Digital Commons Network^™

Nature And Function Of Insulator Protein Binding Sites In The Drosophila Genome, Sarah C. R. Elgin, Et Al

Open Access Publications

No abstract provided.

Music: Identifying Mutational Significance In Cancer Genomes, Nathan D. Dees, Qunyuan Zhang, Cyriac Kandoth, Michael C. Wendl, William Schierding, Daniel C. Kobolt, Thomas B. Mooney, Matthew B. Callaway, David Dooling, Elaine R. Mardis, Richard K. Wilson, Li Ding

Open Access Publications

No abstract provided.

Chronic Intestinal Inflammation: Inflammatory Bowel Disease And Colitis-Associated Colon Cancer, Deborah C. Rubin, Anisa Shaker, Marc S. Levin

Open Access Publications

No abstract provided.

The Oxytricha Trifallax Mitochondrial Genome, Estienne C. Swart, Mariusz Nowacki, Justine Shum, Heather Stiles, Brian P. Higgins, Thomas G. Doak, Klaas Schotanus, Vincent J. Magrini, Patrick Minx, Elaine R. Mardis, Laura F. Landweber

Open Access Publications

No abstract provided.

Sexually Dimorphic Effect Of Aging On Skeletal Muscle Protein Synthesis, Gordon I. Smith, Dominic N. Reeds, Angela M. Hall, Kari T. Chambers, Brian N. Finck, Bettina Mittendorfer

Open Access Publications

No abstract provided.

Correlations Of Coronary Plaque Wall Thickness With Wall Pressure And Wall Pressure Gradient: A Representative Case Study, Biyue Liu, Jie Zheng, Richard Bach, Dalin Tang

Open Access Publications

No abstract provided.

Chapter 4 Regulation Of Genetically Engineered Microorganisms Under Fifra, Ffdca And Tsca, Chris A. Wozniak, Gwendolyn Mcclung, Joel Gagliardi, Mark Segal, Keith Matthews

United States Environmental Protection Agency: Publications

Since the dawn of civilization, humans have utilized microbial organisms of various sorts for food and agricultural production. More recently, microbes have been used for pesticidal, and environmental management purposes. With the advent of the development of recombinant DNA technology to genetically alter microbes, it became necessary for Federal regulators to assess the appropriate level, format, and application of their regulatory authorities. In 1986, the Of fi ce of Science and Technology Policy issued the Coordinated Framework for Regulation of Biotechnology. The Coordinated Framework constituted a comprehensive regulatory policy for biotechnology that, in essence, concluded that no new statutory authorities …

Characterization Of Pasteurella Multocida Strains Isolated From Geese, Zsuzsanna Varga, Dmitriy V. Volokhov, Laszlo Stipkovits, Akos Thuma, Boglarka Sellyei, Tibor Magyar

United States Food and Drug Administration: Publications

Phenotypic and genotypic diversity of forty-two Pasteurella multocida isolates from geese were characterized by analysis of their capsular type, Heddleston serotype, biotype, fimbrial gene allele type, comparative outer membrane protein (OMP) electrophoresis patterns, and were analyzed using PCR for the presence of virulence-associated genes (toxA, tbpA, pfhA, hgbA, hgbB, nanH, nanB, fimA, hsf-1, and pmHAS). A sequence comparison of the thdF and rpoB housekeeping genes of twenty representative P. multocida strains from three different OMP groups demonstrated that seventeen strains were closely related phylogenetically to previously published strains of P. multocida subsp. multocida and P. multocida subsp. gallicida, and only …

Bird Productivity And Nest Predation In Agricultural Grasslands, C.A. Ribic, Michael Guzy, Travis Anderson, David Sample, Jamie Nack

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Effective conservation strategies for grassland birds in agricultural landscapes require understanding how nesting success varies among different grassland habitats. A key component to this is identifying nest predators and how these predators vary by habitat. We quantified nesting activity of obligate grassland birds in three habitats [remnant prairie, cool-season grass Conservation Reserve Program (CRP) fields, and pastures) in southwest Wisconsin, 2002-2004. We determined nest predators using video cameras and examined predator activity using track stations. Bobolink (Dolichonyx oryzivorus) and Henslow's Sparrow (Ammodramus henslowii) nested primarily in CRP fields, and Grasshopper Sparrow (A. savannarum) in …

Use Of Real-Time Pcr To Detect Canine Parvovirus In Feces Of Free-Ranging Wolves, L. David Mech, Emily S. Almberg, Douglas Smith, Sagar Goyal, Randall S. Singer

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Using real-time PCR, we tested 15 wolf (Canis lupus) feces from the Superior National Forest (SNF), Minnesota, USA, and 191 from Yellowstone National Park (YNP), USA, collected during summer and 13 during winter for canine parvovirus (CPV)-2 DNA. We also tested 20 dog feces for CPV-2 DNA. The PCR assay was 100%sensitive and specific with a minimum detection threshold of 104 50% tissue culture infective dose. Virus was detected in two winter specimens but none of the summer specimens. We suggest applying the technique more broadly especially with winter feces.

Monitoring Of Endangered Roanoke Logperch (Percina Rex) In Smith River Upstream From The Philpott Reservoir On U.S. Army Corps Of Engineers Property Near Martinsville, Virginia, James H. Roberts, Paul L. Angermeier

United States Geological Survey: Publications

The purpose of this study was to continue annual monitoring of Roanoke logperch (Percina rex), an endangered fish, in the Smith River immediately upstream from Philpott Reservoir. This river reach is owned by the U.S. Army Corps of Engineers (USACE), which must ensure that appropriate actions are undertaken to aid in recovery of logperch. Monitoring of fish abundance and habitat conditions provides a means for assessing the species’ status and its responses to USACE management actions.

The Roanoke logperch is a large darter (Percidae: Etheostomatinae) endemic to the Roanoke, Dan, and Nottoway River basins of Virginia and North …

Assessment Of Macroinvertebrate Communities In Adjacent Urban Stream Basins, Kansas City, Missouri, Metropolitan Area, 2007 Through 2011, Eric D. Christensen, Heather M. Krempa

United States Geological Survey: Publications

Macroinvertebrates were collected as part of two separate urban water-quality studies from adjacent basins, the Blue River Basin (Kansas City, Missouri), the Little Blue River and Rock Creek Basins (Independence, Missouri), and their tributaries. Consistent collection and processing procedures between the studies allowed for statistical comparisons. Seven Blue River Basin sites, nine Little Blue River Basin sites, including Rock Creek, and two rural sites representative of Missouri ecological drainage units and the area’s ecoregions were used in the analysis. Different factors or levels of urban intensity may affect the basins and macroinvertebrate community metrics differently, even though both basins are …

Pore-Scale Characterization Of Biogeochemical Controls On Iron And Uranium Speciation Under Flow Conditions, Carolyn I. Pearce, Michael J. Wilkins, Changyong Zhang, Steve M. Heald, James K. Fredrickson, John M. Zachara

United States Department of Energy: Publications

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both Xray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively …

Quantitative 3-D Elemental Mapping By La-Icp-Ms Of A Basaltic Clast From The Hanford 300 Area, Washington, Usa, Sheng Peng, Qinhong Hu, Robert Ewing, Chongxuan Liu, John M. Zachara

United States Department of Energy: Publications

Laser ablation with inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to measure elemental concentrations at the 100-μm scale in a 3-dimensional manner within a basaltic clast sample collected from the Hanford 300 Area in south-central Washington State, United States. A calibration method was developed to quantify the LAICP- MS signal response using a constant-sum mass fraction of eight major elements; the method produced reasonable concentration measurements for both major and trace elements when compared to a standard basalt sample with known concentrations. 3-Dimensional maps (stacked 2-D contour layers, each representing 2100 μm × 2100 μm) show …

Molecular Underpinnings Of Fe(Iii) Oxide Reduction By Shewanella Oneidensis Mr-1, Liang Shi, Kevin Rosso, Tomas Clarke, David Richardson, John M. Zachara, James K. Fredrickson

United States Department of Energy: Publications

In the absence of O₂ and other electron acceptors, the Gram-negative bacterium Shewanella oneidensis MR-1 can use ferric [Fe(III)] (oxy) (hydr) oxideminerals as the terminal electron acceptors for an aerobic respiration. At circumneutral pH and in the absence of strong complexing ligands, Fe(III) oxides are relatively insoluble and thus are external to the bacterial cells. S. oneidensis MR-1 and related strains of metal-reducing Shewanella have evolved machinery (i.e.,metal-reducing or Mtr pathway) for transferring electrons from the inner-membrane, through the periplasmanda cross the outer-membrane to the surface of extracellular Fe(III) oxides. The protein components identified to date for the Mtr …

The ‘Porin–Cytochrome’ Model For Microbe-To-Mineral Electron Transfer, David Richardson, Julea Butt, James K. Fredrickson, John M. Zachara, Liang Shi, Marcus Edwards, Gaye White, Nanakow Baiden, Andrew Gates, Sophie Marritt, Thomas Clarke

United States Department of Energy: Publications

Many species of bacteria can couple anaerobic growth to the respiratory reduction of insoluble minerals containing Fe(III) or Mn(III/IV). It has been suggested that in Shewanella species electrons cross the outer membrane to extracellular substrates via ‘porin–cytochrome’ electron transport modules. The molecular structure of an outer-membrane extracellular-facing deca-haem terminus for such a module has recently been resolved. It is debated how, once outside the cells, electrons are transferred from outer-membrane cytochromes to insoluble electron sinks. This may occur directly or by assemblies of cytochromes, perhaps functioning as ‘nanowires’, or via electron shuttles. Here we review recent work in this field …

State Of The Strait Use Of Remote Sensing And Gis To Better Manage The Huron-Erie Corridor, Steve Francoeur, Luca Cargnelli, Anna Cook, John Hartig, John Gannon, Greg Norwood

United States Fish and Wildlife Service: Publications

Understanding the Patterns and Successes of Our Huron-Erie Corridor

The Huron-Erie Corridor, centered by Detroit, Michigan and Windsor, Ontario, is an exceptional example of a place with a concentration of various natural and human boundaries, contrasts, and complex dynamics. The inherent diversity and abundance of habitats in the Corridor in relation to the North American continent and the Great Lakes Basin gives it a centrality that has long attracted both wildlife and people. Of primary importance is the U.S.-Canada border which bisects the Corridor, oft en cited as the location of the largest flow of transnational trade on Earth. Here, …

Status And Harvests Of Sandhill Cranes: Mid-Continent, Rocky Mountain, Lower Colorado River Valley And Eastern Populations, Kammie L. Kruse, James A. Dubovsky, Thomas R. Cooper

United States Fish and Wildlife Service: Publications

Compared to increases recorded in the 1970s, annual indices to abundance of the Mid-Continent Population (MCP) of sandhill cranes have been relatively stable since the early 1980s. The spring 2012 index for sandhill cranes in the Central Platte River Valley, Nebraska, uncorrected for visibility bias, was 259,576 birds, which was significantly lower than the previous 5 years likely due to later timing of the survey period and an early spring migration. The photocorrected, 3-year average for 2009-11 was 579,863, which is above the established population-objective range of 349,000-472,000 cranes. All Central Flyway States, except Nebraska, allowed crane hunting in portions …

Influence Of Carbon And Lipid Sources On Variation Of Mercury And Other Trace Elements In Polar Bears (Ursus Maritimus), Heli Routti, Robert J. Letcher, Erik W. Born, Marsha Branigan, Rune Dietz, Thomas J. Evans, Melissa A. Mckinney, Elizabeth Peacock, Christian Sonne

United States Fish and Wildlife Service: Publications

In the present study, the authors investigated the influence of carbon and lipid sources on regional differences in liver trace element (As, Cd, Cu, total Hg, Mn, Pb, Rb, Se, and Zn) concentrations measured in polar bears (Ursus maritimus) (n=121) from 10 Alaskan, Canadian Arctic, and East Greenland subpopulations. Carbon and lipid sources were assessed using δ¹³C in muscle tissue and fatty acid (FA) profiles in subcutaneous adipose tissue as chemical tracers. A negative relationship between total Hg and δ¹³C suggested that polar bears feeding in areas with higher riverine inputs of …

From Protozoan Infection In Monarch Butterflies To Colony Collapse Disorder In Bees Are Emerging Infectious Diseases Proliferating In The Insect World?, Rebecca Bartel, Sonia Altizer

United States Fish and Wildlife Service: Publications

In the late 1990S, scientists first noticed mysterious declines in several wild bumble bee species (Bombus spp.) in both eastern and western North America, with one species now possibly extinct (Colla and Packer 2008). These bumble bee losses mirrored declines in the abundance of many other native pollinators (National Research Council 2007). Interestingly, the timing of bumble bee declines in the United States coincided with reports of disease outbreaks in commercial- reared bumble bees sold for use in the production of greenhouse tomatoes and peppers (Evans et al. 2008). This observation, together with reports of a higher incidence of …

Marine Biotoxins: Emergence Of Harmful Algal Blooms As Health Threats To Marine Wildlife, Spencer E. Fire, Frances M. Van Dolah

United States Department of Commerce: Staff Publications

Harmful algal blooms (HABs) affect aquatic ecosystems around the world, adversely affecting marine animal and human health, coastal ecosystem integrity, and economies that depend on coastal resources. Shellfish poisoning events involving humans who had ingested bivalves contaminated with HAB toxins primarily drove early scientific and social interest in HABs. More recently, research efforts have shown that HABs are often temporally and spatially correlated with the occurrence of acute morbidity or mortality of marine animals (Landsberg et al. 2005), and to date at least four classes of algal toxins have been associated with such events. Although fish, seabirds, and many other …

Recent Progress In West Nile Virus Diagnosis And Vaccination, Marina De Filette, Sebastian Ulbert, Mike Diamond, Niek N. Sanders

Open Access Publications

No abstract provided.

Copper Pellets Simulating Oral Exposure To Copper Ammunition: Absence Of Toxicity In American Kestrels (Falco Sparverius), J. Christian Franson, Lesanna L. Lahner, Carol U. Meteyer, Barnett A. Rattner

United States Geological Survey: Staff Publications

To evaluate the potential toxicity of copper

(Cu) in raptors that may consume Cu bullets, shotgun

pellets containing Cu, or Cu fragments as they feed on

wildlife carcasses, we studied the effects of metallic Cu

exposure in a surrogate, the American kestrel (Falco

sparverius). Sixteen kestrels were orally administered

5 mg Cu/g body mass in the form of Cu pellets

(1.18–2.00 mm in diameter) nine times during 38 days and

10 controls were sham gavaged on the same schedule. With

one exception, all birds retained the pellets for at least 1 h,

but most (69%) regurgitated pellets during …

A Thousand Tiny Pieces: The Federal Circuit’S Fractured Myriad Ruling, Lessons To Be Learned, And The Way Forward, Jonathan R. K. Stroud

IP Theory

No abstract provided.

A Sediment Ecotoxicity Assessment Platform For In Situ Measures Of Chemistry, Bioaccumulation And Toxicity. Part 1: System Description And Proof Of Concept, G. Allen Burton Jr., Gunther Rosen, D. Bart Chadwick, Marc S. Greenberg, W. Keith Taulbee, Guilherme R. Lotufo, Danny D. Reible

United States Navy: Publications

In situ-based testing using aquatic organisms has been widely reported, but is often limited in scope and practical usefulness in making decisions on ecological risk and remediation. To provide this capability, an integrated deployment system, the Sediment Ecotoxicity Assessment (SEA) Ring was developed, which incorporates rapid in situ hydrological, chemical, bioaccumulation, and toxicological Lines-of-Evidence (LoE) for assessing sediment and overlying water contamination. The SEA Ring system allows for diver-assisted, or diverless, deployment of multiple species of ecologically relevant and indigenous organisms in three different exposures (overlying water, sediment-water interface, and bulk sediment) for periods ranging from two days to …

The Population Structure Of Escherichia Coli Isolated From Subtropical And Temperate Soils, Muruleedhara N. Byappanahalli, Tao Yan, Matthew J. Hamilton, Satoshi Ishii, Roger S. Fujioka, Richard L. Whitman, Michael J. Sadowsky

United States Geological Survey: Staff Publications

While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and …

Remote Sensing Of Sagebrush Canopy Nitrogen, Jessica J. Mitchell, Nancy F. Glenn, Temuulen T. Sankey, Dewayne R. Derryberry, Matthew J. Germino

United States Geological Survey: Staff Publications

This paper presents a combination of techniques suitable for remotely sensing foliar Nitrogen (N) in semiarid shrublands – a capability that would significantly improve our limited understanding of vegetation functionality in dryland ecosystems. The ability to estimate foliar N distributions across arid and semi-arid environments could help answer process-driven questions related to topics such as controls on canopy photosynthesis, the influence of N on carbon cycling behavior, nutrient pulse dynamics, and post-fire recovery. Our study determined that further exploration into estimating sagebrush canopy N concentrations from an airborne platform is warranted, despite remote sensing challenges inherent to open canopy systems. …

Linking River Management To Species Conservation Using Dynamic Landscape-Scale Models, M. C. Freeman, G. R. Buell, L. E. Hay, W. B. Hughes, R. B. Jacobson, J. W. Jones, S. A. Jones, J. H. Lafontaine, K. R. Odom, J. T. Peterson, J. W. Riley, J. S. Schindler, C. Shea, J. D. Weaver

United States Geological Survey: Staff Publications

Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km² catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. …

Dynamics Of Envelope Evolution In Clade C Shiv-Infected Pig-Tailed Macaques During Disease Progression Analyzed By Ultra-Deep Pyrosequencing, For Yue Tso, Damien C. Tully, Sandra Gonzalez, Christopher Quince, On Ho, Patricia Polacino, Ruth M. Ruprecht, Shiu-Lok Hu, Charles Wood

Nebraska Center for Virology: Faculty Publications

Understanding the evolution of the human immunodeficiency virus type 1 (HIV-1) envelope during disease progression can provide tremendous insights for vaccine development, and simian-human immunodeficiency virus (SHIV) infection of nonhuman primate provides an ideal platform for such studies. A newly developed clade C SHIV, SHIV-1157ipd3N4, which was able to infect rhesus macaques, closely resembled primary HIV-1 in transmission and pathogenesis, was used to infect several pig-tailed macaques. One of the infected animals subsequently progressed to AIDS, whereas one remained a nonprogressor. The viral envelope evolution in the infected animals during disease progression was analyzed by a bioinformatics approach using ultra-deep …

Coxsackievirus B3 Infection Leads To The Generation Of Cardiac Myosin Heavy Chain-Α-Reactive Cd4 T Cells In A/J Mice, Arunakumar Gangaplara, Chandirasegaran Massilamany, Deborah M. Brown, Gustavo A. Delhon, Asit K. Pattnaik, Nora Chapman, Noel Rose, David J. Steffen, Jay Reddy

Jay Reddy Publications

Enteroviruses like coxsackievirus B3 (CVB3) are common suspects in myocarditis/dilated cardiomyopathy patients. Autoimmunity has been proposed as an underlying mechanism, but direct evidence of its role is lacking. To delineate autoimmune response in CVB3 myocarditis, we used IA^k dextramers for cardiac myosin heavy chain (Myhc)-α 334–352. We have demonstrated that myocarditis-susceptible A/J mice infected with CVB3 generate Myhc-α-reactive CD4 T cells and such a repertoire was absent in naïve mice as measured by proliferative response to Myhc-α 334–352 and IA^k dextramer staining. We also detected Myhc-α 334–352 dextramer⁺ cells in the hearts of CVB3-infected mice. The autoreactive …