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Comparative study of protein profiles of Desulfovibrio desulfuricans G20 under different metabolism conditions
Project Lead: Lee Krumholz
Project Lead Institution: University of Oklahoma
Abstract
Abstract: Desulfovibrio has very diversified metabolism styles. It can grow by fermentation using pyruvate, by respiration of organic substrates or hydrogen coupled to sulfate reduction or by syntrophic growth with methanogens. As an important electron carrier and intermediate in redox reaction, H2 is important for every type of metabolism. Desulfovibrio contains unique hydrogen (H2) metabolism pathways, which can produce H2 during the oxidation of organic substrated and also can oxidize H2 and use it co-metabolicaly during the degradation of organic compounds or as sole electron donor. Many proteins involved in above metabolic processes involving H2 production and oxidation, and energy generation pathways under different growth conditions have not been identified. The research proposed here will detect novel proteins possibly involved in these metabolic and energy generation pathways and to investigate metabolism netwoks of H2 production and oxidation in D. desulfuricans G20. For this proposal, we will compare the protein profiles of Desulfovibrio desulfuricans G20 under sulfodogenic (Lactate/sulfate), hydrogentrophic (H2/sulfate), syntrophy (with methanospirillum hungatei JF1 and Syntrophomonas Wolfei) and fermentation (pyruvate) growth. Proteins profiles will be compared to identify proteins that are specifically used for each pathway. Cytochrome c3 is a key electron transfer protein used during respiration and has been shown to be a critical component of the H2 oxidation pathway. We will use co-immunoprecipitation methodology and proteomic analysis to identify proteins interacting with cytochrome c3.
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Fuel-Neutral Studies of Particulate Matter Transportation Emissions
Project Lead: David Foster
Project Lead Institution: University of Wisconsin, Madison
Abstract
Customers and governments are demanding greater fuel efficiency in light duty engine applications. Since the majority of light duty engines in North America are fueled by gasoline, gasoline engine technology must be targeted in order to achieve a dramatic and immediate impact on fuel savings in our region. Efforts to curb carbon dioxide emissions, which have been implicated in global climate change, have added new urgency to the drive towards higher fuel efficiency standards. It is also recognized, however, that higher fuel efficiencies must also be accompanied by reductions in other potentially harmful emissions, including particulates. To this end, novel engine modes and various fuel blends are being examined and re-examined. Spark ignition direct injection (SIDI) gasoline engines are one example of a possible technology for dramatically increasing fuel efficiency in light duty vehicles through combustion modes which are more similar to those found in current diesel engines. One concern, however, is that SIDI engines may just like diesel engines generate more particulate matter (PM) than port fuel injection (PFI) gasoline engines. Diesel particulate filters (DPF)s are considered necessary to meet new particulate emissions limits for diesel engines in Europe, Japan, and North America. Similar measures may also be necessary for gasoline engines employing new combustion technologies such as SIDI. Even if the particulate matter counted on a mass basis is much less than that observed with diesel engines, on a number counted basis the distinction may not be so clear, since the combustion of shorter chain fuels can generally be expected to lead to more and smaller soot particles. In addition to engine operation modes, new flexible engines operated on a variety of fuels are being examined, adding more uncertainty to the nature and quantity of particulate emissions. A study designed to elucidate the effect of engine mode and fuel blend on PM generated in a fuel-neutral engine would therefore be of considerable value in the drive toward future high efficiency transportation in the light duty arena. Understanding the nature of the particulate matter derived from an energy efficient fuel-neutral engine will then enable a pathway to optimal particulate filter technology for this particular application. To meet these challenges, a new initiative comprising Pacific Northwest National Laboratory, GM Research and the University of Wisconsin will examine the properties of particulates derived from a fuel-neutral engine, and then subsequently explore filtration and oxidation strategies for effective mitigation.
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Deployment of EMSL Instruments during the 2010 Carbonaceous Aerosol and Radiative Effects Study (CARES)
Project Lead: Rahul Zaveri
Project Lead Institution: Pacific Northwest National Laboratory
Abstract
The Carbonaceous Aerosol and Radiative Effects Study (CARES) will be conducted during summer 2010 in order to investigate the evolution of carbonaceous aerosols of different types and their optical and hygroscopic properties. CARES will be conducted in central California, with a focus on the Sacramento urban plume. A suite of EMSL instruments are requested to complement an extensive set of measurements planned for this field campaign, which is being organized by the DOE ARM Climate Research Facility (ACRF). Both the instrumentation and expertise of the scientists at EMSL are critical to the successful completion of the CARES objectives described in this proposal.
During summer, the Sacramento urban plume transport is controlled by highly consistent winds that draw polluted air to the northeast over the oak and pine trees in the Blodgett Forest area. The Sacramento-Blodgett Forest corridor therefore effectively serves as a mesoscale (~100 km) daytime flow reactor in which the urban aerosols undergo significant aging due to coagulation, condensation, and photochemical processes. The CARES campaign observation strategy will therefore consist of the DOE G-1 aircraft sampling upwind, within, and outside of the evolving Sacramento urban plume in the morning and again in the afternoon. The aircraft measurements will be complemented by a well-instrumented ground site within the Sacramento urban source area (â??T0") and a ~60 km downwind receptor site ("T1") near Cool, CA, to characterize the diurnal evolution of meteorological variables, trace gases/aerosol precursors, and aerosol composition and properties in freshly polluted and aged urban air. EMSL instruments are requested for deployment on the G-1 and at both the T0 and T1 sites. These include measurements of trace gas mixing ratios, aerosol size distribution and composition, and aerosol optical and CCN activation properties.
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Fundamental understanding of atomic force microscope-induced
nanoscale interfacial reactions through nanostructure characterization
Project Lead: Marco Rolandi
Project Lead Institution: University of Washington
Abstract
The proposed research focuses on the fundamental understanding of the chemical reactions occurring at the nanoscale tip-sample interface during atomic force microscope (AFM) lithography. This understanding requires a detailed characterization of the nanostructures manufactured using different lithography conditions and parameters. In particular, we will focus on features produced with either high field liquid precursor direct write or local anodic oxidation. The proposed research at EMSL would focus on (1) compositional characterization, (2) bonding characterization, and (3) nanostructural characterization. The goal of this research is to understand the mechanisms involved in the fabrication of features within this complex multi-interfacial environment and to enable careful tailoring of processing parameters. This will afford the facile manufacturing of a broad range of nanostructures with several potential applications such as: nanotransistors, multiplexed chemical and biological sensors, nanoscale waveguides, and memory devices. Because of the very small size of the features deposited via AFM lithography (2-3 nm height, 10-50 nm width per line), we must look outside our home institution to the EMSL facility for the instrumentation required for nanoscale characterization.
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In-Situ/Liquid Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) for Environmental Interfaces
Project Lead: James Cowin
Project Lead Institution: Pacific Northwest National Laboratory
Abstract
Chemistry of liquid interfaces is extremely important in environmental and industrial processes but is poorly understood. Liquid layers coat nearly all real-world systems from the oceans to atmospheric particles, and include surface "brines" that coat rocks and soils, and ice, selective membranes for energy storage and production, important industrial catalysts, and even us. New tools are needed to study these inherently inhomogeneous systems, under realistic conditions of humidity and in the presence of trace and reactive gases. We propose an In-Situ/Liquids Time-of-Flight Secondary Ion Mass Spectrometer (ISL-TOFSIMS) system, that will for the first time allow a comprehensive molecular-specific understanding of chemistry at liquid and liquid/solid interfaces. Major recent developments in TOFSIMS (cluster beams) and novel micro-scale chemistry methods make this revolutionary advance possible and timely. The proposed system can measure molecular and ion concentrations, microsecond reaction kinetics with high spatial resolution (120 nm laterally, 1 nm vertically) and 3D mapping capability, and has a unique "in operation" sensitivity calibration. These features will enable exploring pressing issues in interface-specific photochemistry, surface segregation and transport at liquid, brine, ice and mineral surfaces, and transport across aqueous-based membranes and adherent films, all under relevant gaseous conditions.
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Exploring the boundaries of metazoan thermotolerance at hydrothermal vents: Respiration and protein expression of paralvinellid worms
Project Lead: Peter Girguis
Project Lead Institution: Harvard University
Abstract
As evidence of global climate change mounts, there is a growing impetus to examine the responses of metazoan life to increasing thermal pressure. Organismal thermotolerance is the subject of many recent investigations, but the advent of new methods and technologies such as protein sequencing via LC MS/MS now offer new avenues of investigation. Similarly, advances in exploration and engineering have made new habitats available for biological research. Deep-sea vents, only discovered in 1977, provide a unique opportunity to examine thermotolerance in one of the most extreme environments on Earth. Unique to these vents, the annelid worm Paralvinella sulfincola has an exemplary thermal range from approximately 5°C to 55°C, one of the most thermotolerant organisms on the planet.
These worms, amenable to live recovery and experimentation, were maintained in shipboard high pressure respirometry systems under differential thermal regimes. Our objective here is to employ proteomic sequencing and analyses of experimentally treated P. sulfincola to identify suites of biochemical factors that enable extreme thermotolerance. By defining global proteomic responses to thermal changes in extreme environments, we can identify biochemical risk indicators for all organisms, including those living in threatened and sensitive environments. These stress factors will be integral to understanding the capabilities and limitations of organisms to adapt and maintain proper cellular function under increasing thermal pressure. The unique combination of mass spectrometric instrumentation and the expertise that EMSL provides is vital to the success of these objectives. The data provided by these runs, combined with the interpretive knowledge of EMSL staff, will provide the first coupling between biomolecular function and respiratory data for animals under extreme thermal duress. This will be a significant advance in the fields of thermobiology and deep sea biology.
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Growth mechanisms of graphene on thin Ni films
Project Lead: Jing Kong
Project Lead Institution: Massachusetts Institute of Technology
Abstract
The growth of single- to few- layer graphene is implemented by ambient pressure CVD on thin Ni films (~500 nm). ToF-SIMS will be used to investigate the growth mechanisms of graphene over the Ni films. We have carried preliminary studies of the depth profile and 2D mapphing of carbon concentration in the Ni films after CVD which have valuable insights of the growth mechanisms of graphene over the Ni films. Therefore, continuing these studies in more Ni films could enable us to develop a detailed model of graphene growth over our thin Ni films which will be useful in improving the quality of the graphene grown by this method.
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Solid State NMR Characterization of Hydrogenase
Project Lead: Wendy Shaw
Project Lead Institution: Pacific Northwest National Laboratory
Abstract
Hydrogenase is a naturally occurring enzyme that efficiently converts H2->2H+ + 2e- and is reversible. Producing synthetic catalysts with these properties is highly desirable, but current analogs cannot match the low overpotentials and the fastest rates of the enzyme. Understanding how the enzyme works is an essential first step in the intelligent development of synthetic catalysts. A thorough understanding of the structure will likely reveal key details in functional properties of the enzyme. This work proposes to investigate the full structure of hydrogenase using solid state NMR, including the unique 900 MHz capability housed in the EMSL facility.
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Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport
Project Lead: James Mckinley
Project Lead Institution: Pacific Northwest National Laboratory
Abstract
The PNNL Scientific Focus Area (SFA) will resolve critical Hanford and basic subsurface science issues through integrated, multi-disciplinary, science-theme focused research on the role of microenvironments and transition zones in the reactive transport of technetium (Tc), uranium (U), and plutonium (Pu). Microenvironments are small domains within larger ones that exert a disproportionate influence on subsurface contaminant migration. They may be internal fractures or microbiologic niches within porous media lithic fragments; grain coatings, bio-films, or micro-colonies on larger mineral particles; or compact silt/clay stringers in gravel-dominated subsurface sediments. Transition zones are field scale features where chemical, physical, or microbiologic properties change dramatically over relatively short distances (e.g., 1 m). They exhibit steep, transport-controlled gradients of system controlling chemical species such as O2, H+, or organic carbon. Microenvironments and transition zones frequently dominate subsurface contaminant reactivity, with strong effects resulting from the coupling of chemical reaction, physical transport (advection, diffusion), and microbiologic processes. Past EMSP and NABIR research has documented the importance of these zones at the Hanford site.
The overall ten-year goals of the SFA are to develop: i.) an integrated conceptual model for microbial ecology in the Hanford subsurface and its influence on contaminant migration, ii.) a fundamental understanding of chemical reaction, biotransformation, and physical transport processes in microenvironments and transition zones, and iii.) quantitative biogeochemical reactive transport models for Tc, U, and Pu that integrate multi-process coupling at different spatial scales for field-scale application. Targeted contaminant chemical reaction and biotransformation processes include heterogeneous/biologic electron transfer, precipitation and dissolution, and surface complexation. The SFA will emphasize lab-based, coupled computational and experimental research using relevant physical/biologic models, and sediments and microbial isolates from various Hanford settings to explore
molecular, microscopic, and macroscopic processes underlying field-scale contaminant migration. It will also pursue the refinement of geophysical techniques to define, characterize, and map spatial structures and reactive transport properties of microenvironments and transition zones in the field. The SFA will partner with the PNNL Environmental Molecular Sciences Laboratory (EMSL) to develop molecular understandings of key processes, and the Hanford Integrated Field Challenge (IFC) for access to, and samples from subsurface environments where these zones exist and are important.
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Advanced IMPROVE Studies
Project Lead: Douglas Lowenthal
Project Lead Institution: Desert Research Institute
Abstract
The proposed collaboration with Dr. Lizabeth Alexander of PNNL will enable continuous measurement of size-resolved aerosol chemical composition using the EMSL high resolution time-of-flight Aerosol Mass Spectrometer (H-ToF AMS) at Mount Rainier National Park during August, 2009. This experiment is part of a long-term study of the "IMPROVE equation" which estimates particle light scattering from aerosol chemical composition. Similar studies were conducted at Great Smoky Mountains National Park (GRSM) during summer, 2006 and winter, 2008. The revised "IMPROVE" equation calculates PM2.5 light scattering from sulfate, nitrate, organic carbon mass (OCM), and soil concentrations, dry scattering efficiencies, and factors that account for hygroscopic growth. Organics are assumed to be non-hygroscopic. The organic mass to organic carbon (OCM/OC) ratio is assumed to be 1.8. The following aspects of the IMPROVE equation will be studied with ambient and laboratory measurements: 1) concentration-varying dry scattering efficiencies; 2) ambient hydration state (deliquescence, hysteresis, smooth growth; 3) the OCM/OC ratio; and 4) organic hygroscopicity. Concentration-varying dry scattering efficiencies are based on the assumption that as air masses age during transport to remote sites, gas-to-particle conversion, particularly in-cloud oxidation, increases particle size and bulk concentrations of sulfate, nitrate and possibly organics. The H-ToF AMS provides an efficient means (the ToF mass spectrometer provides a complete mass spectrum as a function of particle size) of confirming the relationship between particle size and concentration for various chemical species. The IMPROVE equation assumes that sulfate and nitrate hygroscopic growth follows the upper leg (hysteresis branch) of the ammonium sulfate growth curve. The ambient hygroscopic state depends on the particle composition and mixing state, particularly, the degree of neutralization of sulfate by ammonia. The ambient hygroscopic state will be measured with the Texas A&M Ambient State Hygroscopic Tandem Differential Mobility Analyzer (AS-HTDMA) as a function of particle size. Size-resolved chemical composition measured with the AMS will facilitate interpretation of the AS-HTDMA data by providing the ammonium to sulfate ratio and relative abundance of potentially insoluble organics. The OCM/OC ratio in part determines the contribution of organic carbon (OC) to light scattering. OCM in water extracts treated with XAD resins to remove inorganic ions and in dichloromethane extracts will be measured gravimetrically and OC will be measured by thermal optical reflectance. The H-ToF AMS provides an alternative approach for measuring the OCM/OC ratio as both OCM and OC can be derived from the organic fragments in the AMS mass spectrum. Hygroscopic growth factors (GFs) for isolated WSOC will be measured at Texas A&M with an HTDMA. WSOC GFs of aerosols at GRSM during summer averaged 1.10±0.02, 1.13±0.03, and 1.19±0.04 at 80, 85, and 90% RH, respectively. The AMS has been used to distinguish oxygenated organic aerosols (OOA) from hydrocarbon-like organic aerosols (HOA). Since OOA presumably contains more hydrophilic oxygenated functional groups (COOH, C=O, OH), higher growth factors should be associated with higher ratios of OOA to HOA. The EMSL H-ToF AMS will thus provide invaluable information which will help address all of the major scientific questions in this research.
