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NASA NTRS2000

A Simpler Nucleic Acid

It has been supposed that for a nucleic acid analog to pair with RNA it must, like RNA, have a backbone with at least a sixatom repeat; a shorter backbone presumably would not stretch far enough to bind RNA properly. The Eschenmoser group has shown, however, that this first impression is incorrect.As they report in their new paper, Eschenmoser and co-workers ( I ) have now synthesized a substantial number of these polymers, which are called (L)-a-threofuranosyl oligonucleotides or TNAs. They are composed of bases linked to a threose sugar-phosphate backbone, with phosphodiester bonds connecting the nucleotides. The investigators discovered that pairs of complementary TNAs do indeed form stable Watson-Crick double helices and, perhaps more importantly, that TNAs form stable double helices with complementary RNAs and DNAs.

Orgel, Leslie↗
NASA NTRS2004

Metal/Silicate Partitioning of P, Ga, and W at High Pressures and Temperatures: Dependence on Silicate Melt Composition

The distinctive pattern of element concentrations in the upper mantle provides essential evidence in our attempts to understand the accretion and differentiation of the Earth (e.g., Drake and Righter, 2002; Jones and Drake, 1986; Righter et al., 1997; Wanke 1981). Core formation is best investigated through use of metal/silicate partition coefficients for siderophile elements. The variables influencing partition coefficients are temperature, pressure, the major element compositions of the silicate and metal phases, and oxygen fugacity. Examples of studies investigating the effects of these variables on partitioning behavior are: composition of the metal phase by Capobianco et al. (1999) and Righter et al. (1997); silicate melt composition by Watson (1976), Walter and Thibault (1995), Hillgren et al. (1996), Jana and Walker (1997), and Jaeger and Drake (2000); and oxygen fugacity by Capobianco et al. (1999), and Walter and Thibault (1995). Here we address the relative influences of silicate melt composition, pressure and temperature.

Bailey, Edward↗
NASA NTRS1989

Correlations in alpha-alpha scattering and semi-classical optical models

We show the equivalence of semi-classical solutions to optical model coupled-channel equations derived from Watson's form of the nucleus-nucleus multiple-scattering series to the Glauber multiple-scattering series. A second-order solution to the semi-classical coupled-channel elastic amplitude is shown to be nearly equivalent to a second-order optical-phase-shift approximation to the Glauber amplitude if the densities of all nuclear excited states are approximated by the ground-state density. Using the Jastrow method to model the two-body density we find an average excited-state density to be of negligible importance in the double-scattering region of alpha-alpha scattering.

NASA Discipline Number 04-10↗
NASA NTRS1999

Nucleic acid duplexes incorporating a dissociable covalent base pair

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

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 NTRS2000

Database of non-canonical base pairs found in known RNA structures

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

NASA Discipline Exobiology↗
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 NTRS1996

Gravitational acceleration as a cue for absolute size and distance?

When an object's motion is influenced by gravity, as in the rise and fall of a thrown ball, the vertical component of acceleration is roughly constant at 9.8 m/sec2. In principle, an observer could use this information to estimate the absolute size and distance of the object (Saxberg, 1987a; Watson, Banks, von Hofsten, & Royden, 1992). In five experiments, we examined people's ability to utilize the size and distance information provided by gravitational acceleration. Observers viewed computer simulations of an object rising and falling on a trajectory aligned with the gravitational vector. The simulated objects were balls of different diameters presented across a wide range of simulated distances. Observers were asked to identify the ball that was presented and to estimate its distance. The results showed that observers were much more sensitive to average velocity than to the gravitational acceleration pattern. Likewise, verticality of the motion and visibility of the trajectory's apex had negligible effects on the accuracy of size and distance judgments.

NASA Discipline Space Human Factors↗
NASA NTRS1995

Template switching between PNA and RNA oligonucleotides

The origin of the RNA world is not easily understood, as effective prebiotic syntheses of the components of RNA, the beta-ribofuranoside-5'-phosphates, are hard to envisage. Recognition of this difficulty has led to the proposal that other genetic systems, the components of which are more easily formed, may have preceded RNA. This raises the question of how transitions between one genetic system and another could occur. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine, but has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides bases on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides, we now show that RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa. This suggests that a transition between different genetic systems can occur without loss of information.

NASA Discipline Exobiology↗
NASA NTRS1997

Model Determined for Predicting Fatigue Lives of Metal Matrix Composites Under Mean Stresses

Aircraft engine components invariably are subjected to mean stresses over and above the cyclic loads. In monolithic materials, it has been observed that tensile mean stresses are detrimental and compressive mean stresses are beneficial to fatigue life in comparison to a base of zero mean stress. Several mean stress models exist for monolithic metals, but each differ quantitatively in the extent to which detrimental or beneficial effects are ascribed. There have been limited attempts to apply these models to metal matrix composites. At the NASA Lewis Research Center, several mean stress models--the Smith-Watson- Topper, Walker, Normalized Goodman, and Soderberg models--were examined for applicability to this class of composite materials. The Soderberg approach, which normalizes the mean stress to a 0.02-percent yield strength, was shown to best represent the effect of mean stresses over the range covered. The other models varied significantly in their predictability and often failed to predict the composite behavior at very high tensile mean stresses. This work is the first to systematically demonstrate the influence of mean stresses on metal matrix composites and model their effects. Attention also was given to fatigue-cracking mechanisms in the Ti-15-3 matrix and to micromechanics analyses of mean stress effects.

Lerch, Bradley↗
NASA NTRS2003

Real-Time Imaging of Ground Cover: Relationships with Radiation Capture, Canopy Photosynthesis, and Daily Growth Rate

Cumulative absorbed radiation is highly correlated with crop biomass and yield. In this chapter we describe the use of a digital camera and commercial imaging software for estimating daily radiation capture, canopy photosynthesis, and relative growth rate. Digital images were used to determine percentage of ground cover of lettuce (Lactuca sativa L.) communities grown at five temperatures. Plants were grown in a steady-state, 10-chamber CO2 gas exchange system, which was used to measure canopy photosynthesis and daily carbon gain. Daily measurements of percentage of ground cover were highly correlated with daily measurements of both absorbed radiation (r(sup 2) = 0.99) and daily carbon gain (r(sup 2) = 0.99). Differences among temperature treatments indicated that these relationships were influenced by leaf angle, leaf area index, and chlorophyll content. An analysis of the daily images also provided good estimates of relative growth rates, which were verified by gas exchange measurements of daily carbon gain. In a separate study we found that images taken at hourly intervals were effective for monitoring real-time growth. Our data suggests that hourly images can be used for early detection of plant stress. Applications, limitations, and potential errors are discussed. We have long known that crop yield is determined by the efficiency of four component processes: (i) radiation capture, (ii) quantum yield, (iii) carbon use efficiency, and (iv) carbon partitioning efficiency (Charles-Edwards, 1982; Penning de Vries & van Laar, 1982; Thornley, 1976). More than one-half century ago, Watson (1947, 1952) showed that variation in radiation capture accounted for almost all of the variation in yield between sites in temperate regions, because the three other components are relatively constant when the crop is not severely stressed. More recently, Monteith (1977) reviewed the literature on the close correlation between radiation capture and yield. Bugbee and Monje (1992) demonstrated the close relationship between absorbed radiation and yield in an optimal environment.

Klassen, S. P.↗
NASA NTRS2006

A Brief Summary of Some of the Laboratory Astrophysics Workshop

Our present knowledge of the molecular universe has come primarily from radio observations [ I include here millimeter and submillimeter in this rubric]. There are a number of reasons for this but the primary one is the extremely high spectral resolution. The ease of observing emission from the volume of dense molecular clouds without significant attenuation by scattering from dust has shown this to be the powerful observational tool for molecular astronomy. Finally the relative simplicity of rotational compared to vibrational or electronic spectroscopy allows carrier identification as well as facile evaluation of cloud conditions such as density and temperature. These virtues become tenuous as the astronomical observations are pushed to higher frequencies for enhanced observational sensitivity. Thus precision rest frequencies are mandatory for the search for new species. We may inquire about which new species require particular attention, and which species may be relatively safely predicted on the basis of lower frequency laboratory measurements. For a rigid rotor the three rotational constants are sufficient to completely specify the transition frequencies. The intensities require the three components of the electric dipole moment. For semirigid species, where the centrifugal distortion, may be treated at the quartic level of angular momentum (Bunker et al. 1998), up to five additional constants are required (Watson 1967). There are a number of such species of considerable interest, where laboratory measurements are adequate for astronomical searches.

Klemperer, William↗
NASA NTRS2006

Electron-Impact Ionization and Dissociative Ionization of Biomolecules

It is well recognized that secondary electrons play an important role in radiation damage to humans. Particularly important is the damage of DNA by electrons, potentially leading to mutagenesis. Molecular-level study of electron interaction with DNA provides information on the damage pathways and dominant mechanisms. Our study of electron-impact ionization of DNA fragments uses the improved binary-encounter dipole model and covers DNA bases, sugar phosphate backbone, and nucleotides. An additivity principle is observed. For example, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3(sup prime)- and C5 (sup prime)-deoxyribose-phospate cross sections, differing by less than 5%. Investigation of tandem double lesion initiated by electron-impact dissociative ionization of guanine, followed by proton reaction with the cytosine in the Watson-Crick pair, is currently being studied to see if tandem double lesion can be initiated by electron impact. Up to now only OH-induced tandem double lesion has been studied.

Huo, Winifred M.↗
NASA NTRS2008

Exploiting Lunar Natural and Augmented Thermal Environments for Exploration and Research

Near the poles of the Moon, there are permanently shadowed craters whose surface temperatures never exceed 100 K. Craters within craters, commonly referred to as double-shaded craters, have areas where even colder regions exist with, in many cases, temperatures that should never exceed 50 K. The presence of water ice possibly existing in permanently shaded areas of the moon has been hypothesized, discussed, and studied since Watson et al. [1] predicted the possibility of ice on the moon. Ingersoll et al. [2] estimated that the maximum sublimation rate for ice is less than 1 cm per billion years for these types of environments. These potential ice stores have many uses for lunar exploration, potentially providing precious water and rocket fuel for any human exploration or future colonization. The temperatures within these regions offer unprecedented high-vacuum cryogenic environments, which in their natural state could support cryogenic applications such as high-temperature superconductors and associated devices that could be derived. The potential application of naturally occurring cryogenic environments in conjunction with simple methods to augment these environments to achieve even colder temperatures opens the potential use of many additional cryogenic techniques. Besides ice stores and the potential for continuous solar illumination for power production, the unique cryogenic conditions at the lunar poles provide an environment that could reduce the power, weight, and total mass that would have to be carried from the Earth to the Moon for lunar exploration and research.

Ryan, Robert E.↗
NASA NTRS2006

The 'Biologically-Inspired Computing' Column

The field of Biology changed dramatically in 1953, with the determination by Francis Crick and James Dewey Watson of the double helix structure of DNA. This discovery changed Biology for ever, allowing the sequencing of the human genome, and the emergence of a "new Biology" focused on DNA, genes, proteins, data, and search. Computational Biology and Bioinformatics heavily rely on computing to facilitate research into life and development. Simultaneously, an understanding of the biology of living organisms indicates a parallel with computing systems: molecules in living cells interact, grow, and transform according to the "program" dictated by DNA. Moreover, paradigms of Computing are emerging based on modelling and developing computer-based systems exploiting ideas that are observed in nature. This includes building into computer systems self-management and self-governance mechanisms that are inspired by the human body's autonomic nervous system, modelling evolutionary systems analogous to colonies of ants or other insects, and developing highly-efficient and highly-complex distributed systems from large numbers of (often quite simple) largely homogeneous components to reflect the behaviour of flocks of birds, swarms of bees, herds of animals, or schools of fish. This new field of "Biologically-Inspired Computing", often known in other incarnations by other names, such as: Autonomic Computing, Pervasive Computing, Organic Computing, Biomimetics, and Artificial Life, amongst others, is poised at the intersection of Computer Science, Engineering, Mathematics, and the Life Sciences. Successes have been reported in the fields of drug discovery, data communications, computer animation, control and command, exploration systems for space, undersea, and harsh environments, to name but a few, and augur much promise for future progress.

Hinchey, Mike↗
NASA NTRS2008

Fatigue Behavior of a Third Generation PM Disk Superalloy

The fatigue behavior of a 3rd generation PM disk alloy, LSHR, was studied at 1300 F. Tensile, creep, and fatigue tests were run on smooth and notched (Kt = 2) bars under a variety of conditions. Analysis of smooth bar fatigue data, run under strain and load control with R ratios of 0 and -1, showed that a stress based Smith-Watson-Topper approach could collapse the data set. While the tensile and creep data showed substantial notch strengthening at 1300 F, the fatigue data showed a life deficit for the notch specimens. A viscoplastic finite element model, which accounted for stress relaxation at the notch tip, provided the best correlation between the notched and smooth bar behavior, although the fatigue data was not fully rationalized based on this simplified viscoplastic model of the stresses at the notch tip.Inclusion of a 90 sec dwell at peak load was found to dramatically decrease notch fatigue life. This result was shown to be consistent with a simple linear creep-fatigue damage rule, where creep damage dominated at low stresses and fatigue damage was more prevalent at higher stresses.

Gayda, John↗
NASA NTRS2008

Software Simulates Sight: Flat Panel Mura Detection

In the increasingly sophisticated world of high-definition flat screen monitors and television screens, image clarity and the elimination of distortion are paramount concerns. As the devices that reproduce images become more and more sophisticated, so do the technologies that verify their accuracy. By simulating the manner in which a human eye perceives and interprets a visual stimulus, NASA scientists have found ways to automatically and accurately test new monitors and displays. The Spatial Standard Observer (SSO) software metric, developed by Dr. Andrew B. Watson at Ames Research Center, measures visibility and defects in screens, displays, and interfaces. In the design of such a software tool, a central challenge is determining which aspects of visual function to include while accuracy and generality are important, relative simplicity of the software module is also a key virtue. Based on data collected in ModelFest, a large cooperative multi-lab project hosted by the Optical Society of America, the SSO simulates a simplified model of human spatial vision, operating on a pair of images that are viewed at a specific viewing distance with pixels having a known relation to luminance. The SSO measures the visibility of foveal spatial patterns, or the discriminability of two patterns, by incorporating only a few essential components of vision. These components include local contrast transformation, a contrast sensitivity function, local masking, and local pooling. By this construction, the SSO provides output in units of "just noticeable differences" (JND) a unit of measure based on the assumed smallest difference of sensory input detectable by a human being. Herein is the truly amazing ability of the SSO, while conventional methods can manipulate images, the SSO models human perception. This set of equations actually defines a mathematical way of working with an image that accurately reflects the way in which the human eye and mind behold a stimulus. The SSO is intended for a wide variety of applications, such as evaluating vision from unmanned aerial vehicles, measuring visibility of damage to aircraft and to the space shuttles, predicting outcomes of corrective laser eye surgery, inspecting displays during the manufacturing process, estimating the quality of compressed digital video, evaluating legibility of text, and predicting discriminability of icons or symbols in a graphical user interface.

Source record↗
NASA NTRS2010

How Cold are the Floors of Lunar Polar Shadowed Craters?

Almost five decades ago Watson, et al, [1] speculated that molecules of volatile species might accumulate within the cryogenic environments of permanently shadowed polar craters. The subject was largely a scientific curiosity until recently. In the mid-1980's, people began to seriously discuss the feasibility of long-term or permanent human settlement of the Moon. Given that the Moon was known be missing the compounds need to support life and that importing volatiles from Earth is prohibitively expensive, lunar colonists were pictured as processing the putative polar volatiles. A bistatic radar experiment performed with the Clementine spacecraft was interpreted to suggest the presence of large quantities of ice at some polar locations. [2] The neutron spectrometer aboard the Lunar Prospector spacecraft reported high concentrations of hydrogen in the polar regolith, [3] and some interpretations of the data set pointed to very high concentrations in permanently shadowed craters. The reformulation of civilian space policy in 2004, known as the Vision for Space Exploration, emphasized lunar exploration with eye toward development of economic returns from cislunar space and long-tern human presence on the Moon. The theme of finding lunar resources was an impetus for the inclusion of the Diviner Lunar Radiometer Experiment on the Lunar Reconnaissance Orbiter. Preliminary results from Diviner report an unexpectedly low temperature down to 35K in the depths of some craters. [4]

Mendell, Wendell W.↗