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All sourcesNASA NTRSDOE OSTI
NASA NTRS1988

IRAS 14348-1447, an ultraluminous pair of colliding, gas-rich galaxies - The birth of a quasar?

Ground-baed observations of the object IRAS 14348-1447, which was discovered with the Infrared Astronomical Satellite, show that it is an extremely luminous colliding galaxy system that emits more than 95 percent of its energy at FIR wavelengths. IRAS 14348-1447, which is receeding from the sun at 8 percent of the speed of light, has a bolometric luminosity more than 100 times larger than that of the Galaxy, and is therefore as luminous as optical quasars. New optical, infrared, and spectroscopic measurements suggest that the dominant luminosity source is a dust-enshrouded quasar. The fuel for the intense activity is an enormous supply of molecular gas. Carbon monoxide emission has been detected at a wavelength of 2.6 millimeters by means of a new, more sensitive receiver recently installed on the 12-meter telescope of the National Radio Astronomy Observatory. IRAS 14348-1447 is the most distant and luminous source of carbon monoxide line emission yet detected.

Sanders, D. B.↗
NASA NTRS1988

Atmospheric Trace Molecule Spectroscopy (ATMOS)

The Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment is a space-borne investigation designed to obtain fundamental information related to the chemistry and physics of the earth's upper atmosphere (20 to 120 km altitude). The instrument, a high resolution (0.01/cm) interferometric spectrometer, measures the atmospheric absorption of solar radiation over the wavelength range from 2 to 16 micrometers, a spectral band which encompasses active transitions of all of the molecular species of current importance in upper atmospheric studies. There are two major aspects to the experiment: (1) the determination of the detailed compositional structure of the stratosphere and mesosphere, and its global, seasonal, and long-term variability; and (2) the study of the partitioning of absorbed solar energy at levels in the atmosphere characterized by dissociation of many of the constituents and by the breakdown of thermodynamic equilibrium. Characteristics of ATMOS are given. This experiment will be part of the atmospheric science research payload flown on the Atmospheric Laboratory for Applications and Science (ATLAS 1) NASA mission planned for late 1990.

Farmer, C. B.↗
NASA NTRS1993

The C-terminal region of alpha-crystallin: involvement in protection against heat-induced denaturation

Recent studies have demonstrated that the alpha-crystallins can protect other proteins against heat-induced denaturation and aggregation. To determine the possible involvement of the C-terminal region in this activity, the alpha-crystallins were subjected to limited tryptic digestion, and the amount of cleavage from the N-terminal and C-terminal regions of the alpha-A and alpha-B crystallin chains was assessed using antisera specific for these regions. Limited tryptic digestion resulted in cleavage only from the C-terminal region of alpha-A crystallin. This trypsin-treated alpha-A crystallin preparation showed a decreased ability to protect proteins from heat-induced aggregation using an in vitro assay. Together, these results demonstrate that the C-terminal region of alpha-A crystallin is important for its ability to protect against heat-induced aggregation, which is consistent with the hypothesis that post-translational changes that are known to occur at the C-terminal region may have significant effects on the ability of alpha-A crystallin to protect against protein denaturation in vivo.

NASA Discipline Cell Biology↗
NASA NTRS1985

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

NASA Discipline Exobiology↗
NASA NTRS1993

Review of the biological effects of weightlessness on the human endocrine system

Studies from space flights over the past two decades have demonstrated that there are basic physiological changes in humans during space flight. These changes include cephalad fluid shifts, loss of fluid and electrolytes, loss of muscle mass, space motion sickness, anemia, reduced immune response, and loss of calcium and mineralized bone. The cause of most of these manifestations is not known but the general approach has been to investigate systemic and hormonal changes. However, data from the 1973-1974 Skylabs, Spacelab 3 (SL-3), Spacelab D-I (SL-DI), and now the new SLS-1 missions support a more basic biological response to microgravity that may occur at the tissue, cellular, and molecular level. This report summarizes ground-based and SLS-1 experiments that examined the mechanism of loss of red blood cell mass in humans, the loss of bone mass and lowered osteoblast growth under space flight conditions, and loss of immune function in microgravity.

STS-40 Shuttle Project↗
NASA NTRS2012

Rates of Dinitrogen Fixation and the Abundance of Diazotrophs in North American Coastal Waters Between Cape Hatteras and Georges Bank

We coupled dinitrogen (N2) fixation rate estimates with molecular biological methods to determine the activity and abundance of diazotrophs in coastal waters along the temperate North American Mid-Atlantic continental shelf during multiple seasons and cruises. Volumetric rates of N2 fixation were as high as 49.8 nmol N L(sup -1) d(sup -1) and areal rates as high as 837.9 micromol N m(sup -2) d(sup -1) in our study area. Our results suggest that N2 fixation occurs at high rates in coastal shelf waters that were previously thought to be unimportant sites of N2 fixation and so were excluded from calculations of pelagic marine N2 fixation. Unicellular N2-fixing group A cyanobacteria were the most abundant diazotrophs in the Atlantic coastal waters and their abundance was comparable to, or higher than, that measured in oceanic regimes where they were discovered. High rates of N2 fixation and the high abundance of diazotrophs along the North American Mid-Atlantic continental shelf highlight the need to revise marine N budgets to include coastal N2 fixation. Integrating areal rates of N2 fixation over the continental shelf area between Cape Hatteras and Nova Scotia, the estimated N2 fixation in this temperate shelf system is about 0.02 Tmol N yr(sup -1), the amount previously calculated for the entire North Atlantic continental shelf. Additional studies should provide spatially, temporally, and seasonally resolved rate estimates from coastal systems to better constrain N inputs via N2 fixation from the neritic zone.

Middle Atlantic Bight↗
NASA NTRS2021

Predicting the Functional State of Protein Kinases Using Interpretable Graph Neural Networks

Kinases are a family of proteins that function as molecular switches, regulating several essential cellular activities such as cell proliferation. Dysfunctional kinases are implicated in several types of cancers and hence they are actively pursued as drug targets. Given the vast number of complex kinase structures that are available in the protein data bank (PDB), there is a necessity to develop methodologies that can identify structurally important moieties of the kinases in an automated fashion, for such techniques can be instrumental in identifying novel drug targets. In this work, we develop a graph neural network (GNN) based deep learning framework for classifying the functionally active and inactive states of a large set of eukaryotic protein kinases, making use of their 3D structure from the PDB. We show that GNN based machine learning models can classify protein states with an accuracy greater than 97%. We further use the GNN models to automatically identify regions of the kinases that are important for its function. For this purpose, Gradient-weighted Class Activation Mapping (Grad-CAM) was implemented on the protein graphs. Remarkably, Grad-CAM consistently identifies the highly conserved DFG motif as the most important part of the protein across the entire kinome, without any prior input. Other regions of the hydrophobic core such as the HRD motif were also identified by the interpretable GNN framework, consistent with the literature. We discuss the significance of each of these regions in detail.

Ashwin Ravichandran↗
NASA NTRS1990

Circumnuclear molecular gas in starburst and Seyfert galaxies

In order to investigate circumnuclear molecular gaseous contents and their relation to the nuclear activity, researchers made a search for circumnuclear (12)CO (J=1-0) emission from 28 starburst-nucleus galaxies (SBNs) and 12 Seyfert galaxies with the recession velocities less than 5000 km/s, using the Nobeyama Radio Observatory 45-m telescope. The full half-power beam width of 17 arcsec covers a region of less than about 5 kpc in diameter for the sample galaxies. The circumnuclear CO emission was detected from twelve SBNs (one is marginal) and four Seyfert galaxies. The main results and conclusions are summarized. Researchers derived the circumnuclear surface density of molecular gas which is corrected for inclination of the galaxies. This analysis shows that the surface density spans a wide range over two orders of magnitude. Further, there is no significant difference in the surface densities between types 1 and 2 Seyfert galaxies. Thus, we may conclude that the circumnuclear molecular content is not a key parameter producing the dichotomy of the Seyfert galaxies. It is also shown that there is no significant difference in the circumnuclear surface densities of molecular gas among the Seyfert, starburst, and normal galaxies. This implies that the circumnuclear gaseous content is not a key parameter determining which activity occurs in nuclei. We may conclude that more centrally condensed (i.e., less than 10 - 100 pc in diameter) gas components play an essential role on the occurrence of nuclear activities. Comparing results with the previous ones, researchers deduced radial distribution of surface density of molecular gases. They cannot obtain evidence for strong central concentration of molecular gas in the sample Seyfert galaxies except for NGC 3227. This is consistent with the previous result by Blitz, Mathieu, and Bally (1986). Comparing the CO emission line profiles with the previous ones taken with the larger beams, researchers discovered circumnuclear components of molecular gases. In particular, they found that molecular gas clouds may be absent in the SE of the nucleus of NGC 7469 where the high-excitation emitting region is discovered by Heckman et al. (1986). It is suggested that the nuclear activity (strong radiation and/or wind) may destruct the molecular clouds in that region.

Taniguchi, Yoshiaki↗
NASA NTRS1997

A 2000 Solar Mass Rotating Molecular Disk Around NGC 6334A

We present millimeter and centimeter wave spectroscopic observations of the H II region NGC 6334A. We have mapped the source in several transitions of CO, CS, and NH3. The molecular emission shows a distinct flattened structure in the east-west direction. This structure is probably a thick molecular disk or torus (2.2 x 0.9 pc) responsible for the bipolarity of the near-infrared (NIR) and radio continuum emission which extends in two "lobes" to the north and south of the shell-like H II region. The molecular disk is rotating from west to east (omega approximately equals 2.4 km/s.pc) about an axis approximately parallel to the radio and NIR emission lobes. By assuming virial equilibrium, we find that the molecular disk contains approximately 2000 solar mass. Single-component gas excitation model calculations show that the molecular gas in the disk is warmer and denser (T(sub k) approximately equals 60 K, n approximately equals 3000/cc) than the gas to the north and south (T(sub k) approximately equals 50 K, n approximately equals 400/cc). High resolution (approximately 5 sec) NH3 (3, 3) images of NGC 6334A reveal several small (approximately 0.1 pc) clumps, one of which lies southwest of the radio continuum shell, and is spatially coincident with a near-infrared source, IRS 20. A second NH3 clump is coincident with an H2O maser and the center of a molecular outflow. The dense gas tracers, CS J = 5 approaches 4 and 7 approaches 6, peak near IRS 20 and the H2O maser, not at NGC 6334A. IRS 20 has a substantial far-infrared (FIR) luminosity L(sub FIR) approximately 10(exp 5) solar luminosity, which indicates the presence of an O 7.5 star but has no detected radio continuum (F(sub 6 cm) < 0.02 Jy). The combination of dense gas, a large FIR luminosity and a lack of radio continuum can best be explained if IRS 20 is a protostar. A third clump of NH3 emission lies to the west of IRS 20 but is not associated with any other molecular or continuum features. The star formation activity in the region has moved west of NGC 6334A to IRS 20 and the H2O maser position. We suggest that NGC 6334A, IRS 20, and the H2O maser spot are part of a "protocluster" of stars which is condensing from the massive molecular disk. The similarity between the structure around NGC 6334A and other large (r approximately 1 pc), massive (M approximately 10(exp 3) solar mass), rotating disks (K3-50A and G10.6-0.4) suggests that this may be a common mechanism by which open clusters form.

Kraemer, Kathleen E.↗
NASA NTRS1997

Identification of the prooxidant site of human ceruloplasmin: a model for oxidative damage by copper bound to protein surfaces

Free transition metal ions oxidize lipids and lipoproteins in vitro; however, recent evidence suggests that free metal ion-independent mechanisms are more likely in vivo. We have shown previously that human ceruloplasmin (Cp), a serum protein containing seven Cu atoms, induces low density lipoprotein oxidation in vitro and that the activity depends on the presence of a single, chelatable Cu atom. We here use biochemical and molecular approaches to determine the site responsible for Cp prooxidant activity. Experiments with the His-specific reagent diethylpyrocarbonate (DEPC) showed that one or more His residues was specifically required. Quantitative [14C]DEPC binding studies indicated the importance of a single His residue because only one was exposed upon removal of the prooxidant Cu. Plasmin digestion of [14C]DEPC-treated Cp (and N-terminal sequence analysis of the fragments) showed that the critical His was in a 17-kDa region containing four His residues in the second major sequence homology domain of Cp. A full length human Cp cDNA was modified by site-directed mutagenesis to give His-to-Ala substitutions at each of the four positions and was transfected into COS-7 cells, and low density lipoprotein oxidation was measured. The prooxidant site was localized to a region containing His426 because CpH426A almost completely lacked prooxidant activity whereas the other mutants expressed normal activity. These observations support the hypothesis that Cu bound at specific sites on protein surfaces can cause oxidative damage to macromolecules in their environment. Cp may serve as a model protein for understanding mechanisms of oxidant damage by copper-containing (or -binding) proteins such as Cu, Zn superoxide dismutase, and amyloid precursor protein.

NASA Discipline Regulatory Physiology↗
NASA NTRS1984

ECUT: Energy Conversion and Utilization Technologies program - Biocatalysis research activity

The activities of the Biocatalysis Research Activity are organized into the Biocatalysis and Molecular Modeling work elements and a supporting planning and analysis function. In the Biocatalysis work element, progress is made in developing a method for stabilizing genetically engineered traits in microorganisms, refining a technique for monitoring cells that are genetically engineered, and identifying strains of fungi for highly efficient preprocessing of biomass for optimizing the efficiency of bioreactors. In the Molecular Modeling work element, a preliminary model of the behavior of enzymes is developed. A preliminary investigation of the potential for synthesizing enzymes for use in electrochemical processes is completed. Contact with industry and universities is made to define key biocatalysis technical issues and to broaden the range of potential participants in the activity. Analyses are conducted to identify and evaluate potential concepts for future research funding.

Wilcox, R.↗
NASA NTRS2000

Role of Integrin in Mechanical Loading of Osteoblasts

Mechanical forces generated by gravity, weightbearing, and muscle contraction play a key role in the genesis and maintenance of skeletal structure. The molecular mechanisms that mediate changes in osteoblast activity in response to altered patterns of skeletal loading are not known, and a better understanding of these processes may be essential for developing effective treatment strategies to prevent disuse osteoporosis. We have elucidated specific integrin/ECM (extracellular matrix) interactions that are required for osteoblast differentiation and survival and have developed a useful loading system to further explore the molecular basis of mechano-sensitivity of osteoblasts. The long term goal of our collaborative research is to understand how the ECM and cell adhesion proteins and integrins interaction to mediate the response of osteoblasts and their progenitors to mechanical loading. We suggest that integrin/ECM interactions are crucial for basic cellular processes, including differentiation and survival, as well as to participate in detecting and mediating cellular responses to mechanical stimuli.

Globus, Ruth↗
NASA NTRS2014

Protecting Neural Structures and Cognitive Function During Prolonged Space Flight by Targeting the Brain Derived Neurotrophic Factor Molecular Network

Brain derived neurotrophic factor (BDNF) is the main activity-dependent neurotrophin in the human nervous system. BDNF is implicated in production of new neurons from dentate gyrus stem cells (hippocampal neurogenesis), synapse formation, sprouting of new axons, growth of new axons, sprouting of new dendrites, and neuron survival. Alterations in the amount or activity of BDNF can produce significant detrimental changes to cortical function and synaptic transmission in the human brain. This can result in glial and neuronal dysfunction, which may contribute to a range of clinical conditions, spanning a number of learning, behavioral, and neurological disorders. There is an extensive body of work surrounding the BDNF molecular network, including BDNF gene polymorphisms, methylated BDNF gene promoters, multiple gene transcripts, varied BDNF functional proteins, and different BDNF receptors (whose activation differentially drive the neuron to neurogenesis or apoptosis). BDNF is also closely linked to mitochondrial biogenesis through PGC-1alpha, which can influence brain and muscle metabolic efficiency. BDNF AS A HUMAN SPACE FLIGHT COUNTERMEASURE TARGET Earth-based studies reveal that BDNF is negatively impacted by many of the conditions encountered in the space environment, including oxidative stress, radiation, psychological stressors, sleep deprivation, and many others. A growing body of work suggests that the BDNF network is responsive to a range of diet, nutrition, exercise, drug, and other types of influences. This section explores the BDNF network in the context of 1) protecting the brain and nervous system in the space environment, 2) optimizing neurobehavioral performance in space, and 3) reducing the residual effects of space flight on the nervous system on return to Earth

Schmidt, M. A.↗
NASA NTRS1990

CO excitation in four IR luminous galaxies

The correlation between the CO and far infrared luminosities of spiral galaxies is well established. The luminosity ration, L sub FIR/L sub CO in IR luminous active galaxies is, however, systematically five to ten times higher than in ordinary spirals and molecular clouds in our Galaxy. Furthermore, the masses of molecular hydrogen in luminous galaxies are large, M (H2) approx. equals 10(exp 10) solar magnitude, which indicates the observed luminosity ratios are due to an excess of infrared output, rather than a deficiency of molecular gas. These large amounts of molecular gas may fuel luminous galaxies through either star formation or nuclear activity. This interpretation rests on applying the M (H2)/L sub CO ratio calibrated in our Galaxy to galaxies with strikingly different luminosity ratios. But are the physical conditions of the molecular gas different in galaxies with different luminosity ratios. And, if so, does the proportionality between CO and H2 also vary among galaxies. To investigate these questions researchers observed CO (2 to 1) and (1 to 0) emission from four luminous galaxies with the Institute for Radio Astronomy in the Millimeter range (IRAM) 30 m telescope. Researchers conclude that most of the CO emission from these Arp 193, Arp 220, and Mrk 231 arises in regions with moderate ambient densities similar to the clouds in the Milky Way molecular ring. The emission is neither from dense hot cloud cores nor from the cold low density gas characteristic of the envelopes of dark clouds.

Radford, Simon J. E.↗
NASA NTRS2004

DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation damage, immune response changes and other risks identified for long-duration Space travel.

vanderWoerd, Mark↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗
NASA NTRS1981

Terrestrial evolution of polymerization of amino acids - Heat to ATP

Sets of amino acids containing sufficient trifunctional monomer are thermally polymerized at temperatures such as 65 deg; the amino acids order themselves. Various polymers have diverse catalytic activities. The polymers aggregate, in aqueous solution, to cell-like structures having those activities plus emergent properties, e.g. proliferatability. Polyamino acids containing sufficient lysine catalyze conversion of free amino acids, by ATP, to small peptides and a high molecular weight fraction. The lysine-rich proteinoid is active in solution, within suspensions of cell-like particles, or in other particles composed of lysine-rich proteinoid and homopolyribonucleotide. Selectivities are observed. An archaic polyamino acid prelude to coded protein synthesis is indicated.

Fox, S. W.↗
NASA NTRS1990

CO observations of southern mergers

There are good reasons to believe that the formation of some elliptical galaxies result from the merging of two disk galaxies, as Toomre and Toomre first suggested (1972, Ap. J. 178, 623). Such a process strongly enhances the star-formation activity of the system, thus consuming its molecular gas. This might account for the low cold-gas content of elliptical galaxies compared to that of spirals. Researchers present here CO(1-0) and CO(2-1) observations of a sequence of three objects, NGC 1614, NGC 3256, and NGC 7252, that present characteristic features of merger remnants: single body and extended tidal tails. NGC 3256 and 7252 even exhibit the r(exp 1/4) radial light distribution that is the signature of elliptical galaxies, which indicates that their stellar bodies are in late stages of relaxation. Both NGC 1614 and NGC 3256 undergo extended bursts of star formation revealed by their large far-infrared luminosities, and by the presence in the near-infrared spectrum of the 3.28 microns feature (Morwood: 1986, A. A. 166, 4) attributed to polycyclic aromatic hydrocarbons. On the other hand, NGC 7252 has a milder activity of star formation, as suggested by a lower infrared luminosity, and thus seems to have gone past the starburst phase. The CO data were collected with the Swedish-ESO 15 m Submillimeter Telescope (SEST) (beamsize = 43 seconds at 115 GHz, 23 seconds at 230 GHz). For NGC 7252, researchers have only observed the central position in CO-12(1-0). The spectrum is displayed together with an HI spectrum obtained with the Nancay radiotelescope. Researchers mapped NGC 1614 and NGC 3256 in CO-12(1-0) and CO-12(2-1), and also observed the nucleus of NGC 3256 in CO-13(1-0). The various CO spectra obtained towards the nuclei of both galaxies are presented. Characteristics of the galaxies are gathered, with luminosities and masses in solar units and temperatures in Kelvins.

Casoli, F.↗