Life Sciences Commons^™

Strategic Assessment Of Fisheries Independent Monitoring Programs In The Gulf Of Mexico, Paul Mark Suprenand, Michael Drexler, David L. Jones, Cameron H. Ainsworth

Marine Science Faculty Publications

This study evaluates information produced from 14 fisheries independent monitoring programs (FIM) in the Gulf of Mexico. We consider the uniqueness of information from each program and its usefulness in estimating fisheries management indices. Biomass values of 35 functional groups are extracted from an operating model (Ecospace) in such a way as to replicate the patterns of historic FIM samplings. Observation error is added to these data in order to create a set of pseudo data that replicates the type and quality of information obtained from FIM programs. The pseudo data then are put into a separate fishery assessment model …

Things Fall Apart? The Political Ecology Of Forest Governance In Southern Nigeria, Prakash Kashwan

Journal of Ecological Anthropology

No abstract provided.

A Decline In Benthic Foraminifera Following The Deepwater Horizon Event In The Northeastern Gulf Of Mexico, Patrick Schwing, Isabel Romero, Gregg R. Brooks, David Hastings, Rebekka A. Larson, David Hollander

C-IMAGE Publications

Sediment cores were collected from three sites (1000–1200 m water depth) in the northeastern Gulf of Mexico from December 2010 to June 2011 to assess changes in benthic foraminiferal density related to the Deepwater Horizon (DWH) event (April-July 2010, 1500 m water depth). Short-lived radioisotope geochronologies (²¹⁰Pb, ²³⁴Th), organic geochemical assessments, and redox metal concentrations were determined to relate changes in sediment accumulation rate, contamination, and redox conditions with benthic foraminiferal density. Cores collected in December 2010 indicated a decline in density (80–93%). This decline was characterized by a decrease in benthic foraminiferal density and benthic foraminiferal …

Terrestrial Lidar-Based Automated Counting Of Swiftlet Nests In The Caves Of Gomantong, Sabah, Borneo., Donald A. Mcfarlane, Warren Roberts, Manfred Buchroithner, Guy Van Rentergem, Joyce Lundberg, Stefan Hautz

International Journal of Speleology

High resolution terrestrial laser scanning (TLS) within the Simud Hitam cave, Gomantong, has proven successful at discriminating the nests of black-nest swiftlets from roosting bats in high, inaccessible locations. TLS data was imported into ArcGIS software, allowing for semi-automated counting of nests. Spatial analysis of nest locations has established a maximum packing density of 268 nests/m² in optimum locations, which correspond to roof slopes of >20 degrees. Rhinolophid bats roost adjacent to, but not within nest locations, preferring roof surfaces close to horizontal.

Ocean Currents Generate Large Footprints In Marine Palaeoclimate Proxies, Erik Van Sebille, Paolo Scussolini, Jonathan V. Durgadoo, Frank J. C. Peeters, Arne Biastoch, Wilbert Weijer, Chris Turney, Claire B. Paris, Rainer Zahn

C-IMAGE Publications

Fossils of marine microorganisms such as planktic foraminifera are among the cornerstones of palaeoclimatological studies. It is often assumed that the proxies derived from their shells represent ocean conditions above the location where they were deposited. Planktic foraminifera, however, are carried by ocean currents and, depending on the life traits of the species, potentially incorporate distant ocean conditions. Here we use high-resolution ocean models to assess the footprint of planktic foraminifera and validate our method with proxy analyses from two locations. Results show that foraminifera, and thus recorded palaeoclimatic conditions, may originate from areas up to several thousands of kilometres …

A Decline In Benthic Foraminifera Following The Deepwater Horizon Event In The Northeastern Gulf Of Mexico, Patrick Schwing, Isabel C. Romero, Gregg R Brooks, David W Hastings, Rebekka A Larson, David Hollander

Marine Science Faculty Publications

Sediment cores were collected from three sites (1000-1200 m water depth) in the northeastern Gulf of Mexico from December 2010 to June 2011 to assess changes in benthic foraminiferal density related to the Deepwater Horizon (DWH) event (April-July 2010, 1500 m water depth). Short-lived radioisotope geochronologies (²¹⁰Pb, ²³⁴Th), organic geochemical assessments, and redox metal concentrations were determined to relate changes in sediment accumulation rate, contamination, and redox conditions with benthic foraminiferal density. Cores collected in December 2010 indicated a decline in density (80-93%). This decline was characterized by a decrease in benthic foraminiferal density and benthic foraminiferal accumulation rate (BFAR) …

Observations Of Hysteresis In The Annual Exchange Circulation Of A Large Microtidal Estuary, Steven D. Meyers, Monica Wilson, Mark E. Luther

Marine Science Faculty Publications

A nonlinear relation between the salinity field and the subtidal exchange circulation in the Tampa Bay estuary is demonstrated using observational data from 1999 to 2011. The data are averaged to form mean monthly climatological values of total freshwater discharge ( ), axial and vertical salinity gradients, and subtidal vertical shear. Well‐known steady state solutions indicate that the exchange circulation is linearly proportional to the horizontal salinity gradient, assuming a constant vertical eddy viscosity ( ). The exchange flow is found to be multivalued with respect to the horizontal salinity gradient, forming a hysteresis loop in parameter space that passes …

Promoting Genome Stability Via Multiple Dna Repair Pathways, Scott Cukras

USF Tampa Graduate Theses and Dissertations

Maintaining genome integrity is indispensible for cells to prevent and limit accruement of deleterious mutations and to promote viable cell growth and proliferation. Cells possess a myriad of mechanisms to detect, prevent and repair incurred cellular damage. Here we discuss various proteins and their accompanying cellular pathways that promote genome stability. We first investigate the NEDD8 protein and its role in promoting homologous recombination repair via multiple Cullin E3 ubiquitin ligases. We provide specific mechanisms through which, UBE2M, an E2 conjugating enzyme, neddylates various Cullin ligases to render them catalytically active to degrade their substrates by the proteasome. We show …

Cyanobacteria, Algae And Microfungi Present In Biofilm From Božana Cave (Serbia), Slađana Popović, Gordana Subakov Simić, Miloš Stupar, Nikola Unković, Dragana Predojević, Jelena Jovanović, Milica Ljaljević Grbić

International Journal of Speleology

Phototrophic microorganisms (cyanobacteria and algae) and microfungi, were identified from biofilm on the walls of the entrance of BožanaCavein west Serbia. Temperature, relative humidity and light intensity were measured, and chlorophyll a content determined. Light intensity differed from the entrance inwards. However, Chl a content was not proportional to light intensity, instead it was positively correlated to biofilm weight. Biofilm samples from two sites were also observed using a scanning electron microscope. Coccoid forms of cyanobacteria were abundant at the sampling site with the lowest light intensity, while members of the order Nostocales were predominant at the sampling site with …

The Association Of Cognitive Endophenotypes And Risky Single Nucleotide Polymorphisms Of Alzheimer's Disease Within The Alzheimer's Disease Neuroimaging Initiative (Adni) Database, Kyle Joseph Jennette

USF Tampa Graduate Theses and Dissertations

Objective: The purpose of this study was to assess the influence of three single nucleotide polymorphisms (SNP) previously associated with Alzheimer's disease on specific domains of cognition, when controlling for Apolipoprotein E gene (APOE), in a sample of individuals with Alzheimer's disease. Methods: The data were drawn from the Alzheimer's Disease Neuroimaging Initiative database, a comprehensive, longitudinal database of controls, persons with mild cognitive impairment, and persons with mild Alzheimer's disease. Each subject has a full neuropsychological assessment, neuroimaging, genetic sequencing, and physical evaluation. For the purposes of this study, individuals were selected based on the presence of the three …

A Functional Chlorophyll Biosynthesis Pathway Identified In The Kleptoplastic Sea Slug, Elysia Chlorotica, Julie A. Schwartz

USF Tampa Graduate Theses and Dissertations

The sacoglossan sea slug, Elysia chlorotica, feeds upon and sequesters plastids from the heterokont alga, Vaucheria litorea, and maintains the metabolically active organelles for up to nine months under starvation conditions while utilizing the photosynthate to survive and reproduce. The photosynthetic pigment, chlorophyll a (Chla), is found in all oxygenic photosynthetic organisms and is responsible for capturing photons of light and converting them into chemical energy. Chlorophyll and its associated proteins involved in the light capturing process are subject to photo oxidative damage and must be continually replaced for ongoing photosynthesis to continue; however, genes encoding these proteins are present …

Utilizing Systems Level Approaches To Identify Key Mechanisms Of Drug Resistance In Braf Mutated Melanoma, Kim H.T. Paraiso

USF Tampa Graduate Theses and Dissertations

In the last four years, seven new drugs have been FDA approved for the treatment of late stage melanoma, for the field of melanoma, this marks an incredibly exciting. Three of these new therapies, vemurafenib, dabrafenib and trametinib are small molecule kinase inhibitors that target the MAPK pathway and as such have been approved for the treatment of BRAFV600 mutant melanomas. Yet despite recent advances, mechanisms of intrinsic and acquired BRAF inhibitor resistance continue to undermine uniform and long-lasting therapeutic responses. Several studies have shown that the reactivation of MAPK signaling is a critical event leading to BRAF inhibitor resistance. …

Gamma-Aapeptides As A New Class Of Peptidomimetics: Synthesis, Structures, And Functions, Haifan Wu

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic oligomers that resemble the activities of peptides. Their advantages over peptides include high stability towards proteolysis and enormous chemical diversity. Over the past two decades, there have been extensive efforts to develop peptide mimics, such as beta-peptides, peptoids, D-peptides, etc. The research on peptidomimetics have led to many important applications in both medicinal and material science. In order to explore new functions, the discovery of peptidomimetics with novel frameworks is essential. We reported the synthesis and evaluation of a new class of peptidomimetics, termed as gamma-AApeptides. Previous studies of gamma-AApeptides have revealed that gamma-AApeptides are highly resistant …

Presentations And Posters From The 2015 Research That Matters Sustainable Food Conference: People, Policy, & Practice, Various Authors

Food and Gardening Working Group

The University of South Florida Sustainable Food Conference: People, Policy, & Practice brought together food researchers from USF and the larger Tampa Bay community to share ideas and findings that will pave the path toward more sustainable and resilient communities. It featured research papers and presentations from all disciplines and methodologies addressing issues concerning food production, distribution, retail, and/or consumption.

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

USF Tampa Graduate Theses and Dissertations

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

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

And On Top Of All That… Coping With Ocean Acidification In The Midst Of Many Stressors, Denise L. Breitburg, Joseph Salisbury, Joan M. Bernhard, Wei-Jun Cai, Sam Dupont, Scott C. Doney, Kristy J. Kroeker, Lisa A. Levin, W. Christopher Long, Lisa M. Milke, Seth H. Miller, Beth Phelan, Uta Passow, Brad A. Seibel, Anne E. Todgham, Ann M. Tarrant

Marine Science Faculty Publications

Oceanic and coastal waters are acidifying due to processes dominated in the open ocean by increasing atmospheric CO2 and dominated in estuaries and some coastal waters by nutrient-fueled respiration. The patterns and severity of acidification, as well as its effects, are modified by the host of stressors related to human activities that also influence these habitats. Temperature, deoxygenation, and changes in food webs are particularly important co-stressors because they are pervasive, and both their causes and effects are often mechanistically linked to acidification. Development of a theoretical underpinning to multiple stressor research that considers physiological, ecological, and evolutionary perspectives is …

Quantifying The Resolution Level Where The Grace Satellites Can Separate Greenland's Glacial Mass Balance From Surface Mass Balance, J. A. Bonin, D. P. Chambers

Marine Science Faculty Publications

Mass change over Greenland can be caused by either changes in the glacial dynamic mass balance (DMB) or the surface mass balance (SMB). The GRACE satellite gravity mission cannot directly separate the two physical causes because it measures the sum of the entire mass column with limited spatial resolution. We demonstrate one theoretical way to indirectly separate cumulative SMB from DMB with GRACE, using a least squares inversion technique with knowledge of the location of the glaciers. However, we find that the limited 60 × 60 spherical harmonic representation of current GRACE data does not provide sufficient resolution to adequately …

Evaluation Of Empirical Mode Decomposition For Quantifying Multi-Decadal Variations And Acceleration In Sea Level Records, D. P. Chambers

Marine Science Faculty Publications

The ability of empirical mode decomposition (EMD) to extract multi-decadal variability from sea level records is tested using three simulations: one based on a series of purely sinusoidal modes, one based on scaled climate indices of El Niño and the Pacific decadal oscillation (PDO), and the final one including a single month with an extreme sea level event. All simulations include random noise of similar variance to high-frequency variability in the San Francisco tide gauge record. The intrinsic mode functions (IMFs) computed using EMD were compared to the prescribed oscillations. In all cases, the longest-period modes are significantly distorted, with …

Review Of Wave-Turbulence Interactions In The Stable Atmospheric Boundary Layer, Jielun Sun, Carmen J. Nappo, Larry Mahrt, Danijel Belušić, Branko Grisogono, David R. Stauffer, Manuel Pulido, Chantal Staquet, Qingfang Jiang, Annick Pouquet, Carlos Yagüe, Boris Galperin, Ronald B. Smith, John J. Finnigan, Shane D. Mayor, Gunilla Svensson, Andrey A. Grachev, William D. Neff

Marine Science Faculty Publications

Flow in a stably stratified environment is characterized by anisotropic and intermittent turbulence and wavelike motions of varying amplitudes and periods. Understanding turbulence intermittency and wave-turbulence interactions in a stably stratified flow remains a challenging issue in geosciences including planetary atmospheres and oceans. The stable atmospheric boundary layer (SABL) commonly occurs when the ground surface is cooled by longwave radiation emission such as at night over land surfaces, or even daytime over snow and ice surfaces, and when warm air is advected over cold surfaces. Intermittent turbulence intensification in the SABL impacts human activities and weather variability, yet it cannot …

Subannual Variability Of Total Alkalinity Distributions In The Northeastern Gulf Of Mexico, Bo Yang, Robert H. Byrne, Rik Wanninkhof

Marine Science Faculty Publications

The subannual variability of total alkalinity (TA) distributions in the northeastern Gulf of Mexico was examined through the use of TA data from ship-based water sampling, historical records of riverine TA, and contemporaneous model output of surface currents and salinity. TA variability was restricted to the upper 150 m of the water column, where relationships between salinity and TA were controlled primarily by subannual variations in the extent of mixing between seawater and river water. A transition in TA distribution patterns between the river-dominated northern margin (near the Mississippi-Atchafalaya River System) and the ocean current-dominated eastern margin (West Florida Shelf) …

Solutions For Recovering And Sustaining The Bounty Of The Ocean: Combining Fishery Reforms, Rights-Based Fisheries Management, And Marine Reserves, Allison K. Barner, Jane Lubchenco, Christopher Costello, Steven D. Gaines, Amanda Leland, Brett Jenks, Steven Murawski, Eric Schwaab, Margaret Spring

Marine Science Faculty Publications

This manuscript is based on a keynote lecture given by Jane Lubchenco at One Planet, One Ocean: The 2nd International Ocean Research Conference, Barcelona, Spain, November 17–21, 2014.

Food security, economic opportunities, and other benefits provided by a healthy ocean are in jeopardy because of years of overexploitation of many fisheries, and the challenges will intensify in many locales as climate and the environment continue to change. The good news is that solutions are gaining traction. Mandates to end overfishing that use scientifically determined catch limits and rights-based approaches to fishery management have produced impressive results in ending overfishing and …

Non-Lethal Approach Identifies Variability Of Δ15N Values In The Fin Rays Of Atlantic Goliath Grouper, Epinephelus Itajara, Orian E. Tzadik, Ethan A. Goddard, David J. Hollander, Christopher C. Koenig, Christopher D. Stallings

Marine Science Faculty Publications

The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ¹⁵N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, …

Paleoreconstruction Of Organic Carbon Inputs To An Oxbow Lake In The Mississippi River Watershed: Effects Of Dam Construction And Land Use Change On Regional Inputs, Thomas S. Bianchi, Valier Galy, Brad E. Rosenheim, Michael Shields, Xingqian Cui, Peter Van Metre

Marine Science Faculty Publications

We use a dated sediment core from Lake Whittington (USA) in the lower Mississippi River to reconstruct linkages in the carbon cycling and fluvial sediment dynamics over the past 80 years. Organic carbon (OC) sources were characterized using bulk (δ¹³C, ramped pyrolysis-oxidation (PyrOx) ¹⁴C, δ¹⁵N, and TN:OC ratios) and compound-specific (lignin phenols and fatty acids, including δ¹³C and ¹⁴C of the fatty acids) analyses. Damming of the Missouri River in the 1950s, other hydrological modifications to the river, and soil conservation measures resulted in reduced net OC export, in spite of increasing …

A Severe Red Tide (Tampa Bay, 2005) Causes An Anomalous Decrease In Biological Sound, Katherine L. Indeck, Peter Simard, Shannon Gowans, Susan Lowerre-Barbieri, David A. Mann

Marine Science Faculty Publications

Although harmful algal blooms (HABs) are known to cause morbidity and mortality in marine organisms, their sublethal effects are poorly understood. The purpose of this study was to compare ambient noise levels during a severe HAB event in Tampa Bay, Florida, to those during non-HAB periods. Passive acoustic monitoring was conducted using bottom-mounted autonomous acoustic recorders during a severe HAB in summer 2005, and in summers 2006, 2011 and 2012 (non-severe HAB years). Ambient noise levels were significantly higher during the non-HAB years due to an abundance of snapping shrimp (Alpheidae) sounds and fish chorusing. The difference of …

The Dry Season Shuffle: Gorges Provide Refugia For Animal Communities In Tropical Savannah Ecosystems, J. Sean Doody, Simon Clulow, Geoff Kay, Domenic D'Amore, David Rhind

USF St. Petersburg Campus Faculty Publications

In the wet-dry tropics, animal species face the major challenges of acquiring food, water or shelter during an extended dry season. Although large and conspicuous animals such as ungulates and waterfowl migrate to wetter areas during this time, little is known of how smaller and more cryptic animal species with less mobility meet these challenges. We fenced off the entire entrance of a gorge in the Australian tropical savanna, offering the unique opportunity to determine the composition and seasonal movement patterns of the small vertebrate community. The 1.7 km-long fence was converted to a trapline that was deployed for 18-21 …

Adaptive Plasticity And Epigenetic Variation In Response To Warming In An Alpine Plant, Adrienne B. Nicotra, Deborah L. Segal, Gemma L. Hoyle, Aaron W. Schrey, Koen J. Verhoeven, Christina L. Richards

Integrative Biology Faculty and Staff Publications

Environmentally induced phenotypic plasticity may be a critical component of response to changing environments. We examined local differentiation and adaptive phenotypic plasticity in response to elevated temperature in half-sib lines collected across an elevation gradient for the alpine herb, Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP), we found low but significant genetic differentiation between low- and high-elevation seedlings, and seedlings originating from low elevations grew faster and showed stronger temperature responses (more plasticity) than those from medium and high elevations. Furthermore, plasticity was more often adaptive for plants of low-elevation origin and maladaptive for plants of high elevation. With …

Ebola Cases And Health System Demand In Liberia, John M. Drake, Rajreni B. Kaul, Laura W. Alexander, Suzanne M. O’Regan, Andrew M. Kramer, J. Tomlin Pulliam, Matthew J. Ferrari, Andrew W. Park

Integrative Biology Faculty and Staff Publications

In 2014, a major epidemic of human Ebola virus disease emerged in West Africa, where human-to-human transmission has now been sustained for greater than 12 months. In the summer of 2014, there was great uncertainty about the answers to several key policy questions concerning the path to containment. What is the relative importance of nosocomial transmission compared with community-acquired infection? How much must hospital capacity increase to provide care for the anticipated patient burden? To which interventions will Ebola transmission be most responsive? What must be done to achieve containment? In recent years, epidemic models have been used to guide …

Immigration Can Destabilize Tri-Trophic Interactions: Implications For Conservation Of Top Predators, Kevin L. S. Drury, Jesse D. Suter, Jacob B. Rendall, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

Top predators often have large home ranges and thus are especially vulnerable to habitat loss and fragmentation. Increasing connectance among habitat patches is therefore a common conservation strategy, based in part on models showing that increased migration between subpopulations can reduce vulnerability arising from population isolation. Although three-dimensional models are appropriate for exploring consequences to top predators, the effects of immigration on tri-trophic interactions have rarely been considered. To explore the effects of immigration on the equilibrium abundances of top predators, we studied the effects of immigration in the three-dimensional Rosenzweig-MacArthur model. To investigate the stability of the top predator …

What Happens To Soil Organic Carbon As Coastal Marsh Ecosystems Change In Response To Increasing Salinity? An Exploration Using Ramped Pyrolysis, Elizabeth K. Williams, Brad E. Rosenheim

Marine Science Faculty Publications

Coastal wetlands store vast amounts of organic carbon, globally, and are becoming increasingly vulnerable to the effects of anthropogenic sea level rise. To understand the effect of sea level rise on organic carbon fate and preservation in this global sink, it is necessary to characterize differences in the biogeochemical stability of coastal wetland soil organic carbon (SOC). Here we use ramped pyrolysis/oxidation decomposition characteristics as proxies for SOC stability to understand the fate of carbon storage in coastal wetlands comprising the Mississippi River deltaic plain, undergoing rapid rates of local sea level rise. Soils from three wetland types (fresh, brackish, …