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  • Computer Programming and Software  (8)
  • Molecular Sequence Data  (4)
  • Mechanical Engineering  (3)
  • 2005-2009  (15)
  • 1
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    The Calyptogena magnifica chemoautotrophic symbiont genome (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-17
    Description: Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newton, I L G -- Woyke, T -- Auchtung, T A -- Dilly, G F -- Dutton, R J -- Fisher, M C -- Fontanez, K M -- Lau, E -- Stewart, F J -- Richardson, P M -- Barry, K W -- Saunders, E -- Detter, J C -- Wu, D -- Eisen, J A -- Cavanaugh, C M -- New York, N.Y. -- Science. 2007 Feb 16;315(5814):998-1000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17303757" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bivalvia/*microbiology ; Carbon/metabolism ; Chemoautotrophic Growth ; Gammaproteobacteria/*genetics/isolation & purification/metabolism/ultrastructure ; *Genome, Bacterial ; Molecular Sequence Data ; Photosynthesis ; *Symbiosis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-16
    Description: Phylogenetic analysis indicates that microbial arsenic metabolism is ancient and probably extends back to the primordial Earth. In microbial biofilms growing on the rock surfaces of anoxic brine pools fed by hot springs containing arsenite and sulfide at high concentrations, we discovered light-dependent oxidation of arsenite [As(III)] to arsenate [As(V)] occurring under anoxic conditions. The communities were composed primarily of Ectothiorhodospira-like purple bacteria or Oscillatoria-like cyanobacteria. A pure culture of a photosynthetic bacterium grew as a photoautotroph when As(III) was used as the sole photosynthetic electron donor. The strain contained genes encoding a putative As(V) reductase but no detectable homologs of the As(III) oxidase genes of aerobic chemolithotrophs, suggesting a reverse functionality for the reductase. Production of As(V) by anoxygenic photosynthesis probably opened niches for primordial Earth's first As(V)-respiring prokaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kulp, T R -- Hoeft, S E -- Asao, M -- Madigan, M T -- Hollibaugh, J T -- Fisher, J C -- Stolz, J F -- Culbertson, C W -- Miller, L G -- Oremland, R S -- New York, N.Y. -- Science. 2008 Aug 15;321(5891):967-70. doi: 10.1126/science.1160799.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Geological Survey (USGS), Menlo Park, CA 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18703741" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Arsenate Reductases/genetics/metabolism ; Arsenates/*metabolism ; Arsenites/*metabolism ; Autotrophic Processes ; Biofilms/*growth & development ; California ; Cyanobacteria/growth & development/isolation & purification/*metabolism ; Ectothiorhodospira/classification/growth & development/isolation & ; purification/*metabolism ; Hot Springs/*microbiology ; Light ; Molecular Sequence Data ; Oxidation-Reduction ; *Photosynthesis ; Sulfides/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Oncogenic CARD11 mutations in human diffuse large B cell lymphoma (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-08
    Description: Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma. In the least curable (ABC) subtype of DLBCL, survival of the malignant cells is dependent on constitutive activation of the nuclear factor-kappaB (NF-kappaB) signaling pathway. In normal B cells, antigen receptor-induced NF-kappaB activation requires CARD11, a cytoplasmic scaffolding protein. To determine whether CARD11 contributes to tumorigenesis, we sequenced the CARD11 gene in human DLBCL tumors. We detected missense mutations in 7 of 73 ABC DLBCL biopsies (9.6%), all within exons encoding the coiled-coil domain. Experimental introduction of CARD11 coiled-coil domain mutants into lymphoma cell lines resulted in constitutive NF-kappaB activation and enhanced NF-kappaB activity upon antigen receptor stimulation. These results demonstrate that CARD11 is a bona fide oncogenein DLBCL, providing a genetic rationale for the development of pharmacological inhibitors of the CARD11 pathway for DLBCL therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lenz, Georg -- Davis, R Eric -- Ngo, Vu N -- Lam, Lloyd -- George, Thaddeus C -- Wright, George W -- Dave, Sandeep S -- Zhao, Hong -- Xu, Weihong -- Rosenwald, Andreas -- Ott, German -- Muller-Hermelink, Hans Konrad -- Gascoyne, Randy D -- Connors, Joseph M -- Rimsza, Lisa M -- Campo, Elias -- Jaffe, Elaine S -- Delabie, Jan -- Smeland, Erlend B -- Fisher, Richard I -- Chan, Wing C -- Staudt, Louis M -- UO1-CA84967/CA/NCI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 21;319(5870):1676-9. doi: 10.1126/science.1153629. Epub 2008 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Metabolism Branch, Division of Cancer Treatment and Diagnosis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323416" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apoptosis Regulatory Proteins/chemistry/*genetics/metabolism ; CARD Signaling Adaptor Proteins/chemistry/*genetics/metabolism ; Cell Line, Tumor ; Cytoplasm/metabolism ; Guanylate Cyclase/chemistry/*genetics/metabolism ; Humans ; I-kappa B Kinase/metabolism ; Jurkat Cells ; Lymphoma, Large B-Cell, Diffuse/*genetics ; Molecular Sequence Data ; *Mutation, Missense ; NF-kappa B ; *Oncogenes ; Protein Structure, Tertiary ; Receptors, Antigen, B-Cell/physiology ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    High-throughput sequencing of the zebrafish antibody repertoire (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-09
    Description: Despite tremendous progress in understanding the nature of the immune system, the full diversity of an organism's antibody repertoire is unknown. We used high-throughput sequencing of the variable domain of the antibody heavy chain from 14 zebrafish to analyze VDJ usage and antibody sequence. Zebrafish were found to use between 50 and 86% of all possible VDJ combinations and shared a similar frequency distribution, with some correlation of VDJ patterns between individuals. Zebrafish antibodies retained a few thousand unique heavy chains that also exhibited a shared frequency distribution. We found evidence of convergence, in which different individuals made the same antibody. This approach provides insight into the breadth of the expressed antibody repertoire and immunological diversity at the level of an individual organism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086368/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086368/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weinstein, Joshua A -- Jiang, Ning -- White, Richard A 3rd -- Fisher, Daniel S -- Quake, Stephen R -- DP1 OD000251/OD/NIH HHS/ -- DP1 OD000251-04/OD/NIH HHS/ -- DP1 OD000251-05/OD/NIH HHS/ -- DP1 OD000251-06/OD/NIH HHS/ -- New York, N.Y. -- Science. 2009 May 8;324(5928):807-10. doi: 10.1126/science.1170020.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19423829" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/genetics ; Antibody Diversity ; Base Sequence ; Complementarity Determining Regions/*genetics ; Computational Biology ; Female ; Gene Library ; *Genes, Immunoglobulin Heavy Chain ; Immunoglobulin Heavy Chains/*genetics ; Immunoglobulin Joining Region/genetics ; Immunoglobulin M/*genetics ; Male ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Analysis, DNA ; VDJ Exons ; Zebrafish/genetics/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Development of a Forced Oscillation System for Measuring Dynamic Derivatives of Fluidic Vehicles (2006)
    In:  CASI
    Details
    Publication Date: 2018-06-11
    Description: A new Forced Oscillation System (FOS) has been designed and built at NASA Langley Research Center that provides new capabilities for aerodynamic researchers to investigate the dynamic derivatives of vehicle configurations. Test vehicles may include high performance and general aviation aircraft, re-entry spacecraft, submarines and other fluidic vehicles. The measured data from forced oscillation testing is used in damping characteristic studies and in simulation databases for control algorithm development and performance analyses. The newly developed FOS hardware provides new flexibility for conducting dynamic derivative studies. The design is based on a tracking principle where a desired motion profile is achieved via a fast closed-loop positional controller. The motion profile for the tracking system is numerically generated and thus not limited to sinusoidal motion. This approach permits non-traditional profiles such as constant velocity and Schroeder sweeps. Also, the new system permits changes in profile parameters including nominal offset angle, waveform, and associated parameters such as amplitude and frequency. Most importantly, the changes may be made remotely without halting the FOS and the tunnel. System requirements, system analysis, and the resulting design are addressed for a new FOS in the 12-Foot Low-Speed Wind Tunnel (LSWT). The overall system including mechanical, electrical, and control subsystems is described. The design is complete, and the FOS has been built and installed in the 12-Foot LSWT. System integration and testing have verified design intent and safe operation. Currently it is being validated for wind-tunnel operations and aerodynamic testing. The system is a potential major enhancement to forced oscillation studies. The productivity gain from the motion profile automation will shorten the testing cycles needed for control surface and aircraft control algorithm development. The new motion capabilities also will serve as a test bed for researchers to study and to improve and/or alter future forced oscillation testing techniques.
    Keywords: Mechanical Engineering
    Type: 38th Aerospace Mechanisms Symposium; 387-399; NASA/CP-2006-214290
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  • 6
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    Solid and Liquid Waste Drying Bag (2009)
    In:  CASI
    Details
    Publication Date: 2019-08-13
    Description: Method and system for processing waste from human activities, including solids, liquids and vapors. A fluid-impermeable bag, lined with a liquid-impermeable but vapor-permeable membrane, defining an inner bag, is provided. A vacuum force is provided to extract vapors so that the waste is moved toward a selected region in the inner bag, extracted vapors, including the waste vapors and vaporized portions of the waste liquids are transported across the membrane, and most or all of the solids remain within the liner. Extracted vapors are filtered, and sanitized components thereof are isolated and optionally stored. The solids remaining within the liner are optionally dried and isolated for ultimate disposal.
    Keywords: Mechanical Engineering
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  • 7
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    ABM Drag_Pass Report Generator (2008)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: dragREPORT software was developed in parallel with abmREPORT, which is described in the preceding article. Both programs were built on the capabilities created during that process. This tool generates a drag_pass report that summarizes vital information from the MRO aerobreaking drag_pass build process to facilitate both sequence reviews and provide a high-level summarization of the sequence for mission management. The script extracts information from the ENV, SSF, FRF, SCMFmax, and OPTG files, presenting them in a single, easy-to-check report providing the majority of parameters needed for cross check and verification as part of the sequence review process. Prior to dragReport, all the needed information was spread across a number of different files, each in a different format. This software is a Perl script that extracts vital summarization information and build-process details from a number of source files into a single, concise report format used to aid the MPST sequence review process and to provide a high-level summarization of the sequence for mission management reference. This software could be adapted for future aerobraking missions to provide similar reports, review and summarization information.
    Keywords: Computer Programming and Software
    Type: NPO-44384 , NASA Tech Briefs, June 2008; 15
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  • 8
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    Aerobraking Maneuver (ABM) Report Generator (2008)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: abmREPORT Version 3.1 is a Perl script that extracts vital summarization information from the Mars Reconnaissance Orbiter (MRO) aerobraking ABM build process. This information facilitates sequence reviews, and provides a high-level summarization of the sequence for mission management. The script extracts information from the ENV, SSF, FRF, SCMFmax, and OPTG files and burn magnitude configuration files and presents them in a single, easy-to-check report that provides the majority of the parameters necessary for cross check and verification during the sequence review process. This means that needed information, formerly spread across a number of different files and each in a different format, is all available in this one application. This program is built on the capabilities developed in dragReport and then the scripts evolved as the two tools continued to be developed in parallel.
    Keywords: Computer Programming and Software
    Type: NPO-44382 , NASA Tech Briefs, June 2008; 15
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  • 9
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    Mars Reconnaissance Orbiter Uplink Analysis Tool (2008)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: This software analyzes Mars Reconnaissance Orbiter (MRO) orbital geometry with respect to Mars Exploration Rover (MER) contact windows, and is the first tool of its kind designed specifically to support MRO-MER interface coordination. Prior to this automated tool, this analysis was done manually with Excel and the UNIX command line. In total, the process would take approximately 30 minutes for each analysis. The current automated analysis takes less than 30 seconds. This tool resides on the flight machine and uses a PHP interface that does the entire analysis of the input files and takes into account one-way light time from another input file. Input flies are copied over to the proper directories and are dynamically read into the tool s interface. The user can then choose the corresponding input files based on the time frame desired for analysis. After submission of the Web form, the tool merges the two files into a single, time-ordered listing of events for both spacecraft. The times are converted to the same reference time (Earth Transmit Time) by reading in a light time file and performing the calculations necessary to shift the time formats. The program also has the ability to vary the size of the keep-out window on the main page of the analysis tool by inputting a custom time for padding each MRO event time. The parameters on the form are read in and passed to the second page for analysis. Everything is fully coded in PHP and can be accessed by anyone with access to the machine via Web page. This uplink tool will continue to be used for the duration of the MER mission's needs for X-band uplinks. Future missions also can use the tools to check overflight times as well as potential site observation times. Adaptation of the input files to the proper format, and the window keep-out times, would allow for other analyses. Any operations task that uses the idea of keep-out windows will have a use for this program.
    Keywords: Computer Programming and Software
    Type: NPO-44222 , NASA Tech Briefs, June 2008; 16
    Format: application/pdf
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  • 10
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    Replacement Sequence of Events Generator (2008)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: The soeWINDOW program automates the generation of an ITAR (International Traffic in Arms Regulations)-compliant sub-RSOE (Replacement Sequence of Events) by extracting a specified temporal window from an RSOE while maintaining page header information. RSOEs contain a significant amount of information that is not ITAR-compliant, yet that foreign partners need to see for command details to their instrument, as well as the surrounding commands that provide context for validation. soeWINDOW can serve as an example of how command support products can be made ITAR-compliant for future missions. This software is a Perl script intended for use in the mission operations UNIX environment. It is designed for use to support the MRO (Mars Reconnaissance Orbiter) instrument team. The tool also provides automated DOM (Distributed Object Manager) storage into the special ITAR-okay DOM collection, and can be used for creating focused RSOEs for product review by any of the MRO teams.
    Keywords: Computer Programming and Software
    Type: NPO-44392 , NASA Tech Briefs, June 2008; 17
    Format: application/pdf
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