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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Multi-Omics Analysis of Mouse Retina Following Low Dose Radiation and/or Hindlimb Unloading

Rodent models have been used as analogs for studying the effects of spaceflight. NASA’s GeneLab provides access to omics datasets generated from spaceflight and ground-based experiments allowing for additional retrospective analysis. We used GeneLab’s GLDS-203, a dataset generated by researchers at Loma Linda University to study the impact of prolonged unloading and/or low-dose radiation on mouse retina. The purpose of this study was to understand the effect of gamma radiation and/or hindlimb unloading on mice retinas through a multi-omics analysis. In the experiment that generated the omics data, mice were irradiated with gamma-ray and/or subjected to hindlimb unloading for 21 days and multi-omics analysis was performed at 7 days, 1 month, or 4 months post exposure. In the current study, for each of the three timepoints, we compared epigenomic profiles for retinas from exposed mice against timepoint-matched controls. We identified a total of 5,271 differentially methylated loci (DML) and 321 differentially methylated regions (DMR; using a sliding window and step size of 500 bp) with methylation difference > 10% and q-value < 0.05 (sliding linear model corrected p-value) across the nine exposure groups. Highest correlation in methylation difference was seen for significant DMLs (q-value < 0.05) across different conditions at same post exposure timepoint (Figure 1).The location of DMLs and DMRs were characterized with respect to CpG islands and shores, putative promoters, gene body, and intergenic regions (Table 1). We analyzed RNA-seq counts and performed gene set enrichment analysis using differential expression results from comparing each exposure group to its timepoint-matched control group. Significant pathways (adjusted p-value <0.05) enriched in all three microgravity-only groups were related to morphogenesis of a branching epithelium, skeletal muscle cell differentiation, and response to fibroblast growth factor. Common processes across all timepoints in the radiation-only groups were retina homeostasis, synaptic vesicle exocytosis-endocytosis, and chemotaxis. In the combination groups, regulation of trans-synaptic signaling, and Rho protein signal transduction were enriched at all three timepoints. Processes related to purine nucleotide metabolism were enriched in all nine exposure groups, with activation at 1 month, and suppression at 7 days and 4 months. A total of 14 genes contained at least one DML and were differentially expressed at adjusted p-value < 0.05, including genes implicated in cataract development (Sipa1l3, Crybb3) and those involved in cytoskeletal organization (Plec, Flnb, Eef1a1). This analysis is part of a larger effort to understand the molecular mechanisms following spaceflight exposures that can help translate effects observed in animal models to human impacts.

Prachi Kothiyal↗
NASA NTRS2022

The Zn, S, and Cl Isotope Compositions of Mare Basalts: Implications for the Effects of Eruption Style and Pressure on Volatile Element Stable Isotope Fractionation on the Moon

We compare the stable isotope compositions of Zn, S, and Cl for Apollo mare basalts to better constrain the sources and timescales of lunar volatile loss. Mare basalts have broadly elevated yet limited ranges in δ(66)Zn, δ(34)S, and δ(37)Cl_(SBC+WSC) values of 1.27 ± 0.71, 0.55 ± 0.18, and 4.1 ± 4.0‰, respectively, compared to the silicate Earth at 0.15, –1.28, and 0‰, respectively. We find that the Zn, S, and Cl isotope compositions are similar between the low- and high-Ti mare basalts, providing evidence of a geochemical signature in the mare basalt source region that is inherited from lunar formation and magma ocean crystallization. The uniformity of these compositions implies mixing following mantle overturn, as well as minimal changes associated with subsequent mare magmatism. Degassing of mare magmas and lavas did not contribute to the large variations in Zn, S, and Cl isotope compositions found in some lunar materials (i.e., 15‰ in δ(66)Zn, 60‰ in δ(34)S, and 30‰ in δ(37)Cl). This reflects magma sources that experienced minimal volatile loss due to high confining pressures that generally exceeded their equilibrium saturation pressures. Alternatively, these data indicate effective isotopic fractionation factors were near unity. Our observations of S isotope compositions in mare basalts contrast to those for picritic glasses (Saal and Hauri 2021), which vary widely in S isotope compositions from –14.0 to 1.3‰, explained by extensive degassing of picritic magmas under high-P/P_(Sat) values (>0.9) during pyroclastic eruptions. The difference in the isotope compositions of picritic glass beads and mare basalts may result from differences in effusive (mare) and explosive (picritic) eruption styles, wherein the high-gas contents necessary for magma fragmentation would result in large effective isotopic fractionation factors during degassing of picritic magmas. Additionally, in highly vesiculated basalts, the δ(34)S and δ(37)Cl values of apatite grains are higher and more variable than the corresponding bulk-rock values. The large isotopic range in the vesiculated samples is explained by late-stage low-pressure “vacuum” degassing (P/P-(Sat) ~ 0) of mare lavas wherein vesicle formation and apatite crystallization took place post-eruption. Bulk-rock mare basalts were seemingly unaffected by vacuum degassing. Degassing of mare lavas only became important in the final stages of crystallization recorded in apatite—potentially facilitated by cracks/fractures in the crystallizing flow. We conclude that samples with wide-ranging volatile element isotope compositions are likely explained by localized processes, which do not represent the bulk Moon.

Halogens↗
NASA NTRSDate not supplied

Thermodynamic Modeling of the Vapor in Equilibrium With Apollo 17 Basalts.

Lunar mare basalts sampled during the Apollo 17 mission provide insight to the chemical evolution of mare basalt magmas and their associated vapor as these samples erupted and cooled rapidly at the lunar surface. We focus on minerals present on vesicle and vug surfaces in Apollo 17 basalts, such as 71036, which was opened as part of the Apollo Next Generation Sample Analysis (ANGSA) program. The mineral assemblage observed includes native Fe, SiO2, and a Mg-P mineral, possibly merrillite [1, 2]. The pet-rographic context of these phases suggests that they may have been deposited directly from the vapor phase after eruption. Here we use thermodynamic modeling to assess the plausibility of the vapor-phase deposition hypothesis.

D. L. Thompson↗
NASA NTRS2023

Mineralogical, Elemental, and Tomographic Reconnaissance Investigation for CLPS (METRIC)

METRIC is a robotic science laboratory that can determine the mineralogy, elemental chemistry, micromorphology, and thermophysical properties of planetary regolith. The METRIC suite comprises METRIC XRD/F, an X-ray diffraction/X-ray fluorescence instrument that can determine the mineralogy and elemental chemistry of regolith samples; METRIC XCT, a micro X-ray computed tomography instrument that can be used to evaluate grain/crystallite sizes and textures; METRIC IRS, an imaging spectrometer mounted on a rover that can determine mineralogy and thermophysical properties at the landing site; and a pneumatic sample collection, processing, distribution system developed by Honeybee Robotics. The payload elements could be deployed on a static lander or a rover. Data returned from the METRIC payload would inform origin, formation, and evolution of rocky planetary bodies. METRIC XRD/F draws on heritage from the CheMin instrument on the Mars Science Laboratory (MSL) Curiosity rover [1], with a few important improvements. Like CheMin, METRIC XRD/F operates in transmission geometry and uses piezoelectric actuators on sample cells in a tuning fork geometry to induce convective grain motion of the regolith to create a randomly oriented powder. MSL CheMin uses an energy-sensitive CCD to collect XRD patterns and XRF spectra simultaneously from the same sample cell, resulting in qualitative XRF data. METRIC XRD/F uses two different sample cells, one optimized for XRD and one optimized for XRF, and a silicon drift detector to detect fluoresced X-rays. This improvement to the XRF capabilities provides quantitative geochemical data of major elements down to Z = 11 and allows for the detection of minor and trace elements that are critical for evaluating geologic evolution of the Moon (e.g., P and Th). Modest improvements to the XRD geometry and hardware allow for better angular resolution and the ability to distinguish between members of the pyroxene group. METRIC XCT uses the same geometry and much of the same hardware as METRIC XRD/F, where a CCD would capture images of a regolith sample in a 3 mm diameter sample tube that is rotated 360° in steps <1°. Image brightness can be used to infer compositional data, where brighter materials indicate a higher Z, much like scanning electron microscopy. Data from METRIC XCT complement those from METRIC XRD/F. Particle size, shape, and texture can provide petrologic and provenance information, whereas vesicle size and morphology in volcanic or impact melt lithologies can inform cooling rates. METRIC IRS is a hyperspectral thermal imager that can be mounted to a lander or rover to provide mineralogical data from the broader landing site and help determine whether the samples analyzed by METRIC XRD/F and XCT are representative. The METRIC IRS spectral range (8–14 μm) and resolution (10.8 cm-1) allow for quantitative mineralogy from modelling Reststrahlen bands of major rock-forming minerals (e.g., silicates, phosphates). Radiance cubes can be processed and modelled with an onboard high-performance computer to determine mineral abundances of plagioclase, high-Ca pyroxene, pigeonite, orthopyroxene, olivine, and glass. Regolith samples can be acquired, processed, and delivered to the X-ray instruments via multiple sample handling systems, but the pneumatic sampling systems developed by Honeybee Robotics [e.g., 2] are best suited for relatively low-cost missions that are being competed for the Moon (e.g., NASA’s Payloads and Research Investigations for the Surface of the Moon program). There are pneumatic sampling systems that collect surface material and other systems that pneumatically drill up to ~1 m below the surface, providing material that has not been space weathered and has not been affected by the lander’s exhaust. [1] Blake, D. F., Vaniman, D., Achilles, C., Anderson, R., Bish, D., et al. (2012). Space Sci. Rev. 170, 341-478. https://doi.org/10.1007/s11214-012-9905-1. [2] Zacny, K., Betts, B., Hedlund, M., Long, P., Gramlich, M., Tura, K., Chu, P., Jacob, A., Garcia, A. (2014). IEEE Aerospace Conference, 3-7 March 2014, Big Sky, MT, U.S.A.

X-ray diffraction↗
NASA NTRS2023

Investigating the Effects of Space Weathering in Ryugu Samples Using Coordinated Microanalyses

Airless planetary surfaces are characterized by a distinct lack of an atmosphere or magnetic field, leading to direct exposure to the effects of hypervelocity micrometeoroid impacts and solar wind ion irradiation [1]. These processes, cumulatively known as space weathering, gradually alter the microstructural and chemical properties of the grains on airless surfaces. Signatures of space weathering include vesiculated textures, amorphous grain rims (upper ~100 nm), solar flare tracks, and Fe-bearing nanoparticles (npFe) [2,3]. The accumulation of these microstructural space weathering characteristics, particularly the presence of npFe, alters the spectral properties of airless regoliths resulting in changes in spectral slope and reflectance of the surfaces, and the attenuation of characteristic absorption bands in the visible to near-infrared (Vis-NIR) wavelengths. These spectral changes complicate our ability to accurately interpret the mineralogy of airless bodies via remote sensing spectroscopy [1,4]. Studies of space weathering have primarily focused on anhydrous silicate minerals, reflecting the main components of the available returned samples from the Moon and S-type asteroid Itokawa [3,5,6]. However, our understanding of space weathering of primitive, organic-rich carbonaceous materials is still a work in progress. The Japan Aerospace Exploration Agency (JAXA)’s Hayabusa2 mission offered the first opportunity to directly investigate carbonaceous asteroids by returning samples from C-type asteroid (162173) Ryugu. Initial studies of Ryugu samples show mineralogical similarities to CI chondrites along with surface modifications consistent with space weathering. These surface modifications are primarily in the form of μm-thick silicate melts, amorphized phyllosilicates, glassy spherules, and burst vesicles [3,7]. Here, we report results from coordinated microanalytical techniques to further our understanding of the mineralogy and space weathering of carbonaceous materials.

L E Melendez↗
DOE OSTI2016

Cell-based composite materials with programmed structures and functions

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Biological Small Angle Scattering: Techniques, Strategies and Tips

This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins, and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications.The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS.The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for exploring the diversity of solution SAS methods and applications.

Chaudhuri, Barnali↗
DOE OSTI2018

Cell-based composite materials with programmed structures and functions

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Cell-based composite materials with programmed structures and functions

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Hierarchical Membrane Dynamics in Phase-Separated Model Membranes

Lipid membranes, the primary matrix of cell membranes, exhibit a hierarchy of dynamics from molecular motions to collective undulations, which control spatiotemporal membrane phenomena and regulate various cellular functions. Thus, understanding how various dynamic modes influence membrane behavior is crucial to uncovering the design rules of cell membranes and implementing them in future technologies. Previous membrane dynamics studies using neutron spin-echo spectroscopy (NSE) have shed light on the dependence of collective membrane fluctuations on viscoelastic membrane properties, demonstrating that thickness fluctuation modes (100ns) are dictated by membrane viscosity, which directly governs fast (ps) molecular diffusive motions. Here, we focus on phase-separating lipid membranes, composed of DMPC:DSPC mixtures, to understand the effect of domain formation/growth on hierarchical matrix dynamics using selective lipid deuteration and different neutron spectroscopy techniques. NSE measurements on DMPC:DSPC-d83 (70:30 mol%) show that bending rigidity of the DMPC-rich matrix graduallyincreases with decreasing temperature - as the fully-fluid membrane approaches the upper phase transition (i.e. with the formation of transient DSPC clusters) - and increases further in the phase coexistence region with the growth of DSPC domains. Comparatively, NSE measurements on DMPC-d54:DSPC-d83 vesicles show pronounced matrix thickness fluctuations in the fully-fluid phase and drastic suppression of this fluctuation mode in the gel-fluid coexistence phase, even when the DMPC-rich matrix is still in its fluid phase. This suppression in fluctuations suggests an increase in the matrix viscosity with the growth of gel DSPC domains, which is further investigated by selectively measuring lipid diffusion in the DMPC-rich matrix using neutron backscattering spectroscopy. Comparisons of the experimental results with coarse-grained MD simulationsillustrate the underlying coupling mechanisms. Overall, these observations indicate a clear mechanical and viscoelastic coupling betweenlipid domains and their host matrix, suggesting that domain formation influences membrane properties beyond local effects.

Carrillo, Jan Michael↗
DOE OSTI2023

MEMPHIS (Mesoscle Multiphysics Phase Field Simulator v.0

SAND2024-01427O Mesoscale Multiphysics Phase Field Simulator (MEMPHIS) is used for solving interfacial problems and can be applied to many evolutionary problems. Some examples are solidification dynamics, viscous fingering, fracture mechanics, hydrogen embrittlement, vesicle dynamics, electro-mechanical degradation of batteries, aging of microstructures, and segregation. MEMPHIS is written in Fortran 90 in a modular fashion, where model and numerical solvers are decoupled from one another. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Dingreville, Remi↗
DOE OSTI2017

Electrostatic Control of Polymorphism in Charged Amphiphile Assemblies

Stimuli-induced structural transformations of molecular assemblies in aqueous solutions are integral to nanotechnological applications and biological processes. In particular, pH responsive amphiphiles as well as proteins with various degrees of ionization can reconfigure in response to pH variations. Here, we use in situ small and wide-angle X-ray scattering (SAXS/WAXS), transmission electron microscopy (TEM), and Monte Carlo simulations to show how charge regulation via pH induces morphological changes in the assembly of a positively charged peptide amphiphile (PA). Monte Carlo simulations and pH titration measurements reveal that ionic correlations in the PA assemblies shift the ionizable amine pK ~ 8 from pK ~ 10 in the lysine headgroup. SAXS and TEM show that with increasing pH, the assembly undergoes spherical micelle to cylindrical nanofiber to planar bilayer transitions. SAXS/WAXS reveal that the bilayer leaflets are interdigitated with the tilted PA lipid tails crystallized on a rectangular lattice. The details of the molecular packing in the membrane result from interplay between steric and van der Waals interactions. We speculate that this packing motif is a general feature of bilayers comprised of amphiphilic lipids with large ionic headgroups. Altogether, our studies correlate the molecular charge and the morphology for a pH-responsive PA system and provide insights into the Å-scale molecular packing in such assemblies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Relaxing Wrinkles in Jammed Interfacial Assemblies

Dynamic covalent bonding has emerged as a mean by which stresses in a network can be relaxed. Here, the strength of the bonding of ligands to nanoparticles at the interface between two immiscible liquids affect the same results in jammed assemblies of nanoparticle surfactants. Beyond a critical degree of overcrowding induced by the compression of jammed interfacial assemblies, the bonding of ligands to nanoparticles (NPs) can be broken, resulting in a desorption of the NPs from the interface. This reduces the areal density of nanoparticle surfactants at the interface, allowing the assemblies to relax, not to a fluid state but rather another jammed state. The relaxation of the wrinkles caused by the compression reflects the tendency of these assemblies to eliminate areas of high curvature, favoring a more planar geometry. Importantly, this enabled the generation of giant vesicular and multivesicular structures from these assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

X-ray Structure of the Mature Ectodomain of Phogrin

Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretion, ensuring proper granulogenesis, and β-cell proliferation. The role of their cytoplasmic tail has been partially unveiled, while that of their luminal region remains unclear. To advance the understanding of its structure–function relationship, the X-ray structure of the mature ectodomain of phogrin (ME phogrin) at pH 7.4 and 4.6 has been solved at 1.95- and 2.01-Å resolution, respectively. Likewise to the ME of ICA512, ME phogrin adopts a ferredoxin-like fold: a sheet of four antiparallel β-strands packed against two α-helices. Furthermore, sequence conservation among vertebrates, plants and insects suggests that the structural similarity extends to all the receptor family. Crystallized ME phogrin is monomeric, in agreement with solution studies but in striking contrast with the behavior of homodimeric ME ICA512. The structural details that may cause the quaternary structure differences are analyzed. The results provide a basis for building models of the overall orientation and oligomerization state of the receptor in biological membranes.

dense-core vesicle↗
DOE OSTI2016

Cyanobacterial ultrastructure in light of genomic sequence data

Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high magnification transmission electron micrographs of sequenced representatives of each of the five morphological Subsections. We place the image data in the context of tabulated protein domains--which are the structural, functional and evolutionary units of proteins--from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provide a guidebook to morphological features.

59 BASIC BIOLOGICAL SCIENCES↗