National Library of Energy BETA

Sample records for nucleic acid database

  1. Nucleic Acid Database: a Repository of Three-Dimensional Information about Nucleic Acids

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B.

    The Nucleic Acid Database (NDB) provides 3-D structural information about nucleic acids. It is a relational database designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures and structures may be viewed in several different formats, including the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. Browsing structure images created directly from coordinates in the repository can also be done. More than 7000 structures have been released as of May 2014. This website also includes a number of specialized tools and interfaces. The NDB Project is funded by the National Institutes of Health and has been funded by the National Science Foundation and the Department of Energy in the past.

  2. Nucleic Acid Database: a Repository of Three-Dimensional Information about Nucleic Acids

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B.

    The Nucleic Acid Database (NDB) provides 3-D structural information about nucleic acids.  It is a relational database designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures and structures may be viewed in several different formats, including the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. Browsing structure images created directly from coordinates in the repository can also be done. More than 7000 structures have been released as of May 2014. This website also includes a number of specialized tools and interfaces. The NDB Project is funded by the National Institutes of Health and has been funded by the National Science Foundation and the Department of Energy in the past.

  3. Nucleic acid detection compositions

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James L.

    2008-08-05

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  4. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2000-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  5. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow; Mary Ann D.; Dahlberg, James E.

    2010-11-09

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  6. Nucleic acid detection assays

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

    2005-04-05

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  7. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor L.; Brow, Mary Ann D.; Dahlberg, James E.

    2007-12-11

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  8. Nucleic acid detection kits

    DOE Patents [OSTI]

    Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann; Kwiatkowski, Robert W.; Vavra, Stephanie H.

    2005-03-29

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of nucleic acid from various viruses in a sample.

  9. Method for isolating nucleic acids

    DOE Patents [OSTI]

    Hurt, Jr., Richard Ashley; Elias, Dwayne A.

    2015-09-29

    The current disclosure provides methods and kits for isolating nucleic acid from an environmental sample. The current methods and compositions further provide methods for isolating nucleic acids by reducing adsorption of nucleic acids by charged ions and particles within an environmental sample. The methods of the current disclosure provide methods for isolating nucleic acids by releasing adsorbed nucleic acids from charged particles during the nucleic acid isolation process. The current disclosure facilitates the isolation of nucleic acids of sufficient quality and quantity to enable one of ordinary skill in the art to utilize or analyze the isolated nucleic acids for a wide variety of applications including, sequencing or species population analysis.

  10. Composition for nucleic acid sequencing

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-08-26

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  11. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  12. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  13. Functional nucleic acid probes and uses thereof

    DOE Patents [OSTI]

    Nilsen-Hamilton, Marit

    2006-10-03

    The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regulating nucleic acid only in the presence of a regulating nucleic acid target. In its activated state the functional nucleic acid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleic acid, or catalyzing a reaction.

  14. Nucleic acid detection methods

    DOE Patents [OSTI]

    Smith, C.L.; Yaar, R.; Szafranski, P.; Cantor, C.R.

    1998-05-19

    The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3{prime}-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated. 18 figs.

  15. Nucleic Acid Detection Methods

    DOE Patents [OSTI]

    Smith, Cassandra L.; Yaar, Ron; Szafranski, Przemyslaw; Cantor, Charles R.

    1998-05-19

    The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated.

  16. Nucleic acid arrays and methods of synthesis

    DOE Patents [OSTI]

    Sabanayagam, Chandran R.; Sano, Takeshi; Misasi, John; Hatch, Anson; Cantor, Charles

    2001-01-01

    The present invention generally relates to high density nucleic acid arrays and methods of synthesizing nucleic acid sequences on a solid surface. Specifically, the present invention contemplates the use of stabilized nucleic acid primer sequences immobilized on solid surfaces, and circular nucleic acid sequence templates combined with the use of isothermal rolling circle amplification to thereby increase nucleic acid sequence concentrations in a sample or on an array of nucleic acid sequences.

  17. Identifying a base in a nucleic acid

    DOE Patents [OSTI]

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2005-02-08

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  18. High speed nucleic acid sequencing

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

  19. Replica amplification of nucleic acid arrays

    DOE Patents [OSTI]

    Church, George M.

    2002-01-01

    A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

  20. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-06-06

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  1. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-05-30

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  2. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, C.R.; Niemeyer, C.M.; Smith, C.L.; Sano, Takeshi; Hnatowich, D.J.; Rusckowski, M.

    1996-10-01

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products. 5 figs.

  3. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, Charles R.; Niemeyer, Christof M.; Smith, Cassandra L.; Sano, Takeshi; Hnatowich, Donald J.; Rusckowski, Mary

    1999-10-12

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  4. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, Charles R.; Niemeyer, Christof M.; Smith, Cassandra L.; Sano, Takeshi; Hnatowich, Donald J.; Rusckowski, Mary

    1996-01-01

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  5. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  6. Chip-based sequencing nucleic acids

    DOE Patents [OSTI]

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  7. Methods for analyzing nucleic acid sequences

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid. The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The time duration of the signal from labeled nucleotides or nucleotide analogs that become incorporated is distinguished from freely diffusing labels by a longer retention in the observation volume for the nucleotides or nucleotide analogs that become incorporated than for the freely diffusing labels.

  8. Replica amplification of nucleic acid arrays

    DOE Patents [OSTI]

    Church, George M.; Mitra, Robi D.

    2010-08-31

    Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

  9. Amplification of trace amounts of nucleic acids

    DOE Patents [OSTI]

    Church, George M.; Zhang, Kun

    2008-06-17

    Methods of reducing background during amplification of small amounts of nucleic acids employ careful analysis of sources of low level contamination. Ultraviolet light can be used to reduce nucleic acid contaminants in reagents and equipment. "Primer-dimer" background can be reduced by judicious design of primers. We have shown clean signal-to-noise with as little as starting material as one single human cell (.about.6 picogram), E. coli cell (.about.5 femtogram) or Prochlorococcus cell (.about.3 femtogram).

  10. Method of Identifying a Base in a Nucleic Acid

    DOE Patents [OSTI]

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    1999-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  11. Hybridization and sequencing of nucleic acids using base pair mismatches

    DOE Patents [OSTI]

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  12. Probe kit for identifying a base in a nucleic acid

    DOE Patents [OSTI]

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  13. Detection of nucleic acid sequences by invader-directed cleavage

    DOE Patents [OSTI]

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  14. Nucleic acid based fluorescent sensor for copper detection

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2013-04-02

    A nucleic acid enzyme responsive to copper, comprising an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1, wherein the nucleic acid enzyme is not self-cleaving.

  15. Method for identifying and quantifying nucleic acid sequence aberrations

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    1998-01-01

    A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

  16. Nucleic acid-coupled colorimetric analyte detectors

    DOE Patents [OSTI]

    Charych, Deborah H.; Jonas, Ulrich

    2001-01-01

    The present invention relates to methods and compositions for the direct detection of analytes and membrane conformational changes through the detection of color changes in biopolymeric materials. In particular, the present invention provide for the direct colorimetric detection of analytes using nucleic acid ligands at surfaces of polydiacetylene liposomes and related molecular layer systems.

  17. Quantification of false positive reduction in nucleic acid purificatio...

    Office of Scientific and Technical Information (OSTI)

    Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES; DNA; ELECTRODYNAMICS; FEVER; GENETICS; HYBRIDIZATION; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PURIFICATION; TARGETS; TESTING ...

  18. Method for nucleic acid isolation using supercritical fluids

    DOE Patents [OSTI]

    Nivens, David E.; Applegate, Bruce M.

    1999-01-01

    A method for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification.

  19. Method for nucleic acid isolation using supercritical fluids

    DOE Patents [OSTI]

    Nivens, D.E.; Applegate, B.M.

    1999-07-13

    A method is disclosed for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification. 4 figs.

  20. Nucleic acid analysis using terminal-phosphate-labeled nucleotides

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-04-22

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  1. Detection of nucleic acids by multiple sequential invasive cleavages 02

    DOE Patents [OSTI]

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  2. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

    Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

    2012-10-16

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  3. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

    Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann D.

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  4. Nucleic acid compositions and the encoding proteins

    DOE Patents [OSTI]

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  5. Nucleic acids, compositions and uses thereof

    DOE Patents [OSTI]

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2012-02-21

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  6. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOE Patents [OSTI]

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  7. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOE Patents [OSTI]

    Ramsey, J. Michael (Knoxville, TN); Foote, Robert S. (Oak Ridge, TN)

    2002-01-01

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  8. Nucleic acid amplification using modular branched primers

    DOE Patents [OSTI]

    Ulanovsky, Levy

    2001-01-01

    Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

  9. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOE Patents [OSTI]

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  10. Quantification of false positive reduction in nucleic acid purification on

    Office of Scientific and Technical Information (OSTI)

    hemorrhagic fever DNA. (Technical Report) | SciTech Connect Quantification of false positive reduction in nucleic acid purification on hemorrhagic fever DNA. Citation Details In-Document Search Title: Quantification of false positive reduction in nucleic acid purification on hemorrhagic fever DNA. Columbia University has developed a sensitive highly multiplexed system for genetic identification of nucleic acid targets. The primary obstacle to implementing this technology is the high rate of

  11. Quantification of false positive reduction in nucleic acid purificatio...

    Office of Scientific and Technical Information (OSTI)

    hemorrhagic fever DNA. Citation Details In-Document Search Title: Quantification of false positive reduction in nucleic acid purification on hemorrhagic fever DNA. You are ...

  12. CRC handbook of chromatography: Nucleic acids and related compounds

    SciTech Connect (OSTI)

    Krstulovic, A.M.

    1987-01-01

    This book's contents include: Structure Elucidation of Nucleic Acid Components; Fundamentals of HPLC; Analysis of Nucleic Acids and Oligonucleotides; Extraction of Nucleic Acids from Tissues; Gel Filtration Chromatography of RNAs and DNS Fragments; Separation of tRNAs and Oligonucleotides by Mixed Mode Chromatography; Anion-Exchange and Reversed-Phase HPLC of Synthetic Oligonucleotides; Nucleic Acid Components in Biological Fluids; RPLC Separation of RNA and DNA Hydrolysates; Nucleotides in Tissue Extracts; and Determination of Adenine Nucleotides and Creatine Phosphate in Various Mammalian Tissues.

  13. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2013-07-16

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  14. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2012-02-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  15. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2015-04-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  16. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2014-02-25

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  17. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2008-04-01

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  18. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2009-05-05

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  19. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2010-10-12

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  20. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2010-10-05

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  1. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2008-11-11

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  2. EGVIII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-23

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl8, and the corresponding EGVIII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVIII, recombinant EGVIII proteins and methods for producing the same.

  3. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-06-06

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  4. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  5. Nucleic acid based fluorescent sensor for mercury detection

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2013-02-05

    A nucleic acid enzyme comprises an oligonucleotide containing thymine bases. The nucleic acid enzyme is dependent on both Hg.sup.2+and a second ion as cofactors, to produce a product from a substrate. The substrate comprises a ribonucleotide, a deoxyribonucleotide, or both.

  6. Solid phase sequencing of double-stranded nucleic acids

    DOE Patents [OSTI]

    Fu, Dong-Jing (Waltham, MA); Cantor, Charles R. (Boston, MA); Koster, Hubert (Concord, MA); Smith, Cassandra L. (Boston, MA)

    2002-01-01

    This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

  7. Nucleic acids encoding metal uptake transporters and their uses

    DOE Patents [OSTI]

    Schroeder, Julian I.; Antosiewicz, Danuta M.; Schachtman, Daniel P.; Clemens, Stephan

    1999-01-01

    The invention provides LCT1 nucleic acids which encode metal ion uptake transporters. The invention also provides methods of modulating heavy metal and alkali metal uptake in plants. The methods involve producing transgenic plants comprising a recombinant expression cassette containing an LCT1 nucleic acid linked to a plant promoter.

  8. Methods and compositions for efficient nucleic acid sequencing

    DOE Patents [OSTI]

    Drmanac, Radoje

    2002-01-01

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  9. Methods and compositions for efficient nucleic acid sequencing

    DOE Patents [OSTI]

    Drmanac, Radoje

    2006-07-04

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  10. Nucleic acid detection system and method for detecting influenza

    DOE Patents [OSTI]

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  11. Isolated menthone reductase and nucleic acid molecules encoding same

    DOE Patents [OSTI]

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  12. Methods for separating particles and/or nucleic acids using

    Office of Scientific and Technical Information (OSTI)

    isotachophoresis (Patent) | SciTech Connect Methods for separating particles and/or nucleic acids using isotachophoresis Citation Details In-Document Search Title: Methods for separating particles and/or nucleic acids using isotachophoresis According to one embodiment, a method includes co-feeding fluids comprising a leading electrolyte, a trailing electrolyte, and at least one of DNA and RNA to a channel, and applying an electric field to the fluids in a direction perpendicular to an axis

  13. Methods for separating particles and/or nucleic acids using

    Office of Scientific and Technical Information (OSTI)

    isotachophoresis (Patent) | SciTech Connect Methods for separating particles and/or nucleic acids using isotachophoresis Citation Details In-Document Search Title: Methods for separating particles and/or nucleic acids using isotachophoresis × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information (OSTI) and is provided as a public service. Visit OSTI to utilize additional information

  14. Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids

    DOE Patents [OSTI]

    Miller, P.S.; Ts'o, P.O.P.

    1999-06-15

    A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid is provided. It includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional. 16 figs.

  15. Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids

    DOE Patents [OSTI]

    Miller, Paul S.; Ts'o, Paul O.P.

    1999-06-15

    A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid and includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional.

  16. Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

    DOE Patents [OSTI]

    Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

    2005-08-30

    Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

  17. Method for nucleic acid hybridization using single-stranded DNA binding protein

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-01-01

    Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

  18. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the target sequence.

  19. Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz (Livermore, CA)

    2011-01-11

    A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

  20. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2012-10-16

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  1. Arrays of nucleic acid probes on biological chips

    DOE Patents [OSTI]

    Chee, Mark; Cronin, Maureen T.; Fodor, Stephen P. A.; Huang, Xiaohua X.; Hubbell, Earl A.; Lipshutz, Robert J.; Lobban, Peter E.; Morris, MacDonald S.; Sheldon, Edward L.

    1998-11-17

    DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

  2. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    DOE Patents [OSTI]

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  3. Cell cycle nucleic acids, polypeptides and uses thereof

    DOE Patents [OSTI]

    Gordon-Kamm, William J. (Urbandale, IA); Lowe, Keith S. (Johnston, IA); Larkins, Brian A. (Tucson, AZ); Dilkes, Brian R. (Tucson, AZ); Sun, Yuejin (Westfield, IN)

    2007-08-14

    The invention provides isolated nucleic acids and their encoded proteins that are involved in cell cycle regulation. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions. The present invention provides methods and compositions relating to altering cell cycle protein content, cell cycle progression, cell number and/or composition of plants.

  4. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  5. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2010-06-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  6. Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-04-20

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from fungal fermentation broths. Nucleic acids that encode the antipathogenic polypeptides are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  7. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  8. Method for promoting specific alignment of short oligonucleotides on nucleic acids

    DOE Patents [OSTI]

    Studier, F. William; Kieleczawa, Jan; Dunn, John J.

    1996-01-01

    Disclosed is a method for promoting specific alignment of short oligonucleotides on a nucleic acid polymer. The nucleic acid polymer is incubated in a solution containing a single-stranded DNA-binding protein and a plurality of oligonucleotides which are perfectly complementary to distinct but adjacent regions of a predetermined contiguous nucleotide sequence in the nucleic acid polymer. The plurality of oligonucleotides anneal to the nucleic acid polymer to form a contiguous region of double stranded nucleic acid. Specific application of the methods disclosed include priming DNA synthesis and template-directed ligation.

  9. Universal nucleic acids sample preparation method for cells, spores and their mixture

    DOE Patents [OSTI]

    Bavykin, Sergei

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  10. Method and apparatus for staining immobilized nucleic acids

    DOE Patents [OSTI]

    Ramsey, J. Michael; Foote, Robert S.; Jacobson, Stephen C.

    2000-01-01

    A method for staining immobilized nucleic acids includes the steps of affixing DNA probes to a solid substrate, moving target DNA material into proximity with the DNA probes, whereby the target DNA hybridized with specific ones of the DNA probes, and moving a fluorescent dye into proximity with the hybridized target DNA, whereby the fluorescent dye binds to the hybridized DNA to enable subsequent detection of fluorescence.

  11. Nucleic acids encoding human trithorax protein

    DOE Patents [OSTI]

    Evans, Glen A.; Djabali, Malek; Selleri, Licia; Parry, Pauline

    2001-01-01

    In accordance with the present invention, there is provided an isolated peptide having the characteristics of human trithorax protein (as well as DNA encoding same, antisense DNA derived therefrom and antagonists therefor). The invention peptide is characterized by having a DNA binding domain comprising multiple zinc fingers and at least 40% amino acid identity with respect to the DNA binding domain of Drosophila trithorax protein and at least 70% conserved sequence with respect to the DNA binding domain of Drosophila trithorax protein, and wherein said peptide is encoded by a gene located at chromosome 11 of the human genome at q23. Also provided are methods for the treatment of subject(s) suffering from immunodeficiency, developmental abnormality, inherited disease, or cancer by administering to said subject a therapeutically effective amount of one of the above-described agents (i.e., peptide, antagonist therefor, DNA encoding said peptide or antisense DNA derived therefrom). Also provided is a method for the diagnosis, in a subject, of immunodeficiency, developmental abnormality, inherited disease, or cancer associated with disruption of chromosome 11 at q23.

  12. Human jagged polypeptide, encoding nucleic acids and methods of use

    DOE Patents [OSTI]

    Li, Linheng; Hood, Leroy

    2000-01-01

    The present invention provides an isolated polypeptide exhibiting substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the polypeptide does not have the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. The invention further provides an isolated nucleic acid molecule containing a nucleotide sequence encoding substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the nucleotide sequence does not encode the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. Also provided herein is a method of inhibiting differentiation of hematopoietic progenitor cells by contacting the progenitor cells with an isolated JAGGED polypeptide, or active fragment thereof. The invention additionally provides a method of diagnosing Alagille Syndrome in an individual. The method consists of detecting an Alagille Syndrome disease-associated mutation linked to a JAGGED locus.

  13. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    SciTech Connect (OSTI)

    Cary, Robert E.

    2015-12-08

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

  14. Methods for point-of-care detection of nucleic acid in a sample...

    Office of Scientific and Technical Information (OSTI)

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample ... Sponsoring Org: USDOE Country of Publication: United States Language: English Subject: 59 ...

  15. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2012-10-30

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  16. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2013-01-29

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  17. BGL6 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2012-10-02

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  18. BGL4 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2011-12-06

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  19. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2015-04-14

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  20. BGL6 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2015-08-11

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  1. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-25

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  2. BGL6 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-04

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  3. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2008-04-01

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  4. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2008-03-18

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  5. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2007-09-25

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  6. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2008-08-05

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  7. BGL6 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2009-09-01

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  8. BGL4 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2008-01-22

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  9. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2011-06-14

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  10. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-02-28

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  11. BGL4 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  12. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    DOE Patents [OSTI]

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  13. Methods for point-of-care detection of nucleic acid in a sample

    DOE Patents [OSTI]

    Bearinger, Jane P.; Dugan, Lawrence C.

    2015-12-29

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  14. Nucleic acids encoding mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

    DOE Patents [OSTI]

    Korber, Bette T; Fischer, William; Liao, Hua-Xin; Haynes, Barton F; Letvin, Norman; Hahn, Beatrice H

    2015-04-21

    The present invention relates to nucleic acids encoding mosaic clade M HIV-1 Env polypeptides and to compositions and vectors comprising same. The nucleic acids of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  15. The present invention relates to automated methods of introducing multiple nucleic acid sequences into one or more target cells.

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Wang, Harris H. (Cambridge, MA); Isaacs, Farren J. (Brookline, MA)

    2012-04-10

    The present invention relates to automated methods of introducing multiple nucleic acid sequences into one or more target cells.

  16. Method for producing labeled single-stranded nucleic acid probes

    DOE Patents [OSTI]

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  17. Plants having modified response to ethylene by transformation with an ETR nucleic acid

    DOE Patents [OSTI]

    Meyerowitz, Elliott M.; Chang, Caren; Bleecker, Anthony B.

    2001-01-01

    The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

  18. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  19. 5'to 3' nucleic acid synthesis using 3'-photoremovable protecting group

    DOE Patents [OSTI]

    Pirrung, Michael C.; Shuey, Steven W.; Bradley, Jean-Claude

    1999-01-01

    The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5' to 3' nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5' end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

  20. 5[prime] to 3[prime] nucleic acid synthesis using 3[prime]-photoremovable protecting group

    DOE Patents [OSTI]

    Pirrung, M.C.; Shuey, S.W.; Bradley, J.C.

    1999-06-01

    The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5[prime] to 3[prime] nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5[prime] end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

  1. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOE Patents [OSTI]

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  2. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  3. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

    DOE Patents [OSTI]

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2006-10-03

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  4. Label-free functional nucleic acid sensors for detecting target agents

    SciTech Connect (OSTI)

    Lu, Yi; Xiang, Yu

    2015-01-13

    A general methodology to design label-free fluorescent functional nucleic acid sensors using a vacant site approach and an abasic site approach is described. In one example, a method for designing label-free fluorescent functional nucleic acid sensors (e.g., those that include a DNAzyme, aptamer or aptazyme) that have a tunable dynamic range through the introduction of an abasic site (e.g., dSpacer) or a vacant site into the functional nucleic acids. Also provided is a general method for designing label-free fluorescent aptamer sensors based on the regulation of malachite green (MG) fluorescence. A general method for designing label-free fluorescent catalytic and molecular beacons (CAMBs) is also provided. The methods demonstrated here can be used to design many other label-free fluorescent sensors to detect a wide range of analytes. Sensors and methods of using the disclosed sensors are also provided.

  5. Methods and kits for nucleic acid analysis using fluorescence resonance energy transfer

    DOE Patents [OSTI]

    Kwok, Pui-Yan; Chen, Xiangning

    1999-01-01

    A method for detecting the presence of a target nucleotide or sequence of nucleotides in a nucleic acid is disclosed. The method is comprised of forming an oligonucleotide labeled with two fluorophores on the nucleic acid target site. The doubly labeled oligonucleotide is formed by addition of a singly labeled dideoxynucleoside triphosphate to a singly labeled polynucleotide or by ligation of two singly labeled polynucleotides. Detection of fluorescence resonance energy transfer upon denaturation indicates the presence of the target. Kits are also provided. The method is particularly applicable to genotyping.

  6. Nucleic acids encoding modified human immunodeficiency virus type 1 (HIV-1) group M consensus envelope glycoproteins

    DOE Patents [OSTI]

    Haynes, Barton F.; Gao, Feng; Korber, Bette T.; Hahn, Beatrice H.; Shaw, George M.; Kothe, Denise; Li, Ying Ying; Decker, Julie; Liao, Hua-Xin

    2011-12-06

    The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralizes a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

  7. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    DOE Patents [OSTI]

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  8. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

    SciTech Connect (OSTI)

    Myers, G.; Foley, B.; Korber, B.; Mellors, J.W.; Jeang, K.T.; Wain-Hobson, S.

    1997-04-01

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.

  9. Nucleic Acid Encoding A Lectin-Derived Progenitor Cell Preservation Factor

    DOE Patents [OSTI]

    Colucci, M. Gabriella; Chrispeels, Maarten J.; Moore, Jeffrey G.

    2001-10-30

    The invention relates to an isolated nucleic acid molecule that encodes a protein that is effective to preserve progenitor cells, such as hematopoietic progenitor cells. The nucleic acid comprises a sequence defined by SEQ ID NO:1, a homolog thereof, or a fragment thereof. The encoded protein has an amino acid sequence that comprises a sequence defined by SEQ ID NO:2, a homolog thereof, or a fragment thereof that contains an amino acid sequence TNNVLQVT. Methods of using the encoded protein for preserving progenitor cells in vitro, ex vivo, and in vivo are also described. The invention, therefore, include methods such as myeloablation therapies for cancer treatment wherein myeloid reconstitution is facilitated by means of the specified protein. Other therapeutic utilities are also enabled through the invention, for example, expanding progenitor cell populations ex vivo to increase chances of engraftation, improving conditions for transporting and storing progenitor cells, and facilitating gene therapy to treat and cure a broad range of life-threatening hematologic diseases.

  10. Modified pseudomonas oleovorans phaC1 nucleic acids encoding bispecific polyhydroxyalkanoate polymerase

    DOE Patents [OSTI]

    Srienc, Friedrich; Jackson, John K.; Somers, David A.

    2000-01-01

    A genetically engineered Pseudomonas oleovorans phaC1 polyhydroxyalkanoate (PHA) polymerase having tailored substrate specificity is provided. The modified PHA polymerase is preferably a "bispecific" PHA polymerase capable of copolymerizing a short chain length monomer and a medium chain length monomer is provided. Methods for making the modified PHA polymerase and for making nucleic acids encoding the modified PHA polymerase are also disclosed, as are methods of producing PHA using the modified PHA polymerase. The invention further includes methods to assay for altered substrate specificity.

  11. Nucleic acid encoding DS-CAM proteins and products related thereto

    DOE Patents [OSTI]

    Korenberg, Julie R.

    2005-11-01

    In accordance with the present invention, there are provided Down Syndrome-Cell Adhesion Molecule (DS-CAM) proteins. Nucleic acid sequences encoding such proteins and assays employing same are also disclosed. The invention DS-CAM proteins can be employed in a variety of ways, for example, for the production of anti-DS-CAM antibodies thereto, in therapeutic compositions and methods employing such proteins and/or antibodies. DS-CAM proteins are also useful in bioassays to identify agonists and antagonists thereto.

  12. Nucleic acids encoding plant glutamine phenylpyruvate transaminase (GPT) and uses thereof

    DOE Patents [OSTI]

    Unkefer, Pat J.; Anderson, Penelope S.; Knight, Thomas J.

    2016-03-29

    Glutamine phenylpyruvate transaminase (GPT) proteins, nucleic acid molecules encoding GPT proteins, and uses thereof are disclosed. Provided herein are various GPT proteins and GPT gene coding sequences isolated from a number of plant species. As disclosed herein, GPT proteins share remarkable structural similarity within plant species, and are active in catalyzing the synthesis of 2-hydroxy-5-oxoproline (2-oxoglutaramate), a powerful signal metabolite which regulates the function of a large number of genes involved in the photosynthesis apparatus, carbon fixation and nitrogen metabolism.

  13. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOE Patents [OSTI]

    Studier, F. William

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

  14. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOE Patents [OSTI]

    Studier, F.W.

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

  15. Aptamer- and nucleic acid enzyme-based systems for simultaneous detection of multiple analytes

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2011-11-15

    The present invention provides aptamer- and nucleic acid enzyme-based systems for simultaneously determining the presence and optionally the concentration of multiple analytes in a sample. Methods of utilizing the system and kits that include the sensor components are also provided. The system includes a first reactive polynucleotide that reacts to a first analyte; a second reactive polynucleotide that reacts to a second analyte; a third polynucleotide; a fourth polynucleotide; a first particle, coupled to the third polynucleotide; a second particle, coupled to the fourth polynucleotide; and at least one quencher, for quenching emissions of the first and second quantum dots, coupled to the first and second reactive polynucleotides. The first particle includes a quantum dot having a first emission wavelength. The second particle includes a second quantum dot having a second emission wavelength different from the first emission wavelength. The third polynucleotide and the fourth polynucleotide are different.

  16. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2014-04-08

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  17. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Ward, Thomas E.

    2016-03-22

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  18. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2013-07-23

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  19. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOE Patents [OSTI]

    Weier, Heinz-Ulrich G.; Gray, Joe W.

    1995-01-01

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

  20. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOE Patents [OSTI]

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

  1. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  2. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, an d analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: (1) to assess the potential terrorist threat to U.S. agricultural crops, (2) to determine whether suitable assays exist to monitor that threat, and (3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  3. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2010-04-06

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  4. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Patel, Kamlesh D [Ken]; SNL,

    2013-01-25

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  5. Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V

    SciTech Connect (OSTI)

    Myers, G.; Korber, B.; Wain-Hobson, S.; Smith, R.F.; Pavlakis, G.N.

    1993-12-31

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (I) HIV and SIV Nucleotide Sequences; (II) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.

  6. Nucleic acid molecules encoding isopentenyl monophosphate kinase, and methods of use

    DOE Patents [OSTI]

    Croteau, Rodney B.; Lange, Bernd M.

    2001-01-01

    A cDNA encoding isopentenyl monophosphate kinase (IPK) from peppermint (Mentha x piperita) has been isolated and sequenced, and the corresponding amino acid sequence has been determined. Accordingly, an isolated DNA sequence (SEQ ID NO:1) is provided which codes for the expression of isopentenyl monophosphate kinase (SEQ ID NO:2), from peppermint (Mentha x piperita). In other aspects, replicable recombinant cloning vehicles are provided which code for isopentenyl monophosphate kinase, or for a base sequence sufficiently complementary to at least a portion of isopentenyl monophosphate kinase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding isopentenyl monophosphate kinase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant isopentenyl monophosphate kinase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant isopentenyl monophosphate kinase may be used to obtain expression or enhanced expression of isopentenyl monophosphate kinase in plants in order to enhance the production of isopentenyl monophosphate kinase, or isoprenoids derived therefrom, or may be otherwise employed for the regulation or expression of isopentenyl monophosphate kinase, or the production of its products.

  7. Nucleic and amino acid sequences relating to a novel transketolase, and methods for the expression thereof

    DOE Patents [OSTI]

    Croteau, Rodney Bruce; Wildung, Mark Raymond; Lange, Bernd Markus; McCaskill, David G.

    2001-01-01

    cDNAs encoding 1-deoxyxylulose-5-phosphate synthase from peppermint (Mentha piperita) have been isolated and sequenced, and the corresponding amino acid sequences have been determined. Accordingly, isolated DNA sequences (SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7) are provided which code for the expression of 1-deoxyxylulose-5-phosphate synthase from plants. In another aspect the present invention provides for isolated, recombinant DXPS proteins, such as the proteins having the sequences set forth in SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8. In other aspects, replicable recombinant cloning vehicles are provided which code for plant 1-deoxyxylulose-5-phosphate synthases, or for a base sequence sufficiently complementary to at least a portion of 1-deoxyxylulose-5-phosphate synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding a plant 1-deoxyxylulose-5-phosphate synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant 1-deoxyxylulose-5-phosphate synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant 1-deoxyxylulose-5-phosphate synthase may be used to obtain expression or enhanced expression of 1-deoxyxylulose-5-phosphate synthase in plants in order to enhance the production of 1-deoxyxylulose-5-phosphate, or its derivatives such as isopentenyl diphosphate (BP), or may be otherwise employed for the regulation or expression of 1-deoxyxylulose-5-phosphate synthase, or the production of its products.

  8. Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Databases Databases NERSC supports the provisioning of databases to hold large scientific datasets, as part of the science gateways effort. Data-centric science often benefits from database solutions to store scientific data or metadata about data stored in more traditional file formats. Our database offereings are targeted toward large data sets and high performance. Currently we support: MySQL PostgreSQL MongoDB SciDB If you would like to discuss databases at NERSC please fill out this form

  9. Nucleic acid biosensors

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2009-11-03

    Sensors comprising aptazymes capable of detecting the presence and concentration of effectors, as well as methods of using such sensors, are disclosed.

  10. Nucleic acid indexing

    DOE Patents [OSTI]

    Guilfoyle, Richard A.; Guo, Zhen

    1999-01-01

    A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

  11. Nucleic acid indexing

    DOE Patents [OSTI]

    Guilfoyle, Richard A.; Guo, Zhen

    2001-01-01

    A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

  12. Nucleic acid isolation

    DOE Patents [OSTI]

    Longmire, J.L.; Lewis, A.K.; Hildebrand, C.E.

    1988-01-21

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduces the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without effect on the protocol.

  13. Nucleic acid isolation process

    DOE Patents [OSTI]

    Longmire, Jonathan L.; Lewis, Annette K.; Hildebrand, Carl E.

    1990-01-01

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduce the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without affect on the protocol.

  14. Databases

    Broader source: Energy.gov [DOE]

    The Fuel Cell Technologies Office is developing databases to make it easier for users to find up-to-date information on hydrogen and fuel cells.

  15. Databases

    Broader source: Energy.gov [DOE]

    DOE has supported the development of several combined heat and power (CHP) and distributed energy databases that have proven to be "go-to" resources for end users. These resources include an...

  16. Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3;#8242;-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

    SciTech Connect (OSTI)

    Egli, Martin; Pallan, Pradeep S.; Allerson, Charles R.; Prakash, Thazha P.; Berdeja, Andres; Yu, Jinghua; Lee, Sam; Watt, Andrew; Gaus, Hans; Bhat, Balkrishen; Swayze, Eric E.; Seth, Punit P.

    2012-03-16

    The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F {hor_ellipsis} H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py) {hor_ellipsis} H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

  17. Accumulated SET protein up-regulates and interacts with hnRNPK, increasing its binding to nucleic acids, the Bcl-xS repression, and cellular proliferation

    SciTech Connect (OSTI)

    Almeida, Luciana O.; Garcia, Cristiana B.; Matos-Silva, Flavia A.; Curti, Carlos; Leopoldino, Andria M.

    2014-02-28

    Highlights: hnRNPK is a new target of SET. SET regulates hnRNPK. SET and hnRNPK accumulation promotes tumorigenesis. SET accumulation is a potential model to study genes regulated by SET-hnRNPK. - Abstract: SET and hnRNPK are proteins involved in gene expression and regulation of cellular signaling. We previously demonstrated that SET accumulates in head and neck squamous cell carcinoma (HNSCC); hnRNPK is a prognostic marker in cancer. Here, we postulate that SET and hnRNPK proteins interact to promote tumorigenesis. We performed studies in HEK293 and HNSCC (HN6, HN12, and HN13) cell lines with SET/hnRNPK overexpression and knockdown, respectively. We found that SET and/or hnRNPK protein accumulation increased cellular proliferation. SET accumulation up-regulated hnRNPK mRNA and total/phosphorylated protein, promoted hnRNPK nuclear location, and reduced Bcl-x mRNA levels. SET protein directly interacted with hnRNPK, increasing both its binding to nucleic acids and Bcl-xS repression. We propose that hnRNPK should be a new target of SET and that SEThnRNPK interaction, in turn, has potential implications in cell survival and malignant transformation.

  18. Structural Rationalization of a Large Difference in RNA Affinity Despite a Small Difference in Chemistry between Two 2'-O-Modified Nucleic Acid Analogs

    SciTech Connect (OSTI)

    Pattanayek, R.; Sethaphong, L.; Pan, C.; Prhavc, M.; Prakash, T.P.; Manoharan, M.; Egli, M.

    2010-03-08

    Chemical modification of nucleic acids at the 2'-position of ribose has generated antisense oligonucleotides (AONs) with a range of desirable properties. Electron-withdrawing substituents such as 2'-O-[2-(methoxy)ethyl] (MOE) confer enhanced RNA affinity relative to that of DNA by conformationally preorganizing an AON for pairing with the RNA target and by improving backbone hydration. 2'-Substitution of the ribose has also been shown to increase nuclease resistance and cellular uptake via changes in lipophilicity. Interestingly, incorporation of either 2'-O-[2-(methylamino)-2-oxoethyl]- (NMA) or 2'-O-(N-methylcarbamate)-modified (NMC) residues into AONs has divergent effects on RNA affinity. Incorporation of 2'-O-NMA-T considerably improves RNA affinity while incorporation of 2'-O-NMC-T drastically reduces RNA affinity. Crystal structures at high resolution of A-form DNA duplexes containing either 2'-O-NMA-T or 2'-O-NMC-T shed light on the structural origins of the surprisingly large difference in stability given the relatively minor difference in chemistry between NMA and NMC. NMA substituents adopt an extended conformation and use either their carbonyl oxygen or amino nitrogen to trap water molecules between phosphate group and sugar. The conformational properties of NMA and the observed hydration patterns are reminiscent of those found in the structures of 2'-O-MOE-modified RNA. Conversely, the carbonyl oxygen of NMC and O2 of T are in close contact, providing evidence that an unfavorable electrostatic interaction and the absence of a stable water structure are the main reasons for the loss in thermodynamic stability as a result of incorporation of 2'-O-NMC-modified residues.

  19. Method of increasing conversion of a fatty acid to its corresponding dicarboxylic acid

    DOE Patents [OSTI]

    Craft, David L.; Wilson, C. Ron; Eirich, Dudley; Zhang, Yeyan

    2004-09-14

    A nucleic acid sequence including a CYP promoter operably linked to nucleic acid encoding a heterologous protein is provided to increase transcription of the nucleic acid. Expression vectors and host cells containing the nucleic acid sequence are also provided. The methods and compositions described herein are especially useful in the production of polycarboxylic acids by yeast cells.

  20. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    (Specialized Interface)

  1. Databases for rRNA gene profiling of microbial communities

    DOE Patents [OSTI]

    Ashby, Matthew

    2013-07-02

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  2. Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

    SciTech Connect (OSTI)

    Eric E. Roden

    2009-07-08

    This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Area 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.

  3. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1996-03-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

  4. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  5. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

    de la Chapelle, Albert; Vogelstein, Bert; Kinzler, Kenneth W.

    1997-01-01

    The human MSH2 gene, responsible for hereditary non-polyposis colorectal cancer, was identified by virtue of its homology to the MutS class of genes, which are involved in DNA mismatch repair. The sequence of cDNA clones of the human gene are provided, and the sequence of the gene can be used to demonstrate the existence of germ line mutations in hereditary non-polyposis colorectal cancer (HNPCC) kindreds, as well as in replication error.sup.+ (RER.sup.+) tumor cells.

  6. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

    Chapelle, A. de la; Vogelstein, B.; Kinzler, K.W.

    1997-12-02

    The human MSH2 gene, responsible for hereditary non-polyposis colorectal cancer, was identified by virtue of its homology to the MutS class of genes, which are involved in DNA mismatch repair. The sequence of cDNA clones of the human gene are provided, and the sequence of the gene can be used to demonstrate the existence of germ line mutations in hereditary non-polyposis colorectal cancer (HNPCC) kindreds, as well as in replication error{sup +}(RER{sup +}) tumor cells. 19 figs.

  7. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect (OSTI)

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  8. Piperazine-based nucleic acid analogs

    DOE Patents [OSTI]

    Schmidt, Jurgen; Silks, Louis A.; Michalczyk, Ryszard

    2005-01-11

    A novel nucleoside analog is disclosed which comprises a piperazine ring in the place of the ring ribose or deoxyribose sugar. Monomers utilizing a broad variety of nucleobases are disclosed, as well as oligomers comprising the monomers disclosed herein linked by a variety of linkages, including amide, phosphonamide, and sulfonamide linkages. A method of synthesizing the nucleoside analogs is also disclosed.

  9. Fatty acid-producing hosts

    DOE Patents [OSTI]

    Pfleger, Brian F; Lennen, Rebecca M

    2013-12-31

    Described are hosts for overproducing a fatty acid product such as a fatty acid. The hosts include an exogenous nucleic acid encoding a thioesterase and, optionally, an exogenous nucleic acid encoding an acetyl-CoA carboxylase, wherein an acyl-CoA synthetase in the hosts are functionally delected. The hosts prefereably include the nucleic acid encoding the thioesterase at an intermediate copy number. The hosts are preferably recominantly stable and growth-competent at 37.degree. C. Methods of producing a fatty acid product comprising culturing such hosts at 37.degree. C. are also described.

  10. Humic acids: Characterization and interactions in natural and wastewater systems. (Latest citations from Pollution Abstracts database). Published Search

    SciTech Connect (OSTI)

    Not Available

    1993-09-01

    The bibliography contains citations concerning the absorptive and complexation properties of humic and fulvic acids. Characterization and the occurrence of these acids in wastewater systems and natural systems are studied. The interaction of humic substances with metallic pollutants and chlorinated hydrocarbons, and removal of humic acids by precipitation are among the topics discussed. Wastewater treatment processes are discussed in separate bibliographies. (Contains 250 citations and includes a subject term index and title list.)

  11. MvirDB: Microbial Database of Protein Toxins, Virulence Factors and Antibiotic Resistance Genes for Bio-Defense Applications

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Zhou, C. E.; Smith, J.; Lam, M.; Zemla, M. D.; Slezak, T.

    MvirDB is a cenntralized resource (data warehouse) comprising all publicly accessible, organized sequence data for protein toxins, virulence factors, and antibiotic resistance genes. Protein entries in MvirDB are annotated using a high-throughput, fully automated computational annotation system; annotations are updated periodically to ensure that results are derived using current public database and open-source tool releases. Tools provided for using MvirDB include a web-based browser tool and BLAST interfaces. MvirDB serves researchers in the bio-defense and medical fields. (taken from page 3 of PI's paper of same title published in Nucleic Acids Research, 2007, Vol.35, Database Issue (Open Source)

  12. Database Search

    National Nuclear Security Administration (NNSA)

    ... mountain ranges, faults that have both normal and strike slip. Dip Database Search http:gldims.cr.usgs.govwebappscfusionsitesqfaultqfwebdisp.cfm?... 1 of 1 3292010 6:23

  13. Database Search

    National Nuclear Security Administration (NNSA)

    ... fault were found, so its displacement sense is uncertain. Dip Database Search http:gldims.cr.usgs.govwebappscfusionSitesqfaultqfwebdisp.cfm?... 1 of 1 1292010 2:54

  14. Buildings Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Energy Efficiency & Renewable Energy EERE Home | Programs & Offices | Consumer Information Buildings Database Welcome Guest Log In | Register | Contact Us Home About All Projects...

  15. Database Help

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    other services. What databases does LinkSeeker appear in? Primo, Web of Knowledge, ProQuest, PubMed, MathSciNet, and the classic Library Catalog When I click the LinkSeeker...

  16. Methods for immobilizing nucleic acids on a gel substrate

    DOE Patents [OSTI]

    Mirzabekov, Andrei Darievich; Proudnikov, Dimitri Y.; Timofeev, Edward N.; Kochetkova, Svetlana V.; Florentiev, Vladimir L.; Shick, Valentine V.

    1999-01-01

    A method for labeling oligonucleotide molecules, and for immobilizing oligonucleotide and DNA molecules is provided comprising modifying the molecules to create a chemically active group, and contacting activated fluorescent dyes to the region. A method for preparing an immobilization substrate is also provided comprising modifying a gel to contain desired functional groups which covalently interact with certain moieties of the oligonucleotide molecules. A method for immobilizing biomolecules and other molecules within a gel by copolymerization of allyl-substituted oligonucleotides, DNA and proteins with acrylamide is also provided.

  17. Rapid microfluidic thermal cycler for nucleic acid amplification

    DOE Patents [OSTI]

    Beer, Neil Reginald; Vafai, Kambiz

    2015-11-06

    A system for thermal cycling a material to be thermal cycled including a microfluidic heat exchanger; a porous medium in the microfluidic heat exchanger; a microfluidic thermal cycling chamber containing the material to be thermal cycled, the microfluidic thermal cycling chamber operatively connected to the microfluidic heat exchanger; a working fluid at first temperature; a first system for transmitting the working fluid at first temperature to the microfluidic heat exchanger; a working fluid at a second temperature, a second system for transmitting the working fluid at second temperature to the microfluidic heat exchanger; a pump for flowing the working fluid at the first temperature from the first system to the microfluidic heat exchanger and through the porous medium; and flowing the working fluid at the second temperature from the second system to the heat exchanger and through the porous medium.

  18. Method for replicating an array of nucleic acid probes

    DOE Patents [OSTI]

    Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

    1998-08-18

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

  19. Replica amplification of nucleic acid arrays (Patent) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    7,785,790 US patent application 11745,806 DOE Contract Number: FG02-87ER60565 Resource Type: Patent Research Org: President and Fellows of Harvard College (Cambridge, MA)...

  20. Rapid microfluidic thermal cycler for nucleic acid amplification

    DOE Patents [OSTI]

    Beer, Neil Reginald; Vafai, Kambiz

    2015-10-27

    A system for thermal cycling a material to be thermal cycled including a microfluidic heat exchanger; a porous medium in the microfluidic heat exchanger; a microfluidic thermal cycling chamber containing the material to be thermal cycled, the microfluidic thermal cycling chamber operatively connected to the microfluidic heat exchanger; a working fluid at first temperature; a first system for transmitting the working fluid at first temperature to the microfluidic heat exchanger; a working fluid at a second temperature, a second system for transmitting the working fluid at second temperature to the microfluidic heat exchanger; a pump for flowing the working fluid at the first temperature from the first system to the microfluidic heat exchanger and through the porous medium; and flowing the working fluid at the second temperature from the second system to the heat exchanger and through the porous medium.

  1. Methods for separating particles and/or nucleic acids usingisotachoph...

    Office of Scientific and Technical Information (OSTI)

    Other methods of isotachophoresis are disclosed in addition to these. Authors: Jung, Byoungsok ; Ness, Kevin ; Rose, Klint A. Publication Date: 2016-03-15 OSTI Identifier: 1243046 ...

  2. Method for replicating an array of nucleic acid probes

    DOE Patents [OSTI]

    Cantor, Charles R.; Przetakiewicz, Marek; Smith, Cassandra L.; Sano, Takeshi

    1998-01-01

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

  3. Digital microfluidic hub for automated nucleic acid sample preparation.

    SciTech Connect (OSTI)

    He, Jim; Bartsch, Michael S.; Patel, Kamlesh D.; Kittlaus, Eric A.; Remillared, Erin M.; Pezzola, Genevieve L.; Renzi, Ronald F.; Kim, Hanyoup

    2010-07-01

    We have designed, fabricated, and characterized a digital microfluidic (DMF) platform to function as a central hub for interfacing multiple lab-on-a-chip sample processing modules towards automating the preparation of clinically-derived DNA samples for ultrahigh throughput sequencing (UHTS). The platform enables plug-and-play installation of a two-plate DMF device with consistent spacing, offers flexible connectivity for transferring samples between modules, and uses an intuitive programmable interface to control droplet/electrode actuations. Additionally, the hub platform uses transparent indium-tin oxide (ITO) electrodes to allow complete top and bottom optical access to the droplets on the DMF array, providing additional flexibility for various detection schemes.

  4. CREW Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Database - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs Advanced Nuclear Energy

  5. Plant fatty acid hydroxylase

    DOE Patents [OSTI]

    Somerville, Chris; van de Loo, Frank

    2000-01-01

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  6. Thermal and acid tolerant beta-xylosidases, genes encoding, related organisms, and methods

    DOE Patents [OSTI]

    Thompson, David N.; Thompson, Vicki S.; Schaller, Kastli D.; Apel, William A.; Lacey, Jeffrey A.; Reed, David W.

    2011-04-12

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof are provided. Further provided are methods of at least partially degrading xylotriose and/or xylobiose using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof.

  7. Thermal and acid tolerant beta xylosidases, arabinofuranosidases, genes encoding, related organisms, and methods

    DOE Patents [OSTI]

    Thompson, David N; Thompson, Vicki S; Schaller, Kastli D; Apel, William A; Reed, David W; Lacey, Jeffrey A

    2013-04-30

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof are provided. Further provided are methods of at least partially degrading xylotriose, xylobiose, and/or arabinofuranose-substituted xylan using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof.

  8. Security of databases

    SciTech Connect (OSTI)

    Yeh, Y.S.

    1985-01-01

    In this thesis, the security of databases using cryptographic methods is considered. An algebra for encrypted relational databases is considered and examined. Other database cryptosystems are presented, namely multilevel secure databases including three different approaches; multikey multilevel, cumulative key multilevel, and permutational multilevel secure databases. Finally, entity-relationship encryption is examined.

  9. Databases | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Information Resources » Databases Databases This page contains several databases that provide comprehensive information to expand your biomass knowledge. Use the descriptions and links provided to access the database that best meets your research needs. Alternative Fuels & Advanced Vehicles Data Center (AFDC) Publications Database: There are thousands of publications in AFDC's comprehensive alternative fuels and advanced transportation database. Sponsored by the U.S. Department of Energy's

  10. ARM Publications Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DatabaseSearch Publications Database Search Submit a Publication Would your publication make a good research highlight? Submit one now. Comments? Need a change to an existing...

  11. ARM Publications Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    govPublicationsPublications Database Publications Database Submit a Publication Would your publication make a good research highlight? Submit one now. Comments? Need a change to an...

  12. ARM Publications Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DatabaseSearchTips Publications Database Search Submit a Publication Would your publication make a good research highlight? Submit one now. Comments? Need a change to an existing...

  13. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

    Katz, Leonard; Fortman, Jeffrey L; Keasling, Jay D

    2013-10-29

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing a dicarboxylic acid (diacid). Such diacids include diketide-diacids and triketide-diacids. The invention includes recombinant nucleic acid encoding the PKS, and host cells comprising the PKS. The invention also includes methods for producing the diacids.

  14. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

    Katz, Leonard; Fortman, Jeffrey L.; Keasling, Jay D.

    2015-05-26

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing a dicarboxylic acid (diacid). Such diacids include diketide-diacids and triketide-diacids. The invention includes recombinant nucleic acid encoding the PKS, and host cells comprising the PKS. The invention also includes methods for producing the diacids.

  15. Network II Database

    Energy Science and Technology Software Center (OSTI)

    1994-11-07

    The Oak Ridge National Laboratory (ORNL) Rail and Barge Network II Database is a representation of the rail and barge system of the United States. The network is derived from the Federal Rail Administration (FRA) rail database.

  16. Pathogen Research Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Pathogen Databases Pathogen Research Databases A new research frontier awaits! Our door is open and we thrive on mutually beneficial partnerships, collaborations that drive innovations and new technologies. HIV Databases The HIV and HCV databases contain data on viral genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. The websites also gives access to a large number of tools that can be used to analyze these data. These projects are funded by the

  17. Benchmarking Database - JCAP

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ©bobpaz.com0121.JPG Benchmarking Database Research Why Solar Fuels Goals & Objectives Thrust 1 Thrust 2 Thrust 3 Thrust 4 Publications Research Highlights Videos Innovations User Facilities Expert Team Benchmarking Database Device Simulation Tool XPS Spectral Database Research Introduction Why Solar Fuels? Goals & Objectives Thrusts Thrust 1 Thrust 2 Thrust 3 Thrust 4 Library Publications Research Highlights Videos Resources User Facilities Expert Team Benchmarking Database Device

  18. Deep Sky Astronomical Image Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Deep Sky Astronomical Image Database Deep Sky Astronomical Image Database Key Challenges: Develop, store, analyze, and make available an astronomical image database of...

  19. databases | netl.doe.gov

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The database is available in Microsoft Access 2002 format. Download 6.35 MB COA Database Heavy Oil Database: 2004. The Heavy Oil Database contains information on over 500 ...

  20. 2010 Worldwide Gasification Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

  1. Databases | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Databases Databases CORPORATE REPORTING AND SAFETY PERFORMANCE ANALYSIS chart The Office of Environment, Health, Safety and Security (EHSS) manages corporate reporting databases and provides analysis of DOE-wide performance in protecting the public, the workers and the environment while performing the missions of DOE. EHSS manages a number of viable safety indicators applicable to most DOE contractor operations that provide Departmental leadership, line management, and stakeholders with timely

  2. Cambridge Structural Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Cambridge Structural Database Cambridge Structural Database LANL researchers can access WebCSD from offsite via Remote Access. Question? 667-5809 Email Cambridge Structural Database (CSD) includes bibliographic, chemical, and crystallographic information for organic molecules and metal-organic compounds. The crystal structure data comes from the open literature or direct deposits by researchers. The CSD System incorporations a suite of flexible search and analysis tools. The Research Library

  3. Gasification Plant Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Plant Databases Welcome to the U. S. Department of Energy, National Energy Technology Laboratory's Gasification Plant Databases Within these databases you will find current publicly available information on proposed projects and projects undergoing construction and initial operation within the United States and worldwide. Currently operating projects are excluded. The data have been compiled here to keep the public informed of the technologies and investments in major industrial coal

  4. SWNVF: database contents

    National Nuclear Security Administration (NNSA)

    Nevada Test Site (NTS). The database complies with protocols of Structured Query Language (SQL), allowing construction of relationships among these data, from...

  5. Lessons Learned Database

    Broader source: Energy.gov [DOE]

    The DOE Corporate Lessons Learned Database provides a central clearinghouse that allows ready access to and communication about collected information on a timely, unimpeded basis by all DOE...

  6. Find Articles/Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Geology Looking for data? Chemical Data and Structures: SciFinder information CRC Handbook of Chemistry and Physics Protein Data Bank Cambridge Structural Database (and ...

  7. BioImaging Database

    Energy Science and Technology Software Center (OSTI)

    2006-10-25

    The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

  8. Hazard Analysis Database Report

    SciTech Connect (OSTI)

    GAULT, G.W.

    1999-10-13

    The Hazard Analysis Database was developed in conjunction with the hazard analysis activities conducted in accordance with DOE-STD-3009-94, Preparation Guide for US Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, for the Tank Waste Remediation System (TWRS) Final Safety Analysis Report (FSAR). The FSAR is part of the approved TWRS Authorization Basis (AB). This document describes, identifies, and defines the contents and structure of the TWRS FSAR Hazard Analysis Database and documents the configuration control changes made to the database. The TWRS Hazard Analysis Database contains the collection of information generated during the initial hazard evaluations and the subsequent hazard and accident analysis activities. The database supports the preparation of Chapters 3,4, and 5 of the TWRS FSAR and the USQ process and consists of two major, interrelated data sets: (1) Hazard Evaluation Database--Data from the results of the hazard evaluations; and (2) Hazard Topography Database--Data from the system familiarization and hazard identification.

  9. Requirements Management Database

    Energy Science and Technology Software Center (OSTI)

    2009-08-13

    This application is a simplified and customized version of the RBA and CTS databases to capture federal, site, and facility requirements, link to actions that must be performed to maintain compliance with their contractual and other requirements.

  10. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1994-05-27

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  11. Life Cycle Inventory Database

    Broader source: Energy.gov [DOE]

    The U.S. Life Cycle Inventory (LCI) Database serves as a central repository for information about the total energy and resource impacts of developing and using various commercial building materials...

  12. Buildings Performance Database Overview

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Overview Buildings.energy.gov/BPD BuildingsPerformanceDatabase@ee.doe.gov 2 * The BPD statistically analyzes trends in the energy performance and physical & operational characteristics of real commercial and residential buildings. The Buildings Performance Database 3 Design Principles * The BPD contains actual data on existing buildings - not modeled data or anecdotal evidence. * The BPD enables statistical analysis without revealing information about individual buildings. * The BPD cleanses

  13. XPS Spectral Database - JCAP

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Information XML Services Science Search Tools | DOE Collections | Journal Sources | Library Tools Home | U.S. Federal Agencies | Global Databases | Customized Resources XML data services are currently available from several OSTI collections. The XML Services Manual covers the following products: DOE PagesBeta XML Data Services Manual [674-KB PDF] DOE R&D Accomplishments XML Data Services Manual [157-KB PDF] DOepatents database XML Data Services Manual [1089-KB PDF] Geothermal

  14. DIP: The Database of Interacting Proteins

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

  15. Crude Oil Analysis Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Shay, Johanna Y.

    The composition and physical properties of crude oil vary widely from one reservoir to another within an oil field, as well as from one field or region to another. Although all oils consist of hydrocarbons and their derivatives, the proportions of various types of compounds differ greatly. This makes some oils more suitable than others for specific refining processes and uses. To take advantage of this diversity, one needs access to information in a large database of crude oil analyses. The Crude Oil Analysis Database (COADB) currently satisfies this need by offering 9,056 crude oil analyses. Of these, 8,500 are United States domestic oils. The database contains results of analysis of the general properties and chemical composition, as well as the field, formation, and geographic location of the crude oil sample. [Taken from the Introduction to COAMDATA_DESC.pdf, part of the zipped software and database file at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the zipped file to your PC. When opened, it will contain PDF documents and a large Excel spreadsheet. It will also contain the database in Microsoft Access 2002.

  16. OpenEI Community - Database

    Open Energy Info (EERE)

    Announcing New Utility Rate Database and API Features http:en.openei.orgcommunityblogannouncing-new-utility-rate-database-and-api-features

    NREL, in collaboration with...

  17. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1992-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

  18. Mutant fatty acid desaturase

    DOE Patents [OSTI]

    Shanklin, John; Cahoon, Edgar B.

    2004-02-03

    The present invention relates to a method for producing mutants of a fatty acid desaturase having a substantially increased activity towards fatty acid substrates with chains containing fewer than 18 carbons relative to an unmutagenized precursor desaturase having an 18 carbon atom chain length substrate specificity. The method involves inducing one or more mutations in the nucleic acid sequence encoding the precursor desaturase, transforming the mutated sequence into an unsaturated fatty acid auxotroph cell such as MH13 E. coli, culturing the cells in the absence of supplemental unsaturated fatty acids, thereby selecting for recipient cells which have received and which express a mutant fatty acid desaturase with an elevated specificity for fatty acid substrates having chain lengths of less than 18 carbon atoms. A variety of mutants having 16 or fewer carbon atom chain length substrate specificities are produced by this method. Mutant desaturases produced by this method can be introduced via expression vectors into prokaryotic and eukaryotic cells and can also be used in the production of transgenic plants which may be used to produce specific fatty acid products.

  19. Redis database administration tool

    Energy Science and Technology Software Center (OSTI)

    2013-02-13

    MyRedis is a product of the Lorenz subproject under the ASC Scirntific Data Management effort. MyRedis is a web based utility designed to allow easy administration of instances of Redis databases. It can be usedd to view and manipulate data as well as run commands directly against a variety of different Redis hosts.

  20. High Performance Buildings Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The High Performance Buildings Database is a shared resource for the building industry, a unique central repository of in-depth information and data on high-performance, green building projects across the United States and abroad. The database includes information on the energy use, environmental performance, design process, finances, and other aspects of each project. Members of the design and construction teams are listed, as are sources for additional information. In total, up to twelve screens of detailed information are provided for each project profile. Projects range in size from small single-family homes or tenant fit-outs within buildings to large commercial and institutional buildings and even entire campuses. The database is a data repository as well. A series of Web-based data-entry templates allows anyone to enter information about a building project into the database. Once a project has been submitted, each of the partner organizations can review the entry and choose whether or not to publish that particular project on its own Web site.

  1. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1992-11-09

    The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

  2. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1999-01-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilities access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  3. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-11-15

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  4. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-07-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  5. MHK Materials Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Materials Database - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs Advanced

  6. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1998-08-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  7. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1997-02-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  8. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Cain, J.M.

    1993-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

  9. Sample Prep, Workflow Automation and Nucleic Acid Fractionation for Next Generation Sequencing

    SciTech Connect (OSTI)

    Roskey, Mark

    2010-06-03

    Mark Roskey of Caliper LifeSciences discusses how the company's technologies fit into the next generation sequencing workflow on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  10. Method for the detection of specific nucleic acid sequences by polymerase nucleotide incorporation

    DOE Patents [OSTI]

    Castro, Alonso

    2004-06-01

    A method for rapid and efficient detection of a target DNA or RNA sequence is provided. A primer having a 3'-hydroxyl group at one end and having a sequence of nucleotides sufficiently homologous with an identifying sequence of nucleotides in the target DNA is selected. The primer is hybridized to the identifying sequence of nucleotides on the DNA or RNA sequence and a reporter molecule is synthesized on the target sequence by progressively binding complementary nucleotides to the primer, where the complementary nucleotides include nucleotides labeled with a fluorophore. Fluorescence emitted by fluorophores on single reporter molecules is detected to identify the target DNA or RNA sequence.

  11. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2015-07-14

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  12. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2014-04-01

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  13. Disposable and removable nucleic acid extraction and purification cartridges for automated flow-through systems

    DOE Patents [OSTI]

    Regan, John Frederick

    2014-09-09

    Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

  14. Modified SSCP method using sequential electrophoresis of multiple nucleic acid segments

    DOE Patents [OSTI]

    Gatti, Richard A.

    2002-10-01

    The present invention is directed to a method of screening large, complex, polyexonic eukaryotic genes such as the ATM gene for mutations and polymorphisms by an improved version of single strand conformation polymorphism (SSCP) electrophoresis that allows electrophoresis of two or three amplified segments in a single lane. The present invention also is directed to new mutations and polymorphisms in the ATM gene that are useful in performing more accurate screening of human DNA samples for mutations and in distinguishing mutations from polymorphisms, thereby improving the efficiency of automated screening methods.

  15. Xylanases, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A; Dirmeier, Reinhard

    2013-07-16

    The invention relates to enzymes having xylanase, mannanase and/or glucanase activity, e.g., catalyzing hydrolysis of internal .beta.-1,4-xylosidic linkages or endo-.beta.-1,4-glucanase linkages; and/or degrading a linear polysaccharide beta-1,4-xylan into xylose. Thus, the invention provides methods and processes for breaking down hemicellulose, which is a major component of the cell wall of plants, including methods and processes for hydrolyzing hemicelluloses in any plant or wood or wood product, wood waste, paper pulp, paper product or paper waste or byproduct. In addition, methods of designing new xylanases, mannanases and/or glucanases and methods of use thereof are also provided. The xylanases, mannanases and/or glucanases have increased activity and stability at increased pH and temperature.

  16. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOE Patents [OSTI]

    Gray, J.W.; Weier, H.U.

    1999-03-30

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  17. Cellulases, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Blum, David; Gemsch Cuenca, Joslin; Dycaico, Mark

    2013-04-23

    This invention relates to molecular and cellular biology and biochemistry. In one aspect, the invention provides polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or .beta.-glucosidase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or .beta.-glucosidase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts.

  18. Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study

    SciTech Connect (OSTI)

    Pitonak, Michal; Neogrady, Pavel; Hobza, Pavel

    2009-12-18

    Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.

  19. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2012-03-13

    The present invention provides BGL7 polypeptides with the biological activity of a .beta.-glucosidase and a method of producing a recombinant enzyme having .beta.-glucosidase activity.

  20. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-07

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  1. Nucleic acids encoding phloem small RNA-binding proteins and transgenic plants comprising them

    DOE Patents [OSTI]

    Lucas, William J.; Yoo, Byung-Chun; Lough, Tony J.; Varkonyi-Gasic, Erika

    2007-03-13

    The present invention provides a polynucleotide sequence encoding a component of the protein machinery involved in small RNA trafficking, Cucurbita maxima phloem small RNA-binding protein (CmPSRB 1), and the corresponding polypeptide sequence. The invention also provides genetic constructs and transgenic plants comprising the polynucleotide sequence encoding a phloem small RNA-binding protein to alter (e.g., prevent, reduce or elevate) non-cell autonomous signaling events in the plants involving small RNA metabolism. These signaling events are involved in a broad spectrum of plant physiological and biochemical processes, including, for example, systemic resistance to pathogens, responses to environmental stresses, e.g., heat, drought, salinity, and systemic gene silencing (e.g., viral infections).

  2. Amplification of trace amounts of nucleic acids (Patent) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    background can be reduced by judicious design of primers. We have shown clean signal-to-noise with as little as starting material as one single human cell (.about.6...

  3. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOE Patents [OSTI]

    Gray, Joe W.; Weier, Heinz-Ulrich

    2001-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  4. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOE Patents [OSTI]

    Gray, J.W.; Weier, H.U.

    1998-11-24

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  5. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOE Patents [OSTI]

    Gray, Joe W.; Weier, Heinz-Ulrich

    1999-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  6. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOE Patents [OSTI]

    Gray, Joe W.; Weier, Heinz-Ulrich

    1998-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  7. Cellulolytic enzymes, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A.; Zhao, Lishan; Cayouette, Michelle H.

    2012-01-24

    The invention provides polypeptides having any cellulolytic activity, e.g., a cellulase activity, a endoglucanase, a cellobiohydrolase, a beta-glucosidase, a xylanase, a mannanse, a .beta.-xylosidase, an arabinofuranosidase, and/or an oligomerase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, .beta.-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. In one aspect, the invention provides polypeptides having an oligomerase activity, e.g., enzymes that convert recalcitrant soluble oligomers to fermentable sugars in the saccharification of biomass. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

  8. Celluloytic enzymes, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A; Zhao, Lishan; Cayouette, Michelle H

    2015-11-04

    The invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, .beta.-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

  9. Celluloytic enzymes, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A.; Zhao, Lishan; Cayouette, Michelle H.

    2015-09-08

    The invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, .beta.-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

  10. REDD+ Database | Open Energy Information

    Open Energy Info (EERE)

    change mitigation, resource conservation and positive development outcomes through sustainable forest management." References "REDD+ Database" Retrieved from "http:...

  11. Hydrogen Storage Materials Database Demonstration

    Broader source: Energy.gov [DOE]

    Presentation slides from the Fuel Cell Technologies Office webinar "Hydrogen Storage Materials Database Demonstration" held December 13, 2011.

  12. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    DOE Patents [OSTI]

    Jessen, Holly Jean; Liao, Hans H.; Gort, Steven John; Selifonova, Olga V.

    2011-10-04

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  13. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    DOE Patents [OSTI]

    Jessen, Holly Jean; Liao, Hans H; Gort, Steven John; Selifonova, Olga V

    2014-11-18

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  14. Building Performance Database

    Broader source: Energy.gov [DOE]

    The Building Performance Database (BPD) unlocks the power of building data by providing access to the largest publicly-available dataset of information about the physical and operational characteristics of real buildings. The BPD enables users to perform statistical analysis on an anonymous dataset of hundreds of thousands of commercial and residential buildings from across the country. Users can examine specific building types and geographic areas, compare performance trends among similar buildings, identify and prioritize cost-saving energy efficiency improvements, and assess the range of likely savings from these improvements.

  15. Construction of file database management

    SciTech Connect (OSTI)

    MERRILL,KYLE J.

    2000-03-01

    This work created a database for tracking data analysis files from multiple lab techniques and equipment stored on a central file server. Experimental details appropriate for each file type are pulled from the file header and stored in a searchable database. The database also stores specific location and self-directory structure for each data file. Queries can be run on the database according to file type, sample type or other experimental parameters. The database was constructed in Microsoft Access and Visual Basic was used for extraction of information from the file header.

  16. Montana State Antiquities Database | Open Energy Information

    Open Energy Info (EERE)

    Antiquities Database Jump to: navigation, search OpenEI Reference LibraryAdd to library Web Site: Montana State Antiquities Database Abstract Database contains cultural resource...

  17. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Mallick, Parag; Rice, Danny; Eisenberg, David

    How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  18. Ribosomal Database Project II

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences. As of March 2008, RDP Release 10 is available and currently (August 2009) contains 1,074,075 aligned 16S rRNA sequences. Data that can be downloaded include zipped GenBank and FASTA alignment files, a histogram (in Excel) of the number of RDP sequences spanning each base position, data in the Functional Gene Pipeline Repository, and various user submitted data. The RDP-II website also provides numerous analysis tools.[From the RDP-II home page at http://rdp.cme.msu.edu/index.jsp

  19. National Residential Efficiency Measures Database Webinar Slides...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    National Residential Efficiency Measures Database Webinar Slides National Residential Efficiency Measures Database Webinar Slides Presentation slides for the Building Technologies ...

  20. WTO Subsidy Notifications Database | Open Energy Information

    Open Energy Info (EERE)

    Dataset Website: www.globalsubsidies.orgprivatemodulesknowledgeboxexternalindex.ph WTO Subsidy Notifications Database Screenshot References: WTO Subsidy Database1...

  1. Buildings Performance Database Overview | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Buildings Performance Database Overview Buildings Performance Database Overview Buildings Performance Database Overview, from the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy. PDF icon bpd_overview_2014.pdf More Documents & Publications Buildings Performance Database (BPD) - 2014 BTO Peer Review Buildings Performance Database - 2013 BTO Peer Review Data Preparation Process for the Buildings Performance Database

  2. Database | OpenEI Community

    Open Energy Info (EERE)

    State University, with funding from the Department of Energy Sunshot Program, has enhanced the U.S. Utility Rate Database with the following new features: Kyoung's picture...

  3. 09-Databases-Wahid.pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wahid Bhimji (wbhimji@lbl.gov) https:www.nersc.govusersdata- analyticsdata-management Databases and IO --- 1 --- Systems Services Tools Capabilities Transfer Processing...

  4. Sandia Wind Turbine Loads Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wind Turbine Loads Database - Sandia Energy Energy Search Icon Sandia Home Locations ... Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power ...

  5. Energy Citations Database (ECD) - Architecture

    Office of Scientific and Technical Information (OSTI)

    Search Architecture - What Is under the hood? The Energy Citations Database makes searchable over two million bibliographic citations for energy and energy related STI from the...

  6. Energy Citations Database (ECD) - About

    Office of Scientific and Technical Information (OSTI)

    About ECD The Energy Citations Database (1943 - Present) was developed by the U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) to improve...

  7. Energy Citations Database (ECD) - Widget

    Office of Scientific and Technical Information (OSTI)

    Energy Citations Database Widget You can access key features from the Department of Energy's Office of Scientific and Technical Information (DOEOSTI) by downloading the Energy...

  8. Hanford Site technical baseline database

    SciTech Connect (OSTI)

    Porter, P.E., Westinghouse Hanford

    1996-05-10

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of May 10, 1996. The cassette tape also includes the delta files that delineate the differences between this revision and revision 3 (April 10, 1996) of the Hanford Site Technical Baseline Database.

  9. Wind turbine reliability database update.

    SciTech Connect (OSTI)

    Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.; Veers, Paul S.

    2009-03-01

    This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

  10. GOTTCHA Database, Version 1

    Energy Science and Technology Software Center (OSTI)

    2015-08-03

    One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discoverymore » rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions.In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure.During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably.During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.The DATABASE provided is the result of the algorithm described.« less

  11. ORISE: Human Subjects Research Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human Subjects Research Database Section 10, Part 745 of the Code of Federal Regulations and U.S. Department of Energy (DOE) Orders 443.1 and 481.1 require the maintenance of...

  12. Marine and Hydrokinetic Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    DOE’s Marine and Hydrokinetic Technology Database provides up-to-date information on marine and hydrokinetic renewable energy, both in the U.S. and around the world. The database includes wave, tidal, current, and ocean thermal energy, and contains information on the various energy conversion technologies, companies active in the field, and development of projects in the water. Depending on the needs of the user, the database can present a snapshot of projects in a given region, assess the progress of a certain technology type, or provide a comprehensive view of the entire marine and hydrokinetic energy industry. Results are displayed as a list of technologies, companies, or projects. Data can be filtered by a number of criteria, including country/region, technology type, generation capacity, and technology or project stage. The database was updated in 2009 to include ocean thermal energy technologies, companies, and projects.

  13. Marine and Hydrokinetic Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    DOEs Marine and Hydrokinetic Technology Database provides up-to-date information on marine and hydrokinetic renewable energy, both in the U.S. and around the world. The database includes wave, tidal, current, and ocean thermal energy, and contains information on the various energy conversion technologies, companies active in the field, and development of projects in the water. Depending on the needs of the user, the database can present a snapshot of projects in a given region, assess the progress of a certain technology type, or provide a comprehensive view of the entire marine and hydrokinetic energy industry. Results are displayed as a list of technologies, companies, or projects. Data can be filtered by a number of criteria, including country/region, technology type, generation capacity, and technology or project stage. The database was updated in 2009 to include ocean thermal energy technologies, companies, and projects.

  14. Energy Citations Database (ECD) - Comments

    Office of Scientific and Technical Information (OSTI)

    Contact Us If you have a question about Energy Citations Database, we recommend you check frequently asked questions. If your question still has not been answered or if you wish to...

  15. National Residential Efficiency Measures Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    National Residential Efficiency Measures Database Development Document, v3.0 Final Draft, June 2012 National Renewable Energy Laboratory 15013 Denver West Parkway Golden, Colorado i Executive Summary The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most

  16. ORISE: Human Subjects Research Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human Subjects Research Database Section 10, Part 745 of the Code of Federal Regulations and U.S. Department of Energy (DOE) Orders 443.1 and 481.1 require the maintenance of information on all research projects that involve human subjects and that are funded by DOE, conducted in DOE facilities, performed by DOE personnel or involve DOE or contract personnel. The Oak Ridge Institute for Science and Education (ORISE) maintains the Human Subjects Research Database (HSRD) for the Office of

  17. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  18. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris; van de Loo, Frank

    2002-01-01

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  19. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, C.; Loo, F. van de

    1998-09-01

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds. 35 figs.

  20. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris; van de Loo, Frank

    1998-01-01

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  1. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris; van de Loo, Frank

    1997-01-01

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  2. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, C.; Loo, F. van de

    1997-09-16

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds. 35 figs.

  3. International Forest Policy Database | Open Energy Information

    Open Energy Info (EERE)

    Database Jump to: navigation, search Tool Summary LAUNCH TOOL Name: International Forest Policy Database AgencyCompany Organization: GTZ Sector: Land Focus Area: Forestry...

  4. Biomass Feedstock Composition and Property Database () | Data...

    Office of Scientific and Technical Information (OSTI)

    Biomass Feedstock Composition and Property Database Title: Biomass Feedstock Composition and Property Database The Office of Energy Efficiency and Renewable Energy's Biomass ...

  5. IPCC Emission Factor Database | Open Energy Information

    Open Energy Info (EERE)

    Emission Factor Database Jump to: navigation, search Tool Summary LAUNCH TOOL Name: IPCC Emission Factor Database AgencyCompany Organization: World Meteorological Organization,...

  6. National Residential Efficiency Measures Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Software developers who require residential retrofit performance and cost data for applications that evaluate residential efficiency measures are the primary audience for this database. In addition, home performance contractors and manufacturers of residential materials and equipment may find this information useful. The database offers the following types of retrofit measures: 1) Appliances, 2) Domestic Hot Water, 3) Enclosure, 4) Heating, Ventilating, and Air Conditioning (HVAC), 5) Lighting, 6) Miscellaneous.

  7. DOE Global Energy Storage Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DOE International Energy Storage Database has more than 400 documented energy storage projects from 34 countries around the world. The database provides free, up-to-date information on grid-connected energy storage projects and relevant state and federal policies. More than 50 energy storage technologies are represented worldwide, including multiple battery technologies, compressed air energy storage, flywheels, gravel energy storage, hydrogen energy storage, pumped hydroelectric, superconducting magnetic energy storage, and thermal energy storage. The policy section of the database shows 18 federal and state policies addressing grid-connected energy storage, from rules and regulations to tariffs and other financial incentives. It is funded through DOEs Sandia National Laboratories, and has been operating since January 2012.

  8. DOE Global Energy Storage Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DOE International Energy Storage Database has more than 400 documented energy storage projects from 34 countries around the world. The database provides free, up-to-date information on grid-connected energy storage projects and relevant state and federal policies. More than 50 energy storage technologies are represented worldwide, including multiple battery technologies, compressed air energy storage, flywheels, gravel energy storage, hydrogen energy storage, pumped hydroelectric, superconducting magnetic energy storage, and thermal energy storage. The policy section of the database shows 18 federal and state policies addressing grid-connected energy storage, from rules and regulations to tariffs and other financial incentives. It is funded through DOE’s Sandia National Laboratories, and has been operating since January 2012.

  9. WMC Database Evaluation. Case Study Report

    SciTech Connect (OSTI)

    Palounek, Andrea P. T

    2015-10-29

    The WMC Database is ultimately envisioned to hold a collection of experimental data, design information, and information from computational models. This project was a first attempt at using the Database to access experimental data and extract information from it. This evaluation shows that the Database concept is sound and robust, and that the Database, once fully populated, should remain eminently usable for future researchers.

  10. About the Building Performance Database

    Broader source: Energy.gov [DOE]

    Recent technology, market and policy drivers - smart meters, energy performance disclosure laws, etc. - are resulting in a rapid increase in generation of data about buildings and their energy performance. But this data is still hard to access, and analyze because it is being housed in many decentralized and often proprietary databases. The DOE Building Performance Database (BPD) aims to bridge this gap by compiling and cleansing a large dataset required to assess the likely performance of energy efficiency retrofit measures and services. By making the data available anonymously and in aggregate, the BPD enables the public to gain value from the data while addressing the privacy needs of contributors.

  11. Sandia Wind Turbine Loads Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wind Turbine Loads Database - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs

  12. Montana 310 Permit Database | Open Energy Information

    Open Energy Info (EERE)

    0 Permit Database Jump to: navigation, search OpenEI Reference LibraryAdd to library Web Site: Montana 310 Permit Database Abstract Provides access to Montana's 310 permit mapping...

  13. Hydrodynamic Testing Facilities Database | Open Energy Information

    Open Energy Info (EERE)

    Hydrodynamic Testing Facilities Database (Redirected from Hydrodynamic Testing Facilities) Jump to: navigation, search Facility Operators By viewing Hydrodynamic Testing Facilities...

  14. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  15. National Residential Efficiency Measures Database Webinar Slides

    Broader source: Energy.gov [DOE]

    Presentation slides for the Building Technologies Program Webinar on the National Residential Efficiency Measures Database on January 18, 2011.

  16. Multimedia-Modeling Environmental Database Editor

    Energy Science and Technology Software Center (OSTI)

    1996-05-09

    MMEDE is a software tool designed by Battelle, PNL to support the maintenance of an environmental risk computation database.

  17. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOE Patents [OSTI]

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  18. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey. Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  19. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

    DOE Patents [OSTI]

    Chee, Mark; Gingeras, Thomas R.; Fodor, Stephen P. A.; Hubble, Earl A.; Morris, MacDonald S.

    1999-01-19

    The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

  20. Isotopic Studies on Structure-function Relationships of Nucleic Acids and Enzymes. Three Year Progress Report, May 1972 -- October 1975

    DOE R&D Accomplishments [OSTI]

    Boyer, P. D.

    1975-01-01

    The most important accomplishments and major contributions are tabulated with citations to published work. The more important unpublished contributions deal with the early events in ATP formation by chloroplasts, energy linkage in reaction steps of oxidative phosphorylation, molecular integrity of parental DNA, bound pyrophosphate and {sup 18}O-exchanges by inorganic pyrophosphatase, and glutamine synthetase exchanges and mechanisms. These are being prepared for publication. (JSR)

  1. Database specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB)

    SciTech Connect (OSTI)

    Faby, E.Z.; Fluker, J.; Hancock, B.R.; Grubb, J.W.; Russell, D.L.; Loftis, J.P.; Shipe, P.C.; Truett, L.F.

    1994-03-01

    This Database Specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB) describes the database organization and storage allocation, provides the detailed data model of the logical and physical designs, and provides information for the construction of parts of the database such as tables, data elements, and associated dictionaries and diagrams.

  2. Deep Sky Astronomical Image Database Project at NERSC

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Deep Sky Astronomical Image Database Deep Sky Astronomical Image Database Key Challenges: Develop, store, analyze, and make available an astronomical image database of...

  3. EM Soil and Groundwater Database Reports | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EM Soil and Groundwater Database Reports EM Soil and Groundwater Database Reports Brookhaven National Laboratory - HFBR Tritium Groundwater Database Report - Brookhaven National ...

  4. Renewable Energy and Defense Geospatial Database | Open Energy...

    Open Energy Info (EERE)

    Database Jump to: navigation, search OpenEI Reference LibraryAdd to library Web Site: Renewable Energy and Defense Geospatial Database Abstract This database provides GIS data...

  5. Overview of selected molecular biological databases

    SciTech Connect (OSTI)

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  6. PDS: A Performance Database Server

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; Letsche, Todd A.

    1994-01-01

    The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore » benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

  7. Sandia Wind Turbine Loads Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Sandia Wind Turbine Loads Database is divided into six files, each corresponding to approximately 16 years of simulation. The files are text files with data in columnar format. The 424MB zipped file containing six data files can be downloaded by the public. The files simulate 10-minute maximum loads for the NREL 5MW wind turbine. The details of the loads simulations can be found in the paper: Decades of Wind Turbine Loads Simulations, M. Barone, J. Paquette, B. Resor, and L. Manuel, AIAA2012-1288 (3.69MB PDF). Note that the site-average wind speed is 10 m/s (class I-B), not the 8.5 m/s reported in the paper.

  8. Catalog of databases and reports

    SciTech Connect (OSTI)

    Burtis, M.D.

    1997-04-01

    This catalog provides information about the many reports and materials made available by the US Department of Energy`s (DOE`s) Global Change Research Program (GCRP) and the Carbon Dioxide Information Analysis Center (CDIAC). The catalog is divided into nine sections plus the author and title indexes: Section A--US Department of Energy Global Change Research Program Research Plans and Summaries; Section B--US Department of Energy Global Change Research Program Technical Reports; Section C--US Department of Energy Atmospheric Radiation Measurement (ARM) Program Reports; Section D--Other US Department of Energy Reports; Section E--CDIAC Reports; Section F--CDIAC Numeric Data and Computer Model Distribution; Section G--Other Databases Distributed by CDIAC; Section H--US Department of Agriculture Reports on Response of Vegetation to Carbon Dioxide; and Section I--Other Publications.

  9. Sandia Wind Turbine Loads Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Sandia Wind Turbine Loads Database is divided into six files, each corresponding to approximately 16 years of simulation. The files are text files with data in columnar format. The 424MB zipped file containing six data files can be downloaded by the public. The files simulate 10-minute maximum loads for the NREL 5MW wind turbine. The details of the loads simulations can be found in the paper: “Decades of Wind Turbine Loads Simulations”, M. Barone, J. Paquette, B. Resor, and L. Manuel, AIAA2012-1288 (3.69MB PDF). Note that the site-average wind speed is 10 m/s (class I-B), not the 8.5 m/s reported in the paper.

  10. Nuclear Concrete Materials Database Phase I Development

    SciTech Connect (OSTI)

    Ren, Weiju; Naus, Dan J

    2012-05-01

    The FY 2011 accomplishments in Phase I development of the Nuclear Concrete Materials Database to support the Light Water Reactor Sustainability Program are summarized. The database has been developed using the ORNL materials database infrastructure established for the Gen IV Materials Handbook to achieve cost reduction and development efficiency. In this Phase I development, the database has been successfully designed and constructed to manage documents in the Portable Document Format generated from the Structural Materials Handbook that contains nuclear concrete materials data and related information. The completion of the Phase I database has established a solid foundation for Phase II development, in which a digital database will be designed and constructed to manage nuclear concrete materials data in various digitized formats to facilitate electronic and mathematical processing for analysis, modeling, and design applications.

  11. Biological & Environmental Research Abstracts Database

    Office of Scientific and Technical Information (OSTI)

    Welcome to the Biological and Environmental Research Abstracts Database The U.S. Department of Energy's Office of Biological and Environmental Research (BER) conducts research in the areas of Climate and Environmental Sciences and Biological Systems Science. This database contains abstracts of research projects supported by the program. Work was performed at DOE Laboratories as well as at nearly 300 universities and other research institutions. This is a historical database that includes the

  12. NREL: National Residential Efficiency Measures Database - Application

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Developer Tools Application Developer Tools Here you will find tools intended to help software application developers access the data in the National Residential Efficiency Measures Database. This database of retrofit measures and associated costs can be used by software applications that evaluate residential efficiency measures. Read more about the database and information about the cost data. Developer Tools Change log-View a list of changes to the National Residential Efficiency Measures

  13. Technology Transitions Facilities Database | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Technology Transitions Facilities Database Technology Transitions Facilities Database Type* Laboratory Name Facilities DataBase The DOE National Laboratories maintain cutting-edge experimental and computational capabilities that can provide unique opportunities for partners from the commercial sector to develop and test new technologies. The data base below lists DOE facilities and can be searched by the Laboratory at which the facility is located and by the type of R&D facility (TYPE) it

  14. Distributed Generation Operational Reliability and Availability Database,

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Final Report, January 2004 | Department of Energy Reliability and Availability Database, Final Report, January 2004 Distributed Generation Operational Reliability and Availability Database, Final Report, January 2004 This final report documents the results of an 18-month project entitled, "Distributed Generation Market Transformation Tools: Distributed Generation Reliability and Availability Database," sponsored by Oak Ridge National Laboratory (ORNL), Energy Solutions Center

  15. Hydrodynamic Testing Facilities Database | Open Energy Information

    Open Energy Info (EERE)

    Hydrodynamic Testing Facilities Database Jump to: navigation, search Facility Operators By viewing Hydrodynamic Testing Facilities in the list accompanying the map, one will be...

  16. HANFORD NUCLEAR CRITICALITY SAFETY PROGRAM DATABASE

    SciTech Connect (OSTI)

    TOFFER, H.

    2005-05-02

    The Hanford Database is a useful information retrieval tool for a criticality safety practitioner. The database contains nuclear criticality literature screened for parameter studies. The entries, characterized with a value index, are segregated into 16 major and six minor categories. A majority of the screened entries have abstracts and a limited number are connected to the Office of Scientific and Technology Information (OSTI) database of full-size documents. Simple and complex searches of the data can be accomplished very rapidly and the end-product of the searches could be a full-size document. The paper contains a description of the database, user instructions, and a number of examples.

  17. REDD Country Activity Database | Open Energy Information

    Open Energy Info (EERE)

    in multiple languages across a broad range of areas including policies, plans, laws, statistics, activities and financing. The REDD Countries Database does not attempt to assess...

  18. Wyoming Interagency Spatial Database & Online Management | Open...

    Open Energy Info (EERE)

    Western Governors' Association, WY Game and Fish Department, WY Geographic Information Science Center (WyGISC), WY Natural Diversity Database, The Nature Conservancy, WY Department...

  19. Buildings Performance Database Recommended Data Fields | Department...

    Broader source: Energy.gov (indexed) [DOE]

    Buildings Performance Database Recommended Data Fields, from the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy. BPD Priority List.pdf More Documents...

  20. Tank waste remediation systems technical baseline database

    SciTech Connect (OSTI)

    Porter, P.E.

    1996-10-16

    This document includes a cassette tape that contains Hanford generated data for the Tank Waste Remediation Systems Technical Baseline Database as of October 09, 1996.

  1. TWRS technical baseline database manager definition document

    SciTech Connect (OSTI)

    Acree, C.D.

    1997-08-13

    This document serves as a guide for using the TWRS Technical Baseline Database Management Systems Engineering (SE) support tool in performing SE activities for the Tank Waste Remediation System (TWRS). This document will provide a consistent interpretation of the relationships between the TWRS Technical Baseline Database Management software and the present TWRS SE practices. The Database Manager currently utilized is the RDD-1000 System manufactured by the Ascent Logic Corporation. In other documents, the term RDD-1000 may be used interchangeably with TWRS Technical Baseline Database Manager.

  2. Basic energy properties of electrolytic solutions database. ...

    Office of Scientific and Technical Information (OSTI)

    Basic energy properties of electrolytic solutions database. Viscosity, thermal conductivity, density, enthalpy Citation Details In-Document Search Title: Basic energy properties ...

  3. Bechtel Environmental Integrated Database Management System

    Energy Science and Technology Software Center (OSTI)

    1995-04-11

    Bechtel Environmental Integrated Data Management System (BEIDMS1.4) is an Oracle based relational database that stores data related to all aspects of environmental data collection.

  4. National Residential Efficiency Measures Database - Building...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    National Residential Efficiency Measures Database - Building America Top Innovation Image of a man insulating the ceiling of a home. Robust cost data for energy-efficiency measures ...

  5. Global Renewable Energy Database | Open Energy Information

    Open Energy Info (EERE)

    LAUNCH TOOL Name: Global Renewable Energy Database AgencyCompany Organization: German Aerospace Center (DLR) Sector: Energy Focus Area: Renewable Energy, Solar, Wind...

  6. Environment/Health/Safety (EHS): Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and to write evaluation reports) HMS - Hazard Management System Laser Management System Lessons Learned Best Practices REMS - Radiation Exposure Monitoring System SJHA Database...

  7. Lessons Learned Database | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    DOE Corporate Lessons Learned Database provides a central clearinghouse that allows ready access to and communication about collected information on a timely, unimpeded basis by...

  8. Buildings Performance Database Recommended Data Fields

    Broader source: Energy.gov [DOE]

    Buildings Performance Database Recommended Data Fields, from the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy.

  9. Database of State Incentives for Renewables & Efficiency

    Broader source: Energy.gov [DOE]

    The Database of State Incentives for Renewables & Efficiency (DSIRE) is the most comprehensive source of information on incentives and policies that support renewables and energy efficiency in...

  10. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Methods for nucleic acid sequencing, nucleic acid assembly and nucleic acid synthesis are also provided. Full Text Available July 2013 Toxin-eating bacteria and bioremediation ...

  11. Methods and compounds for chemical ligation

    DOE Patents [OSTI]

    Church, George M.; Sismour, A. Michael

    2013-07-09

    Compositions and methods for chemical ligation are provided. Methods for nucleic acid sequencing, nucleic acid assembly and nucleic acid synthesis are also provided.

  12. National Spill Test Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Sheesley, David [Western Research Institute

    Western Research Institute established, and ACRC continues to maintain, the National Spill Technology database to provide support to the Liquified Gaseous Fuels Spill Test Facility (now called the National HAZMAT Spill Center) as directed by Congress in Section 118(n) of the Superfund Amendments and Reauthorization Act of 1986 (SARA). The Albany County Research Corporation (ACRC) was established to make publicly funded data developed from research projects available to benefit public safety. The founders since 1987 have been investigating the behavior of toxic chemicals that are deliberately or accidentally spilled, educating emergency response organizations, and maintaining funding to conduct the research at the DOEs HAZMAT Spill Center (HSC) located on the Nevada Test Site. ACRC also supports DOE in collaborative research and development efforts mandated by Congress in the Clean Air Act Amendments. The data files are results of spill tests conducted at various times by the Silicones Environmental Health and Safety Council (SEHSC) and DOE, ANSUL, Dow Chemical, the Center for Chemical Process Safety (CCPS) and DOE, Lawrence Livermore National Laboratory (LLNL), OSHA, and DOT; DuPont, and the Western Research Institute (WRI), Desert Research Institute (DRI), and EPA. Each test data page contains one executable file for each test in the test series as well as a file named DOC.EXE that contains information documenting the test series. These executable files are actually self-extracting zip files that, when executed, create one or more comma separated value (CSV) text files containing the actual test data or other test information.

  13. National Spill Test Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Sheesley, David [Western Research Institute

    Western Research Institute established, and ACRC continues to maintain, the National Spill Technology database to provide support to the Liquified Gaseous Fuels Spill Test Facility (now called the National HAZMAT Spill Center) as directed by Congress in Section 118(n) of the Superfund Amendments and Reauthorization Act of 1986 (SARA). The Albany County Research Corporation (ACRC) was established to make publicly funded data developed from research projects available to benefit public safety. The founders since 1987 have been investigating the behavior of toxic chemicals that are deliberately or accidentally spilled, educating emergency response organizations, and maintaining funding to conduct the research at the DOEÆs HAZMAT Spill Center (HSC) located on the Nevada Test Site. ACRC also supports DOE in collaborative research and development efforts mandated by Congress in the Clean Air Act Amendments. The data files are results of spill tests conducted at various times by the Silicones Environmental Health and Safety Council (SEHSC) and DOE, ANSUL, Dow Chemical, the Center for Chemical Process Safety (CCPS) and DOE, Lawrence Livermore National Laboratory (LLNL), OSHA, and DOT; DuPont, and the Western Research Institute (WRI), Desert Research Institute (DRI), and EPA. Each test data page contains one executable file for each test in the test series as well as a file named DOC.EXE that contains information documenting the test series. These executable files are actually self-extracting zip files that, when executed, create one or more comma separated value (CSV) text files containing the actual test data or other test information.

  14. TWRS information locator database system design description

    SciTech Connect (OSTI)

    Knutson, B.J.

    1996-09-13

    This document gives an overview and description of the Tank Waste Remediation System (TWRS) Information Locator Database (ILD)system design. The TWRS ILD system is an inventory of information used in the TWRS Systems Engineering process to represent the TWRS Technical Baseline. The inventory is maintained in the form of a relational database developed in Paradox 4.5.

  15. NREL: National Residential Efficiency Measures Database - Help

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Help These resources provide help with using the data: Glossary: Definition of terms in the database Application Developer Tools: View the data dictionary, XML schema, and XML file Guide for Application Developers If these resources don't address your question, please send us any questions or comments you have about the database

  16. Environmental release summary (ERS) database CY 1997

    SciTech Connect (OSTI)

    Gleckler, B.P.

    1998-07-01

    This report discusses the Environmental Release Summary (ERS) database. The current needs of the Effluent and Environmental database is continually modified to fulfill monitoring (EEM) program (managed by Waste Management Federal Services of Hanford, Incorporated, Air and Water Services Organization). Changes are made to accurately calculate current releases, to affect how past releases are calculated. This document serves as a snap-shot of the database and software for the CY-1997 data and releases. This document contains all of the relevant data for calculating radioactive-airborne and liquid effluent. The ERS database is the official repository for the CY-1997 ERS release reports and the settings used to generate those reports. As part of the Tri-Party Agreement, FDH is committed to provide a hard copy of the ERS database for Washington State Department of Ecology, upon request. This document also serves as that hard copy for the last complete calendar year.

  17. Hanford Site technical baseline database. Revision 1

    SciTech Connect (OSTI)

    Porter, P.E.

    1995-01-27

    This report lists the Hanford specific files (Table 1) that make up the Hanford Site Technical Baseline Database. Table 2 includes the delta files that delineate the differences between this revision and revision 0 of the Hanford Site Technical Baseline Database. This information is being managed and maintained on the Hanford RDD-100 System, which uses the capabilities of RDD-100, a systems engineering software system of Ascent Logic Corporation (ALC). This revision of the Hanford Site Technical Baseline Database uses RDD-100 version 3.0.2.2 (see Table 3). Directories reflect those controlled by the Hanford RDD-100 System Administrator. Table 4 provides information regarding the platform. A cassette tape containing the Hanford Site Technical Baseline Database is available.

  18. Geothermal/Geochemical Database | Open Energy Information

    Open Energy Info (EERE)

    to library Chart: GeothermalGeochemical DatabaseInfo GraphicMapChart Author Nevada Bureau of Mines and Geology Published Nevada Bureau of Mines and Geology, 2012 DOI Not...

  19. Database Performance Monitoring for the Photovoltaic Systems

    SciTech Connect (OSTI)

    Klise, Katherine A.

    2015-10-01

    The Database Performance Monitoring (DPM) software (copyright in processes) is being developed at Sandia National Laboratories to perform quality control analysis on time series data. The software loads time indexed databases (currently csv format), performs a series of quality control tests defined by the user, and creates reports which include summary statistics, tables, and graphics. DPM can be setup to run on an automated schedule defined by the user. For example, the software can be run once per day to analyze data collected on the previous day. HTML formatted reports can be sent via email or hosted on a website. To compare performance of several databases, summary statistics and graphics can be gathered in a dashboard view which links to detailed reporting information for each database. The software can be customized for specific applications.

  20. NEPA Database | OpenEI Community

    Open Energy Info (EERE)

    NEPA Database Home > Blogs > Kyoung's blog Kyoung's picture Submitted by Kyoung(150) Contributor 25 February, 2013 - 10:19 data NEPA quarterly meeting We are in the process of...

  1. Session title: Distributed and intelligent databases

    SciTech Connect (OSTI)

    Argos, P.; Mewes, H.W.; Frishman, D.

    1996-12-31

    This session focuses on the recent advances in the delivery of information to the biological community concerning genome sequencing and related information. New approaches include interconnecting existing databases, knowledge-based expert systems, interface languages and multiserver management.

  2. Energy Citations Database (ECD) - Alerts Comments

    Office of Scientific and Technical Information (OSTI)

    Alerts Comments If you have a question about Energy Citations Database Alerts, we recommend you check frequently asked questions. If your question still has not been answered or if...

  3. LM FIMS Database | Department of Energy

    Energy Savers [EERE]

    FIMS Database LM FIMS Database January 8, 2013 - 1:06pm Addthis A road is improved at the Grand Junction, Colorado, Disposal Site. A road is improved at the Grand Junction, Colorado, Disposal Site. A building is demolished at the Weldon Spring, Missouri, Site. A building is demolished at the Weldon Spring, Missouri, Site. An innovative cool roof installation increased energy efficiency at the Fernald Preserve, Ohio, offsite administrative building. An innovative cool roof installation increased

  4. Thermodynamic Database Population Software (DBCreate) - Energy Innovation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Portal Geothermal Geothermal Energy Analysis Energy Analysis Find More Like This Return to Search Thermodynamic Database Population Software (DBCreate) DOE Grant Recipients Contact GRANT About This Technology <span id="Caption"><span id="ctl00_MainContentHolder_zoomimage_defaultCaption">Geochemical modeling relies on accurate and up to date thermodynamic databases.</span></span> Geochemical modeling relies on accurate and up to date thermodynamic

  5. EERE Project Management Center Database PIA, The Office of Energy...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EERE Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) EERE Project Management Center Database PIA, The Office of Energy Efficiency and ...

  6. EERE Success Story-Database Aids Building Owners and Operators...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Database Aids Building Owners and Operators in Energy-Efficiency Project Decision Making EERE Success Story-Database Aids Building Owners and Operators in Energy-Efficiency Project ...

  7. Freedom of Information and Privacy Act Database PIA, Idaho Operations...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Information and Privacy Act Database PIA, Idaho Operations Office Freedom of Information and Privacy Act Database PIA, Idaho Operations Office Freedom of Information and Privacy ...

  8. Standard Energy Efficiency Database Platform - 2013 BTO Peer...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Database Platform - 2013 BTO Peer Review Standard Energy Efficiency Database Platform - 2013 BTO Peer Review PDF icon commlbldgs09prindle040313.pdf More Documents & Publications ...

  9. SERN Policy and Regulation Database | Open Energy Information

    Open Energy Info (EERE)

    SERN Policy and Regulation Database Jump to: navigation, search Tool Summary Name: SERN Policy and Regulation Database AgencyCompany Organization: Renewable Energy and Energy...

  10. Database Aids Building Owners and Operators in Energy-Efficiency...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Database Aids Building Owners and Operators in Energy-Efficiency Project Decision Making Database Aids Building Owners and Operators in Energy-Efficiency Project Decision Making ...

  11. Agriculture, Forestry and Other Land Use Mitigation Project Database...

    Open Energy Info (EERE)

    countries. The database currently holds 497 project entries from 11 different databases, including formal crediting scheme registries and third party compilations."...

  12. The Tariff Analysis Project: A Database and Analysis Platform...

    Open Energy Info (EERE)

    Tariff Analysis Project: A Database and Analysis Platform for Electricity Tariffs Jump to: navigation, search Tool Summary LAUNCH TOOL Name: The Tariff Analysis Project: A Database...

  13. Low Carbon Society (LCS) Database | Open Energy Information

    Open Energy Info (EERE)

    (LCS) Database Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Low Carbon Society (LCS) Database AgencyCompany Organization: LCS-RNet Sector: Energy, Land Focus Area:...

  14. Global Offshore Wind Farms Database | Open Energy Information

    Open Energy Info (EERE)

    Wind Farms Database Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Global Offshore Wind Farms Database Focus Area: Renewable Energy Topics: Deployment Data Website:...

  15. Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wind-Wildlife Impacts Literature Database (WILD) What is WILD? The Wind-Wildlife Impacts Literature Database (WILD), developed and main- tained by the National Wind Technology ...

  16. Extension of the JCZ product species database

    SciTech Connect (OSTI)

    Hobbs, M.L.; Baer, M.R.; McGee, B.C.

    1998-09-01

    A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium states for energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. Product species are characterized by r{sup *}, the radius of the minimum pair potential energy, and {var_epsilon}/{kappa}, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) database describing 750 gases listed in the JANNAF tables and were obtained by using literature values of the Lennard-Jones potential, a corresponding states theory, pure liquid shock Hugoniot data, and fit values to an empirical EOS. Detonation velocities predicted with the JCZS database for a wide variety of explosives are in good agreement with data. Improved predictions of low density explosives is attributed to a better description of molecular interactions at intermediate pressures.

  17. Building America Webinar: National Residential Efficiency Measures Database

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Unveiled | Department of Energy National Residential Efficiency Measures Database Unveiled Building America Webinar: National Residential Efficiency Measures Database Unveiled This webinar presented an overview of this database of residential building retrofit measures and associated estimated costs, and progress to date. File webinar_residential_efficiencydb_20110118.wmv More Documents & Publications National Residential Efficiency Measures Database Webinar Slides Building America

  18. The JANA Calibrations and Conditions Database API

    SciTech Connect (OSTI)

    David Lawrence

    2010-07-01

    Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and the environment relieving developers from implementing such details.

  19. A Noisy 10GB Provenance Database

    SciTech Connect (OSTI)

    Cheah, You-Wei; Plale, Beth; Kendall-Morwick, Joey; Leake, David; Ramakrishnan, Lavanya

    2011-06-06

    Provenance of scientific data is a key piece of the metadata record for the data's ongoing discovery and reuse. Provenance collection systems capture provenance on the fly, however, the protocol between application and provenance tool may not be reliable. Consequently, the provenance record can be partial, partitioned, and simply inaccurate. We use a workflow emulator that models faults to construct a large 10GB database of provenance that we know is noisy (that is, has errors). We discuss the process of generating the provenance database, and show early results on the kinds of provenance analysis enabled by the large provenance.

  20. NREL: National Residential Efficiency Measures Database - About the

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Database About the Database Here you will find more information about the purpose, audience, and uses for the National Residential Efficiency Measures Database. Purpose NREL developed this database on behalf of the U.S. Department of Energy. The purpose of this project is to provide a national unified database of residential building retrofit measures and associated costs. These data are accessible to software programs that evaluate most cost-effective retrofit measures to improve the energy

  1. World Gasification Database Now Available from DOE

    Broader source: Energy.gov [DOE]

    A database just released by the U.S. Department of Energy documents the worldwide growth of gasification, the expected technology of choice for future coal-based plants that produce power, fuels, and/or chemicals with near-zero emissions.

  2. CEBAF Large Acceptance Spectrometer (CLAS) Physics Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    A username and password are required to access and search the entire database. However, the Overview page provides links to detailed data pages for each of the experiments available for public access. There are many experiments with data that the public can freely access.

  3. Diffusion Databases for ICME | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    1 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer Evaluation PDF icon lm036_warren_2011_o.pdf More Documents & Publications Diffusion Databases for Mg-ICME Vehicle Technologies Office: 2010 Lightweight Materials R&D Annual Progress Report Low-Cost Direct Bonded Aluminum (DBA) Substrates

  4. Human retroviruses and AIDS 1994

    SciTech Connect (OSTI)

    Myers, G.; Korber, B.; Wain-Hobson, S.; Jeang, Kuan-Teh; Henderson, L.E.; Pavlakis, G.N.

    1995-01-01

    This compendium, including accompanying floppy diskettes, is the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts it comprises: (I) Nucleic Acid Alignments and Sequences; (II) Amino Acid Alignments; (III) Analysis; (IV) Related Sequences; (V) Database communications.

  5. Lessons Learned From Developing Reactor Pressure Vessel Steel Embrittlement Database

    SciTech Connect (OSTI)

    Wang, Jy-An John

    2010-08-01

    Materials behaviors caused by neutron irradiation under fission and/or fusion environments can be little understood without practical examination. Easily accessible material information system with large material database using effective computers is necessary for design of nuclear materials and analyses or simulations of the phenomena. The developed Embrittlement Data Base (EDB) at ORNL is this comprehensive collection of data. EDB database contains power reactor pressure vessel surveillance data, the material test reactor data, foreign reactor data (through bilateral agreements authorized by NRC), and the fracture toughness data. The lessons learned from building EDB program and the associated database management activity regarding Material Database Design Methodology, Architecture and the Embedded QA Protocol are described in this report. The development of IAEA International Database on Reactor Pressure Vessel Materials (IDRPVM) and the comparison of EDB database and IAEA IDRPVM database are provided in the report. The recommended database QA protocol and database infrastructure are also stated in the report.

  6. Interim report on the meteorological database

    SciTech Connect (OSTI)

    Stage, S.A.; Ramsdell, J.V.; Simonen, C.A.; Burk, K.W.

    1993-01-01

    The Hanford Environmental Dose Reconstruction (HEDR) Project is estimating radiation doses that individuals may have received from operations at Hanford from 1944 to the present. An independent Technical Steering Panel (TSP) directs the project, which is being conducted by the Battelle, Pacific Northwest Laboratories in Richland, Washington. The goals of HEDR, as approved by the TSP, include dose estimates and determination of confidence ranges for these estimates. This letter report describes the current status of the meteorological database. The report defines the meteorological data available for use in climate model calculations, describes the data collection procedures and the preparation and control of the meteorological database. This report also provides an initial assessment of the data quality. The available meteorological data are adequate for atmospheric calculations. Initial checks of the data indicate the data entry accuracy meets the data quality objectives.

  7. Rocky Mountain Basins Produced Water Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Historical records for produced water data were collected from multiple sources, including Amoco, British Petroleum, Anadarko Petroleum Corporation, United States Geological Survey (USGS), Wyoming Oil and Gas Commission (WOGC), Denver Earth Resources Library (DERL), Bill Barrett Corporation, Stone Energy, and other operators. In addition, 86 new samples were collected during the summers of 2003 and 2004 from the following areas: Waltman-Cave Gulch, Pinedale, Tablerock and Wild Rose. Samples were tested for standard seven component "Stiff analyses", and strontium and oxygen isotopes. 16,035 analyses were winnowed to 8028 unique records for 3276 wells after a data screening process was completed. [Copied from the Readme document in the zipped file available at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the Zipped file to your PC. When opened, it will contain four versions of the database: ACCESS, EXCEL, DBF, and CSV formats. The information consists of detailed water analyses from basins in the Rocky Mountain region.

  8. DOE Research and Development Accomplishments Database Browse

    Office of Scientific and Technical Information (OSTI)

    Database Browse Sorted by: Most Recently Added Sort List By: -------------------- Most Recently Added Title Author Publication Date Some links on this page may take you to non-federal websites. Their policies may differ from this site. Website Policies/Important Links U.S. Department of Energy Office of Scientific and Technical Information National Library of Energy BETA science.gov WorldWideScience.org U.S. Deparment of Energy Office of Science

  9. Accelerating semantic graph databases on commodity clusters

    SciTech Connect (OSTI)

    Morari, Alessandro; Castellana, Vito G.; Haglin, David J.; Feo, John T.; Weaver, Jesse R.; Tumeo, Antonino; Villa, Oreste

    2013-10-06

    We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

  10. D3 website database | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    2009 DOE Hydrogen Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. PDF icon vssp_19_keller.pdf More Documents & Publications Advanced Vehicle Benchmarking of HEVs and PHEVs Argonne Facilitation of PHEV Standard Testing Procedure (SAE J1711) AVTA: 2012 Toyota Prius PHEV Downloadable Dynamometer Database Reports

  11. Mining Bug Databases for Unidentified Software Vulnerabilities

    SciTech Connect (OSTI)

    Dumidu Wijayasekara; Milos Manic; Jason Wright; Miles McQueen

    2012-06-01

    Identifying software vulnerabilities is becoming more important as critical and sensitive systems increasingly rely on complex software systems. It has been suggested in previous work that some bugs are only identified as vulnerabilities long after the bug has been made public. These vulnerabilities are known as hidden impact vulnerabilities. This paper discusses the feasibility and necessity to mine common publicly available bug databases for vulnerabilities that are yet to be identified. We present bug database analysis of two well known and frequently used software packages, namely Linux kernel and MySQL. It is shown that for both Linux and MySQL, a significant portion of vulnerabilities that were discovered for the time period from January 2006 to April 2011 were hidden impact vulnerabilities. It is also shown that the percentage of hidden impact vulnerabilities has increased in the last two years, for both software packages. We then propose an improved hidden impact vulnerability identification methodology based on text mining bug databases, and conclude by discussing a few potential problems faced by such a classifier.

  12. Oracle Database DBFS Hierarchical Storage Overview

    SciTech Connect (OSTI)

    Rivenes, A

    2011-07-25

    The National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory creates large numbers of images during each shot cycle for the analysis of optics, target inspection and target diagnostics. These images must be readily accessible once they are created and available for the 30 year lifetime of the facility. The Livermore Computing Center (LC) runs a High Performance Storage System (HPSS) that is capable of storing NIF's estimated 1 petabyte of diagnostic images at a fraction of what it would cost NIF to operate its own automated tape library. With Oracle 11g Release 2 database, it is now possible to create an application transparent, hierarchical storage system using the LC's HPSS. Using the Oracle DBMS-LOB and DBMS-DBFS-HS packages a SecureFile LOB can now be archived to storage outside of the database and accessed seamlessly through a DBFS 'link'. NIF has chosen to use this technology to implement a hierarchical store for its image based SecureFile LOBs. Using a modified external store and DBFS links, files are written to and read from a disk 'staging area' using Oracle's backup utility. Database external procedure calls invoke OS based scripts to manage a staging area and the transfer of the backup files between the staging area and the Lab's HPSS.

  13. FRED+free energy database | OpenEI Community

    Open Energy Info (EERE)

    FRED+free energy database Home Dbrodt's picture Submitted by Dbrodt(77) Contributor 22 June, 2012 - 08:35 Hi FRED Team Welcome to our community area FRED+free energy database I...

  14. DOE Science Showcase - Rare Earth Metal Research from DOE Databases |

    Office of Scientific and Technical Information (OSTI)

    OSTI, US Dept of Energy, Office of Scientific and Technical Information Rare Earth Metal Research from DOE Databases Information Bridge Energy Citations Database Highlighted documents of Rare Earth Metal research in DOE databases Information Bridge - Corrosion-resistant metal surfaces DOE R&D Project Summaries - Structural and magnetic studies on heavy rare earth metals at high pressures using designer diamonds Energy Citations Database - Intermultiplet transitions in rare-earth metals

  15. Webinar: Hydrogen Storage Materials Database Demonstration | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy Database Demonstration Webinar: Hydrogen Storage Materials Database Demonstration Below is the text version of the webinar titled "Hydrogen Storage Database Demonstration," originally presented on December 13, 2011. In addition to this text version of the audio, you can view the presentation slides. Lindsay Southerland: Good morning. My name is Lindsay Southerland and I'm with BCS, Inc. It is my pleasure to welcome you to the Hydrogen Storage Materials Database webinar,

  16. EERE Project Management Center Database PIA, The Office of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Efficiency and Renewable Energy (EERE) | Department of Energy EERE Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) EERE Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) EERE Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) PDF icon EERE Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) More

  17. Freedom of Information and Privacy Act Database PIA, Idaho Operations

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Office | Department of Energy Information and Privacy Act Database PIA, Idaho Operations Office Freedom of Information and Privacy Act Database PIA, Idaho Operations Office Freedom of Information and Privacy Act Database PIA, Idaho Operations Office PDF icon Freedom of Information and Privacy Act Database PIA, Idaho Operations Office More Documents & Publications PIA - Security Clearance Work Tracking and Budget System TRAIN-PIA.pdf Occupational Medicine - Assistant PIA, Idaho National

  18. Frequently Asked Questions About the Building Performance Database |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Commercial Buildings » Analysis Tools » Building Performance Database » Frequently Asked Questions About the Building Performance Database Frequently Asked Questions About the Building Performance Database On this page you will find answers to frequently asked questions pertaining to the DOE Buildings Performance Database (BPD). General What is the purpose of the BPD? What building energy performance data is included in the BPD? Access Information How can I access the

  19. Industrial Assistance and Projects Databases | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Industrial Assistance and Projects Databases Industrial Assistance and Projects Databases AMO's databases provide information on energy assessments and recommendations, results and paybacks, and lessons learned by manufacturers who implement projects to save energy. Also review case studies from manufacturers. Combined Heat and Power (CHP) Project Profiles Database Arrow DOE's CHP Technical Assistance Partnerships (CHP TAPs) have compiled a select number of CHP project profiles. The documents

  20. The BABAR Database: Challenges, Trends and Projections (Technical Report) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect The BABAR Database: Challenges, Trends and Projections Citation Details In-Document Search Title: The BABAR Database: Challenges, Trends and Projections The BABAR database, based upon the Objectivity OO database management system, has been in production since early 1999. It has met its initial design requirements which were to accommodate a 100Hz event rate from the experiment at a scale of 200TB per year. However, with increased luminosity and changes in the physics

  1. The CEBAF Element Database and Related Operational Software

    SciTech Connect (OSTI)

    Larrieu, Theodore; Slominski, Christopher; Keesee, Marie; Turner, Dennison; Joyce, Michele

    2015-09-01

    The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

  2. A database for The Geysers geothermal field

    SciTech Connect (OSTI)

    Bodvarsson, G.S.; Cox, B.L.; Fuller, P.; Ripperda, M.; Tulinius, H.; Witherspoon, P.A.; Goldstein, N.; Flexser, S.; Pruess, K. ); Truesdell, A. )

    1989-09-01

    In Fiscal Year 1985-1986 the Earth Sciences Division of Lawrence Berkeley Laboratory (LBL) began a multi-year project for SLC to organize and analyze the field data from The Geysers. In the first year, most of the work concentrated on the development of a comprehensive database for The Geysers, and conventional reservoir engineering analysis of the data. Essentially, all non-proprietary data for wells at The Geysers have been incorporated into the database, as well as proprietary data from wells located on State leases. In following years, a more detailed analysis of The Geysers data has been carried out. This report is a summary of the non- proprietary work performed in FY 1985--1986. It describes various aspects of the database and also includes: review sections on Field Development, Geology, Geophysics, Geochemistry and Reservoir Engineering. It should be emphasized that these background chapters were written in 1986, and therefore only summarize the information available at that time. The appendices contain individual plots of wellhead pressures, degree of superheat, steam flow rates, cumulative mass flows, injection rates and cumulative injection through 1988 for approximately 250 wells. All of the data contained in this report are non-proprietary, from State and non-State leases. The production/injection and heat flow data from the wells were obtained from the California State Division of Oil and gas (DOG) (courtesy of Dick Thomas). Most of the other data were obtained from SLC files in Sacramento (courtesy of Charles Priddy), or DOG files in Santa Rosa (courtesy of Ken Stelling). 159 refs., 23 figs., 3 tabs.

  3. DOE Research and Development Accomplishments Database Browse

    Office of Scientific and Technical Information (OSTI)

    Database Browse Measurement of the Cosmic Ray and Neutrino-Induced Muon Flux at the Sudbury Neutrino Observatory; SNO collaboration; Aharmim, B.; Ahmed, S. N.; Andersen, T. C.; Anthony, A. E.; Barros, N.; Beier, E. W.; Bellerive, A.; Beltran, B.; Bergevin, M.; Biller, S. D.; Boudjemline, K.; Boulay, M. G.; Burritt, T. H.; Cai, B.; Chan, Y. D.; Chen, M.; Chon, M. C.; Cleveland, B. T.; Cox-Mobrand, G. A.; Currat, C. A.; Dai, X.; Dalnoki-Veress, F.; Deng, H.; Detwiler, J.; Doe, P. J.; Dosanjh, R.

  4. Pre-Validated Signal Database Management System

    Energy Science and Technology Software Center (OSTI)

    1996-12-18

    SPRT/DBMS is a pre-validated experimental database management system for industries where large volumes of process signals are acquired and archived. This system implements a new and powerful pattern recognition method, the spectrum transformed sequential testing (STST or ST2) procedure. A network of interacting ST2 modules deployed in parallel is integrated with a relational DBMS to fully validate process signals as they are archived. This reliable, secure DBMS then provides system modelers, code developers, and safetymore » analysts with an easily accessible source of fully validated process data.« less

  5. DNA sequence similarity recognition by hybridization to short oligomers

    DOE Patents [OSTI]

    Milosavljevic, Aleksandar

    1999-01-01

    Methods are disclosed for the comparison of nucleic acid sequences. Data is generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated is manipulated simultaneously with respect to both (i) matching between oligomers and (ii) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.

  6. MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kaufman, Markus; Pal, Debnath; Eisenberg, David

    Proteins up- and down- regulated in Mycobacterium tuberculosis grown under conditions mimicking infection are included in this database. It also includes information on proteins that are regulated by selected transcription factors or other regulatory proteins. The literature data provided here is complimentary to the databases provided by Michael Strong that include recent TB computational functional linkages and the Prolinks Database by Peter Bowers. The experimental condition, the experimental dataset and a literature reference will be displayed, including links to the computationally linked proteins in the Prolinks Database and the entry in the Mycobacterium tuberculosis Structural Genomics Database.[Copied from information at http://www.doe-mbi.ucla.edu/Services/MTBreg/

  7. Ceramic Technology Project database: September 1990 summary report

    SciTech Connect (OSTI)

    Keyes, B.L.P.

    1992-06-01

    Data generated within the Ceramic Technology Project (CTP) represent a valuable resource for both research and industry. The CTP database was created to provide easy access to this information in electronic and hardcopy forms by using a computerized database and by issuing periodic hardcopy reports on the database contents. This report is the sixth in a series of semiannual database summaries and covers recent additions to the database, including joined brazed specimen test data. It covers 1 SiC, 34 SiN, 10 whisker-reinforced SiN, 2 zirconia-toughened aluminas, 8 zirconias, and 34 joints.

  8. Hydroxycarboxylic acids and salts

    DOE Patents [OSTI]

    Kiely, Donald E; Hash, Kirk R; Kramer-Presta, Kylie; Smith, Tyler N

    2015-02-24

    Compositions which inhibit corrosion and alter the physical properties of concrete (admixtures) are prepared from salt mixtures of hydroxycarboxylic acids, carboxylic acids, and nitric acid. The salt mixtures are prepared by neutralizing acid product mixtures from the oxidation of polyols using nitric acid and oxygen as the oxidizing agents. Nitric acid is removed from the hydroxycarboxylic acids by evaporation and diffusion dialysis.

  9. Dynamic graph system for a semantic database

    DOE Patents [OSTI]

    Mizell, David

    2016-04-12

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  10. Dynamic graph system for a semantic database

    DOE Patents [OSTI]

    Mizell, David

    2015-01-27

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  11. Prokaryotic Genomes from Microbes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways The database contains more than 430 genomes. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  12. Biomass Feedstock Composition and Property Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Office of Energy Efficiency and Renewable Energy's Biomass Program works with industry, academia and national laboratory partners on a balanced portfolio of research in biomass feedstocks and conversion technologies. Through research, development, and demonstration efforts geared at the development of integrated biorefineries, the Biomass Program is helping transform the nation's renewable and abundant biomass resources into cost competitive, high performance biofuels, bioproducts, and biopower.(From the Biomass Program's home page at http://www1.eere.energy.gov/biomass/) The Biomass Feedstock Composition and Property Database allows the user to choose from more than 150 types of biomass samples. The specialized interface then guides the user through choices within the sample (such as "Ash" as a choice in the "Hardwood" sample and displays tables based on choice of composition properties, structure properties, elemental properties, extractive properties, etc.

  13. Los Alamos National Laboratory 4D Database

    SciTech Connect (OSTI)

    Atencio, Julian J.

    2014-05-02

    4D is an integrated development platform - a single product comprised of the components you need to create and distribute professional applications. You get a graphical design environment, SQL database, a programming language, integrated PHP execution, HTTP server, application server, executable generator, and much more. 4D offers multi-platform development and deployment, meaning whatever you create on a Mac can be used on Windows, and vice-versa. Beyond productive development, 4D is renowned for its great flexibility in maintenance and modification of existing applications, and its extreme ease of implementation in its numerous deployment options. Your professional application can be put into production more quickly, at a lower cost, and will always be instantly scalable. 4D makes it easy, whether you're looking to create a classic desktop application, a client-server system, a distributed solution for Web or mobile clients - or all of the above!

  14. Final Report: Efficient Databases for MPC Microdata

    SciTech Connect (OSTI)

    Michael A. Bender; Martin Farach-Colton; Bradley C. Kuszmaul

    2011-08-31

    The purpose of this grant was to develop the theory and practice of high-performance databases for massive streamed datasets. Over the last three years, we have developed fast indexing technology, that is, technology for rapidly ingesting data and storing that data so that it can be efficiently queried and analyzed. During this project we developed the technology so that high-bandwidth data streams can be indexed and queried efficiently. Our technology has been proven to work data sets composed of tens of billions of rows when the data streams arrives at over 40,000 rows per second. We achieved these numbers even on a single disk driven by two cores. Our work comprised (1) new write-optimized data structures with better asymptotic complexity than traditional structures, (2) implementation, and (3) benchmarking. We furthermore developed a prototype of TokuFS, a middleware layer that can handle microdata I/O packaged up in an MPI-IO abstraction.

  15. Los Alamos National Laboratory transuranic database analysis

    SciTech Connect (OSTI)

    Christensen, D.V.; Rogers, P.S.Z.; Kosiewicz, S.T.; LeBrun, D.B.

    1997-02-01

    This paper represents an overview of analyses conducted on the TRU database maintained by the Los Alamos National Laboratory (LANL). This evaluation was conducted to support the ``TRU Waste Workoff Strategies`` document and provides an estimation of the waste volume that potentially could be certified and ready for shipment to (WIPP) in April of 1998. Criteria defined in the WIPP WAC, including container type, weight limits, plutonium fissile gram equivalents and decay heat, were used to evaluated the waste for compliance. LANL evaluated the containers by facility and by waste stream to determining the most efficient plan for characterization and certification of the waste. Evaluation of the waste presently in storage suggested that 40- 60% potentially meets the WIPP WAC Rev. 5 criteria.

  16. NREL: National Residential Efficiency Measures Database Home Page

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Learn more about the database. By accessing the database, the user agrees to the terms and conditions of use. View Data Now

  17. DOE Science Showcase - Neutron Science Research from DOE Databases | OSTI,

    Office of Scientific and Technical Information (OSTI)

    US Dept of Energy, Office of Scientific and Technical Information DOE Science Showcase - Neutron Science Research from DOE Databases Additional neutron science research in DOE Databases Information Bridge Neutron scattering research was pioneered in 1946 by ORNL's Clifford G. Shull, winner of 1994 Nobel Prize in Physics. Access Shull's early research records in Energy Citations Database. Neutron scattering research was pioneered in 1946 by ORNL's Clifford G. Shull, winner of 1994 Nobel Prize

  18. V-036: EMC Smarts Network Configuration Manager Database Authentication

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Bypass Vulnerability | Department of Energy 6: EMC Smarts Network Configuration Manager Database Authentication Bypass Vulnerability V-036: EMC Smarts Network Configuration Manager Database Authentication Bypass Vulnerability November 29, 2012 - 3:30am Addthis PROBLEM: EMC Smarts Network Configuration Manager Database Authentication Bypass Vulnerability PLATFORM: EMC Smarts Network Configuration Manager (NCM) all versions prior 9.1 ABSTRACT: Two vulnerabilities were reported in EMC Smarts

  19. Webinar: What Can We Learn from Hydrogen Safety Event Databases? |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy What Can We Learn from Hydrogen Safety Event Databases? Webinar: What Can We Learn from Hydrogen Safety Event Databases? Above is the webinar recording for the Fuel Cell Technologies Office webinar, "What Can We Learn from Hydrogen Safety Event Databases?" originally held on September 10, 2013. In addition to this recording, you can access the presentation slides. A text version of this recording will be available soon

  20. Fact Sheet: Energy Storage Database (October 2012) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Database (October 2012) Fact Sheet: Energy Storage Database (October 2012) DOE and Sandia National Laboratories are developing a database of energy storage projects and policies that will present current information about energy storage projects worldwide and U.S. energy storage policy in an easy-to-use and intuitive format. Users will be able to search by region, technology, service territory, benefit stream, and other project or policy statistics. For more information about how OE performs

  1. Argonne Geothermal Geochemical Database v2.0

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Harto, Christopher

    2013-05-22

    A database of geochemical data from potential geothermal sources aggregated from multiple sources as of March 2010. The database contains fields for the location, depth, temperature, pH, total dissolved solids concentration, chemical composition, and date of sampling. A separate tab contains data on non-condensible gas compositions. The database contains records for over 50,000 wells, although many entries are incomplete. Current versions of source documentation are listed in the dataset.

  2. National Residential Efficiency Measures Database Guide for Application Developers

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    National Residential Efficiency Measures Database Guide for Application Developers March, 2013 National Renewable Energy Laboratory 15013 Denver West Parkway Golden, CO 80401 i Executive Summary This document provides guidance to users of the National Residential Efficiency Measures Database, sponsored by the U.S. Department of Energy (DOE) Office of Energy Efficiency and Renewable Energy (EERE). The database project is being developed and maintained by the National Renewable Energy Laboratory

  3. Marine and Hydrokinetic (MHK) Databases and Systems Fact Sheet | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy (MHK) Databases and Systems Fact Sheet Marine and Hydrokinetic (MHK) Databases and Systems Fact Sheet The following online information resources are designed to provide the public access to information pertaining to MHK technologies, projects, and research. PDF icon Marine and Hydrokinetic (MHK) Databases and Systems Fact Sheet More Documents & Publications Before the Subcommittee on Water and Power - Senate Committee on Energy and Natural Resourses Categorizing and Evaluating

  4. Argonne Geothermal Geochemical Database v2.0

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Harto, Christopher

    A database of geochemical data from potential geothermal sources aggregated from multiple sources as of March 2010. The database contains fields for the location, depth, temperature, pH, total dissolved solids concentration, chemical composition, and date of sampling. A separate tab contains data on non-condensible gas compositions. The database contains records for over 50,000 wells, although many entries are incomplete. Current versions of source documentation are listed in the dataset.

  5. NREL: Wind-Wildlife Impacts Literature Database (WILD) Home Page

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NREL - National Renewable Energy Laboratory Wind-Wildlife Impacts Literature Database (WILD) Wind Research WILD WILD Browse By Reset All Geography Africa (45) Apply Africa filter...

  6. A Web-Based Nuclear Criticality Safety Bibliographic Database

    SciTech Connect (OSTI)

    Koponen, B L; Huang, S

    2007-02-22

    A bibliographic criticality safety database of over 13,000 records is available on the Internet as part of the U.S. Department of Energy's (DOE) Nuclear Criticality Safety Program (NCSP) website. This database is easy to access via the Internet and gets substantial daily usage. This database and other criticality safety resources are available at ncsp.llnl.gov. The web database has evolved from more than thirty years of effort at Lawrence Livermore National Laboratory (LLNL), beginning with compilations of critical experiment reports and American Nuclear Society Transactions.

  7. Motivate Homeowner Action With Updated DOE Incentives Database...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Motivate Homeowner Action With Updated DOE Incentives Database Is customer motivation a barrier to marketing upgrades in your community? You can find ideas for incentives faster ...

  8. Data Preparation Process for the Buildings Performance Database...

    Broader source: Energy.gov (indexed) [DOE]

    Data Preparation Process for the Buildings Performance Database, from the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy, and Lawrence Berkeley...

  9. Databases | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Databases Nuclear Physics (NP) NP Home About Research Facilities Science Highlights Benefits of NP Funding Opportunities Nuclear Science Advisory Committee (NSAC) Community ...

  10. Federal Transit Administration-National Transit Database (NTD...

    Open Energy Info (EERE)

    Type: Dataset User Interface: Website Website: www.ntdprogram.govntdprogram Cost: Free Language: English Federal Transit Administration-National Transit Database (NTD)...

  11. Greenhouse Gas Initiative Scenario Database | Open Energy Information

    Open Energy Info (EERE)

    TOOL Name: Greenhouse Gas Initiative Scenario Database AgencyCompany Organization: Science for Global Insight Sector: Climate, Energy, Land Topics: Baseline projection, GHG...

  12. Single Particle Database of Natural Ice Crystals: Dimensions

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particle Database of Natural Ice Crystals: Dimensions and Aspect Ratios For original submission and image(s), see ARM Research Highlights http:www.arm.govsciencehighlights...

  13. NREL: U.S. Life Cycle Inventory Database Home Page

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    U.S. Life-Cycle Inventory Database Buildings Research Photo of a green field with an ocean in the background. U.S. Life Cycle Inventory Database NREL and its partners created the U.S. Life Cycle Inventory (LCI) Database to help life cycle assessment (LCA) practitioners answer questions about environmental impact. This database provides individual gate-to-gate, cradle-to-gate and cradle-to-grave accounting of the energy and material flows into and out of the environment that are associated with

  14. The Transparent Cost Database (TCDB) | OpenEI Community

    Open Energy Info (EERE)

    the database that already includes published historical and projected cost estimates for electricity generation, biofuels, and vehicle technologies. To access the TCDB at...

  15. Continuous Reliability Enhancement for Wind (CREW) Database and...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Continuous Reliability Enhancement for Wind (CREW) Database and Analysis Program HomeStationary PowerEnergy Conversion EfficiencyWind EnergyMaterials, Reliability, & Standards...

  16. Database (Report) of U.S. CHP Installations Incorporating Thermal...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Turbine Inlet Cooling (TIC), 2004 Database (Report) of U.S. CHP Installations Incorporating Thermal Energy Storage (TES) andor Turbine Inlet Cooling (TIC), 2004 The primary ...

  17. T-614: Cisco Unified Communications Manager Database Security...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    T-614: Cisco Unified Communications Manager Database Security Vulnerability May 3, 2011 - ... Configuration and Execute Arbitrary Code T-622: Adobe Acrobat and Reader Unspecified ...

  18. Global Bus Rapid Transit (BRT) Database | Open Energy Information

    Open Energy Info (EERE)

    URI: cleanenergysolutions.orgcontentglobal-bus-rapid-transit-brt-database Language: English Related Tools GIZ Sourcebook Module 4e: Intelligent Transport Systems...

  19. IEA-Electricity Access Database | Open Energy Information

    Open Energy Info (EERE)

    - Energy Access Resource Type: Dataset Website: www.iea.orgweoelectricity.asp Language: English IEA-Electricity Access Database Screenshot References: Electricity Access...

  20. Sandia Energy - DOE International Energy Storage Database Has...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    International Energy Storage Database Has Logged 420 Energy Storage Projects Worldwide with 123 GW of Installed Capacity Home Energy Assurance Infrastructure Security Energy Surety...

  1. Heat Flow Database Expansion for NGDS Data Development, Collection...

    Open Energy Info (EERE)

    Database Expansion for NGDS Data Development, Collection and Maintenance Geothermal Project Jump to: navigation, search Last modified on July 22, 2011. Project Title Heat Flow...

  2. V-036: EMC Smarts Network Configuration Manager Database Authenticatio...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    V-036: EMC Smarts Network Configuration Manager Database Authentication Bypass ... Tomcat and JBOSS. Addthis Related Articles V-120: EMC Smarts Network Configuration ...

  3. Category:MHK Instrumentation & Sensor Database | Open Energy...

    Open Energy Info (EERE)

    Community Login | Sign Up Search Category Edit History Category:MHK Instrumentation & Sensor Database Jump to: navigation, search Dictionary.png Looking for the MHK...

  4. Heat Flow Database Expansion for NGDS Data Development, Collection...

    Broader source: Energy.gov (indexed) [DOE]

    Heat Flow Database Expansion for NGDS Data Development, Collection and Maintenance (SMU) presentation at the April 2013 peer review meeting held in Denver, Colorado. PDF icon ...

  5. Data Preparation Process for the Buildings Performance Database

    Broader source: Energy.gov [DOE]

    Data Preparation Process for the Buildings Performance Database, from the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy, and Lawrence Berkeley Laboratory.

  6. CHIANTI-AN ATOMIC DATABASE FOR EMISSION LINES. XII. VERSION 7 OF THE DATABASE

    SciTech Connect (OSTI)

    Landi, E.; Del Zanna, G.; Mason, H. E.; Young, P. R.; Dere, K. P.

    2012-01-10

    The CHIANTI spectral code consists of an atomic database and a suite of computer programs to calculate the optically thin spectrum of astrophysical objects and carry out spectroscopic plasma diagnostics. The database includes atomic energy levels, wavelengths, radiative transition probabilities, collision excitation rate coefficients, and ionization and recombination rate coefficients, as well as data to calculate free-free, free-bound, and two-photon continuum emission. Version 7 has been released, which includes several new ions, significant updates to existing ions, as well as Chianti-Py, the implementation of CHIANTI software in the Python programming language. All data and programs are freely available at http://www.chiantidatabase.org, while the Python interface to CHIANTI can be found at http://chiantipy.sourceforge.net.

  7. TWRS information locator database system administrator`s manual

    SciTech Connect (OSTI)

    Knutson, B.J., Westinghouse Hanford

    1996-09-13

    This document is a guide for use by the Tank Waste Remediation System (TWRS) Information Locator Database (ILD) System Administrator. The TWRS ILD System is an inventory of information used in the TWRS Systems Engineering process to represent the TWRS Technical Baseline. The inventory is maintained in the form of a relational database developed in Paradox 4.5.

  8. Stirling engines. (Latest citations from the Aerospace database). Published

    Office of Scientific and Technical Information (OSTI)

    Search (Technical Report) | SciTech Connect Technical Report: Stirling engines. (Latest citations from the Aerospace database). Published Search Citation Details In-Document Search Title: Stirling engines. (Latest citations from the Aerospace database). Published Search The bibliography contains citations concerning fuel consumption, engine design and testing, computerized simulation, and lubrication systems relative to the Stirling cycle engine. Solar energy conversion research,

  9. Quality Assurance Procedures for ModCat Database Code Files

    SciTech Connect (OSTI)

    Siciliano, Edward R.; Devanathan, Ram; Guillen, Zoe C.; Kouzes, Richard T.; Schweppe, John E.

    2014-04-01

    The Quality Assurance procedures used for the initial phase of the Model Catalog Project were developed to attain two objectives, referred to as basic functionality and visualization. To ensure the Monte Carlo N-Particle model input files posted into the ModCat database meet those goals, all models considered as candidates for the database are tested, revised, and re-tested.

  10. DOE technology information management system database study report

    SciTech Connect (OSTI)

    Widing, M.A.; Blodgett, D.W.; Braun, M.D.; Jusko, M.J.; Keisler, J.M.; Love, R.J.; Robinson, G.L.

    1994-11-01

    To support the missions of the US Department of Energy (DOE) Special Technologies Program, Argonne National Laboratory is defining the requirements for an automated software system that will search electronic databases on technology. This report examines the work done and results to date. Argonne studied existing commercial and government sources of technology databases in five general areas: on-line services, patent database sources, government sources, aerospace technology sources, and general technology sources. First, it conducted a preliminary investigation of these sources to obtain information on the content, cost, frequency of updates, and other aspects of their databases. The Laboratory then performed detailed examinations of at least one source in each area. On this basis, Argonne recommended which databases should be incorporated in DOE`s Technology Information Management System.

  11. A+M Collisional Databases in ALADDIN Format

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    ALADDIN (A Labelled Atomic Data Interface) is a database system developed in order to provide a standard and flexible format and interface for the exchange and management of atomic, molecular and plasma-material interaction data of interest to fusion research. As part of the Atomic and Molecular Data Information System (AMDIS), introduced by the IAEA Atomic and Molecular Data Unit, the ALADDIN interface is available on-line. Twelve databases from DOE and IAEA sources are available from the CFADC website under the heading A+M Collisional Databases.

  12. Webinar: NREL's Fuel Cell Contaminant Database | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    NREL's Fuel Cell Contaminant Database Webinar: NREL's Fuel Cell Contaminant Database Below is the text version of the webinar titled "NREL's Fuel Cell Contaminant Database," originally presented on May 27, 2014. In addition to this text version of the audio, you can access the presentation slides. Alli Aman: I'm just going to go through a few housekeeping items before I turn it over to today's speaker. Today's webinar is being recorded. So a recording along with slides will be posted

  13. A snapshot in time - the new TRUplanner database

    SciTech Connect (OSTI)

    Estill, Wesley Gordon; Crawford, Beverly; Van Soest, Greg

    2010-01-01

    A new database was developed to augment transuranic (TRU) waste inventory information already captured within the Comprehensive Inventory Database (CID). This new database, known as the TRUplanner, includes information focused on site capability for TRU waste certification and availability to ship to either the Waste Isolation Pilot Plant (WIPP) or Idaho National Laboratory for final characterization and certification before coming to WIPP. Waste stream specific data is imported from the CID to the TRUplanner, and additional data is collected and entered as a result of interviews and site visits. This data is continuously updated as sites are visited.

  14. Materials Databases Infrastructure Constructed by First Principles Calculations: A Review

    SciTech Connect (OSTI)

    Lin, Lianshan

    2015-10-13

    The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hot applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.

  15. Creating Large Scale Database Servers (Technical Report) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    To date, over 70TB of data have been placed in ObjectivityDB, making it one of the largest databases in the world. Providing access to such a large quantity of data through a ...

  16. OpenEI Community - FRED+free energy database

    Open Energy Info (EERE)

    p> http:en.openei.orgcommunitydiscussionhi-fred-team-welcome-our-community-areacomments FRED+free energy database FRED Fri, 22 Jun 2012 15:35:00 +0000 Dbrodt 35 at http...

  17. NREL Updates Solar Radiation Database - News Releases | NREL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Solar Radiation Database, a web-based technical report that provides critical information about solar and meteorological data for 1,454 locations in the U.S. and its territories. ...

  18. Data Preparation Process for the Buildings Performance Database

    SciTech Connect (OSTI)

    Walter, Travis; Dunn, Laurel; Mercado, Andrea; Brown, Richard E.; Mathew, Paul

    2014-06-30

    The Buildings Performance Database (BPD) includes empirically measured data from a variety of data sources with varying degrees of data quality and data availability. The purpose of the data preparation process is to maintain data quality within the database and to ensure that all database entries have sufficient data for meaningful analysis and for the database API. Data preparation is a systematic process of mapping data into the Building Energy Data Exchange Specification (BEDES), cleansing data using a set of criteria and rules of thumb, and deriving values such as energy totals and dominant asset types. The data preparation process takes the most amount of effort and time therefore most of the cleansing process has been automated. The process also needs to adapt as more data is contributed to the BPD and as building technologies over time. The data preparation process is an essential step between data contributed by providers and data published to the public in the BPD.

  19. UN-Energy Statistics Database | Open Energy Information

    Open Energy Info (EERE)

    PV, Wind Resource Type: Dataset Website: data.un.orgExplorer.aspx?dEDATA Cost: Free Language: English UN-Energy Statistics Database Screenshot References: UN Data1 "The United...

  20. National Solar Radiation Database 1991-2010 Update: User's Manual

    SciTech Connect (OSTI)

    Wilcox, S. M.

    2012-08-01

    This user's manual provides information on the updated 1991-2010 National Solar Radiation Database. Included are data format descriptions, data sources, production processes, and information about data uncertainty.

  1. National Solar Radiation Database 1991-2005 Update: User's Manual

    SciTech Connect (OSTI)

    Wilcox, S.

    2007-04-01

    This manual describes how to obtain and interpret the data products from the updated 1991-2005 National Solar Radiation Database (NSRDB). This is an update of the original 1961-1990 NSRDB released in 1992.

  2. NREL-LCI Database Project | Open Energy Information

    Open Energy Info (EERE)

    and compare analysis results that are based on similar data collection and analysis methods. NREL-LCI Database Project Screenshot This article is a stub. You can help OpenEI by...

  3. Regional Geology: GIS Database for Alternative Host Rocks and...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    The objective of this work is to develop a spatial database that integrates both geologic data for alternative host-rock formations and information that has been historically used ...

  4. National Residential Efficiency Measures Database Unveiled (text version)

    Broader source: Energy.gov [DOE]

    Below is the text version of the Webinar titled "National Residential Efficiency Measures Database Unveiled," originally presented on January 18, 2011. In addition to this text version of the audio...

  5. Motivate Homeowner Action With Updated DOE Incentives Database

    Broader source: Energy.gov [DOE]

    Is customer motivation a barrier to marketing upgrades in your community? You can find ideas for incentives faster with DOE’s updated Database of State Incentives for Renewables and Efficiency ...

  6. DOE Science Showcase - Carbon Capture research in DOE Databases | OSTI,

    Office of Scientific and Technical Information (OSTI)

    US Dept of Energy, Office of Scientific and Technical Information DOE Science Showcase - Carbon Capture research in DOE Databases Information Bridge : Natural materials for carbon capture. ... Realistic costs of carbon capture ... Technology and international climate policy Energy Citations Database : What Can China Do? China's Best Alternative Outcome for Energy Efficiency and CO2 Emissions ... Effects of warming on the structure and function of a boreal black spruce forest ...

  7. Buildings Performance Database (BPD) - 2014 BTO Peer Review | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy (BPD) - 2014 BTO Peer Review Buildings Performance Database (BPD) - 2014 BTO Peer Review Project Objective The overall goal of the Buildings Performance Database (BPD) is to provide public access to high-quality building characteristics and energy consumption data to incentivize, analyze, and validate energy efficiency investments. The project's objectives for this year are to: (1) significantly increase data acquisition, mapping, and cleansing, including an enhanced process for

  8. Indian Renewable Energy and Energy Efficiency Policy Database (Fact Sheet)

    SciTech Connect (OSTI)

    Bushe, S.

    2013-09-01

    This fact sheet provides an overview of the Indian Renewable Energy and Energy Efficiency Policy Database (IREEED) developed in collaboration by the United States Department of Energy and India's Ministry of New and Renewable Energy. IREEED provides succinct summaries of India's central and state government policies and incentives related to renewable energy and energy efficiency. The online, public database was developed under the U.S.- India Energy Dialogue and the Clean Energy Solution Center.

  9. NREL: National Residential Efficiency Measures Database - Retrofit Measures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Submit Questions/Comments Retrofit Measures This page provides the types for all retrofit measures available in the National Residential Efficiency Measures Database. Select a component type below to see the retrofit measure data. For more information, read about the database, learn about the cost data, and see the glossary. Airflow Air Leakage Mechanical Ventilation Ceilings/Roofs Finished Roof Radiant Barrier Roof Material Unfinished Attic Foundation/Floors Crawlspace Slab Unfinished Basement

  10. Expanding the World's Largest Database of Elastic Properties

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Expanding the World's Largest Database of Elastic Properties Expanding the World's Largest Database of Elastic Properties NERSC, Materials Project Help Scientists Increase Available Data Almost Ten-Fold April 7, 2015 Contact: Julie Chao, jchao@lbl.gov, 510.486.6491 Scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have published the world's largest set of data on the complete elastic properties of inorganic compounds, increasing by an order of

  11. Nuclear Energy Infrastructure Database Fitness and Suitability Review

    SciTech Connect (OSTI)

    Heidrich, Brenden

    2015-03-01

    In 2014, the Deputy Assistant Secretary for Science and Technology Innovation (NE-4) initiated the Nuclear Energy-Infrastructure Management Project by tasking the Nuclear Science User Facilities (NSUF) to create a searchable and interactive database of all pertinent NE supported or related infrastructure. This database will be used for analyses to establish needs, redundancies, efficiencies, distributions, etc. in order to best understand the utility of NE’s infrastructure and inform the content of the infrastructure calls. The NSUF developed the database by utilizing data and policy direction from a wide variety of reports from the Department of Energy, the National Research Council, the International Atomic Energy Agency and various other federal and civilian resources. The NEID contains data on 802 R&D instruments housed in 377 facilities at 84 institutions in the US and abroad. A Database Review Panel (DRP) was formed to review and provide advice on the development, implementation and utilization of the NEID. The panel is comprised of five members with expertise in nuclear energy-associated research. It was intended that they represent the major constituencies associated with nuclear energy research: academia, industry, research reactor, national laboratory, and Department of Energy program management. The Nuclear Energy Infrastructure Database Review Panel concludes that the NSUF has succeeded in creating a capability and infrastructure database that identifies and documents the major nuclear energy research and development capabilities across the DOE complex. The effort to maintain and expand the database will be ongoing. Detailed information on many facilities must be gathered from associated institutions added to complete the database. The data must be validated and kept current to capture facility and instrumentation status as well as to cover new acquisitions and retirements.

  12. The BABAR Database: Challenges, Trends and Projections (Technical Report) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect The BABAR Database: Challenges, Trends and Projections Citation Details In-Document Search Title: The BABAR Database: Challenges, Trends and Projections × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information (OSTI) and is provided as a public service. Visit OSTI to utilize additional information resources in energy science and technology. A paper copy of this

  13. Benefits of an International Database for UF6 Cylinders

    SciTech Connect (OSTI)

    Babcock, R A; Whitaker, J M; Murphy, J; Oakberg, J

    2008-06-30

    A reasonable expectation regarding the nuclear energy renaissance is that the location of fuel cycle nuclear materials throughout the world will be known. We ask--would an international system for uranium hexafluoride (UF{sub 6}) cylinders provide the effective assurances expected for international fuel supply and of the international fuel centers? This paper introduces the question and discusses the potential benefits of tracking UF{sub 6} cylinders through the development of an international database. The nonproliferation benefits of an international database for UF{sub 6} cylinders being used in the fuel cycle include an enhanced capability to reconcile nuclear material imports and exports. Currently, import and export declarations only require the reporting of total 'rolled up' quantities of nuclear materials contained in all items--not the quantities of materials in individual items like individual UF{sub 6} cylinders. The database could provide supplier countries with more assurance on the location of the UF{sub 6} cylinders they export. Additionally, a comprehensive database on all declared cylinders would be a valuable resource in detecting and recognizing undeclared cylinders. The database could potentially be administered by the IAEA and be accessible to authorized countries around the world. During the nuclear renaissance, the general public, as well as the participants will expect transparency and quality information about movement of nuclear fuel cycle nuclear materials. We will discuss the potential benefits of such a database for the suppliers, inspectorates, and general public.

  14. In-Memory Graph Databases for Web-Scale Data

    SciTech Connect (OSTI)

    Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.; Tumeo, Antonino; Haglin, David J.; Villa, Oreste; Feo, John

    2015-03-01

    RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++ compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.

  15. Nuclear Energy Infrastructure Database Description and User’s Manual

    SciTech Connect (OSTI)

    Heidrich, Brenden

    2015-11-01

    In 2014, the Deputy Assistant Secretary for Science and Technology Innovation initiated the Nuclear Energy (NE)–Infrastructure Management Project by tasking the Nuclear Science User Facilities, formerly the Advanced Test Reactor National Scientific User Facility, to create a searchable and interactive database of all pertinent NE-supported and -related infrastructure. This database, known as the Nuclear Energy Infrastructure Database (NEID), is used for analyses to establish needs, redundancies, efficiencies, distributions, etc., to best understand the utility of NE’s infrastructure and inform the content of infrastructure calls. The Nuclear Science User Facilities developed the database by utilizing data and policy direction from a variety of reports from the U.S. Department of Energy, the National Research Council, the International Atomic Energy Agency, and various other federal and civilian resources. The NEID currently contains data on 802 research and development instruments housed in 377 facilities at 84 institutions in the United States and abroad. The effort to maintain and expand the database is ongoing. Detailed information on many facilities must be gathered from associated institutions and added to complete the database. The data must be validated and kept current to capture facility and instrumentation status as well as to cover new acquisitions and retirements. This document provides a short tutorial on the navigation of the NEID web portal at NSUF-Infrastructure.INL.gov.

  16. View discovery in OLAP databases through statistical combinatorial optimization

    SciTech Connect (OSTI)

    Hengartner, Nick W; Burke, John; Critchlow, Terence; Joslyn, Cliff; Hogan, Emilie

    2009-01-01

    OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.

  17. High-Performance Secure Database Access Technologies for HEP Grids

    SciTech Connect (OSTI)

    Matthew Vranicar; John Weicher

    2006-04-17

    The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysis capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist’s computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that "Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications.” There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the secure authorization is pushed into the database engine will eliminate inefficient data transfer bottlenecks. Furthermore, traditionally separated database and security layers provide an extra vulnerability, leaving a weak clear-text password authorization as the only protection on the database core systems. Due to the legacy limitations of the systems’ security models, the allowed passwords often can not even comply with the DOE password guideline requirements. We see an opportunity for the tight integration of the secure authorization layer with the database server engine resulting in both improved performance and improved security. Phase I has focused on the development of a proof-of-concept prototype using Argonne National Laboratory’s (ANL) Argonne Tandem-Linac Accelerator System (ATLAS) project as a test scenario. By developing a grid-security enabled version of the ATLAS project’s current relation database solution, MySQL, PIOCON Technologies aims to offer a more efficient solution to secure database access.

  18. SRTC input to DOE-HQ R and D database for FY99

    SciTech Connect (OSTI)

    Chandler, L.R. Jr.

    2000-01-05

    This is a database of the Savannah River Site input to the DOE Research and Development database. The report contains approximately 50 project abstracts.

  19. UNEP-Risoe CDM/JI Pipeline Analysis and Database | Open Energy...

    Open Energy Info (EERE)

    Risoe CDMJI Pipeline Analysis and Database (Redirected from UNEP Risoe CDMJI Pipeline Analysis and Database) Jump to: navigation, search Tool Summary LAUNCH TOOL Name: UNEP Risoe...

  20. UNEP-Risoe CDM/JI Pipeline Analysis and Database | Open Energy...

    Open Energy Info (EERE)

    UNEP-Risoe CDMJI Pipeline Analysis and Database Jump to: navigation, search Tool Summary LAUNCH TOOL Name: UNEP Risoe CDMJI Pipeline Analysis and Database AgencyCompany...

  1. Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)

    SciTech Connect (OSTI)

    Timothy R. Carr; Scott W. White

    2002-06-01

    This annual report describes progress of the project entitled ''Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)''. This project, funded by the Department of Energy, is a cooperative project that assembles a consortium of five states (Indiana, Illinois, Kansas, Kentucky and Ohio) to construct an online distributed Relational Database Management System (RDBMS) and Geographic Information System (GIS) covering aspects of carbon dioxide geologic sequestration (http://www.midcarb.org). The system links the five states in the consortium into a coordinated regional database system consisting of datasets useful to industry, regulators and the public. The project is working to provide advanced distributed computing solutions to link database servers across the five states into a single system where data is maintained at the local level but is accessed through a single Web portal and can be queried, assembled, analyzed and displayed. Each individual state has strengths in data gathering, data manipulation and data display, including GIS mapping, custom application development, web development, and database design. Sharing of expertise provides the critical mass of technical expertise to improve CO{sub 2} databases and data access in all states. This project improves the flow of data across servers in the five states and increases the amount and quality of available digital data. The MIDCARB project is developing improved online tools to provide real-time display and analyze CO{sub 2} sequestration data. The system links together data from sources, sinks and transportation within a spatial database that can be queried online. Visualization of high quality and current data can assist decision makers by providing access to common sets of high quality data in a consistent manner.

  2. PACIFICA (PACIFic ocean Interior CArbon) Database: A Data Synthesis Resource (NDP-92, ORNL/CDIAC-159)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Suzuki, T.; Ishii, M.; Aoyama, M. R; Christian, J. R.; Enyo, K.; Kawano, T.; Key, R. M.; Kosugi, N.; Kozyr, A.; Miller, L. A.; Murata, A.; Nakano, T.; Ono, T.; Saino, T.; Sasaki, K.; Sasano, D; Takatani, Y.; Wakita, M.; Sabine, C.

    PACIFICA (PACIFic ocean Interior CArbon) was an international collaborative project for synthesis of data on ocean interior carbon and its related parameters in the Pacific Ocean. The North Pacific Marine Science Organization (PICES), Section on Carbon and Climate (S-CC) supported the project. Hydrographic/hydrochemical datasets have been merged from a total of 272 cruises, including those from cruises conducted between the late 1980s and 2000 but not included in GLODAP, as well as CLIVAR/CO2 Repeat Hydrography datasets from the 2000s. Adjustments were calculated to account for analytical offsets in dissolved inorganic carbon, total alkalinity, salinity, oxygen, and nutrients (nitrate and nitrite, phosphate, and silicic acid) for each cruise as a result of the secondary quality control procedure, based on crossover analysis using data from deep layers (Tanhua et al., 2010). A total of 59 adjusted datasets from Line P off the west coast of Canada were also merged. Finally, the authors have produced the adjusted PACIFICA database that consists of datasets from a total of 306 cruises that also includes 34 datasets from WOCE Hydrographic Program cruises in the Pacific Ocean conducted in the 1990s. The PACIFICA database is available free of charge as a numeric data package (NDP-92) from the Carbon Dioxide Information Analysis Center (CDIAC) and the primary PACIFICA data site at pacifica.pices.jp. The NDP consists of the original cruise data files, adjusted data product, and the documentation.

  3. A compute-Efficient Bitmap Compression Index for Database Applications

    Energy Science and Technology Software Center (OSTI)

    2006-01-01

    FastBit: A Compute-Efficient Bitmap Compression Index for Database Applications The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is highly efficient for performing search and retrieval operations on large datasets. The WAH technique is optimized for computational efficiency. The WAH-based bitmap indexing software, called FastBit, is particularly appropriate to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry. Some commercial database products already include some Version of a bitmap index,more » which could possibly be replaced by the WAR bitmap compression techniques for potentially large operational speedup. Experimental results show performance improvements by an average factor of 10 over bitmap technology used by industry, as well as increased efficiencies in constructing compressed bitmaps. FastBit can be use as a stand-alone index, or integrated into a database system. ien integrated into a database system, this technique may be particularly useful for real-time business analysis applications. Additional FastRit applications may include efficient real-time exploration of scientific models, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization. FastBit was proven theoretically to be time-optimal because it provides a search time proportional to the number of elements selected by the index.« less

  4. Pollution Prevention Successes Database (P2SDb) user guide

    SciTech Connect (OSTI)

    1995-07-01

    When Pollution Prevention Opportunity Assessments (P2OAs) were launched at the Hanford Site during the summer of 1994, the first comment received from those using them expressed the desire for a method to report assessments electronically. As a temporary measure, macros were developed for use on word processing systems, but a more formal database was obviously needed. Additionally, increased DOE and Washington state reporting requirements for pollution prevention suggested that a database system would streamline the reporting process. The Pollution Prevention Group of Westinghouse Hanford Company (WHC) contracted with the Data Automation Engineering Department from ICF Kaiser Hanford Company (ICFKH) to develop the system. The scope was to develop a database that will track P2OAs conducted by the facilities and contractors at the Hanford Site. It will also track pollution prevention accomplishments that are not the result of P2OAs and document a portion of the Process Waste Assessments conducted in the past. To accommodate the above criteria, yet complete the system in a timely manner, the Pollution Prevention Successes Database (P2SDb) is being implemented in three phases. The first phase will automate the worksheets to provide both input and output of the data associated with the worksheets. The second phase will automate standard summary reports and ad hoc reports. The third phase will provide automated searching of the database to facilitate the sharing of pollution prevention experiences among various users. This User`s Guide addresses only the Phase 1 system.

  5. Status of the database for solid breeder materials

    SciTech Connect (OSTI)

    1996-12-31

    The databases for solid breeder ceramics (Li{sub 2}O, Li{sub 4}SiO{sub 4}, Li{sub 2}ZrO{sub 3} and LiAl0{sub 2}) and beryllium multiplier material were critically reviewed and evaluated as part of the ITER/CDA design effort (1988-1990). The results have been documented in a detailed technical report which includes progress made in expanding the solid breeder and beryllium databases up through September 1993. Emphasis was placed on the physical, thermal, mechanical, chemical-stability/compatibility, tritium retention/release and radiation stability properties which are needed to assess the performance of these materials in a fusion reactor environment. Materials properties correlations were selected for use in design analysis, and ranges of input parameters (e.g., temperature, porosity, etc.) were established. The need for updating the ceramic breeder database was discussed at the Third Ceramic Breeder Blanket Interactions (CBBI-3) workshop at UCLA in June 1994. Progress made in expanding the ceramic breeder database and plans for updating the database are discussed.

  6. Fatty acid analogs

    DOE Patents [OSTI]

    Elmaleh, David R.; Livni, Eli

    1985-01-01

    In one aspect, a radioactively labeled analog of a fatty acid which is capable of being taken up by mammalian tissue and which exhibits an in vivo beta-oxidation rate below that with a corresponding radioactively labeled fatty acid.

  7. Mixed Acid Oxidation

    SciTech Connect (OSTI)

    Pierce, R.A.

    1999-10-26

    Several non-thermal processes have been developed to destroy organic waste compounds using chemicals with high oxidation potentials. These efforts have focused on developing technologies that work at low temperatures, relative to incineration, to overcome many of the regulatory issues associated with obtaining permits for waste incinerators. One such technique with great flexibility is mixed acid oxidation. Mixed acid oxidation, developed at the Savannah River Site, uses a mixture of an oxidant (nitric acid) and a carrier acid (phosphoric acid). The carrier acid acts as a non-volatile holding medium for the somewhat volatile oxidant. The combination of acids allows appreciable amounts of the concentrated oxidant to remain in the carrier acid well above the oxidant''s normal boiling point.

  8. Plant fatty acid hydroxylases

    DOE Patents [OSTI]

    Somerville, Chris; Broun, Pierre; van de Loo, Frank

    2001-01-01

    This invention relates to plant fatty acyl hydroxylases. Methods to use conserved amino acid or nucleotide sequences to obtain plant fatty acyl hydroxylases are described. Also described is the use of cDNA clones encoding a plant hydroxylase to produce a family of hydroxylated fatty acids in transgenic plants. In addition, the use of genes encoding fatty acid hydroxylases or desaturases to alter the level of lipid fatty acid unsaturation in transgenic plants is described.

  9. PRODUCTION OF TRIFLUOROACETIC ACID

    DOE Patents [OSTI]

    Haworth, W.N.; Stacey, M.

    1949-07-19

    A method is given for the production of improved yields of trifluoroacetic acid. The compound is prepared by oxidizing m-aminobenzotrifluoride with an alkali metal or alkaline earth metal permanganate at a temperature in the range of 80 deg C to 100 deg C while dissolved ln a mixture of water with glacial acetic acid and/or trifluoroacetic acid. Preferably a mixture of water and trifluoroacetic acid ls used as the solvent.

  10. Modular microfluidic system for biological sample preparation...

    Office of Scientific and Technical Information (OSTI)

    module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter. ...

  11. A snapshot in time - the new TRUplanner database - 10400

    SciTech Connect (OSTI)

    Estill, Wes; Crawford, Beverly A; Van Soest, Gregory D

    2009-01-01

    A new database was developed to augment transuranic (TRU) waste inventory information already captured within the Comprehensive Inventory Database (CID). This new database, known as the TRUplanner, includes information focused on site capability for TRU waste certification and availability to ship to either the Waste Isolation Pilot Plant (WIPP) or Idaho National Laboratory for final characterization and certification before coming to WIPP. Waste stream specific data is imported from the CID to the TRUplanner, and additional data is collected and entered as a result of interviews and site visits. This data is continuously updated as sites are visited. TRU waste information such as facility, equipment, and container information for waste streams, has been captured within the TRUplanner, and supports the Department of Energy, Carlsbad Field Office (CBFO) decision making and strategic planning activities. This infonnation is delivered via three built-in TRUplanner reports that are provided to CBFO management, Acceptable Knowledge (AK) Experts and the TRU Waste Inventory Team.

  12. DATATRIEVE used in a control-system database

    SciTech Connect (OSTI)

    Greene, N.E.

    1983-01-01

    Process control of the Proton Storage Ring at Los Alamos will be accomplished by LSI-11/23 computers networked with a VAX-11/750. The database contains descriptions, status, and parameters of the hardware channels and equipment connected to the LSIs. Database entry and processing occur on the VAX, largely through DATATRIEVE user-friendly procedures. Data validity is checked during and after data entry by DATATRIEVE and FORTRAN language procedures. The database then is distilled into a machine-efficient form and distributed to the LSIs and VAX for use by the process-control software. This paper includes an overview of our application, an overview of DATATRIEVE, examples of DATATRIEVE concepts, features of DATATRIEVE that have been especially useful, features of DATATRIEVE that have been troublesome in this project, notes about the conversion from DATATRIEVE-11 to VAX-11 DATATRIEVE, and observations on data-management software in a control-system environment.

  13. RTDB: A memory resident real-time object database

    SciTech Connect (OSTI)

    Jerzy M. Nogiec; Eugene Desavouret

    2003-06-04

    RTDB is a fast, memory-resident object database with built-in support for distribution. It constitutes an attractive alternative for architecting real-time solutions with multiple, possibly distributed, processes or agents sharing data. RTDB offers both direct and navigational access to stored objects, with local and remote random access by object identifiers, and immediate direct access via object indices. The database supports transparent access to objects stored in multiple collaborating dispersed databases and includes a built-in cache mechanism that allows for keeping local copies of remote objects, with specifiable invalidation deadlines. Additional features of RTDB include a trigger mechanism on objects that allows for issuing events or activating handlers when objects are accessed or modified and a very fast, attribute based search/query mechanism. The overall architecture and application of RTDB in a control and monitoring system is presented.

  14. Materials Inventory Database for the Light Water Reactor Sustainability Program

    SciTech Connect (OSTI)

    Kazi Ahmed; Shannon M. Bragg-Sitton

    2013-08-01

    Scientific research involves the purchasing, processing, characterization, and fabrication of many sample materials. The history of such materials can become complicated over their lifetime – materials might be cut into pieces or moved to various storage locations, for example. A database with built-in functions to track these kinds of processes facilitates well-organized research. The Material Inventory Database Accounting System (MIDAS) is an easy-to-use tracking and reference system for such items. The Light Water Reactor Sustainability Program (LWRS), which seeks to advance the long-term reliability and productivity of existing nuclear reactors in the United States through multiple research pathways, proposed MIDAS as an efficient way to organize and track all items used in its research. The database software ensures traceability of all items used in research using built-in functions which can emulate actions on tracked items – fabrication, processing, splitting, and more – by performing operations on the data. MIDAS can recover and display the complete history of any item as a simple report. To ensure the database functions suitably for the organization of research, it was developed alongside a specific experiment to test accident tolerant nuclear fuel cladding under the LWRS Advanced Light Water Reactor Nuclear Fuels Pathway. MIDAS kept track of materials used in this experiment from receipt at the laboratory through all processes, test conduct and, ultimately, post-test analysis. By the end of this process, the database proved to be right tool for this program. The database software will help LWRS more efficiently conduct research experiments, from simple characterization tests to in-reactor experiments. Furthermore, MIDAS is a universal tool that any other research team could use to organize their material inventory.

  15. T-614: Cisco Unified Communications Manager Database Security Vulnerability

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    | Department of Energy 14: Cisco Unified Communications Manager Database Security Vulnerability T-614: Cisco Unified Communications Manager Database Security Vulnerability May 3, 2011 - 7:37am Addthis PROBLEM: Cisco Unified Communications Manager contains a vulnerability that could allow an authenticated, remote attacker to inject arbitrary script code on a targeted system. PLATFORM: Cisco Unified Communications Manager versions prior to 8.5(1), 8.0(3), 7.1(5)su1, and 6.1(5)su2 are

  16. NREL: National Residential Efficiency Measures Database - Data Dictionary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Dictionary This page features the data dictionary for the National Residential Efficiency Measures Database, which supplies users with information about the database organization such as table structure, field names, and data element type and length. tblAction Column name Data type Length Description ActionID int 4 Primary key for actions sName varchar 255 Action name idComponentTypeID int 4 The component type to which this action may be applied (foreign key) idActionTypeID int 4 The action type

  17. NREL: National Residential Efficiency Measures Database - Data Use

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Disclaimer Agreement Before accessing the data from the National Residential Efficiency Measures Database, users must read and accept this agreement ("Agreement"). Database version: v3.0.0. See the Change Log for information about the version. This data and software ("Data") is provided by the National Renewable Energy Laboratory ("NREL"), which is operated by the Alliance for Sustainable Energy, LLC ("ALLIANCE") for the U.S. Department Of Energy

  18. Early Site Permit Demonstration Program: Nuclear Power Plant Siting Database

    Energy Science and Technology Software Center (OSTI)

    1994-01-28

    This database is a repository of comprehensive licensing and technical reviews of siting regulatory processes and acceptance criteria for advanced light water reactor (ALWR) nuclear power plants. The program is designed to be used by applicants for an early site permit or combined construction permit/operating license (10CFRR522, Subparts A and C) as input for the development of the application. The database is a complete, menu-driven, self-contained package that can search and sort the supplied datamore » by topic, keyword, or other input. The software is designed for operation on IBM compatible computers with DOS.« less

  19. Evaluating parallel relational databases for medical data analysis.

    SciTech Connect (OSTI)

    Rintoul, Mark Daniel; Wilson, Andrew T.

    2012-03-01

    Hospitals have always generated and consumed large amounts of data concerning patients, treatment and outcomes. As computers and networks have permeated the hospital environment it has become feasible to collect and organize all of this data. This raises naturally the question of how to deal with the resulting mountain of information. In this report we detail a proof-of-concept test using two commercially available parallel database systems to analyze a set of real, de-identified medical records. We examine database scalability as data sizes increase as well as responsiveness under load from multiple users.

  20. RNAcentral: an international database of ncRNA sequences

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Williams, Kelly Porter

    2014-10-28

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

  1. Process for the preparation of lactic acid and glyceric acid

    DOE Patents [OSTI]

    Jackson, James E [Haslett, MI; Miller, Dennis J [Okemos, MI; Marincean, Simona [Dewitt, MI

    2008-12-02

    Hexose and pentose monosaccharides are degraded to lactic acid and glyceric acid in an aqueous solution in the presence of an excess of a strongly anionic exchange resin, such as AMBERLITE IRN78 and AMBERLITE IRA400. The glyceric acid and lactic acid can be separated from the aqueous solution. Lactic acid and glyceric acid are staple articles of commerce.

  2. Geothermal NEPA Database on OpenEI (Poster)

    SciTech Connect (OSTI)

    Young, K. R.; Levine, A.

    2014-09-01

    The National Renewable Energy Laboratory (NREL) developed the Geothermal National Environmental Policy Act (NEPA) Database as a platform for government agencies and industry to access and maintain information related to geothermal NEPA documents. The data were collected to inform analyses of NEPA timelines, and the collected data were made publically available via this tool in case others might find the data useful. NREL staff and contractors collected documents from agency websites, during visits to the two busiest Bureau of Land Management (BLM) field offices for geothermal development, and through email and phone call requests from other BLM field offices. They then entered the information into the database, hosted by Open Energy Information (http://en.openei.org/wiki/RAPID/NEPA). The long-term success of the project will depend on the willingness of federal agencies, industry, and others to populate the database with NEPA and related documents, and to use the data for their own analyses. As the information and capabilities of the database expand, developers and agencies can save time on new NEPA reports by accessing a single location to research related activities, their potential impacts, and previously proposed and imposed mitigation measures. NREL used a wiki platform to allow industry and agencies to maintain the content in the future so that it continues to provide relevant and accurate information to users.

  3. Ceramic Technology Project database: March 1990 summary report

    SciTech Connect (OSTI)

    Keyes, B.L.P.

    1992-07-01

    This report is the fifth in a series of semiannual data summary reports on information being stored in the Ceramic Technology Project (CTP) database. The overall system status as of March 31, 1990, is summarized, and the latest additions of ceramic mechanical properties data are given for zirconia, silicon carbide, and silicon nitride ceramic mechanical properties data, including some properties on brazed specimens.

  4. Final Report- National Database of Utility Rates and Rate Structure

    Broader source: Energy.gov [DOE]

    One of the key informational barriers for consumers, installers, regulators and policymakers, is the proper comparison cost of utility-supplied electricity that will be replaced with a Photovoltaic (PV) system. Oftentimes, these comparisons are made with national or statewide averages which results in inaccurate comparisons and conclusions. Illinois State University seeks to meet the need for accurate information about electricity costs and rate structure by building a national database of utility rates and rate structures. The database will build upon the excellent framework that was developed by the OpenEI.org initiative and extend it in several important ways. First, the data will be populated and monitored by a team of trained regulatory economists. Second, the database will be more comprehensive because it will be populated with data from newer competitive retail suppliers for states that have restructured their electricity markets to allow such suppliers. Third, the University and its Institute for Regulatory Policy Studies will maintain the database and ensure that it contains the most recent rate information.

  5. Energy science and technology database (on the internet). Online data

    SciTech Connect (OSTI)

    1997-12-01

    The Energy Science and Technology Database (EDB) is a multidisciplinary file containing worldwide references to basic and applied scientific and technical research literature. The information is collected for use by government managers, researchers at the national laboratories, and other research efforts sponsored by the U.S. Department of Energy, and the results of this research are transferred to the public. Abstracts are included for records from 1976 to the present. The EDB also contains the Nuclear Science Abstracts which is a comprehensive abstract and index collection to the international nuclear science and technology literature for the period 1948 through 1976. Included are scientific and technical reports of the U.S. Atomic Energy Commission, U.S. Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Approximately 25% of the records in the file contain abstracts. Nuclear Science Abstracts contains over 900,000 bibliographic records. The entire Energy Science and Technology Database contains over 3 million bibliographic records. This database is now available for searching through the GOV. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.

  6. Building America Top Innovations 2012: National Residential Efficiency Measures Database

    SciTech Connect (OSTI)

    none,

    2013-01-01

    This Building America Top Innovations profile describes the DOE-sponsored National Residential Efficiency Measures Database, which contains performance characteristics and cost estimates for nearly 3,000 energy retrofit measures. To date, it is used in four prominent DOE software packages to help optimize energy-efficiency recommendations.

  7. Evaluation of database technologies for the CTBT Knowledge Base prototype

    SciTech Connect (OSTI)

    Keyser, R.; Shepard-Dombroski, E.; Baur, D.; Hipp, J.; Moore, S.; Young, C.; Chael, E.

    1996-11-01

    This document examines a number of different software technologies in the rapidly changing field of database management systems, evaluates these systems in light of the expected needs of the Comprehensive Test Ban Treaty (CTBT) Knowledge Base, and makes some recommendations for the initial prototypes of the Knowledge Base. The Knowledge Base requirements are examined and then used as criteria for evaluation of the database management options. A mock-up of the data expected in the Knowledge Base is used as a basis for examining how four different database technologies deal with the problems of storing and retrieving the data. Based on these requirement and the results of the evaluation, the recommendation is that the Illustra database be considered for the initial prototype of the Knowledge Base. Illustra offers a unique blend of performance, flexibility, and features that will aid in the implementation of the prototype. At the same time, Illustra provides a high level of compatibility with the hardware and software environments present at the US NDC (National Data Center) and the PIDC (Prototype International Data Center).

  8. Materials Databases Infrastructure Constructed by First Principles Calculations: A Review

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lin, Lianshan

    2015-10-13

    The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hotmore » applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.« less

  9. Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2015-01-01

    The Wind-Wildlife Impacts Literature Database (WILD), developed and maintained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is comprised of over 1,000 citations pertaining to the effects of land-based wind, offshore wind, marine and hydrokinetic, power lines, and communication and television towers on wildlife.

  10. National Residential Efficiency Measures Database- Building America Top Innovation

    Broader source: Energy.gov [DOE]

    This Building America Innovations profile describes the DOE-sponsored National Residential Efficiency Measures Database, which contains performance characteristics and cost estimates for nearly 3,000 energy retrofit measures. To date, it is used in four prominent DOE software packages to help optimize energy-efficiency recommendations.

  11. DOE's Public Database for Green Building Case Studies: Preprint

    SciTech Connect (OSTI)

    Torcellini, P. A.; Crawley, D. B.

    2003-11-01

    To help capture valuable information on''green building'' case studies, the U.S. Department of Energy has created an online database for collecting, standardizing, and disseminating information about high-performance, green projects. Type of information collected includes green features, design processes, energy performance, and comparison to other high-performance, green buildings.

  12. Diffusion Databases for Mg-ICME | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    2 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting PDF icon lm036_kulkarni_2012_o.pdf More Documents & Publications Diffusion Databases for ICME Vehicle Technologies Office: 2010 Lightweight Materials R&D Annual Progress Report Low-Cost Magnesium Sheet Production using the Twin Roll Casting Process and Asymmetric Rolling

  13. Microorganisms for producing organic acids

    DOE Patents [OSTI]

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-09-30

    Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

  14. Recovery of organic acids

    DOE Patents [OSTI]

    Verser, Dan W. (Menlo Park, CA); Eggeman, Timothy J. (Lakewood, CO)

    2011-11-01

    A method is disclosed for the recovery of an organic acid from a dilute salt solution in which the cation of the salt forms an insoluble carbonate salt. A tertiary amine and CO.sub.2 are introduced to the solution to form the insoluble carbonate salt and a complex between the acid and an amine. A water immiscible solvent, such as an alcohol, is added to extract the acid/amine complex from the dilute salt solution to a reaction phase. The reaction phase is continuously dried and a product between the acid and the solvent, such as an ester, is formed.

  15. Reversible Acid Gas Capture

    ScienceCinema (OSTI)

    Dave Heldebrant

    2012-12-31

    Pacific Northwest National Laboratory scientist David Heldebrant demonstrates how a new process called reversible acid gas capture works to pull carbon dioxide out of power plant emissions.

  16. Myriant Succinic Acid Biorefinery

    Broader source: Energy.gov [DOE]

    This American Recovery and Reinvestment Act project will focus on the production of bio-succinic acid from a variety of feedstocks.

  17. Recovery of organic acids

    DOE Patents [OSTI]

    Verser, Dan W. (Golden, CO); Eggeman, Timothy J. (Lakewood, CO)

    2009-10-13

    A method is disclosed for the recovery of an organic acid from a dilute salt solution in which the cation of the salt forms an insoluble carbonate salt. A tertiary amine and CO.sub.2 are introduced to the solution to form the insoluble carbonate salt and a complex between the acid and an amine. A water immiscible solvent, such as an alcohol, is added to extract the acid/amine complex from the dilute salt solution to a reaction phase. The reaction phase is continuously dried and a product between the acid and the solvent, such as an ester, is formed.

  18. Use of CYP52A2A promoter to increase gene expression in yeast

    DOE Patents [OSTI]

    Craft, David L.; Wilson, C. Ron; Eirich, Dudley; Zhang, Yeyan

    2004-01-06

    A nucleic acid sequence including a CYP promoter operably linked to nucleic acid encoding a heterologous protein is provided to increase transcription of the nucleic acid. Expression vectors and host cells containing the nucleic acid sequence are also provided. The methods and compositions described herein are especially useful in the production of polycarboxylic acids by yeast cells.

  19. NGNP Risk Management Database: A Model for Managing Risk

    SciTech Connect (OSTI)

    John Collins

    2009-09-01

    To facilitate the implementation of the Risk Management Plan, the Next Generation Nuclear Plant (NGNP) Project has developed and employed an analytical software tool called the NGNP Risk Management System (RMS). A relational database developed in Microsoft Access, the RMS provides conventional database utility including data maintenance, archiving, configuration control, and query ability. Additionally, the tools design provides a number of unique capabilities specifically designed to facilitate the development and execution of activities outlined in the Risk Management Plan. Specifically, the RMS provides the capability to establish the risk baseline, document and analyze the risk reduction plan, track the current risk reduction status, organize risks by reference configuration system, subsystem, and component (SSC) and Area, and increase the level of NGNP decision making.

  20. NGNP Risk Management Database: A Model for Managing Risk

    SciTech Connect (OSTI)

    John Collins; John M. Beck

    2011-11-01

    The Next Generation Nuclear Plant (NGNP) Risk Management System (RMS) is a database used to maintain the project risk register. The RMS also maps risk reduction activities to specific identified risks. Further functionality of the RMS includes mapping reactor suppliers Design Data Needs (DDNs) to risk reduction tasks and mapping Phenomena Identification Ranking Table (PIRTs) to associated risks. This document outlines the basic instructions on how to use the RMS. This document constitutes Revision 1 of the NGNP Risk Management Database: A Model for Managing Risk. It incorporates the latest enhancements to the RMS. The enhancements include six new custom views of risk data - Impact/Consequence, Tasks by Project Phase, Tasks by Status, Tasks by Project Phase/Status, Tasks by Impact/WBS, and Tasks by Phase/Impact/WBS.