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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays

Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

Non-NASA Center↗
NASA NTRS2003

Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro

The human Rad51 protein is essential for DNA repair by homologous recombination. In addition to Rad51 protein, five paralogs have been identified: Rad51B/Rad51L1, Rad51C/Rad51L2, Rad51D/Rad51L3, XRCC2, and XRCC3. To further characterize a subset of these proteins, recombinant Rad51, Rad51B-(His)(6), and Rad51C proteins were individually expressed employing the baculovirus system, and each was purified from Sf9 insect cells. Evidence from nickel-nitrilotriacetic acid pull-down experiments demonstrates a highly stable Rad51B.Rad51C heterodimer, which interacts weakly with Rad51. Rad51B and Rad51C proteins were found to bind single- and double-stranded DNA and to preferentially bind 3'-end-tailed double-stranded DNA. The ability to bind DNA was elevated with mixed Rad51 and Rad51C, as well as with mixed Rad51B and Rad51C, compared with that of the individual protein. In addition, both Rad51B and Rad51C exhibit DNA-stimulated ATPase activity. Rad51C displays an ATP-independent apparent DNA strand exchange activity, whereas Rad51B shows no such activity; this apparent strand exchange ability results actually from a duplex DNA destabilization capability of Rad51C. By analogy to the yeast Rad55 and Rad57, our results suggest that Rad51B and Rad51C function through interactions with the human Rad51 recombinase and play a crucial role in the homologous recombinational repair pathway.

Non-NASA Center↗
NASA NTRS1999

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

Non-NASA Center↗
NASA NTRS1995

Insights to primitive replication derived from structures of small oligonucleotides

Available information on the structure of small oligonucleotides is surveyed. It is observed that even small oligomers typically exhibit defined structures over a wide range of pH and temperature. These structures rely on a plethora of non-standard base-base interactions in addition to the traditional Watson-Crick pairings. Stable duplexes, though typically antiparallel, can be parallel or staggered and perfect complementarity is not essential. These results imply that primitive template directed reactions do not require high fidelity. Hence, the extensive use of Watson-Crick complementarity in genes rather than being a direct consequence of the primitive condensation process, may instead reflect subsequent selection based on the advantage of accuracy in maintaining the primitive genetic machinery once it arose.

Review↗
NASA NTRS1996

Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3'-5' phosphodiester bonds

We have found that nonenzymatic, template-directed ligation reactions of oligoribonucleotides display high selectivity for the formation of 3'-5' rather than 2'-5' phosphodiester bonds. Formation of the 3'-5'-linked product is favored regardless of the metal ion catalyst or the leaving group, and for several different ligation junction sequences. The degree of selectivity depends on the leaving group: the ratio of 3'-5'- to 2'-5'-linked products was 10-15:1 when the 5'-phosphate was activated as the imidazolide, and 60-80:1 when the 5'-phosphate was activated by the formation of a 5'-triphosphate. Comparison of oligonucleotide ligation reactions with previously characterized single nucleotide primer extension reactions suggests that the strong preference for 3'-5'-linkages in oligonucleotide ligation is primarily due to occurence of ligation within the context of an extended Watston-Crick duplex. The ability of RNA to correctly self-assemble by template-directed ligation is an intrinsic consequence of its chemical structure and need not be imposed by an external catalyst (i.e., an enzyme polymerase); RNA therefore provides a reasonable structural basis for a self-replicating system in a prebiological world.

Non-NASA Center↗
NASA NTRS1999

A complex ligase ribozyme evolved in vitro from a group I ribozyme domain

Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.

NASA Discipline Exobiology↗
NASA NTRS1997

Energetics of the lattice: packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice--these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine.cytosine+ (C.C+) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other--for example, when folded in more complicated higher order structures, such as mRNA and chromatin.

Non-NASA Center↗
NASA NTRS1997

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

NASA Discipline Exobiology↗
NASA NTRS2004

Transmission Bearing Damage Detection Using Decision Fusion Analysis

A diagnostic tool was developed for detecting fatigue damage to rolling element bearings in an OH-58 main rotor transmission. Two different monitoring technologies, oil debris analysis and vibration, were integrated using data fusion into a health monitoring system for detecting bearing surface fatigue pitting damage. This integrated system showed improved detection and decision-making capabilities as compared to using individual monitoring technologies. This diagnostic tool was evaluated by collecting vibration and oil debris data from tests performed in the NASA Glenn 500 hp Helicopter Transmission Test Stand. Data was collected during experiments performed in this test rig when two unanticipated bearing failures occurred. Results show that combining the vibration and oil debris measurement technologies improves the detection of pitting damage on spiral bevel gears duplex ball bearings and spiral bevel pinion triplex ball bearings in a main rotor transmission.

Dempsey, Paula J.↗
NASA NTRS1992

Crystal structure of an Okazaki fragment at 2-A resolution

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Non-NASA Center↗
NASA NTRS2005

The Development of Real-Time Physiological Monitoring and Training Software for Remote Applications

Autogenic Feedback Training Exercise (AFTE) is an protocol and technology developed by Dr. Patricia Cowings and her associates at NASA Ames Research Center as a means to facilitate astronaut adaptation to space and exposure to the microgravity. AFTE is a training method which involves teaching subjects to voluntarily control several of their own physiological responses to environmental stressors. As the procedures matured, the training program was expanded to determine if technology developed to facilitate astronaut adaptation to space would be valuable in treating patients suffering from autonomic and vestibular pathologies and symptomatic relief from nausea and/or blood pressure control anomalies such as hypo- or hypertension. The present study, performed in conjunction with Morehouse School of Medicine, Biomedical Engineering at The University of Akron and NASA Ames Research Center has demonstrated that this technology can be successfully applied over vast distances. The specific purpose of this research was to develop a PC based system which could handle processing of twenty channels of acquired physiological data in addition to the necessary duplex communication protocols that would, for example, permit a patient in Atlanta, GA to be trained by a clinician stationed in San Jose, CA. Sixteen channels of physiological data and 20 channels of processed data are included.

Source record↗
NASA NTRS2002

Fail-Safe Operation of a High-Temperature Magnetic Bearing Investigated for Gas Turbine Engine Applications

The Structural Mechanics and Dynamics Branch at the NASA Glenn Research Center has developed a three-axis high-temperature magnetic bearing suspension rig to enhance the safety of the bearing system up to 1000 F. This test rig can accommodate thrust and radial bearings up to a 22.84 cm (9 in.) diameter with a maximum axial loading of 22.25 kN (5000 lb) and a maximum radial loading up to 4.45 kN (1000 lb). The test facility was set up to test magnetic bearings under high-temperature (1100 F) and high-speed (20,000 rpm) conditions. The magnetic bearing is located at the center of gravity of the rotor between two high-temperature grease-packed mechanical ball bearings. The drive-end duplex angular contact ball bearing, which is in full contact, acts as a moment release and provides axial stability. The outboard end ball bearing has a 0.015-in. radial clearance between the rotor to act as a backup bearing and to compensate for axial thermal expansion. There is a 0.020-in. radial air gap between the stator pole and the rotor. The stator was wrapped with three 1-kW band heaters to create a localized hot section; the mechanical ball bearings were outside this section. Eight threaded rods supported the stator. These incorporated a plunger and Bellville washers to compensate for radial thermal expansion and provide rotor-to-stator alignment. The stator was instrumented with thermocouples and a current sensor for each coil. Eight air-cooled position sensors were mounted outside the hot section to monitor the rotor. Another sensor monitored this rotation of the outboard backup bearing. Ground fault circuit interrupts were incorporated into all power amplifier loops for personnel safety. All instrumentation was monitored and recorded on a LabView-based data acquisition system. Currently, this 12-pole heteropolar magnetic bearing has 13 thermal cycles and over 26 hr of operation at 1000 F.

Choi, Benjamin B.↗
NASA NTRS1994

K/Ka-band Antenna for Broadband Aeronautical Mobile Application

The Jet Propulsion Laboratory (JPL) has recently begun the development of a Broadband Aeronauical Terminal (BAT) for duplex video satellite communications on commercial or business class aircraft. The BAT is designed for use with NASA's K/Ka-band Advanced Communications Technology Satellite (ACTS).

Broadband Aeronautica Terminal (BAT) aircraft ante↗
NASA NTRS2005

A low-volume, low-mass, low-power UHF proximity micro-transceiver for Mars Exploration

UHF half-duplex micro-transceiver measuring 1 cubic centimeter, weighing less than 10 grams, and operating at 40 mW on receive and 50mW, 300mW, or 3W on transmit is described. The micro-transceiver is being designed for future Mars exploration missions, but can be adapted for other proximity links. It supports transmission rates up to 256 ksps and higher in BPSK or QPSK format for data return and receives command/control instructions at up to 8 ksps. In addition to its low mass/power features, temperature compensated circuit and system design and radiation tolerance allow operation outside of large shielded enclosures, further reducing the mass and complexity of exploration vehicles.

Silicon-on-Sapphire (SOS)↗
NASA NTRS2004

Relative Sensor with 4Pi Coverage for Formation Flying Missions

The Terrestrial Planet Finder (TPF) pre-project, an element of NASA s Origins program, is currently developing two architectures for a mission to search for earth-like planets around nearby stars. One of the architectures being developed is the Formation Flying Interferometer (FFI). The FFI is envisioned to consist of up to seven spacecraft (as many as six "collectors" with IR telescopes, and a "combiner") flying in precise formation within +/-1 cm of pre-determined trajectories for synchronized observations. The spacecraft-to-spacecraft separations are variable between 20 m and 100 m or more during observations to support various configurations of the interferometer in the planet-finding mode. The challenges involved with TPF autonomous operations, ranging from formation acquisition and formation maneuvering to high precision formation control during science observations, are unprecedented. In this paper we discuss the development of the formation acquisition sensor, which uses novel modulation and duplexing schemes to enable fast signal acquisition, multiple-spacecraft operation, and mitigation of inherent jamming conditions, while providing precise formation sensing and integrated radar capability. This approach performs delay synthesis and carrier cycle ambiguity resolution to improve range measurement, and uses differential carrier cycle ambiguity resolution to make precise bearing angle measurements without calibration maneuvers.

Tien, Jeffrey Y.↗
NASA NTRS2006

Northwest Africa 428: Impact-induced Annealing of an L6 Chondrite Breccia

Northwest Africa (NWA) 428 is an L chondrite that was successively thermally metamorphosed to petrologic type-6, shocked to stage S4-S5, brecciated, and annealed to approximately petrologic type-4. Its thermal and shock history resembles that of the previously studied LL6 chondrite, Miller Range (MIL) 99301, which formed on a different asteroid. The petrologic type-6 classification of NWA 428 is based on its highly recrystallized texture, coarse metal (150 +/- 150 micron), troilite (100 +/- 170 micron), and plagioclase (20-60 micron) grains, and relatively homogeneous olivine (Fa(sub 24.4 +/- 0.6)), low-Ca pyroxene (FS(sub 2.5+/- 0~,4) , and plagioclase (Ab(sub 84.2 +/- 0.4) compositions. The petrographic criteria that indicate shock stage S4-S5 include the presence of chromite veinlets, chromite-plagioclase assemblages, numerous occurrences of metallic Cu, irregular troilite grains within metallic Fe-Ni, polycrystalline troilite, duplex plessite, metal and troilite veins, large troilite nodules, and low-Ca clinopyroxene with polysynthetic twins. If the rock had been shocked before thermal metamorphism, low-Ca clinopyroxene produced by the shock event would have transformed into orthopyroxene. Post-shock brecciation is indicated by the presence of recrystallized clasts and highly shocked clasts that form sharp boundaries with the host. Post-shock annealing is indicated by the sharp optical extinction of the olivine grains; during annealing, the damaged olivine crystal lattices healed. If temperatures exceeded those approximating petrologic type-4 (approximately 600-700 C) during annealing, the low-Ca clinopyroxene would have transformed into orthopyroxene. The other shock indicators, likewise, survived the mild annealing. An impact event is the most plausible source of post-metamorphic, post-shock annealing because any A1-26 that may have been present when the asteroid accreted would have decayed away by the time NWA 428 was annealed. The similar inferred histories of NWA 428 (L6) and MIL 99301 (LL6) indicate that impact heating affected more than 1 ordinary chondrite parent body.

Rubin, Alan E.↗
NASA NTRS2006

Spade: An H Chondrite Impact-melt Breccia that Experienced Post-shock Annealing

The low modal abundances of relict chondrules (1.8 Vol%) and of coarse (i.e. >= 2200 micron-size) isolated mafic silicate grains (1.8 Vol%) in Spade relative to mean H6 chondrites (11.4 and 9.8 vol%, respectively) show Spade to be a rock that has experienced a significant degree of melting. Various petrographic features (e.g., chromite-plagioclase assemblages, chromite veinlets, silicate darkening) indicate that melting was caused by shock. Plagioclase was melted during the shock event and flowed so that it partially to completely surrounded nearby mafic silicate grains. During crystallization, plagioclase developed igneous zoning. Low-Ca pyroxene that crystallized from the melt (or equilibrated with the melt at high temperatures) acquired relatively high amounts of CaO. Metallic Fe-Ni cooled rapidly below the Fe-Ni solws and transformed into martensite. Subsequent reheating of the rock caused transformation of martensite into abundant duplex plessite. Ambiguities exist in the shock stage assignment of Spade. The extensive silicate darkening, the occurrence of chromite-plagioclase assemblages, and the impact-melted characteristics of Spade are consistent with shock stage S6. Low shock (stage S2) is indicated by the undulose extinction and lack of planar fractures in olivine. This suggests that Spade reached a maximum prior shock level equivalent to stage S6 and then experienced post-shock annealing (probably to stage Sl). These events were followed by a less intense impact that produced the undulose extinction in the olivine, characteristic of shock stage S2. Annealing could have occurred if Spade were emplaced near impact melts beneath the crater floor or deposited in close proximity to hot debris within an ejecta blanket. Spade firmly establishes the case for post-shock annealing. This may have been a common process on ordinary chondrites (OC) asteroids.

Rubin, Alan E.↗
NASA NTRS2007

Interactions of the C-terminal Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku(sub 70/80) complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The C-terminal domain of Ku70 (Ku70c, residues 559-609), contains an helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the Ku70c/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the subunit Ku70c and a 14 base pairs DNA duplex, whose starting structures are designed to be variable so as to mimic their different binding modes. By analyzing conformational changes and energetic properties of the complex during MD simulations, we found that interactions are preferred at DNA ends, and within the major groove, which is consistent with previous experimental investigations. In addition, the results indicate that cooperation of Ku70c with other subunits of Ku(sub 70/80) is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗