1
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Blanford J, Zhai Z, Baer MD, Guo G, Liu H, Liu Q, Raugei S, Shanklin J. Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1. Sci Adv 2024; 10:eadn0895. [PMID: 38758793 PMCID: PMC11100557 DOI: 10.1126/sciadv.adn0895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to GEMINIVIRUS REP-INTERACTING KINASE1 (GRIK1), KIN10's activation T-loop reorients into GRIK1's active site, enabling its phosphorylation and activation. Trehalose 6-phosphate (T6P) is a proxy for cellular sugar status and a potent inhibitor of SnRK1. T6P binds to KIN10, a SnRK1 catalytic subunit, weakening its affinity for GRIK1. Here, we investigate the molecular details of T6P inhibition of KIN10. Molecular dynamics simulations and in vitro phosphorylation assays identified and validated the T6P binding site on KIN10. Under high-sugar conditions, T6P binds to KIN10, blocking the reorientation of its activation loop and preventing its phosphorylation and activation by GRIK1. Under these conditions, SnRK1 maintains only basal activity levels, minimizing phosphorylation of its target proteins, thereby facilitating a general shift from catabolism to anabolism.
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Affiliation(s)
- Jantana Blanford
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Zhiyang Zhai
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Marcel D. Baer
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gongrui Guo
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hui Liu
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
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2
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Zhou C, Mun J, Yao J, Anbalagan AK, Hossain MD, McLellan RA, Li R, Kisslinger K, Li G, Tong X, Head AR, Weiland C, Hulbert SL, Walter AL, Li Q, Zhu Y, Sushko PV, Liu M. Ultrathin Magnesium-Based Coating as an Efficient Oxygen Barrier for Superconducting Circuit Materials. Adv Mater 2024; 36:e2310280. [PMID: 38197525 DOI: 10.1002/adma.202310280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Scaling up superconducting quantum circuits based on transmon qubits necessitates substantial enhancements in qubit coherence time. Over recent years, tantalum (Ta) has emerged as a promising candidate for transmon qubits, surpassing conventional counterparts in terms of coherence time. However, amorphous surface Ta oxide layer may introduce dielectric loss, ultimately placing a limit on the coherence time. In this study, a novel approach for suppressing the formation of tantalum oxide using an ultrathin magnesium (Mg) capping layer is presented. Synchrotron-based X-ray photoelectron spectroscopy studies demonstrate that oxide is confined to an extremely thin region directly beneath the Mg/Ta interface. Additionally, it is demonstrated that the superconducting properties of thin Ta films are improved following the Mg capping, exhibiting sharper and higher-temperature transitions to superconductive and magnetically ordered states. Moreover, an atomic-scale mechanistic understanding of the role of the capping layer in protecting Ta from oxidation is established based on computational modeling. This work provides valuable insights into the formation mechanism and functionality of surface tantalum oxide, as well as a new materials design principle with the potential to reduce dielectric loss in superconducting quantum materials. Ultimately, the findings pave the way for the realization of large-scale, high-performance quantum computing systems.
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Affiliation(s)
- Chenyu Zhou
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Junsik Mun
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
- The Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Juntao Yao
- The Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Aswin Kumar Anbalagan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Mohammad D Hossain
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Russell A McLellan
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Ruoshui Li
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Kim Kisslinger
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Gengnan Li
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Xiao Tong
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Ashley R Head
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Conan Weiland
- Material Measurement Laboratory, National Institute of Standard and Technology, Gaithersburg, MD, 20899, USA
| | - Steven L Hulbert
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Andrew L Walter
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Qiang Li
- The Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Yimei Zhu
- The Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Peter V Sushko
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Mingzhao Liu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
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3
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Feingold G, Ghate VP, Russell LM, Blossey P, Cantrell W, Christensen MW, Diamond MS, Gettelman A, Glassmeier F, Gryspeerdt E, Haywood J, Hoffmann F, Kaul CM, Lebsock M, McComiskey AC, McCoy DT, Ming Y, Mülmenstädt J, Possner A, Prabhakaran P, Quinn PK, Schmidt KS, Shaw RA, Singer CE, Sorooshian A, Toll V, Wan JS, Wood R, Yang F, Zhang J, Zheng X. Physical science research needed to evaluate the viability and risks of marine cloud brightening. Sci Adv 2024; 10:eadi8594. [PMID: 38507486 PMCID: PMC10954212 DOI: 10.1126/sciadv.adi8594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/14/2024] [Indexed: 03/22/2024]
Abstract
Marine cloud brightening (MCB) is the deliberate injection of aerosol particles into shallow marine clouds to increase their reflection of solar radiation and reduce the amount of energy absorbed by the climate system. From the physical science perspective, the consensus of a broad international group of scientists is that the viability of MCB will ultimately depend on whether observations and models can robustly assess the scale-up of local-to-global brightening in today's climate and identify strategies that will ensure an equitable geographical distribution of the benefits and risks associated with projected regional changes in temperature and precipitation. To address the physical science knowledge gaps required to assess the societal implications of MCB, we propose a substantial and targeted program of research-field and laboratory experiments, monitoring, and numerical modeling across a range of scales.
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Affiliation(s)
| | | | - Lynn M. Russell
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | - Will Cantrell
- Michigan Technological University, Houghton, MI, USA
| | | | | | | | | | | | | | | | | | - Matthew Lebsock
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Yi Ming
- Boston College, Chestnut Hill, MA, USA
| | | | | | - Prasanth Prabhakaran
- NOAA Chemical Sciences Laboratory, Boulder, CO, USA
- CIRES, University of Colorado, Boulder, CO, USA
| | | | | | | | | | | | | | - Jessica S. Wan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | - Fan Yang
- National Center for Atmospheric Research, Boulder, CO, USA
| | - Jianhao Zhang
- NOAA Chemical Sciences Laboratory, Boulder, CO, USA
- CIRES, University of Colorado, Boulder, CO, USA
| | - Xue Zheng
- Lawrence Livermore National Laboratory, Livermore, CA, USA
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4
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Fu J, McKinley B, James B, Chrisler W, Markillie LM, Gaffrey MJ, Mitchell HD, Riaz MR, Marcial B, Orr G, Swaminathan K, Mullet J, Marshall-Colon A. Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems. Plant J 2024. [PMID: 38407828 DOI: 10.1111/tpj.16690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/17/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).
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Affiliation(s)
- Jie Fu
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Brandon James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - William Chrisler
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | | | - Matthew J Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Muhammad Rizwan Riaz
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Brenda Marcial
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
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5
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Yuan Y, Xie Z, Turaczy KK, Hwang S, Zhou J, Chen JG. Controlling Product Distribution of Polyethylene Hydrogenolysis Using Bimetallic RuM 3 (M = Fe, Co, Ni) Catalysts. Chem Bio Eng 2024; 1:67-75. [PMID: 38434798 PMCID: PMC10906090 DOI: 10.1021/cbe.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 03/05/2024]
Abstract
Plastic hydrogenolysis is an attractive approach for producing value-added chemicals due to its mild reaction conditions, but controlling product distribution is challenging due to the formation of undesired CH4. This work reports several bimetallic RuM3/CeO2 (M = Fe, Co, Ni) catalysts that shift the product of low-density polyethylene hydrogenolysis toward longer-chain hydrocarbons. These catalysts were characterized by using X-ray absorption fine structure spectroscopy, electron microscopy imaging, and H2 temperature-programmed reduction. The combined catalytic evaluation and characterization results revealed that the product distribution was regulated by the formation of bimetallic alloys. A model compound, n-hexadecane, was selected to further understand the differences in hydrogenolysis over the Ru-based catalysts. Although a longer reaction time shifted the product toward smaller molecules, the bimetallic (RuCo3/CeO2) catalyst limited the further conversion of C2-C5 into CH4. This work highlights the role of bimetallic alloys in tailoring the interaction with hydrocarbons, thereby controlling the product distribution of polymer hydrogenolysis.
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Affiliation(s)
- Yong Yuan
- Chemistry
Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Zhenhua Xie
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Kevin K. Turaczy
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Sooyeon Hwang
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Jiahua Zhou
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jingguang G. Chen
- Chemistry
Division, Brookhaven National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
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6
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Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024; 11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.
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Affiliation(s)
- Doo Nam Kim
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Andrew D McNaughton
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
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7
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Yama NS, Chen IT, Chakravarthi S, Li B, Pederson C, Matthews BE, Spurgeon SR, Perea DE, Wirth MG, Sushko PV, Li M, Fu KMC. Silicon-Lattice-Matched Boron-Doped Gallium Phosphide: A Scalable Acousto-Optic Platform. Adv Mater 2024; 36:e2305434. [PMID: 37660285 DOI: 10.1002/adma.202305434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/17/2023] [Indexed: 09/04/2023]
Abstract
The compact size, scalability, and strongly confined fields in integrated photonic devices enable new functionalities in photonic networking and information processing, both classical and quantum. Gallium phosphide (GaP) is a promising material for active integrated photonics due to its high refractive index, wide bandgap, strong nonlinear properties, and large acousto-optic figure of merit. This study demonstrates that silicon-lattice-matched boron-doped GaP (BGaP), grown at the 12-inch wafer scale, provides similar functionalities as GaP. BGaP optical resonators exhibit intrinsic quality factors exceeding 25,000 and 200,000 at visible and telecom wavelengths, respectively. It further demonstrates the electromechanical generation of low-loss acoustic waves and an integrated acousto-optic (AO) modulator. High-resolution spatial and compositional mapping, combined with ab initio calculations, indicate two candidates for the excess optical loss in the visible band: the silicon-GaP interface and boron dimers. These results demonstrate the promise of the BGaP material platform for the development of scalable AO technologies at telecom and provide potential pathways toward higher performance at shorter wavelengths.
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Affiliation(s)
- Nicholas S Yama
- Electrical and Computer Engineering Department, University of Washington, Seattle, WA, 98105, USA
| | - I-Tung Chen
- Electrical and Computer Engineering Department, University of Washington, Seattle, WA, 98105, USA
| | | | - Bingzhao Li
- Electrical and Computer Engineering Department, University of Washington, Seattle, WA, 98105, USA
| | | | - Bethany E Matthews
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Steven R Spurgeon
- Physics Department, University of Washington, Seattle, WA, 98105, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Daniel E Perea
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mark G Wirth
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Peter V Sushko
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mo Li
- Electrical and Computer Engineering Department, University of Washington, Seattle, WA, 98105, USA
- Physics Department, University of Washington, Seattle, WA, 98105, USA
| | - Kai-Mei C Fu
- Electrical and Computer Engineering Department, University of Washington, Seattle, WA, 98105, USA
- Physics Department, University of Washington, Seattle, WA, 98105, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
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8
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Fiedler KR, Olszta MJ, Yano KH, Doty C, Hopkins D, Akers S, Spurgeon SR. Evaluating Stage Motion for Automated Electron Microscopy. Microsc Microanal 2023; 29:1931-1939. [PMID: 37832144 DOI: 10.1093/micmic/ozad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Precise control is an essential and elusive quality of emerging self-driving transmission electron microscopes (TEMs). It is widely understood these instruments must be capable of performing rapid, high-volume, and arbitrary movements for practical self-driving operation. However, stage movements are difficult to automate at scale, owing to mechanical instability, hysteresis, and thermal drift. Such difficulties pose major barriers to artificial intelligence-directed microscope designs that require repeatable, precise movements. To guide design of emerging instruments, it is necessary to understand the behavior of existing mechanisms to identify rate limiting steps for full autonomy. Here, we describe a general framework to evaluate stage motion in any TEM. We define metrics to evaluate stage degrees of freedom, propose solutions to improve performance, and comment on fundamental limits to automated experimentation using present hardware.
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Affiliation(s)
- Kevin R Fiedler
- College of Arts and Sciences, Washington State University-Tri-Cities, Richland, WA 99354, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew J Olszta
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kayla H Yano
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christina Doty
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Derek Hopkins
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah Akers
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Steven R Spurgeon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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9
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Kazimierczuk K, Barrows SE, Olarte MV, Qafoku NP. Decarbonization of Agriculture: The Greenhouse Gas Impacts and Economics of Existing and Emerging Climate-Smart Practices. ACS Eng Au 2023; 3:426-442. [PMID: 38144676 PMCID: PMC10739617 DOI: 10.1021/acsengineeringau.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 12/26/2023]
Abstract
The worldwide emphasis on reducing greenhouse gas (GHG) emissions has increased focus on the potential to mitigate emissions through climate-smart agricultural practices, including regenerative, digital, and controlled environment farming systems. The effectiveness of these solutions largely depends on their ability to address environmental concerns, generate economic returns, and meet supply chain needs. In this Review, we summarize the state of knowledge on the GHG impacts and profitability of these three existing and emerging farming systems. Although we find potential for CO2 mitigation in all three approaches (depending on site-specific and climatic factors), we point to the greater level of research covering the efficacy of regenerative and digital agriculture in tackling non-CO2 emissions (i.e., N2O and CH4), which account for the majority of agriculture's GHG footprint. Despite this greater research coverage, we still find significant methodological and data limitations in accounting for the major GHG fluxes of these practices, especially the lifetime CH4 footprint of more nascent climate-smart regenerative agriculture practices. Across the approaches explored, uncertainties remain about the overall efficacy and persistence of mitigation-particularly with respect to the offsetting of soil carbon sequestration gains by N2O emissions and the lifecycle emissions of controlled environment agriculture systems compared to traditional systems. We find that the economic feasibility of these practices is also system-specific, although regenerative agriculture is generally the most accessible climate-smart approach. Robust incentives (including carbon credit considerations), investments, and policy changes would make these practices more financially accessible to farmers.
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Affiliation(s)
- Kamila Kazimierczuk
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sarah E. Barrows
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mariefel V. Olarte
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nikolla P. Qafoku
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Civil and Environmental Engineering, University of Washington, Seattle, Washington 99195, United States
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10
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Trinh TK, Jian T, Jin B, Nguyen DT, Zuckermann RN, Chen CL. Designed Metal-Containing Peptoid Membranes as Enzyme Mimetics for Catalytic Organophosphate Degradation. ACS Appl Mater Interfaces 2023; 15:51191-51203. [PMID: 37879106 PMCID: PMC10636725 DOI: 10.1021/acsami.3c11816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
The detoxification of lethal organophosphate (OP) residues in the environment is crucial to prevent human exposure and protect modern society. Despite serving as excellent catalysts for OP degradation, natural enzymes require costly preparation and readily deactivate upon exposure to environmental conditions. Herein, we designed and prepared a series of phosphotriesterase mimics based on stable, self-assembled peptoid membranes to overcome these limitations of the enzymes and effectively catalyze the hydrolysis of dimethyl p-nitrophenyl phosphate (DMNP)─a nerve agent simulant. By covalently attaching metal-binding ligands to peptoid N-termini, we attained enzyme mimetics in the form of surface-functionalized crystalline nanomembranes. These nanomembranes display a precisely controlled arrangement of coordinated metal ions, which resemble the active sites found in phosphotriesterases to promote DMNP hydrolysis. Moreover, using these highly programmable peptoid nanomembranes allows for tuning the local chemical environment of the coordinated metal ion to achieve enhanced hydrolysis activity. Among the crystalline membranes that are active for DMNP degradation, those assembled from peptoids containing bis-quinoline ligands with an adjacent phenyl side chain showed the highest hydrolytic activity with a 219-fold rate acceleration over the background, demonstrating the important role of the hydrophobic environment in proximity to the active sites. Furthermore, these membranes exhibited remarkable stability and were able to retain their catalytic activity after heating to 60 °C and after multiple uses. This work provides insights into the principal features to construct a new class of biomimetic materials with high catalytic efficiency, cost-effectiveness, and reusability applied in nerve agent detoxification.
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Affiliation(s)
- Thi Kim
Hoang Trinh
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Tengyue Jian
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Biao Jin
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dan-Thien Nguyen
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National
Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, United States
| | - Chun-Long Chen
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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11
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Latta D, Rosso KM, Scherer MM. Tracking Initial Fe(II)-Driven Ferrihydrite Transformations: A Mössbauer Spectroscopy and Isotope Investigation. ACS Earth Space Chem 2023; 7:1814-1824. [PMID: 37876661 PMCID: PMC10591510 DOI: 10.1021/acsearthspacechem.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/22/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023]
Abstract
Transformation of nanocrystalline ferrihydrite to more stable microcrystalline Fe(III) oxides is rapidly accelerated under reducing conditions with aqueous Fe(II) present. While the major steps of Fe(II)-catalyzed ferrihydrite transformation are known, processes in the initial phase that lead to nucleation and the growth of product minerals remain unclear. To track ferrihydrite-Fe(II) interactions during this initial phase, we used Fe isotopes, Mössbauer spectroscopy, and extractions to monitor the structural, magnetic, and isotope composition changes of ferrihydrite within ∼30 min of Fe(II) exposure. We observed rapid isotope mixing between aqueous Fe(II) and ferrihydrite during this initial lag phase. Our findings from Mössbauer spectroscopy indicate that a more magnetically ordered Fe(III) phase initially forms that is distinct from ferrihydrite and bulk crystalline transformation products. The signature of this phase is consistent with the early stage emergence of lepidocrocite-like lamellae observed in previous transmission electron microscopy studies. Its signature is furthermore removed by xylenol extraction of Fe(III), the same approach used to identify a chemically labile form of Fe(III) resulting from Fe(II) contact that is correlated to the ultimate emergence of crystalline product phases detectable by X-ray diffraction. Our work indicates that the mineralogical changes in the initial lag phase of Fh transformation initiated by Fe(II)-Fh electron transfer are critical to understanding ferrihydrite behavior in soils and sediments, particularly with regard to metal uptake and release.
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Affiliation(s)
- Drew Latta
- Department
of Civil and Environmental Engineering/IIHR, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin M. Rosso
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99345, United States
| | - Michelle M. Scherer
- Department
of Civil and Environmental Engineering/IIHR, The University of Iowa, Iowa City, Iowa 52242, United States
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12
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Nakayasu ES, Gritsenko MA, Kim YM, Kyle JE, Stratton KG, Nicora CD, Munoz N, Navarro KM, Claborne D, Gao Y, Weitz KK, Paurus VL, Bloodsworth KJ, Allen KA, Bramer LM, Montes F, Clark KA, Tietje G, Teeguarden J, Burnum-Johnson KE. Elucidating regulatory processes of intense physical activity by multi-omics analysis. Mil Med Res 2023; 10:48. [PMID: 37853489 PMCID: PMC10583322 DOI: 10.1186/s40779-023-00477-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/28/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. METHODS To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student's t-test followed by pathway analysis and comparison between the different omics modalities. RESULTS Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. CONCLUSION This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Nathalie Munoz
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kathleen M Navarro
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Western States Division, Denver, CO, 80204, USA
| | - Daniel Claborne
- Computational Analytics Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kelsey A Allen
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Fernando Montes
- Los Angeles County Fire Department, Los Angeles, CA, 90063, USA
| | - Kathleen A Clark
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Respiratory Health Division, Morgantown, WV, 26505, USA
| | - Grant Tietje
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Justin Teeguarden
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Kristin E Burnum-Johnson
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
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13
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Lim WG, Li X, Reed D. Understanding the Role of Zinc Hydroxide Sulfate and its Analogues in Mildly Acidic Aqueous Zinc Batteries: A Review. Small Methods 2023:e2300965. [PMID: 37803913 DOI: 10.1002/smtd.202300965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/12/2023] [Indexed: 10/08/2023]
Abstract
Mildly acidic aqueous zinc batteries (AZBs) have attracted tremendous attention for grid storage applications with the expectation to tackle the issues of Li-ion batteries on high cost and poor safety. However, the performance, particularly energy density and cycle stability of AZBs are still unsatisfactory when compared with LIBs. To help the development of AZBs, a lot of effort have been made to understand the battery reaction mechanisms and precedent microscopic and spectroscopic analyses have shown flake-like large particles of zinc hydroxide sulfate (ZHS) and its analogues formed on the surfaces of cathodes and anodes in sulfate and other electrolyte systems during cycling. However, because of the complexity of the thermodynamics and kinetics of aqueous reactions to understand different battery conditions, controversies still exist. This article will review the roles of ZHS discussed in recent representative references aiming to shine light on the fundamental mechanisms of AZBs and pave ways to further improve the battery performance.
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Affiliation(s)
- Won-Gwang Lim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Xiaolin Li
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - David Reed
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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14
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Shishkina EA, Napier BA, Preston DL, Degteva MO. Dose estimates and their uncertainties for use in epidemiological studies of radiation-exposed populations in the Russian Southern Urals. PLoS One 2023; 18:e0288479. [PMID: 37561738 PMCID: PMC10414627 DOI: 10.1371/journal.pone.0288479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 08/12/2023] Open
Abstract
Many residents of the Russian Southern Urals were exposed to radioactive environmental pollution created by the operations of the Mayak Production Association in the mid- 20th century. There were two major releases: the discharge of about 1x1017 Bq of liquid waste into the Techa River between 1949 and 1959; and the atmospheric release of 7.4 * 1016 Bq as a result an explosion in the radioactive waste-storage facility in 1957. The releases into the Techa River resulted in the exposure of more than 30,000 people who lived in riverside villages between 1950 and 1961. The 1957 accident contaminated a larger area with the highest exposure levels in an area that is called the East Urals Radioactive Trace (EURT). Current epidemiologic studies of the exposed populations are based on dose estimates obtained using a Monte-Carlo dosimetry system (TRDS-2016MC) that provides multiple realizations of the annual doses for each cohort member. These dose realizations provide a central estimate of the individual dose and information on the uncertainty of these dose estimates. In addition, the correlation of individual annual doses over realizations provides important information on shared uncertainties that can be used to assess the impact of shared dose uncertainties on risk estimate uncertainty.This paper considers dose uncertainties in the TRDS-2016MC. Individual doses from external and internal radiation sources were reconstructed for 48,036 people based on environmental contamination patterns, residential histories, individual 90Sr body-burden measurements and dietary intakes. Dietary intake of 90Sr resulted in doses accumulated in active bone marrow (or simply, marrow) that were an order of magnitude greater than those in soft tissues. About 84% of the marrow dose and 50% of the stomach dose was associated with internal exposures. The lognormal distribution is well-fitted to the individual dose realizations, which, therefore, could be expressed and easily operated in terms of geometric mean (GM) and geometric standard deviation (GSD). Cohort average GM for marrow and stomach cumulative doses are 0.21 and 0.03 Gy, respectively. Cohort average dose uncertainties in terms of GSD are as follows: for marrow it is 2.93 (90%CI: 2.02-4.34); for stomach and the other non-calcified tissues it is 2.32 (90% CI: 1.78-2.9).
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Affiliation(s)
- Elena A. Shishkina
- Biophysics Laboratory, Urals Research Center for Radiation Medicine, Chelyabinsk, Russia
- Chelyabinsk State University, Chelyabinsk, Russia
| | - Bruce A. Napier
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Dale L. Preston
- Hirosoft International LLC, Eureka, California, United States of America
| | - Marina O. Degteva
- Biophysics Laboratory, Urals Research Center for Radiation Medicine, Chelyabinsk, Russia
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15
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Zambare N, Arey B, Qafoku O, Koirala KP, Kovarik L, Dohnalkova A. Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy. Microsc Microanal 2023; 29:1467-1473. [PMID: 37488814 DOI: 10.1093/micmic/ozad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 07/26/2023]
Abstract
Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.
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Affiliation(s)
- Neerja Zambare
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Bruce Arey
- National Security Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Odeta Qafoku
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Krishna Prasad Koirala
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Libor Kovarik
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
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16
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Evans PE, Wang Y, Sushko PV, Dohnálek Z. Understanding palladium-tellurium cluster formation on WTe 2: From a kinetically hindered distribution to thermodynamically controlled monodispersity. PNAS Nexus 2023; 2:pgad212. [PMID: 37416870 PMCID: PMC10321376 DOI: 10.1093/pnasnexus/pgad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
A fundamental understanding of the transition metal dichalcogenide (TMDC)-metal interface is critical for their utilization in a broad range of applications. We investigate how the deposition of palladium (Pd), as a model metal, on WTe2(001), leads to the assembly of Pd into clusters and nanoparticles. Using X-ray photoemission spectroscopy, scanning tunneling microscopy imaging, and ab initio simulations, we find that Pd nucleation is driven by the interaction with and the availability of mobile excess tellurium (Te) leading to the formation of Pd-Te clusters at room temperature. Surprisingly, the nucleation of Pd-Te clusters is not affected by intrinsic surface defects, even at elevated temperatures. Upon annealing, the Pd-Te nanoclusters adopt an identical nanostructure and are stable up to ∼523 K. Density functional theory calculations provide a foundation for our understanding of the mobility of Pd and Te atoms, preferential nucleation of Pd-Te clusters, and the origin of their annealing-induced monodispersity. These results highlight the role the excess chalcogenide atoms may play in the metal deposition process. More broadly, the discoveries of synthetic pathways yielding thermally robust monodispersed nanostructures on TMDCs are critical to the manufacturing of novel quantum and microelectronics devices and catalytically active nano-alloy centers.
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Affiliation(s)
- Prescott E Evans
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yang Wang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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17
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Zhang S, Hettige JJ, Li Y, Jian T, Yang W, Yao YC, Zheng R, Lin Z, Tao J, De Yoreo JJ, Baer M, Noy A, Chen CL. Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes. Small 2023; 19:e2206810. [PMID: 36811318 DOI: 10.1002/smll.202206810] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/06/2023] [Indexed: 05/25/2023]
Abstract
Robust and cost-effective membrane-based separations are essential to solving many global crises, such as the lack of clean water. Even though the current polymer-based membranes are widely used for separations, their performance and precision can be enhanced by using a biomimetic membrane architecture that consists of highly permeable and selective channels embedded in a universal membrane matrix. Researchers have shown that artificial water and ion channels, such as carbon nanotube porins (CNTPs), embedded in lipid membranes can deliver strong separation performance. However, their applications are limited by the relative fragility and low stability of the lipid matrix. In this work, we demonstrate that CNTPs can co-assemble into two dimension (2D) peptoid membrane nanosheets, opening up a way to produce highly programmable synthetic membranes with superior crystallinity and robustness. A combination of molecular dynamics (MD) simulations, Raman spectroscopy, X-ray diffraction (XRD), and atomic force microscopy (AFM) measurements to verify the co-assembly of CNTP and peptoids are used and show that it does not disrupt peptoid monomer packing within the membrane. These results provide a new option for designing affordable artificial membranes and highly robust nanoporous solids.
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Affiliation(s)
- Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Jeevapani J Hettige
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yuhao Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yun-Chiao Yao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Renyu Zheng
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Zhixing Lin
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Jinhui Tao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Marcel Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
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18
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Baweja JA, Fallon CK, Jefferson BA. Opportunities for human factors in machine learning. Front Artif Intell 2023; 6:1130190. [PMID: 37152975 PMCID: PMC10157195 DOI: 10.3389/frai.2023.1130190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction The field of machine learning and its subfield of deep learning have grown rapidly in recent years. With the speed of advancement, it is nearly impossible for data scientists to maintain expert knowledge of cutting-edge techniques. This study applies human factors methods to the field of machine learning to address these difficulties. Methods Using semi-structured interviews with data scientists at a National Laboratory, we sought to understand the process used when working with machine learning models, the challenges encountered, and the ways that human factors might contribute to addressing those challenges. Results Results of the interviews were analyzed to create a generalization of the process of working with machine learning models. Issues encountered during each process step are described. Discussion Recommendations and areas for collaboration between data scientists and human factors experts are provided, with the goal of creating better tools, knowledge, and guidance for machine learning scientists.
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19
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Lin Z, Ammal SC, Denny SR, Rykov SA, You KE, Heyden A, Chen JG. Unraveling Unique Surface Chemistry of Transition Metal Nitrides in Controlling Selective C-O Bond Scission Pathways of Glycerol. JACS Au 2022; 2:367-379. [PMID: 35252987 PMCID: PMC8889611 DOI: 10.1021/jacsau.1c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 05/24/2023]
Abstract
Controlled C-O bond scission is an important step for upgrading glycerol, a major byproduct from the continuously increasing biodiesel production. Transition metal nitride catalysts have been identified as promising hydrodeoxygenation (HDO) catalysts, but fundamental understanding regarding the active sites of the catalysts and reaction mechanism remains unclear. This work demonstrates a fundamental surface science study of Mo2N and Cu/Mo2N for the selective HDO reaction of glycerol, using a combination of model surface experiments and first-principles calculations. Temperature-programmed desorption (TPD) experiments showed that clean Mo2N cleaved two or three C-O bonds of glycerol to produce allyl alcohol, propanal, and propylene. The addition of Cu to Mo2N changed the reaction pathway to one C-O bond scission to produce acetol. High-resolution electron energy loss spectroscopy (HREELS) results identified the surface intermediates, showing a facile C-H bond activation on Mo2N. Density functional theory (DFT) calculations revealed that the surface N on Mo2N interacted with the H atoms in glycerol and blocked some Mo sites to enable selective C-O bond scission. This work shows that Mo2N and Cu/Mo2N are active and selective for the controlled C-O bond scission of glycerol and in turn provides insights into the rational catalyst design for selective oxygen removal of relevant biomass-derived oxygenates.
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Affiliation(s)
- Zhexi Lin
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Salai C. Ammal
- Department
of Chemical Engineering, University of South
Carolina, Columbia, South Carolina 29208, United States
| | - Steven R. Denny
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Sergei A. Rykov
- Department
of Semiconductors Physics and Nano-electronics, Peter the Great St. Petersburg Polytechnic University 195251 St. Petersburg, Russia
| | - Kyung-Eun You
- Department
of Chemical Engineering, University of South
Carolina, Columbia, South Carolina 29208, United States
| | - Andreas Heyden
- Department
of Chemical Engineering, University of South
Carolina, Columbia, South Carolina 29208, United States
| | - Jingguang G. Chen
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Chemistry
Division, Brookhaven National Laboratory, Upton, New York 11973, United States
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20
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Zaveri RA, Wang J, Fan J, Zhang Y, Shilling JE, Zelenyuk A, Mei F, Newsom R, Pekour M, Tomlinson J, Comstock JM, Shrivastava M, Fortner E, Machado LAT, Artaxo P, Martin ST. Rapid growth of anthropogenic organic nanoparticles greatly alters cloud life cycle in the Amazon rainforest. Sci Adv 2022; 8:eabj0329. [PMID: 35020441 PMCID: PMC8754412 DOI: 10.1126/sciadv.abj0329] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Aerosol-cloud interactions remain uncertain in assessing climate change. While anthropogenic activities produce copious aerosol nanoparticles smaller than 10 nanometers, they are too small to act as efficient cloud condensation nuclei (CCN). The mechanisms responsible for particle growth to CCN-relevant sizes are poorly understood. Here, we present aircraft observations of rapid growth of anthropogenic nanoparticles downwind of an isolated metropolis in the Amazon rainforest. Model analysis reveals that the sustained particle growth to CCN sizes is predominantly caused by particle-phase diffusion-limited partitioning of semivolatile oxidation products of biogenic hydrocarbons. Cloud-resolving numerical simulations show that the enhanced CCN concentrations in the urban plume substantially alter the formation of shallow convective clouds, suppress precipitation, and enhance the transition to deep convective clouds. The proposed nanoparticle growth mechanism, expressly enabled by the abundantly formed semivolatile organics, suggests an appreciable impact of anthropogenic aerosols on cloud life cycle in previously unpolluted forests of the world.
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Affiliation(s)
- Rahul A. Zaveri
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jian Wang
- Washington University in Saint Louis, Saint Louis, MO 63130, USA
| | - Jiwen Fan
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yuwei Zhang
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Alla Zelenyuk
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Fan Mei
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rob Newsom
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Mikhail Pekour
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jason Tomlinson
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | | | | | - Luiz A. T. Machado
- National Institute for Space Research, São José dos Campos, São Paulo 12227-010, Brazil
| | - Paulo Artaxo
- Institute of Physics, University of São Paulo, São Paulo 05508-090, Brazil
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21
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Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim YM, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, Callister SJ. Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil. PLoS One 2021; 16:e0259937. [PMID: 34879068 PMCID: PMC8654227 DOI: 10.1371/journal.pone.0259937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.
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Affiliation(s)
- Matthew J. Peterson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pubudu P. Handakumbura
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Allison M. Thompson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Zachary R. Russell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Sarah J. Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Montana L. Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason G. Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rosey K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bryan A. Stanfill
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Steven C. Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington, United States of America
| | - Vanessa L. Bailey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
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22
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Wu CY, Dodge HH, Reynolds C, Barnes LL, Silbert LC, Lim MM, Mattek N, Gothard S, Kaye JA, Beattie Z. In-Home Mobility Frequency and Stability in Older Adults Living Alone With or Without MCI: Introduction of New Metrics. Front Digit Health 2021; 3:764510. [PMID: 34766104 PMCID: PMC8575720 DOI: 10.3389/fdgth.2021.764510] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Background: Older adults spend a considerable amount of time inside their residences; however, most research investigates out-of-home mobility and its health correlates. We measured indoor mobility using room-to-room transitions, tested their psychometric properties, and correlated indoor mobility with cognitive and functional status. Materials and Methods: Community-dwelling older adults living alone (n = 139; age = 78.1 ± 8.6 years) from the Oregon Center for Aging & Technology (ORCATECH) and Minority Aging Research Study (MARS) were included in the study. Two indoor mobility features were developed using non-parametric parameters (frequency; stability): Indoor mobility frequency (room-to-room transitions/day) was detected using passive infrared (PIR) motion sensors fixed on the walls in four geographic locations (bathroom; bedroom; kitchen; living room) and using door contact sensors attached to the egress door in the entrance. Indoor mobility stability was estimated by variances of number of room-to-room transitions over a week. Test-retest reliability (Intra-class coefficient, ICC) and the minimal clinically important difference (MCID) defined as the standard error of measurement (SEM) were generated. Generalized estimating equations models related mobility features with mild cognitive impairment (MCI) and functional status (gait speed). Results: An average of 206 days (±127) of sensor data were analyzed per individual. Indoor mobility frequency and stability showed good to excellent test-retest reliability (ICCs = 0.91[0.88-0.94]; 0.59[0.48-0.70]). The MCIDs of mobility frequency and mobility stability were 18 and 0.09, respectively. On average, a higher indoor mobility frequency was associated with faster gait speed (β = 0.53, p = 0.04), suggesting an increase of 5.3 room-to-room transitions per day was associated with an increase of 10 cm/s gait speed. A decrease in mobility stability was associated with MCI (β = -0.04, p = 0.03). Discussion: Mobility frequency and stability in the home are clinically meaningful and reliable features. Pervasive-sensing systems deployed in homes can objectively reveal cognitive and functional status in older adults who live alone.
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Affiliation(s)
- Chao-Yi Wu
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Hiroko H. Dodge
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Christina Reynolds
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Lisa L. Barnes
- Department of Neurological Sciences, Rush Medical College, Chicago, IL, United States
- Rush Alzheimer's Disease Center, Rush Medical College, Chicago, IL, United States
| | - Lisa C. Silbert
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Miranda M. Lim
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Veterans Affairs Portland Health Care System, Portland, OR, United States
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, United States
- National Center for Rehabilitative Auditory Research, Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Nora Mattek
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Sarah Gothard
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Jeffrey A. Kaye
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
| | - Zachary Beattie
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Oregon Center for Aging & Technology (ORCATECH), Oregon Health & Science University, Portland, OR, United States
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23
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Seltzer AM, Bekaert DV, Barry PH, Durkin KE, Mace EK, Aalseth CE, Zappala JC, Mueller P, Jurgens B, Kulongoski JT. Groundwater residence time estimates obscured by anthropogenic carbonate. Sci Adv 2021; 7:7/17/eabf3503. [PMID: 33883137 PMCID: PMC8059937 DOI: 10.1126/sciadv.abf3503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Groundwater is an important source of drinking and irrigation water. Dating groundwater informs its vulnerability to contamination and aids in calibrating flow models. Here, we report measurements of multiple age tracers (14C, 3H, 39Ar, and 85Kr) and parameters relevant to dissolved inorganic carbon (DIC) from 17 wells in California's San Joaquin Valley (SJV), an agricultural region that is heavily reliant on groundwater. We find evidence for a major mid-20th century shift in groundwater DIC input from mostly closed- to mostly open-system carbonate dissolution, which we suggest is driven by input of anthropogenic carbonate soil amendments. Crucially, enhanced open-system dissolution, in which DIC equilibrates with soil CO2, fundamentally affects the initial 14C activity of recently recharged groundwater. Conventional 14C dating of deeper SJV groundwater, assuming an open system, substantially overestimates residence time and thereby underestimates susceptibility to modern contamination. Because carbonate soil amendments are ubiquitous, other groundwater-reliant agricultural regions may be similarly affected.
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Affiliation(s)
- Alan M Seltzer
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - David V Bekaert
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Peter H Barry
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Kathryn E Durkin
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
| | - Emily K Mace
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Craig E Aalseth
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | | | - Bryant Jurgens
- U.S. Geological Survey California Water Science Center, San Diego, CA 92101, USA
| | - Justin T Kulongoski
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
- U.S. Geological Survey California Water Science Center, San Diego, CA 92101, USA
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24
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Gomez MA, Jiang R, Song M, Li D, Lea AS, Ma X, Wang H, Yin X, Wang S, Jia Y. Further insights into the Fe(ii) reduction of 2-line ferrihydrite: a semi in situ and in situ TEM study. Nanoscale Adv 2020; 2:4938-4950. [PMID: 36132886 PMCID: PMC9417501 DOI: 10.1039/d0na00643b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
The biotic or abiotic reduction of nano-crystalline 2-line ferrihydrite (2-line FH) into more thermodynamically stable phases such as lepidocrocite-LP, goethite-GT, magnetite-MG, and hematite-HT plays an important role in the geochemical cycling of elements and nutrients in aqueous systems. In our study, we employed the use of in situ liquid cell (LC) and semi in situ analysis in an environmental TEM to gain further insights at the micro/nano-scale into the reaction mechanisms by which Fe(ii)(aq) catalyzes 2-line FH. We visually observed for the first time the following intermediate steps: (1) formation of round and wire-shaped precursor nano-particles arising only from Fe(ii)(aq), (2) two distinct dissolution mechanisms for 2 line-FH (i.e. reduction of size and density as well as breakage through smaller nano-particles), (3) lack of complete dissolution of 2-line FH (i.e. "induction-period"), (4) an amorphous phase growth ("reactive-FH/labile Fe(iii) phase") on 2 line-FH, (5) deposition of amorphous nano-particles on the surface of 2 line-FH and (6) assemblage of elongated crystalline lamellae to form tabular LP crystals. Furthermore, we observed phenomena consistent with the movement of adsorbate ions from solution onto the surface of a Fe(iii)-oxy/hydroxide crystal. Thus our work here reveals that the catalytic transformation of 2-line FH by Fe(ii)(aq) at the micro/nano scale doesn't simply occur via dissolution-reprecipitation or surface nucleation-solid state conversion mechanisms. Rather, as we demonstrate here, it is an intricate chemical process that goes through a series of intermediate steps not visible through conventional lab or synchrotron bulk techniques. However, such intermediate steps may affect the environmental fate, bioavailability, and transport of elements of such nano-particles in aqueous environments.
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Affiliation(s)
- Mario Alberto Gomez
- Liaoning Engineering Research Center for Treatment and Recycling of Industrially Discharged Heavy Metals, Shenyang University of Chemical Technology Shenyang Liaoning 110142 China +86 15093716277 +86 15140014967
- Department of Geological Sciences, University of Saskatchewan Saskatoon Saskatchewan S7N 5E2 Canada
| | - Ruonan Jiang
- Liaoning Engineering Research Center for Treatment and Recycling of Industrially Discharged Heavy Metals, Shenyang University of Chemical Technology Shenyang Liaoning 110142 China +86 15093716277 +86 15140014967
| | - Miao Song
- Physical and Computational Science Directorate, Pacific Northwest National Laboratory Richland Washington 99352 USA +1 5093716242 +1 5093716277
| | - Dongsheng Li
- Physical and Computational Science Directorate, Pacific Northwest National Laboratory Richland Washington 99352 USA +1 5093716242 +1 5093716277
| | - Alan Scott Lea
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland Washington 99352 USA
| | - Xu Ma
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang 110016 Liaoning China
| | - Haibo Wang
- Liaoning Engineering Research Center for Treatment and Recycling of Industrially Discharged Heavy Metals, Shenyang University of Chemical Technology Shenyang Liaoning 110142 China +86 15093716277 +86 15140014967
| | - Xiuling Yin
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang 110016 Liaoning China
| | - Shaofeng Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang 110016 Liaoning China
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang 110016 Liaoning China
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25
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Sand KK, Jelavić S, Dobberschütz S, Ashby PD, Marshall MJ, Dideriksen K, Stipp SLS, Kerisit SN, Friddle RW, DeYoreo JJ. Mechanistic insight into biopolymer induced iron oxide mineralization through quantification of molecular bonding. Nanoscale Adv 2020; 2:3323-3333. [PMID: 36134299 PMCID: PMC9417541 DOI: 10.1039/d0na00138d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/12/2020] [Indexed: 06/16/2023]
Abstract
Microbial production of iron (oxyhydr)oxides on polysaccharide rich biopolymers occurs on such a vast scale that it impacts the global iron cycle and has been responsible for major biogeochemical events. Yet the physiochemical controls these biopolymers exert on iron (oxyhydr)oxide formation are poorly understood. Here we used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxyhydr)oxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxyhydr)oxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxyhydr)oxide transformation rates. Combined, our results provide a mechanistic basis for understanding how polymer-mineral-water interactions alter iron (oxyhydr)oxides nucleation and growth dynamics and pave the way for an improved understanding of the consequences of polymer induced mineralization in natural systems.
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Affiliation(s)
- K K Sand
- Physical Sciences Division, Pacific Northwest National Laboratory Richland WA USA
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - S Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen Denmark
| | - S Dobberschütz
- Nano-Science Center, Department of Chemistry, University of Copenhagen Denmark
| | - P D Ashby
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - M J Marshall
- Biologic Sciences Division, Pacific Northwest National Laboratory Richland WA USA
| | - K Dideriksen
- Nano-Science Center, Department of Chemistry, University of Copenhagen Denmark
| | - S L S Stipp
- Nano-Science Center, Department of Chemistry, University of Copenhagen Denmark
| | - S N Kerisit
- Physical Sciences Division, Pacific Northwest National Laboratory Richland WA USA
| | - R W Friddle
- Sandia National Laboratories Livermore California 94550 USA
| | - J J DeYoreo
- Physical Sciences Division, Pacific Northwest National Laboratory Richland WA USA
- Department of Material Science and Engineering, University of Washington Seattle WA USA
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26
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Burnet MC, Zamith-Miranda D, Heyman HM, Weitz KK, Bredeweg EL, Nosanchuk JD, Nakayasu ES. Remodeling of the Histoplasma Capsulatum Membrane Induced by Monoclonal Antibodies. Vaccines (Basel) 2020; 8:E269. [PMID: 32498228 PMCID: PMC7349930 DOI: 10.3390/vaccines8020269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 02/06/2023] Open
Abstract
Antibodies play a central role in host immunity by directly inactivating or recognizing an invading pathogen to enhance different immune responses to combat the invader. However, the cellular responses of pathogens to the presence of antibodies are not well-characterized. Here, we used different mass spectrometry techniques to study the cellular responses of the pathogenic fungus Histoplasma capsulatum to monoclonal antibodies (mAb) against HSP60, the surface protein involved in infection. A proteomic analysis of H. capsulatum yeast cells revealed that mAb binding regulates a variety of metabolic and signaling pathways, including fatty acid metabolism, sterol metabolism, MAPK signaling and ubiquitin-mediated proteolysis. The regulation of the fatty acid metabolism was accompanied by increases in the level of polyunsaturated fatty acids, which further augmented the degree of unsaturated lipids in H. capsulatum's membranes and energy storage lipids, such as triacylglycerols, phosphatidylcholines, phosphatidylethanolamines and phosphatidylinositols. MAb treatment also regulated sterol metabolism by increasing the levels of cholesterol and ergosterol in the cells. We also showed that global changes in the lipid profiles resulted in an increased susceptibility of H. capsulatum to the ergosterol-targeting drug amphotericin B. Overall, our data showed that mAb induction of global changes in the composition of H. capsulatum membranes can potentially impact antifungal treatment during histoplasmosis.
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Affiliation(s)
- Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (M.C.B.); (H.M.H.); (K.K.W.)
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Heino M. Heyman
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (M.C.B.); (H.M.H.); (K.K.W.)
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (M.C.B.); (H.M.H.); (K.K.W.)
| | - Erin L. Bredeweg
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA;
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (M.C.B.); (H.M.H.); (K.K.W.)
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27
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Ghods S, Waddell S, Weller E, Renteria C, Jiang HY, Janak JM, Mao SS, Linley TJ, Arola D. On the regeneration of fish scales: structure and mechanical behavior. J Exp Biol 2020; 223:jeb211144. [PMID: 32321752 PMCID: PMC7322541 DOI: 10.1242/jeb.211144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/15/2020] [Indexed: 11/20/2022]
Abstract
Fish scales serve as a dermal armor that provides protection from physical injury. Owing to a number of outstanding properties, fish scales are inspiring new concepts for layered engineered materials and next-generation flexible armors. Although past efforts have primarily focused on the structure and mechanical behavior of ontogenetic scales, the structure-property relationships of regenerated scales have received limited attention. In the present study, common carp (Cyprinus carpio) acquired from the wild were held live in an aquatic laboratory at 10°C and 20°C. Ontogenetic scales were extracted from the fish for analysis, as well as regenerated scales after approximately 1 year of development and growth. Their microstructure was characterized using microscopy and Raman spectroscopy, and the mechanical properties were evaluated in uniaxial tension to failure under hydrated conditions. The strength, strain to fracture and toughness of the regenerated scales were significantly lower than those of ontogenetic scales from the same fish, regardless of the water temperature. Scales that regenerated at 20°C exhibited significantly higher strength, strain to fracture and toughness than those regenerated at 10°C. The regenerated scales exhibited a highly mineralized outer layer, but no distinct limiting layer or external elasmodine; they also possessed a significantly lower number of plies in the basal layer than the ontogenetic scales. The results suggest that a mineralized layer develops preferentially during scale regeneration with the topology needed for protection, prior to the development of other qualities.
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Affiliation(s)
- S Ghods
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - S Waddell
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - E Weller
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - C Renteria
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - H-Y Jiang
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Department of Mechanics, Southeast University, Nanjing 211189, China
| | - J M Janak
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - S S Mao
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, 200 444 Shanghai, China
| | - T J Linley
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - D Arola
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, 200 444 Shanghai, China
- Department of Mechanical Engineering, University of Washington Seattle, Seattle, WA 98195, USA
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28
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Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:53. [PMID: 32299497 PMCID: PMC7164142 DOI: 10.1186/s40168-020-00817-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/02/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent evidence has linked the gut microbiome to host behavior via the gut-brain axis [1-3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut microbiome and memory using the genetically defined Collaborative Cross (CC) mouse cohort, complemented with microbiome and metabolomic analyses in conventional and germ-free (GF) mice. RESULTS A genome-wide association analysis (GWAS) identified 715 of 76,080 single-nucleotide polymorphisms (SNPs) that were significantly associated with short-term memory using the passive avoidance model. The identified SNPs were enriched in genes known to be involved in learning and memory functions. By 16S rRNA gene sequencing of the gut microbial community in the same CC cohort, we identified specific microorganisms that were significantly correlated with longer latencies in our retention test, including a positive correlation with Lactobacillus. Inoculation of GF mice with individual species of Lactobacillus (L. reuteri F275, L. plantarum BDGP2 or L. brevis BDGP6) resulted in significantly improved memory compared to uninoculated or E. coli DH10B inoculated controls. Untargeted metabolomics analysis revealed significantly higher levels of several metabolites, including lactate, in the stools of Lactobacillus-colonized mice, when compared to GF control mice. Moreover, we demonstrate that dietary lactate treatment alone boosted memory in conventional mice. Mechanistically, we show that both inoculation with Lactobacillus or lactate treatment significantly increased the levels of the neurotransmitter, gamma-aminobutyric acid (GABA), in the hippocampus of the mice. CONCLUSION Together, this study provides new evidence for a link between Lactobacillus and memory and our results open possible new avenues for treating memory impairment disorders using specific gut microbial inoculants and/or metabolites. Video Abstract.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Marine College, Shandong University, Weihai, 264209 China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Colin J. Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033 Shandong China
| | - B. Y. Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - David W. Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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29
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Crane MJ, Petrone A, Beck RA, Lim MB, Zhou X, Li X, Stroud RM, Pauzauskie PJ. High-pressure, high-temperature molecular doping of nanodiamond. Sci Adv 2019; 5:eaau6073. [PMID: 31058218 PMCID: PMC6499550 DOI: 10.1126/sciadv.aau6073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/14/2019] [Indexed: 05/05/2023]
Abstract
The development of color centers in diamond as the basis for emerging quantum technologies has been limited by the need for ion implantation to create the appropriate defects. We present a versatile method to dope diamond without ion implantation by synthesis of a doped amorphous carbon precursor and transformation at high temperatures and high pressures. To explore this bottom-up method for color center generation, we rationally create silicon vacancy defects in nanodiamond and investigate them for optical pressure metrology. In addition, we show that this process can generate noble gas defects within diamond from the typically inactive argon pressure medium, which may explain the hysteresis effects observed in other high-pressure experiments and the presence of noble gases in some meteoritic nanodiamonds. Our results illustrate a general method to produce color centers in diamond and may enable the controlled generation of designer defects.
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Affiliation(s)
- M. J. Crane
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA
| | - A. Petrone
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - R. A. Beck
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - M. B. Lim
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195-2120, USA
| | - X. Zhou
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195-2120, USA
| | - X. Li
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - R. M. Stroud
- Materials Science and Technology Division, Naval Research Laboratory, Washington, DC 20375, USA
| | - P. J. Pauzauskie
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195-2120, USA
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Corresponding author.
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30
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Hewins DB, Lee H, Barnes PW, McDowell NG, Pockman WT, Rahn T, Throop HL. Early exposure to UV radiation overshadowed by precipitation and litter quality as drivers of decomposition in the northern Chihuahuan Desert. PLoS One 2019; 14:e0210470. [PMID: 30716078 PMCID: PMC6361422 DOI: 10.1371/journal.pone.0210470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/24/2018] [Indexed: 11/18/2022] Open
Abstract
Dryland ecosystems cover nearly 45% of the Earth’s land area and account for large proportions of terrestrial net primary production and carbon pools. However, predicting rates of plant litter decomposition in these vast ecosystems has proven challenging due to their distinctly dry and often hot climate regimes, and potentially unique physical drivers of decomposition. In this study, we elucidated the role of photopriming, i.e. exposure of standing dead leaf litter to solar radiation prior to litter drop that would chemically change litter and enhance biotic decay of fallen litter. We exposed litter substrates to three different UV radiation treatments simulating three-months of UV radiation exposure in southern New Mexico: no light, UVA+UVB+Visible, and UVA+Visible. There were three litter types: mesquite leaflets (Prosopis glandulosa, litter with high nitrogen (N) concentration), filter paper (pure cellulose), and basswood (Tilia spp, high lignin concentration). We deployed the photoprimed litter in the field within a large scale precipitation manipulation experiment: ∼50% precipitation reduction, ∼150% precipitation addition, and ambient control. Our results revealed the importance of litter substrate, particularly N content, for overall decomposition in drylands, as neither filter paper nor basswood exhibited measurable mass loss over the course of the year-long study, while high N-containing mesquite litter exhibited potential mass loss. We saw no effect of photopriming on subsequent microbial decay. We did observe a precipitation effect on mesquite where the rate of decay was more rapid in ambient and precipitation addition treatments than in the drought treatment. Overall, we found that precipitation and N played a critical role in litter mass loss. In contrast, photopriming had no detected effects on mass loss over the course of our year-long study. These results underpin the importance of biotic-driven decomposition, even in the presence of photopriming, for understanding litter decomposition and biogeochemical cycles in drylands.
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Affiliation(s)
- Daniel B. Hewins
- Biology Department, Rhode Island College, Providence, Rhode Island, United States of America
| | - Hanna Lee
- NORCE Norwegian Research Centre, Bjerknes Centre for Climate Research, Bergen, Norway
- * E-mail:
| | - Paul W. Barnes
- Department of Biological Sciences, Loyola University, New Orleans, Louisiana, United States of America
| | - Nathan G. McDowell
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - William T. Pockman
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Thom Rahn
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Heather L. Throop
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
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31
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Bonneville A, Kouzes R, Yamaoka J, Lintereur A, Flygare J, Varner GS, Mostafanezhad I, Guardincerri E, Rowe C, Mellors R. Borehole muography of subsurface reservoirs. Philos Trans A Math Phys Eng Sci 2018; 377:rsta.2018.0060. [PMID: 30530536 PMCID: PMC6335297 DOI: 10.1098/rsta.2018.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Imaging subsurface rock formations or geological objects like oil and gas reservoirs, mineral deposits, cavities or even magmatic plumbing systems under active volcanoes has been for many years a major quest of geoscientists. Since these subsurface objects cannot be observed directly, different indirect methods have been developed. These methods are all based on variations of certain physical properties of the subsurface materials that can be detected from the ground surface or from boreholes. To determine the density distribution, a new imaging technique using cosmic-ray muon detectors deployed in a borehole has been developed and a first prototype of a borehole muon detector successfully tested. In addition to providing a static image of the subsurface density in three dimensions (or three-dimensional tomography), borehole muography can also inform on the variations of density with time, which recently became of major importance with the injection of large volumes of fluids, mainly water and CO2, in porous subsurface reservoirs (e.g. aquifer storage and recovery, wastewater disposal, enhanced oil recovery and carbon sequestration). This raises several concerns about the risk of leakage and the mechanical integrity of the reservoirs. Determining the field scale induced displacement of fluids by geophysical methods like muography is thus a priority.This article is part of the Theo Murphy meeting issue 'Cosmic-ray muography'.
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Affiliation(s)
| | - Richard Kouzes
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jared Yamaoka
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Joshua Flygare
- Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | - Charlotte Rowe
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert Mellors
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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Bakker C, Halappanavar M, Visweswara Sathanur A. Dynamic graphs, community detection, and Riemannian geometry. Appl Netw Sci 2018; 3:3. [PMID: 30839776 PMCID: PMC6214282 DOI: 10.1007/s41109-018-0059-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/26/2018] [Indexed: 06/09/2023]
Abstract
A community is a subset of a wider network where the members of that subset are more strongly connected to each other than they are to the rest of the network. In this paper, we consider the problem of identifying and tracking communities in graphs that change over time - dynamic community detection - and present a framework based on Riemannian geometry to aid in this task. Our framework currently supports several important operations such as interpolating between and averaging over graph snapshots. We compare these Riemannian methods with entry-wise linear interpolation and find that the Riemannian methods are generally better suited to dynamic community detection. Next steps with the Riemannian framework include producing a Riemannian least-squares regression method for working with noisy data and developing support methods, such as spectral sparsification, to improve the scalability of our current methods.
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Affiliation(s)
- Craig Bakker
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, 99352 WA United States
| | - Mahantesh Halappanavar
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, 99352 WA United States
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Henzler K, Fetisov EO, Galib M, Baer MD, Legg BA, Borca C, Xto JM, Pin S, Fulton JL, Schenter GK, Govind N, Siepmann JI, Mundy CJ, Huthwelker T, De Yoreo JJ. Supersaturated calcium carbonate solutions are classical. Sci Adv 2018; 4:eaao6283. [PMID: 29387793 PMCID: PMC5786440 DOI: 10.1126/sciadv.aao6283] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/15/2017] [Indexed: 05/17/2023]
Abstract
Mechanisms of CaCO3 nucleation from solutions that depend on multistage pathways and the existence of species far more complex than simple ions or ion pairs have recently been proposed. Herein, we provide a tightly coupled theoretical and experimental study on the pathways that precede the initial stages of CaCO3 nucleation. Starting from molecular simulations, we succeed in correctly predicting bulk thermodynamic quantities and experimental data, including equilibrium constants, titration curves, and detailed x-ray absorption spectra taken from the supersaturated CaCO3 solutions. The picture that emerges is in complete agreement with classical views of cluster populations in which ions and ion pairs dominate, with the concomitant free energy landscapes following classical nucleation theory.
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Affiliation(s)
- Katja Henzler
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Evgenii O. Fetisov
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Mirza Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Benjamin A. Legg
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Camelia Borca
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Jacinta M. Xto
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
- Department of Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonia Pin
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - John L. Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - J. Ilja Siepmann
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
- Corresponding author. (C.J.M.); (T.H.); (J.J.D.Y.)
| | - Thomas Huthwelker
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
- Corresponding author. (C.J.M.); (T.H.); (J.J.D.Y.)
| | - James J. De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Corresponding author. (C.J.M.); (T.H.); (J.J.D.Y.)
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Bokhari SH, Pomeroy LW, Janies DA. Reassortment Networks and the evolution of pandemic H1N1 swine-origin influenza. IEEE/ACM Trans Comput Biol Bioinform 2012; 9:214-27. [PMID: 22076498 PMCID: PMC7186031 DOI: 10.1109/tcbb.2011.95] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 03/07/2011] [Accepted: 04/26/2011] [Indexed: 05/31/2023]
Abstract
Prior research developed Reassortment Networks to reconstruct the evolution of segmented viruses under both reassortment and mutation. We report their application to the swine-origin pandemic H1N1 virus (S-OIV). A database of all influenza A viruses, for which complete genome sequences were available in Genbank by October 2009, was created and dynamic programming was used to compute distances between all corresponding segments. A reassortment network was created to obtain the minimum cost evolutionary paths from all viruses to the exemplar S-OIV A/California/04/2009. This analysis took 35 hours on the Cray Extreme Multithreading (XMT) supercomputer, which has special hardware to permit efficient parallelization. Six specific H1N1/H1N2 bottleneck viruses were identified that almost always lie on minimum cost paths to S-OIV. We conjecture that these viruses are crucial to S-OIV evolution and worthy of careful study from a molecular biology viewpoint. In phylogenetics, ancestors are typically medians that have no functional constraints. In our method, ancestors are not inferred, but rather chosen from previously observed viruses along a path of mutation and reassortment leading to the target virus. This specificity and functional constraint render our results actionable for further experiments in vitro and in vivo.
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Affiliation(s)
- Shahid H. Bokhari
- Department of Biomedical InformaticsOhio State University333 W 10th Ave.ColumbusOhio43210
| | - Laura W. Pomeroy
- Department of Biomedical InformaticsOhio State University333 W 10th Ave.ColumbusOhio43210
| | - Daniel A. Janies
- Department of Biomedical InformaticsOhio State University333 W 10th Ave.ColumbusOhio43210
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