Our scheme for the tagless purification of water soluble complexes. 10 g of protein from a crude bacterial extract is first fractionated by ammonium sulfate precipitation and then by a series of chromatographic steps: anion exchange (IEX), hydrophobic interaction (HIC), and finally size exclusion (Gel Filtration). Fractions from the last chromatography step are trypsin digested and peptides labeled with iTRAQ reagents to allow multiplexing and quantitation during mass spectrometric analysis. Elution profiles of identified proteins are then subjected to clustering analysis.

Microbes live in changing environments and change their phenotype via gene regulation in response. Although this transcriptional response is important for fitness, very little is known about how it evolves in microbes. We started by asking a number of high-level questions about the evolution of transcriptional phenotype: (1) To what extent is transcriptional response conserved, i.e. do conserved genes respond similarly to the same condition; (2) To what extent are transcriptional modules conserved; and (3) Does there exist a general stress response to a variety of stressors? To illuminate these questions, we analyzed more than 500 microarray experiments across the bacterial domain. We looked for conservation of transcriptional regulation both in close sister species and vastly divergent clades. In addition, we produced and analyzed an extensive in-house compendium of environmental stress data in three metal-reducing bacteria.

When analyzing field data, the uncertainty in the background continuum emission produces the majority of error in the final gamma-source analysis. The background emission typically dominates an observed spectrum in terms of counts and is highly variable spatially and temporally. The majority of the spectral shape of the background continuum is produced by combinations of cosmic rays, {sup 40}K, {sup 235}U, and {sup 220}Rn, and the continuum is similar in shape to the 15%-20% level for most field observations. However, the goal of spectroscopy analysis is to pick up subtle peaks (<%5) upon this large background. Because the continuum is falling off as energy increases, peak detection algorithms must first define the background surrounding the peak. This definition is difficult when the range of background shapes is considered. The full spectral template matching algorithms are heavily weighted to solving for the background continuum as it produces significant counts over much of the energy range. The most appropriate background mitigation technique is to take a separate background observation without the source of interest. But, it is frequently not possible to record a background observation in the exact location before (or after) a source has been detected. Thus, one uses approximate backgrounds …

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNA from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized …

Carbon dioxide (CO{sub 2}) sensors are often deployed in commercial buildings to obtain CO{sub 2} data that are used, in a process called demand-controlled ventilation, to automatically modulate rates of outdoor air ventilation. The objective is to keep ventilation rates at or above design specifications and code requirements and also to save energy by avoiding excessive ventilation rates. Demand controlled ventilation is most often used in spaces with highly variable and sometime dense occupancy. Reasonably accurate CO{sub 2} measurements are needed for successful demand controlled ventilation; however, prior research has suggested substantial measurement errors. Accordingly, this study evaluated: (a) the accuracy of 208 CO{sub 2} single-location sensors located in 34 commercial buildings, (b) the accuracy of four multi-location CO{sub 2} measurement systems that utilize tubing, valves, and pumps to measure at multiple locations with single CO{sub 2} sensors, and (c) the spatial variability of CO{sub 2} concentrations within meeting rooms. The field studies of the accuracy of single-location CO{sub 2} sensors included multi-concentration calibration checks of 90 sensors in which sensor accuracy was checked at multiple CO{sub 2} concentrations using primary standard calibration gases. From these evaluations, average errors were small, -26 ppm and -9 ppm at 760 and 1010 …

The Norman Landfill is a closed municipal solid waste landfill located on an alluvium associated with the Canadian River in Norman, Oklahoma. It has operated as a research site since 1994 because it is typical of many closed landfill sites across the U.S. Leachate from the unlined landfill forms a groundwater plume that extends downgradient approximately 250 m from the landfill toward the Canadian River. To investigate the impact of the landfill leachate on the diversity and functional structure of microbial communities, groundwater samples were taken from eight monitoring wells at a depth of 5m, and analyzed using a comprehensive functional gene array covering about 50,000 genes involved in key microbial processes, such as biogeochemical cycling of C, N, P, and S, and bioremediation of organic contaminants and metals. Wells are located within a transect along a presumed flow path with different distances to the center of the leachate plume. Our analyses showed that microbial communities were obviously impacted by the leachate-component from the landfill. The number of genes detected and microbial diversity indices in the center (LF2B) and its closest (MLS35) wells were significantly less than those detected in other more downgradient wells, while no significant changes were observed …

Tapered plasma channels are considered for controlling dephasing of a beam with respect to a plasma wave driven by a weakly-relativistic, short-pulse laser. Tapering allows for enhanced energy gain in a single laser plasma accelerator stage. Expressions are derived for the taper, or longitudinal plasma density variation, required to maintain a beam at a constant phase in the longitudinal and/or transverse fields of the plasma wave. In a plasma channel, the phase velocities of the longitudinal and transverse fields differ, and, hence, the required tapering differs. The length over which the tapered plasma density becomes singular is calculated. Linear plasma tapering as well as discontinuous plasma tapering, which moves beams to adjacent plasma wave buckets, are also considered. The energy gain of an accelerated electron in a tapered laser-plasma accelerator is calculated and the laser pulse length to optimize the energy gain is determined.

A literature survey on the dissolution of spent nuclear fuel from the University of Missouri Research Reactor (MURR) has been performed. This survey encompassed both internal and external literature sources for the dissolution of aluminum-clad uranium alloy fuels. The most limiting aspect of dissolution in the current facility configuration involves issues related to the control of the flammability of the off-gas from this process. The primary conclusion of this work is that based on past dissolution of this fuel in H-Canyon, four bundles of this fuel (initial charge) may be safely dissolved in a nitric acid flowsheet catalyzed with 0.002 M mercuric nitrate using a 40 scfm purge to control off-gas flammability. The initial charge may be followed by a second charge of up to five bundles to the same dissolver batch depending on volume and concentration constraints. The safety of this flowsheet relies on composite lower flammability limits (LFL) estimated from prior literature, pilot-scale work on the dissolution of site fuels, and the proposed processing flowsheet. Equipment modifications or improved LFL data offer the potential for improved processing rates. The fuel charging sequence, as well as the acid and catalyst concentrations, will control the dissolution rate during the initial …

Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that …

Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are …

Respiratory versatility and psychrophily are the hallmarks of Shewanella. The ability to utilize a wide range of electron acceptors for respiration is due to the large number of c-type cytochrome genes present in the genome of Shewanella strains. More recently the dissimilatory metal reduction of Shewanella species has been extensively and intensively studied for potential applications in the bioremediation of radioactive wastes of groundwater and subsurface environments. Multiple Shewanella genome sequences are now available in the public databases (Fredrickson et al., 2008). Most of the sequenced Shewanella strains were isolated from marine environments and this genus was believed to be of marine origin (Hau and Gralnick, 2007). However, the well-characterized model strain, S. oneidensis MR-1, was isolated from the freshwater lake sediment of Lake Oneida, New York (Myers and Nealson, 1988) and similar bacteria have also been isolated from other freshwater environments (Venkateswaran et al., 1999). Here we comparatively analyzed the genome sequence and physiological characteristics of S. putrefaciens W3-18-1 and S. oneidensis MR-1, isolated from the marine and freshwater lake sediments, respectively. The anaerobic respirations, carbon source utilization, and cell motility have been experimentally investigated. Large scale horizontal gene transfers have been revealed and the genetic divergence between these …

IMPACT-T is a fully three-dimensional program to track relativistic particles taking into account space charge forces and short-range longitudinal and transverse wakenelds. IMPACT-T is one of the few codes used in the photoinjector community that has a parallel implementation, making it very useful for high statistics simulations of beam halos and beam diagnostics. It has a comprehensive set of beamline elements, and furthermore allows arbitrary overlap of their fields, which gives the IMPACT-T a capability to model both the standing wave structure and traveling wave structure. It is also unique in its use of space-charge solvers based on an integrated Green function to efficiently and accurately treat beams with large aspect ratio, and a shifted Green function to efficiently treat image charge effects of a cathode. It is also unique in its inclusion of energy binning in the space-charge calculation to model beams with large energy spread. IMPACT-T has a flexible data structure that allows particles to be stored in containers with common characteristics; for photoinjector simulations the containers represent multiple slices, but in other applications they could correspond, e.g., to particles of different species. Together, all these features make IMPACT-T a powerful and versatile tool for modeling beams in …

Thermal ionization and gas mass spectrometers are widely used across the Department of Energy (DOE) Complex and contractor laboratories. These instruments support critical missions, where high reliability and low measurement uncertainty are essential. A growing number of these mass spectrometers are significantly older than their original design life. The reality is that manufacturers have declared many of the instrument models obsolete, with direct replacement parts and service no longer available. Some of these obsolete models do not have a next generation, commercially available replacement. Today's budget conscious economy demands for the use of creative funds management. Therefore, the ability to refurbish (or upgrade) these valuable analytical tools and extending their useful life is a cost effective option. The Savannah River Site (SRS) has the proven expertise to breathe new life into older mass spectrometers, at a significant cost savings compared to the purchase and installation of new instruments. A twenty-seven year old Finnigan MAT-261{trademark} Thermal Ionization Mass Spectrometer (TIMS), located at the SRS F/H Area Production Support Laboratory, has been successfully refurbished. Engineers from the Savannah River National Laboratory (SRNL) fabricated and installed the new electronics. These engineers also provide continued instrument maintenance services. With electronic component drawings being DOE …

We present a combined experimental and theoretical work on the ionization energies of polyacetylene -- organic molecules considered as important building blocks to form polycyclic aromatic hydrocarbons (PAHs) in the proto planetary nebulae such as of CRL 618. This set of astrophysical data can be utilized with significant confidence in future astrochemical models of photon-dominated regions and also of the proto planetary nebulae CRL 618. We recommend ionization energies of polyacetylenes from diacetylene up to heptaacetylene with an experimental accuracy of +- 0.05 eV: 10.03 eV (diacetylene), 9.45 eV (triacetylene), 9.08 eV (tetraacetylene), 8.75 eV (pentaacetylene), 8.65 eV (hexaacetylene), and 8.50 eV (heptaacetylene); further, ionization energies and with an accuracy of +- 0.1 eV: 8.32 eV (octaacetylene) and 8.24 eV (nonaacetylene) were computed. Implications of these energies to the redox chemistry involved in the multiply charged metal-ion mediated chemistry of hydrocarbon-rich atmospheres of planets and their moons such as Titan are also discussed.

Recent experience indicates that the LCLS undulator segments must not, at any time following tuning, be allowed to change temperature by more than about {+-}2.5 C or the magnetic center will irreversibly shift outside of acceptable tolerances. This vulnerability raises a concern that under fault conditions the ambient temperature in the Undulator Hall might go outside of the safe range and potentially could require removal and retuning of all the segments. In this note we estimate changes that can be expected in the Undulator Hall air temperature for three fault scenarios: (1) System-wide power failure; (2) Heating Ventilation and Air Conditioning (HVAC) system shutdown; and (3) HVAC system temperature regulation fault. We find that for either a system-wide power failure or an HVAC system shutdown (with the technical equipment left on), the short-term temperature changes of the air would be modest due to the ability of the walls and floor to act as a heat ballast. No action would be needed to protect the undulator system in the event of a system-wide power failure. Some action to adjust the heat balance, in the case of the HVAC power failure with the equipment left on, might be desirable but is not …

Testing of nuclear explosives caused widespread contamination of surface soils on the Nevada Test Site (NTS). Atmospheric tests produced the majority of this contamination. The Radionuclide Inventory and Distribution Program (RIDP) was developed to determine distribution and total inventory of radionuclides in surface soils at the NTS to evaluate areas that may present long-term health hazards. The RIDP achieved this objective with aerial radiological surveys, soil sample results, and in situ gamma spectroscopy. This white paper presents the justification to support the use of RIDP data as a guide for future evaluation and to support closure of Soils Sub-Project sites under the purview of the Federal Facility Agreement and Consent Order. Use of the RIDP data as part of the Data Quality Objective process is expected to provide considerable cost savings and accelerate site closures. The following steps were completed: - Summarize the RIDP data set and evaluate the quality of the data. - Determine the current uses of the RIDP data and cautions associated with its use. - Provide recommendations for enhancing data use through field verification or other methods. The data quality is sufficient to utilize RIDP data during the planning process for site investigation and closure. Project …

This report details the chemical analysis results for the characterization of the May 19, 2010 inadvertent transfer from the Saltstone Production Facility (SPF) to the Saltstone Disposal Facility (SDF). On May 19, 2010, the Saltstone Processing Facility (SPF) inadvertently transferred approximately 1800 gallons of untreated low-level salt solution from the salt feed tank (SFT) to Cell F of Vault 4. The transfer was identified and during safe configuration shutdown, approximately 70 gallons of SFT material was left in the Saltstone hopper. After the shutdown, the material in the hopper was undisturbed, while the SFT has received approximately 1400 gallons of drain water from the Vault 4 bleed system. The drain water path from Vault 4 to the SFT does not include the hopper (Figure 1); therefore it was determined that the material remaining in the hopper was the most representative sample of the salt solution transferred to the vault. To complete item No.5 of Reference 1, Savannah River National Laboratory (SRNL) was asked to analyze the liquid sample retrieved from the hopper for pH, and metals identified by the Resource Conservation and Recovery Act (RCRA). SRNL prepared a report to complete item No.5 and determine the hazardous nature of the …

There is an enduring requirement to improve our ability to detect potential threats and discriminate these from the legitimate commercial and recreational activity ongoing in the nearshore/littoral portion of the maritime domain. The Northwest Maritime Information and Littoral Operations (NW-MILO) Program at PNNL’s Coastal Security Institute in Sequim, Washington is establishing a methodology to detect and classify these threats - in part through developing a better understanding of acoustic signatures in a near-shore environment. The purpose of the acoustic data collection described here is to investigate the acoustic signatures of small vessels. The data is being recorded continuously, 24 hours a day, along with radar track data and imagery. The recording began in August 2008, and to date the data contains tens of thousands of signals from small vessels recorded in a variety of environmental conditions. The quantity and variety of this data collection, with the supporting imagery and radar track data, makes it particularly useful for the development of robust acoustic signature models and advanced algorithms for signal classification and information extraction. The underwater acoustic sensing system is part of a multi-modal sensing system that is operating near the mouth of Sequim Bay. Sequim Bay opens onto the Straight …

Sulfate reducing bacteria (SRB) play an important role in global sulfur and carbon cycling through their ability to completely mineralize organic matter while respiring sulfate to hydrogen sulfide. They are ubiquitous in anaerobic environments and have the ability to reduce toxic metals like Cr(VI) and U(VI). While SRB have been studied for over three decades, bioenergetic modes of this group of microbes are poorly understood. Desulfovibrio vulgaris strain Hildenborough (DvH) has served as a model SRB over the last decade with the accumulation of transcriptomic, proteomic and metabolic data under a wide variety of stressors. To further investigate the three hypothesized modes of energy generation in this anaerobe we conducted a systematic study involving multiple electron donor and acceptor combinations for growth. DvH was grown at 37oC in a defined medium with (a) lactate + thiosulfate, (b) lactate + sulfite (c) lactate + sulfate, (d) pyruvate + sulfate, (e) H2 + acetate + sulfate, (f) formate + acetate + sulfate, g) formate + sulfate and (h) pyruvate fermentation. Cells were harvested at mid-log phase of growth for all conditions for transcriptomics, when the optical density at 600nm was in the range 0.42-0.5. Initial results indicate that cells grown on lactate …

The role of tetraheme cytochrome c3 (CycA) in the metabolism of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was investigated by deletion of the cycA gene using a marker-exchange deletion strategy. A highly abundant periplasmic cytochrome, CycA has the important function of transferring electrons from periplasmic hydrogenases (Hyd, Hyn, Hys) to transmembrane complexes which transport the electrons to the cytoplasm where sulfate is reduced. Previous studies have indicated that during its interaction with periplasmic hydrogenases, CycA is also involved in the reduction of toxic metals. Growth of the cycA mutant strain on lactate as the electron donor and sulfate as the terminal electron acceptor showed that, despite its abundance, CycA is not essential for DvH growth. However, the rate of growth of the mutant strain was significantly lower, and the extent of growth less, than rates and extents of growth of the wild type and complement strains on lactate/sulfate medium. This indicates that a portion of the electrons generated from cytoplasmic lactate oxidation are transported by CycA for energy production, possibly in a hydrogen cycling mechanism employed to generate ATP. Failure of the mutant strain to grow on either formate or H2, with sulfate or sulfite as electron acceptors, further …

The Area 5 Hazardous Waste Storage Unit (HWSU) was established to support testing, research, and remediation activities at the Nevada Test Site (NTS), a large-quantity generator of hazardous waste. The HWSU, located adjacent to the Area 5 Radioactive Waste Management Site (RWMS), is a prefabricated, rigid steel-framed, roofed shelter used to store hazardous nonradioactive waste generated on the NTS. No offsite generated wastes are managed at the HWSU. Waste managed at the HWSU includes the following categories: Flammables/Combustibles; Acid Corrosives; Alkali Corrosives; Oxidizers/Reactives; Toxics/Poisons; and Other Regulated Materials (ORMs). A list of the regulated waste codes accepted for storage at the HWSU is provided in Section B.2. Hazardous wastes stored at the HWSU are stored in U.S. Department of Transportation (DOT) compliant containers, compatible with the stored waste. Waste transfer (between containers) is not allowed at the HWSU and containers remain closed at all times. Containers are stored on secondary containment pallets and the unit is inspected monthly. Table 1 provides the metric conversion factors used in this application. Table 2 provides a list of existing permits. Table 3 lists operational Resource Conservation and Recovery Act (RCRA) units at the NTS and their respective regulatory status.

We describe the scientific motivation for a new type of accelerator, the muon collider. This accelerator would permit an energy-frontier scientific program and yet would fit on the site of an existing laboratory. Such a device is quite challenging, and requires a substantial R&D program. After describing the ingredients of the facility, the ongoing R&D activities of the Muon Accelerator Program are discussed. A possible U.S. scenario that could lead to a muon collider at Fermilab is briefly mentioned.

While more and more studies are being conducted on the effects of global warming, little is known regarding the response of metabolic change of whole soil microbial communities to this phenomenon. In this study, functional gene changes at the mRNA level were analyzed by our new developed GeoChip 3.0. Soil samples were taken from a long-term climate warming experiment site, which has been conducted for ~;;8 years at the Kessler Farm Field Laboratory, a 137.6-ha farm located in the Central Redbed Plains, in McClain County, Oklahoma. The experiment uses a paired factorial design with warming as the primary factor nested with clipping as a secondary factor. An infrared heater was used to simulate global warming, and clipping was used to mimic mowing hay. Twelve 2m x 2m plots were divided into six pairs of warmed and control plots. The heater generates a constant output of ~;;100 Watts m-2 to approximately 2 oC increase in soil temperature above the ambient plots, which is at the low range of the projected climate warming by IPCC. Soil whole microbial communities? mRNA was extracted, amplified, labeled and hybridized with our GeoChip 3.0, a functional gene array covering genes involved in N, C, P, and …

An investigation was conducted to compare and evaluate contaminant transport results of two model codes, GoldSim and Porflow, using a simple 1-D string of elements in each code. Model domains were constructed to be identical with respect to cell numbers and dimensions, matrix material, flow boundary and saturation conditions. One of the codes, GoldSim, does not simulate advective movement of water; therefore the water flux term was specified as a boundary condition. In the other code, Porflow, a steady-state flow field was computed and contaminant transport was simulated within that flow-field. The comparisons were made solely in terms of the ability of each code to perform contaminant transport. The purpose of the investigation was to establish a basis for, and to validate follow-on work that was conducted in which a 1-D GoldSim model developed by abstracting information from Porflow 2-D and 3-D unsaturated and saturated zone models and then benchmarked to produce equivalent contaminant transport results. A handful of contaminants were selected for the code-to-code comparison simulations, including a non-sorbing tracer and several long- and short-lived radionuclides exhibiting both non-sorbing to strongly-sorbing characteristics with respect to the matrix material, including several requiring the simulation of in-growth of daughter radionuclides. The …