Life Sciences Commons^™

Climate Impacts On Zooplankton Population Dynamics In Coastal Marine Ecosystems, Harold P. Batchelder, Kendra L. Daly, Cabell S. Davis, Rubao Ji, Mark D. Ohman, William T. Peterson, Jeffrey A. Runge

Marine Science Faculty Publications

The 20-year US GLOBEC (Global Ocean Ecosystem Dynamics) program examined zooplankton populations and their predators in four coastal marine ecosystems. Program scientists learned that environmental controls on zooplankton vital rates, especially the timing and magnitude of reproduction, growth, life-cycle progression, and mortality, determine species population dynamics, seasonal and spatial distributions, and abundances. Improved knowledge of spatial-temporal abundance and distribution of individual zooplankton taxa coupled with new information linking higher trophic level predators (salmon, cod, haddock, penguins, seals) to their prey yielded mechanistic descriptions of how climate variation impacts regionally important marine resources. Coupled ecological models driven by improved regional-scale climate …

Draft Genome Sequence Of Xylella Fastidiosa Subsp. Multiplex Strain Griffin-1 From Quercus Rubra In Georgia, Jianchi Chen, Hong Huang, Chung-Jan Chang, Drake C. Stenger

School of Information Faculty Publications

The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated from a red oak tree (Quercus rubra) in Georgia, is reported here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames and 50 RNA genes.

Generalized Additive Models Used To Predict Species Abundance In The Gulf Of Mexico: An Ecosystem Modeling Tool, Michael Drexler, Cameron H. Ainsworth

C-IMAGE Publications

Spatially explicit ecosystem models of all types require an initial allocation of biomass, often in areas where fisheries independent abundance estimates do not exist. A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. Despite the presence of a large number of zeros in the data, a single GAM using a negative binomial distribution was suitable …

Blood-Brain Barrier Alterations Provide Evidence Of Subacute Diaschisis In An Ischemic Stroke Rat Model, Svitlana Garbuzova-Davis, Maria C. O. Rodrigues, Diana G. Hernandez-Ontiveros, Naoki Tajiri, Aric Frisna-Deyo, Sean M. Boffeli, Jerry V. Abraham, Mibel Pabon, Andrew Wagner, Hiroto Ishikawa, Kazutaka Shinozuka, Edward M. Haller, Paul Sanberg, Yuji Kaneko, Cesario Borlongan

Integrative Biology Faculty and Staff Publications

Background: Comprehensive stroke studies reveal diaschisis, a loss of function due to pathological deficits in brain areas remote from initial ischemic lesion. However, blood-brain barrier (BBB) competence in subacute diaschisis is uncertain. The present study investigated subacute diaschisis in a focal ischemic stroke rat model. Specific focuses were BBB integrity and related pathogenic processes in contralateral brain areas.

Methodology/Principal Findings: In ipsilateral hemisphere 7 days after transient middle cerebral artery occlusion (tMCAO), significant BBB alterations characterized by large Evans Blue (EB) parenchymal extravasation, autophagosome accumulation, increased reactive astrocytes and activated microglia, demyelinization, and neuronal damage were detected in the striatum, …

Iron Modulates Cell Survival In A Ras- And Mapk-Dependent Manner In Ovarian Cells, K. A. Bauckman, Edward M. Haller, I. Flores, M. Nanjundan

Integrative Biology Faculty and Staff Publications

Ovarian cancer is a leading cause of cancer death in women in the United States. While the majority of ovarian cancers are serous, some rarer subtypes (i.e. clear cell) are often associated with endometriosis, a benign gynecological disease. Iron is rich in the cyst fluid of endometriosis-associated ovarian cancers and induces persistent oxidative stress. The role of iron, an essential nutrient involved in multiple cellular functions, in normal ovarian cell survival and ovarian cancer remains unclear. Iron, presented as ferric ammonium citrate (FAC), dramatically inhibits cell survival in ovarian cancer cell types associated with Ras mutations, while it is without …

Inter-Annual To Decadal Sea-Level Variability In The Coastal Zones Of The Norwegian And Siberian Seas: The Role Of Atmospheric Forcing, F. M. Calafat, D. P. Chambers, M. N. Tsimplis

Marine Science Faculty Publications

[1] Inter-annual to decadal sea-level variations from tide gauge records in the coastal zones of the Norwegian and Siberian Seas are examined for the period 1950–2010 using a combination of hydrographic observations, wind data, and theory. We identify two large areas of highly coherent sea-level variability: one that includes the Norwegian, Barents, and Kara Seas, and another one that includes the Laptev, East Siberian, and Chukchi Seas. We provide evidence of a new contribution to the sea-level variability along the Norwegian coast associated with the poleward propagation of sea-level fluctuations along the eastern boundary of the North Atlantic. When this …

Changes In Vegetative Coverage Of The Hongze Lake National Wetland Nature Reserve: A Decade-Long Assessment Using Modis Medium-Resolution Data, Kun Yu, Chuanmin Hu

Marine Science Faculty Publications

Wetlands are important ecosystems on Earth. However, global wetland coverage is being reduced due to both anthropogenic and natural effects. Thus, assessment of temporal changes in vegetative coverage, as a measure of the wetland health, is critical to help implement effective management plans and provide inputs for climate-related research. In this work, 596 moderate-resolution imaging spectroradiometer (MODIS) 250-m resolution images of the Hongze Lake national wetland nature reserve from 2000 to 2009 were used to study the vegetative coverage (above the water surface) of the reserve. Three vegetation indices [normalized difference vegetation index (NDVI), enhanced VI (EVI), and floating algae …

Extracellular Proteases Are Key Mediators Of Staphylococcus Aureus Virulence Via The Global Modulation Of Virulence-Determinant Stability, Stacey L. Kolar, J. Antonio Ibarra, Frances E. Rivera, Joe M. Mootz, Jessica E. Davenport, Stanley M. Stevens Jr., Alexander R. Horswill, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

Staphylococcus aureus is a highly virulent and successful pathogen that causes a diverse array of diseases. Recently, an increase of severe infections in healthy subjects has been observed, caused by community-associated methicillin-resistant S. aureus (CA-MRSA). The reason for enhanced CA-MRSA virulence is unclear; however, work suggests that it results from hypersecretion of agr-regulated toxins, including secreted proteases. In this study, we explore the contribution of exo-proteases to CA-MRSA pathogenesis using a mutant lacking all 10 enzymes. We show that they are required for growth in peptide-rich environments, serum, in the presence of antimicrobial peptides (AMPs), and in human blood. …

Bacterial Colonization And Extinction On Marine Aggregates: Stochastic Model Of Species Presence And Abundance, Andrew M. Kramer, M. Maille Lyons, Fred C. Dobbs, John M. Drake

Integrative Biology Faculty and Staff Publications

Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while …

Optical Contrast Of Oil Dispersed In Seawater Under Windy Conditions, Z. Otremba, O. Zielinski, Chuanmin Hu

C-IMAGE Publications

Oil pollution of natural waters represents a serious threat for aquatic ecosystems, and the assessment of the degree of pollution requiresmeasurement strategies including remote sensing and modeling. While surface oil pollution is relatively easy to detect with radar or opticalremote sensing, underwater oil emulsions can only be detected using visible light as an information carrier. Here the Michelson contrast ofsea area polluted by an oil-in-water emulsion under various wind conditions is simulated through Monte-Carlo modeling. The results showthe premise for optimal direction of observations in which the possibility of detecting the emulsified oil is maximized.

Long-Term Statistical Assessment Of Aqua-Modis Aerosol Optical Depth Over Coastal Regions: Bias Characteristics And Uncertainty Sources, Jacob C. Anderson, Jun Wang, Jing Zeng, Gregory Leptoukh, Maksym Petrenko, Charles Ichoku, Chuanmin Hu

Marine Science Faculty Publications

Coastal regions around the globe represent a major source for anthropogenic aerosols in the atmosphere, but the surface characteristics may not be optimal for the Moderate Resolution Imaging Spectroradiometer (MODIS) algorithms designed for aerosol retrievals over dark land or ocean surfaces. Using data collected from 62 coastal stations worldwide by the Aerosol Robotic Network (AERONET) in 2002–2011, statistical assessments of uncertainties are conducted for coastal aerosol optical depth (AOD) retrieved from MODIS measurements aboard the Aqua satellite (i.e., the Collection 5.1 MYD04 data product generated by the MODIS atmosphere group). It is found that coastal AODs (at 550 nm) characterised …

Identification Of Proteins At Active, Stalled, And Collapsed Replication Forks Using Isolation Of Proteins On Nascent Dna (Ipond) Coupled With Mass Spectrometry, Bianca M. Sirbu, W. Hayes Mcdonald, Huzefa Dungrawala, Akosua Badu-Nkansah, Gina M. Kavanaugh, Yaoyi Chen, David L. Tabb, David Cortez

Molecular Biosciences Faculty Publications

Both DNA and chromatin need to be duplicated during each cell division cycle. Replication happens in the context of defects in the DNA template and other forms of replication stress that present challenges to both genetic and epigenetic inheritance. The replication machinery is highly regulated by replication stress responses to accomplish this goal. To identify important replication and stress response proteins, we combined isolation of proteins on nascent DNA (iPOND) with quantitative mass spectrometry. We identified 290 proteins enriched on newly replicated DNA at active, stalled, and collapsed replication forks. Approximately 16% of these proteins are known replication or DNA …

Satellite-Observed Black Water Events Off Southwest Florida: Implications For Coral Reef Health In The Florida Keys National Marine Sanctuary, Jun Zhao, Chuanmin Hu, Brian Lapointe, Nelson Melo, Elizabeth M. Johns, Ryan H. Smith

Marine Science Faculty Publications

A “black water” event, as observed from satellites, occurred off southwest Florida in 2012. Satellite observations suggested that the event started in early January and ended in mid-April 2012. The black water patch formed off central west Florida and advected southward towards Florida Bay and the Florida Keys with the shelf circulation, which was confirmed by satellite-tracked surface drifter trajectories. Compared with a previous black water event in 2002, the 2012 event was weaker in terms of spatial and temporal coverage. An in situ survey indicated that the 2012 black water patch contained toxic K. brevis and had relatively low …

Changing The Paradigm Of Response To Coastal Storms, Cheryl J. Hapke, Hilary F. Stockdon, William C. Schwab, Mary K. Foley

Marine Science Faculty Publications

Federal, state, and local agencies mounted a massive preparation and response to post–tropical storm Sandy, which made landfall along the northern New Jersey coast on 29 October 2012. The data collected and knowledge gained in response to Sandy are unprecedented and provide critical information to agencies, local emergency responders, and coastal managers and planners.

Distinct Lineage Of Vesiculovirus From Big Brown Bats, United States, Terry Fei Fan Ng, Cindy Driscoll, Maria Paz Carlos, Algernon Prioleau, Robert Schmieder, Bhakti Dwivedi, Jakk Wong, Yunhee Cha, Steven Head, Mya Breitbart, Eric Delwart

Marine Science Faculty Publications

We identified a novel rhabdovirus, American bat vesiculovirus, from postmortem tissue samples from 120 rabies-negative big brown bats with a history of human contact. Five percent of the tested bats were infected with this virus. The extent of zoonotic exposure and possible health effects in humans from this virus are unknown.

The Maredat Global Database Of High Performance Liquid Chromatography Marine Pigment Measurements, Frank E. Muller-Karger

Marine Science Faculty Publications

A global pigment database consisting of 35 634 pigment suites measured by high performance liquid chromatography was assembled in support of the MARine Ecosytem DATa (MAREDAT) initiative. These data originate from 136 field surveys within the global ocean, were solicited from investigators and databases, compiled, and then quality controlled. Nearly one quarter of the data originates from the Laboratoire d'Océanographie de Villefranche (LOV), with an additional 17% and 19% stemming from the US JGOFS and LTER programs, respectively. The MAREDAT pigment database provides high quality measurements of the major taxonomic pigments including chlorophylls a and b, 19'-butanoyloxyfucoxanthin, 19'-hexanoyloxyfucoxanthin, alloxanthin, divinyl …

The Effect Of The Nao On Sea Level And On Mass Changes In The Mediterranean Sea, M. N. Tsimplis, F. M. Calafat, M. Marcos, G. Jordà, D. Gomis, L. Fenoglio-Marc, M. V. Struglia, S. A. Josey, D. P. Chambers

Marine Science Faculty Publications

[1] Sea level in the Mediterranean Sea over the period 1993–2011 is studied on the basis of altimetry, temperature, and salinity data and gravity measurements from Gravity Recovery and Climate Experiment (GRACE) (2002–2010). An observed increase in sea level corresponds to a linear sea level trend of 3.0 ± 0.5 mm/yr dominated by the increase in the oceanic mass in the basin. The increase in sea level does not, however, take place linearly but over two 2–3 year periods, each contributing 2–3 cm of sea level. Variability in the basin sea level and its mass component is dominated by the …

The Real Limits To Marine Life: A Further Critique Of The Respiration Index, B. A. Seibel, J. J. Childress

Marine Science Faculty Publications

The recently proposed "Respiration Index" (RI = log PO2/PCO2) suggests that aerobic metabolism is limited by the ratio of reactants (oxygen) to products (carbon dioxide) according to the thermodynamics of cellular respiration. Here, we demonstrate further that, because of the large standard free energy change for organic carbon oxidation (ΔG° = −686 kcal mol−1), carbon dioxide can never reach concentrations that would limit the thermodynamics of this reaction. A PCO2 to PO2 ratio of 10503 would be required to reach equilibrium (equilibrium constant, Keq = 10503), where ΔG = 0. Thus, …

Satellite-Based Virtual Buoy System To Monitor Coastal Water Quality, Chuanmin Hu, Brian B. Barnes, Brock Murch, Paul R. Carlson

Marine Science Faculty Publications

There is a pressing need to assess coastal and estuarine water quality state and anomaly events to facilitate coastal management, but such a need is hindered by lack of resources to conduct frequent ship-based or buoy-based measurements. Here, we established a virtual buoy system (VBS) to facilitate satellite data visualization and interpretation of water quality assessment. The VBS is based on a virtual antenna system (VAS) that obtains low-level satellite data and generates higher-level data products using both National Aeronautics and Space Administration standard algorithms and regionally customized algorithms in near real time. The VB stations are predefined and carefully …

Indirect Effects Of Conservation Policies On The Coupled Human-Natural Ecosystem Of The Upper Gulf Of California, Hem Nalini Morzaria-Luna, Cameron H. Ainsworth, Isaac C. Kaplan, Phillip S. Levin, Elizabeth A. Fulton

Marine Science Faculty Publications

High bycatch of non-target species and species of conservation concern often drives the implementation of fisheries policies. However, species- or fishery-specific policies may lead to indirect consequences, positive or negative, for other species or fisheries. We use an Atlantis ecosystem model of the Northern Gulf of California to evaluate the effects of fisheries policies directed at reducing bycatch of vaquita (Phocoena sinus) on other species of conservation concern, priority target species, and metrics of ecosystem function and structure. Vaquita, a Critically Endangered porpoise endemic to the Upper Gulf of California, are frequently entangled by finfish gillnets and shrimp driftnets. We …

Physical–Chemical Characterization Of Purified Cresol Red For Spectrophotometric Ph Measurements In Seawater, Mark C. Patsavas, Robert H. Byrne, Xuewu Liu

Marine Science Faculty Publications

The use of impure cresol red in spectrophotometric seawater pH measurements can introduce systematic inaccuracies greater than 0.1. Cresol red has been purified on a bulk scale to address this problem, but a characterization of the dye's physical–chemical properties has not been provided to date. This work reports the physical–chemical characteristics of purified cresol red for use in spectrophotometric seawater pH measurements over a range of temperatures and salinities. Seawater pH is expressed on the total hydrogen ion concentration scale (pHT) in terms of the ratio (R) of cresol red absorbances (A) at 433 and 573 nm (RCR = 573A/433A): …

Generalized Additive Models Used To Predict Species Abundance In The Gulf Of Mexico: An Ecosystem Modeling Tool, Michael Drexler, Cameron H. Ainsworth

Marine Science Faculty Publications

Spatially explicit ecosystem models of all types require an initial allocation of biomass, often in areas where fisheries independent abundance estimates do not exist. A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. Despite the presence of a large number of zeros in the data, a single GAM using a negative binomial distribution was suitable …

Penetration Of Uv-Visible Solar Radiation In The Global Oceans: Insights From Ocean Color Remote Sensing, Zhongping Lee, Chuanmin Hu, Shaoling Shang, Keping Du, Marlon Lewis, Robert Arnone, Robert Brewin

Marine Science Faculty Publications

Penetration of solar radiation in the ocean is determined by the attenuation coefficient (K_d(λ)). Following radiative transfer theory, K_d is a function of angular distribution of incident light and water's absorption and backscattering coefficients. Because these optical products are now generated routinely from satellite measurements, it is logical to evolve the empirical K_d to a semianalytical K_d that is not only spectrally flexible, but also the sun-angle effect is accounted for explicitly. Here, the semianalytical model developed in Lee et al. (2005b) is revised to account for the shift of phase …

Coastal Change From Hurricane Sandy And The 2012–13 Winter Storm Season: Fire Island, New York, Cheryl J. Hapke, Owen Brenner, Rachel Hehre, B. J. Reynolds

Marine Science Faculty Publications

The U.S. Geological Survey (USGS) mounted a substantial effort in response to Hurricane Sandy including an assessment of the morphological impacts to the beach and dune system at Fire Island, New York. Field surveys of the beach and dunes collected just prior to and after landfall were used to quantify change in several focus areas. In order to quantify morphologic change along the length of the island, pre-storm (May 2012) and post-storm (November 2012) lidar and aerial photography were used to assess changes to the shoreline and beach, and to measure volumetric changes. The extent and thicknesses of overwash deposits …

A Transient Α-Helical Molecular Recognition Element In The Disordered N-Terminus Of The Sgs1 Helicase Is Critical For Chromosome Stability And Binding Of Top3/Rmi1, Jessica A. Kennedy, Gary W. Daughdrill, Kristina H. Schmidt

Molecular Biosciences Faculty Publications

The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays …

Validation Of The Diurnal Cycles In Atmospheric Reanalyses Over Antarctic Sea Ice, Esa-Matti Tastula, Timo Vihma, Edgar L. Andreas, Boris Galperin

Marine Science Faculty Publications

The diurnal cycles of near-surface meteorological parameters over Antarctic sea ice in six widely used atmospheric reanalyses are validated against observations from Ice Station Weddell. The station drifted from February through May 1992 and provided the most extensive set of meteorological observations ever collected in the Antarctic sea ice zone. For the radiative and turbulent surface fluxes, both the amplitude and shape of the diurnal cycles vary considerably among different reanalyses. Near-surface temperature, specific humidity, and wind speed in the reanalyses all feature small diurnal ranges, which, in most cases, fall within the uncertainties of the observed cycle. A skill …

Seabed Corrugations Beneath An Antarctic Ice Shelf Revealed By Autonomous Underwater Vehicle Survey: Origin And Implications For The History Of Pine Island Glacier, Alastair G. Graham, Pierre Dutrieux, David G. Vaughan, Frank O. Nitsche, Richard Gyllencreutz, Sarah L. Greenwood, Robert D. Larter, Adrian Jenkins

Marine Science Faculty Publications

[1] Ice shelves are critical features in the debate about West Antarctic ice sheet change and sea level rise, both because they limit ice discharge and because they are sensitive to change in the surrounding ocean. The Pine Island Glacier ice shelf has been thinning rapidly since at least the early 1990s, which has caused its trunk to accelerate and retreat. Although the ice shelf front has remained stable for the past six decades, past periods of ice shelf collapse have been inferred from relict seabed “corrugations” (corrugated ridges), preserved 340 km from the glacier in Pine Island Trough. Here …

Quantifying Recent Acceleration In Sea Level Unrelated To Internal Climate Variability, F. M. Calafat, D. P. Chambers

Marine Science Faculty Publications

[1] Sea level observations suggest that the rate of sea level rise has accelerated during the last 20 years. However, the presence of considerable decadal-scale variability, especially on a regional scale, makes it difficult to assess whether the observed changes are due to natural or anthropogenic causes. Here we use a regression model with atmospheric pressure, wind, and climate indices as independent variables to quantify the contribution of internal climate variability to the sea level at nine tide gauges from around the world for the period 1920–2011. Removing this contribution reveals a statistically significant acceleration (0.022 ± 0.015 mm/yr^{2 …}

Biogenic Nitrogen Gas Production At The Oxic-Anoxic Interface In The Cariaco Basin, Venezuela, Enrique Montes, M. A. Altabet, Frank E. Muller-Karger, M. I. Scranton, R. Thunell, C. Benitez-Nelson, Laura Lorenzoni, Y. M. Astor

Marine Science Faculty Publications

Excess nitrogen gas (N2xs) was measured in samples collected at six locations in the eastern and western sub-basins of the Cariaco Basin, Venezuela, in September 2008 (non-upwelling conditions) and March 2009 (upwelling conditions). During both sampling periods, N2xs concentrations were below detection in surface waters, increasing to ∼ 22 μmol N kg-1 at the oxic-anoxic interface ([O2] ∼ 4 μmol kg-1, ∼ 250 m). Below the oxic-anoxic interface (300-400 m), the average concentration of N2xs was 24.7 ± 1.9 μmol N kg-1 in September 2008 and 27.5 ± 2.0 μmol N kg-1 in March 2009, i.e., N2xs concentrations within this …

Ocean Bottom Pressure Seasonal Cycles And Decadal Trends From Grace Release-05: Ocean Circulation Implications, Gregory C. Johnson, Don P. Chambers

Marine Science Faculty Publications

[1] Ocean mass variations are important for diagnosing sea level budgets, the hydrological cycle, the global energy budget, and ocean circulation variability. Here seasonal cycles and decadal trends of ocean mass from January 2003 to December 2012, both global and regional, are analyzed using GRACE Release-05 data. The trend of global flux of mass into the ocean approaches 2 cm decade−1 in equivalent sea level rise. Regional trends are of similar magnitude, with the North Pacific, South Atlantic, and South Indian oceans generally gaining mass and other regions losing mass. These trends suggest a spin-down of the North Pacific western …