Life Sciences Commons^™

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 …

The Problem Of Too Many Statistical Tests: Subgroup Analyses In A Study Comparing The Effectiveness Of Online And Live Lectures, David M. Lane

Numeracy

The more statistical analyses performed in the analysis of research data, the more likely it is that one or more of the conclusions will be in error. Multiple statistical analyses can occur when the sample contains several subgroups and the researchers perform separate analyses for each subgroup. For example, separate analyses may be done for different ethnic groups, different levels of education, and/or for both genders. Media reports of research frequently omit information on the number of subgroup analyses performed thus leaving the reader with insufficient information to assess the validity of the conclusions. This article discusses the problems with …

Prioritizing Caves For Karst Invertebrate Recovery In Central Texas, Cyndee Watson

National Cave and Karst Management Symposium 2013

Prioritizing caves known to contain endangered karst invertebrates in central Texas is more challenging than one may think. Here, we outline a strategy to achieve this goal while thinking of what is best for these species including addressing future impacts from climate change, and what works for landowners that are bound to permit restrictions. For example, there are two entities in the Austin, Texas area that hold regional Section 10(a) (1)(B) incidental take permits issued by the U.S. Fish and Wildlife Service. When developing the Habitat Conservation Plan for one of these permits several years ago, they listed several caves …

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 …}

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 …

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 …

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, …

River Discharge Influences On Particulate Organic Carbon Age Structure In The Mississippi/Atchafalaya River System, Brad E. Rosenheim, Kimberly M. Roe, Brian J. Roberts, Alexander S. Kolker, Mead A. Allison, Karen H. Johannesson

Marine Science Faculty Publications

[1] Applying ramped pyrolysis radiocarbon analysis to suspended river sediments, we generate radiocarbon (¹⁴C) age spectra for particulate organic carbon (POC) from the lower Mississippi-Atchafalaya River system (MARS) to better understand a major river system's role in carbon transport. Ramped pyrolysis ¹⁴C analysis generates age distributions of bulk carbon based on thermochemical stability of different organic components. Our results indicate higher proportions of older material in the POC during higher discharge. Ages increase throughout the high-discharge age spectra, indicating that no single component of the POC is responsible for the overall age increases observed. Instead, older material …

Linking Ramped Pyrolysis Isotope Data To Oil Content Through Pah Analysis, Matthew A. Pendergraft, Zeynep Dincer, José L. Sericano, Terry L. Wade, Joanna Kolasinski, Brad E. Rosenheim

Marine Science Faculty Publications

Ramped pyrolysis isotope (¹³C and ¹⁴C) analysis coupled with polycyclic aromatic hydrocarbon (PAH) analysis demonstrates the utility of ramped pyrolysis in screening for oil content in sediments. Here, sediments from Barataria Bay, Louisiana, USA that were contaminated by oil from the 2010 BP Deepwater Horizon spill display relationships between oil contamination, pyrolysis profiles, and isotopic composition. Sediment samples with low PAH concentrations are thermochemically stable until higher temperatures, while samples containing high concentrations of PAHs pyrolyze at low temperatures. High PAH samples are also depleted in radiocarbon (¹⁴C), especially in the fractions that pyrolyze at …

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 …

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 …

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 …

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.

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 …

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 …

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 …

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 …

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. …

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 …

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 …

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.

Free-Living Amoebae In Sediments From The Lascaux Cave In France, Angela M. Garcia-Sanchez, Concepcion Ariza, Jose M. Ubeda, Pedro M. Martin-Sanchez, Valme Jurado, Fabiola Bastian, Claude Alabouvette, Cesareo Saiz Jimenez

International Journal of Speleology

The Lascaux Cave in France is an old karstic channel where the running waters are collected in a pool and pumped to the exterior. It is well-known that water bodies in the vicinity of humans are suspected to be reservoirs of amoebae and associated bacteria. In fact, the free-living amoebae Acanthamoeba astronyxis, Acanthamoeba castellanii, Acanthamoeba sp. and Hartmannella vermiformis were identified in the sediments of the cave using phylogenetic analyses and morphological traits. Lascaux Cave sediments and rock walls are wet due to a relative humidity near saturation and water condensation, and this environment and the presence of abundant bacterial …

The Cave Environment Influencing The Lipid Profile And Hepatic Lipogenesis Of The Fish Ancistrus Cryptophthalmus Reis, 1987 (Siluriformes: Loricariidae), Valquíria Aparecida Alves Bastos, Rodrigo Lopes Ferreira, Daniel Cardoso Carvalho, Marina Lages Pugedo, Luciana De Matos Alves Pinto

International Journal of Speleology

The metabolism of hypogean organisms is frequently molded by the cave environment traits, especially food scarcity. The aim of the present work was to evaluate the influence of such environment on lipid composition and hepatic lipogenesis in the fish Ancistrus cryptophthalmus. For this, the species was compared to an epigean population of the same species. A greater accumulation of total lipids was observed in the cave-dwelling fish (18.36 g/100 g tissue) compared to the surface fish (14.09 g/100 g tissue). The muscle fatty acid profile also varied between the populations. Arachidonic acid was only detected in the epigean fish, while …

Phototactic Behaviour Of Subterranean Copionodontinae Pinna, 1992 Catfishes (Siluriformes, Trichomycteridae) From Chapada Diamantina, Central Bahia, Northeastern Brazil, Bianca Rantin, Maria Elina Bichuette

International Journal of Speleology

The phototactic behaviour of three Copionodontinae (Trichomycteridae) catfish species (two troglobites and one epigean) from Chapada Diamantina was studied in order to detect modifications related to isolation in the subterranean environment. Differences in response under different luminosities were detected and, unlike other cavefish, Copionodontinae cave species have shown to be more photophobic than the epigean syntopic to them. The troglobitic Glaphyropoma spinosum is the most photophobic, presenting this behaviour under all light intensities, and more homogeneous regarding morphological characters. It suggests that this population is probably isolated for a longer time in the subterranean environment compared to Copionodon sp. n., …

La Serreta Endokarst (Se Spain): A Sustainable Value?, Antonia D. Asencio, Teodoro Espinosa

International Journal of Speleology

La Serreta endokarst (SE Spain), which UNESCO declared a World Heritage Site in 1998, was considered a sanctuary with cave art and one of the most important archaeological sites in the Mediterranean region for both the remains it hosts and the spectacular karstic landscape at the site.

To coincide with the 40th anniversary of its discovery, the La Serreta cave-chasm was adapted for public use with the intention of showing visitors the remains, which date back to prehistoric times. The solution included attempts to minimize contact with the valuables in the cave in order to alter the existing remains as …

The Effects Of Uv Light On The Antimicrobial Activities Of Cave Actinomycetes, Devon Rule, Naowarat Cheeptham

International Journal of Speleology

The goal of this study was to determine whether actinomycetes isolated from a volcanic cave in western Canada could produce novel antimicrobial compounds against six multidrugresistant pathogens when exposed to UV light. One hundred and seventy-six actinomycete strains isolated from Helmcken Falls Cave, Wells Gray Provincial Park, BC, were screened against six pathogens using the “plug assay” in UV light and no light conditions. Of the 176 strains tested, 100 or 57% of the cave actinomycete strains had antimicrobial activities against the pathogens in 124 different instances: 35 instances when exposed to UV and no light, 30 when exposed to …

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 …