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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Amino acid racemization in amber-entombed insects: implications for DNA preservation

DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from <100 years to 130 million years. The amino acids present in 40 to 130 million year old amber-entombed insects resemble those in a modern fly and are probably the most ancient, unaltered amino acids found so far on Earth. In comparison to other geochemical environments on the surface of the Earth, the amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

NASA Discipline Exobiology↗
NASA NTRS1994

Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

Non-NASA Center↗
NASA NTRS2000

A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation

DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from > 100 Mbp down to < 0.01 Mbp, is modeled using computer simulations and analytic equations. A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. The chromatin model neglects molecular details but systematically incorporates an increase in average spatial separation between two DNA loci as the number of base-pairs between the loci increases. Fragment-size distributions obtained using DNAbreak match data on large fragments about as well as distributions previously obtained with a less mechanistic approach. Dose-response relations, linear at small doses of high linear energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data.

DNA/radiation effects↗
NASA NTRS1999

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

Non-NASA Center↗
NASA NTRS1998

Nerve-responsive troponin I slow promoter does not respond to unloading

We examined the regulation of the troponin I slow (TnIs) promoter during skeletal muscle unloading-induced protein isoform transition, by using a transgenic mouse line harboring the -4,200 to +12 base pairs region of the human TnIs promoter. Eighteen female transgenic mice ( approximately 30 g body mass) were randomly divided into two groups: weight-bearing (WB) controls (n = 9) and hindlimb unloaded (HU; n = 9). The HU mice were tail suspended for 7 days. Body mass was unchanged in the WB group but was reduced (-6%; P < 0.05) after the HU treatment. Absolute soleus muscle mass (-25%) and soleus mass relative to body mass (-16%) were both lower (P < 0.05) in the HU group compared with the WB mice. Northern blot analyses indicate that 7 days of HU result in a 64% decrease (P < 0.05) in the abundance of endogenous TnIs mRNA (microg/mg muscle) in the mouse soleus. Furthermore, there is a trend for the abundance of the fast troponin I mRNA to be increased (+34%). Analysis of transgenic chloramphenicol acetyltransferase activity in the soleus muscle revealed no difference (P > 0.05) between WB and HU groups. We conclude that additional elements are necessary for the TnIs gene to respond to an unloading-induced, slow-to-fast isoform transition stimulus.

Non-NASA Center↗
NASA NTRS1997

Information transfer from peptide nucleic acids to RNA by template-directed syntheses

Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. A PNA C10 oligomer has been shown to act as template for efficient formation of oligoguanylates from activated guanosine ribonucleotides. In a previous paper we used heterosequences of DNA as templates in sequence-dependent polymerization of PNA dimers. In this paper we show that information can be transferred from PNA to RNA. We describe the reactions of activated mononucleotides on heterosequences of PNA. Adenylic, cytidylic and guanylic acids were incorporated into the products opposite their complement on PNA, although less efficiently than on DNA templates.

NASA Discipline Exobiology↗
NASA NTRS1997

Information transfer from DNA to peptide nucleic acids by template-directed syntheses

Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. Oligocytidylates have been shown to act as templates for formation of longer oligomers of G from PNA G2 dimers. In this paper we show that information can be transferred from DNA to PNA. DNA C4T2C4 is an efficient template for synthesis of PNA G4A2G4 using G2 and A2 units as substrates. The corresponding synthesis of PNA G4C2G4 on DNA C4G2C4 is less efficient. Incorporation of PNA T2 into PNA products on DNA C4A2C4 is the least efficient of the three reactions. These results, obtained using PNA dimers as substrates, parallel those obtained using monomeric activated nucleotides.

NASA Discipline Exobiology↗
NASA NTRS1996

Promoter-dependent and -independent activation of insulin-like growth factor binding protein-5 gene expression by prostaglandin E2 in primary rat osteoblasts

Insulin-like growth factor (IGF) action is mediated by high affinity cell surface IGF receptors and modulated by a family of secreted IGF binding proteins (IGFBPs). IGFBP-5, the most conserved of six IGFBPs characterized to date, uniquely potentiates the anabolic actions of IGF-I for skeletal cells. In osteoblasts, IGFBP-5 production is stimulated by prostaglandin E2 (PGE2), a local factor that mediates certain effects induced by parathyroid hormone, cytokines such as interleukin-1 and transforming growth factor-beta, and mechanical strain. In this study, we show that transcriptional and post-transcriptional events initiated by PGE2 collaborate to enhance IGFBP-5 gene expression in primary fetal rat osteoblast cultures. PGE2 treatment stimulated up to a 7-fold rise in steady-state levels of IGFBP-5 mRNA throughout 32 h of incubation. Analysis of nascent IGFBP-5 mRNA suggested that PGE2 had only a modest stimulatory effect on IGFBP-5 gene transcription, and transient transfection studies with IGFBP-5 promoter-reporter genes confirmed that PGE2 enhanced promoter activity by approximately 2-fold. Similar stimulatory effects were seen with forskolin. A DNA fragment with only 51 base pairs of the 5'-flanking sequence retained hormonal responsiveness, which may be mediated by a binding site for transcription factor AP-2 located at positions -44 to -36 in the proximal IGFBP-5 promoter. Incubation of osteoblasts with the mRNA transcriptional inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole demonstrated that PGE2 enhanced IGFBP-5 mRNA stability by 2-fold, increasing the t1/2 from 9 to 18 h. The effects of PGE2 on steady-state IGFBP-5 transcripts were abrogated by preincubating cells with cycloheximide, indicating that the effects of PGE2 on both gene transcription and mRNA stability required ongoing protein synthesis. Therefore, both promoter-dependent and -independent pathways converge to enhance IGFBP-5 gene expression in response to PGE2 in osteoblasts.

Non-NASA Center↗
NASA NTRS1996

Cellular and molecular analysis of mutagenesis induced by charged particles of defined linear energy transfer

Mutation induction by charged particles of defined linear energy transfer (LET) and gamma rays was scored using human-hamster hybrid AL cells. The LET values for charged particles accelerated at the Radiological Research Accelerator Facility ranged from 10 keV/microm protons to 150 keV/microm 4He ions. The induced mutant fractions at both the S1 and HGPRT loci were dependent on the dose and LET. In addition, for each dose examined, the mutant yield at the S1 locus was 30-60 fold higher than at the corresponding HGPRT locus. To determine whether the mutation spectrum was comparably dependent on dose and LET, independent S1- and HGPRT- mutants induced by 150 keV/microm 4He ions and gamma rays were isolated, and their DNA was analyzed by both Southern blotting and multiplex PCR methods. While the majority of radiation-induced mutants showed deletions of varying sizes, the relative percentage of large deletions was found to be related to both the dose and LET of the radiation examined. Using a mutation system that can detect multilocus changes, results of the present study show that radiation-induced chromosomal loss can be in the millions of base pairs.

NASA Discipline Radiation Health↗
NASA NTRS1995

Mutational analysis of photosystem I polypeptides in the cyanobacterium Synechocystis sp. PCC 6803. Targeted inactivation of psaI reveals the function of psaI in the structural organization of psaL

We cloned, characterized, and inactivated the psaI gene encoding a 4-kDa hydrophobic subunit of photosystem I from the cyanobacterium Synechocystis sp. PCC 6803. The psaI gene is located 90 base pairs downstream from psaL, and is transcribed on 0.94- and 0.32-kilobase transcripts. To identify the function of PsaI, we generated a cyanobacterial strain in which psaI has been interrupted by a gene for chloramphenicol resistance. The wild-type and the mutant cells showed comparable rates of photoautotrophic growth at 25 degrees C. However, the mutant cells grew slower and contained less chlorophyll than the wild-type cells, when grown at 40 degrees C. The PsaI-less membranes from cells grown at either temperature showed a small decrease in NADP+ photoreduction rate when compared to the wild-type membranes. Inactivation of psaI led to an 80% decrease in the PsaL level in the photosynthetic membranes and to a complete loss of PsaL in the purified photosystem I preparations, but had little effect on the accumulation of other photosystem I subunits. Upon solubilization with nonionic detergents, photosystem I trimers could be obtained from the wild-type, but not from the PsaI-less membranes. The PsaI-less photosystem I monomers did not contain detectable levels of PsaL. Therefore, a structural interaction between PsaL and PsaI may stabilize the association of PsaL with the photosystem I core. PsaL in the wild-type and PsaI-less membranes showed equal resistance to removal by chaotropic agents. However, PsaL in the PsaI-less strain exhibited an increased susceptibility to proteolysis. From these data, we conclude that PsaI has a crucial role in aiding normal structural organization of PsaL within the photosystem I complex and the absence of PsaI alters PsaL organization, leading to a small, but physiologically significant, defect in photosystem I function.

NASA Discipline Cell Biology↗
NASA NTRS1995

Heavy ion mutagenesis: linear energy transfer effects and genetic linkage

We have characterized a series of 69 independent mutants at the endogenous hprt locus of human TK6 lymphoblasts and over 200 independent S1-deficient mutants of the human x hamster hybrid cell line AL arising spontaneously or following low-fluence exposures to densely ionizing Fe ions (600 MeV/amu, linear energy transfer = 190 keV/microns). We find that large deletions are common. The entire hprt gene (> 44 kb) was missing in 19/39 Fe-induced mutants, while only 2/30 spontaneous mutants lost the entire hprt coding sequence. When the gene of interest (S1 locus = M1C1 gene) is located on a nonessential human chromosome 11, multilocus deletions of several million base pairs are observed frequently. The S1 mutation frequency is more than 50-fold greater than the frequency of hprt mutants in the same cells. Taken together, these results suggest that low-fluence exposures to Fe ions are often cytotoxic due to their ability to create multilocus deletions that may often include the loss of essential genes. In addition, the tumorigenic potential of these HZE heavy ions may be due to the high potential for loss of tumor suppressor genes. The relative insensitivity of the hprt locus to mutation is likely due to tight linkage to a gene that is required for viability.

NASA Discipline Radiation Health↗
NASA NTRS1994

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Non-NASA Center↗
NASA NTRS2000

Trajectory Orientation: A Technology-Enabled Concept Requiring a Shift in Controller Roles and Responsibilities

The development of a decision support tool (DST) for the en-route domain with accurate conflict prediction time horizons of 20 minutes has introduced an interesting problem. A 20 minute time horizon for conflict prediction often results in the predicted conflict occurring one or more sectors downstream from the sector controller who "owns" (i-e., is responsible for the safe separation of aircraft) one or both of the aircraft in the conflict pair. Based on current roles and responsibilities of today's en route controllers, the upstream controller would not resolve this conflict. In most cases, the downstream controller would wait until the conflicting aircraft entered higher sector before resolving the conflict. This results in a delay of several minutes from the time when the conflict was initially predicted. This delay is inefficient from both a controller workload and user's cost of operations perspective. Trajectory orientation, a new concept for facilitating an efficient, conflict-free flight path across several sectors while conforming to metering or miles-in-trail spacing, is proposed as an alternative to today's sector-oriented method. This concept necessitates a fundamental shift in thinking about inter-sector coordination. Instead of operating independently, with the main focus on protecting their internal airspace, controllers would work cooperatively, depending on each other for well-planned, conflict-free flow of aircraft. To support the trajectory orientation concept, a long time horizon (15 to 20 minutes) for conflict prediction and resolution would most likely be a primary requirement. In addition, new tools, such as controller-pilot data link will be identified to determine their necessity and applicability for trajectory orientation. Finally, with significant controller participation from selected Air Route Traffic Control Centers, potential shifts in R-side/D-side roles and responsibilities as well as the creation of a new controller position for multi-sector planning will be examined to determine the most viable solutions.

Leiden, Ken↗
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↗
NASA NTRS2006

A Climatology of Midlatitude Continental Clouds from the ARM SGP Central Facility: Cloud Fraction and Radiative Forcing - Part II

Data collected at the Department of Energy Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) central facility are analyzed for determining the variability of cloud fraction and radiative forcing at several temporal scales between January 1997 and December 2002. Cloud fractions are estimated for total cloud cover and for single-layer low (0-3 km), middle (3-6 km), and high clouds (greater than 6 km) using ARM SGP ground-based paired lidar-radar measurements. Shortwave (SW), longwave (LW), and net cloud radiative forcings (CRF) are derived from up- and down-looking standard precision spectral pyranometers and precision infrared radiometer measurements. The annual averages of total, and single-layer, nonoverlapped low, middle and high cloud fractions are 0.49, 0.11, 0.03, and 0.17, respectively. Total and low cloud amounts were greatest from December through March and least during July and August. The monthly variation of high cloud amount is relatively small with a broad maximum from May to August. During winter, total cloud cover varies diurnally with a small amplitude, mid-morning maximum and early evening minimum, and during summer it changes by more than 0.14 over the daily cycle with a pronounced early evening minimum. The diurnal variations of mean single-layer cloud cover change with season and cloud height. Annual averages of all-sky, total, and single-layer high, middle, and low LW CRFs are 21.4, 40.2, 16.7, 27.2, and 55.0 Wm(sup -2), respectively; and their SW CRFs are -41.5, -77.2, -37.0, -47.0, and -90.5 Wm(sup -2). Their net CRFs range from -20 to -37 Wm(sup -2). For all-sky, total, and low clouds, the maximum negative net CRFs of -40.1, -70, and -69.5 Wm(sup -2), occur during April; while the respective minimum values of -3.9, -5.7, and -4.6 Wm(sup -2), are found during December. July is the month having maximum negative net CRF of -46.2 Wm(sup -2) for middle clouds, and May has the maximum value of -45.9 Wm(sup -2) for high clouds. An uncertainty analysis demonstrates that the calculated CRFs are not significantly affected by the difference between clear-sky and cloudy conditions. A more comprehensive cloud fraction study from both surface and satellite observations will follow.

Dong, Xiquan↗
NASA NTRS2006

A Climatology of Midlatitude Continental Clouds from the ARM SGP Site: Cloud Fraction and Surface Radiative Forcing - Part II

Data collected at the Department of Energy Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) Central Facility (SCF) are analyzed to determine the monthly and hourly variations of cloud fraction and radiative forcing between January 1997 and December 2002. Cloud fractions are estimated for total cloud cover and for single-layered low (0-3 km), middle (3-6 km), and high clouds (more than 6 km) using ARM SCG ground-based paired lidar-radar measurements. Shortwave (SW) and longwave (LW) fluxes are derived from up- and down-looking standard precision spectral pyranometers and precision infrared radiometer measurements with uncertainties of approximately 10 Wm(exp -2). The annual averages of total, and single-layered low, middle and high cloud fractions are 0.49, 0.11, 0.03, and 0.17, respectively. Both total and low cloud amounts peak during January and February and reach a minimum during July and August, high clouds occur more frequently than other types of clouds with a peak in summer. The average annual downwelling surface SW fluxes for total and low clouds (151 and 138 Wm(exp-2), respectively) are less than those under middle and high clouds (188 and 201 Wm(exp -2), respectively), but the downwelling LW fluxes (349 and 356 Wm(exp -2)) underneath total and low clouds are greater than those from middle and high clouds (337 and 333 Wm(exp -2)). Low clouds produce the largest LW warming (55 Wm(exp -2) and SW cooling (-91 Wm(exp -2)) effects with maximum and minimum absolute values in spring and summer, respectively. High clouds have the smallest LW warming (17 Wm(exp -2)) and SW cooling (-37 Wm(exp -2)) effects at the surface. All-sky SW CRF decreases and LW CRF increases with increasing cloud fraction with mean slopes of -0.984 and 0.616 Wm(exp -2)%(exp -1), respectively. Over the entire diurnal cycle, clouds deplete the amount of surface insolation more than they add to the downwelling LW flux. The calculated CRFs do not appear to be significantly affected by uncertainties in data sampling and clear-sky screening. Traditionally, cloud radiative forcing includes, not only the radiative impact of the hydrometeors, but also the changes in the environment. Taken together over the ARM SCF, changes in humidity and surface albedo between clear and cloudy conditions offset approximately 20% of the NET radiative forcing caused by the cloud hydrometeors alone. Variations in water vapor, on average, account for 10% and 83% of the SW and LW CRFs, respectively, in total cloud cover conditions. The error analysis further reveals that the cloud hydrometeors dominate the SW CRF, while water vapor changes are most important for LW flux changes in cloudy skies. Similar studies over other locales are encouraged where water and surface albedo changes from clear to cloudy conditions may be much different than observed over the ARM SCF.

Xi, B.↗
NASA NTRS2007

Automated Identification of Nucleotide Sequences

STITCH is a computer program that processes raw nucleotide-sequence data to automatically remove unwanted vector information, perform reverse-complement comparison, stitch shorter sequences together to make longer ones to which the shorter ones presumably belong, and search against the user s choice of private and Internet-accessible public 16S rRNA databases. ["16S rRNA" denotes a ribosomal ribonucleic acid (rRNA) sequence that is common to all organisms.] In STITCH, a template 16S rRNA sequence is used to position forward and reverse reads. STITCH then automatically searches known 16S rRNA sequences in the user s chosen database(s) to find the sequence most similar to (the sequence that lies at the smallest edit distance from) each spliced sequence. The result of processing by STITCH is the identification of the most similar well-described bacterium. Whereas previously commercially available software for analyzing genetic sequences operates on one sequence at a time, STITCH can manipulate multiple sequences simultaneously to perform the aforementioned operations. A typical analysis of several dozen sequences (length of the order of 103 base pairs) by use of STITCH is completed in a few minutes, whereas such an analysis performed by use of prior software takes hours or days.

Osman, Shariff↗