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DOE OSTI2022

Are enzymes transported in soils by water fluxes?

Transport of extracellular hydrolytic enzymes in soils has always been a subject of doubt. The considerations against its importance are that (i) enzymes benefit their producers the most when they remain in close proximity; and (ii) enzymes are large molecules with low mobility due to high affinity to fine soil particles and organic matter. However, soil mineral colloids (SMC), to which extracellular enzymes also have an affinity and which are known to facilitate transport of a broad variety of chemicals and microorganisms in soils, can serve as vehicles for enzyme transport as well. Since current literature lacks information on enzyme transport in soils, our goal was to determine whether enzymes are transported and, if so, whether they are transported in a free- or in a colloid-associated form. We conducted column transport experiments with four hydrolytic enzymes, namely, β-glucosidase, acid-phosphatase, cellobiohydrolase, and xylosidase, in soils with contrasting textures. The eluents containing enzymes were applied on top of soil columns, while enzyme activities, SMC, and electrical conductivity were measured in the effluents from the columns. Our results provided evidence of joint enzyme transport with soil colloids. The enzymes associated with the coarse SMC (1 μm < Ø) contributed 52–88% of the total enzyme activity in the effluents. The remaining enzyme activity was attributed to the enzymes associated with organic colloids, fine SMC (Ø < 1 μm) and free enzymes in solution. Furthermore, this study suggested a dual effect of ionic strength in the soil suspension on enzyme activity and their release from soils with soil colloids.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2011

Biogeochemical Impact of Long-Range Transported Dust over Northern South China Sea

Transpacific transport and impact of Asian dust aerosols have been well documented (e.g., results from ACE-Asia and regional follow-on campaigns), but little is known about dust invasion to the South China Sea (SCS). On 19-21 March 2010, a fierce Asian dust storm affected large areas from the Gobi deserts to the West Pacific, including Taiwan and Hong Kong. As a pilot study of the 7-SEAS (Seven South East Asian Studies) in the northern SCS, detailed characteristics of long-range transported dust aerosols were first observed by a comprehensive set of ground-based instruments deployed at the Dongsha islands (20deg42'52" N, 116deg43'51" E). Aerosol measurements such as particle mass concentrations, size distribution, optical properties, hygroscopicity, and vertical profiles help illustrate the evolution of this dust outbreak. Our results indicate that these dust particles were mixed with anthropogenic and marine aerosols, and transported near the surface. Satellite assessment of biogeochemical impact of dust deposition into open oceans is hindered by our current inability in retrieving areal dust properties and ocean colors over an extensive period of time, particularly under the influence of cloudy conditions. In this paper, we analyze the changes of retrieved Chlorophyll-a (Chl-a) concentration over the northern SCS, considered as oligotophic waters in the spring, from long-term SeaWiFS measurements since 1997. Over the past decade, six long-range transported dust events are identified based on spatiotemporal evolutions of PM10 measurements from regional monitoring stations, with the aid of trajectory analysis. Multi-year composites of Chl-a imagery for dust event and non-dust background during March-April are applied to overcome insufficient retrievals of Chl-a due to cloudy environment. Due to anthropogenic modification within a shallow boundary layer off the densely populated and industrial southeast coast of China, the iron ion activation of deliquescent dust particles enhances the efficiency of fertilization for biological productivity. Compared to the West Pacific, the marine ecosystem in the northern SCS is much more susceptible to the biogeochemical impact of long-range transported Asian dust.

Tsay, Si-Chee↗

DOE OSTI2025

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Nanobodies against the metal binding domains of ATP7B as tools to study copper transport in the cell

Abstract Nanobodies are genetically engineered single domain antibodies derived from the unusual heavy-chain only antibodies found in llamas and camels. The small size of the nanobodies and flexible selection schemes make them uniquely versatile tools for protein biochemistry and cell biology. We have developed a panel of nanobodies against the metal binding domains of the human copper transporter ATP7B, a multidomain membrane protein with a complex regulation of enzymatic activity and intracellular localization. To enable the use of the nanobodies as tools to investigate copper transport in the cell, we characterized their binding sites and affinity by isothermal titration calorimetry and NMR. We have identified nanobodies against each of the first four metal binding domains of ATP7B, with a wide affinity range, as evidenced by dissociation constants from below 10−9 to 10−6 M. We found both the inhibitory and activating nanobodies among those tested. The diverse properties of the nanobodies make the panel useful for the structural studies of ATP7B, immunoaffinity purification of the protein, modulation of its activity in the cell, protein dynamics studies, and as mimics of copper chaperone ATOX1, the natural interaction partner of ATP7B.

Uhlemann, Eva-Maria E.↗

DOE OSTI2021

Sugar transporters in grasses: Function and modulation in source and storage tissues

Carbohydrate partitioning, the process of transporting carbohydrates from photosynthetic (source) tissues, such as leaves, to non-photosynthetic (sink) tissues, such as stems, roots, and reproductive structures, is vital not only for the growth and development of plants but also for withstanding biotic and abiotic stress. In many plants, sucrose is the primary form of carbohydrate loaded into the phloem for long-distance transport and unloaded into the sink tissues for utilization or storage. Here, we highlight recent findings about 1) phloem loading in grasses, 2) the principal families of sugar transporters involved in sucrose transport, and 3) novel mechanisms by which the activities of sugar transporters are modulated. We discuss exciting discoveries from eudicot species that provide valuable insights regarding the regulation of these sugar transporters, which may be translatable to monocot species. As we better understand the intricate pathways that control the activities of various sugar transporters, we can utilize this knowledge for developing improved crop varieties.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2016

Hollow Fiber Membrane Bioreactor Systems for Wastewater Processing: Effects of Environmental Stresses Including Dormancy Cycling and Antibiotic Dosing

Membrane-aerated biofilm reactors (MABRs) have been studied for a number of years as an alternate approach for treating wastewater streams during space exploration. While the technology provides a promising pre-treatment for lowering organic carbon and nitrogen content without the need for harsh stabilization chemicals, several challenges must be addressed before adoption of the technology in future missions. One challenge is the transportation of bioreactors containing intact, active biofilms as a means for rapid start-up on the International Space Station or beyond. Similarly, there could be a need for placing these biological systems into a dormant state for extended periods when the system is not in use, along with the ability for rapid restart. Previous studies indicated that there was little influence of storage condition (4 or 25 C, with or without bulk fluid) on recovery of bioreactors with immature biofilms (48 days old), but that an extensive recovery time was required (20+ days). Bioreactors with fully established biofilms (13 months) were able to recover from a 7-month dormancy within 4 days (approximately 1 residence). Further dormancy and recovery testing is presented here that examines the role of biofilm age on recovery requirements, repeated dormancy cycle capabilities, and effects of long-duration dormancy cycles (8-9 months) on HFMB systems. Another challenge that must be addressed is the possibility of antibiotics entering the wastewater stream. Currently, for most laboratory tests of biological water processors, donors providing urine may not contribute to the study when taking antibiotics because the effects on the system are yet uncharacterized. A simulated urinary tract infection event, where an opportunistic, pathogenic organism, E. coli, was introduced to the HFMBs followed by dosing with an antibiotic, ciprofloxacin, was completed to study the effect of the antibiotic on reactor performance and to also examine the development of antibiotic-resistant communities within the system.

Bioreactor Systems↗

DOE OSTI2020

Redox Stability Controls the Cellular Uptake and Activity of Ruthenium‐Based Inhibitors of the Mitochondrial Calcium Uniporter (MCU)

Abstract The mitochondrial calcium uniporter (MCU) is the ion channel that mediates Ca 2+ uptake in mitochondria. Inhibitors of the MCU are valuable as potential therapeutic agents and tools to study mitochondrial Ca 2+ . The best‐known inhibitor of the MCU is the ruthenium compound Ru360. Although this compound is effective in permeabilized cells, it does not work in intact biological systems. We have recently reported the synthesis and characterization of Ru265, a complex that selectively inhibits the MCU in intact cells. Here, the physical and biological properties of Ru265 and Ru360 are described in detail. Using atomic absorption spectroscopy and X‐ray fluorescence imaging, we show that Ru265 is transported by organic cation transporter 3 (OCT3) and taken up more effectively than Ru360. As an explanation for the poor cell uptake of Ru360, we show that Ru360 is deactivated by biological reductants. These data highlight how structural modifications in metal complexes can have profound effects on their biological activities.

Woods, Joshua J.↗

DOE OSTI2021

TOUGHREACT V4.12

TOUGHREACT V4.12 is a 3-D reactive transport code that handles to non-isothermal, multiphase/multicomponent fluid flow, heat transport, aqueous and gaseous species advection-diffusion, and equilibrium/kinetic water-gas-rock-biological reactions. TOUGHREACT V4.12 is based on TOUGHREACT V3.3, with several new features including: an option to compute activity coefficients using the Pitzer ion interaction model; implementation of ECO2N V2.0 for temperatures up to 300 C; options to simulate forward and reverse osmosis, including 2D Poiseuille flow; addition of EOS8 and revisions for EOS5 and EWASG with H2(g); addition of gas species decay, various new output formats and time step control options; many bug fixes.

Spycher, Nicolas↗

NASA NTRS2013

Galactic Cosmic Ray Event-Based Risk Model (GERM) Code

This software describes the transport and energy deposition of the passage of galactic cosmic rays in astronaut tissues during space travel, or heavy ion beams in patients in cancer therapy. Space radiation risk is a probability distribution, and time-dependent biological events must be accounted for physical description of space radiation transport in tissues and cells. A stochastic model can calculate the probability density directly without unverified assumptions about shape of probability density function. The prior art of transport codes calculates the average flux and dose of particles behind spacecraft and tissue shielding. Because of the signaling times for activation and relaxation in the cell and tissue, transport code must describe temporal and microspatial density of functions to correlate DNA and oxidative damage with non-targeted effects of signals, bystander, etc. These are absolutely ignored or impossible in the prior art. The GERM code provides scientists data interpretation of experiments; modeling of beam line, shielding of target samples, and sample holders; and estimation of basic physical and biological outputs of their experiments. For mono-energetic ion beams, basic physical and biological properties are calculated for a selected ion type, such as kinetic energy, mass, charge number, absorbed dose, or fluence. Evaluated quantities are linear energy transfer (LET), range (R), absorption and fragmentation cross-sections, and the probability of nuclear interactions after 1 or 5 cm of water equivalent material. In addition, a set of biophysical properties is evaluated, such as the Poisson distribution for a specified cellular area, cell survival curves, and DNA damage yields per cell. Also, the GERM code calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle in a selected material. The GERM code makes the numerical estimates of basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the first option, properties of monoenergetic beams are treated. In the second option, the transport of beams in different materials is treated. Similar biophysical properties as in the first option are evaluated for the primary ion and its secondary particles. Additional properties related to the nuclear fragmentation of the beam are evaluated. The GERM code is a computationally efficient Monte-Carlo heavy-ion-beam model. It includes accurate models of LET, range, residual energy, and straggling, and the quantum multiple scattering fragmentation (QMSGRG) nuclear database.

Cucinotta, Francis A.↗

DOE OSTI2023

Genomes to ecosystem function: Targeting critical knowledge gaps in methanogenesis and translation to updated global biogeochemical models

Natural freshwater temperate wetland systems currently represent the largest natural source of atmospheric methane, but are relatively understudied using systems biology tools (e.g. meta-omics) compared to other high producing methane systems (e.g. peat, tropical, or reconstructed wetlands). Using field investigations at the NOAA operated sentinel site on Lake Erie, methane producing activities and responses to geochemical conditions will be determined along seasonal and spatial gradients (Objective 1). Here, a combination of high-throughput activity and gas measurements, combined with high-resolution systems biology and analytical methods, will provide in depth knowledge of the microbiological, chemical, and physical constraints on methane production in wetlands. Using laboratory microcosms, the formation of anoxic microsites and their capacity to facilitate methane production in wetland soils will be simulated (Objective 2). This objective will validate the findings from the field investigations, offering a more controlled environment for teasing out the role of different yet interrelated variables. Lastly, these field and laboratory data will be used for multi-scale, process-level evaluation of an ecosystem biogeochemical model that accommodates these newly identified processes and parameterizes representation of these processes along relevant environmental gradients (Objective 3).This research will identify multiple interacting geochemical, ecological, and metabolic constraints that are poorly understood, oversimplified, or missing in global biogeochemical methane models. This proposal targets the role of oxygen limitation on methane processes in soil domains, to improve reactive transport models of microbial carbon cycling across terrestrial-aquatic soils and generate data on nutrient cycling activities in Great Lake wetlands. This information could provide new insights into the microbial controllers of Lake Erie eutrophication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein–protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Permeability-Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems

In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability-configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer-sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell-free protein synthesis system sustains multicycle protein production; ≈100 000 compartments are repeatedly used in a five-cycle synthesis, featuring a yield of 2.2 mg mL -1 . Further, the engineered bacteria-enclosing compartments possess near-perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole-cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability-engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Materials processing in space - New challenges for industry

A summary is presented of NASA's activity in materials research in zero-g. Very simple experiments to determine the effects of zero-g upon solidification processes, upon heat flow, convection and mass transport, and upon the separation of biological cells were conducted during three Apollo flights. The investigations were continued in a series of experiments conducted on Skylab. The experiments provided data on a wide range of space-processing topics. The various tests and the results obtained in them are discussed. Attention is also given to experiments planned for the Apollo-Soyuz experiment, studies to be conducted with the aid of sounding rockets, and an evaluation of the possibilities provided by space processing for industry.

Bredt, J. H.↗

DOE OSTI2022

Grape ASR Regulates Glucose Transport, Metabolism and Signaling

To decipher the mediator role of the grape Abscisic acid, Stress, Ripening (ASR) protein, VvMSA, in the pathways of glucose signaling through the regulation of its target, the promoter of hexose transporter VvHT1, we overexpressed and repressed VvMSA in embryogenic and non-embryogenic grapevine cells. The embryogenic cells with organized cell proliferation were chosen as an appropriate model for high sensitivity to the glucose signal, due to their very low intracellular glucose content and low glycolysis flux. In contrast, the non-embryogenic cells displaying anarchic cell proliferation, supported by high glycolysis flux and a partial switch to fermentation, appeared particularly sensitive to inhibitors of glucose metabolism. By using different glucose analogs to discriminate between distinct pathways of glucose signal transduction, we revealed VvMSA positioning as a transcriptional regulator of the glucose transporter gene VvHT1 in glycolysis-dependent glucose signaling. The effects of both the overexpression and repression of VvMSA on glucose transport and metabolism via glycolysis were analyzed, and the results demonstrated its role as a mediator in the interplay of glucose metabolism, transport and signaling. The overexpression of VvMSA in the Arabidopsis mutant abi8 provided evidence for its partial functional complementation by improving glucose absorption activity.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Assessment of Anthropogenic and Climatic Impacts on the Global Carbon Cycle Using a 3-D Model Constrained by Isotopic Carbon Measurements and Remote Sensing of Vegetation

Our original proposal called for improved modeling of the terrestrial biospheric carbon cycle, specifically using biome-specific process models to account for both the energy and water budgets of plant growth, to facilitate investigations into recent changes in global atmospheric CO2 abundance and regional distribution. The carbon fluxes predicted by these models were to be incorporated into a global model of CO2 transport to establish large-scale regional fluxes of CO2 to and from the terrestrial biosphere subject to constraints imposed by direct measurements of atmospheric CO2 and its 13C/12C isotopic ratio. Our work was coordinated with a NASA project (NASA NAGW-3151) at the University of Montana under the direction of Steven Running, and was partially funded by the Electric Power Research Institute. The primary objective of this project was to develop and test the Biome-BGC model, a global biological process model with a daily time step which simulates the water, energy and carbon budgets of plant growth. The primary product, the unique global gridded daily land temperature, and the precipitation data set which was used to drive the process model is described. The Biome-BGC model was tested by comparison with a simpler biological model driven by satellite-derived (NDVI) Normalized Difference Vegetation Index and (PAR) Photosynthetically Active Radiation data and by comparison with atmospheric CO2 observations. The simple NDVI model is also described. To facilitate the comparison with atmospheric CO2 observations, a three-dimensional atmospheric transport model was used to produce predictions of atmospheric CO2 variations given CO2 fluxes owing to (NPP) Net Primary Productivity and heterotrophic respiration that were produced by the Biome-BGC model and by the NDVI model. The transport model that we used in this project, and errors associated with transport simulations, were characterized by a comparison of 12 transport models.

Keeling, Charles D.↗

DOE OSTI2026

Biocatalyst discovery and design for plastics deconstruction: A multi‐scale perspective

Plastic waste accumulation poses significant environmental challenges due to a lack of economical solutions for the molecular deconstruction of diverse synthetic polymers. Biological‐based degradation offers promise but is hindered by the crystallinity, hydrophobicity, and additive complexity of plastics, which restrict biocatalyst access and activity. To address these problems, we propose a multi‐scale framework that combines detailed materials characterization, optimization of plastic‐biomolecular interfacial interactions, and enhancement of biocatalytic kinetics to develop effective plastic‐deconstructing enzymes. This approach leverages principles from reaction kinetics, transport and interfacial phenomena, and enzyme engineering to systematically address barriers across diverse plastic types. Our framework aims to accelerate the discovery and optimization of biocatalysts capable of scalable, selective, and efficient deconstruction of plastic waste. These advances hold potential to enable sustainable biological recycling and upcycling pathways, contributing to global efforts in mitigating plastic pollution and promoting circular material economies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2007

Physical Laws for Mechanobiology

Higher-level physical laws applicable to biological tissues are presented that will permit the modeling of metabolic activity at the cellular level, including variations in the mass of a tissue. Here the tissue is represented as a fluid/solid mixture, wherein molecular solutes transport within the fluid, and cells can migrate throughout the porous solid. Variations in mass can arise via exchanges in mass between the constituent phases within a control volume such that mass is conserved in the tissue overall. The governing balance laws for mass, momentum, energy, and entropy are a special case of those describing a chemically reacting mixture with diffusion. Thermodynamic constraints on the constitutive structure are addressed. Biophysics; Biomechanics; Brownian motion; Cell migration; Mixture theory; Thermodynamic laws; Tissue mechanics

Freed, Alan D.↗

NASA NTRS1991

Evolution of ore deposits on terrestrial planets

Ore deposits on terrestrial planets materialized after core formation, mantle evolution, crustal development, interactions of surface rocks with the hydrosphere and atmosphere, and, where life exists on a planet, the involvement of biological activity. Core formation removed most of the siderophilic and chalcophilic elements, leaving mantles depleted in many of the strategic and noble metals relative to their chondritic abundances. Basaltic magma derived from partial melting of the mantle transported to the surface several metals contained in immiscible silicate and sulfide melts. Magmatic ore deposits were formed during cooling, fractional crystallization and density stratification from the basaltic melts. Such ore deposits found in earth's Archean rocks were probably generated during early histories of all terrestrial planets and may be the only types of igneous ores on Mars. Where plate tectonic activity was prevalent on a terrestrial planet, temporal evolution of ore deposits took place. Repetitive episodes of subduction modified the chemical compositions of the crust and upper mantles, leading to porphyry copper and molybdenum ores in calc-alkaline igneous rocks and granite-hosted tin and tungsten deposits. Such plate tectonic-induced mineralization in relatively young igneous rocks on earth may also have produced hydrothermal ore deposits on Venus in addition to the massive sulfide and cumulate chromite ores associated with Venusian mafic igneous rock. Sedimentary ore deposits resulting from mechanical and chemical weathering in reducing atmospheres in Archean earth included placer deposits (e.g., uraninite, gold, pyrite ores). Chromite, ilmenite, and other dense unreactive minerals could also be present on channel floors and in valley networks on Mars, while banded iron formations might underlie the Martian northern plains regions. As oxygen evolved in earth's atmosphere, so too did oxide ores. By analogy, gossans above sulfide ores probably occur on Mars, but not submarine ferromanganese nodules and crusts which have precipitated in oxygenated seawater on earth.

Burns, R. G.↗