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All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Abundant raw material for cis-regulatory evolution in humans

Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

NASA Discipline Evolutionary Biology↗
NASA NTRS1981

Stability of goethite /alpha-FeOOH/ and lepidocrocite /gamma-FeOOH/ to dehydration by UV radiation - Implications for their occurrence on the Martian surface

The geochemistry of the FeOOH polymorphs is an important consideration when evaluating the likelihood of an occurrence of detectable amounts of these minerals on Mars. An investigation is conducted regarding the stability of the FeOOH polymorphs geothite and lepidocrocite to dehydration in the presence of UV radiation. A thorough characterization of the FeOOH powders used in the laboratory experiments is presented, and the irradiational facility and experimental procedures are described. The results obtained in the conducted experiments are discussed. It is found that there is as yet no basis in laboratory experiments for inferring that perceptible UV photodehydration of FeOOH polymorphs will occur naturally on the surface of Mars on a time scale of at least 10-100 years.

Morris, R. V.↗
NASA NTRS1988

Possible significance of cubic water-ice, H2O-Ic, in the atmospheric water cycle of Mars

The possible formation and potential significance of the cubic ice polymorph on Mars is discussed. When water-ice crystallizes on Earth, the ambient conditions of temperature and pressure result in the formation of the hexagonal ice polymorph; however, on Mars, the much lower termperature and pressures may permit the crystallization of the cubic polymorph. Cubic ice has two properties of possible importance on Mars: it is an excellant nucleator of other volatiles (such as CO2), and it undergoes an exothermic transition to hexagonal ice at temperatures above 170 K. These properties may have significant implications for both martian cloud formation and the development of the seasonal polar caps.

Gooding, James L.↗
NASA NTRS1991

Glass formation and crystallization in high-temperature glass-ceramics and Si3N4

The softening of glassy grain boundaries in ceramic matrix composites and Si3N4 at high temperatures reduces mechanical strength and the upper-use temperature. By crystallizing this glass to a more refractory crystalline phase, a material which performs at higher temperatures may result. Three systems were examined: a cordierite composition with ZrO2 as a nucleating agent; celsian compositions; and yttrium silicate glasses both in bulk and intergranular in Si3N4. For the cordierite compositions, a series of metastable phases was obtained. The crystallization of these compositions was summarized in terms of metastable ternary isothermal sections. Zircon formed at the expense of ZrO2 and spinel. In SiC composites, the transformations were slower. In celsian, two polymorphs were crystallized. One phase, hexacelsian, which always crystallized, even when metastable, had an undesirable volume change. The other phase, celsian, was very difficult to crystallize. In yttrium silicate bulk glasses, similar in composition to the intergranular glass in Si3N4, a number of polymorphs of Y2Si2O7 were crystallized. The conditions under which these polymorphs formed are compared with crystallization in Si3N4.

Drummond, Charles H., III↗
NASA NTRS1997

Mineralogy of Meteorite Groups

Approximately 275 mineral species have been identified in meteorites, reflecting diverse redox environments, and, in some cases, unusual nebular formation conditions. Anhydrous ordinary, carbonaceous and R chondrites contain major olivine, pyroxene and plagioclase; major opaque phases include metallic Fe-Ni, troilite and chromite. Primitive achondrites are mineralogically similar. The highly reduced enstatite chondrites and achondrites contain major enstatite, plagioclase, free silica and kamacite as well as nitrides, a silicide and Ca-, Mg-, Mn-, Na-, Cr-, K- and Ti-rich sulfides. Aqueously altered carbonaceous chondrites contain major amounts of hydrous phyllosilicates, complex organic compounds, magnetite, various sulfates and sulfides, and carbonates. In addition to kamacite and taenite, iron meteorites contain carbides, elemental C, nitrides, phosphates, phosphides, chromite and sulfides. Silicate inclusions in IAB/IIICD and lIE iron meteorites consist of mafic silicates, plagioclase and various sulfides, oxides and phosphates. Eucrites, howardites and diogenites have basaltic to orthopyroxenitic compositions and consist of major pyroxene and calcic plagioclase and several accessory oxides. Ureilttes .are made up mainly of calcic, chromian olivine and low-Ca clinopyroxene embedded in a carbonaceous matrix; accessory phases include the C polymorphs graphite, diamond, lonsdaleite and chaoite as well as metallic Fe-Ni, troilite and halides. Angrites are achondrites rich in fassaitic pyroxene (i.e. , AI-Ti diopside); minor olivine with included magnesian kirschsteinite is also present. Martian meteorites comprise basalts, Iherzolites, a dunite and an orthopyroxenite. Major phases include various pyroxenes and olivine; minor to accessory phases include various sulfides, magnetite, chromite and Ca-phosphates. Lunar meteorites comprise mare basalts with major augite and calcic plagioclase and anorthositic breccias with major calcic plagioclase. Several meteoritic phases were formed by shock metamorphism. Martensite (a2-fe,Ni) has a distorted body-centered-cubic structure and formed by a shear transformation from taenite during shock reheating and rapid cooling. The C polymorphs diamond, lonsdaleite and chaoite formed by shock from graphite. Suessite formed in the North Haig ureilite by reduction of Fe and Si (possibly from olivine) via reaction with carbonaceous matrix material. Ringwoodite, the spinel form of (Mg,Fe)2Si04, and majorite, a polymorph of (Mg,Fe)Si03 with the garnet structure, formed inside shock veins in highly shocked ordinary chondrites. Secondary minerals in meteorite finds that formed during terrestrial weathering include oxides and hy-. droxides formed directly from metallic Fe-Ni by oxidation, phosphates formed by the alteration of schreibersite, and sulfates formed by alteration of troilite.

Rubin, Alan E.↗
NASA NTRSDate not supplied

One-Carbon Metabolism and SANS 2022 Update

Spaceflight Associated Neuro-ocular Syndrome, or SANS, affects a subset of astronauts (1, 2), and biochemical evidence has documented differences in those astronauts (3). Specifically, they had higher circulating concentrations of metabolites of the one-carbon metabolic pathway (1C), including homocysteine, and these concentrations were higher before flight (3). After ruling out many potential confounding factors in these otherwise healthy individuals (e.g., sex, kidney function, vitamin status, coffee consumption), a study of genetics was warranted. In an initial pilot effort, we documented a genetic predisposition to develop ophthalmic changes after long-duration space flight (4). That is, from a limited study of 5 single-nucleotide polymorphisms (SNPs), we found that the G allele for the MTRR A66G SNP was associated with a greater risk of choroidal folds and cotton-wool spots after flight, and the C allele for SHMT1 C1420T was protective against optic disc edema (4). These data provide a potential pathway for understanding why some individuals develop SANS, while others do not. The initial pilot study of 5 SNPs yielded striking findings, but the 1C pathway is far more complex. An effort was undertaken to examine more than 500 1C SNPs to see if a broader examination could help illuminate this association. That work is ongoing. The astronaut findings led us to advocate for the inclusion of 1C pathway genetic and biochemistry testing on other SANS-related projects, noting that genetics might help identify responders, non-responders, or outliers. The first such effort yielded evidence of an association of specific forms of the MTRR and SHMT-1 SNPs and vitamin B12 status with end-tidal CO2 after acute carbon dioxide exposure (5). The second such effort led to the identification that individuals exposed to strict head-down tilt and CO2 for 30-d who developed optic disc edema also had risk alleles for the two SNPs described above (6). Additionally, we identified a clinical population with many characteristics either attributed or purported to be involved in the ocular changes seen in affected astronauts: women with polycystic ovary syndrome (PCOS). PCOS is a condition of androgen excess and anovulatory menstrual cycles. The shared characteristics and clinical findings between SANS and PCOS generally include higher circulating homocysteine concentrations, increased retinal nerve fiber layer thickness, increased androgen concentrations (or responses), and altered carbohydrate metabolism. To our knowledge, no study has examined whether women with PCOS have asymptomatic ophthalmic anomalies observed in astronauts with SANS. While researchers have evaluated the one-carbon metabolism pathway polymorphisms of PCOS patients, and initial studies show an association with certain one-carbon polymorphisms, none have looked at the set of SNPs identified in our studies that are associated with ophthalmic changes in astronauts. Accordingly, we designed a study to evaluate the association of one-carbon pathway SNPs and ophthalmic findings in patients with PCOS and/or IIH compared to controls. Subjects provided blood samples for vitamin and one carbon biochemistry analyses, an extensive analysis of >500 SNPs associated with one carbon metabolism and had eye examinations and ocular imaging. Data analysis are underway. The data collected to date have shown associations between one carbon pathway biochemistry and genetics and incidence of SANS. The mechanisms for SANS has yet to be identified, although many hypotheses exist. Based on our data, we have developed (8, 9) and expanded (6) a multi-hit hypothesis for how these seemingly disparate findings could be linked. While intriguing, the hypothesis represents the starting point for further research. We aim to clarify the relationship between B-vitamin status and genetics with regard to the risk of SANS. Ultimately, understanding the mechanism(s) behind this will provide a means to predict, prevent, or treat these ophthalmologic pathologies in astronauts, and terrestrial populations.

S M Smith↗
NASA NTRS2001

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

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.

Non-NASA Center↗
NASA NTRS2023

Microstructural Changes and Pb Mobility During the Zircon to Reidite Transformation: Implications for Planetary Impact Chronology

Impact events modify and leave behind a complex history of rock metamorphism on terrestrial planets. Evidence for an impact event may be recorded in physical changes to minerals, such as mineral deformation and formation of high P-T polymorphs, but also in the form of chemical fingerprints, such as enhanced elemental diffusion and isotopic mixing. Here we explore laboratory shock-induced physical and chemical changes to zircon and feldspar, the former of which is of interest because its trace elements abundances and isotope ratios are used extensively in geochemistry and geochronology. To this end, a granular mixture of Bishop Tuff sanidine and Kuehl Lake zircon, both with well characterized Pb isotope compositions, was prepared and then shocked via a flat plate accelerator. The peak pressure of the experiment, as calculated by the impedance matching method, was ~24 GPa although a broader range of P-T conditions is anticipated due to starting sample porosity. Unshocked and shocked materials were characterized via scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), and Raman spectroscopy. These methods show that the starting zircon material had abundant metamict regions, and the conversion of the feldspar to glass in the post-shock material. Analyses of the shocked product also yielded multiple occurrences of the high-pressure ZrSiO 4 polymorph reidite, with some domains up to 300 μm across. The possibility of U-Pb system disturbance was evaluated via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and secondary ion mass spectrometry (SIMS). The isotopic data reveal that disturbance of the U-Pb geochronometer in the reidite was minimal (<2% for the main U-Pb geochronometers). To better constrain the P-T conditions during the shock experiment, we complement impedance matching pressure calculations with iSALE2D impact simulations. The simulated results yield a range of P-T conditions experienced during the experiment and show that much of the sample may have reached >30 GPa, which is consistent with formation of reidite. In the recovered shocked material, we identified lamellae of reidite, some of which interlock with zircon lamellae. Reidite {112} twins were identified, which we interpret to have formed to reduce stress between the crystal structure of the host zircon and reidite. These two findings support the interpretation that shear transformation enabled the transition of zircon to reidite. The size and presence of reidite found here indicate that this phase is probably common in impact-shocked crustal rocks that experienced ~25 to ~35 GPa, especially when the target material has porosity. Additionally, shock loading of the zircon and transformation to reidite at these pressures in porous materials is unlikely to significantly disturb the U-Pb system in zircon and that the reidite inherits the primary U and Pb elemental and isotopic ratios from the zircon.

Bishop Tuff↗
NASA NTRS1979

Infrared spectra of the Orgueil /C-1/ chondrite and serpentine minerals

Infrared spectroscopy of the Orgueil C-1 chondrite and polymorphs of serpentine was performed in order to further define the mineralogy of Orgueil. Spectra of the meteorite and a synthetic serpentine (Mg3(Si2O5)(OH)4) were obtained in the regions from 1400 to 200 and from 4000 to 2500 kayers using a double beam infrared spectrometer. The spectra of Orgueil are found to be incompatible with those of the chrysotile, antigorite and lizardite polymorphs of serpentine, indicating a very low abundance of these minerals in the meteorite. It is suggested that chamosite or minerals related to chamosites may prove to be compatible with the compositional, structural and infrared properties of Orgueil.

Zaikowski, A.↗
NASA NTRS1982

The tectonics of Ganymede

Evidence of tectonic activity has been found on the Jupiter moon Ganymede, which is the largest solar system icy object known. The transition of dense ice polymorphs in the deep interior of large icy bodies to either less dense polymorphs or liquid water at shallow depths, as internal differentiation and formation of a silicate core occurs, could increase Ganymede's surface area by as much as 7%. If the tectonic evolution of Ganymede is to be described by a progressive fragmentation of an initially uniform lithosphere in response to planetary expansion, the stress transmitted across different areas of bright terrain must differ significantly. Alternatively, lithospheric thickness variations or such other mechanisms as tidal distortion or convection stresses beneath the lithosphere may have been important.

Parmentier, E. M.↗
NASA NTRS1982

Spectral characteristics of the iron oxides with application to the Martian bright region mineralogy

Reflectance spectra of eight polymorphs of FeOOH and Fe2O3 are determined in order to clarify the nature and significance of the iron oxide mineralogy on Mars. The effect of other components that might interfere with iron oxide absorption features is qualitatively constrained through the use of the Kebulka-Munk theory. It is found that the effect of temperature complicates the identification of a given Fe(3+) phase based on the position of the 6A1-4T1 absorption feature. While the Fe(3+) crystal field transitions are spin forbidden, most of the iron oxide polymorphs exhibit anomalously intense crystal field absorption features due to magnetic coupling between adjacent FeO6 octahedra. It is suggested that the resulting deviations from observed remotely sensed reflectance spectra of Mars may provide a basis for the exclusion of many iron oxide phases as significant components of the Martian Fe(3+) mineralogy. A comparison of these results with the visible region spectra of Martian bright regions indicates that the predominant Fe(3+)-bearing phase may be a magnetically disordered material, such as amorphous gels, some ferric sulphates, and other minerals in which Fe(3+) ions in the crystal structure are not magnetically coupled.

Sherman, D. M.↗
NASA NTRS1987

Hydrogenated amorphous carbon (a:C-H) in the planetary nebula NGC 7027

A spectroscopic identification of the infrared continuum radiation is proposed for the planetary nebula NGC 7027. Hydrogenated amorphous carbon (a:C-H) is shown to account for the undulating spectrum between 5 and 15 microns. The unidentified infrared emission bands lie at the peaks in the a:C-H spectrum, pointing to their association with a carbon polymorph, possibly a:C-H or polycyclic aromatic hydrocarbon molecules. Except for atomic emission lines, all the infrared emission from NGC 7027 comes from one or another polymorph of carbon.

Goebel, John H.↗
NASA NTRS1994

The structural changes of water ice I during warmup

The polymorph transitions of vapor deposited water ice I during warmup from 15 K to 210 K was mapped by means of selected area electron diffraction. The polymorph transitions account for many phenomena observed in laboratory analog studies of cometary outgassing and radial diffusion in UV photolyzed interstellar ices.

Jenniskens, Peter↗
NASA NTRS1994

Spectral reflectance properties of carbon-bearing materials

The 0.3-2.6 micrometers spectral reflectance properties of carbon polymorphs (graphite, carbon black, diamond), carbides (silicon carbide, cementite), and macromolecular organic-bearing materials (coal, coal tar extract, oil sand, oil shale) are found to vary from sample to sample and among groups. The carbon polymorphs are readily distinguishable on the basis of their visible-near infrared spectral slopes and shapes. The spectra of macromolecular organic-bearing materials show increases in reflectance toward longer wavelengths, exceeding the reflectance rise of more carbon-rich materials. Reflectance spectra of carbonaceous materials are affected by the crystal structure, composition, and degree of order/disorder of the samples. The characteristic spectral properties can potentially be exploited to identify individual carbonaceous grains in meteorites (as separates or in situ) or to conduct remote sensing geothermometry and identification of carbonaceous phases on asteroids.

Cloutis, Edward A.↗
NASA NTRS1999

Genetic Regulation of Charged Particle Mutagenesis in Human Cells

Our studies use a series of syngeneic, and where possible, isogenic human B-lymphoblastoid cell lines to assess the genetic factors that modulate susceptibility apoptosis and their impact on the mutagenic risks of low fluence exposures to 1 GeV Fe ions and 55 MeV protons. These ions are representative of the types of charged particle radiation that are of particular significance for human health in the space radiation environment. The model system employs cell lines derived from the male donor WIL-2. These cells have a single X chromosome and they are hemizygous for one mutation marker, hypoxanthine phosphoribosyltransferase (HPRT). TK6 and WTK1 cells were each derived from descendants of WIL-2 and were each selected as heterozygotes for a second mutation marker, the thymidine kinase (TK) gene located on chromosome 17q. The HPRT and TK loci can detect many different types of mutations, from single basepair substitutions up to large scale loss of heterozygosity (LOH). The single expressing copy of TK in the TK6 and WTKI cell lines is found on the same copy of chromosome 17, and this allele can be identified by a restriction fragment length polymorphism (RFLP) identified when high molecular weight DNA is digested by the SacI restriction endonuclease and hybridized against the cDNA probe for TK. A large series of polymorphic linked markers has been identified that span more than 60 cM of DNA (approx. 60 megabasepairs) and distinguish the copy of chromosome 17 bearing the initially active TK allele from the copy of chromosome 17 bearing the silent TK allele in both TK6 and WTKI cells. TK6 cells express normal p53 protein while WTKI cells express homozygous mutant p53. Expression of mutant p53 can increase susceptibility to x-ray-induced mutations. It's been suggested that the increased mutagenesis in p53 mutant cells might be due to reduced apoptosis.

Kronenberg, Amy↗
NASA NTRS2003

Crystallization Physics in Biomacromolecular Systems

The crystals are built of molecules of protein, nucleic acid and their complexes, like viruses, approx. 5x10(exp 3)+ 3x10(exp 6) Da in weight and 2 + 20 nm in effective diameter. This size strongly exceeds action range of molecular forces and makes a big difference with inorganic crystals. Intermolecular contacts form patches on the biomacromolecular surface. Each patch may occupy only a small percent of the whole surface and vary from polymorph to polymorph of the same protein. Thus, under different conditions (pH, solution chemistry, temperature, any area on the macromolecular surface may form a contact. The crystal Young moduli, E approx. equals 0.1 + 0.5 GPa are more than 10 times lower than that of inorganics and the biomolecules themselves. Water within biocrystals (30-70%) is unable to flow unless typical deformation time is longer than approx. 10(exp -5)s. This explains the discrepancy between light scattering and static measurements of E. Nucleation and Growth requires typically concentrations exceeding the equilibrium ones up to 100 times - because of the new size scale results in 10 - 10(exp 3) times lower kinetic coefficients than that needed for inorganic solution growth. All phenomena observed in the latter occur with protein crystallization and are even better studied by AFM. Crystals are typically facetted. Among unexpected findings of general significance are - net molecular exchange flux at kinks is much lower than that expected from supersaturation, steps with low (< approx. 10(exp -2)) kink density at steps follow Gibbs-Thomson law only at very low supersaturations, step segment growth rate may be independent of step energy. Crystal perfection is a must of biocrystallization to achieve the major goal to find 3-D atomic structure of biomacromolecules by x-ray diffraction. Poor diffraction resolution (> 3Angstrom) makes crystallization a bottleneck for structural biology. All defects typical of small molecule crystals are found in biocrystals, but the defects responsible for poor resolution are not identified. Conformational changes are one of them. Biocrystallization in microgravity reportedly results in 20% cases of better crystals. The mechanism of how lack of convection can do this is still not clear. Lower supersaturation, self-purification &om preferentially trapped homologous impurities and step bunching are viable hypotheses.

Chernov, A. A.↗
NASA NTRS2001

A comparison of mutations induced by accelerated iron particles versus those induced by low earth orbit space radiation in the FEM-3 gene of Caenorhabditis elegans

The fem-3 gene of Caenorhabditis elegans was employed to determine the mutation frequency as well as the nature of mutations induced by low earth orbit space radiation ambient to Space Shuttle flight STS-76. Recovered mutations were compared to those induced by accelerated iron ions generated by the AGS synchrotron accelerator at Brookhaven National Laboratory. For logistical reasons, dauer larvae were prepared at TCU, transported to either Kennedy Space Center or Brookhaven National Laboratory, flown in space or irradiated, returned to TCU and screened for mutants. A total of 25 fem-3 mutants were recovered after the shuttle flight and yielded a mutation frequency of 2.1x10(-5), roughly 3.3-fold higher than the spontaneous rate of 6.3x10(-6). Four of the mutations were homozygous inviable, suggesting that they were large deletions encompassing fem-3 as well as neighboring, essential genes. Southern blot analyses revealed that one of the 25 contained a polymorphism in fem-3, further evidence that space radiation can induce deletions. While no polymorphisms were detected among the iron ion-induced mutations, three of the 15 mutants were homozygous inviable, which is in keeping with previous observations that high LET iron particles generate deficiencies. These data provide evidence, albeit indirect, that an important mutagenic component of ambient space radiation is high LET charged particles such as iron ions.

short duration↗
NASA NTRS2006

Genetic mutation underlying orthostatic intolerance and diagnostic and therapeutic methods relating thereto

Isolated polynucleotide molecules and peptides encoded by these molecules are used in the analysis of human norepinephrine (NE) transporter variants, as well as in diagnostic and therapeutic applications, relating to a human NE transporter polymorphism. By analyzing genomic DNA or amplified genomic DNA, or amplified cDNA derived from mRNA, it is possible to type a human NE transporter with regard to the human NE transporter polymorphism, for example, in the context of diagnosing and treating NE transport impairments, and disorders associated with NE transport impairments, such as orthostatic intolerance.

Robertson, David↗