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  • richardmitnick 1:59 pm on September 26, 2014 Permalink | Reply
    Tags: , , , Pacific Northwest National Laboratory   

    From PNNL: “Off-shore Power Potential Floating in the Wind” 


    PNNL Lab

    September 2014
    Web Publishing Services

    Results
    : Two bright yellow buoys – each worth $1.3 million – are being deployed by Pacific Northwest National Laboratory in Washington State’s Sequim Bay. The massive, 20,000-pound buoys are decked out with the latest in meteorological and oceanographic equipment to enable more accurate predictions of the power-producing potential of winds that blow off U.S. shores. Starting in November, they will be commissioned for up to a year at two offshore wind demonstration projects: one near Coos Bay, Oregon, and another near Virginia Beach, Virginia.

    off
    PNNL staff conduct tests in Sequim Bay, Washington, while aboard one of two new research buoys being commissioned to more accurately predict offshore wind’s power-producing potential.

    “We know offshore winds are powerful, but these buoys will allow us to better understand exactly how strong they really are at the heights of wind turbines,” said PNNL atmospheric scientist Dr. William J. Shaw. “Data provided by the buoys will give us a much clearer picture of how much power can be generated at specific sites along the American coastline – and enable us to generate that clean, renewable power sooner.”

    Why It Matters: Offshore wind is a new frontier for U.S. renewable energy developers. There’s tremendous power-producing potential, but limited information is available about ocean-based wind resources. A recent report estimated the U.S. could power nearly 17 million homes by generating more than 54 gigawatts of offshore wind energy, but more information is needed.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 11:13 am on September 19, 2014 Permalink | Reply
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    From PNNL: “As Light Dims and Food Sources Are Limited, Key Changes in Proteins Occur in Cyanobacteria” 


    PNNL Lab

    September 2014
    Web Publishing Services

    As Light Dims and Food Sources Are Limited, Key Changes in Proteins Occur in Cyanobacteria
    Identification of redox-sensitive enzymes can enrich biofuel production research

    Results: Using a chemical biology approach, scientists at Pacific Northwest National Laboratory (PNNL) identified more than 300 proteins in a bacterium adept at converting carbon dioxide into other molecules of interest to energy researchers. These proteins are involved in generating macromolecule synthesis and carbon flux through central metabolic pathways and may also be involved in cell signaling and response mechanisms.

    The team’s research also suggests that dynamic redox changes in response to specific nutrient limitations, including carbon and nitrogen limitations, contribute to the regulatory changes driven by a shift from light to dark.

    They also observed that the number of labeled proteins under nitrogen or carbon limitation was ~50 percent greater than in nutrient-replete cultures, suggesting that nitrogen or carbon limitation results in increased probe labeling of proteins, indicative of a more reduced cellular environment.

    “Together, our results contribute to a high-level understanding of post-translational mechanisms that regulate flux distributions and suggest potential metabolic engineering targets for redirecting carbon toward biofuel precursors,” said Dr. Charles Ansong, PNNL scientist and co-first author of the research publication that appears in Frontiers in Microbiology. “Our identification of redox-sensitive enzymes involved in these processes can potentially enrich the experimental design of research in biofuel production.”

    image
    Overview of the chemical biology technique used by PNNL scientists to determine Synechococcus sp. PCC 7002 cells’ protein redox status in real time and identify redox-sensitive proteins as they occurred under induced nutrient perturbations including C and N limitation and transition from light to dark environments. Cell-permeable chemical probes derived from iodoacetamide (IAM-RP) and n-ethylmaleimide (Mal-RP) (top right) were applied to living cells. Once applied, the chemical probes irreversibly labeled proteins with reduced cysteines (bottom middle). The probe-labeled proteins were subsequently isolated for identification by high-resolution LC-MS (bottom right).

    Why It Matters: Plants or organisms that use sunlight to convert inorganic materials to organic ones for chemical compound production and respiration, among other functions, are called phototrophs. Scientists are interested in them because their conversion properties could translate into research experiments for biofuel production. But a key step toward such research is understanding protein redox chemistry-a reaction that can alter protein structure thereby regulating function. The lack of such understanding is a major void in knowledge about photoautotrophic system regulation and signaling processes.

    To decrease that void, the PNNL team analyzed redox-sensitive proteins in live Synechococcus sp. PCC 7002 cells in both light and dark periods, and to understand how cellular redox balance is disrupted during nutrient perturbation.

    Research Team: Charles Ansong, Natalie C. Sadler, Eric A. Hill, Michael P. Lewis, Erika M. Zink, Richard D. Smith, Alexander S. Beliaev, Allan E. Konopka, and Aaron T. Wright, all PNNL.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 1:30 pm on September 4, 2014 Permalink | Reply
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    From PNNL: “Birth of a mineral” 


    PNNL Lab

    September 04, 2014
    Mary Beckman, PNNL, (509) 375-3688

    One of the most important molecules on earth, calcium carbonate crystallizes into chalk, shells and minerals the world over. In a study led by the Department of Energy’s Pacific Northwest National Laboratory, researchers used a powerful microscope that allows them to see the birth of crystals in real time, giving them a peek at how different calcium carbonate crystals form, they report September 5 in Science.

    The results might help scientists understand how to lock carbon dioxide out of the atmosphere as well as how to better reconstruct ancient climates.

    “Carbonates are most important for what they represent, interactions between biology and Earth,” said lead researcher James De Yoreo, a materials scientist at PNNL. “For a decade, we’ve been studying the formation pathways of carbonates using high-powered microscopes, but we hadn’t had the tools to watch the crystals form in real time. Now we know the pathways are far more complicated than envisioned in the models established in the twentieth century.”

    Earth’s Reserve

    Calcium carbonate is the largest reservoir of carbon on the planet. It is found in rocks the world over, shells of both land- and water-dwelling creatures, and pearls, coral, marble and limestone. When carbon resides within calcium carbonate, it is not hanging out in the atmosphere as carbon dioxide, warming the world. Understanding how calcium carbonate turns into various minerals could help scientists control its formation to keep carbon dioxide from getting into the atmosphere.

    Calcium carbonate deposits also contain a record of Earth’s history. Researchers reconstructing ancient climates delve into the mineral for a record of temperature and atmospheric composition, environmental conditions and the state of the ocean at the time those minerals formed. A better understanding of its formation pathways will likely provide insights into those events.

    To get a handle on mineral formation, researchers at PNNL, the University of California, Berkeley, and Lawrence Berkeley National Laboratory [LBNL] examined the earliest step to becoming a mineral, called nucleation. In nucleation, molecules assemble into a tiny crystal that then grows with great speed. Nucleation has been difficult to study because it happens suddenly and unpredictably, so the scientists needed a microscope that could watch the process in real time.

    Come to Order

    In the 20th century, researchers established a theory that crystals formed in an orderly fashion. Once the ordered nucleus formed, more molecules added to the crystal, growing the mineral but not changing its structure. Recently, however, scientists have wondered if the process might be more complicated, with other things contributing to mineral formation. For example, in previous experiments they’ve seen forms of calcium carbonate that appear to be dense liquids that could be sources for minerals.

    Researchers have also wondered if calcite forms from less stable varieties or directly from calcium and carbonate dissolved in the liquid. Aragonite and vaterite are calcium carbonate minerals with slightly different crystal architectures than calcite and could represent a step in calcite’s formation. The fourth form called amorphous calcium carbonate — or ACC, which could be liquid or solid, might also be a reservoir for sprouting minerals.

    To find out, the team created a miniature lab under a transmission electron microscope at the Molecular Foundry, a DOE Office of Science User Facility at LBNL. In this miniature lab, they mixed sodium bicarbonate (used to make club soda) and calcium chloride (similar to table salt) in water. At high enough concentrations, crystals grew. Videos of nucleating and growing crystals recorded what happened:

    tem
    transmission electron microscope at LBNL

    Morphing Minerals

    The videos revealed that mineral growth took many pathways. Some crystals formed through a two-step process. For example, droplet-like particles of ACC formed, then crystals of aragonite or vaterite appeared on the surface of the droplets. As the new crystals formed, they consumed the calcium carbonate within the drop on which they nucleated.

    Other crystals formed directly from the solution, appearing by themselves far away from any ACC particles. Multiple forms often nucleated in a single experiment — at least one calcite crystal formed on top of an aragonite crystal while vaterite crystals grew nearby.

    What the team didn’t see in and among the many options, however, was calcite forming from ACC even though researchers widely expect it to happen. Whether that means it never does, De Yoreo can’t say for certain. But after looking at hundreds of nucleation events, he said it is a very unlikely event.

    “This is the first time we have directly visualized the formation process,” said De Yoreo. “We observed many pathways happening simultaneously. And they happened randomly. We were never able to predict what was going to come up next. In order to control the process, we’d need to introduce some kind of template that can direct which crystal forms and where.”

    In future work, De Yoreo and colleagues plan to investigate how living organisms control the nucleation process to build their shells and pearls. Biological organisms keep a store of mineral components in their cells and have evolved ways to make nucleation happen when and where needed. The team is curious to know how they use cellular molecules to achieve this control.

    This work was supported by the Department of Energy Office of Science.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 4:29 pm on August 28, 2014 Permalink | Reply
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    From PNNL Lab: “Playing Twenty Questions with Molecules at Plasmonic Junctions” 


    PNNL Lab

    August 2014
    Toward engineering ultrasensitive probes of nanoscale physical and chemical processes

    Results: Sometimes, it seems as if molecules struggle to communicate with scientists. When it comes to junction plasmons, essentially light waves trapped at tiny gaps between noble metals, what the molecules have to say could radically change the design of detectors used for science and security. Single molecule detection sensitivity is feasible through Raman scattering from molecules coaxed into plasmonic junctions. Scientists at Pacific Northwest National Laboratory (PNNL) found that sequences of Raman spectra recorded at a plasmonic junction, formed by a gold tip and a silver surface, exhibit dramatic intensity fluctuations, accompanied by switching from familiar vibrational line spectra of a molecule to broad band spectra of the same origin. The fluctuations confirm the team’s earlier model that assigns enhanced band spectra in Raman scattering from plasmonic nanojunctions to shorting of the junction plasmon through intervening molecular bridges.

    “It’s all about asking it the right questions and listening to what it has to say,” said Dr. Patrick El-Khoury, who has been working on this project for 2 years.

    charts
    “This is a paradigm shift in molecular spectroscopy, as we are no longer after molecular properties. Rather, we use those properties — in this study the symmetry of the observable vibrational modes — to tell us about the rich environments in which molecules reside,” said Dr. Patrick El-Khoury. (A) Time evolution of contact mode spectra of DMS on a 15 nm silver film. (B) Cross-correlation map of the individually normalized spectra shown in the image on the top. Copyright 2014: American Chemical Society

    Why It Matters: A host of emerging state-of-the-art devices and instruments rely on molecule-plasmon interactions. Recent works demonstrated yoctomolar detection sensitivity in Raman scattering from plasmonic nanojunctions, or the ability to detect 1 molecule in 602,214,000,000,000,000,000,000. Plasmonic sensors operating at this detection limit are able to determine the chemical identity of minute quantities of radioactive and environmental hazards. The development of single molecule chemical nanoscopes could answer fundamental questions about physical and chemical processes taking place over nanometer length scales. The fundamentals gained from this study could impact the design of ultrasensitive plasmonic sensors and chemical nanoscopes used to understand the fundamental chemistry behind energy storage and production, as well as the blueprints of extremely tiny electronic devices.

    “Before you can engineer the devices you need, you need to know how molecules behave over length scales comparable to their characteristic dimensions. Our research is fundamental, providing novel insights into how molecules interact with junction plasmons,” said Dr. Wayne Hess, a chemical physicist at PNNL

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 4:55 am on July 29, 2014 Permalink | Reply
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    From PNNL Lab: “Mapping Molecules in the Human Lung” 


    PNNL Lab

    July 2014
    Molecular atlas could reduce mortality in premature infants caused by undeveloped lungs

    A team of investigators at Pacific Northwest National Laboratory (PNNL) will perform an unprecedented, systematic study, mapping the molecular components of normal lung development during late term and early childhood. They recently were awarded $4.5 million over 5 years by the National Heart Lung and Blood Institute (NHLBI) to develop a molecular atlas of the developing human lung (LungMAP).

    baby
    Expanding understanding of early human lung development is a critical step toward promoting proper lung formation in preterm infants.

    Why It Matters. Lung development from ~4 months before birth through ~24 months post-birth is crucial to the lifelong health of an individual and remains the critical factor in newborn viability. However, little is known of human lung development at this critical period. Thus, expanding understanding of early human lung development is a critical step toward promoting proper lung formation in preterm infants. This has significant implications toward reducing the high mortality rate in prematurely born infants in the United States.

    The multi-investigator PNNL LungMAP project is led by PNNL scientists Dr. Charles Ansong and Dr. Richard Corley and former PNNL scientist Dr. James Carson, now at Texas Advanced Computing Center. They will generate high-quality data using cutting-edge technologies for linking molecular information-including genes, proteins, lipids, and metabolites-to locations in the developing lung, as well as to specific cell types.

    two
    Mass spectrometry imaging showing spatial localization of lipids in lung tissue. Cell-type specific multi-omic profiling done at PNNL and EMSL will complement spatial imaging in research to better understand lung formation in preterm infants.

    The project leverages several PNNL signature strengths, in mass spectrometry-based imaging, proteomics, metabolomics and lipidomics technologies, image analysis and registration, organ/cellular atlas development, and multi-scale computational modeling. A portion of the work will be done at EMSL, a Department of Energy national user facility located at PNNL.

    “It’s an honor to be part of this consortium, which is important to NHLBI and will be highly visible,” said Corley. “Our involvement connects PNNL to some of the leading pulmonary developmental biologists in the field, which is also a significant honor.”

    The results of this new initiative will create the first spatial-temporal molecular atlas of the mammalian lung during alveologenesis-the ultimate phase of lung development.

    “Through our research over the next 5 years, we hope to fill the current knowledge gaps in lung development and set the foundation for answering a new generation of hypotheses in the context of prenatal and early childhood lung development,” said Ansong.

    Co-investigators and collaborators on the project include Dr. Cecilia Ljungberg (Baylor College of Medicine); Drs. Charles Frevert and Sina Gharib (University of Washington); and Drs. Julia Laskin, Richard Smith, Thomas Metz, Aaron Wright, and Wei-Jun Qian (all PNNL).

    About : LungMAP is a national consortium of four Research Centers including PNNL, Cincinnati Children’s Hospital Medical Center, University of Alabama at Birmingham, Children’s Hospital Los Angeles, a Data Coordination Center at Duke University, and a Human Tissue Core at University of Rochester, all working to produce information on human lung development that can be openly accessed and shared by the research community and the public.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 12:17 pm on July 7, 2014 Permalink | Reply
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    From DOE Pulse: “Satisfying metals’ thirst vital for high-capacity batteries” 

    pulse

    See the full article here.

    July 7, 2014
    Kristin Manke, 509.372.6011,
    kristin.manke@pnnl.gov]

    Imagine a cell phone battery that worked for days between charges. At DOE’s Pacific Northwest National Laboratory, scientists are answering fundamental science questions that could make batteries work more efficiently. Replacing lithium, which is in the +1 oxidation state, with metals that can carry multiple charges could potentially increase battery capacity.

    PNNL Campus
    PNNL Campus

    “Our initial efforts focused on understanding the behavior of metals that have +2 or +3 oxidation states in an aqueous solution,” said Dr. Sotiris Xantheas, who led the research at PNNL. “This would double or triple the amount of charge that could be stored in a battery, but before this study, we had no insights on how the charge on the ions is either stabilized or destabilized when their local environment changes.”

    A roadblock to this future is understanding how to keep multiply charged ions stable with respect to hydrolysis channels.

    When a multiply charged ion, such as aluminum (Al+3), encounters a single water molecule, the result can be explosive. The metal ion rips an electron from the water molecule, causing a molecular-level explosion due to Coulombic forces. But multiply charged metal cations exist in water in countless ways, such as the calcium ions in your chocolate milkshake.

    The PNNL scientists, post-doctoral fellow Evangleos Miliordos and Laboratory Fellow Sotiris Xantheas, determined the paths that lead to either the hydrolysis of water or the creation of stable metal ion clusters peaceably surrounded by water. It comes down to the pH of the solution, the number of water molecules nearby and the energy needed to remove electrons from the metal, known as the ionization potential.

    This research was featured on the cover of Physical Chemistry Chemical Physics and in a special issue of Theoretical Chemistry Accounts dedicated to Prof. Thomas H. Dunning, Jr. on the occasion of his 70th birthday.

    “This paper describes an elegant use of computational modeling to understand a phenomena that is of fundamental importance in chemistry, yet has many practical applications as well,” said Dunning, co-director of the Northwest Institute for Advanced Computing, operated by PNNL and the University of Washington.

    What’s next? The researchers are now working to extend their computational protocol to the solution phase and at interfaces. Extending the methodology will allow the team to better understand the dynamic interactions occurring, eventually leading to better battery technologies.

    This research was sponsored by DOE’s Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Resources at the National Energy Research Scientific Computing Center were used.

    DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

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  • richardmitnick 8:43 pm on May 13, 2014 Permalink | Reply
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    From PNNL Lab: “Cyanobacterial Consortia Shed New Light on Phototrophic Biofilm Assembly” 


    PNNL Lab

    May 2014
    Cyanobacterial Consortia Shed New Light on Phototrophic Biofilm Assembly
    Model “microecosystems” used to study producer-consumer interaction networks in microbial mats

    Results: As part of their ongoing studies of the complex world of microbial communities, scientists at Pacific Northwest National Laboratory recently isolated two bacterial consortia from a microbial mat in Hot Lake, located in north-central Washington State. They characterized each consortia’s membership and metabolic function to identify the interactions thought to recruit and maintain genetic and functional diversity in the consortia over time.

    The team’s results shed light on the principles that govern microbial communities, principles needed for scientists to move closer to the goal of being able to predict, engineer, and manipulate microbial communities of importance to global carbon and energy cycling.

    These consortia are each anchored by a single cyanobacterium-a type of autotroph-that obtains energy from sunlight through photosynthesis and uses the energy to produce sugars from carbon dioxide. In turn, the autotrophs supply many heterotrophs-organisms that consume carbon produced by other organisms-with the carbon and oxygen they need to harvest energy and produce biomass.

    map
    Overview of cycle between autotrophs and heterotrophs

    “Primary production by microbial autotrophs and consumption by heterotrophs are occurring everywhere,” said Dr. Steve Lindemann, PNNL microbiologist and lead author of the study, which appears in Frontiers in Microbiology. “If you don’t understand the interactions, you can’t predict how communities will respond to changing environmental conditions or engineer them to sustainably perform a useful function; for example, making them more productive-to generate more biomass for bioenergy applications-or resilient, so they recover quickly from environmental shocks. It’s a big deal.”

    The relative simplicity and tractability of the consortia make them useful model systems for deciphering the interspecies interactions and principles of microbial community assembly.

    The PNNL scientists found that though the consortia shared all their members except for the cyanobacteria, they contained very different abundances of each member as the communities assembled into a biofilm. This suggested that specific interactions between the cyanobacteria and heterotrophs generate a different network of interactions. These networks likely create related but unique niches that support different population sizes of each heterotroph.

    The scientists also found that autotroph growth rates dominated early in assembly but yielded to heterotroph growth rates late in the growth cycle. Although the heterotrophic species composition was similar in both consortia, the population dynamics of different species varied significantly as their biofilms matured. These data suggest that, although the niches provided by the cyanobacterial metabolisms are sufficiently broad to retain the same species, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions in each consortium are likely distinct.

    Why It Matters: Much like members of a growing village, microbial community members occupy niches that support their own growth, but in turn also promote other members’ growth; analogous, perhaps, to a microbe’s “occupation” within its community. Though different microbial “villages” require similar resources for growth, the way those resources are produced and move through the community will depend upon which niche each microbe is filling and its abundance. Consequently, though similar kinds of niches may be created in each community, there will be distinctions in the numbers or specialties of members occupying those niches depending upon other members and the community’s circumstances.

    As Lindemann explains, “For example, while two villages will require farmers for food production, whether those farmers are growing wheat, rice, or corn will impact the roles of other members of the community-in this example, perhaps in the amounts and types of bread made by bakers. Similarly, different primary producers are likely to interact with heterotrophic consumers in similar but unique ways. These differences will then have cascading effects upon interactions between heterotrophic members.”

    Such disparities in the network of interactions between two microbial communities are likely to create distinct niches in each, support different population sizes of each member species, and affect a community’s overall functions and properties. Comparing interactions occurring within these two consortia therefore brings scientists closer to understanding the principles governing similar interactions in the wild-and may allow them to better predict and control microbial communities.

    Process for isolation and cultivation of the unicyanobacterial consortia.

    Methods: The PNNL team defined the membership and examined the spatial structure and phototroph-heterotroph succession of unicyanobacterial consortia as they assembled into biofilms. Earlier studies were limited to quantifying populations of cultivable organisms and were therefore unable to estimate the diversity of potential colonizers in experimental “microecosystems.”

    “Next-generation sequencing has greatly expanded our ability to comprehensively characterize a community’s membership, and molecular quantitation at the species level allows us to assess heterotroph abundance independent of cultivation,” Lindemann said. “We can now track the dynamics of all of the community’s members, whether we can grow them by themselves or not.”

    Interestingly, though different cyanobacteria were primary producers in each consortium, both retained the same suite of heterotrophic species.

    What’s Next? The team plans to subject the consortia to environmental perturbation (such as variations in salinity, light, temperature, or availability of specific nutrients) to examine how changing conditions affect the structure and composition of the assembling consortial biofilms.

    Acknowledgments:

    Sponsors: This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), Genomic Science Program (GSP), as part of the PNNL Foundational Scientific Focus Area. Portions of this work were performed at the DOE Joint Genome Institute (JGI), and in EMSL, a BER-sponsored national scientific user facility located at PNNL.

    Research Team: Jessica K Cole, Janine R Hutchison, Ryan S Renslow, Young-Mo Kim, William B Chrisler, Heather E Engelmann, Alice Dohnalkova, Dehong Hu, Thomas O Metz, Jim K Fredrickson, and Stephen R Lindemann, all PNNL.

    Research Area: Biological Systems Science

    See the full article here.

    [I have a particular affinity for cyanobacteria, the first providers of oxygen here on Earth. I developed thi affinity from watching the PBS Nova program on the Gaia theory of the universe and its theorist James Ephraim Lovelock. I still have my undigitized VCR tape of that very special program.

    jel
    Lovelock in 2005

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 4:20 pm on May 1, 2014 Permalink | Reply
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    From PNNL Lab: ” Whales hear us more than we realize” 


    PNNL Lab

    May 01, 2014
    Tom Rickey, PNNL, (509) 375-3732

    Sonar signal “leaks” likely audible to some marine mammals

    Killer whales and other marine mammals likely hear sonar signals more than we’ve known.

    That’s because commercially available sonar systems, which are designed to create signals beyond the range of hearing of such animals, also emit signals known to be within their hearing range, scientists have discovered.

    whale
    A sperm whale off the coast of southern California.
    Photo taken under NMFS permit #14534; credit A. Friedlaender.

    The sound is likely very soft and audible only when the animals are within a few hundred meters of the source, say the authors of a new study. The signals would not cause any actual tissue damage, but it’s possible that they affect the behavior of some marine mammals, which rely heavily on sound to communicate, navigate, and find food.

    The findings come from a team of researchers at the Department of Energy’s Pacific Northwest National Laboratory, working together with marine mammal expert Brandon Southall of Southall Environmental Associates. The findings were published April 15 in the journal PLOS ONE.

    A team led by Zhiqun (Daniel) Deng, a chief scientist at PNNL, evaluated the signals from three commercially available sonar systems designed to transmit signals at 200 kilohertz. The impact of such systems on marine mammals is not typically analyzed because signals at 200 kilohertz can’t be heard by the animals.

    The team found that while most of the energy is transmitted near the intended frequency of 200 kilohertz, some of the sound leaks out to lower frequencies within the hearing range of killer whales and other animals such as harbor porpoises, dolphins and beluga whales. The three systems studied produced signals as low as 90, 105 and 130 kilohertz.

    At the levels measured, the sounds would be quieter than many other sounds in the ocean, including the sounds the animals themselves make, and they wouldn’t be heard at all by the animals beyond a few hundred meters.

    “These signals are quiet, but they are audible to the animals, and they would be relatively novel since marine mammals don’t encounter many sounds in this range,” said Southall, who is the former director of the Ocean Acoustics Program of the National Oceanic and Atmospheric Administration.

    “These sounds have the potential to affect animal behavior, even though the main frequency is above what they primarily hear. It may be that environmental assessments should include the effects of these systems. This may not be a major issue, but it deserves further exploration,” added Southall.

    The new findings have their roots in a project to track marine mammals in Puget Sound, which was part of a broader effort to provide information on the environmental impact of a planned tidal energy project there near Seattle. Researchers had planned to use sonar to help locate killer whales, but some marine mammal experts had observed that the animals might actually be hearing the sonar. Those observations led to the study, which was funded by Depart of Energy’s Office of Energy Efficiency and Renewable Energy.

    How do the sonar signals actually sound to marine mammals like killer whales? Since high-frequency sonar pings several times per second, it’s possible that it sounds like one continuous, high-pitched hum or ping.

    “If you think of a keyboard on a piano, the ships would be hitting the low notes quite hard, the middle keys would be most of the sounds of the animals themselves, and the sonar systems we studied would be relatively quieter sounds in the top few octaves on the right of the keyboard,” said Southall.

    The authors of the paper did not directly study the hearing capability of whales and other marine mammals. Instead, the study focused on the sounds produced by sonar systems, discovering that commercial sonar systems are emitting signals within the animals’ known hearing range. Deng and colleagues are currently considering ways to limit signal leakage to reduce the amount of sound from high-frequency sonar systems that would be audible to marine mammals.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 3:10 pm on April 24, 2014 Permalink | Reply
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    From PNNL Lab: “How a plant beckons the bacteria that will do it harm” 


    PNNL Lab

    April 24, 2014
    Tom Rickey, PNNL, (509) 375-3732

    Work on microbial signaling offers a window into better biofuels, human health

    A common plant puts out a welcome mat to bacteria seeking to invade, and scientists have discovered the mat’s molecular mix.

    The study published this week in the Proceedings of the National Academy of Sciences reveals new targets during the battle between microbe and host that researchers can exploit to protect plants.

    The team showed that the humble and oft-studied plant Arabidopsis puts out a molecular signal that invites an attack from a pathogen. It’s as if a hostile army were unknowingly passing by a castle, and the sentry stood up and yelled, “Over here!” — focusing the attackers on a target they would have otherwise simply passed by.

    “This signaling system triggers a structure in bacteria that actually looks a lot like a syringe, which is used to inject virulence proteins into its target. It’s exciting to learn that metabolites excreted by the host can play a role in triggering this system in bacteria,” said Thomas Metz, an author of the paper and a chemist at the Department of Energy’s Pacific Northwest National Laboratory.

    The findings come from a collaboration of scientists led by Scott Peck of the University of Missouri that includes researchers from Missouri, the Biological Sciences Division at PNNL, and EMSL, DOE’s Environmental Molecular Sciences Laboratory.

    The research examines a key moment in the relationship between microbe and host, when a microbe recognizes a host as a potential target and employs its molecular machinery to pierce it, injecting its contents into the plant’s cells — a crucial step in infecting an organism.

    The work focused on bacteria known as Pseudomonas syringae pv. tomato DC3000, which can ruin tomatoes as well as Arabidopsis. The bacteria employ a molecular system known as the Type 3 Secretion System, or T3SS, to infect plants. In tomatoes, the infection leads to unsightly brown spots.

    rot
    Infection of tomatoes by Pseudomonas syringae
    Image courtesy of Cornell University.

    Peck’s team at the University of Missouri had discovered a mutant type of the plant, known as Arabidopsis mkp1, which is resistant to infection by Pseudomonas syringae. The Missouri and PNNL groups compared levels of metabolites in Arabidopsis to those in the mutant mkp1 form of the plant. Peck’s group used those findings as a guide to find the compounds that had the biggest effect — a combination that invites infection.

    The researchers discovered a group of five acids that collectively had the biggest effect on turning on the bacteria’s T3SS: pyroglutamic, citric, shikimic, 4-hydroxybenzoic, and aspartic acids.

    They found that the mutant has a much lower level of these cellular products on the surface of the plant than found in normal plants. Since the resistant plants don’t have high levels of these acids, it stops the bacteria from unfurling the “syringe” in the presence of the plant. But when the combination of acids is introduced onto mkp1, it quickly becomes a target for infection.

    “We know that microbes can disguise themselves by altering the proteins or molecules that the plant uses to recognize the bacteria, as a strategy for evading detection,” said Peck, associate professor of biochemistry at the University of Missouri and lead author of the PNAS paper. “Our results now show that the plant can also disguise itself from pathogen recognition by removing the signals needed by the pathogen to become fully virulent.”

    While Peck’s study focused on bacteria known mostly for damaging tomatoes, the findings also could have implications for people. The same molecular machinery employed by Pseudomonas syringae is also used by a host of microbes to cause diseases that afflict people, including salmonella, the plague, respiratory disease, and chlamydia.

    On the energy front, the findings will help scientists grow plants that can serve as an energy source and are more resistant to infection. Also, a better understanding of the signals that microbes use helps scientists who rely on such organisms for converting materials like switchgrass and wood chips into useable fuel.

    The work opens the door to new ways to rendering harmful bacteria harmless, by modifying plants so they don’t become invasive.

    “There isn’t a single solution for disease resistance in the field, which is part of the reason these findings are important,” said Peck. “The concept of another layer of interaction between host and microbe provides an additional conceptual strategy for how resistance might be manipulated. Rather than trying to kill the bacteria, eliminating the recognition signals in the plant makes the bacteria fairly innocuous, giving the natural immune system more time to defend itself.”

    The research was funded by the National Science Foundation, and some of the research took place at EMSL. PNNL authors of the paper include Metz, Young-Mo Kim, and Ljiljana Pasa-Tolic. Missouri authors include Peck, Ying Wan, and first author Jeffrey C. Anderson.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 11:55 am on April 23, 2014 Permalink | Reply
    Tags: , , , , Pacific Northwest National Laboratory   

    From PNNL Lab: “Halving hydrogen” 

    PNNL Lab

    April 23, 2014
    Mary Beckman

    – Like a hungry diner ripping open a dinner roll, a fuel cell catalyst that converts hydrogen into electricity must tear open a hydrogen molecule. Now researchers have captured a view of such a catalyst holding onto the two halves of its hydrogen feast. The view confirms previous hypotheses and provides insight into how to make the catalyst work better for alternative energy uses.

    cat
    Neutron crystallography shows this iron catalyst gripping two hydrogen atoms (red spheres). This arrangement allows an unusual dihydrogen bond to form between the hydrogen atoms (red dots).

    This study is the first time scientists have shown precisely where the hydrogen halves end up in the structure of a molecular catalyst that breaks down hydrogen, the team reported online April 22 in Angewandte Chemie International Edition. The design of this catalyst was inspired by the innards of a natural protein called a hydrogenase enzyme.
    “The catalyst shows us what likely happens in the natural hydrogenase system,” said Morris Bullock of the Department of Energy’s Pacific Northwest National Laboratory. “The catalyst is where the action is, but the natural enzyme has a huge protein surrounding the catalytic site. It would be hard to see what we have seen with our catalyst because of the complexity of the protein.”

    Ironing Out Expense

    Hydrogen-powered fuel cells offer an alternative to burning fossil fuels, which generates greenhouse gases. Molecular hydrogen — two hydrogen atoms linked by an energy-rich chemical bond — feeds a fuel cell. Generating electricity through chemical reactions, the fuel cell spits out water and power.

    If renewable power is used to store energy in molecular hydrogen, these fuel cells can be carbon-neutral. But fuel cells aren’t cheap enough for everyday use.
    To make fuel cells less expensive, researchers turned to natural hydrogenase enzymes for inspiration. These enzymes break hydrogen for energy in the same way a fuel cell would. But while conventional fuel cell catalysts require expensive platinum, natural enzymes use cheap iron or nickel at their core.
    Researchers have been designing catalysts inspired by hydrogenase cores and testing them. In this work, an important step in breaking a hydrogen molecule so the bond’s energy can be captured as electricity is to break the bond unevenly. Instead of producing two equal hydrogen atoms, this catalyst must produce a positively charged proton and a negatively charged hydride.

    The physical shape of a catalyst — along with electrochemical information — can reveal how it does that. So far, scientists have determined the overall structure of catalysts with cheap metals using X-ray crystallography, but hydrogen atoms can’t be located accurately using X-rays. Based on chemistry and X-ray methods, researchers have a best guess for the position of hydrogen atoms, but imagination is no substitute for reality.

    Bullock, Tianbiao “Leo” Liu and their colleagues at the Center for Molecular Electrocatalysis at PNNL, one of DOE’s Energy Frontier Research Centers, collaborated with scientists at the Spallation Neutron Source at Oak Ridge National Laboratory in Tennessee to find the lurking proton and hydride. Using a beam of neutrons like a flashlight allows researchers to pinpoint the nucleus of atoms that form the backbone architecture of their iron-based catalyst.

    Bonding Jamboree

    To use their iron-based catalyst in neutron crystallography, the team had to modify it chemically so it would react with the hydrogen molecule in just the right way. Neutron crystallography also requires larger crystals as starting material compared to X-ray crystallography.

    “We were designing a molecule that represented an intermediate in the chemical reaction, and it required special experimental techniques,” Liu said. “It took more than six months to find the right conditions to grow large single crystals suitable for neutron diffraction. And another six months to pinpoint the position of the split H2 molecule.”

    Crystallizing their catalyst of interest into a nugget almost 40 times the size needed for X-rays, the team succeeded in determining the structure of the iron-based catalyst.
    The structure, they found, confirmed theories based on chemical analyses. For example, the barbell-shaped hydrogen molecule snuggles into the catalyst core. On being split, the negatively charged hydride attaches to the iron at the center of the catalyst; meanwhile, the positively charged proton attaches to a nitrogen atom across the catalytic core. The researchers expected this set-up, but no one had accurately characterized it in an actual structure before.

    In this form, the hydride and proton form a type of bond uncommonly seen by scientists — a dihydrogen bond. The energy-rich chemical bond between two hydrogen atoms in a molecule is called a covalent bond and is very strong. Another bond called a “hydrogen bond” is a weak one formed between a slightly positive hydrogen and another, slightly negative atom.
    Hydrogen bonds stabilize the structure of molecules by tacking down chains as they fold over within a molecule or between two independent molecules. Hydrogen bonds are also key to water surface tension, ice’s ability to float and even a snowflake’s shape.

    The dihydrogen bond seen in the structure is much stronger than a single hydrogen bond. Measuring the distance between atoms reveals how tight the bond is. The team found that the dihydrogen bond was much shorter than typical hydrogen bonds but longer than typical covalent bonds. In fact, the dihydrogen bond is the shortest of its type so far identified, the researchers report.

    This unusually strong dihydrogen bond likely plays into how well the catalyst balances tearing the hydrogen molecule apart and putting it back together. This balance allows the catalyst to work efficiently.

    “We’re not too far from acceptable with its efficiency,” said Bullock. “Now we just want to make it a little more efficient and faster.”

    This work was supported by the Department of Energy Office of Science.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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