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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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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Bacterial flagellar capping proteins adopt diverse oligomeric states

Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD from Pseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find that Pseudomonas FliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Calpain-7 protease functions together with the ESCRT-III protein IST1 within the midbody to regulate the timing and completion of abscission

The Endosomal Sorting Complexes Required for Transport (ESCRT) machinery mediates the membrane fission step that completes cytokinetic abscission and separates dividing cells. Filaments composed of ESCRT-III subunits constrict membranes of the intercellular bridge midbody to the abscission point. These filaments also bind and recruit cofactors whose activities help execute abscission and/or delay abscission timing in response to mitotic errors via the NoCut/Abscission checkpoint. We previously showed that the ESCRT-III subunit IST1 binds the cysteine protease Calpain-7 (CAPN7) and that CAPN7 is required for both efficient abscission and NoCut checkpoint maintenance. Here, we report biochemical and crystallographic studies showing that the tandem microtubule-interacting and trafficking (MIT) domains of CAPN7 bind simultaneously to two distinct IST1 MIT interaction motifs. Structure-guided point mutations in either CAPN7 MIT domain disrupted IST1 binding in vitro and in cells, and depletion/rescue experiments showed that the CAPN7-IST1 interaction is required for (1) CAPN7 recruitment to midbodies, (2) efficient abscission, and (3) NoCut checkpoint arrest. CAPN7 proteolytic activity is also required for abscission and checkpoint maintenance. Hence, IST1 recruits CAPN7 to midbodies, where its proteolytic activity is required to regulate and complete abscission.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗
DOE OSTI2011

Methods, systems, and computer program products for network firewall policy optimization

Methods, systems, and computer program products for firewall policy optimization are disclosed. According to one method, a firewall policy including an ordered list of firewall rules is defined. For each rule, a probability indicating a likelihood of receiving a packet matching the rule is determined. The rules are sorted in order of non-increasing probability in a manner that preserves the firewall policy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Combining multi-layered bitmap files using network specific hardware

Images and video can be produced by compositing or alpha blending a group of image layers or video layers. Increasing resolution or the number of layers results in increased computational demands. As such, the available computational resources limit the images and videos that can be produced. A computational architecture in which the image layers are packetized and streamed through processors can be easily scaled so to handle many image layers and high resolutions. The image layers are packetized to produce packet streams. The packets in the streams are received, placed in queues, and processed. For alpha blending, ingress queues receive the packetized image layers which are then z sorted and sent to egress queues. The egress queue packets are alpha blended to produce an output image or video.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Crowds bringing power, payoff to entrepreneurs

Monthly economic diversity column for Tri-City Herald; excerpt here: As I walk through my garden, marveling at the fresh treats in store and wondering what I’ll do when 47 bell peppers ripen at once, I also wistfully think of the one crop that continues to elude even the greenest of thumbs. The money tree. It’s fun to imagine the possibilities a money tree would offer, branch after branch reaching out to support one’s life pursuits. Go ahead, take a minute... Back in reality, I realize how valuable this concept could be to many entrepreneurs out there in possession of the next game-changing idea, without the capital to move forward. Enter Kickstarter.com, a highly successful example in a growing genre of websites devoted to crowdfunding. In the past few years, crowdfunding has become a disruptive element in the startup process, enabling inventors and promoters of numerous causes to generate capital through a consensus of virtual supporters, a money giving tree of sorts, without sacrificing equity in their projects or circling the globe chasing venture capital and angel money.

Madison, Alison L.↗
DOE OSTI2013

Affinity+: Semi-Structured Brainstorming on Large Displays

Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

large display, natural user interface, ubiquitous ↗
DOE OSTI2013

Structure and Function of Subsurface Microbial Communities Affecting Radionuclide Transport and Bio-immobilization

The goal of this research project was to employ a multi-disciplinary team to investigate the DOE-ERSP Field Research Center at Oak Ridge, TN (ORFRC), which contains well-defined subsurface contaminant plumes with contrasting pH and redox conditions. Part of the team would pursue cultivation-independent characterization of the microbial groups catalyzing relevant biogeochemical reactions to gain an understanding of the physiological mechanisms controlling radionuclide immobilization. Other team members would focus on cultivation and physiological characterization of model microorganisms from the site using single cell sorting methods. In order to understand and predict the in situ function of microbial communities, the PIs hope to develop new strategies for cultivation and to couple phylogenetic structure with microbial community function. Specific objectives by the Rutgers group was to discern the active bacteria at the Oak Ridge Research Field Challenge Site: 1. by applying stable isotope probing techniques to enrichment cultures developed from Florida State University; 2. by fingerprinting intact rRNA from groundwater samples obtained along the various flow pathways at ORFRC; and 3. by identifying functional genes for N and S cycling along the flowpaths to aid in detection of active bacteria.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Modern Atmospheric Pressure Surface Sampling/Ionization Techniques in Mass Spectrometry

Over the last few years, there has been a rapid increase in atmospheric pressure surface sampling/ionization techniques for mass spectrometry, dramatically expanding the range of sample types that can be analyzed. The growth in this field of mass spectrometry has also resulted in a plethora of new acronyms. In this encyclopedia article, the various techniques are first sorted into four major categories based on the method used for analyte desorption and then subcategorized by ionization method. The underlying principles of operation are explained and some representative applications are described.

Pasilis, Sofie P↗
DOE OSTI2014

Fermentation process using specific oxygen uptake rates as a process control

Specific oxygen uptake (OUR) is used as a process control parameter in fermentation processes. OUR is determined during at least the production phase of a fermentation process, and process parameters are adjusted to maintain the OUR within desired ranges. The invention is particularly applicable when the fermentation is conducted using a microorganism having a natural PDC pathway that has been disrupted so that it no longer functions. Microorganisms of this sort often produce poorly under strictly anaerobic conditions. Microaeration controlled by monitoring OUR allows the performance of the microorganism to be optimized.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

F Reactor Inspection

Workers from Mission Support Alliance, LLC., removed the welds around the steel door of the F Reactor before stepping inside the reactor to complete its periodic inspection. This is the first time the Department of Energy (DOE) has had the reactor open since 2008. The F Reactor is one of nine reactors along the Columbia River at the Department's Hanford Site in southeastern Washington State, where environmental cleanup has been ongoing since 1989. As part of the Tri-Party Agreement, the Department completes surveillance and maintenance activities of cocooned reactors periodically to evaluate the structural integrity of the safe storage enclosure and to ensure confinement of any remaining hazardous materials. "This entry marks a transition of sorts because the Hanford Long-Term Stewardship Program, for the first time, was responsible for conducting the entry and surveillance and maintenance activities," said Keith Grindstaff, Energy Department Long-Term Stewardship Program Manager. "As the River Corridor cleanup work is completed and transitioned to long-term stewardship, our program will manage any on-going requirements."

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2013

Expediting Scientific Data Analysis with Reorganization of Data

Data producers typically optimize the layout of data files to minimize the write time. In most cases, data analysis tasks read these files in access patterns different from the write patterns causing poor read performance. In this paper, we introduce Scientific Data Services (SDS), a framework for bridging the performance gap between writing and reading scientific data. SDS reorganizes data to match the read patterns of analysis tasks and enables transparent data reads from the reorganized data. We implemented a HDF5 Virtual Object Layer (VOL) plugin to redirect the HDF5 dataset read calls to the reorganized data. To demonstrate the effectiveness of SDS, we applied two parallel data organization techniques: a sort-based organization on a plasma physics data and a transpose-based organization on mass spectrometry imaging data. We also extended the HDF5 data access API to allow selection of data based on their values through a query interface, called SDS Query. We evaluated the execution time in accessing various subsets of data through existing HDF5 Read API and SDS Query. We showed that reading the reorganized data using SDS is up to 55X faster than reading the original data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Building America Case Study: Community-Scale Energy Modeling (Fact Sheet)

IBACOS analyzed pre-retrofit daily utility data to sort homes by energy consumption, allowing for better targeting of homes for physical audits. Following ASHRAE Guideline 14 normalization procedures, electricity consumption of 1,166 all electric production-built homes' was modeled. The homes were in two communities--one built in the 1970s and the other in the mid-2000s.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2015

Zeolites: Exploring Molecular Channels

Synthetic zeolites contain microscopic channels, sort of like a sponge. They have many uses, such as helping laundry detergent lather, absorbing liquid in kitty litter, and as catalysts to produce fuel. Of the hundreds of types of zeolites, only about 15 are used for catalysis. PNNL catalysis scientists Ilke Arslan and Mirek Derewinksi are studying these zeolites to understand what make them special. By exploring the mystery of these microscopic channels, their fundamental findings will help design better catalysts for applications such as biofuel production.

09 BIOMASS FUELS↗
DOE OSTI2014

Iodine Standard Materials: Preparation and Inter-Laboratory Comparisons

The Idaho National Laboratory is preparing to enter the community of AMS practioners who analyze for 129Iodine. We expect to take delivery of a 0.5 MV compact accelerator mass spectrometry system, built by NEC, in the early summer of 2014. The primary mission for this instrument is iodine; it is designed to analyze iodine in the +3 charge state. As part of the acceptance testing for this instrument, both at NEC and on-site in our laboratory, some sort of standard or reference material is needed to verify performance. Appropriate standard materials are not readily available in the commercial marketplace. Small quantities can sometimes be acquired from other laboratories already engaged in iodine analyses. In the longer-term, meaningful quantities of standard materials are needed for routine use in analyses, and for quality control functions1. We have prepared some standard materials, starting with elemental Woodward iodine and NIST SRM 3231 [Iodine-129 Isotopic Standard (high level)] 10-6 solution. The goal was to make mixtures at the 5x10-10, 5x10-11, 5x10-12 ratio levels, along with some unmodified Woodward, in the chemical form of silver iodide. Approximately twenty grams of each of these mixtures were prepared. The elemental Woodward iodine was dissolved in chloroform, then reduced to iodide using sodium bisulfite in water. At this point the NIST spike material was added, in the form of sodium iodide. The mixed iodides were oxidized back to iodine in chloroform using hydrogen peroxide. This oxidation step was essential for isotopic equilibration of the 127 and 129 atoms. The iodine was reduced to iodide using sodium bisulfite as before. Excess sulfites and sulfates were precipitated with barium nitrate. After decanting, silver nitrate was used to precipitate the desired silver iodide. Once the silver iodide was produced, the material was kept in darkness as much as possible to minimize photo-oxidation. The various mixtures were synthesized independently of each other; there were no serial dilutions involved. Aliquots of these four materials have been submitted to five established AMS laboratories where iodine analyses are routinely performed: ETH (Zurich), CNA (Seville), PRIME (Purdue), LLNL (California), and Isotrace (Toronto.) Results from four of these laboratories have been received; in general they indicate that the desired 129/127 ratios have been achieved. We will discuss the results of this informal round-robin exercise. If the installation of the instrument in Idaho goes well, we may have some very preliminary results from the new system. An integral part of data reporting is the approach to data reduction. Accordingly, there will also be some discussion of various philosophies of data handling in regard to the use of standards to adjust data, and background subtraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Existing Whole-House Solutions Case Study: Community-Scale Energy Modeling - Southeastern United States

Community-scale energy modeling and testing are useful for determining energy conservation measures that will effectively reduce energy use. To that end, IBACOS analyzed pre-retrofit daily utility data to sort homes by energy consumption, allowing for better targeting of homes for physical audits. Following ASHRAE Guideline 14 normalization procedures, electricity consumption of 1,166 all-electric, production-built homes was modeled. The homes were in two communities: one built in the 1970s and the other in the mid-2000s.

ASHRAE GUIDELINE 14↗
DOE OSTI2015

Relative permeability of hydrate-bearing sediments from percolation theory and critical path analysis: theoretical and experimental results

Relative permeabilities to water and gas are important parameters for accurate modeling of the formation of methane hydrate deposits and production of methane from hydrate reservoirs. Experimental measurements of gas and water permeability in the presence of hydrate are difficult to obtain. The few datasets that do exist suggest that relative permeability obeys a power law relationship with water or gas saturation with exponents ranging from around 2 to greater than 10. Critical path analysis and percolation theory provide a framework for interpreting the saturation-dependence of relative permeability based on percolation thresholds and the breadth of pore size distributions, which may be determined easily from 3-D images or gas adsorption-desorption hysteresis. We show that the exponent of the permeability-saturation relationship for relative permeability to water is related to the breadth of the pore size distribution, with broader pore size distributions corresponding to larger exponents. Relative permeability to water in well-sorted sediments with narrow pore size distributions, such as Berea sandstone or Toyoura sand, follows percolation scaling with an exponent of 2. On the other hand, pore-size distributions determined from argon adsorption measurements we performed on clays from the Nankai Trough suggest that relative permeability to water in fine-grained intervals may be characterized by exponents as large as 10 as determined from critical path analysis. We also show that relative permeability to the gas phase follows percolation scaling with a quadratic dependence on gas saturation, but the threshold gas saturation for percolation changes with hydrate saturation, which is an important consideration in systems in which both hydrate and gas are present, such as during production from a hydrate reservoir. Our work shows how measurements of pore size distributions from 3-D imaging or gas adsorption may be used to determine relative permeabilities.

Daigle, Hugh↗