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At least 109 records · Page 6

Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes

Numerous complete mitochondrial DNA sequences have been determined for species within two arthropod groups, insects and crustaceans, but there are none for a third, the chelicerates. Most mitochondrial gene arrangements reported for crustaceans and insect species are identical or nearly identical to that of Drosophila yakuba. Sequences across 36 of the gene boundaries in the mitochondrial DNA (mtDNA) of a representative chelicerate. Limulus polyphemus L., also reveal an arrangement like that of Drosophila yakuba. Only the position of the tRNA(LEU)(UUR) gene differs; in Limulus it is between the genes for tRNA(LEU)(CUN) and ND1. This positioning is also found in onychophorans, mollusks, and annelids, but not in insects and crustaceans, and indicates that tRNA(LEU)(CUN)-tRNA(LEU)(UUR)-ND1 was the ancestral gene arrangement for these groups, as suggested earlier. There are no differences in the relative arrangements of protein-coding and ribosomal RNA genes between Limulus and Drosophila, and none have been observed within arthropods. The high degree of similarity of mitochondrial gene arrangements within arthropods is striking, since some taxa last shared a common ancestor before the Cambrian, and contrasts with the extensive mtDNA rearrangements occasionally observed within some other metazoan phyla (e.g., mollusks and nematodes).

Non-NASA Center↗

Robot acting on moving bodies (RAMBO): Preliminary results

A robot system called RAMBO is being developed. It is equipped with a camera, which, given a sequence of simple tasks, can perform these tasks on a moving object. RAMBO is given a complete geometric model of the object. A low level vision module extracts and groups characteristic features in images of the object. The positions of the object are determined in a sequence of images, and a motion estimate of the object is obtained. This motion estimate is used to plan trajectories of the robot tool to relative locations nearby the object sufficient for achieving the tasks. More specifically, low level vision uses parallel algorithms for image enchancement by symmetric nearest neighbor filtering, edge detection by local gradient operators, and corner extraction by sector filtering. The object pose estimation is a Hough transform method accumulating position hypotheses obtained by matching triples of image features (corners) to triples of model features. To maximize computing speed, the estimate of the position in space of a triple of features is obtained by decomposing its perspective view into a product of rotations and a scaled orthographic projection. This allows the use of 2-D lookup tables at each stage of the decomposition. The position hypotheses for each possible match of model feature triples and image feature triples are calculated in parallel. Trajectory planning combines heuristic and dynamic programming techniques. Then trajectories are created using parametric cubic splines between initial and goal trajectories. All the parallel algorithms run on a Connection Machine CM-2 with 16K processors.

Davis, Larry S.↗

Robot Acting on Moving Bodies (RAMBO): Interaction with tumbling objects

Interaction with tumbling objects will become more common as human activities in space expand. Attempting to interact with a large complex object translating and rotating in space, a human operator using only his visual and mental capacities may not be able to estimate the object motion, plan actions or control those actions. A robot system (RAMBO) equipped with a camera, which, given a sequence of simple tasks, can perform these tasks on a tumbling object, is being developed. RAMBO is given a complete geometric model of the object. A low level vision module extracts and groups characteristic features in images of the object. The positions of the object are determined in a sequence of images, and a motion estimate of the object is obtained. This motion estimate is used to plan trajectories of the robot tool to relative locations rearby the object sufficient for achieving the tasks. More specifically, low level vision uses parallel algorithms for image enhancement by symmetric nearest neighbor filtering, edge detection by local gradient operators, and corner extraction by sector filtering. The object pose estimation is a Hough transform method accumulating position hypotheses obtained by matching triples of image features (corners) to triples of model features. To maximize computing speed, the estimate of the position in space of a triple of features is obtained by decomposing its perspective view into a product of rotations and a scaled orthographic projection. This allows use of 2-D lookup tables at each stage of the decomposition. The position hypotheses for each possible match of model feature triples and image feature triples are calculated in parallel. Trajectory planning combines heuristic and dynamic programming techniques. Then trajectories are created using dynamic interpolations between initial and goal trajectories. All the parallel algorithms run on a Connection Machine CM-2 with 16K processors.

Davis, Larry S.↗

Stellar evolution from the zero-age main sequence

A consistent set of 247 evolutionary sequences extending from the ZAMS to the red-giant branch is presented for Y from 0.10 to 0.40, Z from 0.00001 to 0.10, and masses of 0.55 to 6.90 solar masses. Each sequence is started from a homogeneous ZAMS model, and almost all are evolved to the base of the red-giant branch. It is shown that: (1) the relative position of the main sequence can be determined as a function of composition; (2) theoretical luminosity functions can be derived from the relative evolutionary time scales; (3) a dip in luminosity sometimes occurs at the base of the red-giant branch and is most pronounced at larger Z values; (4) metal-poor stars evolve farther up along the main sequence before turning off toward the red-giant branch; and (5) the onset of helium burning halts the evolution across the Hertzsprung gap for the most massive and most metal-poor models, so that the star remains blue during its phase of core-helium burning.

Mengel, J. G.↗

Identification of a nuclear localization sequence in the polyomavirus capsid protein VP2

A nuclear localization signal (NLS) has been identified in the C-terminal (Glu307-Glu-Asp-Gly-Pro-Gln-Lys-Lys-Lys-Arg-Arg-Leu318) amino acid sequence of the polyomavirus minor capsid protein VP2. The importance of this amino acid sequence for nuclear transport of newly synthesized VP2 was demonstrated by a genetic "subtractive" study using the constructs pSG5VP2 (expressing full-length VP2) and pSG5 delta 3VP2 (expressing truncated VP2, lacking amino acids Glu307-Leu318). These constructs were transfected into COS-7 cells, and the intracellular localization of the VP2 protein was determined by indirect immunofluorescence. These studies revealed that the full-length VP2 was localized in the nucleus, while the truncated VP2 protein was localized in the cytoplasm and not transported to the nucleus. A biochemical "additive" approach was also used to determine whether this sequence could target nonnuclear proteins to the nucleus. A synthetic peptide identical to VP2 amino acids Glu307-Leu318 was cross-linked to the nonnuclear proteins bovine serum albumin (BSA) or immunoglobulin G (IgG). The conjugates were then labeled with fluorescein isothiocyanate and microinjected into the cytoplasm of NIH 3T6 cells. Both conjugates localized in the nucleus of the microinjected cells, whereas unconjugated BSA and IgG remained in the cytoplasm. Taken together, these genetic subtractive and biochemical additive approaches have identified the C-terminal sequence of polyoma-virus VP2 (containing amino acids Glu307-Leu318) as the NLS of this protein.

Non-NASA Center↗

Developing a Genetic Variant Calling Pipeline for Quantifying the Complex Mutagenic Load Accumulated in BioNutrients-1 Production Pack Samples

Microorganisms hold great promise for on demand production of labile nutrients and pharmaceuticals as well recycling and in situ resource utilization. The utilization of microorganisms for such tasks on space missions is hindered by the limited data on how microbes respond to spaceflight. For example, the genetic stability of microorganisms, and the genomic engineered traits added to deliver desired functions, over long-term storage in the spacecraft environment is poorly understood. The BioNutrients-1 (BN-1) mission conducted a 5-year study of desiccated storage in Low Earth Orbit (LEO) to evaluate the suitability of eight synthetic biology chassis organisms for long-duration space missions. We are employing high-depth, whole genome sequencing (WGS) to determine the mutagenic load that accumulated during long-term storage. Mutation analysis pipelines are well established for homogenous culture grown from a single colony, but the mutational landscape of the BN-1 samples present a unique analysis challenge, as every cell in the BN-1 samples had a unique genetic journey of DNA damage and repair. Consequently, sequence variants are expected at low allele frequency within samples. To address this genetic complexity, we apply two distinct computational approaches to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO. For reference genome free mutation detection, we utilized DiscoSNP++, which is a de Bruijn graph approach. For reference genome-based mutation detection we utilize GATK for Microbes, which is a Bayesian probabilistic approach. We will benchmark these approaches against the mutations originally identified using CRISP, a method optimized for pooled samples. Ultimately, quantifying the mutation load imposed by storage or growth on the ISS will help identify chassis organisms with both high levels of genome stability and viability, which are desirable traits for implementation of bioproduction in long-duration missions.

SNP↗

Seed surface sanitization and persistence of E.coli through different tissues of ‘Red Robin’ Tomato (Solanum lycopersicum cv. Red Robin)

Seed surface sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed surface sanitization on the plants’ microbiome, sanitized and unsanitized seeds from ‘Red Robin’ Tomato (Solanumlycopersicum cv. Red Robin) were exposed to Escherichia coli (E. coli) and grown in a controlled environment growth chamber simulating environmental conditions aboard the International Space Station (ISS). Plants were harvested at four intervals, days 11, 33,42 and 76 post-germination. Changes in the microbial communities of leaf, stem, root, and fruit because of E. coli exposure and the persistence of E. coli itself were investigated using aerobic plate count (APC), qPCR and 16S rRNA sequencing. It was determined that E. coli persisted for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf or stem tissue. E. coli was not detected in fruits raised from either sanitized or unsanitized seeds. The 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in all tissue types studied. We observed minimal or no changes in the alpha diversity of leaf stem and fruit tissue with time, or between sanitized and unsanitized seeds. Roots showed significant differences in alpha diversity with time and seed sanitization status. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. Members of phyla Proteobacteria and Bacteroidetes were found to be differentially abundant across leaf, stem and root tissue. Our results indicated that the seed surface sanitization, although a requirement for sending seeds to space, might influence the developing microbiome. This research was funded by NASA’s Space Life and Physical Sciences Research and Applications.

Anirudha R Dixit↗

Performance of code division multiple access systems

The performance of code division multiple-access (CDMA) systems is determined using direct sequence spectral spreading. Under relatively ideal conditions, the degradation in system performance as a function of the number of users is shown to have a threshold effect. This basic limitation in the number of users of the system is further limited if the powers are unequal. For two users, system performance as a function of their power ratio also has a threshold effect. System performance as a function of the amount of spectral spreading is determined. The performance of both coded and uncoded systems is predicted.

Weber, C. L.↗

Equally parsimonious pathways through an RNA sequence space are not equally likely

An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.

NASA Discipline Exobiology↗

Network device interface for digitally interfacing data channels to a controller a via network

The present invention provides a network device interface and method for digitally connecting a plurality of data channels to a controller using a network bus. The network device interface interprets commands and data received from the controller and polls the data channels in accordance with these commands. Specifically, the network device interface receives digital commands and data from the controller, and based on these commands and data, communicates with the data channels to either retrieve data in the case of a sensor or send data to activate an actuator. In one embodiment, the bus controller transmits messages to the network device interface containing a plurality of bits having a value defined by a transition between first and second states in the bits. The network device interface determines timing of the data sequence of the message and uses the determined timing to communicate with the bus controller.

Ellerbrock, Philip J.↗

The determination of the helium abundance in main-sequence B stars

It is pointed out that the abundances of deuterium, helium, and lithium provide fundamental constraints on cosmological models. The central question is related to the compatibility of the observed abundances with big bang models of primordial nucleosynthesis, taking into account a modification by subsequent nuclear processing in stars or a modification of standard models. The present paper has the objective to assess critically the feasibility of deriving accurate helium abundances from measurements of the photospheric lines in main-sequence B-type stars. A method is established for assigning atmospheric parameters to main-sequence stars with spectral types in the range (approximately) B1-B5. It is found that an analysis of stars in distant anticenter H II regions and clusters offer an alternative method which seems capable of determining relative abundances with more than the requisite accuracy.

Wolff, S. C.↗

Application of the steepest ascent optimization method to a reentry trajectory problem

The direct optimization method is presented in detail. Nominal values of the control variables are input parameters. Perturbations are introduced into the control variables and the resulting first order predictions of changes in the payoff, and constraint functions are then determined. Through a sequence of prescribed cycles, a trajectory is eventually obtained which is reasonably close to the optimum. The method is successfully applied to an Apollo three-dimensional reentry problem. The study of this Apollo application problem has resulted in the development of a highly flexible computer program that can be modified to consider other trajectory optimization problems.

Junkin, B. G.↗

Thermogravimetric-quadrupole mass-spectrometric analysis of geochemical samples.

Thermogravimetric-quadrupole mass-spectrometric-analysis techniques can be used to study a wide variety of problems involving decomposition processes and identification of released volatile components. A recording vacuum thermoanalyzer has been coupled with a quadrupole mass spectrometer. The rapid scan capabilities of the quadrupole mass spectrometer are used to identify the gaseous components released. The capability of the thermogravimetric-quadrupole mass spectrometer to provide analytical data for identification of the released volatile components, for determination of their sequence of release and for correlation of thermal-decomposition studies is illustrated by an analysis of the Orgueil carbonaceous chondrite.

Gibson, E. K., Jr.↗

Structural analysis of vibroacoustical processes

The method of automatic identification of acoustical signals, by means of the segmentation was used to investigate noises and vibrations in machines and mechanisms, for cybernetic diagnostics. The structural analysis consists of presentation of a noise or vibroacoustical signal as a sequence of segments, determined by the time quantization, in which each segment is characterized by specific spectral characteristics. The structural spectrum is plotted as a histogram of the segments, also as a relation of the probability density of appearance of a segment to the segment type. It is assumed that the conditions of ergodic processes are maintained.

Gromov, A. P.↗

Postural effects on the noninvasive baselines of ventricular performance

The effects of posture on time-based noninvasive measurements were determined utilizing the sequence supine-sitting-standing in a formal protocol in which observer biases were eliminated by blinding the measurement and calculation phases. Compared to the supine posture, the sitting and standing postures produced significant increases in heart rate, isovolumic contraction time, pre-ejection period and pre-ejection period/left-ventricular ejection time and significant decreases in ejection time and ejection time index. The response patterns are consistent with the hemodynamic correlates cited in the literature which show increased adrenergic activity and decreased venous return in the sitting and standing postures, the effect on venous return being dominant.

Lance, V. Q.↗

Solar calibration of stellar rotation tracers

A study of the time variability of the disk-integrated solar magnetic flux, with a view to the behavior of emission-line intensity variations observed in lower main sequence stars, has determined that solar rotation modulation of the integrated flux is present in 75% of all rotations. For observing intervals of more than twice the lifetime of the features causing rotational modulation, the correct rotation period is identified in more than 90% of all cases. The optimum time for measuring rotational modulation is the decay phase of the activity cycle, and the solar rotation period is measured with an accuracy of a few percent. The lifetime of a rotational modulation period is approximately five rotations, and a sensitivity limit of Delta S= 0.005 is found for the Vaughan et al (1981) stellar rotation measures.

Labonte, B. J.↗

Evidence for a complex archean deformational history; southwestern Michipicoten Greenstone Belt, Ontario

The Michipicoten Greenstone Belt extends for about 150 km ENE from the northeastern angle of Lake Superior. In common with many other Archean greenstone belts, it is characterized by generally steep bedding dips and a distribution of major lithologic types suggesting a crudely synclinal structure for the belt as a whole. Detailed mapping and determination of structural sequence demonstrates that the structure is much more complex. The Archean history of the belt includes formation of at least three regionally significant cleavages, kilometer-scale overturning, extensive shearing, and diabase intrusion. Most well defined, mappable 'packages' of sedimentary rocks appear to be bounded by faults. These faults were active relatively early in the structural history of the belt, when extensive overturning also occurred. Steepening of dips, NW-SE shortening, development of steep NE cleavage, and pervasive shearing all postdate the early faulting and the regional overturning, obscuring much of the detail needed to define the geometry of the earlier structures. The results obtained so far suggest, however, that the Michipicoten Greenstone Belt underwent an early stage of thrusting and associated isoclinal folding, probably in a convergent tectonic environment.

Mcgill, George E.↗

Photogeological inferences of Martian surface composition

Photogeological mapping provides a systematic documentation of geologic observations and included the identification of surface materials and structures, and determination of their sequence of formation. It is concluded that photogeologic mapping shows the presence of a wide range of materials on Mars. Many of which appear to be volcanic. The knowledge of the composition of these materials is poorly constrained. Inferences drawn from the morphology of individual flows would suggest that most of the materials had rheological properties similar to basalt or other mafic magmas.

Greeley, R.↗