Life Sciences Commons^™

Network Inference Driven Drug Discovery, Gergely Zahoránszky-Kőhalmi, Tudor I. Oprea, Cristian G. Bologa, Subramani Mani, Oleg Ursu

Biomedical Sciences ETDs

The application of rational drug design principles in the era of network-pharmacology requires the investigation of drug-target and target-target interactions in order to design new drugs. The presented research was aimed at developing novel computational methods that enable the efficient analysis of complex biomedical data and to promote the hypothesis generation in the context of translational research. The three chapters of the Dissertation relate to various segments of drug discovery and development process.

The first chapter introduces the integrated predictive drug discovery platform „SmartGraph”. The novel collaborative-filtering based algorithm „Target Based Recommender (TBR)” was developed in the framework of this …

Regulation Of Palmitoylation Enzymes And Substrates By Intrinsically Disordered Regions, Krishna D. Reddy

USF Tampa Graduate Theses and Dissertations

Protein palmitoylation refers to the process of adding a 16-carbon saturated fatty acid to the cysteine of a substrate protein, and this can in turn affect the substrate’s localization, stability, folding, and several other processes. This process is catalyzed by a family of 23 mammalian protein acyltransferases (PATs), a family of transmembrane enzymes that modify an estimated 10% of the proteome. At this point in time, no structure of a protein in this family has been solved, and therefore there is poor understanding about the regulation of the enzymes and their substrates. Most proteins, including palmitoylation enzymes and substrates, have …

Quantitative And Qualitative Nutritional Analysis Of Gvsu Managed Honey Bee Colonies, Emily Noordyke, Anne Marie Fauvel

Student Summer Scholars Manuscripts

Managed honeybee colonies are in significant decline worldwide. The interaction between poor nutrition, pests and diseases, and pesticide use are most cited as potential culprits for the precarious state of the beekeeping industry. By evaluating food coming into the hive, conclusions can be drawn about the quality of hive location and forage availability. Pollen from an apiary with historically low honey production and poor colony health was compared to pollen from an apiary with high honey production and good colony health. Pollen was collected weekly in a 24-hour period, hive weight was monitored, and colonies were assessed for overall growth …

An Iron Detection System Determines Bacterial Swarming Initiation And Biofilm Formation, Chuan-Sheng Lin, Yu-Huan Tsai, Chih-Jung Chang, Shun-Fu Tseng, Tseng-Ru Wu, Chia-Chen Lu, Ting-Shu Wu, Jang-Jih Lu, Jim-Tong Horng, Jan Martel, David M. Ojcius, Hsin-Chih Lai, John Ding-E. Young

All Dugoni School of Dentistry Faculty Articles

Iron availability affects swarming and biofilm formation in various bacterial species. However, how bacteria sense iron and coordinate swarming and biofilm formation remains unclear. Using Serratia marcescens as a model organism, we identify here a stage-specific iron-regulatory machinery comprising a two-component system (TCS) and the TCS-regulated iron chelator 2-isocyano-6,7-dihydroxycoumarin (ICDH-Coumarin) that directly senses and modulates environmental ferric iron (Fe3+) availability to determine swarming initiation and biofilm formation. We demonstrate that the two-component system RssA-RssB (RssAB) directly senses environmental ferric iron (Fe³⁺) and transcriptionally modulates biosynthesis of flagella and the iron chelator ICDH-Coumarin whose production requires the pvc cluster. …

Toxic Effect Of Lead Chloride On Antioxidant Enzyme In The Liver And Kidney Of Fish, Bakhtawar Raza, Muhammad Javed, Faiza Ambreen, Fariha Latif

Journal of Bioresource Management

The contamination of aquatic habitats has become a serious problem for sustainability of the fisheries sector in Pakistan. Among different pollutants, heavy metals are very toxic. Their toxicity can be assessed by using antioxidant enzymes as biomarkers. These enzymes protect the living organisms from the oxidative stress caused by the heavy metals. Therefore, the effect of lead chloride (PbCl2) on the peroxidase enzyme activity in the tissues (liver and kidney) of Cirrhinamrigala was investigated. Four groups of Cirrhinamrigala were exposed, separately, to 96-hr LC50 concentration of PbCl2 along with its sub-lethal concentrations, viz.2/3rd, 1/4th and 1/5th for a period of …

Plant-Biocrust Interactions Mediated By The Fungal Loop, Eva Dettweiler-Robinson

Biology ETDs

Plant-microbial interactions influence biogeochemical cycles. Plants and biological soil crusts are primary producers in drylands. Biocrusts include cyanobacteria, lichens, mosses, algae, fungi, bacteria, and archaea on the soil surface, some of which fix atmospheric nitrogen. I investigated controls on biocrust carbon fluxes and their contribution to ecosystem fluxes, the incorporation of plant-derived carbon into biocrusts, and the role of soil fungi in promoting performance of plants and biocrusts. Biocrusts responded to temperature and moisture differently by biome. Biocrusts in grasslands/shrublands contributed >25% of total summertime ecosystem respiration, but biocrusts in savannas/woodlands contributed < 1%. Biocrusts contributed < 2% to GPP in any biome. To augment their native photosynthesis, biocrusts may include 16% plant-derived carbon. Fungal connections improved plant and biocrust performance and reduced differences in the CN ratio between organisms compared to when connections were impeded. Investigation of interactions among biocrusts, plants, and fungi has improved understanding of resource cycling in drylands.

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

The Molecular Systematics And Phylogeography Of The Widespread North American Meadow Vole (Microtus Pennsylvanicus), Donavan J. Jackson

Biology ETDs

The climatic and environmental fluctuations of the Quaternary played an integral role in geographic distribution and genetic structure within many organisms today. Understanding how these historical biogeographic events may have partitioned genetic variation throughout the landscape is critical to forecasting the implications of modern climate change and how animals will respond to projected climate shifts. Through geographic and taxonomically comprehensive sampling, we used multi-locus and species delimitation analyses along with niche modeling methods to investigate the evolutionary and biogeographic history of the meadow vole, Microtus pennsylvanicus. The findings of this study highlight the vulnerability and importance that special consideration …

Shifts In The Relative Importance Of Competition And Mutualism For Communities And Ecosystems, Lukas Patrick Bell-Dereske

Biology ETDs

Plant species interact with at least one, likely many, microbial mutualist throughout their life cycles. These microbial mutualists can have strong effects on plant communities and ecosystem processes. Fungal endophytes within the genus Epichloë associate with ~20%–30% of grass species and have been shown to have strong effects on plant communities. Here I described the effect of Epichloë amarillans associated with the dominant grass species, Ammophila breviligulata, on nutrient cycling, below-ground microbial community, and compare the strength of its effects on plant communities to plant-plant competition.

In chapters one and two, I examine the effects of Epichloë on litter …

Meador, Thomas (Sc 3074), Manuscripts & Folklife Archives

Manuscript Collection Finding Aids

Finding aid, scan and typescript (Click on "Additional Files" below) for Manuscripts Small Collection 3074. Agreement, 25 February 1854, between O. S. Warner and Thomas Meador setting out the terms of Meador’s employment on Warner’s farm in Breckinridge County, Kentucky. The agreement provides for payment, the provision of housing and produce from an orchard, and the use of pasture by Meador. Meador’s 12-month, full-time engagement makes allowances for his family and business, and for “unnecessary exposure” to “wet weather or heavy dews.”

Engineering Small Molecule Based Dimerization To Induce Translation And Provide Optogenetic Control, Catherine Wright

Chemistry and Chemical Biology ETDs

We wanted to develop a system that combines the spatial control of photoactivation and control of translation to build a tool to spatially control translation in neurons. This kind of tool could be used to investigate the role of spatially controlled translation of any protein in neural behavior. In this way the development and growth of neural processes could be studied to elucidate the mechanisms for spatially sensitive events such as pathfinding, repair, or long-term potentiation.

Chemically induced dimerization was used to install a switch into the activation of translation for specific genes. An abscisic acid (ABA) dependent dimerization of …

A Compilation Of Iron Speciation Data For Open Oceanic Waters, Salvatore Caprara, Kristen N. Buck, Loes J. A. Gerringa, Micha J. A. Rijkenberg, Damiano Monticelli

Marine Science Faculty Publications

No abstract provided.

Towards Deeper Understanding In Neuroimaging, Rex Devon Hjelm

Computer Science ETDs

Neuroimaging is a growing domain of research, with advances in machine learning having tremendous potential to expand understanding in neuroscience and improve public health. Deep neural networks have recently and rapidly achieved historic success in numerous domains, and as a consequence have completely redefined the landscape of automated learners, giving promise of significant advances in numerous domains of research. Despite recent advances and advantages over traditional machine learning methods, deep neural networks have yet to have permeated significantly into neuroscience studies, particularly as a tool for discovery. This dissertation presents well-established and novel tools for unsupervised learning which aid in …

Current And Emerging Uses Of Statins In Clinical Therapeutics: A Review, Jonathan T. Davies, Spencer F. Delfino, Chad E. Feinberg, Meghan F. Johnson, Veronica L. Nappi, Joshua T. Olinger, Anthony P. Schwab, Hollie I. Swanson

Pharmacology and Nutritional Sciences Faculty Publications

Statins, a class of cholesterol-lowering medications that inhibit 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase, are commonly administered to treat atherosclerotic cardiovascular disease. Statin use may expand considerably given its potential for treating an array of cholesterol-independent diseases. However, the lack of conclusive evidence supporting these emerging therapeutic uses of statins brings to the fore a number of unanswered questions including uncertainties regarding patient-to-patient variability in response to statins, the most appropriate statin to be used for the desired effect, and the efficacy of statins in treating cholesterol-independent diseases. In this review, the adverse effects, costs, and drug–drug and drug–food interactions associated with statin …

The Interplay Of Tlr9, Myeloid Cells, And A20 In Periodontal Inflammation, Katie E. Crump, Jennifer C. Oakley, Xia Xia-Juan, Theandra C. Madu, Swathi Devaki, Erin C. Mooney, Sinem E. Sahingur

Biology Faculty Articles

TLR9 deficient (TLR9^-/-) mice are resistant to periodontitis, a disease characterized by a dysbiotic microbiota and deregulated immune response resulting in tooth loss and various systemic conditions. However, the mechanisms and biological pathways by which TLR9 instigates periodontal inflammation are yet to be identified. In a ligature-induced model of periodontitis, we demonstrate TLR9^-/- mice exhibited significantly less alveolar bone loss compared to their wild-type (WT) counterparts. Consistent with the disease phenotype, gingival tissues showed significantly more inflammatory cell infiltrate in the WT ligated but not in the TLR9^-/- ligated mice compared to their unligated controls. Peritoneal …

Constituting Agricultural And Food Policy In Malawi: The Role Of The State And International Donors In The Farm Input Subsidy Program (Fisp), Peter Rock Nkhoma

USF Tampa Graduate Theses and Dissertations

Numerous studies have been undertaken on the political economy of agricultural policies in developing countries. These studies have explained agricultural policies in terms of urban bias, economic reforms, and domestic politics. Recently, the emphasis has been on explanations that reference the existence of a rational-legal and patronage element within the African state. Such explanations tend to underplay the extent to which agricultural policies are devised in a context of power asymmetries between the state and international donors or financial institutions. In the Malawian context specifically, limited attention has been paid to the possibility that policies are a negotiated outcome of …

Influence Of Water Quality On Stony Coral Diversity And Net Community Productivity In The Florida Keys, María Vega-Rodriguez

USF Tampa Graduate Theses and Dissertations

Worldwide, coral cover has declined at rates that have often exceeded 5% per year since the 1980’s. Populations of scleractinians (stony corals) in the Florida Keys reef tract have declined as well, with some communities declining at rates > 3% per year. Decreased water quality (e.g., steady increases in the ocean water temperatures and increased pollution, nutrients, or water turbidity due to coastal runoff) are commonly attributed to this decline. But actual linkages between variability and trends in these environmental parameters, and in stony coral diversity and ecosystem functions such as net community production, have not yet been well characterized.

With …

Tai Chi Can Improve Postural Stability As Measured By Resistance To Perturbation Related To Upper Limb Movement Among Healthy Older Adults, Jiahao Pan, Cuixian Liu, Shuqi Zhang, Li Li

Health Sciences & Kinesiology: Faculty Publications

Purpose: The aim of the study was to examine the effects of Tai Chi (TC) training on postural control when upright standing was perturbed by upper limb movement.

Methods: Three groups, TC, Brisk walk (BW), and sedentary (SE), of thirty-six participants aged from 65 to 75 years were recruited from local community centers. Participants performed static balance task (quiet standing for 30 s with eyes open and closed) and fitting task (two different reaching distances X three different opening sizes to fit objects through). During tasks, the COP data was recorded while standing on the force plate. Criteria measures calculated …

Smokejumper Obituary: Seim, Keith Douglas (Missoula 1966), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Photovoice Of Obesity On Murray State University's Campus, Karley Wray, Melissa Godby

Scholars Week

The issue we decided to discuss on campus using Photovoice was obesity. Obesity is becoming a very big topic that we all need to start focusing on. Obesity is defined as having a BMI at or above 30. This is becoming more common with our cultural change. We are becoming more fast food eaters and are not exercising as much as we should. It is even getting worse on college campuses. We all knew of what was called the freshmen 15, but now it is becoming a four year 15. It is becoming more common for college students to become …

The Role Of Fatty Acids And Cigarette Smoke Toxicants In Cigarette Smoke-Induced Cardiovascular Disease, Elani Fourie Wiest

Biomedical Sciences ETDs

Young, healthy smokers have an increased risk of developing cardiovascular disease (CVD), but early identification of these individuals can prevent progression to more severe cardiovascular diseases like atherosclerosis, stroke, and heart attacks. However, methods developed to detect cardiovascular disease in its early stages are limited and very costly. The goal of this project is to identify biomarkers that can be tested in a single blood draw from smokers in order to both assess their risk of developing cardiovascular disease and identify possible therapeutic targets to prevent disease progression.

The long term goals of this project are to investigate the association …

Montane Valley Grassland Plant Communities Are Highly Resistant To Wildfire, Martina M. Suazo

Biology ETDs

Understanding the ecological role of fire in fire-adapted plant communities is of great importance for restoration and preservation; however, limited research has been conducted on the response of upper elevation, C₃ grassland plant communities to wildfire. This study investigates the effects of the Las Conchas wildfire of 2011 on plant community structure and function in the montane valley grasslands of the Valles Caldera National Preserve, Jemez Mountains, New Mexico, USA. Long term monitoring of nine burned and seven unburned grassland sites was used to measure vegetation composition and dynamics both spatially and temporally relative to fire. Results show that …

Ordination Obscures The Influence Of Environment On Plankton Metacommunity Structure, Tad Dallas, Andrew M. Kramer, Marcus Zokan, John M. Drake

Faculty Publications

The composition of plankton communities in individual habitats is often influenced by environmental conditions like pH or hydroperiod. At larger scales, environmental gradients can influence community structure across interconnected local communities. Detecting the role of environmental and spatial factors on metacommunity structure depends on the ordering of sites and species prior to analysis. We investigated this ordination in two wetland metacommunities; a well-sampled, hyper-diverse zooplankton metacommunity, and a Central American phytoplankton metacommunity. We calculated coherence, turnover, and boundary clumping to classify the structure of the metacommunity, and we propose a statistic that responds to variation in both coherence and turnover. …

Human Amplified Changes In Precipitation-Runoff Patterns In Large River Basins Of The Midwestern United States, Sara A. Kelly, Zeinab Takbiri, Patrick Belmont, Efi Foufoula-Georgiou

Watershed Sciences Faculty Publications

Complete transformations of land cover from prairie, wetlands, and hardwood forests to homogenous row crop agriculture scattered with urban centers are thought to have caused profound changes in hydrology in the Upper Midwestern US since the 1800s. Continued intensification of land use and drainage practices combined with increased precipitation have caused many Midwest watersheds to exhibit higher streamflows today than in the historical past. While changes in crop type and farming practices have been well documented over the past few decades, changes in artificial surface (ditch) and subsurface (tile) drainage systems have not. This makes it difficult to quantitatively disentangle …

How To Restore Phragmites-Invaded Wetlands, Christine Rohal, Keith Hambrecht, Chad Cranney, Karin M. Kettenring

UAES Publications

Phragmites grows in tall, dense stands that shade out native plants. It spreads rapidly and overtakes important habitat for shorebirds and waterfowl, reducing the availability of nesting, loafing, and foraging areas. Phragmites makes large areas of wetlands inaccessible to wildlife and humans alike.

Broad-Sense Heritability And Genetic Gain For Powdery Mildew Resistance In Multiple Pseudo-F2 Populations Of Flowering Dogwoods (Cornus Florida L.), Lipi Parikh, Margaret T. Mmbaga, Srikanth Kodati, Matthew W. Blair, Dafeng Hui, Geoffrey Meru

Agricultural and Environmental Sciences Faculty Research

Powdery mildew caused by Erysiphe pulchra is one of the most destructive diseases of flowering dogwoods (Cornus florida L.). Control of powdery mildew relies heavily on chemical fungicides. Developing genetic resistance and planting powdery mildew resistant cultivars is a desirable long term control strategy for the disease. Information on inheritance characteristics associated with powdery mildew resistance in C. florida is needed to facilitate development of breeding strategies for a new generation of powdery mildew resistant cultivars. The objectives of this study were to determine broad-sense heritability, genetic gain and minimum number of effective genes associated with resistance to powdery mildew …

Genome Of The Asian Longhorned Beetle (Anoplophora Glabripennis), A Globally Significant Invasive Species, Reveals Key Functional And Evolutionary Innovations At The Beetle-Plant Interface, Duane D. Mckenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung-Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stephanie Haddad, Yi Han, Daniel S. T. Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, David R. Lance, Chien-Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba R. Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Ann M. Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards

Entomology Faculty Publications

Background: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.

Results: …

Survey Of The Heritability And Sparse Architecture Of Gene Expression Traits Across Human Tissues., Heather E. Wheeler, Kaanan P. Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, Gtex-Consortium, Nancy J. Cox, Dan L. Nicolae, Hae Kyung Im

Bioinformatics Faculty Publications

Understanding the genetic architecture of gene expression traits is key to elucidating the underlying mechanisms of complex traits. Here, for the first time, we perform a systematic survey of the heritability and the distribution of effect sizes across all representative tissues in the human body. We find that local h² can be relatively well characterized with 59% of expressed genes showing significant h² (FDR < 0.1) in the DGN whole blood cohort. However, current sample sizes (n ≤ 922) do not allow us to compute distal h². Bayesian Sparse Linear Mixed Model (BSLMM) analysis provides strong evidence that the genetic contribution to local expression traits is dominated by …

Historical Fire In Longleaf Pine (Pinus Palustris) Forests Of South Mississippi And Its Relation To Land Use And Climate, Charles Raymond White, Grant L. Harley

Faculty Publications

We characterized historical fire regimes in Pinus palustris (longleaf pine) forests of southern Mississippi with regard to global and regional coupled climate systems (e.g., El Niño–Southern Oscillation) and past human activity. The composite fire chronology spanned 1756–2013 with 132 individual scars representing 89 separate fire events. The mean fire interval was 2.9 yr, and mean intervals were significantly different between identified time periods (e.g., settlement period vs. management period). Evidence of biannual fire activity (up to three fires occurring within a 12‐ to 15‐month period) was found coeval with a peak in livestock grazing and logging from the 1850s through …

An Ecosystem-Based Approach To Reef Fish Management In The Gulf Of Mexico, Michelle D. Masi

USF Tampa Graduate Theses and Dissertations

Fisheries managers have the potential to significantly improve reef fish management in the Gulf of Mexico through the use of ecosystem-based approaches to fisheries management. Ecosystem-based approaches are needed to address the effects of fishing on trophodynamic interactions, to better account for ecosystem-scale processes in model projections, and to recognize the short and long-term biomass tradeoffs associated with making regulatory choices. My research was concentrated around three objectives: (1) characterizing the trophodynamic interactions between Gulf of Mexico fishes, in order to construct an invaluable tool (a Gulf of Mexico Atlantis model) to be used in ecological hypothesis testing and policy …