in the field and in the lab. In order to understand higher order bloom behavior and dynamics it is imperative to understand K. brevis at the cellular level. In growing K. brevis in vitro under a variety of …

Modeling Uric Acid Kidney Stones Disease In D. Melanogaster Using Rnai And Dietary Modulation, Hai T.H. Lu

Dissertations, Masters Theses, Capstones, and Culminating Projects

In humans, the major predictor for gout and forming uric acid kidney stones is elevated uric acid in the serum and urine respectively. It is known that uric acid is an end metabolite of purine degradation in humans, but in other species from D. melanogaster to lower apes, uric acid can be further metabolized by urate oxidase into readily excreted allantoin. We hypothesize that if urate oxidase enzyme activity and dietary purine are both critical in uric acid kidney stone formation, then urate oxidase knockdown in combination with dietary purine supplementation will increase uric acid and induce uric acid kidney …

Forest Sustainability In An Altered Landscape Requires Human Intervention, Adam C. Labatore

Biology Theses

Recruitment success determines the abundance and composition of plant communities. Successful recruitment can be summarized as a simple dichotomy of establishment versus seed limitations. Establishment limitation occurs when plant populations are inhibited by habitat availability and quality, whereas seed limitation occurs when seeds fail to arrive in necessary densities. Recruitment failure undermines overstory sustainability if the existing trees cannot replace themselves. Preliminary analysis indicated tree recruitment failure at an urban nature preserve with too few tree seedlings to replace mature canopy trees. These data suggested that the urban forest was not sustainable. The overarching goal of the study was to …

Seasonal Variation In Corticosterone, Stress Responses, And Physiology In The Northern Cardinal Cardinalis Cardinalis, Benjamin Matthew Duckworth

Master's Theses

Seasonal regulation of the adrenocortical response (e.g., ‘stress response’) appears to be ubiquitous in mid- to high-latitude vertebrates. Northern Cardinals (Cardinalis cardinalis) are a Temperate dwelling passerine of Tropical-descent with a wide species range (tropics to Northern Temperate zones). This species encounters a wide variety of environmental conditions and strong seasonality, however corticosterone (CORT, the main adrenal stress hormone) has not been studied with regards to changes in seasonal levels. I initially analyzed samples from cardinals collected between 2007-2011 from the Lake Thoreau Environmental Research and Educational Center (Hattiesburg, Mississippi, USA). The data suggested seasonal differences of CORT, with higher …

Actions Of Pi3k-Delta Inhibitor, Idelalisib, And Its Combination With Bendamustine In Chronic Lymphocytic Leukemia, Prexy Modi

Dissertations and Theses (Open Access)

Class I phosphatidylinositol 3-kinase isoforms (α, β, δ, and γ) play a major role in cancer cell growth and survival. PI3K α and β are most studied. PI3K pathway is highly dysregulated in many cancers and aberrant PI3K signaling is associated with oncogene mutations and disease progression in solid tumors and in hematologic malignancies.

Chronic lymphocytic leukemia (CLL) is driven by B-cell receptor (BCR) signaling that promotes B-cell proliferation and survival. PI3K is a critical node in BCR pathway and PI3Kδ has a pivotal role in B-cell development and maintenance and this isoform is over-expressed in many B-cell malignancies, including …

Phytoextraction Of Lead From Contaminated Urban Soils By Panicum Virgatum Enhanced With Phytohormone, Edta, Benomyl, And Citric Acid Application, Matthew Aderholt

Master of Science in Integrative Biology Theses

Lead (Pb) contamination in soil represents a threat to human health and cleanup efforts often requires expensive or environmentally disruptive techniques. Phytoextraction has gained attention as a possible alternative to traditional remediation methods because of lower cost and minimal soil disruption. Panicum virgatum L. (switchgrass) was chemically enhanced with applications of the soil-fungicide benomyl, chelates (EDTA and citric acid), and phytohormones for phytoextraction of Pb from contaminated urban soils in Atlanta, GA. EDTA is often regarded as the most effective chelate, but has potential problems associated with its use due to long persistence time in soil and possible Pb mobilization …

An Investigation Of The Effects Of Increased Tidal Inundation, Competition, And Facilitation On Salt Marsh Systems, Jennifer A. Hyder

USF Tampa Graduate Theses and Dissertations

The low-lying topographic nature of salt marshes makes plants in these communities particularly vulnerable to increased salinity and inundation exposure associated with sea level rise. Both increased salinity and inundation have been cited as major causes of reduced plant performance and survival in marsh and areas fringing marsh. In addition to limitations imposed by physical stress, interspecific interactions have also been shown to mediate the performance and survival of salt marsh and salt marsh fringing species. The Stress Gradient Hypothesis (SGH) postulates that species interactions shift from competitive to facilitative as stress levels increase and predicts that (a) the frequency …

Targeted Single Molecule Sequencing Methodology For Ovarian Hyperstimulation Syndrome., Funda Orkunoglu-Suer, Arthur F. Harralson, David Frankfurter, Paul Gindoff, Travis J. O'Brien

Genomics and Precision Medicine Faculty Publications

BACKGROUND: One of the most significant issues surrounding next generation sequencing is the cost and the difficulty assembling short read lengths. Targeted capture enrichment of longer fragments using single molecule sequencing (SMS) is expected to improve both sequence assembly and base-call accuracy but, at present, there are very few examples of successful application of these technologic advances in translational research and clinical testing. We developed a targeted single molecule sequencing (T-SMS) panel for genes implicated in ovarian response to controlled ovarian hyperstimulation (COH) for infertility.

RESULTS: Target enrichment was carried out using droplet-base multiplex polymerase chain reaction (PCR) technology (RainDance®) …

The Proteomic Response Of The Carcinus Maenas Y-Organ Over The Course Of The Molt Cycle, Mark S. Hamer

Master's Theses

Molting in arthropods is a complex process governed by regulatory mechanisms that have evolved and adapted over millennia to allow these animals to grow, despite being confined by a hardened exoskeleton. We isolated the molt-regulating Y-organs (YO) from the common shore crab Carcinus maenas at molt stages B, C_1-3, C₄, and D₀ to assess how changes in protein abundances might underline the unique physiology of each of these stages. We found that changes in protein abundance were most notable in the postmolt stages (B and C_1-3), where an increase in energy metabolism and …

Status Of A Translocated Florida Sand Skink Population After Six Years: Establishing And Evaluating Criteria For Success, Adam Ryan Emerick

USF Tampa Graduate Theses and Dissertations

The translocation of organisms is becoming a frequently used tool in conservation biology. There are, however, a disproportionate number of unsuccessful attempts translocating populations of herpetofauna. Logistical and temporal limits of monitoring, combined with ambiguous metrics concerning "success," have led to few advances regarding reptile translocations. Successfully established and persistent populations are those in which both the founding population and subsequent generations show consistent or positive levels of survival and reproduction. A small population of the threatened Florida Sand Skink (Plestiodon reynoldsi) was translocated in 2007. Data collected from 2007 to 2009 confirmed survival and reproduction among the founding individuals, …