A pinboard by
Greg Tebbutt

I'm Sparrho and I curated this pinboard collection after being given some basic subject guidance


A collection illustrating the depth and breadth of the science research published by NASA


Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments.

Abstract: A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Pub.: 07 Feb '01, Pinned: 17 Feb '17

Organic protomolecule assembly in igneous minerals.

Abstract: CH stretching bands, nu(CH), in the infrared spectrum of single crystals of nominally high purity, of laboratory-grown MgO, and of natural upper mantle olivine, provide an "organic" signature that closely resembles the symmetrical and asymmetrical C--H stretching modes of aliphatic -CH(2) units. The nu(CH) bands indicate that H(2)O and CO(2), dissolved in the matrix of these minerals, converted to form H(2) and chemically reduced C, which in turn formed C--H entities, probably through segregation into defects such as dislocations. Heating causes the C--H bonds to pyrolyze and the nu(CH) bands to disappear, but annealing at 70 degrees C causes them to reappear within a few days or weeks. Modeling dislocations in MgO suggests that the segregation of C can lead to C(x) chains, x = 4, with the terminal C atoms anchored to the MgO matrix by bonding to two O(-). Allowing H(2) to react with such C(x) chains leads to [O(2)C(CH(2))(2)CO(2)] or similar precipitates. It is suggested that such C(x)--H(y)--O(z) entities represent protomolecules from which derive the short-chain carboxylic and dicarboxylic and the medium-chain fatty acids that have been solvent-extracted from crushed MgO and olivine single crystals, respectively. Thus, it appears that the hard, dense matrix of igneous minerals represents a medium in which protomolecular units can be assembled. During weathering of rocks, the protomolecular units turn into complex organic molecules. These processes may have provided stereochemically constrained organics to the early Earth that were crucial to the emergence of life.

Pub.: 28 Feb '01, Pinned: 17 Feb '17

Constraints on nebular dynamics and chemistry based on observations of annealed magnesium silicate grains in comets and in disks surrounding Herbig Ae/Be stars.

Abstract: Understanding dynamic conditions in the Solar Nebula is the key to prediction of the material to be found in comets. We suggest that a dynamic, large-scale circulation pattern brings processed dust and gas from the inner nebula back out into the region of cometesimal formation-extending possibly hundreds of astronomical units (AU) from the sun-and that the composition of comets is determined by a chemical reaction network closely coupled to the dynamic transport of dust and gas in the system. This scenario is supported by laboratory studies of Mg silicates and the astronomical data for comets and for protoplanetary disks associated with young stars, which demonstrate that annealing of nebular silicates must occur in conjunction with a large-scale circulation. Mass recycling of dust should have a significant effect on the chemical kinetics of the outer nebula by introducing reduced, gas-phase species produced in the higher temperature and pressure environment of the inner nebula, along with freshly processed grains with "clean" catalytic surfaces to the region of cometesimal formation. Because comets probably form throughout the lifetime of the Solar Nebula and processed (crystalline) grains are not immediately available for incorporation into the first generation of comets, an increasing fraction of dust incorporated into a growing comet should be crystalline olivine and this fraction can serve as a crude chronometer of the relative ages of comets. The formation and evolution of key organic and biogenic molecules in comets are potentially of great consequence to astrobiology.

Pub.: 28 Feb '01, Pinned: 17 Feb '17

Relationship between Inner-Ear Fluid Pressure and Semicircular Canal Afferent Nerve Discharge

Abstract: The present study was designed to determine (1) the transcupular fluid pressure (Δ) generated across the semicircular canal cupula in response to sinusoidal head rotation, (2) the translabyrinthine dilational pressure () generated across the membranous labyrinth in response to an increase in endolymph fluid volume (hydrops), (3) afferent nerve discharge patterns generated by these distinct pressure stimuli and, (4) threshold values of Δ and required to elicit afferent neural responses. The experimental model was the oyster toadfish, Micromechanical indentation of the horizontal canal (HC) duct and utricular vestibule was used to simulate sinusoidal head rotation and fluid volume injection. Single-unit neural spike trains and endolymph pressure within the ampulla, on both sides of the cupula, were recorded simultaneously. Δ averaged 0.013 Pa per 1°/s of sinusoidal angular head velocity and averaged 0.2 Pa per 1 nL of endolymph volume injection. The most responsive afferents had a threshold sensitivity to Δ of 10 Pa and to of 5 × 10 Pa based on a discharge modulation criterion of 1 impulse/s per cycle for 2 Hz pressure stimuli. Neural sensitivity to Δ was expected on the basis of transverse cupular and hair bundle deflections. Analysis of mechanics of the end organ, neuronal projections into the crista, and individual neural firing patterns indicates that sensitivity resulted from pressure-induced distension of the ampulla that led to a nonuniform cupular deformation pattern and hair bundle deflections. This explanation is consistent with predictions of a finite element model of the end organ. Results have implications regarding the role of Δ in angular motion transduction and the role of under transient hydropic conditions.

Pub.: 31 Aug '01, Pinned: 17 Feb '17

Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates.

Abstract: Although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. We examined several intact samples of naturally occurring gas hydrate from the Gulf of Mexico for evidence of microbes. All samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. The delta(13)C of hydrate-bound methane varied from -45.1 per thousand Peedee belemnite (PDB) to -74.7 per thousand PDB, reflecting different gas origins. Stable isotope composition data indicated microbial consumption of methane or propane in some of the samples. Evidence of the presence of microbes was initially determined by 4,6-diamidino 2-phenylindole dihydrochloride (DAPI) total direct counts of hydrate-associated sediments (mean = 1.5 x 10(9) cells g(-1)) and gas hydrate (mean = 1.0 x 10(6) cells ml(-1)). Small-subunit rRNA phylogenetic characterization was performed to assess the composition of the microbial community in one gas hydrate sample (AT425) that had no detectable associated sediment and showed evidence of microbial methane consumption. Bacteria were moderately diverse within AT425 and were dominated by gene sequences related to several groups of Proteobacteria, as well as Actinobacteria and low-G + C Firmicutes. In contrast, there was low diversity of Archaea, nearly all of which were related to methanogenic Archaea, with the majority specifically related to Methanosaeta spp. The results of this study suggest that there is a direct association between microbes and gas hydrate, a finding that may have significance for hydrocarbon flux into the Gulf of Mexico and for life in extreme environments.

Pub.: 27 Oct '01, Pinned: 17 Feb '17

Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives.

Abstract: The molecular and isotopic compositions of lipid biomarkers of cultured Aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring. Thermocrinis ruber, Thermocrinis sp. strain HI 11/12, Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus, and Aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. The n-C(20:1) and cy-C(21) fatty acids dominated all of the Aquificales, while the alkyl glycerol ethers were mainly C(18:0). These Aquificales biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C(18) and C(20) alkyl groups were prevalent. Phospholipid fatty acids included both the Aquificales n-C(20:1) and cy-C(21), plus a series of iso-branched fatty acids (i-C(15:0) to i-C(21:0)), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in (13)C relative to source water CO(2) by 10.9 and 17.2 per thousand, respectively. The C(20-21) fatty acids of the PSC were less depleted than the iso-branched fatty acids, 18.4 and 22.6 per thousand, respectively. The biomass of T. ruber grown on CO(2) was depleted in (13)C by only 3.3 per thousand relative to C source. In contrast, biomass was depleted by 19.7 per thousand when formate was the C source. Independent of carbon source, T. ruber lipids were heavier than biomass (+1.3 per thousand). The depletion in the C(20-21) fatty acids from the PSC indicates that Thermocrinis biomass must be similarly depleted and too light to be explained by growth on CO(2). Accordingly, Thermocrinis in the PSC is likely to have utilized formate, presumably generated in the spring source region.

Pub.: 27 Oct '01, Pinned: 17 Feb '17

Three-dimensional tissue assemblies: novel models for the study of Salmonella enterica serovar Typhimurium pathogenesis.

Abstract: The lack of readily available experimental systems has limited knowledge pertaining to the development of Salmonella-induced gastroenteritis and diarrheal disease in humans. We used a novel low-shear stress cell culture system developed at the National Aeronautics and Space Administration in conjunction with cultivation of three-dimensional (3-D) aggregates of human intestinal tissue to study the infectivity of Salmonella enterica serovar Typhimurium for human intestinal epithelium. Immunohistochemical characterization and microscopic analysis of 3-D aggregates of the human intestinal epithelial cell line Int-407 revealed that the 3-D cells more accurately modeled human in vivo differentiated tissues than did conventional monolayer cultures of the same cells. Results from infectivity studies showed that Salmonella established infection of the 3-D cells in a much different manner than that observed for monolayers. Following the same time course of infection with Salmonella, 3-D Int-407 cells displayed minimal loss of structural integrity compared to that of Int-407 monolayers. Furthermore, Salmonella exhibited significantly lower abilities to adhere to, invade, and induce apoptosis of 3-D Int-407 cells than it did for infected Int-407 monolayers. Analysis of cytokine expression profiles of 3-D Int-407 cells and monolayers following infection with Salmonella revealed significant differences in expression of interleukin 1alpha (IL-1alpha), IL-1beta, IL-6, IL-1Ra, and tumor necrosis factor alpha mRNAs between the two cultures. In addition, uninfected 3-D Int-407 cells constitutively expressed higher levels of transforming growth factor beta1 mRNA and prostaglandin E2 than did uninfected Int-407 monolayers. By more accurately modeling many aspects of human in vivo tissues, the 3-D intestinal cell model generated in this study offers a novel approach for studying microbial infectivity from the perspective of the host-pathogen interaction.

Pub.: 13 Oct '01, Pinned: 17 Feb '17

Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming.

Abstract: Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 +/- 22 EM root tips/core in forest soil; 68 +/- 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 +/- 0.5 species/core in forest soil; 1.2 +/- 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.

Pub.: 28 Nov '01, Pinned: 17 Feb '17

Predicting the risk of Lyme disease: habitat suitability for Ixodes scapularis in the north central United States.

Abstract: The distribution and abundance of Ixodes scapularis were studied in Wisconsin, northern Illinois, and portions of the Upper Peninsula of Michigan by inspecting small mammals for ticks and by collecting questing ticks at 138 locations in state parks and natural areas. Environmental data were gathered at a local level (i.e., micro and meso levels), and a geographic information system (GIS) was used with several digitized coverages of environmental data to create a habitat profile for each site and a grid map for Wisconsin and Illinois. Results showed that the presence and abundance of I. scapularis varied, even when the host population was adequate. Tick presence was positively associated with deciduous, dry to mesic forests and alfisol-type soils of sandy or loam-sand textures overlying sedimentary rock. Tick absence was associated with grasslands, conifer forests, wet to wet/mesic forests, acidic soils of low fertility and a clay soil texture, and Precambrian bedrock. We performed a discriminant analysis to determine environmental differences between positive and negative tick sites and derived a regression equation to examine the probability of I. scapularis presence per grid. Both analyses indicated that soil order and land cover were the dominant contributors to tick presence. We then constructed a risk map indicating suitable habitats within areas where I. scapularis is already established. The risk map also shows areas of high probability the tick will become established if introduced. Thus, this risk analysis has both explanatory power and predictive capability.

Pub.: 03 Apr '02, Pinned: 17 Feb '17

Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon.

Abstract: The low-shear environment of optimized rotation suspension culture allows both eukaryotic and prokaryotic cells to assume physiologically relevant phenotypes that have led to significant advances in fundamental investigations of medical and biological importance. This culture environment has also been used to model microgravity for ground-based studies regarding the impact of space flight on eukaryotic and prokaryotic physiology. We have previously demonstrated that low-shear modeled microgravity (LSMMG) under optimized rotation suspension culture is a novel environmental signal that regulates the virulence, stress resistance, and protein expression levels of Salmonella enterica serovar Typhimurium. However, the mechanisms used by the cells of any species, including Salmonella, to sense and respond to LSMMG and identities of the genes involved are unknown. In this study, we used DNA microarrays to elucidate the global transcriptional response of Salmonella to LSMMG. When compared with identical growth conditions under normal gravity (1 x g), LSMMG differentially regulated the expression of 163 genes distributed throughout the chromosome, representing functionally diverse groups including transcriptional regulators, virulence factors, lipopolysaccharide biosynthetic enzymes, iron-utilization enzymes, and proteins of unknown function. Many of the LSMMG-regulated genes were organized in clusters or operons. The microarray results were further validated by RT-PCR and phenotypic analyses, and they indicate that the ferric uptake regulator is involved in the LSMMG response. The results provide important insight about the Salmonella LSMMG response and could provide clues for the functioning of known Salmonella virulence systems or the identification of uncharacterized bacterial virulence strategies.

Pub.: 09 Oct '02, Pinned: 17 Feb '17

Radiometric Measurement Comparison on the Integrating Sphere Source Used to Calibrate the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Landsat 7 Enhanced Thematic Mapper Plus (ETM+)

Abstract: As part of a continuing effort to validate the radiometric scales assigned to integrating sphere sources used in the calibration of Earth Observing System (EOS) instruments, a radiometric measurement comparison was held in May 1998 at Raytheon/Santa Barbara Remote Sensing (SBRS). This comparison was conducted in support of the calibration of the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Landsat 7 Enhanced Thematic Mapper Plus (ETM+) instruments. The radiometric scale assigned to the Spherical Integrating Source (SIS100) by SBRS was validated through a comparison with radiometric measurements made by a number of stable, well-characterized transfer radiometers from the National Institute of Standards and Technology (NIST), the National Aeronautics and Space Administration’s Goddard Space Flight Center (NASA’s GSFC), and the University of Arizona Optical Sciences Center (UA). The measured radiances from the radiometers differed by ±3 % in the visible to near infrared when compared to the SBRS calibration of the sphere, and the overall agreement was within the combined uncertainties of the individual measurements. In general, the transfer radiometers gave higher values than the SBRS calibration in the near infrared and lower values in the blue. The measurements of the radiometers differed by ±4 % from 800 nm to 1800 nm compared to the SBRS calibration of the sphere, and the overall agreement was within the combined uncertainties of the individual measurements for wavelengths less than 2200 nm. The results of the radiometric measurement comparison presented here supplement the results of previous measurement comparisons on the integrating sphere sources used to calibrate the Multi-angle Imaging SpectroRadiometer (MISR) at NASA’s Jet Propulsion Laboratory (JPL), Pasadena, CA and the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) at NEC Corporation, Yokohama, Japan.

Pub.: 01 Jun '03, Pinned: 17 Feb '17

Functional profiling of a human cytomegalovirus genome.

Abstract: Human cytomegalovirus (HCMV), a ubiquitous herpesvirus, causes a lifelong subclinical infection in healthy adults but leads to significant morbidity and mortality in neonates and immunocompromised individuals. Its ability to grow in different cell types is responsible for HCMV-associated diseases, including mental retardation and retinitis, and vascular disorders. To globally assess viral gene function for replication in cells, we determined the genomic sequence of a bacterial artificial chromosome (BAC)-based clone of HCMV Towne strain and used this information to delete each of its 162 unique ORFs and generate a collection of viral mutants. The growth of these mutants in different cultured cells was examined to systematically investigate the necessity of each ORF for replication. Our results showed that 45 ORFs are essential for viral replication in fibroblasts and 117 are nonessential. Some genes were found to be required for viral replication in retinal pigment epithelial cells and microvascular endothelial cells, but not in fibroblasts, indicating their role as tropism factors. Interestingly, several viral mutants grew 10- to 500-fold better than the parental strain in different cell types, suggesting that the deleted ORFs encode replication temperance or repressing functions. Thus, HCMV encodes supportive and suppressive growth regulators for optimizing its replication in human fibroblasts, epithelial, and endothelial cells. Suppression of viral replication by virus-encoded temperance factors represents a novel mechanism for regulating the growth of an animal virus, and may contribute to HCMV's optimal infection of different tissues and successful proliferation among the human population.

Pub.: 19 Nov '03, Pinned: 17 Feb '17

Linking field-based ecological data with remotely sensed data using a geographic information system in two malaria endemic urban areas of Kenya.

Abstract: BACKGROUND: Remote sensing technology provides detailed spectral and thermal images of the earth's surface from which surrogate ecological indicators of complex processes can be measured. METHODS: Remote sensing data were overlaid onto georeferenced entomological and human ecological data randomly sampled during April and May 2001 in the cities of Kisumu (population asymptotically equal to 320,000) and Malindi (population asymptotically equal to 81,000), Kenya. Grid cells of 270 meters x 270 meters were used to generate spatial sampling units for each city for the collection of entomological and human ecological field-based data. Multispectral Thermal Imager (MTI) satellite data in the visible spectrum at five meter resolution were acquired for Kisumu and Malindi during February and March 2001, respectively. The MTI data were fit and aggregated to the 270 meter x 270 meter grid cells used in field-based sampling using a geographic information system. The normalized difference vegetation index (NDVI) was calculated and scaled from MTI data for selected grid cells. Regression analysis was used to assess associations between NDVI values and entomological and human ecological variables at the grid cell level. RESULTS: Multivariate linear regression showed that as household density increased, mean grid cell NDVI decreased (global F-test = 9.81, df 3,72, P-value = <0.01; adjusted R2 = 0.26). Given household density, the number of potential anopheline larval habitats per grid cell also increased with increasing values of mean grid cell NDVI (global F-test = 14.29, df 3,36, P-value = <0.01; adjusted R2 = 0.51). CONCLUSIONS: NDVI values obtained from MTI data were successfully overlaid onto georeferenced entomological and human ecological data spatially sampled at a scale of 270 meters x 270 meters. Results demonstrate that NDVI at such a scale was sufficient to describe variations in entomological and human ecological parameters across both cities.

Pub.: 12 Dec '03, Pinned: 17 Feb '17

Intracellular localization of a group II chaperonin indicates a membrane-related function.

Abstract: Chaperonins are protein complexes that are believed to function as part of a protein folding system in the cytoplasm of the cell. We observed, however, that the group II chaperonins known as rosettasomes in the hyperthermophilic archaeon Sulfolobus shibatae, are not cytoplasmic but membrane associated. This association was observed in cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C by using immunofluorescence microscopy and in thick sections of rapidly frozen cells grown at 76 degrees C by using immunogold electron microscopy. We observed that increased abundance of rosettasomes after heat shock correlated with decreased membrane permeability at lethal temperature (92 degrees C). This change in permeability was not seen in cells heat-shocked in the presence of the amino acid analogue azetidine 2-carboxylic acid, indicating functional protein synthesis influences permeability. Azetidine experiments also indicated that observed heat-induced changes in lipid composition in S. shibatae could not account for changes in membrane permeability. Rosettasomes purified from cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C bind to liposomes made from either the bipolar tetraether lipids of Sulfolobus or a variety of artificial lipid mixtures. The presence of rosettasomes did not significantly change the transition temperature of liposomes, as indicated by differential scanning calorimetry, or the proton permeability of liposomes, as indicated by pyranine fluorescence. We propose that these group II chaperonins function as a structural element in the natural membrane based on their intracellular location, the correlation between their functional abundance and membrane permeability, and their potential distribution on the membrane surface.

Pub.: 16 Dec '03, Pinned: 17 Feb '17