Img/M: The Integrated Metagenome Data
Management And Comparative Analysis System,
2011
Lawrence Berkeley National Laboratory
Img/M: The Integrated Metagenome Data Management And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides
United States Department of Energy: Publications
The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M’s data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl
B-30929, A Novel Strain From A Commercial Ethanol Plant,
2011
National Center for Agricultural Utilization Research
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl B-30929, A Novel Strain From A Commercial Ethanol Plant, Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, David A. Mills
United States Department of Energy: Publications
Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium.
Vista Region Viewer (Rviewer)—A Computational System For
Prioritizing Genomic Intervals For Biomedical Studies,
2011
Lawrence Berkeley National Laboratory
Vista Region Viewer (Rviewer)—A Computational System For Prioritizing Genomic Intervals For Biomedical Studies, Igor Lukashin, Pavel Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak
United States Department of Energy: Publications
Summary:
Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (RViewer), an interactive online tool that allows for efficient screening and prioritization of regions of the human genome for follow-up studies. The tool takes as input genetic variation data from different biomedical studies, determines a number of various functional parameters for both coding …
Complete Genome Sequence Of The Plant Growth-Promoting
Endophyte Burkholderia Phytofirmans Strain Psjn,
2011
AIT Austrian Institute of Technology GmbH
Complete Genome Sequence Of The Plant Growth-Promoting Endophyte Burkholderia Phytofirmans Strain Psjn, Alexandra Weilharter, Birgit Mitter, Maria V. Shin, Patrick S. G. Chain, Jerzy Nowak, Angela Sessitsch
United States Department of Energy: Publications
Burkholderia phytofirmans PsJNT is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.
Characterization Of The Intragranular Water Regime Within
Subsurface Sediments: Pore Volume, Surface Area, And Mass
Transfer Limitations,
2011
U.S. Geological Survey
Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara
United States Department of Energy: Publications
Although ‘‘intragranular’’ pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted …
Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion,
2011
Pacific Northwest National Laboratory
Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara
United States Department of Energy: Publications
Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found …
Transient Groundwater Chemistry Near A River: Effects On U(Vi)
Transport In Laboratory Column Experiments,
2011
Oregon State University
Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara
United States Department of Energy: Publications
In the 300 Area of a U(VI)-contaminated aquifer at Hanford, Washington, USA, inorganic carbon and major cations, which have large impacts on U(VI) transport, change on an hourly and seasonal basis near the Columbia River. Batch and column experiments were conducted to investigate the factors controlling U(VI) adsorption/desorption by changing chemical conditions over time. Low alkalinity and low Ca concentrations (Columbia River water) enhanced adsorption and reduced aqueous concentrations. Conversely, high alkalinity and high Ca concentrations (Hanford groundwater) reduced adsorption and increased aqueous concentrations of U(VI). An equilibrium surface complexation model calibrated using laboratory batch experiments accounted for the decrease …
Simulating Adsorption Of U(Vi) Under Transient Groundwater
Flow And Hydrochemistry: Physical Versus Chemical
Nonequilibrium Model,
2011
CSIRO Land and Water
Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara
United States Department of Energy: Publications
Coupled intragrain diffusional mass transfer and nonlinear surface complexation processes play an important role in the transport behavior of U(VI) in contaminated aquifers. Two alternative model approaches for simulating these coupled processes were analyzed and compared: (1) the physical nonequilibrium approach that explicitly accounts for aqueous speciation and instantaneous surface complexation reactions in the intragrain regions and approximates the diffusive mass exchange between the immobile intragrain pore water and the advective pore water as multirate first-order mass transfer and (2) the chemical nonequilibrium approach that approximates the diffusion-limited intragrain surface complexation reactions by a set of multiple first-order surface complexation …
Transition Of Cellulose Crystalline Structure And Surface Morphology
Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation
To Enzymatic Hydrolysis,
2011
Joint BioEnergy Institute
Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh
United States Department of Energy: Publications
Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of themajor factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine (Pinus radiata), and eucalyptus (Eucalyptus globulus), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160°C for 1, 3, 6, and 12 …
Absolute High-Resolution Se+ Photoionization Cross-Section Measurements
With Rydberg-Series Analysis,
2011
University of Nevada - Reno
Absolute High-Resolution Se+ Photoionization Cross-Section Measurements With Rydberg-Series Analysis, D. A. Esteves, R. C. Bilodeau, N. C. Sterling, R. A. Phaneuf, A. L. D. Kilcoyne, E. C. Red, A. Aguilar
United States Department of Energy: Publications
Absolute single photoionization cross-section measurements for Se+ ions were performed at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory using the photo-ion merged-beams technique. Measurements were made at a photon energy resolution of 5.5 meV from 17.75 to 21.85 eV spanning the 4s24p34So3/2 ground-state ionization threshold and the 2Po3/2,2Po1/2,2Do5/2, and2Do3/2 metastable state thresholds. Extensive analysis of the complex resonant structure in this region identified numerous Rydberg series of resonances and …
Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+,
2011
University of Nevada - Reno
Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+, M. F. Gharaibeh, A. Aguilar, A. M. Covington, E. D. Emmons, S. W. J. Scully, R. A. Phaneuf, A. Muller, J. D. Bozek, A. L. D. Kilcoyne, A. S. Schlachter, I. Alvarez, C. Cisneros, G. Hinojosa
United States Department of Energy: Publications
Cross sections for single photoionization of Fe3+, Fe5+, and Fe7+ ions were measured at spectral resolutions of 0.04, 0.15, and 0.13 eV, respectively, by merging mass- and charge-selected ion beams with a beam of monochromatized synchrotron undulator radiation. The measurements span photon energy ranges beginning at the ionization thresholds and extending several tens of electron volts to include the most important resonant contributions due to 3p–nd transitions to autoionizing states. The photoion yield spectra are characterized by narrow resonances and also broad features in Fe3+ and Fe5+ that are believed to result …
An Approach To Crystallizing Proteins By
Metal-Mediated Synthetic Symmetrization,
2011
University of California - Los Angeles
An Approach To Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization, Arthur Laganowsky, Minglei Zhao, Angela B. Soriaga, Michael R. Sawaya, Duilio Cascio, Todd O. Yeates
United States Department of Energy: Publications
Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu …
Modification Of Native Grasses For Biofuel Production May
Increase Virus Susceptibility,
2011
Michigan State University, East Lansing
Modification Of Native Grasses For Biofuel Production May Increase Virus Susceptibility, Abbie C. Schrotenboer, Michael S. Allen, Carolyn M. Malmstrom
United States Department of Energy: Publications
Bioenergy production is driving modifications to native plant species for use as novel biofuel crops. Key aims are to increase crop growth rates and to enhance conversion efficiency by reducing biomass recalcitrance to digestion. However, selection for these biofuel-valuable traits has potential to compromise plant defenses and alter interactions with pests and pathogens. Insect-vectored plant viruses are of particular concern because perennial crops have potential to serve as virus reservoirs that influence regional disease dynamics. In this study, we examined relationships between growth rates and biomass recalcitrance in five switchgrass (Panicum virgatum) populations, ranging from near wild type …
2011 Nebraska Water Monitoring
Programs Report,
2011
NDEQ
2011 Nebraska Water Monitoring Programs Report, Marty Link
Nebraska Department of Environmental Quality: Reports
The Nebraska Department of Environmental Quality (NDEQ) is charged with monitoring, assessing, and to the extent possible, managing the state’s water resources. The purpose of this work is to protect and maintain good quality water and encourage or execute activities to improve poor water quality. Monitoring is done on the over 18,000 miles of flowing rivers and streams, our greater than 280,000 acres of surface water in lakes and reservoirs, and the vast storage of groundwater in Nebraska’s aquifers.
Charge And Fluence Lifetime Measurements Of A Dc High Voltage Gaas Photogun
At High Average Current,
2011
Thomas Jefferson National Accelerator Facility
Charge And Fluence Lifetime Measurements Of A Dc High Voltage Gaas Photogun At High Average Current, J. Grames, R. Suleiman, P. A. Adderley, J. Clark, J. Hansknecht, D. Machie, M. Poelker, M. L. Stutzman
United States Department of Energy: Publications
GaAs-based dc high voltage photoguns used at accelerators with extensive user programs must exhibit long photocathode operating lifetime. Achieving this goal represents a significant challenge for proposed high average current facilities that must operate at tens of milliamperes or more. This paper describes techniques to maintain good vacuum while delivering beam, and techniques that minimize the ill effects of ion bombardment, the dominant mechanism that reduces photocathode yield of a GaAs-based dc high voltage photogun. Experimental results presented here demonstrate enhanced lifetime at high beam currents by: (a) operating with the drive laser beam positioned away from the electrostatic center …
Zinc Speciation In Power Plant Burning Mixtures Of Coal And Tires,
2011
Environmental Science and Nanotechnology Department, Catarinense Institute of Environmental Research and Human Development– IPADHC, Capivari de Baixo, Santa Catarina, Brazil.
Zinc Speciation In Power Plant Burning Mixtures Of Coal And Tires, Luis F.O. Silva, Marcos L.S. Oliveira, Carmen Serra, James C. Hower
Coal Combustion and Gasification Products Journal Archive
Fly ash from the cyclone-boiler co-combustion of high-S, high volatile bituminous coal and tire-derived fuel (tdf) was studied using a variety of chemical, optical, and microbeam techniques. Fly ash, dominated by Al-Si glass with lesser amounts of coalderived carbons, Fe-spinels, and tire-derived carbons, has Zn concentrations ranging from 2200 ppm (1st ESP row) to 6900 ppm Zn (3rd ESP row). Zinc occurs in Zn-rich nanoparticles in the Al-Si glass phases and as ZnO in amorphous and crystalline nanominerals, Fe- and Zn-sulfides, Pb-Al-Fe sulfates, and Zn sulfates. Iron-rich, Al- and Ti-bearing spinels contain accessory Zn2+,Cr3+,Mn2+, and Pb2+. Fe-sulfates and phosphates nanoparticles …
Co-Disposal Of Dry Fgd By-Product With Coal Gasification Ash And Inorganic Brines,
2011
SASOL Technology (Pty) Ltd, Environmental Sciences and Engineering, P/Bag x 1034, Secunda, South Africa, 2302
Co-Disposal Of Dry Fgd By-Product With Coal Gasification Ash And Inorganic Brines, Jabulani S. Mahlaba, P.C. Pretorius, Subal Maharajh, M.P. Augustyn
Coal Combustion and Gasification Products Journal Archive
There is a growing pressure from the environmental authorities and public bodies to reduce anthropogenic pollution. Stringent environmental legislation is being implemented for industries around the world, even more so for coal consuming industries. Control of gaseous emissions is one of the areas that are receiving considerable attention towards sustainable development. Coal combustion in coal-fired power utilities emits SO~x~ to the atmosphere. Dry flue gas desulphurisation (FGD) is a well known technology often used to mitigate sulphur emissions in coal-fired power utilities. It traditionally uses lime to neutralise SO~x~, and forms a mixture of anhydrite (CaSO~4~), and calcium sulphite (CaSO~3~). …
Magnetite Nanoparticles For Medical Mr Imaging,
2011
University of Washington, Seattle
Magnetite Nanoparticles For Medical Mr Imaging, Zachary R. Stephen, Forrest M. Kievit, Miqin Zhang
Department of Agricultural and Biological Systems Engineering: Faculty Publications
Magnetic resonance imaging (MRI) has become one of the most widely used and powerful tools for non-invasive clinical diagnosis due to its high soft tissue contrast, spatial resolution, and penetration depth1. In addition, images are acquired without the use of ionizing radiation or radiotracers that would cause unwanted harmful side-effects. A considerable amount of research in medical MR imaging is focused on the development of contrast agents that can provide better delineation between healthy and diseased tissue. Magnetic nanoparticles (MNPs) are a major class of nanoscale material currently under extensive development for improved diagnosis of a wide range of diseases, …
A Multi-Analytical Approach To Understand The Chemistry Of Fe-Minerals In Feed Coals And Ashes,
2011
Development Department of Touristic Opportunities, Catarinense Institute of Environmental Research and Human Development– IPADHC, Capivari de Baixo, Santa Catarina, Brazil
A Multi-Analytical Approach To Understand The Chemistry Of Fe-Minerals In Feed Coals And Ashes, Marcos L.S. Oliveira, Frans Waanders, Luis F.O. Silva, Andre Jasper, Carlos H. Sampaio, Dursman Mchabe, Rachel S. Hatch, James C. Hower
Coal Combustion and Gasification Products Journal Archive
Seven feed coals used in the Brazilian power generation industry were obtained and subsequently analysed together with fly ash and bottom ash from a major Brazilian power plant. The samples were investigated by means of room temperature FeMo¨ssbauer analyses, X-ray diffraction, Raman spectroscopy, scanning electron microscope and petrographic analysis. In addition, nanometer-sized crystalline phases in coals and ashes were characterised using an energy-dispersive X-ray spectrometer and a high-resolution transmission electron microscope. The major identified Fe-bearing minerals in the coals were found to be actinolite, ankerite, chalcopyrite, chlorite, goethite, illite, ilmenite, magnesioferrite, natrojarosite, pyrite, pyrrhotite, and siderite; whilst in the fly …
Compositional Variations In Pilot Gasifier And Laboratory-Produced Slags And Their Impacts On Slag Viscosity And Coal Assessment,
2011
CSIRO Energy Technology, PO Box 883, Kenmore QLD 4069 Australia
Compositional Variations In Pilot Gasifier And Laboratory-Produced Slags And Their Impacts On Slag Viscosity And Coal Assessment, Alexander Ilyushechkin, Daniel Roberts, David Harris
Coal Combustion and Gasification Products Journal Archive
The flow behaviour of coal mineral matter at high temperatures is an important parameter for coal use in entrained-flow gasification technologies. Recently, gasification performance data was obtained from a series of pilot-scale gasification tests on a suite of well-characterised Australian black coals. Evaluation of the results of the pilot tests and the detailed laboratory investigations provided the opportunity for evaluation of the practical applicability of different laboratory and modelling techniques for coal assessment in terms of mineral matter behaviour in entrained flow gasification. A series of viscosity measurements was made over the range 1200–1600uC using slags produced in a pilot …
