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When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.
A new engineering environment constructed for the purposes of analyzing and designing Reusable Launch Vehicles (RLVs) is presented. The new environment has been developed to allow NASA to perform independent analysis and design of emerging RLV architectures and technologies. The new Advanced Engineering Environment (AEE) is both collaborative and distributed. It facilitates integration of the analyses by both vehicle performance disciplines and life-cycle disciplines. Current performance disciplines supported include: weights and sizing, aerodynamics, trajectories, propulsion, structural loads, and CAD-based geometries. Current life-cycle disciplines supported include: DDT&E cost, production costs, operations costs, flight rates, safety and reliability, and system economics. Involving six NASA centers (ARC, LaRC, MSFC, KSC, GRC and JSC), AEE has been tailored to serve as a web-accessed agency-wide source for all of NASA's future launch vehicle systems engineering functions. Thus, it is configured to facilitate (a) data management, (b) automated tool/process integration and execution, and (c) data visualization and presentation. The core components of the integrated framework are a customized PTC Windchill product data management server, a set of RLV analysis and design tools integrated using Phoenix Integration's Model Center, and an XML-based data capture and transfer protocol. The AEE system has seen production use during the Initial Architecture and Technology Review for the NASA 2nd Generation RLV program, and it continues to undergo development and enhancements in support of its current main customer, the NASA Next Generation Launch Technology (NGLT) program.
The NASTRAN thermal analyzer (NTA) which performs large-scale unified thermo-structural analyses with the NASTRAN (NASA structural analysis) computer program is described. The mathematical similitude between these two distinct disciplines of thermal and structure is examined. It serves as the theoretical basis upon which the implementation of the thermal capability in NASTRAN was accomplished. The program structure, the functional flow, the solution algorithms, the organization of an input data deck and the solution capabilities of NTA are summarized. Emphasis is placed on the interface of the unified approach in thermo-structural analyses where stresses, deflections, vibrations and bucklings induced by the effect of temperature change are of concern. Attentions are also directed to the preprocessor and post processors. As a specially designed preprocessor, the VIEW program is capable of generating exchange factors which can be output, at user's option, in formats compatible with that required by NTA. Two post processors that serve specific objectives are included. They are the thermal variance analysis and the graphical displaying capability of temperatures in color or black and white.
The Suomi National Polar-orbiting Partnership (SNPP) satellite was successfully launched into a polar orbit on October 28, 2011 carrying 5 remote sensing instruments designed to provide data to improve weather forecasts and to increase understanding of long-term climate change. SNPP provides operational continuity of satellite-based observations for NOAA's Polar-orbiting Operational Environmental Satellites (POES) and continues the long-term record of climate quality observations established by NASA's Earth Observing System (EOS) satellites. In the 2003 to 2011 pre-launch timeframe, NASA's SNPP Science Team assessed the adequacy of the operational Raw Data Records (RDRs), Sensor Data Records (SDRs), and Environmental Data Records (EDRs) from the SNPP instruments for use in NASA Earth Science research, examined the operational algorithms used to produce those data records, and proposed a path forward for the production of climate quality products from SNPP. In order to perform these tasks, a distributed data system, the NASA Science Data Segment (SDS), ingested RDRs, SDRs, and EDRs from the NOAA Archive and Distribution and Interface Data Processing Segments, ADS and IDPS, respectively. The SDS also obtained operational algorithms for evaluation purposes from the NOAA Government Resource for Algorithm Verification, Independent Testing and Evaluation (GRAVITE). Within the NASA SDS, five Product Evaluation and Test Elements (PEATEs) received, ingested, and stored data and performed NASA's data processing, evaluation, and analysis activities. The distributed nature of this data distribution system was established by physically housing each PEATE within one of five Climate Analysis Research Systems (CARS) located at either at a NASA or a university institution. The CARS were organized around 5 key EDRs directly in support of the following NASA Earth Science focus areas: atmospheric sounding, ocean, land, ozone, and atmospheric composition products. The PEATES provided the system level interface with members of the NASA SNPP Science Team and other science investigators within each CARS. A sixth Earth Radiation Budget CARS was established at NASA Langley Research Center (NASA LaRC) to support instrument performance, data evaluation, and analysis for the SNPP Clouds and the Earth's Radiant Budget Energy System (CERES) instrument. Following the 2011 launch of SNPP, spacecraft commissioning, and instrument activation, the NASA SNPP Science Team evaluated the operational RDRs, SDRs, and EDRs produced by the NOAA ADS and IDPS. A key part in that evaluation was the NASA Science Team's independent processing of operational RDRs and SDRs to EDRs using the latest NASA science algorithms. The NASA science evaluation was completed in the December 2012 to April 2014 timeframe with the release of a series of NASA Science Team Discipline Reports. In summary, these reports indicated that the RDRs produced by the SNPP instruments were of sufficiently high quality to be used to create data products suitable for NASA Earth System science and applications. However, the quality of the SDRs and EDRs were found to vary greatly when considering suitability for NASA science. The need for improvements in operational algorithms, adoption of different algorithmic approaches, greater monitoring of on-orbit instrument calibration, greater attention to data product validation, and data reprocessing were prominent findings in the reports. In response to these findings, NASA, in late 2013, directed the NASA SNPP Science Team to use SNPP instrument data to develop data products of sufficiently high quality to enable the continuation of EOS time series data records and to develop innovative, practical applications of SNPP data. This direction necessitated a transition of the SDS data system from its pre-launch assessment mode to one of full data processing and production. To do this, the PEATES, which served as NASA's data product testing environment during the prelaunch and early on-orbit periods, were transitioned to Science Investigator-led Processing Systems (SIPS). The distributed data architecture was maintained in this new system by locating the SIPS at the same institutions at which the CARS and PEATES were located. The SIPS acquire raw SNPP instrument Level 0 (i.e. RDR) data over the full SNPP mission from the NOAA ADS and IDPS through the NASA SDS Data Distribution and Depository Element (SD3E). The SIPS process those data into NASA Level 1, Level 2, and global, gridded Level 3 standard products using peer-reviewed algorithms provided by members of the NASA Science Team. The SIPS work with the NASA SNPP Science Team in obtaining enhanced, refined, or alternate real-time algorithms to support the capabilities of the Direct Readout Laboratory (DRL). All data products, algorithm source codes, coefficients, and auxiliary data used in product generation are archived in an assigned NASA Distributed Active Archive Center (DAAC).
A Xanthomonas oryzae pv. oryzae gene with sequence similarity to an Escherichia coli phosphate-binding protein gene (phoS) produces a periplasmic protein of apparent M(r) 35,000 when expressed in E. coli. Amino terminal sequencing revealed that a signal peptide is removed during transport to the periplasm in E. coli.
NASA devotes approximately 40 percent of its budget to R&D. Twelve NASA Research Centers and their contractors conduct this R&D, which ranges across many disciplines and is fueled by information about previous endeavors. Locating the right information is crucial. While NASA researchers use peer contacts as their primary source of scientific and technical information (STI), on-line bibliographic data bases - both Government-owned and commercial - are also frequently consulted. Once identified, the STI must be delivered in a usable format. This report assesses the appropriateness of developing an intelligent gateway interface for the NASA R&D community as a means of obtaining improved access to relevant STI resources outside of NASA's Remote Console (RECON) on-line bibliographic database. A study was conducted to determine (1) the information requirements of the R&D community, (2) the information sources to meet those requirements, and (3) ways of facilitating access to those information sources. Findings indicate that NASA researchers need more comprehensive STI coverage of disciplines not now represented in the RECON database. This augmented subject coverage should preferably be provided by both domestic and foreign STI sources. It was also found that NASA researchers frequently request rapid delivery of STI, in its original format. Finally, it was found that researchers need a better system for alerting them to recent developments in their areas of interest. A gateway that provides access to domestic and international information sources can also solve several shortcomings in the present STI delivery system. NASA should further test the practicality of a gateway as a mechanism for improved STI access.
Exposure, pathology and mortality data for mice, dogs and humans were examined to determine whether accurate interspecies predictions of radiation-induced mortality could be achieved. The analyses revealed that (1) days of life lost per unit dose can be estimated for a species even without information on radiation effects in that species, and (2) accurate predictions of age-specific radiation-induced mortality in beagles and the atomic bomb survivors can be obtained from a dose-response model for comparably exposed mice. These findings illustrate the value of comparative mortality analyses and the relevance of animal data to the study of human health effects.
Bacteriochlorophyll (BChl) c and a similar model compound, Mg-methyl bacteriopheophorbide d, form several types of aggregates in nonpolar solvents. One of these aggregates is highly fluorescent, with a quantum yield higher than that of the monomer. This aggregate is also unusual in that it shows a rise time in its fluorescence emission decay at certain wavelengths, which is ascribed to a change in conformation of the aggregate. An analysis of fluorescence depolarization data is consistent with either a linear aggregate of four or five monomers or preferably a cyclic arrangement of three dimers.
Three small blue copper proteins designated auracyanin A, auracyanin B-1, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus. All three auracyanins are peripheral membrane proteins. Auracyanin A was described previously (Trost, J. T., McManus, J. D., Freeman, J. C., Ramakrishna, B. L., and Blankenship, R. E. (1988) Biochemistry 27, 7858-7863) and is not glycosylated. The two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis apparent monomer molecular masses are 14 (A), 18 (B-2), and 22 (B-1) kDa. The amino acid sequences of the B forms are presented. All three proteins have similar absorbance, circular dichroism, and resonance Raman spectra, but the electron spin resonance signals are quite different. Laser flash photolysis kinetic analysis of the reactions of the three forms of auracyanin with lumiflavin and flavin mononucleotide semiquinones indicates that the site of electron transfer is negatively charged and has an accessibility similar to that found in other blue copper proteins. Copper analysis indicates that all three proteins contain 1 mol of copper per mol of protein. All three auracyanins exhibit a midpoint redox potential of +240 mV. Light-induced absorbance changes and electron spin resonance signals suggest that auracyanin A may play a role in photosynthetic electron transfer. Kinetic data indicate that all three proteins can donate electrons to cytochrome c-554, the electron donor to the photosynthetic reaction center.
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.
Muscle wasting is a debilitating consequence of fasting, inactivity, cancer, and other systemic diseases that results primarily from accelerated protein degradation by the ubiquitin-proteasome pathway. To identify key factors in this process, we have used cDNA microarrays to compare normal and atrophying muscles and found a unique gene fragment that is induced more than ninefold in muscles of fasted mice. We cloned this gene, which is expressed specifically in striated muscles. Because this mRNA also markedly increases in muscles atrophying because of diabetes, cancer, and renal failure, we named it atrogin-1. It contains a functional F-box domain that binds to Skp1 and thereby to Roc1 and Cul1, the other components of SCF-type Ub-protein ligases (E3s), as well as a nuclear localization sequence and PDZ-binding domain. On fasting, atrogin-1 mRNA levels increase specifically in skeletal muscle and before atrophy occurs. Atrogin-1 is one of the few examples of an F-box protein or Ub-protein ligase (E3) expressed in a tissue-specific manner and appears to be a critical component in the enhanced proteolysis leading to muscle atrophy in diverse diseases.
RNA sequence analysis has been used to examine the phylogenetic position and structure of the genus Campylobacter. A complete 5S rRNA sequence was determined for two strains of Campylobacter jejuni and extensive partial sequences of the 16S rRNA were obtained for several strains of C. jejuni and Wolinella succinogenes. In addition limited partial sequence data were obtained from the 16S rRNAs of isolates of C. coli, C. laridis, C. fetus, C. fecalis, and C. pyloridis. It was found that W. succinogenes is specifically related to, but not included, in the genus Campylobacter as presently constituted. Within the genus significant diversity was noted. C. jejuni, C. coli and C. laridis are very closely related but the other species are distinctly different from one another. C. pyloridis is without question the most divergent of the Campylobacter isolates examined here and is sufficiently distinct to warrant inclusion in a separate genus. In terms of overall position in bacterial phylogeny, the Campylobacter/Wolinella cluster represents a deep branching most probably located within an expanded version of the Division containing the purple photosynthetic bacteria and their relatives. The Campylobacter/Wolinella cluster is not specifically includable in either the alpha, beta or gamma subdivisions of the purple bacteria.
Intrinsic rhythmic changes in the diameter of pial cerebral arterioles (30-70 microns) in anesthetized normotensive and hypertensive rats were assessed in vivo to determine if any significant differences exist between the two strains. All diameter measurements were analyzed using a traditional graphic analysis technique and a new frequency spectrum analysis technique known as the Prony Spectral Line Estimator. Graphic analysis of the data revealed that spontaneously hypertensive rats (SHR) possess a significantly greater fundamental frequency (5.57 +/- 0.28 cycles/min) of vasomotion compared to the control Wistar-Kyoto normotensive rats (WKY) (1.95 +/- 0.37 cycles/min). Furthermore, the SHR cerebral arterioles exhibited a significantly greater amplitude of vasomotion (10.07 +/- 0.70 microns) when compared to the WKY cerebral arterioles of the same diameter (8.10 +/- 0.70 microns). Diameter measurements processed with the Prony technique revealed that the fundamental frequency of vasomotion in SHR cerebral arterioles (6.14 +/- 0.39 cycles/min) was also significantly greater than that of the WKY cerebral arterioles (2.99 +/- 0.42 cycles/min). The mean amplitudes of vasomotion in the SHR and WKY strains obtained by the Prony analysis were found not to be statistically significant in contrast to the graphic analysis of the vasomotion amplitude of the arterioles. In addition, the Prony system was able to consistently uncover a very low frequency of vasomotion in both strains of rats that was typically less than 1 cycle/min and was not significantly different between the two strains. The amplitude of this slow frequency was also not significantly different between the two strains. The amplitude of the slow frequency of vasomotion (less than 1 cycle/min) was not different from the amplitude of the higher frequency (2-6 cycles/min) vasomotion by Prony or graphic analysis. These data suggest that a fundamental intrinsic defect exists in the spontaneously hypertensive rat that may contribute to the pathogenesis of hypertension in these animals.
No abstract available
The search for radio signals from extraterrestrial intelligent beings (SETI) requires the use of large instantaneous bandwidth (500 MHz) and high resolution (20 Hz) spectrometers. Digital systems with a high degree of modularity can be used to provide this capability, and this method has been widely discussed. Another technique for meeting the SETI requirement is to use a crossed Bragg cell spectrometer as described by Psaltis and Casasent. This technique makes use of the Folded Spectrum concept, introduced by Thomas. The Folded Spectrum is a 2-D Fourier Transform of a raster scanned 1-D signal. It is directly related to the long 1-D spectrum of the original signal and is ideally suited for optical signal processing. The folded spectrum technique has received little attention to date, primarily because early systems made use of photographic film which are unsuitable for the real time data analysis and voluminous data requirements of SETI. An analysis of the crossed Bragg cell spectrometer is presented as a method to achieve the spectral processing requirements for SETI. Systematic noise contributions unique to the Bragg cell system will be discussed.
The effect of sleep deprivation (40 h) on topographic and temporal aspects of electroencephalographic (EEG) activity during sleep was investigated by all night spectral analysis in six young volunteers. The sleep-deprivation-induced increase of EEG power density in the delta and theta frequencies (1-7 Hz) during nonREM sleep, assessed along the antero-posterior axis (midline: Fz, Cz, Pz, Oz), was significantly larger in the more frontal derivations (Fz, Cz) than in the more parietal derivations (Pz, Oz). This frequency-specific frontal predominance was already present in the first 30 min of recovery sleep, and dissipated in the course of the 8-h sleep episode. The data demonstrate that the enhancement of slow wave EEG activity during sleep following extended wakefulness is most pronounced in frontal cortical areas.
A strategy suggested by comparative genomic studies was used to amplify the entire Vibrio proteolyticus (Vp) gene for ribosomal protein L18. Vp L18 and its flanking regions were sequenced and compared with the deduced amino acid (aa) sequences of other known L18 proteins. A 26-aa residue segment at the carboxy terminus contains many strongly conserved residues and may be critical for the L18 interaction with 5S rRNA. This approach should allow rapid characterization of L18 from large numbers of bacteria. Both Vp L18 and Escherichia coli (Ec) L18 were overproduced and purified using a T7 expression vector which fuses an N-terminal peptide segment (His-tag) containing 6 histidine residues to the recombinant protein. The purified fusion proteins, Vp His::L18 and Ec His::L18, were both found to bind to either the Vp 5S or Ec 5S rRNAs in vitro. Vp His::L18 protein was also shown to incorporate into Ec ribosomes in vivo. This His-tag strategy likely will have general applicability for the study of ribosomal proteins in vitro and in vivo.
Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.