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NASA NTRS1987

Mechanical and thermal properties of planetologically important ices

Two squences of ice composition were proposed for the icy satellites: a dense nebula model and a solar nebula model. Careful modeling of the structure, composition, and thermal history of satellites composed of these various ices requires quantitative information on the density, compressibility, thermal expansion, heat capacity, and thermal conductivity. Equations of state were fitted to the density data of the molecular ices. The unusual thermal and mechanical properties of the molecular and binary ices suggest a larger range of phenomena than previously anticipated, sufficiently complex perhaps to account for many of the unusual geologic phenomena found on the icy satellites.

Croft, Steven K.↗

NASA NTRS1989

Solar nebula condensates and the composition of comets

Interpretation of the volatile abundances in Halley's comet in terms of models for chemical and physical processes in the solar nebula are discussed. Key ratios of the oxidized and reduced species of nitrogen and carbon are identified which tell something of the chemical history of the environment in which cometary grains accreted to form the nucleus. Isotopic abundances are also applied to this problem. It will be shown that the abundances of methane and carbon monoxide are consistent both with models of solar nebula chemistry and chemical processing on grains in star-forming regions. Ultimately, limitations of the current data set on molecular abundances in comets and star-forming regions prevent a definitive choice between the two. Processes important to the composition of outer solar system bodies are: (1) gas phase chemistry in the solar nebula; (2) imperfect mixing in the solar nebula; (3) condensation; (4) clathration; (5) adsorption; and (6) processing of interstellar material.

Lunine, J. I.↗

NASA NTRS1992

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Herren, B.↗

NASA NTRS1994

Magnetic field structure in Monoceros R2

We have carried out polarimetric observations to investigate the geometry of the magnetic field in the giant molecular cloud Monoceros R2. This study is based upon deep R-band charge coupled device (CCD) polarimetry, covering a total area of 0.5 deg(exp 2) of the giant molecular cloud. The data were calibrated using a new technique that relies on obtaining broad-band photometry of stars simultaneously with polarimetric photometry of the Mon R2 fields, thus providing an accurate means of measuring the electric vectors of starlight which is polarized by the fore-ground dust grains aligned by the magnetic field in the Mon R2 GMC. In this work, (1) we were able to continuously trace magnetic field lines from the largest scales in Mon R2 to the detailed structure of the field in the dense core, as determined from infrared polarimetry; and (2) we have found that the ambient field is apparently modified by a large-scale structure in the Mon R2 cloud. The mean angle of polarization for the complete sample we measured is 158 deg, which is roughly coincident with the local Galactic magnetic field (155 deg). The dispersion in the angle of polarization is 33 deg, similar to that found in the Orion GMC. The dispersion in angle of polarization for stars located along the western side of the three CCD fields is 22 deg. The CCD fields are bisected by a dense ridge of gas defining the boundary of an expanding gas shell that recent observational results at millimeter wavelengths now reveal dominates the Mon R2 GMC. Our results suggest th at the expanding shell has distorted the magnetic field lines extending from the core to the northern gas structure comprising Mon R2.

Jarrett, T. H.↗

NASA NTRS2002

Charge Transfer Calculations and Database for Astrophysics

A variety of theoretical approaches, having different but overlapping energy ranges of applicability, are applied to investigate charge transfer processes for collisions of atomic ions with atoms and molecules. The methods include quantal molecular-orbital close-coupling, classical trajectory Monte Carlo, and continuum distorted wave methods. Recent collision systems studied include S(+4) + H, S(+4) + He, N(+7) + He, H2O, CO, and CO2, O(+q)(q = 1 - 8) + H, H2, and S(+q)(q = 1 - 16) + H2. The database effort is concentrating on astrophysically important reactions of atomic ions X(+q)(X=H-Zn, q=1-4, and selected higher charges) with H, He, various metal atoms, H2, and other selected molecular targets. Existing data, much of it produced by us, has been compiled and critically evaluated. Data for many reactions missing in the literature are estimated using the multichannel Landau-Zener approximation. Fits to cross sections and rate coefficients using standard functions are provided as well as tabulations of the raw data. The database is available on the World Wide Web at cfadc.phy.ornl.gov/astro/ps/data.

Wang, J. G.↗

NASA NTRS2000

Evolutionary conservation of the presumptive neural plate markers AmphiSox1/2/3 and AmphiNeurogenin in the invertebrate chordate amphioxus

Amphioxus, as the closest living invertebrate relative of the vertebrates, can give insights into the evolutionary origin of the vertebrate body plan. Therefore, to investigate the evolution of genetic mechanisms for establishing and patterning the neuroectoderm, we cloned and determined the embryonic expression of two amphioxus transcription factors, AmphiSox1/2/3 and AmphiNeurogenin. These genes are the earliest known markers for presumptive neuroectoderm in amphioxus. By the early neurula stage, AmphiNeurogenin expression becomes restricted to two bilateral columns of segmentally arranged neural plate cells, which probably include precursors of motor neurons. This is the earliest indication of segmentation in the amphioxus nerve cord. Later, expression extends to dorsal cells in the nerve cord, which may include precursors of sensory neurons. By the midneurula, AmphiSox1/2/3 expression becomes limited to the dorsal part of the forming neural tube. These patterns resemble those of their vertebrate and Drosophila homologs. Taken together with the evolutionarily conserved expression of the dorsoventral patterning genes, BMP2/4 and chordin, in nonneural and neural ectoderm, respectively, of chordates and Drosophila, our results are consistent with the evolution of the chordate dorsal nerve cord and the insect ventral nerve cord from a longitudinal nerve cord in a common bilaterian ancestor. However, AmphiSox1/2/3 differs from its vertebrate homologs in not being expressed outside the CNS, suggesting that additional roles for this gene have evolved in connection with gene duplication in the vertebrate lineage. In contrast, expression in the midgut of AmphiNeurogenin together with the gene encoding the insulin-like peptide suggests that amphioxus may have homologs of vertebrate pancreatic islet cells, which express neurogenin3. In addition, AmphiNeurogenin, like its vertebrate and Drosophila homologs, is expressed in apparent precursors of epidermal chemosensory and possibly mechanosensory cells, suggesting a common origin for protostome and deuterostome epidermal sensory cells in the ancestral bilaterian. Copyright 2000 Academic Press.

NASA Discipline Evolutionary Biology↗

NASA NTRS1992

Cloning of the cDNA for U1 small nuclear ribonucleoprotein particle 70K protein from Arabidopsis thaliana

We cloned and sequenced a plant cDNA that encodes U1 small nuclear ribonucleoprotein (snRNP) 70K protein. The plant U1 snRNP 70K protein cDNA is not full length and lacks the coding region for 68 amino acids in the amino-terminal region as compared to human U1 snRNP 70K protein. Comparison of the deduced amino acid sequence of the plant U1 snRNP 70K protein with the amino acid sequence of animal and yeast U1 snRNP 70K protein showed a high degree of homology. The plant U1 snRNP 70K protein is more closely related to the human counter part than to the yeast 70K protein. The carboxy-terminal half is less well conserved but, like the vertebrate 70K proteins, is rich in charged amino acids. Northern analysis with the RNA isolated from different parts of the plant indicates that the snRNP 70K gene is expressed in all of the parts tested. Southern blotting of genomic DNA using the cDNA indicates that the U1 snRNP 70K protein is coded by a single gene.

NASA Discipline Plant Biology↗

NASA NTRS2005

DNA Damage by Ionizing Radiation: Tandem Double Lesions by Charged Particles

Oxidative damages by ionizing radiation are the source of radiation-induced carcinogenesis, damage to the central nervous system, lowering of the immune response, as well as other radiation-induced damages to human health. Monte Carlo track simulations and kinetic modeling of radiation damages to the DNA employ available molecular and cellular data to simulate the biological effect of high and low LET radiation io the DNA. While the simulations predict single and double strand breaks and base damages, so far all complex lesions are the result of stochastic coincidence from independent processes. Tandem double lesions have not yet been taken into account. Unlike the standard double lesions that are produced by two separate attacks by charged particles or radicals, tandem double lesions are produced by one single attack. The standard double lesions dominate at the high dosage regime. On the other hand, tandem double lesions do not depend on stochastic coincidences and become important at the low dosage regime of particular interest to NASA. Tandem double lesions by hydroxyl radical attack of guanine in isolated DNA have been reported at a dosage of radiation as low as 10 Gy. The formation of two tandem base lesions was found to be linear with the applied doses, a characteristic of tandem lesions. However, tandem double lesions from attack by a charged particle have not been reported.

Huo, Winifred M.↗

NASA NTRS2004

Spectroscopic Investigations of Fragment Species in the Coma

The content of the gaseous coma of a comet is dominated by fragment species produced by photolysis of the parent molecules issuing directly from the icy nucleus of the comet. Spectroscopy of these species provides complementary information on the physical state of the coma to that obtained from observations of the parent species. Extraction of physical parameters requires detailed molecular and atomic data together with reliable high-resolution spectra and absolute fluxes of the primary source of excitation, the Sun. The large database of observations, dating back more than a century, provides a means to assess the chemical and evolutionary diversity of comets.

Feldman, Paul D.↗

NASA NTRS2008

NASA Tech Briefs, January 2008

Topics covered include: Induction Charge Detector with Multiple Sensing Stages; Generic Helicopter-Based Testbed for Surface Terrain Imaging Sensors; Robot Electronics Architecture; Optimized Geometry for Superconducting Sensing Coils; Sensing a Changing Chemical Mixture Using an Electronic Nose; Inertial Orientation Trackers with Drift Compensation; Microstrip Yagi Antenna with Dual Aperture-Coupled Feed; Patterned Ferroelectric Films for Tunable Microwave Devices; Micron-Accurate Laser Fresnel-Diffraction Ranging System; Efficient G(sup 4)FET-Based Logic Circuits; Web-Enabled Optoelectronic Particle-Fallout Monitor; SiO2/TiO2 Composite for Removing Hg from Combustion Exhaust; Lightweight Tanks for Storing Liquefied Natural Gas; Hybrid Wound Filaments for Greater Resistance to Impacts; Making High-Tensile-Strength Amalgam Components; Bonding by Hydroxide-Catalyzed Hydration and Dehydration; Balanced Flow Meters without Moving Parts; Deflection-Compensating Beam for Use inside a Cylinder; Four-Point-Latching Microactuator; Curved Piezoelectric Actuators for Stretching Optical Fibers; Tunable Optical Assembly with Vibration Dampening; Passive Porous Treatment for Reducing Flap Side-Edge Noise; Cylindrical Piezoelectric Fiber Composite Actuators; Patterning of Indium Tin Oxide Films; Gimballed Shoulders for Friction Stir Welding; Improved Thermal Modulator for Gas Chromatography; Nuclear-Spin Gyroscope Based on an Atomic Co-Magnetometer; Utilizing Ion-Mobility Data to Estimate Molecular Masses; Optical Displacement Sensor for Sub-Hertz Applications; Polarization/Spatial Combining of Laser-Diode Pump Beams; Spatial Combining of Laser-Diode Beams for Pumping an NPRO; Algorithm Optimally Orders Forward-Chaining Inference Rules; Project Integration Architecture; High Power Amplifier and Power Supply; Estimating Mixing Heights Using Microwave Temperature Profiler; and Multiple-Cone Sunshade for a Spaceborne Telescope.

Source record↗

NASA NTRS2003

Algorithms for Haptic Rendering of 3D Objects

Algorithms have been developed to provide haptic rendering of three-dimensional (3D) objects in virtual (that is, computationally simulated) environments. The goal of haptic rendering is to generate tactual displays of the shapes, hardnesses, surface textures, and frictional properties of 3D objects in real time. Haptic rendering is a major element of the emerging field of computer haptics, which invites comparison with computer graphics. We have already seen various applications of computer haptics in the areas of medicine (surgical simulation, telemedicine, haptic user interfaces for blind people, and rehabilitation of patients with neurological disorders), entertainment (3D painting, character animation, morphing, and sculpting), mechanical design (path planning and assembly sequencing), and scientific visualization (geophysical data analysis and molecular manipulation).

Basdogan, Cagatay↗

NASA NTRS2018

Enabling Experimental Evolution: Multi-Parameter Sensor System Integration into a Culture/Stressor Biofluidics System

Experimental evolution (EE) exposes microbial communities to ecological stressors, simulating dynamics up to near-extinction events. Combined with comparative sequencing and other molecular tools, such data can inform the genetic and other biological mechanisms underlying extremophile adaptation, and other observed effects. Automating this type of experiment using biofluidics can mitigate many traditional obstacles, including delays in assay results and environment adjustment and the need for many replicates. A first-generation device for automating EE procedures, the Automated Adaptive Directed Evolution Chamber (AADEC), was developed at NASA Ames. UV-C radiation was the stressor, an LED-photodiode array measured optical density, magnetic agitation and peristaltic pump systems ensured nutrient availability, and Arduino microcontrollers provided control. Escherichia coli in LB kanamycin media was used for testing and performance verification. A manual laboratory procedure with timed exposure to UV-C was performed to typify tolerance acquisition. Approximately a 106 factor increase in survival ratio was recorded over multiple iterations. Currently, a second-generation device is being developed integrating more real-time sensors: redox potential (ORP), indicating available/consumed metabolic energy; dissolved oxygen (DO), indicating aerobic/anaerobic growth; pH, indicating metabolic products; and electrical conductivity (EC), another indicator of metabolic products. The EC sensor system was constructed and calibrated in-house and matched commercial sensors in the required range. A Raspberry Pi computer automated the electrical system, allowing real-time data acquisition. The fluidics card was made of CNC-milled polycarbonate for biocompatibility. Each sensor parameter can also be used as a selection pressure alone or in combination with others to create extreme microbial environments. As a proof of concept, this work demonstrated sensor operation in one pair of growth-sensor chambers. It can be expanded to a multi-chamber system to enable inter-culture comparisons and multi-population studies. The prior Arduino system will be ported to the RPi system. Future stressors to be added include thermal, reactive oxygen species, and varying nutrient availability.

Govinda Raj, Chinmayee↗

DOE OSTI2024

Dataset for "Large Language Models as molecular design engines"

This dataset contains data and results associated with the paper "Large Language Models as molecular design engines" The paper investigates the use of large language models, specifically Claude 3 Opus, for generating and analyzing chemical structures based on various prompts from A-H (as mentioned in the manuscript), and guided design related to electron-withdrawing groups (EWG), electron-donating groups (EDG).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter across Laboratories

Non-targeted liquid chromatography tandem highresolution mass spectrometry (LC−MS/MS) is increasingly applied for the structure-resolved chemical analysis of dissolved organic matter (DOM). With new developments in MS instrumentation and analysis software, the approach has gained substantial momentum over the past decade. However, achieving high-quality analytical data that is reproducible and comparable across laboratories can be a bottleneck in non-targeted metabolomics and organic matter chemical analysis, especially for data reuse in repository-scale analyses. Understanding the capabilities as well as challenges of comparing LC−MS/MS data from different laboratories is necessary for inferring global trends from public data sets. To illuminate instrumentation factors that drive differences and variability, we used a standardized data analysis pipeline, including classical (CMN) and featurebased molecular networking (FBMN), to analyze data from a ring trial by 24 laboratories on identical sample sets of algal and DOM extracts that were mixed in predefined concentrations and spiked with standards. Our results showed that data sets from similar mass spectrometer types with unified instrument parameters were qualitatively comparable, resolving the same general trends and shared mass spectral features. Interlaboratory comparability was best for high-intensity features, while low-intensity features showed greater detection variability. Our analysis also highlights challenges when comparing data from instruments with different acquisition rates or operating with less standardized methods. Lastly, we provide recommendations for data integration, public data sharing, standardization, and best practices for standardized LC−MS/MS data acquisition, which will be critical for long-term time series and intercomparability of DOM chemical analyses.

DOM↗

NASA NTRS2016

Proteomic Assessment of Fluid Shifts and Association with Visual Impairment and Intracranial Pressure in Twin Astronauts

BACKGROUND: Astronauts participating in long duration space missions are at an increased risk of physiological disruptions. The development of visual impairment and intracranial pressure (VIIP) syndrome is one of the leading health concerns for crew members on long-duration space missions; microgravity-induced fluid shifts and chronic elevated cabin CO2 may be contributing factors. By studying physiological and molecular changes in one identical twin during his 1-year ISS mission and his ground-based co-twin, this work extends a current NASA-funded investigation to assess space flight induced "Fluid Shifts" in association with the development of VIIP. This twin study uniquely integrates physiological and -omic signatures to further our understanding of the molecular mechanisms underlying space flight-induced VIIP. We are: (i) conducting longitudinal proteomic assessments of plasma to identify fluid regulation-related molecular pathways altered by long-term space flight; and (ii) integrating physiological and proteomic data with genomic data to understand the genomic mechanism by which these proteomic signatures are regulated. PURPOSE: We are exploring proteomic signatures and genomic mechanisms underlying space flight-induced VIIP symptoms with the future goal of developing early biomarkers to detect and monitor the progression of VIIP. This study is first to employ a male monozygous twin pair to systematically determine the impact of fluid distribution in microgravity, integrating a comprehensive set of structural and functional measures with proteomic, metabolomic and genomic data. This project has a broader impact on Earth-based clinical areas, such as traumatic brain injury-induced elevations of intracranial pressure, hydrocephalus, and glaucoma. HYPOTHESIS: We predict that the space-flown twin will experience a space flight-induced alteration in proteins and peptides related to fluid balance, fluid control and brain injury as compared to his pre-flight protein/peptide signatures. Conversely, the trajectory of these protein signatures will remain relatively constant in his ground based co-twin. METHODS: We are using proteomic and standard immunoelectrophoresis techniques to delineate the change in protein signatures throughout the course of a long duration space flight in relation to the development of VIIP. We are also applying a novel cell-based metaboloic organ system assay ("Organs on a Plate") to address how these circulating biomarkers affect physiological processes at the cellular and organ level which could result in VIIP symptoms. These molecular data will be correlated with physiological measures (eg. extra and intracellular fluid volume, vascular filling/flow patterns, MRI, and Optic Coherence Tomography. DISCUSSION: Pre- and in-flight data collection is in progress for the space-flown twin, and similar data have been obtained from the ground-based twin. Biosamples will be batch processed when received from ISS after the conclusion of the 1-year mission. Omic and Physiological measures from the twin astronauts will be compared to similar data being collected on twin subjects who participated in simulated microgravity study. bed rest study.

Rana, Brinda K.↗

DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Interaction of plant chimeric calcium/calmodulin-dependent protein kinase with a homolog of eukaryotic elongation factor-1alpha

A chimeric Ca2+/calmodulin-dependent protein kinase (CCaMK) was previously cloned and characterized in this laboratory. To investigate the biological functions of CCaMK, the yeast two-hybrid system was used to isolate genes encoding proteins that interact with CCaMK. One of the cDNA clones obtained from the screening (LlEF-1alpha1) has high similarity with the eukaryotic elongation factor-1alpha (EF-1alpha). CCaMK phosphorylated LlEF-1alpha1 in a Ca2+/calmodulin-dependent manner. The phosphorylation site for CCaMK (Thr-257) was identified by site-directed mutagenesis. Interestingly, Thr-257 is located in the putative tRNA-binding region of LlEF-1alpha1. An isoform of Ca2+-dependent protein kinase (CDPK) phosphorylated multiple sites of LlEF-1alpha1 in a Ca2+-dependent but calmodulin-independent manner. Unlike CDPK, CCaMK phosphorylated only one site, and this site is different from CDPK phosphorylation sites. This suggests that the phosphorylation of EF-1alpha by these two kinases may have different functional significance. Although the phosphorylation of LlEF-1alpha1 by CCaMK is Ca2+/calmodulin-dependent, in vitro binding assays revealed that CCaMK binds to LlEF-1alpha1 in a Ca2+-independent manner. This was further substantiated by coimmunoprecipitation of CCaMK and EF-1alpha using the protein extract from lily anthers. Dissociation of CCaMK from EF-1alpha by Ca2+ and phosphorylation of EF-1alpha by CCaMK in a Ca2+/calmodulin-dependent manner suggests that these interactions may play a role in regulating the biological functions of EF-1alpha.

Non-NASA Center↗

NASA NTRS1995

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

NASA Discipline Exobiology↗