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NASA NTRS2021

Recovery: Fast and Slow—Vegetation Response During the 2012–2016 California Drought

The 2012–2016 California Drought severely impacted natural vegetation across a wide range of environmental gradient. Although several studies have reported an increase in plant water stress and mortality, the spatiotemporal variations of ecosystem productivity responses and the associated environmental and biological drivers remain unclear. Here, using Enhanced Vegetation Index from the Moderate resolution imaging spectrometer, we found that 45% of the natural ecosystems showed an abrupt change (breakpoint [BP]) in productivity during 2012–2016. There were three major contrasting temporal patterns of productivity responses: (i) a steady increase under higher temperature followed by a decline due to accumulated moisture depletion (high elevation forest) or temperature decrease (high elevation nonforest), (ii) gradual decline during the drought followed by a rapid recovery within 1 year after drought stress was partially relieved, and (iii) both a gradual decline and an abrupt decline. The magnitude of abrupt changes was negatively correlated (r = −0.80, p < 0.001) with initial gradual changes. Overall, changes during BP offset, on average, 57% of the preceding gradual responses. The spatial variability in ecosystem response patterns is driven by both environmental and biological factors. Particularly, for forests, positive BP was driven by increasing rainfall and decreasing temperature, while negative BP was mainly driven by the precipitation anomaly. By 2019, 33% of the natural vegetation have recovered to the level of EVI in 2010. Ecosystem responses to multiyear droughts can influence ecosystem dynamics in a complex pattern. Multiple ecohydrological factors should be considered to understand and predict the long-term drought impacts on ecosystems.

Xi Yang↗

DOE OSTI2021

Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover

Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). Additionally, the highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2023

Relativistic ultrafast electron diffraction at high repetition rates

The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are being developed that are aimed at increasing the beam brightness in order to observe structural signatures, but so far they have been limited to low average current beams. Here, we present the technical design and capabilities of the HiRES (High Repetition-rate Electron Scattering) instrument, which blends relativistic electrons and high repetition rates to achieve orders of magnitude improvement in average beam current compared to the existing state-of-the-art instruments. The setup utilizes a novel electron source to deliver femtosecond duration electron pulses at up to MHz repetition rates for UED experiments. Instrument response function of sub-500 fs is demonstrated with < 100 fs time resolution targeted in future. We provide example cases of diffraction measurements on solid-state and gas-phase samples, including both micro- and nanodiffraction (featuring 100 nm beam size) modes, which showcase the potential of the instrument for novel UED experiments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

A Brief Overview of Reactive Transport Codes Used in CO 2 Applications

Reactive transport modelling consists of computational and numerical models that describe the coupled physical, chemical, mechanical, and biological processes interacting with each other over a broad range of spatial and temporal scales. This report reviews some of the reactive transport codes available in the literature for carbon dioxide (CO 2 ) applications and can assist the scientific community with the applicability of each code to solve a specific problem. Approaches implemented in these codes can be categorized in three groups: (i) continuum-scale, (ii) pore-scale, and (iii) hybrid-scale approaches. Theoretical foundations, numerical implementations, and application examples using the models are described. In the continuum approach, flow and transport are formulated in terms of a representative control volume of the medium and coupled with geochemical reactions. The medium is characterized by bulk parameters such as porosity, permeability, or reactive surface area. In the pore-scale approach, each point of space in the pore network is occupied by either a fluid or solid phase. The pore-scale approach requires an exact knowledge of the spatial and temporal phase distribution. In the hybrid-scale approach, media are described by multiple characteristic length-scales, with some regions using a pore-scale approach while others used a continuum approach.

01 COAL, LIGNITE, AND PEAT↗

NASA NTRS1980

Separating liquid and gaseous solutions

Clusius-Dickel separation (CDS) technique, currently used in laboratoryscale separation of certain isotopes, may find more effective applications in low-gravity, space environments. Many advantages in power supply, mechanical stresses, and spatial arragement can be realized in space, making technique suitable for biological and polymer separations.

Benefield, J. W.↗

DOE OSTI2023

Methods and systems of proteome analysis and imaging

Provided herein are methods and systems for proteome analysis that are at least partially automated and/or performed robotically. In some aspects, the methods and systems described herein can rapidly and efficiently provide protein identification of each of the proteins from a proteome, or a complement of proteins, obtained from extremely small amounts of biological samples. The identified proteins can be imaged quantitatively over a spatial region. Automation and robotics facilitates the throughput of the methods and systems, which enables protein imaging and/or rapid proteome analysis.

Piehowski, Paul D.↗

NASA NTRS1995

Effect of the nonlinearity of the carbonate system on partial pressure of carbon dioxide in the oceans

Partial pressure of CO2 is a nonlinear function of several seawater properties. Due to the nonlinearity in this relationship, the partial pressure of a uniform ocean would be different from that of a nonuniform ocean with the same bulk seawater properties. Assuming uniformity of seawater properties at some temporal and spatial scales in carbon models leads to systematic errors in partial pressure of CO2. In this paper we evaluate the magnitude of these errors. We partition the Geochemical Ocean Sections Study and Transient Tracers in the Oceans data according to the horizontal structure of several box models from the literature. Our results suggest that assumption of uniformity at large scales leads to understanding of underestimation of global surface ocean partial pressure of CO2 by at least 3 - 12 microatm. Nonlinear effects also introduce systematic errors in the buffer factor estimated from bulk seawater properties. We find the standard deviation of partial pressure of CO2 to be an indicator of the magnitude of the nonlinear effects. We discuss the implications of these errors for some conclusions drawn from carbon models. Biogeochemical processes, such as mixing, gas exchange, or biological activity, influence the distribution of the seawater properties. A shift in spatial or temporal patterns of these processes can modify the nonuniformity of the seawater properties and thus alter the partial pressure of the surface waters, even if the mean intensities of the processes remain constant.

Trela, Piotr↗

DOE OSTI2026

Spatial analysis of cell patterning to aid genetic and phenotypic understanding of grass stomatal density: A case study in maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2018

Satellite Radiation Products for Ocean Biology and Biogeochemistry: Needs, State-Of-The-Art, Gaps, Development Priorities, and Opportunities

Knowing the spatial and temporal distribution of the underwater light field, i.e., the spectral and angular structure of the radiant intensity at any point in the water column, is essential to understanding the biogeochemical processes that control the composition and evolution of aquatic ecosystems and their impact on climate and reaction to climate change. At present, only a few properties are reliably retrieved from space, either directly or via water-leaving radiance. Existing satellite products are limited to planar photosynthetically available radiation (PAR) and ultraviolet (UV) irradiance above the surface and diffuse attenuation coefficient. Examples of operational products are provided, and their advantages and drawbacks are examined. The usefulness and convenience of these products notwithstanding, there is a need, as expressed by the user community, for other products, i.e., sub-surface planar and scalar fluxes, average cosine, spectral fluxes (UV to visible), diurnal fluxes, absorbed fraction of PAR by live algae (APAR), surface albedo, vertical attenuation, and heating rate, and for associating uncertainties to any product on a pixel-by-pixel basis. Methodologies to obtain the new products are qualitatively discussed in view of most recent scientific knowledge and current and future satellite missions, and specific algorithms are presented for some new products, namely sub-surface fluxes and average cosine. A strategy and roadmap (short, medium, and long term) for usage and development priorities is provided, taking into account needs and readiness level. Combining observations from satellites overpassing at different times and geostationary satellites should be pursued to improve the quality of daily-integrated radiation fields, and products should be generated without gaps to provide boundary conditions for general circulation and biogeochemical models. Examples of new products, i.e., daily scalar PAR below the surface, daily average cosine for PAR, and sub-surface spectral scalar fluxes are presented. A procedure to estimate algorithm uncertainties in the total uncertainty budget for above-surface daily PAR, based on radiative simulations for expected situations, is described. In the future, space-borne lidars with ocean profiling capability offer the best hope for improving our knowledge of sub-surface fields. To maximize temporal coverage, space agencies should consider placing ocean-color instruments in L1 orbit, where the sunlit part of the Earth can be frequently observed.

Frouin, Robert↗

NASA NTRS1999

Near-Field Scanning Optical Microscopy of Soft, Biological, or Rough Objects in Aqueous Environment: Challenges and some Remedies to Circumvent

Near-field scanning optical microscopy is an established technique for sub-wavelength spatial resolution in imaging, spectroscopy, material science, surface chemistry, polarimetry, etc. A significant amount of confidence has been established for thin hard specimens in air. However when soft, biological, rough, in aqueous environment object, or a combination is involved, the progress has been slow. The tip-sample mechanical interaction, heat effects to sample, drag effects to the probe, difficulty in controlling tip-sample separation in case of rough objects, light scattering from sample thickness, etc. create problems. Although these problems are not even fully understood, there have been attempts to study them with the aim of performing reliable operations. In this review we describe these attempts. Starting with general problems encountered, various effects like polarization, thermal, and media are covered. The roles of independent tip-sample distance control tools in the relevant situations are then described. Finally progress in fluid cell aspect has been summarized.

Vikram, C. S.↗

DOE OSTI2020

Nanomechanical sampling of material for nanoscale mass spectrometry chemical analysis

The ability to spatially resolve the chemical distribution of compounds on a surface is important in many applications ranging from biological to material science. To this extent, we have recently introduced a hybrid atomic force microscopy (AFM)-mass spectrometry (MS) system for direct thermal desorption and pyrolysis of material with nanoscale chemical resolution. However, spatially resolved direct surface heating using local thermal desorption becomes challenging on material surfaces with low melting points, because the material will undergo a melting phase transition due to heat dissipation prior to onset of thermal desorption. Therefore, here we developed an approach using mechanical sampling and collection of surface materials on an AFM cantilever probe tip for real-time analysis directly from the AFM tip. This approach allows for material to be concentrated directly onto the probe for subsequent MS analysis. We evaluate the performance metrics of the technique and demonstrate localized MS sampling from a candelilla wax matrix containing UV stabilizers avobenzone and oxinoxate from areas down to 250 nm × 250 nm. Overall, this approach removes heat dissipation into the bulk material allowing for a faster desorption and concentration of the gas phase analyte from a single heating pulse enabling higher signal levels from a given amount of material in a single sampling spot.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2004

Characterization of Asian Dust Properties Near Source Region During ACE-Asia

Asian dust typically originates in desert areas far from polluted urban regions. During transport, dust layers can interact with anthropogenic sulfate and soot aerosols from heavily polluted urban areas. Added to the complex effects of clouds and natural marine aerosols, dust particles reaching the marine environment can have drastically different properties than those from the source. Thus, understanding the unique temporal and spatial variations of Asian aerosols is of special importance in regional-to-global climate issues such as radiative forcing, the hydrological cycle, and primary biological productivity in the mid-Pacific Ocean. During ACE-Asia campaign, we have acquired ground- based (temporal) and satellite (spatial) measurements to infer aerosol physical/optical/radiative properties, column precipitable water amount, and surface reflectivity over this region. The inclusion of flux measurements permits the determination of aerosol radiative flux in addition to measurements of loading and optical depth. At the time of the Terra/MODIS, SeaWiFS, TOMS and other satellite overpasses, these ground-based observations can provide valuable data to compare with satellite retrievals over land. In this paper, we will demonstrate new capability of the Deep Blue algorithm to track the evolution of the Asian dust storm from sources to sinks. Although there are large areas often covered by clouds in the dust season in East Asia, this algorithm is able to distinguish heavy dust from clouds over the entire regions. Examination of the retrieved daily maps of dust plumes over East Asia clearly identifies the sources contributing to the dust loading in the atmosphe~~. We have compared the satellite retrieved aerosol optical thickness to the ground-based measurements and obtained a reasonable agreement between these two. Our results also indicate that there is a large difference in the retrieved value of spectral single scattering albedo of windblown dust between different sources in East Asia.

Tsay, Si-Chee↗

NASA NTRS1998

Integration of GIS, Geostatistics, and 3-D Technology to Assess the Spatial Distribution of Soil Moisture

The spatial and temporal distribution of near surface soil moisture is of fundamental importance to many physical, biological, biogeochemical, and hydrological processes. However, knowledge of these space-time dynamics and the processes which control them remains unclear. The integration of geographic information systems (GIS) and geostatistics together promise a simple mechanism to evaluate and display the spatial and temporal distribution of this vital hydrologic and physical variable. Therefore, this research demonstrates the use of geostatistics and GIS to predict and display soil moisture distribution under vegetated and non-vegetated plots. The research was conducted at the Winfred Thomas Agricultural Experiment Station (WTAES), Hazel Green, Alabama. Soil moisture measurement were done on a 10 by 10 m grid from tall fescue grass (GR), alfalfa (AA), bare rough (BR), and bare smooth (BS) plots. Results indicated that variance associated with soil moisture was higher for vegetated plots than non-vegetated plots. The presence of vegetation in general contributed to the spatial variability of soil moisture. Integration of geostatistics and GIS can improve the productivity of farm lands and the precision of farming.

Betts, M.↗

DOE OSTI2023

Enzymatically hydrolyzed fluorescence-based chemical probe enables in situ mapping of chitinase activity in the rhizosphere

Rhizosphere microbiomes and root exudates play a pivotal biochemical role in helping to catalyze chitin catabolism. Chitin is a recalcitrant and ubiquitous soil biopolymer, estimated to be the second most abundant organic soil biopolymer on Earth. Despite its abundance, role as a source of C and N in soil, and importance to ecosystem function, the biochemical mechanisms controlling chitin fate in the rhizosphere are elusive and poorly understood. To enable spatial mapping of chitinase activity in the rhizosphere, we designed and synthesized an enzymatically activated fluorogenic substrate, chitotriose-TokyoGreen (chitotriose-TG), by incorporating a fluorescein derivative (TG) onto the trimeric unit of chitin. This non-fluorescent substrate is selectively hydrolyzed by chitinase to release TG and yield a high fluorescence signal, which can be used to spatially image and measure chitinase activity in the rhizosphere. To demonstrate the application of this technique, we grew switchgrass (Panicum virgatum) in rhizoboxes amended with a horizontal layer of chitin. We extracted mobile proteins from the rhizobox using a nitrocellulose membrane blotting technique which offer non-destructive enzyme extraction while preserving the 2D spatial position of the enzymes. We then subjected these membranes to the synthesized chitotriose-TG stain to spatially visualize the distribution of chitinase activity within the rhizosphere. Furthermore, we observed increased chitinase activity near plant roots and higher activity within the soil zone enriched in chitin, showing an adaptive response of chitinase activity with spatial focusing in areas of higher chitin abundance. Thus, the enzyme extraction and visualization strategy we describe here can help enlighten efforts to better understand spatial controls on chitin breakdown in rhizosphere, further elucidating the role of chitin as a C and N source in these systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Confinement-induced chirality in phase-separated achiral polymer solutions

Self-organization of polymers in constrained geometries largely determines their applications in high-strength materials, photonics, and electronics. Chiral organization under confinement is well established for polymers with intrinsic molecular chirality; however, it has not been observed for achiral polymers. Here, we report the emergence of chirality in spatially confined solutions of achiral rigid-rod polymers. We show that kinetically arrested phase separation of polymer solutions confined to narrow capillaries resulted in alternating segments of isotropic and chiral nematic phases. The chiral structure of the nematic segments originated from the interplay between the constrained geometry, surface anchoring, orientational wetting, and elastic anisotropy of rigid-rod polymers. The catenoidal shape of the chiral structure recapitulated the morphology of biological chiral structures. These findings provide insight into the organization of soft matter under spatial confinement and offer a straightforward way to form chiral structures from achiral synthetic polymers.

Science & Technology - Other Topics↗

DOE OSTI2025

Challenges in spatial metabolomics and proteomics for functional tissue unit and single-cell resolution

While transcriptomics is the most broadly applied technology for global spatial and single cell measurements in healthy and diseased tissues. Transcripts are often used as a proxy for protein and even metabolite measurements, but it has become commonly accepted that extrapolating this kind of information is a poor proxy and not a substitute for direct measurement. Within the last decade advanced developments of mass spectrometry-based assays have made these direct measurements not only possible, but routine. Where mass spectrometry has become an enabling technology, and various methods can now detect hundreds of metabolites and thousands of proteins from samples. Not only can this be performed within bulk measurements, but much effort has been directed into translating these measurements to single cells and tissues at cellular resolution. The information obtained from mass spectrometry is now able to trace metabolic events and decipher feedback loops across anatomical regions, connecting genetic and metabolic networks that define phenotypes. Herein, we will broadly overview developments in the field over the past decade, leading into several case studies which highlight the direct measurement of metabolites, proteins, and proteoforms from thinly sliced tissues. Much of this work is feasible due to multidisciplinary team science, and we offer brief perspective on paths forward and the challenges that persist with adoption and application of spatial omics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Damage-free Analysis of Biological Materials by Vibrational Spectroscopy in the EM

In summary, vibrational spectroscopy in the electron microscope promises to probe biological materials in a way that is similar to infrared spectroscopy, at a spatial resolution of about 30-50 nm, while circumventing radiation damage. Herein we are now focused on developing this technique fully, using a side-entry cryotransfer holder in a Nion HERMES electron microscope equipped with a fast and efficient EELS direct detector [10], and capable of 5 meV (and better) energy resolution. The results of these investigations will be reported at the meeting.

59 BASIC BIOLOGICAL SCIENCES↗