Search NASA⌕ Search

SEARCH · Search NASA

Results for “spatial biology”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16

The MOSAiC Distributed Network: Observing the coupled Arctic system with multidisciplinary, coordinated platforms

Central Arctic properties and processes are important to the regional and global coupled climate system. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Distributed Network (DN) of autonomous ice-tethered systems aimed to bridge gaps in our understanding of temporal and spatial scales, in particular with respect to the resolution of Earth system models. By characterizing variability around local measurements made at a Central Observatory, the DN covers both the coupled system interactions involving the ocean-ice-atmosphere interfaces as well as three-dimensional processes in the ocean, sea ice, and atmosphere. The more than 200 autonomous instruments (“buoys”) were of varying complexity and set up at different sites mostly within 50 km of the Central Observatory. During an exemplary midwinter month, the DN observations captured the spatial variability of atmospheric processes on sub-monthly time scales, but less so for monthly means. They show significant variability in snow depth and ice thickness, and provide a temporally and spatially resolved characterization of ice motion and deformation, showing coherency at the DN scale but less at smaller spatial scales. Ocean data show the background gradient across the DN as well as spatially dependent time variability due to local mixed layer sub-mesoscale and mesoscale processes, influenced by a variable ice cover. The second case (May–June 2020) illustrates the utility of the DN during the absence of manually obtained data by providing continuity of physical and biological observations during this key transitional period. We show examples of synergies between the extensive MOSAiC remote sensing observations and numerical modeling, such as estimating the skill of ice drift forecasts and evaluating coupled system modeling. The MOSAiC DN has been proven to enable analysis of local to mesoscale processes in the coupled atmosphere-ice-ocean system and has the potential to improve model parameterizations of important, unresolved processes in the future.

54 ENVIRONMENTAL SCIENCES↗

Size-Resolved Chemical Composition of Particles Collected Using STAC at the Ground Site During the SAIL Campaign in Gunnison, Colorado

Aerosol particles were collected using a four-stage Size and Time-resolved Aerosol Collector (STAC) during the SAIL field campaign. Each stage of STAC separates particles into distinct aerodynamic size fractions with 50% cut-off diameters: Stage A: 2.27 µm Stage B: 0.615 µm Stage C: 0.421 µm Stage D: 0.119 µm Each stage provides both size- and time-resolved sampling, enabling investigation of particle composition across different atmospheric regimes. Only a subset of samples was selected for analysis based on prevailing meteorological conditions (e.g., temperature, humidity, and air-mass influence) to capture representative aerosol types under distinct weather patterns. Collected substrates were first examined under Scanning Electron Microscopy (SEM) to evaluate particle loading, morphology, and spatial distribution. Subsequently, Computer-Controlled Scanning Electron Microscopy with Energy-Dispersive X-ray Spectroscopy (CCSEM/EDX) was performed to obtain size-resolved elemental composition of individual particles. A rule-based classification scheme was applied to categorize particles into major compositional groups (e.g., biological, carbonaceous, dust, sulfate, Na-rich, and mixed types). This dataset provides high-resolution morphological and chemical information on atmospheric particles collected during the SAIL campaign, offering insights into the influence of meteorology on aerosol composition and mixing state.

Size and Time-resolved Aerosol Collector↗

Integrating fine root diameter and watershed mapping to characterize rhizosphere hydrology

Root morphology and soil hydraulic characteristics were integrated using watershed distance mapping to show water distribution and uptake across the plant-soil interface. Poplar (Populus deltoides, P. trichocarpa), maize (Zea mays), juniper (Juniperus virginiana), grape (Vitis rotundifolia) and maple (Acer saccharum) seedlings were grown in sand, after which root diameter and soil water dynamics were assessed via sequential neutron radiography. Three local soil regions (root-soil interface or edge, rhizosphere, bulk soil) were classified based on both radial distance from the root surface and diameter of the nearest root, from which changes in water content and distribution were characterized using digital image processing. Water content dynamics across the rhizosphere showed two different species-independent processes: a consistently elevated water content at the root-soil edge interface which increased with root diameter, and hysteresis as the rhizosphere transitioned to bulk soil (~0.5 cm from the root), independent of root diameter. Water uptake per unit root surface area declined exponentially with root diameter, independent of species. Results highlight the species-independent hydrologic characteristics of the rhizosphere and the potential for evaluating them in a local spatially connected soil context. Avenues for improved integration of soil and root characteristics are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold

Abstract Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.

59 BASIC BIOLOGICAL SCIENCES↗

Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations

Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.

97 MATHEMATICS AND COMPUTING↗

Strong Potential Gradients and Electron Confinement in ZnO Nanoparticle Films: Implications for Charge-Carrier Transport and Photocatalysis

We report that zinc oxide (ZnO) nanomaterials are promising components for chemical and biological sensors and photocatalytic conversion and operate as electron collectors in photovoltaic technologies. Many of these applications involve nanostructures in contact with liquids or exposed to ambient atmosphere. Under these conditions, single-crystal ZnO surfaces are known to form narrow electron accumulation layers with few nanometer spatial penetration into the bulk. A key question is to what extent such pronounced surface potential gradients can develop in the nanophases of ZnO, where they would dominate the catalytic activity by modulating charge-carrier mobility and lifetimes. Here, we follow the temperature-dependent surface electronic structure of nanoporous ZnO with photoemission spectroscopy to reveal a sizable, spatially averaged downward band bending for the hydroxylated state and a conservative upper bound of < 6 nm for the spatial extent of the associated potential gradient. This nanoscale confinement of conduction-band electrons to the nanoparticle film surface is crucial for a microscopic understanding and further optimization of charge transport and photocatalytic function in complex ZnO nanomaterials.

36 MATERIALS SCIENCE↗

Hollow fiber mid-ID spectrometer with UV laser ablation sampling for fine spatial reoslution of isotope ratios in solids

We describe a system that combines isotope ratio analysis via mid-infrared (Mid-IR) laser absorption spectroscopy with fine spatial resolution sampling using a UV pulsed laser. The UV laser ablates a pit in a solid on the order of 10 microns in diameter. The sample-derived particulates resulting from laser ablation pass through a micro-combustor, and the resulting gas is analyzed using Mid-IR laser absorption spectroscopy in a capillary absorption spectrometer (CAS). The CAS uses a hollow fiber optic waveguide with a reflective inner coating and a small internal volume on the order of 1ml. The hollow fiber both guides the laser light from source to detector and contains the gas sample at reduced pressure. Near unity overlap between the laser beam and sample enables sensitive analysis with ultra-small sample size. A prototype system has been demonstrated to enable stable carbon isotopic analysis (d13C) with 1 per mil precision using <1 picomole of carbon and is currently being used to study nutrient exchange in soil/root/microbial rhizosphere studies. The smaller sample size of this system is enabling fine spatial resolution analysis (on the order of 10 microns), which is roughly an order of magnitude smaller than was possible with an isotope ratio mass spectrometer (IRMS). In addition to rhizosphere studies, the system can provide a useful tool for fine scale isotope analysis with applications in biological, forensic, and environmental science.

capillary absorption spectroscopy, laser ablation,↗

Estimating biotic integrity to capture existence value of freshwater ecosystems

The US Environmental Protection Agency (EPA) uses a water quality index (WQI) to estimate benefits of proposed Clean Water Act regulations. The WQI is relevant to human use value, such as recreation, but may not fully capture aspects of nonuse value, such as existence value. Here, we identify an index of biological integrity to supplement the WQI in a forthcoming national stated preference survey that seeks to capture existence value of streams and lakes more accurately within the conterminous United States (CONUS). We used literature and focus group research to evaluate aquatic indices regularly reported by the EPA’s National Aquatic Resource Surveys. We chose an index that quantifies loss in biodiversity as the observed-to-expected (O/E) ratio of taxonomic composition because focus group participants easily understood its meaning and the environmental changes that would result in incremental improvements. However, available datasets of this index do not provide the spatial coverage to account for how conditions near survey respondents affect their willingness to pay for its improvement. Therefore, we modeled and interpolated the values of this index from sampled sites to 1.1 million stream segments and 297,071 lakes across the CONUS to provide the required coverage. The models explained 13 to 36% of the variation in O/E scores and demonstrate how modeling can provide data at the required density for benefits estimation. We close by discussing future work to improve performance of the models and to link biological condition with water quality and habitat models that will allow us to forecast changes resulting from regulatory options.

59 BASIC BIOLOGICAL SCIENCES↗

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping microhabitats of lignocellulose decomposition by a microbial consortium

The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Invited article: X-ray phase contrast imaging in inertial confinement fusion and high energy density research

X-ray phase contrast imaging (XPCI) provides enhanced image contrast beyond absorption-based x-ray imaging alone due to refraction and diffraction from gradients in the object material density. It is sensitive to small variations in density, such as internal voids, cracks, grains, defects, and material flow, as well as to stronger density variations such as from a shock wave. Beyond its initial use in biology and materials science, XPCI is now routinely used in inertial confinement fusion (ICF) and high energy density (HED) research, first to characterize ICF capsules and targets, and later applied in dynamic experiments, where coherent x-ray sources, ultrafast x-ray pulses, and high temporal and spatial resolution are required. In this Review article, XPCI image formation theory is presented, its diverse use in ICF and HED research is discussed, the unique requirements for ultrafast XPCI imaging are given, as well as current challenges and issues in its use.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The impact of long-range dispersal on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

59 BASIC BIOLOGICAL SCIENCES↗

End-of-Winter Snow Depth, Temperature, Density and SWE Measurements at Teller Road Site, Seward Peninsula, Alaska, 2016-2018

Measurements of end-of-winter snow properties were collected at the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) for three consecutive years - 2016, 2017, and 2018. This dataset contains one *.pdf user guide and four *.csv data files spatially distributed values of snow depth, snow water equivalent (SWE), temperature at the snow surface and at the bottom of the snowpack, and snow density as a function of depth from top of snowpack. Data was collected toward the end of the winter season, typically in late March or early April, when the snowpack would be near its maximum. In 2016, snow depth measurements were taken using either a thaw probe or avalanche probe. In 2017 and 2018 a Snow-Hydro MagnaProbe http://www.snowhydro.com/products/column2.html was used to improve collection efficiency and enhance spatial coverage. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

Yang, Yunqi↗

Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging↗

Little vertical and circumferential variations in stem xylem water Δ 2 H and Δ 18 O in three tree species

Vertical and circumferential patterns of xylem water isotope signatures in large trees are rarely characterized but may influence interpretation of water source investigations and soil/xylem water isotope offsets. Furthermore, to examine vertical and circumferential variation in xylem water δ 2 H and δ 18 O, we collected xylem tissue at 5 heights (0, 1, 4, 7 and 10 m) from three replicate trees of three species with contrasting xylem anatomy, two angiosperms (Liquidambar styraciflua and Quercus nigra) and one gymnosperm (Pinus taeda). Concurrently, we also determined δ 2 H and δ 18 O of groundwater, soil water, and recent precipitation. On a different day, we collected circumferential samples at 1 m from the same trees to test for sectorality effects. Water from stem and soil samples were cryogenically extracted and analyzed for δ 2 H and δ 18 O. Mean xylem water δ 2 H and δ 18 O were significantly different between species, both vertically and circumferentially. We did not find significant (p = 0.05) systematic variation in δ 2 H or δ 18 O with height. We found no significant evidence for sectorality effects on δ 2 H, δ 18 O. Variances of vertical synoptic xylem water δ 2 H or δ 18 O were similar between species, 7.2–10.4‰ for δ 2 H and 0.58–0.81‰ for δ 18 O. Circumferential variances were also similar between species, 4.0–6.0 for δ 2 H and 0.37–0.44 for δ 18 O. A mixing model showed that sweetgum, water oak and loblolly pine, were drawing most of their water from deep soil from 45 to 190 cm (84.7, 68.4 and 53.2%, respectively) however, soil water-excess values indicate δ 2 H fractionation effects on these estimates. Dual isotope mixing model evaluation with single and multiple sample configurations showed that source water estimates were not affected by within tree variability of xylem water signatures. Xylem water δ 2 H and δ 18 O variability with height or circumference, was 3.2 and 2.7 times less than between tree variation because of transient temporal and spatial processes and is, therefore, not likely to affect interpretations of water sourcing in these three species.

59 BASIC BIOLOGICAL SCIENCES↗

Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells

Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. Patterning within cells can extend down to the level of individual proteins and mRNA. But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning - the giant ciliate Stentor coeruleus. Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning. A Stentor cell is roughly 2mmlong, allowing a ‘‘proteomic dissection’’ in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell’s anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗