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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 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

New Modeling Approaches to Study DNA Damage by the Direct and Indirect Effects of Ionizing Radiation

DNA is damaged both by the direct and indirect effects of radiation. In the direct effect, the DNA itself is ionized, whereas the indirect effect involves the radiolysis of the water molecules surrounding the DNA and the subsequent reaction of the DNA with radical products. While this problem has been studied for many years, many unknowns still exist. To study this problem, we have developed the computer code RITRACKS [1], which simulates the radiation track structure for heavy ions and electrons, calculating all energy deposition events and the coordinates of all species produced by the water radiolysis. In this work, we plan to simulate DNA damage by using the crystal structure of a nucleosome and calculations performed by RITRACKS. The energy deposition events are used to calculate the dose deposited in nanovolumes [2] and therefore can be used to simulate the direct effect of the radiation. Using the positions of the radiolytic species with a radiation chemistry code [3] it will be possible to simulate DNA damage by indirect effect. The simulation results can be compared with results from previous calculations such as the frequencies of simple and complex strand breaks [4] and with newer experimental data using surrogate markers of DNA double ]strand breaks such as . ]H2AX foci [5].

Plante, Ianik↗
NASA NTRS2004

Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.

Stolc, Viktor↗
NASA NTRS2005

Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php

Ioana, Cozmuta↗
NASA NTRS2010

Latent Virus Reactivation: From Space to Earth

Reactivation of latent viruses is a recognized consequence of decreased immunity. More recently viral reactivation has been identified as an important in vivo indicator of clinically relevant immune changes. Viral reactivation can be determined quickly and easily by the presence of virus in saliva and other body fluids. Real-time polymerase chain reaction (PCR) is a highly sensitive and specific molecular method to detect the presence of specific viral DNA. Studies in astronauts demonstrated that herpes simplex virus type 1(HSV-1), Epstein-Barr Virus (EBV), cytomegalovirus (CMV), and varicella zoster virus (VZV) reactivate at rates above normal during and after spaceflight in response to moderately decreased T-cell immunity. This technology was expanded to patients on Earth beginning with human immune deficiency virus (HIV) immuno-compromised patients. The HIV patients shed EBV in saliva at rates 9-fold higher than observed in astronauts demonstrating that the level of EBV shedding reflects the severity of impaired immunity. Whereas EBV reactivation is not expected to produce serious effects in astronauts on missions of 6 months or less, VZV reactivation in astronauts could produce shingles. Reactivation of live, infectious VZV in astronauts with no symptoms was demonstrated in astronauts during and after spaceflight. We applied our technology to study VZV-induced shingles in patients. In a study of 54 shingles patients, we showed salivary VZV was present in every patient on the day antiviral (acyclovir) treatment was initiated. Pain and skin lesions decreased with antiviral treatment. Corresponding decreases in levels of VZV were also observed and accompanied recovery. Although the level of VZV in shingles patients before the treatment was generally higher than those found in astronauts, lower range of VZV numbers in shingles patients overlapped with astronaut s levels. This suggests a potential risk of shingles to astronauts resulting from reactivation of VZV. In another clinical study of 25 shingles patients, PCR technology detected VZV in the serum and peripheral blood mononuclear cells of all 25 patients demonstrating for the first time that viremia is a common manifestation of herpes shingles.

Mehta, Satish K.↗
NASA NTRS2002

Photoabsorption Study of Bacillus megaterium, DNA and Related Biological Materials in the Phosphorus K-edge Region

We have measured the x-ray transmission spectra of several biologically related samples in the phosphorus K-edge absorption region. These include elemental red phosphorus, hydrated sodium phosphate (Na3PO4.12H2O), deoxyribonucleic acid (DNA), adenosinetriphosphate (ATP), diolylphosphatidyl choline (DOPC), and Bacillus megaterium spores. Elemental red phosphorus essentially displays an edge-jump. All other spectra are similar in form and energy position. Each spectrum for these substances is dominated by a narrower, more intense first peak and a broader but less intense second peak. The corresponding K-edge absorption thresholds are shifted towards higher energy relative to that for elemental red phosphorus, as expected for increasing degrees of phosphorus oxidation. The B. megaterium spectrum has aspects common to both the phosphate and DNA spectra and is therefore interpreted as a composite of spectra arising from DNA/RNA and phosphates within the spore. The B. megaterium spore spectrum provides needed information for resonant radiation damage studies in the phosphorus K-edge absorption region by identifying candidate photoexcitations. In addition,the absorption spectra will be useful in macromolecular crystallography studies employing anomalous dispersion effects at the phosphorus K-edge.

Frigo, Sean P.↗
NASA NTRS2003

Photoabsorption study of Bacillus megaterium, DNA and Related Biological Materials in the Phosphorus K-edge Region

We have measured the x-ray transmission spectra of several biologically related samples in the phosphorus K-edge absorption region. These include red phosphorus, hydrated sodium phosphate (Na3PO4 12 H2O), deoxyribonucleic acid (DNA), adenosinetriphosphate (ATP), diolylphosphatidyl choline (DOPC), and Bacillus megaterium spores. Red phosphorus essentially displays an edge-jump. All other spectra are similar in form and energy position, where each is dominated by a narrower, more intense first peak and a broader but less intense second peak. The corresponding K-edge absorption thresholds are shifted towards higher energy relative to that for red phosphorus, as expected for increasing degrees of phosphorus oxidation. The B.meguterium spectrum has aspects common to both the phosphate and DNA spectra and is therefore interpreted as a composite of spectra arising from DNA/RNA and phosphates within the spore. The B. megaterium spore spectrum provides needed information for resonant radiation damage studies in the phosphorus K-edge absorption region by identifying candidate photoexcitations. In addition, the absorption spectra will be useful in macromolecular crystallography studies employing anomalous dispersion effects at the phosphorus K-edge.

Frigo, Sean P.↗
NASA NTRS1999

A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

Oligodeoxyribonucleotides/chemistry/metabolism↗
NASA NTRS2014

A Radiation Chemistry Code Based on the Green's Function of the Diffusion Equation

Stochastic radiation track structure codes are of great interest for space radiation studies and hadron therapy in medicine. These codes are used for a many purposes, notably for microdosimetry and DNA damage studies. In the last two decades, they were also used with the Independent Reaction Times (IRT) method in the simulation of chemical reactions, to calculate the yield of various radiolytic species produced during the radiolysis of water and in chemical dosimeters. Recently, we have developed a Green's function based code to simulate reversible chemical reactions with an intermediate state, which yielded results in excellent agreement with those obtained by using the IRT method. This code was also used to simulate and the interaction of particles with membrane receptors. We are in the process of including this program for use with the Monte‐Carlo track structure code Relativistic Ion Tracks (RITRACKS). This recent addition should greatly expand the capabilities of RITRACKS, notably to simulate DNA damage by both the direct and indirect effect.

Plante, Ianik↗
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 NTRS2007

Interactions of the SAP 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 Ku70/80 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 SAP domain of Ku70 (residues 556-609), contains an a 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 SAP/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the SAP domain of Ku70 and a 10 base pairs DNA duplex. Large-scale conformational changes were observed and some putative binding modes were suggested based on energetic analysis. These modes are consistent with previous experimental investigations. In addition, the results indicate that cooperation of SAP with other domains of Ku70/80 is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗
NASA NTRS2002

Analysis of unrejoined chromosomal breakage in human fibroblast cells exposed to low- and high-LET radiation

Reported studies of DNA breakage induced by radiation of various qualities have generally shown a higher fraction of unrejoined residual breaks after high-LET exposure. This observation is supported by the argument that high-LET radiation induced DNA breaks that are more complex in nature and, thus, less likely to be repaired. In most cases the doses used in these studies were very high. We have studied unrejoined chromosome breaks by analyzing chromosome aberrations using a fluorescence in situ hybridization (FISH) technique with a combination of whole chromosome specific probes and probes specific for the telomere region of the chromosomes. Confluent human fibroblast cells (AG1522) were irradiated with gamma rays, 490 MeV/nucleon Si, or with Fe ions at either 200 and 500 MeV/nucleon, and were allowed to repair at 37 degrees C for 24 hours after exposure. A chemically induced premature chromosome condensation (PCC) technique was used to condense chromosomes in the G2 phase of the cell cycle. Results showed that the frequency of unrejoined chromosome breaks was higher after high-LET radiation, and the ratio of unrejoined to misrejoined chromosome breaks increased steadily with LET up a peak value at 440 keV/microm.

NASA Discipline Radiation Health↗
NASA NTRS2008

Novel Species of Non-Spore-Forming Bacteria

While cataloging cultivatable microbes from the airborne biological diversity of the atmosphere of the Regenerative Enclosed life-support Module Simulator (REMS) system at Marshall Space Flight Center, two strains that belong to one novel bacterial species were isolated. Based on 16S rRNA gene sequencing and the unique morphology and the taxonomic characteristics of these strains, it is shown that they belong to the family Intrasporangiaceae, related to the genus Tetrasphaera, with phylogenetic distances from any validly described species of the genus Tetrasphaera ranging from 96.71 to 97.76 percent. The fatty acid profile supported the affiliation of these novel strains to the genus Tetrasphaera except for the presence of higher concentrations of octadecenoic acid (C18:0) and cis-9-octadecenoic acid (C18:1), which discriminates these strains from other valid species. In addition, DNA-DNA hybridization studies indicate that these strains belong to a novel species that could be readily distinguished from its nearest neighbor, Tetrasphaera japonica AMC 5116T, with less than 20 percent DNA relatedness. Physiological and biochemical tests show few phenotypic dissimilarities, but genotypic analysis allowed the differentiation of these gelatin-liquefying strains from previously reported strains. The name Tetrasphaera remsis sp. Nov. is proposed with the type strain 3-M5-R-4(sup T) (=ATCC BAA-1496(sup T)=CIP 109413(sup T). The cells are Gram-positive, nonmotile, cocci, in tetrad arrangement and clusters. Spore formation is not observed. No species of Tetrashpaera has ever been isolated from airborne samples. Previous discoveries have come from soil and activated sludge samples. As other species of this genus have demonstrated enhanced biological phosphorus removal activity, further tests are required to determine if this newly discovered species would have bioremediation applications.

Briegel, Ariane↗
NASA NTRS2018

How to Kill a Tardigrade - Without Even Trying

Tardigrades are small aquatic animals that are known for their ability to tolerate extreme dessication as well as ionizing radiation. The extent to which different tardigrade species are able to survive extreme doses of radiation has been previously defined, yet the molecular mechanisms underlying such radiation resistance has not been fully characterized. In Ramazzottius varieornatus, high dose radiation resistance been attributed to the presence of a tardigrade-unique DNA-associated protein Dsup, a protein that facilitates in the reduction of DNA fragmentation immediately after radiation exposure. This suggests that tardigrades possess a unique set of proteins that confer enhanced DNA protection as opposed to DNA repair. Previous studies have suggested that tolerance to radiation resistance in the tardigrade Hypsibius dujardini is inversely correlated with cellular division and mitotic activity, yet the molecular mechanisms and identities of such radiation resistance are poorly understood. In the current study, we plan to examine DNA damage by X-ray irradiation of metabolically active Hypsibius dujardini at three different developmental stages (egg, juvenile and adult) to quantitate the relative amount of double-strand breaks per unit DNA. These values will be compared to quantitation using Deinococcus radiodurans and Saccharomyces cerevisiae, at similar X-ray doses. X-ray exposure of D. radiodurans induces many double-stranded DNA breaks from which recovers by efficient repair. S. cerevisiae is not inherently radiation tolerant. Protection of DNA would be evidenced by reduced numbers of DNA double strand breaks in H. dujardini per unit DNA relative to the other two species.

Tardigrades↗
NASA NTRS2004

gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group

Bacillus anthracis, the causative agent of the human disease anthrax, Bacillus cereus, a food-borne pathogen capable of causing human illness, and Bacillus thuringiensis, a well-characterized insecticidal toxin producer, all cluster together within a very tight clade (B. cereus group) phylogenetically and are indistinguishable from one another via 16S rDNA sequence analysis. As new pathogens are continually emerging, it is imperative to devise a system capable of rapidly and accurately differentiating closely related, yet phenotypically distinct species. Although the gyrB gene has proven useful in discriminating closely related species, its sequence analysis has not yet been validated by DNA:DNA hybridization, the taxonomically accepted "gold standard". We phylogenetically characterized the gyrB sequences of various species and serotypes encompassed in the "B. cereus group," including lab strains and environmental isolates. Results were compared to those obtained from analyses of phenotypic characteristics, 16S rDNA sequence, DNA:DNA hybridization, and virulence factors. The gyrB gene proved more highly differential than 16S, while, at the same time, as analytical as costly and laborious DNA:DNA hybridization techniques in differentiating species within the B. cereus group.

Phylogeny↗
NASA NTRS2000

A comparison of RNA with DNA in template-directed synthesis

Nonenzymatic template-directed copying of RNA sequences rich in cytidylic acid using nucleoside 5'-(2-methylimidazol-1-yl phosphates) as substrates is substantially more efficient than the copying of corresponding DNA sequences. However, many sequences cannot be copied, and the prospect of replication in this system is remote, even for RNA. Surprisingly, wobble-pairing leads to much more efficient incorporation of G opposite U on RNA templates than of G opposite T on DNA templates.

Non-NASA Center↗
NASA NTRS2002

Spatial distribution and yield of DNA double-strand breaks induced by 3-7 MeV helium ions in human fibroblasts

Accelerated helium ions with mean energies at the target location of 3-7 MeV were used to simulate alpha-particle radiation from radon daughters. The experimental setup and calibration procedure allowed determination of the helium-ion energy distribution and dose in the nuclei of irradiated cells. Using this system, the induction of DNA double-strand breaks and their spatial distributions along DNA were studied in irradiated human fibroblasts. It was found that the apparent number of double-strand breaks as measured by a standard pulsed-field gel assay (FAR assay) decreased with increasing LET in the range 67-120 keV/microm (corresponding to the energy of 7-3 MeV). On the other hand, the generation of small and intermediate-size DNA fragments (0.1-100 kbp) increased with LET, indicating an increased intratrack long-range clustering of breaks. The fragment size distribution was measured in several size classes down to the smallest class of 0.1-2 kbp. When the clustering was taken into account, the actual number of DNA double-strand breaks (separated by at least 0.1 kbp) could be calculated and was found to be in the range 0.010-0.012 breaks/Mbp Gy(-1). This is two- to threefold higher than the apparent yield obtained by the FAR assay. The measured yield of double-strand breaks as a function of LET is compared with theoretical Monte Carlo calculations that simulate the track structure of energy depositions from helium ions as they interact with the 30-nm chromatin fiber. When the calculation is performed to include fragments larger than 0.1 kbp (to correspond to the experimental measurements), there is good agreement between experiment and theory.

NASA Program Biomedical Research and Countermeasur↗
NASA NTRS1994

The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

Non-NASA Center↗