Digital Commons Network^™

Assessing The Effects Of Exposure Timing On Biomarker Expression Using Β-Estradiol, K. M. Hyndman, A. Biales, S. E. Bartell, H. L. Schoenfuss

United States Environmental Protection Agency: Publications

Temporal and spatial variability in estrogenicity has been documented formanytreated wastewater effluents with the consequences of this variability on the expression of biomarkers of endocrine disruption being largely unknown. Laboratory exposure studies usually utilize constant exposure concentrations which may produce biological effects that differ from those observed in organisms exposed in natural environments. In this study, we investigated the effects of differential timing of exposures with 17β - estradiol (E2) on a range of fathead minnow biomarkers to simulate diverse environmentally relevant exposure profiles. Two 21-day, replicate experiments were performed exposing mature male fathead minnows to E2 at time-weighted mean …

Severe Systemic Toxicity And Urinary Bladder Cytotoxicity And Regenerative Hyperplasia Induced By Arsenite In Arsenic (+3 Oxidation State) Methyltransferase Knockout Mice. A Preliminary Report, Masanao Yokohira, Lora L. Arnold, Karen L. Pennington, Shugo Suzuki, Satoko Kakiuchi-Kiyota, Karen Herbin-Davis, David J. Thomas, Samuel M. Cohen

United States Environmental Protection Agency: Publications

Arsenic (+3 oxidation state) methyltransferase (As3mt) catalyzes reactions which convert inorganic arsenic to methylated metabolites. This study determined whether the As3mt null genotype in the mouse modifies cytotoxic and proliferative effects seen in urinary bladders of wild type mice after exposure to inorganic arsenic. Female wild type C57BL/6 mice and As3mt KO mice were divided into 3 groups each (n=8) with free access to a diet containing 0, 100 or 150 ppm of arsenic as arsenite (As^III). During the first week of As^III exposure, As3mt KO mice exhibited severe and lethal systemic toxicity. At termination, …

Integration Of Metabolomics And In Vitro Metabolism Assays For Investigating The Stereoselective Transformation Of Triadimefon In Rainbow Trout, John F. Kenneke, Drew R. Ekman, Chris S. Mazur, Brad J. Konwick, Aaron T. Fisk, Jimmy K. Avants, A. Wayne Garrison

United States Environmental Protection Agency: Publications

Triadimefon is a systemic agricultural fungicide of the triazole class whose major metabolite, triadimenol, also a commercial fungicide, provides the majority of the actual fungicidal activity, i.e., inhibition of steroid demethylation. Both chemicals are chiral: triadimefon has one chiral center with two enantiomers while its enzymatic reduction to triadimenol produces a second chiral center and two diastereomers with two enantiomers each. All six stereoisomers of the two fungicides were separated from each other using a chiral BGB-172 column on a GC-MS system so as to follow stereospecificity in metabolism by rainbow trout hepatic microsomes. In these microsomes the S-(+) enantiomer …

Habitat-Related Benthic Macrofaunal Assemblages Of Bays And Estuaries Of The Western United States, J. Ananda Ranasinghe, Kathy I. Welch, Peter N. Slattery, David E. Montagne, David D. Huff, Henry Lee Ii, Jeffrey L. Hyland, Bruce Thompson, Stephen B. Weisberg, James M. Oakden, Donald B. Caiden, Ronald G. Velarde

United States Environmental Protection Agency: Publications

Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q-mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) …

Genetic Evidence Of Illegal Trade In Protected Whales Links Japan With The Us And South Korea, C. Scott Baker, Debbie Steel, Yeyong Choi, Hang Lee, Kyung Seok Kim, Sung Kyoung Choi, Yong-Un Ma, Charles Hambleton, Louie Psihoyos, R. L. Brownell Jr,, Naoko Funahashi

United States Department of Commerce: Staff Publications

We report on genetic identification of ‘whale meat’ purchased in sushi restaurants in Los Angeles, CA (USA) in October 2009 and in Seoul, South Korea in June and September 2009. Phylogenetic analyses of mtDNA cytochrome b sequences confirmed that the products included three species of whale currently killed in the controversial scientific whaling program of Japan, but which are protected from international trade: the fin, sei and Antarctic minke. The DNA profile of the fin whale sold in Seoul established a match to products purchased previously in Japan in September 2007, confirming unauthorized trade between these two countries. Following species …

A Note On The Unprecedented Strandings Of 56 Deep-Diving Whales Along The Uk And Irish Coast, Sarah J. Dolman, Eunice Pinn, Robert J. Reid, Jason P. Barley, Rob Deaville, Paul D. Jepson, Mick O’Connell, Simon Berrow, Rod S. Penrose, Peter T. Stevick, Susannah Calderan, Kevin P. Robinson, Robert L. Brownell Jr., Mark P. Simmonds

United States Department of Commerce: Staff Publications

In the first seven months of 2008, eighteen Cuvier’s beaked whales (Ziphius cavirostris), four Sowerby’s beaked whales (Mesoplodon bidens), five unidentified beaked whales and twenty-nine long-finned pilot whales (Globicephala melas) were reported stranded in the UK and Ireland. Decomposition of those animals investigated puts the predicted time of death at mid-January. Concerns that an unusual mortality event had taken place prompted further investigations. Most carcasses were too decomposed for necropsy. A summary of findings is presented here. Although the initial stranding of five Cuvier’s beaked whales in Scotland shared some similarities with atypical mass …

The Traceability/Trackability Of Illegal Trade In Whale Products: A Proposal To Evaluate The Technical Functionality Of Dna Registers, C. Scott Baker, R. L. Brownell Jr.

United States Department of Commerce: Staff Publications

The Government of Japan, through the Institute for Cetacean Research (Tokyo), has established a DNA register for whales taken under special permit or otherwise destined for commercial markets (IWC 2005; IWC 2010a). The functionality of this DNA register, for the purposes of traceability/trackability, is critical to the current negotiations on the future of the IWC (IWC 2010b). Here we request access to the DNA register for 3 species of whales (fin, sei and Antarctic minke) for the purposes of tracking the origins of whale products purchased at commercial outlets in Seoul, South Korea and Santa Monica, US, as described in …

Fast Computing Of Some Generalized Linear Mixed Pseudo-Models With Temporal Autocorrelation, Jay M. Ver Hoef, Josh M. London, Peter L. Boveng

United States Department of Commerce: Staff Publications

This paper considers ways to increase computational speed in generalized linear mixed pseudo-models for the case of many repeated measurements on subjects. We obtain linearly increasing computing time with number of observations, as opposed to O(n³) increasing computing time using numerical optimization. We also find a surprising result; that incomplete optimization for covariance parameters within the larger parameter estimation algorithm actually decreases time to convergence. After comparing various computing algorithms and choosing the best one, we fit a generalized linear mixed model to a binary time series data set with over 100 fixed effects, 50 random effects, …

Social Cohesion Among Kin, Gene Flow Without Dispersal And The Evolution Of Population Genetic Structure In The Killer Whale (Orcinus Orca), M. Pilot, M. E. Dahlheim, A. R. Hoelzel

United States Department of Commerce: Staff Publications

In social species, breeding system and gregarious behavior are key factors influencing the evolution of large-scale population genetic structure. The killer whale is a highly social apex predator showing genetic differentiation in sympatry between populations of foraging specialists (ecotypes), and low levels of genetic diversity overall. Our comparative assessments of kinship, parentage and dispersal reveal high levels of kinship within local populations and ongoing male-mediated gene flow among them, including among ecotypes that are maximally divergent within the mtDNA phylogeny. Dispersal from natal populations was rare, implying that gene flow occurs without dispersal, as a result of reproduction during temporary …

Long-Term Survival Of Humpback Whales Radio-Tagged In Alaska From 1976 Through 1978, Sally Mizroch, Michael F. Tillman, Susan Jurasz, Janice Straley, Olga Von Ziegesar, Louis Herman, Adam Pack, Scott Baker, Jim Darling, Debbie Glockner-Ferrari, Mark Ferrari, Dan Salden, P J. Clapham

United States Department of Commerce: Staff Publications

Invasive tags designed to provide information on animal movements through radio or satellite monitoring have tremendous potential for the study of whales and other cetaceans. However, to date there have been no published studies on the survival of tagged animals over periods of years or decades. Researchers from the National Marine Mammal Laboratory and the Woods Hole Oceanographic Institution tracked five humpback whales with implanted radio tags in southeastern Alaska in August 1976 and July 1977, and tracked two humpback whales in Prince William Sound, Alaska, in June 1978. All seven of these individually identified humpback whales were resighted at …

Movements Of Satellite-Monitored Humpback Whales From New Caledonia, Claire Garrigue, Alexandre N. Zerbini, Ygor Geyer, Mads-Peter Heide-Jørgensen, Wakao Hanaoka, Phil Clapham

United States Department of Commerce: Staff Publications

Knowledge of the local and migratory movements of humpback whales (Megaptera novaeangliae) from New Caledonia is very limited. To investigate this topic, we attached satellite-monitored tags to 12 whales off southern New Caledonia. Tag longevity ranged from 1 to 52 days (X = 22.5 days). Tagged whales generally moved to the south or southeast, with several spending time in a previously unknown seamount habitat named Antigonia before resuming movement, generally toward Norfolk Island or New Zealand. However, 1 female with a calf traveled the entire length of the western coast of New Caledonia (~450 km) and then …

Seasonal Home Ranges And Fidelity To Breeding Sites Among Ringed Seals, Brendan P. Kelly, Oriana H. Badajos, Mervi Kunnasranta, John R. Moran, Micaela Martinez-Bakker, Peter Boveng, Douglas Wartzok

United States Department of Commerce: Staff Publications

Population structure and patterns of habitat use among ringed seals (Phoca hispida) are poorly known, in part because seasonal movements have not been adequately documented. We monitored the movements of 98 ringed seals in the Beaufort and Chukchi seas between 1990 and 2006 using three forms of telemetry. In the winter—spring period (when the seals were occupying shorefast ice), we used radio and ultra-sonic tags to track movements above and below the ice, respectively. We used satellite-linked transmitters in summer and fall (when the seals ranged away from their winter sites) to track at-sea movements. In the shorefast …

A Mixed-Model Moving-Average Approach To Geostatistical Modeling In Stream Networks, Erin E. Peterson, Jay M. Ver Hoef

United States Department of Commerce: Staff Publications

Spatial autocorrelation is an intrinsic characteristic in freshwater stream environments where nested watersheds and flow connectivity may produce patterns that are not captured by Euclidean distance. Yet, many common autocovariance functions used in geostatistical models are statistically invalid when Euclidean distance is replaced with hydrologic distance. We use simple worked examples to illustrate a recently developed moving-average approach used to construct two types of valid autocovariance models that are based on hydrologic distances. These models were designed to represent the spatial configuration, longitudinal connectivity, discharge, and flow direction in a stream network. They also exhibit a different covariance structure than …

Validation Of A Homologous Canine Relaxin Radioimmunoassay And Application With Pregnant And Non-Pregnant Northern Fur Seals (Callorhinus Ursinus), Don R. Bergfelt, Bernard G. Steinetz, J. Lawrence Dunn, Shannon Atkinson, J. Ward Testa, Gregg P. Adams

United States Department of Commerce: Staff Publications

The primary objectives of this study were to validate a canine relaxin RIA for use in otariids and phocids and consider practical applications. For 6 captive Northern fur seal females, serum samples were grouped and examined according to pregnancy (n = 13), post-partum (n = 8) and non-pregnancy (n = 6), and, for 2 captive Northern fur seal males, serum samples were grouped and examined together regardless of age (2 mo–15 yrs, n = 6). Placental tissue was available for examination from one Northern fur seal, Steller sea lion and harbor seal. The validation process involved several steps using an …

Foraging Effort Of Juvenile Steller Sea Lions Eumetopias Jubatus With Respect To Heterogeneity Of Sea Surface Temperature, Michelle E. Lander, Thomas R. Loughlin, Miles G. Logsdon, Glenn R. Vanblaricom, Brian Fadely

United States Department of Commerce: Staff Publications

Among many other factors, the decline of the western distinct population segment of Steller sea lions Eumetopias jubatus in Alaska (USA) has been attributed to changes in the distribution or abundance of prey due to the cumulative effects of fisheries and large-scale climate change. However, the depletion of localized prey resources due to small-scale environmental variability and perturbations may be impeding recovery, resulting in the need to understand how the environment currently affects this species on smaller spatial and temporal scales. The objective of this study, there-fore, was to assess how Steller sea lions respond to changes in localized environmental …

Distance Software: Design And Analysis Of Distance Sampling Surveys For Estimating Population Size, Len Thomas, Stephen T. Buckland, Eric A. Rexstad, Jeff L. Laake, Samantha Strindberg, Sharon L. Hedley, Jon R.B. Bishop, Tiago A. Marques, Kenneth P. Burnham

United States Department of Commerce: Staff Publications

1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance.

2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use.

3. Good survey design is a crucial prerequisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated.

4. A first step in analysis of …

System Dynamics Modeling Of Corn Ethanol As A Bio Transportation Fuel In The United States, Deogratias Kibira, Guodong Shao, Stephen Nowak

United States Department of Commerce: Staff Publications

The production capacity of corn ethanol as a transportation fuel is experiencing rapid growth in the United States. The demand is driven by increased prices of gasoline, government mandates, incentives, desire for cleaner fuels, and the need to achieve energy independence. Continued strong growth of the corn ethanol industry will depend on profitability by both suppliers and producers. This in turn will be influenced by several factors such as demand, government incentives, feedstock availability and prices, processing plant capacity, and efficient farm and ethanol processing technologies. How and to what extent will the projected growth of the corn ethanol industry …

Can Bottom-Up Ocean Co2 Fluxes Be Reconciled With Atmospheric 13C Observations?, Caroline B. Alden, John B. Miller, James W. C. White

United States Department of Commerce: Staff Publications

The rare stable carbon isotope, ¹³C, has been used previously to partition CO₂ fluxes into land and ocean components. Net ocean and land fluxes impose distinctive and predictable fractionation patterns upon the stable isotope ratio, making it an excellent tool for distinguishing between them. Historically, isotope constrained inverse methods for calculating CO₂ surface fluxes—the ‘double deconvolution’—have disagreed with bottom-up ocean flux estimates. In this study, we use the double deconvolution framework, but add, as a constraint, independent estimates of time histories of ocean fluxes to the atmospheric observations of CO₂ and ¹³CO₂. We …

Vertical Profiles Of Co2 Above Eastern Amazonia Suggest A Net Carbon Flux To The Atmosphere And Balanced Biosphere Between 2000 And 2009, L. V. Gatti, J. B. Miller, M. T. S. D'Amelio, A. Martinewski, L. S. Basso, M. E. Gloor, S. Wofsy, P. Tans

United States Department of Commerce: Staff Publications

From 2000 until January 2010 vertical profiles were collected above eastern Amazonia to help determine regional-scale (∼10⁵–10⁶ km²) fluxes of carbon cycle-related greenhouse gases. Samples were collected aboard light aircraft between the surface and 4.3 km and a column integration technique was used to determine the CO₂ flux. Measured CO₂ profiles were differenced from the CO₂ background determined from measurements in the tropical Atlantic. The observed annual flux between the coast and measurement sites was 0.40 ± 0.27 gC m⁻² d⁻¹ (90% confidence interval using a bootstrap analysis). The wet …

Predicting The Occurrence Of Atlantic Bluefin Tuna (Thunnus Thynnus) Larvae In The Northern Gulf Of Mexico: Building A Classification Model From Archival Data, Barbara A. Muhling, John T. Lamkin, Mitchell A. Roffer

United States Department of Commerce: Staff Publications

Although bluefin tuna are found throughout the Atlantic Ocean, spawning in the western Atlantic has been recorded predominantly in the Gulf of Mexico (GOM) in spring. Larval bluefin tuna abundances from the northern GOM are formulated into an index used to tune the adult stock assessment, and the variability of this index is currently high. This study investigated whether some of the variability in larval bluefin tuna abundances was related to environmental conditions, by defining associations between larval bluefin tuna catch locations, and a suite of environmental variables. We hypothesized that certain habitat types, as defined by environmental variables, would …

Interacting Effects Of Phenotypic Plasticity And Evolution On Population Persistence In A Changing Climate, Thomas E. Reed, Daniel E. Schindler, Robin Waples

United States Department of Commerce: Staff Publications

Climate change affects individual organisms by altering development, physiology, behavior, and fitness, and populations by altering genetic and phenotypic composition, vital rates, and dynamics. We sought to clarify how selection, phenotypic plasticity, and demography are linked in the context of climate change. On the basis of theory and results of recent empirical studies of plants and animals, we believe the ecological and evolutionary issues relevant to population persistence as climate changes are the rate, type, magnitude, and spatial pattern of climate-induced abiotic and biotic change; generation time and life history of the organism; extent and type of phenotypic plasticity; amount …

Eco-Evolutionary Dynamics: Fluctuations In Population Growth Rate Reduce Effective Population Size In Chinook Salmon, Robin Waples, David Jensen, Michelle Mcclure

United States Department of Commerce: Staff Publications

We empirically assess the relationship between population growth rate (λ, a parameter central to ecology) and effective population size (N_e, a key parameter in evolutionary biology). Recent theoretical and numerical studies indicate that in semelparous species with variable age at maturity (such as Pacific salmon, many monocarpic plants, and various other species), differences in mean reproductive success among individuals reproducing in different years leads to variation in λ, and this in turn can reduce N_e. However, this phenomenon has received little empirical evaluation. We examined time series of abundance data for 56 populations of chinook …

An Epitope From Acanthamoeba Castellanii That Cross-React With Proteolipid Protein 139-151-Reactive T Cells Induces Autoimmune Encephalomyelitis In Sjl Mice, Chandirasegaran Massilamany, David Steffan, Jay Reddy

Jay Reddy Publications

We report here that an epitope (aa, 83-95) derived from Acanthamoeba castellanii (ACA) induces clinical signs of experimental autoimmune encephalomyelitis (EAE) in SJL/J mice reminiscent of the disease induced with myelin proteolipid protein (PLP) 139-151. By using IA^s/tetramers, we demonstrate that both ACA 83-95 and PLP 139-151 generate antigen-specific cross-reactive CD4 T cells and the T cells secrete identical patterns of cytokines and induce EAE with a similar severity. These results may provide insights into the pathogenesis of multiple sclerosis and ACA-induced granulomatous encephalitis.

The Influence Of Nutrients And Physical Habitat In Regulating Algal Biomass In Agricultural Streams, Mark D. Munn, Jeffrey Frey, Anthony Tesoriero

United States Geological Survey: Water Reports and Publications

This study examined the relative influence of nutrients (nitrogen and phosphorus) and habitat on algal biomass in five agricultural regions of the United States. Sites were selected to capture a range of nutrient conditions, with 136 sites distributed over five study areas. Samples were collected in either 2003 or 2004, and analyzed for nutrients (nitrogen and phosphorous) and algal biomass (chlorophyll a). Chlorophyll a was measured in three types of samples, fine-grained benthic material (CHLFG), coarse-grained stable substrate as in rock or wood (CHLCG), and water column (CHLS). Stream and riparian habitat were characterized at each site. TP ranged from …

Mercury Concentrations In Fish From A Sierra Nevada Foothill Reservoir Located Downstream From Historic Gold-Mining Operations, Michael K. Saiki, Barbara A. Martin, Thomas W. May, Charles N. Alpers

United States Geological Survey: Staff Publications

This study examined mercury concentrations in whole fish from Camp Far West Reservoir, an 830-ha reservoir in northern California, USA, located downstream from lands mined for gold during and following the Gold Rush of 1848–1864. Total mercury (reported as dry weight concentrations) was highest in spotted bass (mean, 0.93 μg/g; range, 0.16–4.41 μg/g) and lower in bluegill (mean, 0.45 μg/g; range, 0.22– 1.96 μg/g) and threadfin shad (0.44 μg/g; range, 0.21–1.34 μg/g). Spatial patterns for mercury in fish indicated high concentrations upstream in the Bear River arm and generally lower concentrations elsewhere, including downstream near the dam. These findings coincided …

A Macroinvertebrate Assessment Of Ozark Streams Located In Lead–Zinc Mining Areas Of The Viburnum Trend In Southeastern Missouri, Usa, Barry Poulton, Ann L. Allert, John M. Besser, Christopher J. Schmitt, William G. Brumbaugh, James F. Fairchild

United States Geological Survey: Staff Publications

The Viburnum Trend lead–zinc mining subdistrict is located in the southeast Missouri portion of the Ozark Plateau. In 2003 and 2004, we assessed the ecological effects of mining in several watersheds in the region. We included macroinvertebrate surveys, habitat assessments, and analysis of metals in sediment, pore water, and aquatic biota. Macroinvertebrates were sampled at 21 sites to determine aquatic life impairment status (full, partial, or nonsupport) and relative biotic condition scores. Macroinvertebrate biotic condition scores were significantly correlated with cadmium, nickel, lead, zinc, and specific conductance in 2003 (r = −0.61 to −0.68) and with cadmium, lead, and …

Vulnerability Of Age-0 Pallid Sturgeon Scaphirhynchus Albus To Fish Predation, W. E. French, Brian D. S. Graeb, S. R. Chipps, Katie N. Bertrand, T. M. Selch, R. A. Klumb

United States Geological Survey: Staff Publications

Stocking is a commonly employed conservation strategy for endangered species such as the pallid sturgeon, Scaphirhynchus albus. However, decisions about when, where and at what size pallid sturgeon should be stocked are hindered because vulnerability of pallid sturgeon to fish predation is not known. The objective of this study was to evaluate the vulnerability of age-0 pallid sturgeon to predation by two Missouri River predators under different flow regimes, and in combination with alternative prey. To document vulnerability, age-0 pallid sturgeon (<100 mm) were offered to channel catfish Ictalurus punctatus and smallmouth bass Micropterus dolomieu in laboratory experiments. Selection of pallid sturgeon by both …

Biological Opinion On The Operation Of The Missouri River Main Stem System, Operation And Maintenance Of The Missouri River Bank Stabilization And Navigation Project, And Operation Of The Kansas River Reservoir System

United States Army Corps of Engineers, Omaha District

This Annual Report summarizes implementation efforts in response to the Biological Opinion on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project, and Operation of the Kansas River Reservoir System. The document improves upon the previous annual Biological Opinion (BiOp) compliance reports by incorporating:

• The first combined U.S. Fish and Wildlife (USFWS) and U.S. Army Corps of Engineers (Corps) report documenting recovery efforts on the Missouri River satisfying reporting requirements of the 2003 Amended BiOp on the Operation of the Missouri River Main Stem System (System), Operation …

Use Biomedical Laboratories In Physics To Develop Student Reasoning, Robert G. Fuller

Robert G. Fuller Publications

The results of the “intrinsic motivation for learning” work by Thomas Malone (1) can be combined with the “development of reasoning” work by Robert Karplus (2) to create introductory physics laboratories that feature biomedical applications of physics. This presentation will discuss the attributes of the work of Malone and Karplus and illustrate how they can work together to construct physics laboratories that encourage the development of reasoning by students as well as intrigue them with biomedical applications. A concrete example will be given in a six-week module “How Do We See Color?” that was developed as part of the Humanized …

Traveling Wave Solutions For A Nonlocal Reaction-Diffusion Model Of Influenza A Drift, Joaquin Riviera, Yi Li

Mathematics and Statistics Faculty Publications

In this paper we discuss the existence of traveling wave solutions for a nonlocal reaction-diffusion model of Influenza A proposed in Lin et. al. (2003). The proof for the existence of the traveling wave takes advantage of the different time scales between the evolution of the disease and the progress of the disease in the population. Under this framework we are able to use the techniques from geometric singular perturbation theory to prove the existence of the traveling wave.