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  • richardmitnick 10:25 pm on January 11, 2013 Permalink | Reply
    Tags: , , , Pacific Northwest National Laboratory   

    From PNNL Lab: “Metabolomics Key to Identifying Disease Pathway” 

    Research reveals lactic acid’s role in lung disease

    January 2013
    Suraiya Farukhi
    Christine Sharp

    Results:Expertise at Pacific Northwest National Laboratory contributed to the understanding of the role of cellular metabolism in the pathogenesis of a currently untreatable lung disease. This research, reported in the American Journal of Respiratory and Critical Care Medicine, highlights the importance of PNNL’s nuclear magnetic resonance (NMR) metabolomics in the field of biomedicine.

    graphs
    Top: Lactic acid concentrations were measured in whole lung homogenates using ¹H-PASS nuclear magnetic resonance (NMR) spectroscopy obtained from patients with idiopathic pulmonary fibrosis (IPF) and compared with healthy control subjects. Bottom: Lactate dehydrogenase-5 (LDH5) expression is elevated in fibroblasts and lung tissue from IPF patients. LDH5 is responsible for the generation of lactic acid. Immunohistochemistry is shown for LDH5 performed on lung tissue sections from a healthy control subject (left) and a patient with IPF (right). LDH5 expression, shown as the reddish-brown stained area, is increased in the lung tissue of patients with IPF.

    Why It Matters: Scientists increasingly recognize that dysregulated, or impaired, cellular metabolism impacts disease processes. However, they know little about the role of cellular metabolism as it relates to lung disease. Greater understanding of the dysregulated processes in human diseases will help in developing improved diagnostic and treatment strategies.”

    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 1:23 pm on January 3, 2013 Permalink | Reply
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    From PNNL: “A Pathway for Protons” 

    Efficient delivery to material’s center turns oxygen cleanly into water

    January 2013
    No Writer Credit

    Results : Pushing protons around may sound like a small task, but it is a big part of energy independence for the United States. Moving four relatively large protons to where they are needed is easier if you build a path, as is being done by scientists at the Center for Molecular Electrocatalysis. The research team has built two iron-based compounds that help protons move from the exterior to where they are needed. Once delivered, the protons bond with molecular oxygen, O2, and create water. In previous compounds, the protons often don’t arrive in time or go to the wrong place, which leads to forming the unwanted byproduct hydrogen peroxide (H2O2). The new compounds direct the protons in ways that help separate the two oxygen atoms in O2, and thereby drives the reaction to completion.

    ‘While water is the end product, it is not the goal of our work. These studies show that we can take the knowledge that the Center for Molecular Electrocatalysis has learned for reactions that move two protons and apply that knowledge to the challenge of relaying four protons,’ said Dr. James Mayer, an expert in proton-coupled electron transfer reactions and a professor at the University of Washington, who led this research.

    Why It Matters: Understanding how to move protons efficiently lets scientists design new materials that can turn electrons generated by wind turbines and solar farms into fuels, creating easily transported, use-any-time alternatives to coal and oil.

    ‘We want to generate as much power as we can when the conditions are right and store the energy,’ said Dr. Monte Helm, Deputy Director for the Center for Molecular Electrocatalysis. ‘This research is directly related to storing that energy in chemical bonds, so we can get the energy out at a future time, when necessary.’”

    q2
    Scientists from the Center for Molecular Electrocatalysis have built two iron-based compounds that help protons move from the exterior to where they are needed. Once delivered, the protons bond with molecular oxygen and create water. No image credit

    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 3:34 pm on December 12, 2012 Permalink | Reply
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    From PNNL: “Carbon dioxide reveals a predilection for tumbling alone and lining up together” 

    Pacific Northwest National Laboratory

    Carbon Dioxide emissions are very important, so this research is very important.

    December 2012
    Suraiya Farukhi
    Christine Sharp

    Results: Crowded together on a titanium dioxide surface, carbon dioxide molecules relinquish their free-tumbling ways to form crooked lines and cling to molecules in nearby lines, according to scientists at Pacific Northwest National Laboratory. Bringing together a trio of instruments and a supercomputer, the team joined experiments and theory to understand carbon dioxide’s behavior.

    ‘We want to build our understanding from the ground up,’ said Dr. Zdenek Dohnalek, an experimental chemist on the study. ‘We want to understand the interaction of carbon dioxide with well-known models of oxides, such as titanium dioxide.’

    tit
    Carbon dioxide diffuses on titanium rows by a tumbling mechanism. Once bound to a titanium atom, the carbon dioxide’s axis tilts. No image credit.

    Why It Matters: Understanding how carbon dioxide molecules behave is basic science needed by the energy sector to facilitate carbon sequestration and fuel production. Sequestration stores carbon dioxide emissions from power plants underground. Fuel production uses the carbon dioxide as a building block to create fuels.

    ‘While titanium dioxide is a model material that will likely not be used to sequester carbon dioxide or serve as a catalyst for fuel conversion, the fundamental aspects of carbon dioxide reactivity revealed in our study are very intriguing,’ said Dr. Xiao Lin, a Linus Pauling Postdoctoral Fellow at PNNL, who proposed this research as part of his fellowship.”

    See the full article here.

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    “Located in Richland, Washington, PNNL is one among ten U.S. Department of Energy (DOE) national laboratories managed by DOE’s Office of Science. Our research strengthens the U.S. foundation for innovation, and we help find solutions for not only DOE, but for the U.S. Department of Homeland Security, the National Nuclear Security Administration, other government agencies, universities and industry.”


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  • richardmitnick 12:02 pm on August 17, 2012 Permalink | Reply
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    From PNNL Lab: “New Protein Discovered Gives Insights to Iron’s Fate Underground” 

    August 2012
    Christine Sharp
    Suraiya Farukhi

    Scientists identify molecule that steals electrons, leaving iron stuck in the mud

    Results: It’s almost an evil twin story; a protein that steals electrons from iron in one microbe looks a lot like one that adds electrons in another microbe, according to scientists at Pacific Northwest National Laboratory and the University of East Anglia. Their survey of the genes of common groundwater bacterium Sideroxydans lithotrophicus ES-1, which removes electrons from iron, revealed that it contained genes in common with Shewanella oneidensis MR-1, which adds electrons to iron.

    image
    Proposed roles of MtoAB and CymAES-1 in Sideroxydans lithotrophicus ES-1-mediated extracellular Fe(II) oxidation. Decaheme c-Cyt MtoA, which is inserted into the porin-like, outer membrane (OM) protein MtoB, oxidizes Fe(II) directly on the bacterial surface and transfers the released electrons across the OM to the periplasmic proteins that have yet to be identified. The periplasmic proteins relay the electrons through the periplasm (PS) to the tetraheme c-Cyt CymAES-1. CymAES-1, located in the cytoplasmic or inner membrane (IM), reduces quinone to quinol. c-Cyts are labeled in red, and the direction of electron transfer is indicated by a yellow arrows. No image credit

    Their results contribute to understanding of the molecular mechanisms by which microorganisms change the electron configuration of iron and, thus, change its mobility. The research was published in Frontiers in Microbiological Chemistry.

    ‘Recent studies indicate that aerobic Fe(II)-oxidizing bacteria, FeOB, would play a key role in niches having low levels of oxygen concentration, where microbial Fe(II)-oxidation can compete with the chemical oxidation of Fe(II),’ said PNNL biogeochemist Dr. Juan Liu, first author of the study paper.

    Why It Matters: Science has realized the importance of microorganisms in research on processes such as carbon sequestration, the generation of new energy sources, and the movement and ultimate resting place of contaminants. Scientists are interested in the oxidation state, or loss of electrons, of iron because it dramatically affects the metal’s solubility in water, in which electron transfer proteins play critical roles. In contrast to Fe(II), trivalent iron, Fe(III), is not water soluble.

    The difference in solubility between Fe(II) and Fe(III) also means that iron acquisition tends to be much more of a problem for organisms that use oxygen than for those that don’t, because anaerobic environments favor the more soluble Fe(II).

    ‘We have shown the generality of these reaction mechanisms in metal oxidizing and reducing bacteria,’ said Dr. Liang Shi, a PNNL microbiologist who led the study. ‘Whether it’s Fe(II) or Fe(III), iron’s solubility affects its accessibility to microorganisms. To access these different phases of Fe, some microorganisms seem to adopt a common mechanism.’”

    See the full article here.
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  • richardmitnick 3:16 pm on July 25, 2012 Permalink | Reply
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    From PNNL Lab: “Listening to Life” 


    Pacific Northwest National Laboratory (PNNL)

    New chemical imaging method probes the communications of live microbial colonies

    July 2012
    Suraiya Farukhi
    Christine Sharp

    Results: Once impossible, scientists can now eavesdrop on microbes, thanks to a new technique from scientists at Pacific Northwest National Laboratory and three universities. Microbes converse by releasing simple and complex molecules, called metabolites. The metabolites interact with and alter their environment and nearby cells. To listen in, the team combined nanospray desorption electrospray ionization mass spectrometry, or nanoDESI, and a new bioinformatics technique. This approach allows scientists to identify and quantify, in time and space, the metabolites around living bacterial colonies.

    nano
    Image of the nanoDESI setup with a microbial colony grown on an agar surface

    ‘This is a real discovery tool—showing us how microbial communities interact,’ said Dr. Julia Laskin, a PNNL chemist who has been successfully advancing the frontiers of nanoDESI for three years.

    Why It Matters: Understanding the timing and distribution of metabolite exchanges will help interpret and potentially manipulate microbial communities. For example, by studying how Shewanella oneidensis colonies respond to their environment and other strains of bacteria, scientists can gain insights into how the microbe makes mobile uranium stationary. Another example, scientists can determine how brain cells respond to nicotine and other toxins. The new nanoDESI-based technique offers the insights scientists want.

    ‘Microbial biology covers topics from biofuel production to bioremediation to health to defense,’ said Laskin. ‘And, it is all of these different areas of research that the tool may impact—that’s why it is so exciting.’”

    See the full article here.

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  • richardmitnick 9:29 am on July 24, 2012 Permalink | Reply
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    From PNNL Lab: “Mother Nature as a Wire Manufacturer” 


    Pacific Northwest National Laboratory (PNNL)

    With computational models, scientists see how microbe directs electrons

    July 2012
    Suraiya Farukhi
    Christine Sharp

    Results: For the first time, each step an electron takes as it moves along a “wire” from a microbe’s interior to the outside world is known, thanks to modeling by University College London and Pacific Northwest National Laboratory. The wire is a twisted molecule, known as a cytochrome. The cytochrome is made of 10 iron-based clusters, called hemes, held in a particular arrangement by a protein that serves as a backbone. The hemes are positioned end-to-end in a staggered cross, to comprise the electron transfer interface between the interior of Shewanella oneidensis, a bacteria found in the soil, and metals and minerals beyond the cell’s wall.

    image
    Scientists elucidated the molecular details of electron transport along the 10-heme chains in the Shewanella oneidensis’ cytochrome (right) using complex, dynamic molecular simulations.

    image2
    Shewanella may send out tiny wires that contact metals and minerals. Within these wires are thought to be proteins containing hemes that pass electrons outward. In 2011, a collaborative team from the University of East Anglia and Pacific Northwest National Laboratory determined the structure of the first of these protein components. This research expands on that study, showing how the electrons hopscotch across the tiny wires.

    ‘This is the first look at how nature would design a molecular wire for transport on nanometer length scales,’ said Dr. Kevin Rosso, a geochemist at PNNL and a corresponding author on the study.

    Why It Matters: To understand how these microbes influence contaminated water and soil, as well as to answer the clamor for smaller and smaller computer circuits, scientists are looking to bacteria. Optimized over eons, bacteria are very proficient at moving electrons using molecular complexes. This study provides details about the molecules that move the electrons and how they work. It is opening doors to designing molecule-sized circuits and to research related to how these microbes affect contaminated water and soil.”

    See the full article here.

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  • richardmitnick 11:03 am on July 23, 2012 Permalink | Reply
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    From PNNL Lab: “Unique Protein Fold Flags Potentially Unique Function” 

    Crystal structure of a cyanobacterial protein associated with nitrogen fixation

    July 2012
    No Writer Credit

    Results: The crystal structure of a protein in a bacterium being studied for its renewable energy potential suggests that the protein’s biological function may be unique to a process leading to hydrogen gas production, according to researchers from Pacific Northwest National Laboratory and Brookhaven National Laboratory. They determined the structure for a protein that falls into a family of proteins with a “Domain of Unknown Function,” annotated DUF269, from Cyanothece 51142, a photosynthetic bacterium with a completely different lifestyle in the day and the night.

    cyano
    Crystal structure of DUF269 (3NJ2). The β-sheets at the dimer interface, highlighted in red, form the framework for a solvent-accessible cleft.No image credit.

    They found that a solvent-accessible cleft with conserved charged residues at the interface of the asymmetric unit of the crystal (see figure) could be an active site or ligand-binding surface for the protein’s biological function. The protein fold observed for the Cyanothece appears to be unique to the DUF269 family of proteins.

    Why It Matters: By day Cyanothece 51142 uses sunlight to convert carbon dioxide into molecular oxygen and glucose, a process called photosynthesis. At night it uses the glucose to convert atmospheric N2 into biologically available ammonia, a process called nitrogen fixation.”

    See the full article here.

    doe

     
  • richardmitnick 5:32 pm on July 17, 2012 Permalink | Reply
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    From PNNL Lab: “Iron Center and Pendant Nitrogen Needed to Achieve Catalyst’s Goal” 


    Pacific Northwest National Laboratory (PNNL)

    Scientists built catalysts that cleave bonds for platinum-free fuel cells

    July 2012
    No writer credit

    Results: To crack hydrogen molecules and free the electrons, scientists at Pacific Northwest National Laboratory built nature-inspired molecules that get the job done. These designer molecules, or catalysts, rely on an iron center and small, dangling molecular chains with strategically placed nitrogen atoms. Known as pendant amines, these chains draw in the hydrogen molecule and position it just so. The iron center breaks apart the hydrogen into protons and electrons. The pendant amines shuttle the protons off, and the process starts all over again.

    cat
    Scientists at Pacific Northwest National Laboratory built a nature-inspired catalyst with an iron center and small, dangling molecular chains with strategically placed nitrogen atoms to crack hydrogen molecules and free the electrons needed for fuel cells.No image credit

    ‘We’re not trying to precisely mimic nature, just incorporate the salient features that make natural catalysts function, said Dr. Morris Bullock, Director of the Center for Molecular Electrocatalysis, led by PNNL. The results were published in the Journal of the American Chemical Society.

    Why It Matters: Using fossil fuels to power cars and heat homes continues to raise economic, environmental, and security issues. A popular alternative is the fuel cell, which converts hydrogen, methanol, or other chemicals into water, and in the process it turns out electricity. But the catalyst of choice for the fuel cells is platinum, which is expensive and scarce. In contrast, iron is far less expensive and is the Earth’s most abundant metal.

    See the full article here.

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  • richardmitnick 1:03 pm on June 20, 2012 Permalink | Reply
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    From PNNL Lab: “Watching Molecules in Slow Motion” 


    Pacific Northwest National Laboratory (PNNL)

    By supercooling liquids, scientists can determine the physics happening in glasses

    June 2012
    No Writer Credit

    Results: The whereabouts of exceedingly slow-moving molecules in glasses can be quickly and efficiently measured, thanks to a new technique that uses vapor and extreme cold to drop the molecules’ speed a trillion times. Designed by Dr. Scott Smith and Dr. Bruce Kay at Pacific Northwest National Laboratory, the method supercools vapor molecules turning them into a glassy film. Then, they heat the film just enough to get the molecules moving at the desired speed to study. An overview of this new method appears in an invited Perspective article in Journal of Physical Chemistry Letters.

    Why It Matters: While glass is ubiquitous in the world today, from fiber optic cables to fuel cells to pharmaceuticals, and even nuclear waste storage, fundamental glass properties are not clearly understood. Knowledge gaps exist, in part, because supercooling alcohols, water and other small molecular liquids was not easy. This difficulty meant that fundamental questions were the purview of computer simulations and models. With this new technique, scientists can get precise data. The data will answer basic questions, and one day may guide transformations into key industries.

    glass
    As liquids cool, they can take on different states depending on various conditions. A liquid can cool to become a supercooled liquid and then a glass, given the right conditions. The more common route is for the liquid to cool into a crystalline solid. (No image credit)

    fios
    From fiber optic cables to fuel cells, and even nuclear waste storage, glass is pervasive in today’s world; however, the fundamental properties of glass are not clearly understood.

    See the full article here.

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  • richardmitnick 1:01 pm on May 1, 2012 Permalink | Reply
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    From PNNL Lab: “Annotating Plague with Proteogenomics” 

    May 2012
    No writer credit

    Multifaceted strategies help refine annotations of three Yersinia strains

    Results: Strains of bacteria from the genus Yersinia are infectious and virulent: Y. pseudotuberculosis causes intestinal distress, and Y. pestis causes the plague. To better understand and potentially design ways to mitigate Yersinia’s effects on human health, researchers from Pacific Northwest National Laboratory, the J. Craig Venter Institute, and the University of Texas Medical Branch took on the task of refining the genome maps of three Yersinia strains. They used the proteome and transcriptome, collections of proteins and transcripts in the bacteria, to discover new information about the genome. Their results appear in PLoS ONE.

    yp
    3D representation of Yersina pestis, the cause of bubonic plague

    Why it matters: This new multi-faceted approach layers several types of evidence and substantially improves the genome annotation process. Importantly, the team’s work established refined genome annotations that provide essential information needed for a better understanding of how the plague functions, may provide new targets for therapeutics, and should speed the characterization of other pathogenic bacteria.”

    See the full article here.

    Pacific Northwest National Laboratory is a Department of Energy Office of Science national laboratory where interdisciplinary teams advance science and technology and deliver solutions to America’s most intractable problems in energy, the environment and national security.
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