Life Sciences Commons^™

Interpreting The Role Of Ph On Stable Isotopes In Large Benthic Foraminifera, L. L. Robbins, P. O. Knorr, J. G. Wynn, Pamela Hallock, P. J. Harries

Marine Science Faculty Publications

Large benthic foraminifera (LBF) are prolific producers of calcium carbonate sediments in shallow, tropical environments that are being influenced by ocean acidification (OA). Two LBF species, Amphistegina gibbosa (Order Rotaliida) with low-Mg calcite tests and Archaias angulatus (Order Miliolida) with high-Mg calcite tests, were studied to assess the effects of pH 7.6 on oxygen and carbon isotopic fractionation between test calcite and ambient seawater. The δ 18O and δ 13C values of terminal chambers and of whole adult tests of both species after 6 weeks were not significantly different between pH treatments of 8.0 and 7.6. However, tests of juveniles …

Challenges In Methane Column Retrievals From Aviris-Ng Imagery Over Spectrally Cluttered Surfaces: A Sensitivity Analysis, Minwei Zhang, Ira Leifer, Chuanmin Hu

Marine Science Faculty Publications

A comparison between efforts to detect methane anomalies by a simple band ratio approach from the Airborne Visual Infrared Imaging Spectrometer-Classic (AVIRIS-C) data for the Kern Front oil field, Central California, and the Coal Oil Point marine hydrocarbon seep field, offshore southern California, was conducted. The detection succeeded for the marine source and failed for the terrestrial source, despite these sources being of comparable strength. Scene differences were investigated in higher spectral and spatial resolution collected by the AVIRIS-C successor instrument, AVIRIS Next Generation (AVIRIS-NG), by a sensitivity study. Sensitivity to factors including water vapor, aerosol, planetary boundary layer (PBL) …

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 …

Requirement Of Minimal Signal-To-Noise Ratios Of Ocean Color Sensors And Uncertainties Of Ocean Color Products, Lin Qi, Zhongping Lee, Chuanmin Hu, Menghua Wang

Marine Science Faculty Publications

Using simulations, error propagation theory, and measurements from the Moderate Resolution Imaging Spectroradiometer (MODIS), we determined the minimal signal-to-noise ratio (SNR) required for ocean color measurements and product uncertainties at different spatial and temporal scales. First, based on typical top-of-atmosphere (TOA) radiance over the ocean, we evaluate the uncertainties in satellite-derived R_rs in the visible wavelengths (ΔR_rs(vis)) due to sensor noise in both the near-infrared (NIR) and the visible bands. While the former induces noise in R_rs(vis) through atmospheric correction, the latter has a direct impact on R_rs(vis). Such estimated uncertainties are …

Remote-Sensing Estimation Of Phytoplankton Size Classes From Goci Satellite Measurements In Bohai Sea And Yellow Sea, Deyong Sun, Yu Huan, Zhongfeng Qiu, Chuanmin Hu, Shengqiang Wang, Yijun He

Marine Science Faculty Publications

Phytoplankton size class (PSC), a measure of different phytoplankton functional and structural groups, is a key parameter to the understanding of many marine ecological and biogeochemical processes. In turbid waters where optical properties may be influenced by terrigenous discharge and nonphytoplankton water constituents, remote estimation of PSC is still a challenging task. Here based on measurements of phytoplankton diagnostic pigments, total chlorophyll a, and spectral reflectance in turbid waters of Bohai Sea and Yellow Sea during summer 2015, a customized model is developed and validated to estimate PSC in the two semienclosed seas. Five diagnostic pigments determined through high-performance …

Estimating Particulate Inorganic Carbon Concentrations Of The Global Ocean From Ocean Color Measurements Using A Reflectance Difference Approach, C. Mitchell, C. Hu, B. Bowler, D. Drapeau, W. M. Balch

Marine Science Faculty Publications

A new algorithm for estimating particulate inorganic carbon (PIC) concentrations from ocean color measurements is presented. PIC plays an important role in the global carbon cycle through the oceanic carbonate pump, therefore accurate estimations of PIC concentrations from satellite remote sensing are crucial for observing changes on a global scale. An extensive global data set was created from field and satellite observations for investigating the relationship between PIC concentrations and differences in the remote sensing reflectance (R_rs) at green, red, and near-infrared (NIR) wavebands. Three color indices were defined: two as the relative height of R_{rs …}

Towards The Complete Proteinaceous Regulome Of Acinetobacter Baumannii, Leila G. Casella, Andy Weiss, Ernesto Pérez-Rueda, J Antonio Ibarra, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so …

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 …

Accuracy Of Climate-Based Forecasts Of Pathogen Spread, Annakate M. Schatz, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

Species distribution models (SDMs) are a tool for predicting the eventual geographical range of an emerging pathogen. Most SDMs, however, rely on an assumption of equilibrium with the environment, which an emerging pathogen, by definition, has not reached. To determine if some SDM approaches work better than others for modelling the spread of emerging, non-equilibrium pathogens, we studied time-sensitive predictive performance of SDMs for Batrachochytrium dendrobatidis, a devastating infectious fungus of amphibians, using multiple methods trained on time-incremented subsets of the available data. We split our data into timeline-based training and testing sets, and evaluated models on each set …

Evaluation Of Filtration And Dna Extraction Methods For Environmental Dna Biodiversity Assessments Across Multiple Trophic Levels, Anni Djurhuus, Jesse Port, Collin Closek, Kevan Yamahara, Ofelia Romero-Maraccini, Kristine Walz, Dawn Goldsmith, Reiko Michisaki, Mya Breitbart, Alexandria Boehm, Francisco Chavez

Marine Science Faculty Publications

Metabarcoding of marine environmental DNA (eDNA), originating from tissue, cells, or extracellular DNA, offers the opportunity to survey the biological composition of communities across multiple trophic levels from a non-invasive seawater sample. Here we compare results of eDNA metabarcoding of multiple trophic levels from individual seawater samples collected from a kelp forest in Monterey Bay, California in order to establish methods for future cross-trophic level eDNA analysis. Triplicate 1 L water samples were filtered using five different 47 mm diameter membrane filters (PVDF, PES, GFF, PCTE, and NC) and DNA was extracted from triplicates of each filter-type using three widely-used …

Spatial Variability Of Spanish Sardine (Sardinella Aurita) Abundance As Related To The Upwelling Cycle Off The Southeastern Caribbean Sea, Digna Rueda-Roa, Jeremy Mendoza, Frank E. Muller-Karger, Juan José Cárdenas, Alina Achury, Yrene Astor

Marine Science Faculty Publications

The Sardinella aurita fishery off northeastern Venezuela, region of seasonal wind-driven coastal-upwelling, accounts for 90% of the Caribbean Sea small pelagic catch. This law-protected artisanal fishery takes place up to ∼10 km offshore. The spatial distribution, number of schools, and biomass of S. aurita were studied using eight hydro-acoustic surveys (1995-1998). The study included the analysis of satellite-derived sea surface temperature and chlorophyll-a. Surveys were grouped by strong, weak, and transitional upwelling seasons. Relationships between these observations were analyzed using Generalized Additive Models. Results show that during the primary upwelling season (January-May) sardines were widely distributed in upwelling plumes that …

Remote Estimation Of Biomass Of Ulva Prolifera Macroalgae In The Yellow Sea, Lianbo Hu, Chuanmin Hu, He Ming-Xia

Marine Science Faculty Publications

Since 2008, macroalgal blooms of Ulva prolifera (also called green tides) occurred every summer in the Yellow Sea (YS), causing environmental and economic problems. A number of studies have used satellite observations to estimate the severity of the blooms through estimating the bloom size and duration. However, a critical bloom parameter, namely biomass, has never been objectively determined due to lack of measurements. In this study, laboratory experiments were conducted to measure U. prolifera biomass (wet weight) per unit area and the corresponding spectral reflectance, through which a robust relationship has been established to link biomass per area to …

Isolation And Characterization Of A Shewanella Phage–Host System From The Gut Of The Tunicate, Ciona Intestinalis, Brittany Leigh, Charlotte Karrer, John P. Cannon, Mya Breitbart, Larry J. Dishaw

Marine Science Faculty Publications

Outnumbering all other biological entities on earth, bacteriophages (phages) play critical roles in structuring microbial communities through bacterial infection and subsequent lysis, as well as through horizontal gene transfer. While numerous studies have examined the effects of phages on free-living bacterial cells, much less is known regarding the role of phage infection in host-associated biofilms, which help to stabilize adherent microbial communities. Here we report the cultivation and characterization of a novel strain of Shewanella fidelis from the gut of the marine tunicate Ciona intestinalis, inducible prophages from the S. fidelis genome, and a strain-specific lytic phage recovered from surrounding …

Short Organic Carbon Turnover Time And Narrow 14C Age Spectra In Early Holocene Wetland Paleosols, Lael Vetter, Brad E. Rosenheim, Alvaro Fernandez, Torbjörn E. Törnqvist

Marine Science Faculty Publications

Paleosols contain information about the rates of soil organic carbon turnover when the soil was actively forming. However, this temporal information is often difficult to interpret without tight stratigraphic control on the age of the paleosol. Here we apply ramped pyrolysis/oxidation (Ramped PyrOx) ¹⁴C analyses to evaluate age spectra of transgressive early Holocene paleosols from the Mississippi Delta in southeastern Louisiana, USA. We find ¹⁴C age spectra from soil organic matter (SOM) in both paleosols and overlying basal peats that represent variability in age that is close to, or only slightly greater than, analytical uncertainty of ¹⁴C …

Ice Formation And The Risk Of Chloride Toxicity In Shallow Wetlands And Lakes, Hilary A. Dugan, Greta Helmueller, John J. Magnuson

Marine Science Faculty Publications

The process of ice formation in shallow waterbodies can increase chloride to toxic levels in waterbodies already impacted by chloride loading from road salt (NaCl deicer) application. Chloride concentrations were measured bi-weekly in a shallow, urban wetland in Madison, Wisconsin. We found that in this shallow waterbody, ice thickening doubled chloride concentrations from ion exclusion as the water froze. To understand the role of ice formation and ion exclusion, we constructed a numerical model to predict chloride concentrations beneath the ice resulting from ion exclusion. Where chloride levels already are elevated above background and flushing rates are low, ice thickening …

High-Resolution Sub-Ice-Shelf Seafloor Records Of Twentieth Century Ungrounding And Retreat Of Pine Island Glacier, West Antarctica, D. Davies, R. G. Bingham, A. G. C. Graham, M. Spagnolo, P. Dutrieux, D. G. Vaughan, A. Jenkins, F. O. Nitsche

Marine Science Faculty Publications

Pine Island Glacier Ice Shelf (PIGIS) has been thinning rapidly over recent decades, resulting in a progressive drawdown of the inland ice and an upstream migration of the grounding line. The resultant ice loss from Pine Island Glacier (PIG) and its neighboring ice streams presently contributes an estimated ∼10% to global sea level rise, motivating efforts to constrain better the rate of future ice retreat. One route toward gaining a better understanding of the processes required to underpin physically based projections is provided by examining assemblages of landforms and sediment exposed over recent decades by the ongoing ungrounding of PIG. …

Predicting Sargassum Blooms In The Caribbean Sea From Modis Observations, Mengqiu Wang, Chuanmin Hu

Marine Science Faculty Publications

Recurrent and significant Sargassum beaching events in the Caribbean Sea (CS) have caused serious environmental and economic problems, calling for a long-term prediction capacity of Sargassum blooms. Here we present predictions based on a hindcast of 2000–2016 observations from Moderate Resolution Imaging Spectroradiometer (MODIS), which showed Sargassum abundance in the CS and the Central West Atlantic (CWA), as well as connectivity between the two regions with time lags. This information was used to derive bloom and nonbloom probability matrices for each 1° square in the CS for the months of May–August, predicted from bloom conditions in a hotspot region in …

Evolving Academic Culture To Meet Societal Needs, Kateryna Wowk, Larry Mckinney, Frank E. Muller-Karger, Russell Moll, Susan Avery, Elva Escobar-Briones, David Yoskowitz, Richard Mclaughlin

Marine Science Faculty Publications

Given today's complex societal challenges, academia should work better with government, industry and others in offering innovative solutions that benefit our society, economy and environment. Researchers across disciplines must work together and with decision-makers to understand how science can have better on-The-ground impacts toward longer-Term, resilient societal outcomes. This includes, for example, by working with end-users in problem formation and throughout research projects to ensure decision-making needs are being met, and by linking physical science to additional fields like economics, risk communication or psychology. However, persistent barriers to collaborating across disciplines and with external decision-makers remain. Despite decades of studies …

Satellite Observation Of Particulate Organic Carbon Dynamics On The Louisiana Continental Shelf, Chengfeng Le, John C. Lehrter, Chuanmin Hu, Hugh Macintyre, Marcus W. Beck

Marine Science Faculty Publications

Particulate organic carbon (POC) plays an important role in coastal carbon cycling and the formation of hypoxia. Yet, coastal POC dynamics are often poorly understood due to a lack of long-term POC observations and the complexity of coastal hydrodynamic and biogeochemical processes that influence POC sources and sinks. Using field observations and satellite ocean color products, we developed a new multiple regression algorithm to estimate POC on the Louisiana Continental Shelf (LCS) from satellite observations. The algorithm had reliable performance with mean relative error (MRE) of ∼40% and root mean square error (RMSE) of ∼50% for MODIS and SeaWiFS images …

Land Adjacency Effects On Modis Aqua Top-Of-Atmosphere Radiance In The Shortwave Infrared: Statistical Assessment And Correction, Lian Feng, Chuanmin Hu

Marine Science Faculty Publications

Satellite measurements of coastal or inland waters near land/water interfaces suffer from land adjacency effects (LAEs), particularly in the short-wave infrared (SWIR) wavelengths. Here a statistical method was developed to quantify the LAEs as the ratio of top-of-atmosphere (TOA) total radiance (L_t, W m⁻² µm⁻¹ sr⁻¹) between near-shore pixels and LAE-free offshore pixels (>12 pixels away from land). The calculations were conducted using MODIS Aqua images between 2003 and 2012 over the Madagascar Island, with results showing the dependency of LAEs on different environmental and observational factors. The LAEs decrease dramatically with increasing …

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 …