MICROSCOPIC CHEMICAL IMAGING: A KEY TO UNDERSTAND ION MOBILITY IN TIGHT FORMATIONS
Abstract not provided
Grolimund, D.↗
SEARCH · Engineering Papers
Results for “KEYING”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Demonstration of a Silicon Photonic Transceiver for Polarization-Based Discrete Variable Quantum Key Distribution.
Abstract not provided.
Cai, Hong↗
Silicon photonic transceiver circuit for high-speed polarization-based discrete variable quantum key distribution
Not Available
97 MATHEMATICS AND COMPUTING↗
Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics
Hepatitis B virus (HBV) infection kinetics in immunodeficient mice reconstituted with humanized livers from inoculation to steady state is highly dynamic despite the absence of an adaptive immune response. To recapitulate the multiphasic viral kinetic patterns, we developed an agent-based model that includes intracellular virion production cycles reflecting the cyclic nature of each individual virus lifecycle. The model fits the data well predicting an increase in production cycles initially starting with a long production cycle of 1 virion per 20 hours that gradually reaches 1 virion per hour after approximately 3–4 days before virion production increases dramatically to reach to a steady state rate of 4 virions per hour per cell. Together, modeling suggests that it is the cyclic nature of the virus lifecycle combined with an initial slow but increasing rate of HBV production from each cell that plays a role in generating the observed multiphasic HBV kinetic patterns in humanized mice.
59 BASIC BIOLOGICAL SCIENCES↗
Disulfide Bonds within the C2 Domain of RAGE Play Key Roles in Its Dimerization and Biogenesis
The receptor for advanced glycation end products (RAGE) on the cell surface transmits inflammatory signals. A member of the immunoglobulin superfamily, RAGE possesses the V, C1, and C2 ectodomains that collectively constitute the receptor’s extracellular structure. However, the molecular mechanism of RAGE biogenesis remains unclear, impeding efforts to control RAGE signaling through cellular regulation. We used co-immunoprecipitation and crossing-linking to study RAGE oligomerization and found that RAGE forms dimer-based oligomers. Via non-reducing SDS-polyacrylamide gel electrophoresis and mutagenesis, we found that cysteines 259 and 301 within the C2 domain form intermolecular disulfide bonds. Using a modified tripartite split GFP complementation strategy and confocal microscopy, we also found that RAGE dimerization occurs in the endoplasmic reticulum (ER), and that RAGE mutant molecules without the double disulfide bridges are unstable, and are subjected to the ER-associated degradation. Disulfide bond-mediated RAGE dimerization in the ER is the critical step of RAGE biogenesis. Without formation of intermolecular disulfide bonds in the C2 region, RAGE fails to reach cell surface. Significance: This is the first report of RAGE intermolecular disulfide bond.
59 BASIC BIOLOGICAL SCIENCES↗
Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function
HNP1 is a human alpha defensin that forms dimers and multimers governed by hydrophobic residues, including Tyr 16 , Ile 20 , Leu 25 , and Phe 28 . Previously, alanine scanning mutagenesis identified each of these residues and other hydrophobic residues as important for function. Here we report further structural and functional studies of residues shown to interact with one another across oligomeric interfaces: I20A-HNP1 and L25A-HNP1, plus the double alanine mutants I20A/L25AHNP1 and Y16A/F28A-HNP1, and the quadruple alanine mutant Y16A/I20A/L25A/F28A-HNP1. We tested binding to HIV-1 gp120 and HNP1 by surface plasmon resonance, binding to HIV-1 gp41 and HNP1 by fluorescence polarization, inhibition of anthrax lethal factor, and antibacterial activity using the virtual colony count assay. Similar to the previously described single mutant W26A-HNP1, the quadruple mutant displayed the least activity in all functional assays, followed by the double mutant Y16A/F28A-HNP1. The effects of the L25A and I20A single mutations were milder than the double mutant I20A/ L25A-HNP1. Crystallographic studies confirmed the correct folding and disulfide pairing, and depicted an array of dimeric and tetrameric structures. These results indicate that side chain hydrophobicity is the critical factor that determines activity at these positions.
59 BASIC BIOLOGICAL SCIENCES↗
Dissecting the Functional Role of Key Residues in Triheme Cytochrome PpcA: A Path to Rational Design of G. sulfurreducens Strains with Enhanced Electron Transfer Capabilities
PpcA is the most abundant member of a family of five triheme cytochromes c7 in the bacterium Geobacter sulfurreducens (Gs) and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24%) among the family, and it was suggested to be involved in e2/H+ energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys9 (located near heme IV), Lys18 (near heme I) or Lys22 (between hemes I and III) has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys43 (near heme IV), Lys52 (between hemes III and IV) and Lys60 (near heme III) are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e2/H+ transfer pathways. The results showed that the preferred e2/H+ transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e2/H+ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities.
59 BASIC BIOLOGICAL SCIENCES↗
Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations
Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus ; monoculture of Acacia mangium ; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.
Balieiro, Fabiano C.↗
Biophysical characterization and a roadmap towards the NMR solution structure of G0S2, a key enzyme in non-alcoholic fatty liver disease
In the United States non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease, affecting an estimated 80 to 100 million people. It occurs in every age group, but predominantly in people with risk factors such as obesity and type 2 diabetes. NAFLD is marked by fat accumulation in the liver leading to liver inflammation, which may lead to scarring and irreversible damage progressing to cirrhosis and liver failure. In animal models, genetic ablation of the protein G0S2 leads to alleviation of liver damage and insulin resistance in high fat diets. The research presented in this paper aims to aid in rational based drug design for the treatment of NAFLD by providing a pathway for a solution state NMR structure of G0S2. Here we describe the expression of G0S2 in an E. coli system from two different constructs, both of which are confirmed to be functionally active based on the ability to inhibit the activity of Adipose Triglyceride Lipase. In one of the constructs, preliminary NMR spectroscopy measurements show dominant alpha-helical characteristics as well as resonance assignments on the N-terminus of G0S2, allowing for further NMR work with this protein. Additionally, the characterization of G0S2 oligomers are outlined for both constructs, suggesting that G0S2 may defensively exist in a multimeric state to protect and potentially stabilize the small 104 amino acid protein within the cell. This information presented on the structure of G0S2 will further guide future development in the therapy for NAFLD.
59 BASIC BIOLOGICAL SCIENCES↗
Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes
Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.
59 BASIC BIOLOGICAL SCIENCES↗
Key Role of M.G. Nakhodkin’s Insight and Inspiration in Development of UHV STM-Related Techniques and Methods
In this contribution I briefly describe my joint efforts and experiences with M.G. Nakhodkin in the field of scanning tunneling microscopy (STM) including a construction of the home-built microscopes, application of this technique in various scientific endevours, as well as fruitfull and enlightening discusions. Our co-operation was focused on the novel aspects of STM probes preparation and conditioning, coupling the STM junction with laser irradiation, STM-based nanolithography, and also on collaboration at the international scale with M.G. Nakhodkin and members of his scientific group.
Environmental Molecular Sciences Laboratory↗
Identification of key parameters controlling demographically structured vegetation dynamics in a Land Surface Model
This dataset includes outputs of 5000 simulations of CLM4.5(ED) to quantify the sensitivity of the model outputs to changes in model parameters using the Fourier Amplitude Sensitivity Test (FAST). Each simulation is generated by simultaneously sampling from 15% deviations of the default values of >80 vegetation parameters. This dataset includes 1) model codes of CLM4.5(ED) used for the sensitivity analysis; 2) the parameter samples; and 3) the corresponding model outputs of vegetation status (e.g., Gross Primary Production, Leaf Area Index and Biomass) and demography (e.g., diameter growth and mortality rates). The outputs are organized to the format of the FAST toolbox (https://sites.google.com/site/xuchongang/uasatoolbox).
54 ENVIRONMENTAL SCIENCES↗
Solid-state ionics: The key to the discovery and domination of lithium batteries: some learnings from β-alumina and titanium disulfide
We report solid state ionics, the study of fast ion transport in solids, expanded explosively after the discovery of sodium ion transport in b-alumina 50 years ago and has revolutionized energy storage. Lithium ion batteries have come from a dream with titanium disulfide to enabling the communications revolution and are enabling renewable energy. Much can be learnt from these early studies, that will allow the attainment of a fossil-free society and a sustainable environment.
36 MATERIALS SCIENCE↗
SUBTASK 1.7 EVALUATION OF KEY FACTORS AFFECTING SUCCESSFUL OIL PRODUCTION IN THE BAKKEN FORMATION, NORTH DAKOTA PHASE II
Production from the Bakken and Three Forks Formations continues to trend upward as forecasts predict significant production of oil from unconventional resources nationwide. As the U.S. Geological Survey reevaluates the 3.65 billion bbl technically recoverable estimate of 2008, technological advancements continue to unlock greater unconventional oil resources, and new discoveries continue within North Dakota. It is expected that the play will continue to expand to the southwest, newly develop in the northeastern and northwestern corners of the basin in North Dakota, and fully develop in between. Although not all wells are economical, the economic success rate has been near 75% with more than 90% of wells finding oil. Currently, only about 15% of the play has been drilled, and recovery rates are less than 5%, providing a significant future of wells to be drilled and untouched hydrocarbons to be pursued through improved stimulation practices or enhanced oil recovery. This study provides the technical characterizations that are necessary to improve knowledge, provide characterization, validate generalizations, and provide insight relative to hydrocarbon recovery in the Bakken and Three Forks Formations. Oil-saturated rock charged from the Bakken shales and prospective Three Forks can be produced given appropriate stimulation treatments. Highly concentrated fracture stimulations with ceramic- and sand-based proppants appear to be providing the best success for areas outside the Parshall and Sanish Fields. Targeting of specific lithologies can influence production from both natural and induced fracture conductivity. Porosity and permeability are low, but various lithofacies units within the formation are highly saturated and, when targeted with appropriate technology, release highly economical quantities of hydrocarbons.
04 OIL SHALES AND TAR SANDS↗
Low-Temperature Biodiesel Research Reveals Potential Key to Successful Blend Performance [Fact Sheet]
Relatively low-cost solutions could improve reliability while making biodiesel blends an affordable option.
09 BIOMASS FUELS↗