Life Sciences Commons^™

Optical Backscattering Measured By Airborne Lidar And Underwater Glider, James H. Churnside, Richard D. Marchbanks, Chad Lembke, Jordon Beckler

Marine Science Faculty Publications

The optical backscattering from particles in the ocean is an important quantity that has been measured by remote sensing techniques and in situ instruments. In this paper, we compare estimates of this quantity from airborne lidar with those from an in situ instrument on an underwater glider. Both of these technologies allow much denser sampling of backscatter profiles than traditional ship surveys. We found a moderate correlation (R = 0.28, p < 10⁻⁵), with differences that are partially explained by spatial and temporal sampling mismatches, variability in particle composition, and lidar retrieval errors. The data suggest that there are two …

Large-Scale Deposition Of Weathered Oil In The Gulf Of Mexico Following A Deep-Water Oil Spill, Isabel Romero, Gerardo Toro-Farmer, Arne R. Diercks, Patrick Schwing, Frank E. Muller-Karger, Steven Murawski, David Hollander

Marine Science Faculty Publications

The blowout of the Deepwater Horizon (DWH) drilling rig in 2010 released an unprecedented amount of oil at depth (1,500 m) into the Gulf of Mexico (GoM). Sedimentary geochemical data from an extensive area (∼194,000 km2) was used to characterize the amount, chemical signature, distribution, and extent of the DWH oil deposited on the seafloor in 2010–2011 from coastal to deep-sea areas in the GoM. The analysis of numerous hydrocarbon compounds (N = 158) and sediment cores (N = 2,613) suggests that, 1.9 ± 0.9 × 104 metric tons of hydrocarbons (>C9 saturated and aromatic fractions) were deposited in …

Justo Sierra Cruise Sample Data, Southern Gulf Of Mexico, 2015, Patrick Schwing

C-IMAGE data

This dataset includes CTD data from two cruises aboard the B/O Justo Sierra in 2015. Data are in ACSII and RAW format.

Mass-Spectrometry Based Proteomics Of Age-Related Changes In Murine Microglia, Antwoine Flowers

USF Tampa Graduate Theses and Dissertations

The last century has seen a steady increase in the extension of the average lifespan. This has concomitantly produced higher incidences of age-related chronic degenerative diseases like Alzheimer’s and Parkinson’s diseases. Age is the single greatest risk factor for the development of not just these degenerative conditions but cancer as well. The aged niche undergoes a number of maladaptive changes that allow underlying conditions to present and progress. Exactly which changes, contribute to the progression of which disease is currently an area of intense study. However, these answers often present therapeutic targets for disease prevention. Age is characterized by a …

Abundance And Habitat Preferences Of Introduced Muscovy Ducks (Cairina Moschata), Jacqueline Marie Perry Cahanin

USF Tampa Graduate Theses and Dissertations

Muscovy ducks are native only to Central and South America, Mexico, and parts of southern Texas and are considered invasive in some areas outside of their native range. Although they have been introduced worldwide, they remain largely unstudied. The primary focus of this study was to relate Muscovy duck abundance to habitat characteristics of wetlands in Tampa, Florida. Muscovy abundance was measured using point count methods at 21 wetland sites that occur within an eight km radius of the University of South Florida’s main campus. Habitat features at these sites were assessed using field methods and Geographic Information Systems (GIS) …

A Novel Approach To The Discovery Of Natural Products From Actinobacteria, Rahmy Tawfik

USF Tampa Graduate Theses and Dissertations

Actinobacteria, primarily the genus Streptomyces, have led to the development of a number of antibiotics, which result from their secondary metabolites or modified derivatives. Secondary metabolite production can result from competition with neighboring microbes in an effort to disrupt growth, aiding in the competition for vital nutrients in impoverished conditions. Such secondary metabolites have the potential to affect a plethora of cellular functions in target cells, including, cell wall development, protein synthesis, protein function and fatty acid synthesis/metabolism. Due to the pandemic spread of antibiotic resistant bacteria, it is imperative to continue the search for new therapeutic agents …

Analysis Of Antibody-Induced Plasmodium Falciparum Sporozoites Through Scanning Electron Microscopy, Sagorika Bera

USF Tampa Graduate Theses and Dissertations

Malaria is a devastating disease that continues to affect millions of people worldwide every year. Specifically, Plasmodium falciparum is the most common human malaria parasite, particularly in sub-Saharan Africa. P. falciparum causes the most malignant and debilitating symptoms with the highest mortality and complication rates. Even with the worldwide efforts of many researchers and organizations, the road to discovering a vaccine has been difficult and challenging. Due do to the improvements in in vitro liver stage assays as well as rodent models of mammalian malaria, pre-erythrocytic stages of malaria have become a more accessible target for experimental studies. These vaccine …

Tiered Vs. Traditional Daily Undulating Periodization For Improving Powerlifting Performance In Trained Males, Andres Vargas

USF Tampa Graduate Theses and Dissertations

Daily undulating periodization represents an increasingly popular trend in exercise science with which a traditional model has been established. Tiered daily undulating periodization pairs the DUP approach with a tiered training system which allows volume and intensity to be more evenly distributed throughout a given graining cycle. The concept of tiered daily undulating periodization is a novel form of periodization and has not been investigated. As such, a comparison of traditional and tiered daily undulating periodization has yet to be examined. Therefore, the purpose of this study was to compare the effects of traditional and tiered daily undulating periodization models …

Development Of Tools For Stable Transfection In The Human Filarial Parasite Brugia Malayi Via The Piggybac Transposon System, Johan Chabanon

USF Tampa Graduate Theses and Dissertations

Brugia malayi is one of three species of nematode known to cause lymphatic filariasis (LF) in humans. LF infects over 120 million people, causing debilitating disease. Various global programs have been launched in the past 20 years to eliminate LF. These programs have greatly scaled up the resources and efforts allocated to halting the transmission and reducing disease burden. Only a few drugs are used to treat LF, and resistance is thus a devastating possibility. Research aimed at identifying new drug targets could therefore prove essential in elimination of LF.

Genetic manipulation of B. malayi has been limited to transient …

Taxonomy, Ecology, And Behavior Of The Kleptoplastic Sea Slug Elysia Papillosa, William Alan Gowacki

USF Tampa Graduate Theses and Dissertations

Sacoglossan sea slugs are one of the best known examples of specialist herbivores in the marine environment and can be found strongly associated with their algal hosts and food sources. Perhaps the most intriguing characteristic of many sacoglossans is their ability to sequester functional chloroplasts from their algal food sources in a process called kleptoplasty. Despite this, there continues to be issues regarding taxonomic identification of species. In turn, the ecological characteristics of many of these slugs, such as algal host and food source preference, as well as their behavioral aspects, have received little attention. A prime example of these …

Playing-With The World: Toy Story's Aesthetics And Metaphysics Of Play, Jonathan Hendricks

USF Tampa Graduate Theses and Dissertations

Pixar’s Toy Story (John Lassiter, 1995) is not just a story about toys and the children that play with them, but a demonstration of how we interact with the world. This thesis looks at the way in which both main children, Andy and Sid, interact with their toys and how this interaction is one that is structured by way of what Martin Heidegger calls “Enframing.” In this modality of playing, toys and other things and entities in the world, and the world itself, appear to the children as on-hand resources for use at any time and can be molded, as …

A Novel Abi-Domain Protein Controls Virulence Determinant Production In Staphylococcus Aureus, Stephanie Michelle Marroquin

USF Tampa Graduate Theses and Dissertations

A major factor in the success of Staphylococcus aureus as a pathogen is its vast arsenal of virulence determinants and, more importantly, the tight and precisely- timed regulation of these factors. Here we investigate the product of the S. aureus gene, SAUSA300_1984, encoding a putative transmembrane protein. This as yet uncharacterized protein belongs to the Abi (abortive infection) family, which are commonly annotated as CAAX-proteases, and are significantly understudied in prokaryotes. In S. aureus the disruption of SAUSA300_1984 results in a drastic reduction of proteolytic and hemolytic activity, as well as diminished pigmentation. This phenotype appears to be mediated through …

Zonation Pattern And Spatial Arrangement Of A Geukensia Granosissima Population In A Mixed Mangrove Forest Of Tampa Bay, Derrick Shane Hudson

USF Tampa Graduate Theses and Dissertations

Here I provide the first report on Geukensia granosissima patterns of abundance along a tidal gradient within a mixed mangrove stand located in Tampa Bay, Florida, USA. Specifically, I examined 1) the relationship between G. granosissima size and density with mangrove root type (e.g. prop root, pneumatophore), and of density within the intertidal zones; and 2) the possible role of predation in shaping the lower zonation patterns displayed. Transect surveys located along the lower and upper population limit boundaries were conducted every two months over a ten-month period. Variables measured include size distribution, density of mussels, above ground mangrove prop …

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 …

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.

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.

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 …

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 …

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.

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.

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, …