Life Sciences Commons^™

Analyzing And Modeling The Dysfunction Of Inhibitory Neurons In Alzheimer’S Disease, Carlos Perez, Jokubas Ziburkus, Ghamim Ullah

Physics Faculty Publications

Alzheimer’s disease (AD) is characterized by the abnormal proteolytic processing of amyloid precursor protein, resulting in increased production of a self-aggregating form of beta amyloid (Aβ). Several lines of work on AD patients and transgenic mice with high Aβ levels exhibit altered rhythmicity, aberrant neuronal network activity and hyperexcitability reflected in clusters of hyperactive neurons, and spontaneous epileptic activity. Recent studies highlight that abnormal accumulation of Aβ changes intrinsic properties of inhibitory neurons, which is one of the main reasons underlying the impaired network activity. However, specific cellular mechanisms leading to interneuronal dysfunction are not completely …

Generation Of Germ-Free /Ciona Intestinalis For Studies Of Gut-Microbe Interactions, Brittany A Leigh, Assunta Liberti, Larry J Dishaw

Marine Science Faculty Publications

Microbes associate with animal hosts, often providing shelter in a nutrient-rich environment. The gut, however, can be a harsh environment with members of the microbiome settling in distinct niches resulting in more stable, adherent biofilms. These diverse communities can provide orders of magnitude more gene products than the host genome; selection and maintenance of a functionally relevant and useful microbiome is now recognized to be an essential component of homeostasis. Germ-free (GF) model systems allow dissection of host-microbe interactions in a simple and direct way where each member of the symbiosis can be studied in isolation. In addition, because immune …

Population Density, Habitat Dynamic And Aerial Survival Of Relict Cave Bivalves From Genus Congeria In The Dinaric Karst, Olga Jovanović Glavaš, Branko Jalžić, Helena Bilandžija

International Journal of Speleology

Caves are some of the least-known ecosystems on Earth and long-term ecological studies and population size estimates are very rare. Genus Congeria is a Tertiary relict that comprises three species from Dinaric karst area; C. kusceri, C. jalzici and C. mulaomerovici, each with very limited distribution. They are the only known cave bivalves and in contrast to many other cave species, they form populations with high densities. We estimated that the population of C. kusceri in Jama u Predolcu is between 72,454 and 72,906 individuals. The highest density occurred between one and three meters depth, and reached maximum …

Molecular Typing And Virulence Analysis Of Multidrug Resistant Klebsiella Pneumoniae Clinical Isolates Recovered From Egyptian Hospitals, Reham Wasfi, Walid F. Elkhatib, Hossam M. Ashour

Molecular Biosciences Faculty Publications

Klebsiella pneumonia infection rates have increased dramatically. Molecular typing and virulence analysis are powerful tools that can shed light on Klebsiella pneumonia infections. Whereas 77.7% (28/36) of clinical isolates indicated multidrug resistant (MDR) patterns, 50% (18/36) indicated carpabenem resistance. Gene prevalence for the AcrAB efflux pump (82.14%) was more than that of the mdtK efflux pump (32.14%) in the MDR isolates. FimH-1 and mrkD genes were prevalent in wound and blood isolates. FimH-1 gene was prevalent in sputum while mrkD gene was prevalent in urine. Serum resistance associated with outer membrane protein coding gene (traT) was found in all blood …

Integrated Strategy Improves The Prediction Accuracy Of Mirna In Large Dataset., Bin Xue, David Lipps, Sree Devineni

Molecular Biosciences Faculty Publications

MiRNAs are short non-coding RNAs of about 22 nucleotides, which play critical roles in gene expression regulation. The biogenesis of miRNAs is largely determined by the sequence and structural features of their parental RNA molecules. Based on these features, multiple computational tools have been developed to predict if RNA transcripts contain miRNAs or not. Although being very successful, these predictors started to face multiple challenges in recent years. Many predictors were optimized using datasets of hundreds of miRNA samples. The sizes of these datasets are much smaller than the number of known miRNAs. Consequently, the prediction accuracy of these predictors …

An Intercomparison Of Dissolved Iron Speciation At The Bermuda Atlantic Time-Series Study (Bats) Site: Results From Geotraces Crossover Station A, Kristen N. Buck, Loes J. A. Gerringa, Micha J. A. Rijkenberg

Marine Science Faculty Publications

The organic complexation of dissolved iron (Fe) was determined in depth profile samples collected from GEOTRACES Crossover Station A, the Bermuda Atlantic Time-series Study (BATS) site, as part of the Dutch and U.S. GEOTRACES North Atlantic programs in June 2010 and November 2011, respectively. The two groups employed distinct competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-AdCSV) methods, and resulting ligand concentrations and conditional stability constants from each profile were compared. Excellent agreement was found between the total ligand concentrations determined in June 2010 and the strongest, L₁-type, ligand concentrations determined in November 2011. Yet a primary distinction between …

Towards Quantitative Viromics For Both Double-Stranded And Single-Stranded Dna Viruses., Simon Roux, Natalie E Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Mya Breitbart, Matthew B Sullivan

Marine Science Faculty Publications

BACKGROUND: Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).

METHODS: Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation …

Lilliput Effect Dynamics Across The Cretaceous-Paleogene Mass Extinction: Approaches, Prevalence, And Mechanisms, Matthew Brett Jarrett

USF Tampa Graduate Theses and Dissertations

An organism's body size entails both physiological and ecological costs. Furthermore, as a parameter in analyzing organisms, it represents a fundamental and essential morphometric character. Reductions in size following mass extinction is a commonly observed phenomenon in the fossil record. This study examines the evolutionary significance of this phenomenon termed the: 'Lilliput Effect' by proposing that it represents a rapid evolutionary response to altered selection pressures during a mass extinction. This primary hypothesis is evaluated against two additional hypotheses of size reduction: 1) stunted growth as a response to stressed ecosystems, and/or 2) mass extinctions are size selective.

These hypotheses …

Recurring Patterns Among Scrambled Genes In The Encrypted Genome Of The Ciliate Oxytricha Trifallax, Jonathan Burns, Denys Kukushkin, Xiao Chen, Laura F Landweber, Masahico Saito, Nataša Jonoska

Mathematics and Statistics Faculty Publications

Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized "nano-chromosomes". During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt …

A Novel Rrm3 Function In Restricting Dna Replication Via An Orc5-Binding Domain Is Genetically Separable From Rrm3 Function As An Atpase/Helicase In Facilitating Fork Progression, Salahuddin Syed, Claus Desler, Lene J Rasmussen, Kristina H Schmidt

Molecular Biosciences Faculty Publications

In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186-212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role …

Temporal Variability Of Diapycnal Mixing In The Northern South China Sea, Hui Sun, Qingxuan Yang, Wei Zhao, Xinfeng Liang, Jiwei Tian

Marine Science Faculty Publications

Temporal variability of diapycnal mixing over 7 months in the northern South China Sea was examined based on McLane Moored Profiler observations from 850 to 2200 m by employing a finescale parameterization. Intensified diffusivity exceeding the order of 10⁻³ m²/s in magnitude was found over the first half of October 2014, and from 2 December 2014 to 21 January 2015 (a typical wintertime). Strong internal tides and winds in winter were the likely candidates for the high‐level diapycnal mixing in winter. As for the enhanced mixing during October 2014, we suspect the generation of near‐bottom near‐inertial waves …

Reintroducing Environmental Change Drivers In Biodiversity-Ecosystem Functioning Research., Frederik De Laender, Jason R. Rohr, Roman Ashauer, Donald J Baird, Uta Berger, Nico Eisenhauer, Volker Grimm, Udo Hommen, Lorraine Maltby, Carlos J Meliàn

Integrative Biology Faculty and Staff Publications

For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly reintroducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next we show how this reintroduction improves experimental control over community composition and structure, which helps to provide mechanistic insight on how multiple aspects of biodiversity relate to function and how biodiversity and function relate in food webs. We also highlight challenges for the proposed reintroduction and suggest analyses and experiments to better understand how …

Step By Step: Biology Undergraduates' Problem-Solving Procedures During Multiple-Choice Assessment, Luanna B Prevost, Paula P Lemons

Integrative Biology Faculty and Staff Publications

This study uses the theoretical framework of domain-specific problem solving to explore the procedures students use to solve multiple-choice problems about biology concepts. We designed several multiple-choice problems and administered them on four exams. We trained students to produce written descriptions of how they solved the problem, and this allowed us to systematically investigate their problem-solving procedures. We identified a range of procedures and organized them as domain general, domain specific, or hybrid. We also identified domain-general and domain-specific errors made by students during problem solving. We found that students use domain-general and hybrid procedures more frequently when solving lower-order …

The Heat Shock Transcription Factor Hsf1 Induces Ovarian Cancer Epithelial-Mesenchymal Transition In A 3d Spheroid Growth Model., Chase D Powell, Trillitye R Paullin, Candice Aoisa, Christopher J Menzie, Ashley Ubaldini, Sandy D. Westerheid

Molecular Biosciences Faculty Publications

Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. The proteotoxic stress-responsive transcription factor HSF1 is frequently overexpressed in a variety of cancers and is vital to cellular proliferation and invasion in some cancers. Upon analysis of various patient data sets, we find that HSF1 is frequently overexpressed in ovarian tumor samples. In order to determine the role of HSF1 in ovarian cancer, inducible HSF1 knockdown cell lines were created. Knockdown of HSF1 in SKOV3 and HEY ovarian cancer cell lines attenuates the epithelial-to-mesenchymal transition …

The Effects Of Phytohormones And Isoprenoids In Dihydroartemisinin-Induced Dormancy In The Erythrocytic Stages Of Plasmodium Falciparum, Marvin Duvalsaint Duvalsaint

USF Tampa Graduate Theses and Dissertations

Our ability to control malaria has been challenged by increasing antimalarial resistance. Plasmodium falciparum undergoes dormancy in the blood stages which is hypothesized to be a means by which they are able to survive under drug pressure. This helps select for resistant parasites which grow following removal of drug. The mechanisms behind dormancy and the subsequent recrudescence are not fully understood but translating knowledge from related organisms which undergo a similar phenomenon might shed some light. Higher plants utilize dormancy during the early development stages to survive under unfavorable conditions, increasing fitness of the seedling and ensuring viability when this …

Mitochondrial Heteroplasmy Contributes To The Dynamic Atovaquone Resistance Response In Plasmodium Falciparum, Sasha Victoria Siegel

USF Tampa Graduate Theses and Dissertations

Of the considerable challenges researchers face in the control and elimination of malaria, the development of antimalarial drug resistance in parasite populations remains a significant hurdle to progress worldwide. Atovaquone is used in combination with proguanil (Malarone) as an antimalarial treatment in uncomplicated malaria, but is rendered ineffective by the rapid development of atovaquone resistance during treatment. Previous studies have established that de novo mutant parasites confer resistance to atovaquone with a substitution in amino acid 268 in the cytochrome b gene encoded by the parasite mitochondrial genome, yet much is still unknown about how this resistance develops, and whether …

Vdr-Ripk1 Interaction And Its Implications In Cell Death And Cancer Intervention, Waise Quarni

USF Tampa Graduate Theses and Dissertations

Receptor interacting protein kinase 1 (RIPK1) is an enzyme acting downstream of tumor necrosis factor alpha to control cell survival and death. RIPK1 expression has been reported to cause drug resistance in cancer cells; but so far, no published studies have investigated the role of RIPK1 in vitamin D action. In the present study, we investigated whether RIPK1 played any role in 1,25-dihydroxyvitamin D3 (1,25D3)-induced growth suppression. In our studies, RIPK1 decreased the transcriptional activity of vitamin D receptor (VDR) in luciferase reporter assays independently of its kinase activity, suggesting a negative role of RIPK1 in 1,25D3 action. RIPK1 also …

Quantitative Proteomic Investigation Of Disease Models Of Type 2 Diabetes, Mark Gabriel Athanason

USF Tampa Graduate Theses and Dissertations

PANcreatic DERived factor (PANDER, FAM3B) is a member of a superfamily of FAM3 proteins that are uniquely structured and strongly expressed from the endocrine pancreas and co-secreted with insulin. Unique animal models available to our lab have indicated that PANDER can induce a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased. The complexity of the biological networks involved with this process warranted the logical approach of employing quantitative mass spectrometry based proteomic analysis using stable isotope labeling of amino acids in cell culture (SILAC) to identify the global proteome differences between the PANDER …

Gene Expression Profiling And The Role Of Hsf1 In Ovarian Cancer In 3d Spheroid Models, Trillitye Paullin

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. These poor statistics are related to a lack of early symptoms and inadequate screening techniques. This results in the cancer going undetected until later stages when the tumor has metastasized through a process that requires the epithelial to mesenchymal transition (EMT). In lieu of traditional monolayer cell culture, EMT and cancer progression in general is best characterized through the use of 3D spheroid models. In this study, we examine gene expression changes through microarray analysis in …

A Framework For Studying Meshfree Geometry And A Method For Explicit Boundary Determination, Joseph Bradley Alford

USF Tampa Graduate Theses and Dissertations

Patient-specific biomechanical analysis is an important tool used to understand the complex processes that occur in the body due to physical stimulation. Patient-specific models are generated by processing medical images; once an object from the image is identified via segmentation, a point cloud representation of the object is extracted. Generating an analysis suitable representation from the point cloud has traditionally required generating a finite element mesh, which often requires a well defined surface to accomplish. Point clouds lack a well defined geometry, meaning that the surface definition is incomplete at best. Point clouds that have been generated from images have …

Hypercapnic Hyperoxia Increases Free Radical Production And Cellular Excitability In Rat Caudal Solitary Complex Brain Slice Neurons, Geoffrey Edward Ciarlone

USF Tampa Graduate Theses and Dissertations

The caudal solitary complex (cSC) is a cardiorespiratory integrative center in the dorsal medulla oblongata that plays a vital role in the central CO₂-chemoreceptive network. Neurons in this area respond to hypercapnic acidosis (HA) by a depolarization of the membrane potential and increase in firing rate, however a definitive mechanism for this response remains unknown. Likewise, CO₂-chemoreceptive neurons in the cSC respond to hyperoxia in a similar fashion, but via a free radical mediated mechanism. It remains unknown if the response to increased pO₂ is merely an increase in redox signaling, or if it’s the …

Climate Change Drives Outbreaks Of Emerging Infectious Disease And Phenological Shifts, Jeremy Cohen

USF Tampa Graduate Theses and Dissertations

Climate change is expected to impact species by altering infectious disease outcomes, modifying community composition, and causing species to shift their phenology, body sizes and range distributions. However, the outcomes of these impacts are often controversial; for example, scientists have debated whether climate change will exacerbate emerging infectious disease and which species are at greatest risk to advance their phenology. There reason for these controversies may be that climate change is impacting diverse processes across a wide range of ecological scales, as the interplay between fine-scale processes and broad-scale dynamics can often cause unpredictable changes to the biosphere. Therefore, it …

Significance Of Pten Phosphorylation And Its Nuclear Function In Lung Cancer, Prerna Malaney

USF Tampa Graduate Theses and Dissertations

Phosphorylation mediated inactivation of PTEN leads to multiple malignancies with increased severity. However, the consequence of such inactivation on downstream functions of PTEN are poorly understood. Therefore, the objective of my thesis is to ascertain the molecular mechanisms by which PTEN phosphorylation drives lung cancer. PTEN phosphorylation at the C-terminal serine/threonine cluster abrogates its tumor suppressor function. Despite the critical role of the PTEN C-tail in regulating its function, the crystal structure of the C-tail remains unknown. Using bioinformatics and structural analysis, I determined that the PTEN C-tail is an intrinsically disordered region and is a hot spot for post-translational …

Quantitative Proteomic Profiling Reveals Hepatic Lipogenesis And Liver X Receptor Activation In The Pander Transgenic Model., Mark G. Athanason, Whitney A. Ratliff, Dale Chaput, Catherine B. Marelia, Melanie N. Kuehl, Stanley M. Stevens Jr., Brant R. Burkhardt

Molecular Biosciences Faculty Publications

PANcreatic-DERived factor (PANDER) is a member of a superfamily of FAM3 proteins modulating glycemic levels by metabolic regulation of the liver and pancreas. The precise PANDER-induced hepatic signaling mechanism is still being elucidated and has been very complex due to the pleiotropic nature of this novel hormone. Our PANDER transgenic (PANTG) mouse displays a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased, a phenomena observed in type 2 diabetes. To examine the complex PANDER-induced mechanism of SHIR, we utilized quantitative mass spectrometry-based proteomic analysis using Stable Isotope Labeling by Amino Acids in Cell …

Variability Of Particle Size Distributions In The Bohai Sea And The Yellow Sea, Zhongfeng Qui, Deyong Sun, Chuanmin Hu, Sengquiang Wang, Lufei Zheng, Yu Huang, Tian Peng

Marine Science Faculty Publications

Particle size distribution (PSD) is an important parameter that is relevant to many aspects of marine ecosystems, such as phytoplankton functional types, optical absorption and scattering from particulates, sediment fluxes, and carbon export. However, only a handful of studies have documented the PSD variability in different regions. Here, we investigate the PSD properties and variability in two shallow and semi-enclosed seas (the Bohai Sea (BS) and Yellow Sea (YS)), using in situ laser diffraction measurements (LISST-100X Type C) and other measurements at 79 stations in November 2013. The results show large variability in particle concentrations (in both volume and number …

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 …

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.

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 …

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 …