Digital Commons Network^™

Consistency Of Structural Color Across Molts: The Effects Of Environmental Conditions And Stress On Feather Ultraviolet Reflectance, Rebecca Lynn Windsor

USF Tampa Graduate Theses and Dissertations

Across avian systems, plumage ornamentation is often considered a signal of individual fitness, condition, sex, or status, and varies due to genetics or environmental sources. In species with structural coloration, plumage variation results from differences in the amount of energy allocated to feather growth during molt, presenting a unique opportunity to study the link between individual quality and ornamentation. In cooperative breeding species, such as the Florida Scrub-Jay (Aphelocoma coerulescens), the role of structural color as a signal is particularly important because helpers may delay breeding for one to several years and competition for space is high. Florida Scrub-Jay juveniles …

Linkage Mapping And Comparative Genomics Of Red Drum (Sciaenops Ocellatus) Using Next-Generation Sequencing, Christopher M. Hollenbeck, David S. Portnoy, Dana Wetzel, Tracy A. Sherwood, Paul B. Samollow, John R. Gold

C-IMAGE Publications

Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere. We used a prior microsatellite-based linkage map as a framework and incorporated 1794 haplotyped contigs derived from high-throughput, reduced representation DNA sequencing to produce a linkage map containing 1794 haplotyped restriction-site associated DNA (RAD) contigs, 437 anonymous microsatellites, …

Oil Extraction Visible Infrared Imaging Radiometer Suite (Viirs) Imagery, Western Gulf Of Mexico 2005-2013, Mengqiu Wang

C-IMAGE data

This dataset includes MODIS and VIIRS imagery used in the paper "Extracting Oil Slick Features From VIIRS Nighttime Imagery Using a Gaussian Filter and Morphological Constraints" (DOI: 10.1109/LGRS.2015.2444871). For accuracy assessment, the ROI file used as oil slick ground truth, feature extraction results, the VIIRS nighttime imagery used in the test and the final accuracy assessment statistics are also included.

Land Use, Stream Stability, And Benthic Invertebrates In A Dry Forest Watershed Of Western Costa Rica, Jacqueline Ann Demko

USF Tampa Graduate Theses and Dissertations

There is a paucity of data on dry forests, the most threatened biome in the tropics. The Nandamojo is a tropical dry forest watershed in Western Costa Rica that has been impacted by varying degrees of human induced modifications. This research was conducted to examine the influence of land use and channel characteristics on invertebrate communities within a sub basin of the Nandamojo watershed. This study addressed three hypotheses: (1) sites with low tree cover and small riparian buffer zones will have high erosion, (2) macroinvertebrate abundance will be lower at sites with low channel stability values, and (3) benthic …

Subterranean Systems Provide A Suitable Overwintering Habitat For Salamandra Salamandra, Monika Balogová, Dušan Jelić, Michaela Kyselová, Marcel Uhrin

International Journal of Speleology

The fire salamander (Salamandra salamandra) has been repeatedly noted to occur in natural and artificial subterranean systems. Despite the obvious connection of this species with underground shelters, their level of dependence and importance to the species is still not fully understood. In this study, we carried out long-term monitoring based on the capture-mark-recapture method in two wintering populations aggregated in extensive underground habitats. Using the POPAN model we found the population size in a natural shelter to be more than twice that of an artificial underground shelter. Survival and recapture probabilities calculated using the Cormack-Jolly-Seber model were very …

Ixtoc-I Oil Spill Footprints Derived From Coastal Zone Color Scanner And Landsat/Mss Imagery, Shaojie Sun

C-IMAGE data

This dataset contains Coastal Zone Color Scanner (CZCS) and Landsat/MSS images used to identify the surface oil footprints created by the Ixtoc-I oil spill in 1979. There are two periods of imagery: June 1979-March 1980 is the oil spill period; and Jan. 1981-Dec. 1982 is the reference period. Oil slick surface footprints derived from the images are also included in the dataset. They are either in the format of shapefile or ArcGIS personal geodatabase.

Weatherbird Ii Sediment Cruise Sample Data (2016), Patrick Schwing, Steven Murawski

C-IMAGE data

This dataset includes the locations and allotments of multicore sediment samples, water sample locations, and CTD data from cruises aboard the R/V Weatherbird II from 2016.

Krillbase: A Circumpolar Database Of Antarctic Krill And Salp Numerical Densities, 1926–2016, Angus Atkinson, Siemon L. Hill, Evgeny A. Pakhomov, Volker Siegel, Ricardo Anadon, Sanae Chiba, Kendra L. Daly, Rod Downie, Sophie Fielding

Marine Science Faculty Publications

Antarctic krill (Euphausia superba) and salps are major macroplankton contributors to Southern Ocean food webs and krill are also fished commercially. Managing this fishery sustainably, against a backdrop of rapid regional climate change, requires information on distribution and time trends. Many data on the abundance of both taxa have been obtained from net sampling surveys since 1926, but much of this is stored in national archives, sometimes only in notebooks. In order to make these important data accessible we have collated available abundance data (numerical density, no. m⁻² ) of postlarval E. superba and salp individual (multiple …

The Experimental Flow To The Colorado River Delta: Effects On Carbon Mobilization In A Dry Watercourse, Thomas S. Bianchi, David Butman, Peter A. Raymond, Nicholas D. Ward, Rory J. Kates, Karl W. Flessa, Hector Zamora, Ana Arellano, Jorge Ramirez, Eliana Rodriguez

Marine Science Faculty Publications

Here we report on the effects of an experimental flood on the carbon cycling dynamics in the dry watercourse of the Colorado River in Mexico. We observed post-flood differences in the degree of decay, age, and concentration of dissolved organic carbon (DOC), as well as dissolved CH₄ and CO₂ concentrations throughout the study site. Our results indicate that this flooded waterway was a limited source of CH₄ and CO₂ to the atmosphere during the event and that DOC age increased with time of flooding. Based on our findings, we suggest that the interplay between storage and …

Moderate Resolution Imaging Spectroradiometer (Modis) Surface Oil Products For The Gulf Of Mexico, April - July 2010, Chuanmin Hu, Lian Feng

C-IMAGE data

This dataset contains the MODIS surface oil products (with thickness of >0 but 8um as thick) for all the golden days between April and July of 2010.

Deepwater Horizon Incident Oil Slick Morphology Determined From United States Geological Survey Oil Volume Product, May 17 2010, Shaojie Sun

C-IMAGE data

This dataset includes original oil volume product download from USGS, post processing file to remove noise and then classified to different oil thickness class file. All the afterward analysis and statistics are based on the classified oil thickness class file. Ascii files of oil slicks' area and length.

Weatherbird Ii Sediment Cruise Sample Data 2015, Patrick Schwing

C-IMAGE data

This dataset includes the locations and allotments of multicore sediment samples, water sample locations, and CTD data from cruises aboard the R/V Weatherbird II from 2015.

Bioaccumulation Of Metallic Trace Elements And Antioxidant Enzyme Activities In Apfelbeckia Insculpta (L. Koch, 1867) (Diplopoda: Callipodida) From The Cave Hadži-Prodanova Pećina (Serbia), Jelena Vranković, Slavica Borković-Mitić, Bojan Ilić, Milanka Radulović, Slaviša Milošević, Slobodan Makarov, Bojan Mitić

International Journal of Speleology

The concentration of 10 metallic trace elements or MTE (Cu, Fe, Zn, Mn, As, Hg, Pb, Cd, Ni, and Cr) was measured in specimens of the troglophilic millipede Apfelbeckia insculpta (L. Koch, 1867) and sediment of the cave Hadži-Prodanova Pećina in western Serbia. Some MTE, like Fe and Mn, displayed much higher concentrations compared to other elements, both in the sediment and in the body of A. insculpta. On the other hand, estimation of the bioaccumulation factor (BAF) in both males and females of A. insculpta showed values greater than 1 for xenobiotic elements compared to those that are essential. …

Bat Urea-Derived Minerals In Arid Environment. First Identification Of Allantoin, C4H6N4O3, In Kahf Kharrat Najem Cave, United Arab Emirates, Philippe Audra, Pavel Bosák, Fernando Gázquez, Didier Cailhol, Roman Skála, Lenka Lisá, Šárka Jonášová, Amos Frumkin, Martin Knez, Tadej Slabe, Nadja Zupan Hajna, Asma Al-Farraj

International Journal of Speleology

Kahf Kharrat Najem Cave is a small cave in United Arab Emirates (UAE) that hosts a bat colony which is the source of guano deposits and peculiar centimeter-long yellowish stalactites. The mineralogy and geochemistry of these deposits were analyzed using powder X-ray diffraction (XRD), energy dispersive X-ray spectroscopic microanalysis (EDX), scanning electron microscope (SEM), and stable isotope composition (δ¹³C and δ¹⁵N). Urea CO(NH₂)₂ was found to be the main compound of these stalactites, while allantoin C₄H₆N₄O₃ was found to be an accessory urea byproduct. This paper …

Diversity And Biocide Susceptibility Of Fungal Assemblages Dwelling In The Art Gallery Of Magura Cave, Bulgaria, Milena M. Mitova, Mihail Iliev, Alena Nováková, Anna A. Gorbushina, Veneta I. Groudeva, Pedro M. Martin-Sanchez

International Journal of Speleology

Magura Cave, north-western Bulgaria, possesses valuable rock-art paintings made with bat guano and dated from the period between the Eneolithic and Bronze Ages. Since 2008, the Art Gallery is closed to the general public in order to protect the paintings from vandalism, microclimatic changes caused by visitors and artificial illumination, and the consequent growth of fungi and phototrophs. Nevertheless, some tourist visits are allowed under the supervision of cave managers. This study provides the first scientific report on cultivable fungal assemblages dwelling different substrata in the Art Gallery. A total of 78 strains, belonging to 37 OTUs (Ascomycota 81%, Zygomycota …

Dataset For: Sun Glint Requirement For The Remote Detection Of Surface Oil Films, Mengqiu Wang

C-IMAGE data

This dataset includes selected points and their sun glint strength values of image pairs which were used in determining the sun glint threshold required for remotely sensing oil films in the northern Gulf of Mexico. The satellite imagery used in the analyses were collected by Moderate Resolution Imaging Spectroradiometer (MODIS) Terra (MODIST), MODIS Aqua (MODISA), and Visible Infrared Imaging Radiometer Suite (VIIRS) instruments. The dataset includes original raw file lists of the imagery used and information about how they can accessed can be found in the Supplemental Information section of the metadata. Post processing MODIS Rayleigh corrected reflectance (Rrc) data, …

Mechanisms Of Ikbke Activation In Cancer, Sridevi Challa

USF Tampa Graduate Theses and Dissertations

Cancer is the second leading cause of death in the USA and it is expected to surpass heart diseases making it important to understand the underlying mechanisms of cancer. The efforts to target single signaling molecule showed little success in increasing the patient survival and it can be due to increased compensation for cell survival by alternative pathway activations. Hence comprehensive understanding of the alternative signaling pathways may help us treat cancer better. Chronic inflammation is attributed to increased risk of cancer and emerging studies show the growing importance of both canonical and non-canonical IκB kinases such as IKKα, IKKβ, …

Changing The Pathobiological Paradigm In Myelodysplastic Syndromes: The Nlrp3 Inflammasome Drives The Mds Phenotype, Ashley Basiorka

USF Tampa Graduate Theses and Dissertations

Note: Portions of this abstract have been previously published in the journal Blood, Basiorka et al. Blood. 2016 Oct 13, and has been reproduced in this manuscript with permission from the publisher.

Myelodysplastic syndromes (MDS) are genetically diverse hematopoietic stem cell malignancies that share a common phenotype of cytological dysplasia, ineffective hematopoiesis and aberrant myeloid lineage maturation. Apoptotic cell death potentiated by inflammatory cytokines has been considered a fundamental feature of MDS for over two decades. However, this non-inflammatory form of cell death cannot account for the inflammatory nature of these disorders. We report that a hallmark of lower-risk …

How Random Noise And A Graphical Convention Subverted Behavioral Scientists' Explanations Of Self-Assessment Data: Numeracy Underlies Better Alternatives, Edward Nuhfer, Steven Fleisher, Christopher Cogan, Karl Wirth, Eric Gaze

Numeracy

Despite nearly two decades of research, researchers have not resolved whether people generally perceive their skills accurately or inaccurately. In this paper, we trace this lack of resolution to numeracy, specifically to the frequently overlooked complications that arise from the noisy data produced by the paired measures that researchers employ to determine self-assessment accuracy. To illustrate the complications and ways to resolve them, we employ a large dataset (N = 1154) obtained from paired measures of documented reliability to study self-assessed proficiency in science literacy. We collected demographic information that allowed both criterion-referenced and normative-based analyses of self-assessment data. …

Genetic And Epigenetic Variation In Spartina Alterniflora Following The Deepwater Horizon Oil Spill, Marta Robertson, Aaron Schrey, Ashley Shayter, Christina J. Moss, Christina Richards

Integrative Biology Faculty and Staff Publications

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation …

Suitability Of Laurentian Great Lakes For Invasive Species Based On Global Species Distribution Models And Local Habitat, Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng, John M. Drake

Integrative Biology Faculty and Staff Publications

Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model assumptions of data stationarity. Second, predicting potential range of freshwater aquatic species is complicated by the reliance on terrestrial climate measurements to develop occurrence relationships …

Microbe Biogeography Tracks Water Masses In A Dynamic Oceanic Frontal System, Anni Djurhuus, Philipp H. Boersch-Supan, Svein-Ole Mikalse, Alex D. Rogers

Integrative Biology Faculty and Staff Publications

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living …

Permafrost Organic Carbon Mobilization From The Watershed To The Colville River Delta: Evidence From 14C Ramped Pyrolysis And Lignin Biomarkers, Xiaowen Zhang, Thomas S. Bianchi, Xingqian Cui, Brad E. Rosenheim, Chien-Lu Ping, Andrea J. M. Hanna, Mikhail Kanevskiy, Kathryn M. Schreiner, Mead A. Allison

Marine Science Faculty Publications

The deposition of terrestrial-derived permafrost particulate organic carbon (POC) has been recorded in major Arctic river deltas. However, associated transport pathways of permafrost POC from the watershed to the coast have not been well constrained. Here we utilized a combination of ramped pyrolysis-oxidation radiocarbon analysis (RPO ¹⁴C) along with lignin biomarkers, to track the linkages between soils and river and delta sediments. Surface and deep soils showed distinct RPO thermographs which may be related to degradation and organo-mineral interaction. Soil material in the bed load of the river channel was mostly derived from deep old permafrost. Both surface and …

Biogeochemical Sensor Performance In The Soccom Profiling Float Array, Kenneth S. Johnson, Joshua N. Plant, Luke J. Coletti, Hans W. Jannasch, Carole M. Sakamoto, Stephen C. Riser, Dana D. Swift, Nancy L. Williams, Emmanuel Boss, Nils Haëntjens, Lynne D. Talley, Jorge L. Sarmiento

Marine Science Faculty Publications

The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) program has begun deploying a large array of biogeochemical sensors on profiling floats in the Southern Ocean. As of February 2016, 86 floats have been deployed. Here the focus is on 56 floats with quality-controlled and adjusted data that have been in the water at least 6 months. The floats carry oxygen, nitrate, pH, chlorophyll fluorescence, and optical backscatter sensors. The raw data generated by these sensors can suffer from inaccurate initial calibrations and from sensor drift over time. Procedures to correct the data are defined. The initial accuracy of …

Local And Regional Stressors Interact To Drive A Salinization-Induced Outbreak Of Predators On Oyster Reefs, David L. Kimbro, J. Wilson White, Hanna Tillotson, Nikkie Cox, Megan Christopher, Owen Stokes-Cawley, Samantha Yuan, Timothy J. Pusack, Christopher D. Stallings

Marine Science Faculty Publications

Predator outbreaks are predicted to increasingly decimate economically and ecologically important prey populations because global climate change and food-web modifications frequently facilitate predators and stress prey. Natural systems are organized hierarchically, with processes operating at multiple scales giving rise to patterns of biodiversity, so predicting and managing outbreaks requires a framework that accounts for the effects of both local and regional stressors. Here, we used the comparative experimental approach to investigate whether the collapse of a nationally important oyster fishery in the Gulf of Mexico (Apalachicola Bay, Florida) could have been (1) caused proximally by a predator outbreak and (2) …

A Family Of Genus-Specific Rnas In Tandem With Dna-Binding Proteins Control Expression Of The Bada Major Virulence Factor Gene In Bartonella Henselae, Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson

Molecular Biosciences Faculty Publications

Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each …

Cloud And Sun-Glint Statistics Derived From Goes And Modis Observations Over The Intra-Americas Sea For Geo-Cape Mission Planning, Lian Feng, Chuanmin Hu, Brian B. Barnes, Antonio Mannino, Andrew K. Heidinger, Kathleen Strabala, Laura T. Iraci

Marine Science Faculty Publications

Knowledge of cloud cover, frequency, and duration is not only important to study cloud dynamics, but also critical in determining when and where to take ocean measurements from geostationary orbits such as the Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission due to the challenges in achieving complete hemispheric coverage of coastal oceans, estuaries, and inland waters at hourly frequency. Using GOES hourly measurements at 4 km nadir resolution between 2006 and 2011, the number of cloud-free hourly observations per day (N_cf) for solar zenith angle θ_o < 80° was estimated for each 0.1° location of the Intra-Americas Sea. The number of Sun-glint-affected hourly observations per day (N_sg) was also calculated based on the …

Limited Grounding-Line Advance Onto The West Antarctic Continental Shelf In The Easternmost Amundsen Sea Embayment During The Last Glacial Period, Johann P. Klages, Gerhard Kuhn, Claus-Dieter Hillenbrand, James A. Smith, Alastair G. C. Graham, Frank O. Nitsche, Thomas Frederichs, Patrycja E. Jernas, Karsten Gohl, Lukas Wacker

Marine Science Faculty Publications

Precise knowledge about the extent of the West Antarctic Ice Sheet (WAIS) at the Last Glacial Maximum (LGM; c. 26.5–19 cal. ka BP) is important in order to 1) improve paleo-ice sheet reconstructions, 2) provide a robust empirical framework for calibrating paleo-ice sheet models, and 3) locate potential shelf refugia for Antarctic benthos during the last glacial period. However, reliable reconstructions are still lacking for many WAIS sectors, particularly for key areas on the outer continental shelf, where the LGM-ice sheet is assumed to have terminated. In many areas of the outer continental shelf around Antarctica, direct geological data for …

Major Advance Of South Georgia Glaciers During The Antarctic Cold Reversal Following Extensive Sub-Antarctic Glaciation, Alastair G. C. Graham, Gerhard Kuhn, Ove Meisel, Claus-Dieter Hillenbrand, Dominic A. Hodgson, Werner Ehrmann, Lukas Wacker, Paul Wintersteller, Santos Ferreira, Dos Santos Ferreira, Miriam Römer, Duanne White, Gerhard Bohrmann

Marine Science Faculty Publications

The history of glaciations on Southern Hemisphere sub-polar islands is unclear. Debate surrounds the extent and timing of the last glacial advance and termination on sub-Antarctic South Georgia in particular. Here, using sea-floor geophysical data and marine sediment cores, we resolve the record of glaciation offshore of South Georgia through the transition from the Last Glacial Maximum to Holocene. We show a sea-bed landform imprint of a shelf-wide last glacial advance and progressive deglaciation. Renewed glacier resurgence in the fjords between c. 15,170 and 13,340 yr ago coincided with a period of cooler, wetter climate known as the Antarctic Cold …

Importance Of Lateral Flux And Its Percolation Depth On Organic Carbon Export In Arctic Tundra Soil: Implications From A Soil Leaching Experiment, Xiaowen Zhang, Jack A. Hutchings, Thomas S. Bianchi, Yina Liu, Ana Arellano, Edward A. Schuur

Marine Science Faculty Publications

Temperature rise in the Arctic is causing deepening of active layers and resulting in the mobilization of deep permafrost dissolved organic matter (DOM). However, the mechanisms of DOM mobilization from Arctic soils, especially upper soil horizons which are drained most frequently through a year, are poorly understood. Here we conducted a short-term leaching experiment on surface and deep organic active layer soils, from the Yukon River basin, to examine the effects of DOM transport on bulk and molecular characteristics. Our data showed a net release of DOM from surface soils equal to an average of 5% of soil carbon. Conversely, …