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Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA

Although mRNA amplification is necessary for microarray analyses from limited amounts of cells and tissues, the accuracy of transcription profiles following amplification has not been well characterized. We tested the fidelity of differential gene expression following linear amplification by T7-mediated transcription in a well-established in vitro model of cytokine [tumor necrosis factor alpha (TNFalpha)]-stimulated human endothelial cells using filter arrays of 13,824 human cDNAs. Transcriptional profiles generated from amplified antisense RNA (aRNA) (from 100 ng total RNA, approximately 1 ng mRNA) were compared with profiles generated from unamplified RNA originating from the same homogeneous pool. Amplification accurately identified TNFalpha-induced differential expression in 94% of the genes detected using unamplified samples. Furthermore, an additional 1,150 genes were identified as putatively differentially expressed using amplified RNA which remained undetected using unamplified RNA. Of genes sampled from this set, 67% were validated by quantitative real-time PCR as truly differentially expressed. Thus, in addition to demonstrating fidelity in gene expression relative to unamplified samples, linear amplification results in improved sensitivity of detection and enhances the discovery potential of high-throughput screening by microarrays.

Evaluation Studies↗

Complex Organic Materials on Planetary Satellites and Other Small Bodies of the Solar System

The search for organic materials on small bodies of the Solar System is conducted spectroscopically from Earth-based telescopes and from spacecraft. Although the carbonaceous meteorites carry a significant inventory of complex organic solids, the sources of these meteorites have not been identified. Infrared spectra of a sample of the suspected sources, the C- and D-class asteroids, including new data from the Spitzer Space Telescope, show signatures of silicates, but none diagnostic of organic compounds. In the absence of discrete spectral features, the low albedos and colors in the visible and near-IR spectral regions are the principal links between the organic-bearing meteorites and the asteroids. While Pluto and a few trans-neptunian objects show spectral signatures of frozen CH4. Solid CH3OH has been identified on two Centaur objects in the outer Solar System. In some cases the red colors of those objects suggest the presence of tholins. The VIMS instrument aboard the Cassini spacecraft in orbit around Saturn has detected near-IR spectral features on at least three of Saturn's satellites that are indicative or suggestive of organic molecules. One entire hemisphere of the satellite Iapetus is covered with low-albedo material that shows a spectral signature of aromatic hydrocarbons (3.3 microns) and the -CH2 stretching mode bands of an aliphatic component. Organics absorbing at 3.44 microns are suspected in the region of the south pole of Enceladus, and also on the surface of Phoebe. Organic material may originate on icy bodies in the current epoch by various processes of energy deposition into native material, or they may fall to the surface from an external (probably cometary) source. Some organic material may be pre-solar, having originated in the interstellar medium before the formation of the Solar System. Using the techniques of remote sensing, its detection and analysis are slow and difficult.

Cruikshank, Dale P.↗

Analysis of model Titan atmospheric components using ion mobility spectrometry

The Gas Chromatograph-Ion Mobility Spectrometer (GC-IMS) was proposed as an analytical technique for the analysis of Titan's atmosphere during the Cassini Mission. The IMS is an atmospheric pressure, chemical detector that produces an identifying spectrum of each chemical species measured. When the IMS is combined with a GC as a GC-IMS, the GC is used to separate the sample into its individual components, or perhaps small groups of components. The IMS is then used to detect, quantify, and identify each sample component. Conventional IMS detection and identification of sample components depends upon a source of energetic radiation, such as beta radiation, which ionizes the atmospheric pressure host gas. This primary ionization initiates a sequence of ion-molecule reactions leading to the formation of sufficiently energetic positive or negative ions, which in turn ionize most constituents in the sample. In conventional IMS, this reaction sequence is dominated by the water cluster ion. However, many of the light hydrocarbons expected in Titan's atmosphere cannot be analyzed by IMS using this mechanism at the concentrations expected. Research at NASA Ames and PCP Inc., has demonstrated IMS analysis of expected Titan atmospheric components, including saturated aliphatic hydrocarbons, using two alternate sample ionizations mechanisms. The sensitivity of the IMS to hydrocarbons such as propane and butane was increased by several orders of magnitude. Both ultra dry (waterless) IMS sample ionization and metastable ionization were successfully used to analyze a model Titan atmospheric gas mixture.

Kojiro, D. R.↗

Long-term 4.6 µm Variability in Brown Dwarfs and a New Technique for Identifying Brown Dwarf Binary Candidates

Using a sample of 361 nearby brown dwarfs, we have searched for 4.6 μm variability, indicative of large-scale rotational modulations or large-scale, long-term changes on timescales of over 10 yr. Our findings show no statistically significant variability in Spitzer's Infrared Array Camera (IRAC) channel 2 (ch2) or Wide-field Infrared Survey Explorer W2 photometry. For Spitzer the ch2 1σ limits are ∼8 mmag for objects at 11.5 mag and ∼22 mmag for objects at 16 mag. This corresponds to no variability above 4.5% at 11.5 mag and 12.5% at 16 mag. We conclude that highly variable brown dwarfs, at least two previously published examples of which have been shown to have 4.6 μm variability above 80 mmag, are very rare. While analyzing the data, we also developed a new technique for identifying brown dwarf binary candidates in Spitzer data. We find that known binaries have IRAC ch2 point response function (PRF) flux measurements that are consistently dimmer than aperture flux measurements. We have identified 59 objects that exhibit such PRF versus aperture flux differences and are thus excellent binary brown dwarf candidates.

Hunter Brooks↗

Martian Brines in Ancient Salt Lake Beds – A High Priority Target for Mars Sample Return

Mars hosts over 600 chloride deposits as identified from orbital imagery [1-3], including deposits in settings resembling dry, evaporite lacustrine bedforms on Earth. A Mars sample return mission to one of these salt lake beds has a strong potential to directly sample present-day brines originating from ancient martian surface fluids, allowing direct laboratory investigation into fluids, atmosphere, and either potential biology or prebiological conditions on the martian surface at the Noachian through the Hesperian epochs. These sites are extraordinarily well suited for sample return missions because they are favorable for landing and for drill-based sampling, and preserve samples of parent water bodies, including dissolved atmosphere and potential well-preserved biological remains. Such a mission would provide a foundational set of reference samples for understanding Mars’ physiochemical and pre-/biological history, likely to be investigated in depth for generations to come.

brine↗

Detection and Quantification of Nitrogen Compounds in Martian Solid Samples by the Sample Analysis at Mars (SAM) Instrument Suite

The Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover detected both reduced and oxidized nitrogen-bearing compounds during the pyrolysis of surface materials from three sites at Gale Crater. Preliminary detections of nitrogen species include NO, HCN, ClCN, CH3CN, and TFMA (trifluoro-Nmethyl-acetamide). On Earth, nitrogen is a crucial bio-element, and nitrogen availability controls productivity in many environments. Nitrogen has also recently been detected in the form of CN in inclusions in the Martian meteorite Tissint, and isotopically heavy nitrogen (delta N-15 approx +100per mille) has been measured during stepped combustion experiments in several SNC meteorites. The detection of nitrogen-bearing compounds in Martian regolith would have important implications for the habitability of ancient Mars. However, confirmation of indigenous Martian nitrogen bearing compounds will require ruling out their formation from the terrestrial derivatization reagents (e.g. N-methyl-N-tert-butyldimethylsilyl-trifluoroacetamide, MTBSTFA and dimethylformamide, DMF) carried for SAM's wet chemistry experiment that contribute to the SAM background. The nitrogen species we detect in the SAM solid sample analyses can also be produced during laboratory pyrolysis experiments where these reagents are heated in the presence of perchlorate, a compound that has also been identified by SAM in Mars solid samples. However, this does not preclude a Martian origin for some of these compounds, which are present in nanomolar concentrations in SAM evolved gas analyses. Analysis of SAM data and laboratory breadboard tests are underway to determine whether nitrogen species are present at higher concentrations than can be accounted for by maximum estimates of nitrogen contribution from MTBSTFA and DMF. In addition, methods are currently being developed to use GC Column 6, (functionally similar to a commercial Q-Bond column), to separate and identify unretained compounds such as NO, N2O, and NO2, which are difficult to detect by EGA-MS due to mass interferences at 30, 44 and 46, respectively. Here we present evolved gas analysis-mass spectrometry (EGA-MS) and gas chromatography mass spectrometry (GC-MS) data on the identification and quantification of these nitrogen-bearing compounds, and suggestions for their origins

Stern, Jennifer C.↗

Evaluation of the Biolog automated microbial identification system

Biolog's identification system was used to identify 39 American Type Culture Collection reference taxa and 45 gram-negative isolates from water samples. Of the reference strains, 98% were identified to genus level and 76% to species level within 4 to 24 h. Identification of some authentic strains of Enterobacter, Klebsiella, and Serratia was unreliable. A total of 93% of the water isolates were identified.

NASA Program Environmental Health↗

High Resolution Spectroscopy of Vega-like Stars: Abundances and Circumstellar Gas

Vega-like stars are main-sequence stars exhibiting excess infrared emission. In an effort to improve the information available on this class of star, 13 stars have been analyzed which have been classed as Vega-like, or have an infra-red excess attributable to dust in their circumstellar environment. In a separate paper stellar properties such as effective temperature and log g have been derived and in this poster we highlight the results of the photospheric abundance analysis also carried out during this work. King recently drew attention to the possible link between Vega-like stars and the photospheric metal-depleted class of A-stars, the Lambda Bootis stars. Since Vega-like stars are thought to have disks of dust, it might be expected that accretion of depleted gas onto the surface of these stars may cause this same phenomenon. In the 6 stars studied for depletions, none showed the extreme underabundance patterns observed in Lambda Bootis stars. However, depletions of silicon and magnesium were found in two of the sample, suggesting that these elements are in silicate dust grains in the circumstellar environment of these stars. Absorption lines attributed to circumstellar gas have been positively identified in three stars in our sample. Individual cases show evidence either of high-velocity outflowing gas, variability in the circumstellar lines observed, or evidence of circumstellar gas in excited lines of Fe II. No previous identification of circumstellar material has been made for two of the stars in question.

Dunkin, S. K.↗

Detection and Quantification of Nitrogen Compounds in the First Drilled Martian Solid Samples by the Sample Analysis at Mars (SAM) Instrument Suite on the Mars Science Laboratory (MSL)

The Sampl;e Analysis at Mars (sam) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover detected both reduced and oxidized nitrogen bearing compounds during the pyrolysis of surface materials from the three sites at Gale Crater. Preliminary detections of nitrogen species include No, HCN, ClCN, and TFMA ((trifluoro-N-methyl-acetamide), Confirmation of indigenous Martian nitrogen-bearing compounds requires quantifying N contribution from the terrestrial derivatization reagents carried for SAM's wet chemistry experiment that contribute to the SAM background. Nitrogen species detected in the SAM solid sample analyses can also be produced during laboratory pyrolysis experiments where these reagents are heated in the presence of perchlorate a compound that has also been identified by SAM in Mars solid samples.

Stern, Jennifer C.↗

Detection and Quantification of Nitrogen Compounds in the First Drilled Martian Solid Samples by the Sample Analysis at Mars (SAM) Instrument Suite on the Mars Science Laboratory (MSL)

The Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover detected both reduced and oxidized nitrogen-bearing compounds during the pyrolysis of surface materials at Yellowknife Bay in Gale Crater. Preliminary detections of nitrogen species include NO, HCN, ClCN, CH3CN, and TFMA (trifluoro-N-methyl-acetamide). Confirmation of indigenous Martian N-bearing compounds requires quantifying N contribution from the terrestrial derivatization reagents (e.g. N-methyl-N-tertbutyldimethylsilyltrifluoroacetamide, MTBSTFA and dimethylformamide, DMF) carried for SAM's wet chemistry experiment that contribute to the SAM background. Nitrogen species detected in the SAM solid sample analyses can also be produced during laboratory pyrolysis experiments where these reagents are heated in the presence of perchlorate, a compound that has also been identified by SAM in Mars solid samples.

Curiosity rover↗

Mineralogical Analysis of Calcium-Aluminum-Rich Inclusions Provides Insight Into Post-Formation Processes

Introduction: Calcium-aluminum inclusions (CAIs) are cm- to mm-sized intergrowths of refractory phases found in chondritic meteorites [1]. Their mineral compositions closely match the compositions of the solids thought to condense from an extremely hot (>1500K) gas with a bulk solar composition [2-4], suggesting that CAIs were the earliest solids within the Solar System [2-4]. These inclusions provide invaluable insights into the conditions and dynamics of the early Solar System. CAIs must be transported from their formation region near the protosun to the chondrite parent-body accretion region. The nature of their journey could affect how, when, and where the secondary processes recorded in these CAIs occurred [4]. Did these secondary processes occur in the solar nebula or during accretion with the parent body, or both? How were the CAIs affected by varying thermochemical processes? To better answer these questions, we have undertaken an in-depth, textural study of the secondary alteration of select CAI samples. Methods: We chose three CAIs that experienced a range of post-formation processing to gain better understanding of secondary alteration based on previous preliminary examination [5]. Representative CAIs were chosen from NWA 5508 (CV3), NWA 12772 (CV3), and Coolidge (CL4) carbonaceous chondrites. We used scanning electron microscopy (SEM) and electron backscatter diffraction (EBSD) techniques for detailed chemical, mineralogical, and textural analysis of the CAIs. Backscattered electron (BSE) images and X-ray elemental maps were taken of Coolidge and NWA 5508 using the Lunar and Planetary Institute (LPI) Phenom SEM. The JEOL 7900F SEM at NASA Johnson Space Center (JSC) was used to obtain energy dispersive spectroscopy (EDS) chemical maps of all samples. High resolution EBSD analysis identified the mineral phases and textures, providing key information on their nature. Based on the SEM and EBSD data, minerals of interest were selected for quantitative chemical electron probe micro-analysis (EPMA) using the JEOL JXA-8530F at NASA JSC. Results and Discussion: The EDS maps show that the NWA 5508 and NWA 12772 CAIs designated “Saguaro” and “Hoopoe” respectively [5] are enriched in calcium while the Coolidge CAI designated “Cottonwood” is aluminum and magnesium rich. Saguaro. A ~1.5cm diameter igneous Type B CAI with a rounded shape. The dominant phases are melilite, spinel, and Al-Ti pyroxene with minor anorthite. Spinel is subhedral and occurs in clusters. Some of these clusters have a circular geometry which encloses other minerals, known as a palisade structure [6] (Fig. 1). Some palisades form near perfect circles while others are more irregular in shape. Melilite in Saguaro ranges in size from coarse (>250m) to fine-grained (5-7m) and forms intergrown laths. A third of the melilite grains exhibit simple twinning about their <001> axis. The spinel palisades and twinned melilite in Saguaro suggest an igneous history, and the lack of secondary minerals suggests minimal aqueous alteration. At some point in time after the initial condensation of the minerals and formation of the inclusion, the sample was remelted and quickly solidified. The formation of the palisades is still heavily debated. One hypothesis is that the palisades are the rims of smaller CAIs that accreted early on, essentially acting as xenoliths within the larger CAIs [7]. Another hypothesis suggests an igneous origin for palisade structures [6-8] wherein the melt traps gas bubbles, and the spinel nucleates on the surface of this bubble. Based on the WDS spot analyses of 41 melilite grains using EPMA, the data suggest that the composition inside and outside the palisades is nearly identical. This finding indicates that these palisades are likely not exogenous but rather formed from melt-vapor reactions. Our results are consistent with studies by Simon and Grossman,1997 [6] and Zhang et al. (2019) [8]. Hoopoe. A ~0.5cm compact Type A CAI with an irregular shape. The dominant mineral phases are melilite, spinel, and hibonite with minor amounts of anorthite, augite, and perovskite. The melilite ranges in size from ~500 to 50µm. The larger melilite grains have simple twinning along the <001> axis like melilite in Saguaro. Melilite in Hoopoe exhibits crystal-plastic strain with misorientation dominantly about the <010> and <110> axes. Spinel shows subhedral to euhedral morphology and appears in clusters. Hibonite grains are similar to spinel in habit and size but show more plastic strain. The two minerals are often found together with one appearing to replace the other. Perovskite appears in fine grained recrystallized regions alongside fine augite and spinel. The abundant strain and deformation features in the melilite and hibonite suggest that Hoopoe experienced shock. This shock could have occurred in the nebula [9] or from an impact of another body on the parent body asteroid. The appearance of fine-grained (<10m) areas of augite, perovskite, and spinel in the dominantly coarse-grained inclusion suggest recrystallization, possibly due to the sudden increase in pressure and temperature. Cottonwood. This ~0.5cm CAI exhibits distinct mineralogy and textures suggesting a high degree of alteration. It is irregular in shape. The dominant mineral phases are spinel and anorthite with minor amounts of augite and rutile. The two main texture types can be seen in Fig. 2. The first type consists of coarse euhedral to subhedral spinel and anorthite. The second includes fine grained spinel, anorthite, rutile, and iron sulfides. Within these fine-grained regions, the anorthite grains are clustered into domains exhibiting the same crystallographic orientation. Rutile exclusively occurs with fine anorthite indicating a potential relationship between the two. Cottonwood has a clear and unbroken Wark-Lovering [10] rim (Fig. 2) on one side that consists of a sequence of spinel followed by anorthite and an outer layer of augite. The abundance of the fine-grained regions containing iron oxides and iron sulfides, secondary phases such as rutile, and oriented anorthite grains is evidence for recrystallization associated with a high degree of thermal metamorphism. The EPMA analyses on both coarse- and fine-grained spinel show that the fine spinel grains are more enriched in Cr (1-2 wt. %) than their coarse counterparts (0.1-0.5 wt. %). The data suggest thermal metamorphism drove chemical exchange of the previously refractory inclusion, introducing chromium and iron as well as sulfur, which is moderately volatile. Conclusions: The three CAIs analyzed record distinct secondary nebular and parent body processes. Saguaro melted in the nebula as seen by the twinned melilite and spinel palisades. Hoopoe experienced intense shock which deformed its melilite and recrystallized perovskite, augite, and spinel in fine-grained regions. Cottonwood shows evidence of recrystallization and chemical changes consistent with thermal metamorphism occurring after accretion into the parent-body.

V E Burnette↗