Input, Output And Complete Run Files For The Atlantis Ecosystem Model Ixtoc Oil Spill Simulations From Campeche Bay Atlantis Model,
2019
University of South Florida
Input, Output And Complete Run Files For The Atlantis Ecosystem Model Ixtoc Oil Spill Simulations From Campeche Bay Atlantis Model, Cameron Ainsworth
C-IMAGE data
This dataset contains complete input, output, and executable model run files for Atlantis simulations of the Ixtoc-1 oil spill. The model outputs included describes simulations from 1979 to 2015; the spatial domain is the western and southern Gulf of Mexico. The data directory "SGoM_Atlantis_oil" contains the simulation with oil effect acting on fish and the directory "SGoM_Atlantis_nooil" contains a control simulation with no oil effect (no-spill scenario). This dataset supports the paper Ortega-Ortiz et al. (submitted manuscript, 2018).
White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability,
2019
Cornell University; Nova Southeastern University
White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji
Biology Faculty Articles
The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …
An Interactive Application For Tracking The Movement Of The Limulus Polyphemus Throughout Long Island Sound (Lis),
2019
Sacred Heart University
An Interactive Application For Tracking The Movement Of The Limulus Polyphemus Throughout Long Island Sound (Lis), Ismael Youssef, Samah Senbel, Jennifer Mattei
Biology Faculty Publications
Poster presented at the Long Island Sound Research Conference held March 15, 2019 in Port Jefferson, New York.
Petrocarbon Evolution: Ramped Pyrolysis/Oxidation And Isotopic Studies Of Contaminated Oil Sediments From The Deepwater Horizon Oil Spill In The Gulf Of Mexico,
2019
Florida State University
Petrocarbon Evolution: Ramped Pyrolysis/Oxidation And Isotopic Studies Of Contaminated Oil Sediments From The Deepwater Horizon Oil Spill In The Gulf Of Mexico, Kelsey L. Rogers, Samantha H. Bosman, Mary Lardie-Gaylord, Ann Mcnichol, Brad E. Rosenheim, Joseph P. Montoya, Jeffrey P. Chanton
C-IMAGE Publications
Hydrocarbons released during the Deepwater Horizon (DWH) oil spill weathered due to exposure to oxygen, light, and microbes. During weathering, the hydrocarbons’ reactivity and lability was altered, but it remained identifiable as “petrocarbon” due to its retention of the distinctive isotope signatures (14C and 13C) of petroleum. Relative to the initial estimates of the quantity of oil-residue deposited in Gulf sediments based on 2010–2011 data, the overall coverage and quantity of the fossil carbon on the seafloor has been attenuated. To analyze recovery of oil contaminated deep-sea sediments in the northern Gulf of Mexico we tracked the …
Short-Lived Radioisotope (Slrad) Data Collected Aboard R/V Justo Sierra Cruise Js-0815 In The Southern Gulf Of Mexico From 2015-07-31 To 2015-08-08,
2019
Eckerd College
Short-Lived Radioisotope (Slrad) Data Collected Aboard R/V Justo Sierra Cruise Js-0815 In The Southern Gulf Of Mexico From 2015-07-31 To 2015-08-08, Gregg R. Brooks, Rebekka A. Larson
C-IMAGE data
This dataset contains short-lived radioisotope (SLRad) data collected aboard R/V Justo Sierra cruise JS-0815 in the southern Gulf of Mexico from 2015-07-31 to 2015-08-08. SLRad data were generated for selected core sub-samples at 2mm sampling intervals for “surficial unit” and 5mm sampling resolution intervals to the base of cores. SLRad data generated include sample activity as disintegrations per minute per gram (dpm/g) of 1) Excess Thorium-234 (234Thxs) activity, which is calculated by measuring the total Thorium-234 (234ThTot) activity and the subtraction of the measured or estimated “supported” Thorium-234 (234ThSup) activity, 2) Excess Lead-210 (210Pbxs) activity, which is calculated by measuring …
Identifying Causes Of Temporal Changes In Acropora Cervicornis Populations And The Potential For Recovery,
2019
Nova Southeastern University
Identifying Causes Of Temporal Changes In Acropora Cervicornis Populations And The Potential For Recovery, Elizabeth Goergen, Alison L. Moulding, Brian K. Walker, David S. Gilliam
Marine & Environmental Sciences Faculty Articles
Corals, specifically the Atlantic staghorn coral, Acropora cervicornis, are under major threat as disturbance events such as storms and disease and predation outbreaks increase in frequency. Since its population declines due to a wide spread disease event in the early 1980s, limited long-term monitoring studies describing the impact of current threats and potential recovery have been completed. The aim of this study was to document the impacts of environmental (tropical storms, increased wind) and biological (disease and predation) threats on A. cervicornis to further understand its population dynamics and potential for recovery. Two high-density A. cervicornis patches (greater than …
Population Connectivity Of Pelagic Megafauna In The Cuba-Mexico-United States Triangle,
2019
Texas A&M University
Population Connectivity Of Pelagic Megafauna In The Cuba-Mexico-United States Triangle, Jay R. Rooker, Michael A. Dance, R.J. David Wells, Matthew J. Ajemian, Barbara A. Block, Michael R. Castleton, J. Marcus Drymon, Brett J. Falterman, James S. Franks, Neil Hammerschlag, Jill M. Hendon, Eric R. Hoffmayer, Richard T. Kraus, Jennifer A. Mckinney, David H. Secor, Gregory W. Stunz, John F. Walter
Faculty Publications
The timing and extent of international crossings by billfishes, tunas, and sharks in the Cuba-Mexico-United States (U.S.) triangle was investigated using electronic tagging data from eight species that resulted in >22,000 tracking days. Transnational movements of these highly mobile marine predators were pronounced with varying levels of bi- or tri-national population connectivity displayed by each species. Billfishes and tunas moved throughout the Gulf of Mexico and all species investigated (blue marlin, white marlin, Atlantic bluefin tuna, yellowfin tuna) frequently crossed international boundaries and entered the territorial waters of Cuba and/or Mexico. Certain sharks (tiger shark, scalloped hammerhead) displayed prolonged periods …
Report Of The Workshop Evaluating The Nature Of Midwater Mining Plumes And Their Potential Effects On Midwater Ecosystems,
2019
University of Hawaii
Report Of The Workshop Evaluating The Nature Of Midwater Mining Plumes And Their Potential Effects On Midwater Ecosystems, Jeffrey C. Drazen, Craig R. Smith, Kristina Gjerde, Whitlow Au, Jesse Black, Glenn Carter, Malcolm Clark, Jennifer M. Durden, Pierre Dutrieux, Erica Goetze, Steven Haddock, Mariko Hatta, Chris Hauton, Paul Hill, Julian Koslow, Astrid B. Leitner, Chris Measures, Audre Pacini, Frank Parrish, Thomas Peacock, Jessica Perelman, Tracey T. Sutton, Celine Taymans, Verena Tunnicliffe, Les Watling, Hiroyuki Yamamoto, Emily Young, Amanda F. Ziegler
Marine & Environmental Sciences Faculty Articles
The International Seabed Authority (ISA) is developing regulations to control the future exploitation of deep-sea mineral resources including sulphide deposits near hydrothermal vents, polymetallic nodules on the abyssal seafloor, and cobalt crusts on seamounts. Under the UN Convention on the Law of the Sea the ISA is required to adopt are taking measures to ensure the effective protection of the marine environment from harmful effects arising from mining-related activities. Contractors are required to generate environmental baselines and assess the potential environmental consequences of deep seafloor mining. Understandably, nearly all environmental research has focused on the seafloor where the most direct …
Retrieval Of Phytoplankton Pigments From Underway Spectrophotometry In The Fram Strait,
2019
Alfred Wegener Institute Helmholtz Center for Polar and Marine Research
Retrieval Of Phytoplankton Pigments From Underway Spectrophotometry In The Fram Strait, Yangyang Liu, Emmanuel Boss, Alison Chase, Hongyan Xi, Xiaodong Zhang, Rüdiger Röttgers, Yanqun Pan, Astrid Bracher
Faculty Publications
Phytoplankton in the ocean are extremely diverse. The abundance of various intracellular pigments are often used to study phytoplankton physiology and ecology, and identify and quantify different phytoplankton groups. In this study, phytoplankton absorption spectra (αph(λ)) derived from underway flow-through AC-S measurements in the Fram Strait are combined with phytoplankton pigment measurements analyzed by high-performance liquid chromatography (HPLC) to evaluate the retrieval of various pigment concentrations at high spatial resolution. The performances of two approaches, Gaussian decomposition and the matrix inversion technique are investigated and compared. Our study is the first to apply the matrix inversion …
Anaerobic Degradation Of Hexadecane And Phenanthrene Coupled To Sulfate Reduction By Enriched Consortia From Northern Gulf Of Mexico Seafloor Sediment,
2019
Georgia Institute of Technology
Anaerobic Degradation Of Hexadecane And Phenanthrene Coupled To Sulfate Reduction By Enriched Consortia From Northern Gulf Of Mexico Seafloor Sediment, Boryoung Shin, Minjae Kim, Karsten Zengler, Kuk-Jeong Chin, Will A. Overholt, Lisa M. Gieg, Konstantinos T. Konstantinidis, Joel E. Kostka
C-IMAGE Publications
To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), …
Ecological Response Of Phytoplankton To The Oil Spills In The Oceans,
2019
Chinese Academy of Sciences
Ecological Response Of Phytoplankton To The Oil Spills In The Oceans, Danling Tang, Jing Sun, Li Zhou, Sufen Wang, Ramesh P. Singh, Gang Pan
Mathematics, Physics, and Computer Science Faculty Articles and Research
Oil spills in oceans have substantial influence on marine ecosystems. This study investigates 21 oil spills in the world. Analyzing Chlorophyll-a (Chl-a) from Moderate Resolution Imaging Spectroradiomerer (MODIS) data after Penglai oil spills on 4 June 2011, found a bloom with peak value of Chl-a (13.66 mg m−3) spread over an area of 800 km2 during 18–25 June 2011, and a pronounced increase in the monthly Chl-a concentration (6.40 mg m−3) on June 2012 in the Bohai Sea. Out of the 21 oil spills, 14 blooms were observed, while 11 …
Assessing Seasonality And Density From Passive Acoustic Monitoring Of Signals Presumed To Be From Pygmy And Dwarf Sperm Whales In The Gulf Of Mexico,
2019
Scripps Institution of Oceanography
Assessing Seasonality And Density From Passive Acoustic Monitoring Of Signals Presumed To Be From Pygmy And Dwarf Sperm Whales In The Gulf Of Mexico, John A. Hildebrand, Kaitlin E. Fraiser, Simone Baumann-Pickering, Sean M. Wiggins, Karlina P. Merkens, Lance P. Garrison, Melissa S. Soldevilla, Mark A. Mcdonald
C-IMAGE Publications
Pygmy sperm whales (Kogia breviceps) and dwarf sperm whales (Kogia sima) are deep diving cetaceans that commonly strand along the coast of the southeast US, but that are difficult to study visually at sea because of their elusive behavior. Conventional visual surveys are thought to significantly underestimate the presence of Kogia and they have proven difficult to approach for tracking and tagging. An approach is presented for density estimation of signals presumed to be from Kogia spp. based on passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period following …
De Novo Assembly And Transcriptome Dataset Of Liver, Testis And Head Kidney From Red Drum (Sciaenops Ocellatus),
2019
Mote Marine Laboratory
De Novo Assembly And Transcriptome Dataset Of Liver, Testis And Head Kidney From Red Drum (Sciaenops Ocellatus), Tracy A. Sherwood, Kevan L. Main, Dana L. Wetzel
C-IMAGE Publications
Red drum (Sciaenops ocellatus) is an estuarine Sciaenid with high commercial value and recreational demand. During the past 50 years, overfishing has caused declines in the population that resulted in the development of red drum commercial and stock enhancement aquaculture fisheries. Despite the potential high economic value in both wild and aquaculture commercial fisheries the availability of transcriptomic data for red drum in public databases is limited. The data here represents the transcriptome profiles of three tissues: liver, testis and head kidney from red drum. The data was generated using Illumina high-throughput RNA sequencing, Trinity for de novo …
Molecular Cloning And Characterization Of Two Arnt (Arnt-1 And Arnt-2) Genes In Atlantic Croaker And Their Expression During Coexposure To Hypoxia And Pcb77,
2019
The University of Texas Rio Grande Valley
Molecular Cloning And Characterization Of Two Arnt (Arnt-1 And Arnt-2) Genes In Atlantic Croaker And Their Expression During Coexposure To Hypoxia And Pcb77, Md. Saydur Rahman, Peter Thomas
School of Earth, Environmental, & Marine Sciences Faculty Publications
Aryl hydrocarbon receptor nuclear translocator (ARNT) is an important transcriptions factor that binds/coactivates drug-metabolizing genes in vertebrates. In this study, we report the cloning and characterization of two ARNT (ARNT-1 and ARNT-2) genes and their mRNA and protein expression in liver tissues of Atlantic croaker after co-exposure to hypoxia and 3,3',4,4'-tetrachlorobiphenyl (PCB77). The full-length croaker ARNT-1 and ARNT-2 genes encode proteins of 537 and 530 amino acids, respectively, and are highly homologous to ARNT-1 and ARNT-2 genes of other vertebrates. ARNT mRNAs are ubiquitously expressed in all tissues. Hypoxia (dissolved oxygen: 1.7 mg/L) exposure (1-4 weeks) did not affect hepatic …
Ocean Robots Uncover Microbial Secrets,
2019
The University of Texas Rio Grande Valley
Ocean Robots Uncover Microbial Secrets, Susan Evans, Jim Birch, John A. Breier, Michael V. Jakuba, Mak A. Saito, Julie Robidart
School of Earth, Environmental, & Marine Sciences Faculty Publications
Life on Earth began in the sea, and the oceans continue to support life on our planet. Of particular importance is the ability of marine microbes to exist in a complex web of relationships where substances are continually transformed and exchanged.
Correction: New Approaches For Assessing Squid Fin Motions: Coupling Proper Orthogonal Decomposition With Volumetric Particle Tracking Velocimetry (Doi:10.1242/Jeb.176750),
2019
Old Dominion University
Correction: New Approaches For Assessing Squid Fin Motions: Coupling Proper Orthogonal Decomposition With Volumetric Particle Tracking Velocimetry (Doi:10.1242/Jeb.176750), Ian K. Bartol, Paul S. Krueger, Carly A. York, Joseph T. Thompson
Biological Sciences Faculty Publications
Squid, which swim using a coupled fin/jet system powered by muscular hydrostats, pose unique challenges for the study of locomotion. The high flexibility of the fins and complex flow fields generated by distinct propulsion systems require innovative techniques for locomotive assessment. For this study, we used proper orthogonal decomposition (POD) to decouple components of the fin motions and defocusing digital particle tracking velocimetry (DDPTV) to quantify the resultant 3D flow fields. Kinematic footage and DDPTV data were collected from brief squid, Lolliguncula brevis [3.1–6.5 cm dorsal mantle length (DML)], swimming freely in a water tunnel at speeds of 0.39–7.20 DML …
A Heuristic Classification Of Woody Plants Based On Contrasting Shade And Drought Strategies,
2019
The University of Texas Rio Grande Valley
A Heuristic Classification Of Woody Plants Based On Contrasting Shade And Drought Strategies, Liang Wei, Chonggang Xu, Steven Jansen, Hang Zhou, Bradley O. Christoffersen, William T. Pockman, Richard S. Middleton, John D. Marshall, Nate G. Mcdowell
School of Earth, Environmental, & Marine Sciences Faculty Publications
Woody plants vary in their adaptations to drought and shade. For a better prediction of vegetation responses to drought and shade within dynamic global vegetation models, it is critical to group species into functional types with similar adaptations. One of the key challenges is that the adaptations are generally determined by a large number of plant traits that may not be available for a large number of species. In this study, we present two heuristic woody plant groups that were separated using cluster analysis in a three-dimensional trait–environment space based on three key metrics for each species: mean xylem embolism …
Habitat Usage Patterns Of Bottlenose Dolphins (Tursiops Truncatus) In Terrebonne And Timbalier Bays, Louisiana,
2019
Louisiana State University
Habitat Usage Patterns Of Bottlenose Dolphins (Tursiops Truncatus) In Terrebonne And Timbalier Bays, Louisiana, Mary Allison Manning
LSU Master's Theses
I coupled fine-scale environmental data with observed behavior and group composition data to examine overall distribution within the bay system and to characterize the habitat associated with foraging and the presence of calves. Semi-isolated populations of bottlenose dolphins (Tursiops truncatus) along Louisiana’s coast are undergoing increased risks from boat traffic, oil spills, land subsidence, and planned water diversions (CPRA 2017). Characterizing the habitat use of bottlenose dolphins in Terrebonne and Timbalier bays, Louisiana, is important given the likely high site fidelity, small home ranges, and low exchange of individuals with nearby coastal populations (Lane et al. 2015, McDonald …
Predator Water Balance Alters Intraguild Predation In A Streamsidefood Web,
2019
Bowling Green State University
Predator Water Balance Alters Intraguild Predation In A Streamsidefood Web, Israel L. Leinbach, Kevin E. Mccluney, John L. Sabo
Biological Sciences Faculty Publications
Previous work suggests that animal water balance can influence trophic interactions, with predators increasing their consumption of water-laden prey to meet water demands.But it is unclear how the need for water interacts with the need for energy to drive trophic interactions under shifting conditions. Using manipulative field experiments, we show that water balance influences the effects of top predators on prey with contrasting ratios of water and energy, altering the frequency of intraguild predation. Water-stressed top predators (large spiders) negatively affect water-laden basal prey (crickets), especially male prey with higher water content, whereas alleviation of water limitation causes top predators …
Recurring Episodes Of Thermal Stress Shift The Balance From A Dominant Host-Specialist To A Background Host-Generalist Zooxanthella In The Threatened Pillar Coral, Dendrogyra Cylindrus,
2019
Florida Keys Marine Laboratory; Florida International University
Recurring Episodes Of Thermal Stress Shift The Balance From A Dominant Host-Specialist To A Background Host-Generalist Zooxanthella In The Threatened Pillar Coral, Dendrogyra Cylindrus, Cynthia Lewis, Karen L. Neely, Mauricio Rodriguez-Lanetty
Marine & Environmental Sciences Faculty Articles
Most scleractinian corals form obligate symbioses with photosynthetic dinoflagellates (family Symbiodiniaceae), which provide differential tolerances to their host. Previously, research has focused on the influence of symbiont composition and the dynamic processes of symbiont repopulation during single episodes of hyperthermal events, followed by years of less-stressful conditions. In contrast, this study characterized for the first time, the role of Symbiodiniaceae species changes in response to annually recurring hyperthermal events, a scenario soon expected to become the norm. Consecutive hyperthermal events during summer 2014 and 2015 along the Florida Reef Tract offered a unique opportunity to study bleaching susceptibility and recovery …
