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DOE OSTI2022

Predictive Contaminant Transport Simulation with the P2R Model for the Composite Analysis Recharge Sensitivity Case

The Plateau-to-River (P2R) model is a groundwater flow and contaminant fate and transport (F&T) simulation model used to support remedial activities conducted by the Central Plateau Cleanup Company (CPCCo) at the Hanford Site in south-central Washington State. The overall objective of the saturated zone modeling effort is to provide a basis for making informed remedial action decisions based on descriptions of current and expected future contaminant concentrations in groundwater at decision points within and downgradient of the Central Plateau of the Hanford Site. Specifically, the purpose of this environmental calculation file (ECF) is to describe a recharge sensitivity case of the CA base case. The recharge sensitivity case implements a change in the activity contribution from the vadose zone in the A Trenches Area model (for tritium [H-3] and iodine-129 [I-129]), BC Cribs and Trenches model (for I-129 and technetium-99 [Tc-99]), or the Plutonium Uranium Extraction (PUREX) Area model (for H-3 and I-129). All other simulated inventories are identical to the CA base case. The simulation of fate and transport of contaminants reported in this case will support dose predictions as part of the updated Hanford Site CA.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗

DOE OSTI2022

Hanford Site Composite Analysis Special Analysis: P2R Model Predictive Contaminant Transport Simulations - Sensitivity Case

This environmental calculation file (ECF) documents the methodologies, assumptions, and results of predictive fate and transport simulations using the Plateau-to-River (P2R) model. This ECF supports the reevaluation of the representativeness of solid-waste radionuclide inventory and release rate from three solid waste sites included in the recently completed Hanford Site Composite Analysis (CA) (DOE-RL-2019-52, Composite Analysis for Low-Level Waste Disposal in the Hanford Site Central Plateau (FY 2020)). Specifically, this ECF supports the reevaluation of the representativeness of the base case inventory and radionuclide waste release rates from three solid waste sites (i.e., 218-E-12B, 218-W-3A and 218-W-3AE) and two radionuclides (carbon-14 [C-14] and technetium [Tc-99]). These three waste sites and two radionuclides were identified as being the most significant contributors to groundwater contamination and dose in the CA at time periods after the compliance period. The release rates and footprints of the releases from the vadose zone are implemented in the fate and transport modeling utilizing the HSS package.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

User’s Manual for RESRAD-BUILD Code V.4: Vol. 1 – Methodology and Models Used in RESRAD-BUILD Code

The RESRAD-BUILD computer code models radionuclide release and transport in indoor environments and performs pathway analyses to evaluate the potential radiological dose and risk incurred by an individual who works or lives in a building contaminated with radioactive material or housing radioactively contaminated furniture or equipment. The code provides four geometries to characterize a radiation source: point, line, area, and volume, in which radionuclides are homogeneously distributed. Radionuclides contained in a source are considered to be released to the indoor air due to various processes including erosion (mechanically or weathering), diffusion (for tritium and radon in a volume source), or emanation (radon in a point, line, or area source). The release can proceed through different time phases with different rates. In RESRAD-BUILD Version 4.0, a dynamic ventilation model is implemented to simulate the fate and transport of source material particles and radionuclides after their releases. This dynamic ventilation model considers (1) air exchange between rooms in the building and between the rooms and the outdoor environment, (2) deposition from air to floor, (3) resuspension from the floor to the air, and (4) periodical vacuuming that reduces the floor deposition. The fate and transport modeling provides estimates of radionuclide concentrations in the source, in the air, and on the floor at different times, which are then integrated over the exposure duration for the calculation of radiation doses and cancer risks. A single run of the RESRAD-BUILD code can model a building with up to 9 rooms, 10 sources, and 10 receptors. The potential radiation dose and cancer risk incurred by each receptor are calculated for seven exposure pathways: (1) external radiation directly from the sources (accounting for shielding), (2) external radiation from radioactive particles deposited on the floors, (3) external radiation from airborne radionuclides, (4) inhalation of airborne radionuclides, (5) inhalation of radon and radon progenies, (6) inadvertent ingestion of radioactive particles directly from the source, and (7) ingestion of radioactive particles deposited on the floors. Various exposure scenarios can be modeled with RESRAD-BUILD, including but are not limited to, office worker, renovation worker, decontamination worker, building visitor, and resident. Both deterministic and probabilistic analyses can be performed to obtain results in both text reports and graphic displays.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2023

Development and implementation of an in situ high-resolution isotopic microscope for measuring metabolic interactions in soil mesocosms (Final Report)

Many of our planet’s ecosystems rely on the activities of soil microbial communities. These microbes have significant and wide-ranging effects: they metabolize carbon and other nutrients, interact with plants and fungi, and perform other processes important to soil health. However, our ability to directly observe the enzymatic and metabolic activities of microbes within soil is currently limited, not only by the complexity of soil microbial communities themselves, but also by the lack of experimental tools to study them and their molecular interactions in situ. These challenges hinder our understanding of the life-sustaining processes of biomass decomposition and the manner in which it contributes to the movement of freed carbon within soil ecosystems. Here we aimed to develop a novel ultrahigh-resolution isotopic microscope that combines complementary imaging modalities to gain insights into metabolic cycling in soil. This final report covers both the portion of this work that was initially completed at the University of North Carolina at Chapel Hill from 2018 to 2019 (as award DE-SC0019012) and then from 2020 to 2022 (2023 in NCE) at the University of Massachusetts Chan Medical School. This goal was to build an integrated platform consisting of fluorescence microscopy, Raman microspectroscopy, and nanospray desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (nanoDESI-FTICR-MS) to directly investigate microbial activities and molecular transformations occurring in soil by exploiting the use of both fluorescent labels and stable isotope probing. Specifically, our instrument was conceived as integrating: (A) fluorescence detection to localize soil microbes, identify bacteria taking up polysaccharides, and monitor gene expression of enzymes involved in decomposition; (B) Raman microspectroscopy to determine which microbes incorporate decomposition products into their biomass, as well as which decomposers are metabolically active; and (C) nanoDESI-FTICR-MS imaging to spatially probe, in real-time, the metabolites in the surrounding area, which we expect will reveal the distributions of the products of the enzymatic breakdown of polysaccharides, as well as specialized metabolites acting as cell-cell signals between decomposers. To enable these measurements, we exploited fluorescence-based probes to map the microbes that are enzymatically active (per A) and utilized stable isotope-labeled substrates to visualize both the microbial and molecular fate of decomposed biomass (B and C, respectively). To accomplish our goal, we combined the expertise of a multidisciplinary group of scientists to pursue the construction of this microscope and to investigate scientific questions that would be facilitated by such a capability. We aimed to employ this spatially informative, high-resolution isotopic microscope to visualize the critical steps of biomass degradation and the molecular fate of other environmentally relevant substrates within soil mesocosms. Accordingly, this technology will enhance our understanding of the microbial and metabolic interactions occurring within soil communities that are relevant to carbon degradation and other soil processes. The instrument has been developed and housed at EMSL, where it will be available to the entire EMSL User Base, enabling a variety of related DOE-relevant systems to be interrogated in the future by diverse scientific research groups.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Assessment of Carbonated Brine Injection as Low-risk Strategy for Geologic Carbon Storage

The main objective of this early-phase research was to evaluate the techno-economic feasibility and risk associated with combined brine and CO 2 storage in SWD wells using brine dissolution in the North Dakota portion of the Williston Basin. Three simulation studies were conducted to investigate: (1) CO 2 phases at different conditions, (2) wellbore compatibility, and (3) long-term storage fate in reservoir. (1) A simple reservoir model and injection simulations were created using data to represent the BEST (brine extraction and storage test) site, an operational SWD facility located near Watford City, North Dakota. The pressure evolution caused by CO 2 comingled in produced water injectate in a layer cake reservoir was then modeled while tracking aqueous CO 2 throughout the project. The salinity of the injection water, the salinity of the reservoir brine, and the amount of dissolved CO 2 comingled in the injection water were varied. (2) A wellbore corrosion model was performed using the CO 2 concentrations selected based on the reservoir modeling to examine the carbonated produced water impact on wellbore. (3) Reactive transport modeling was conducted with the optimal CO 2 concentration for this injection site to study the rock-fluid interactions and CO 2 fate in the reservoir. Results suggest that CO 2 dissolved in produced water can be injected without appreciably increasing subsurface pressure or leakage risks. Pressure buildup was found to vary with salinity but not with CO 2 mass fraction. Simulation results show that lower CO 2 percent mass fraction leads to a higher amount of CO 2 that can be dissolved at a higher injection salinity. Furthermore, the long-term goal of dissolution trapping in a traditional carbon storage project is accomplished from the start, mitigating risks associated with potential migration of buoyant CO 2 , so long as the reservoir pressure and temperature are used to determine the maximum mass fraction of the dissolved CO 2 .

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Advancements in Multiphysics Microdepletion Analysis of an eVinci TM -like Microreactor Leveraging OpenMC-CRAB Workflow

Nuclear microreactors (MRs) are a class of nuclear reactor technology, characterized by reduced dimensions, modular design, and reduced power output in contrast to conventional Light Water Reactors (LWRs). MRs are proposed for supplying electricity and eventual process heat to remote locations, such as military installations and disaster-affected areas. Current research work sponsored by the US Department of Energy Microreactor Program (MRP) is devoted to the development of novel modeling and simulation tools to better support MR vendors and regulatory bodies. Notably, the NRC is projected to utilize the CRAB multiphysics software driver for executing both design and beyond-design-basis accident analyses. Furthermore, the NRC has been utilizing the MELCOR code to calculate mechanistic source terms during accidents. Since MELCOR relies on isotopic inventory and reactor temperature/power profiles under accident conditions, which theoretically can be derived from CRAB, the goal is to establish a comprehensive CRAB-MELCOR computational framework. Past work was focused on testing and demonstrating CRAB's capability to generate results that can be used to inform mechanistic source term calculations in MELCOR. In particular, a computational workflow leveraging OpenMC-generated microscopic cross sections and CRAB was first applied to perform multiphysics microscopic depletion calculation followed by an accident scenario for a stylized microreactor problem. In fiscal year 2024, the research work has been focused on applying the OpenMC-CRAB workflow, which was first tested in fiscal year 2023, to a realistic 3D heat-pipe cooled MR problem representative of the eVinci TM design. The latter computational problem was developed with inputs from WEC to conserve selected neutronic and thermal characteristics of the eVinci TM design without releasing proprietary data. The results of this simulation, encompassing isotopic inventory, power density distribution, and kinetic parameters, will inform both MELCOR and the WEC-developed FATE code for mechanistic source terms calculations. The results from the two codes will then be compared for code verification purposes. This report contains the design characteristics of the realist heat pipe cooled microreactor developed as a use-case for the verification exercise, and the current results for the multiphysics microscopic depletion performed with the OpenMC-CRAB workflow. The results include eigenvalue as a function of time, power distribution at EOL, in addition to nuclides inventory's time evolution and spatial distribution. Finally, we report improvements to the workflow efficiency achieved through a collaboration with the NEAMS programs. Through this collaborative effort, we were able to strongly decrease the computational time for the multiphysics microdepletion calculation (i.e., from 17.4 hours to 5.7 hours on 280 processors) in addition to simplifying the interface to generate isotopics spatial distribution utilizable by FATE and MELCOR. Future work, including the improvement of the current microscopic cross-sections' library and the simulation of an accident scenario at EOL, is also discussed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Hanford Composite Analysis Special Studies FY2025 - Groundwater Flow Simulation for use in a Comparison of Simulated Concentrations in the Saturated Zone Estimated by the Plateau-to-River Model Versions 8.3 and 9.1

In order to meet the requirements of U.S. Department of Energy (DOE) in DOE O 435.1, Radioactive Waste Management, a composite analysis (CA) must be completed for the Central Plateau at the Hanford Site. The CA requires estimates of fate and transport of radionuclides in the groundwater from multiple sources within the modeling domain. This Environmental Calculation File (ECF) details the application of the Plateau-to-River (P2R) Model (CP-57037, Rev. 3, Model Package Report for the P2R Model: Version 9.1) to predict the flow of groundwater on the Central Plateau for the 10,000-year simulation to support a special analysis associated with the Hanford Site CA. The simulated flow field will support the simulation of fate and transport of contaminants for comparison to the results obtained as part of the CA to evaluate impact of the updated version of the P2R Model.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Inclusion of a cold hardening scheme to represent frost tolerance is essential to model realistic plant hydraulics in the Arctic–boreal zone in CLM5.0-FATES-Hydro

As temperatures decrease in autumn, vegetation of temperate and boreal ecosystems increases its tolerance to freezing. This process, known as hardening, results in a set of physiological changes at the molecular level that initiate modifications of cell membrane composition and the synthesis of anti-freeze proteins. Together with the freezing of extracellular water, anti-freeze proteins reduce plant water potentials and xylem conductivity. To represent the responses of vegetation to climate change, land surface schemes increasingly employ “hydrodynamic” models that represent the explicit fluxes of water from soil and through plants. The functioning of such schemes under frozen soil conditions, however, is poorly understood. Nonetheless, hydraulic processes are of major importance in the dynamics of these systems, which can suffer from, e.g., winter “frost drought” events. In this study, we implement a scheme that represents hardening into CLM5.0-FATES-Hydro. FATES-Hydro is a plant hydrodynamics module in FATES, a cohort model of vegetation physiology, growth, and dynamics hosted in CLM5.0. We find that, in frozen systems, it is necessary to introduce reductions in plant water loss associated with hardening to prevent winter desiccation. This work makes it possible to use CLM5.0-FATES-Hydro to model realistic impacts from frost droughts on vegetation growth and photosynthesis, leading to more reliable projections of how northern ecosystems respond to climate change.

58 GEOSCIENCES↗

DOE OSTI2022

Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC transcriptomic type identity is not specified at mitotic exit, but acquired by gradual, asynchronous restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity emerges. Optimal transport inference identifies groups of RGC precursors with largely nonoverlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1981

A search for neutral hydrogen in D and cD galaxies

Recent X-ray spectroscopic results suggest that 2-3 solar masses/yr of cooling gas may be falling into M87 and as much as 300 solar masses/yr into giant galaxies in rich clusters. The eventual fate of the gas in the radiatively accreting flow is an open question. In an attempt to set some bounds on the evolution of the gas, a sensitive search was performed for H I in a sample of eight D and cD galaxies in rich and poor clusters. Null detections in all cases set upper limits of (4-20) x 10 to the 8th solar masses of H I in the giant galaxies. Possible reasons for these nondetections and alternative evolutionary fates for the accreting gas are discussed.

Burns, J. O.↗

NASA NTRS1983

The role of spicules in hetaing the solar atmosphere Implications of EUV observations

Although spicules hae been obseved for many years, very little is known about their role in the transport of mass and energy between the chromosphere and the higher layers of the atmospere. Athay and Holzer (1982) demonstrated that the rise and fall of spicular material can supply the thermal energy required for heating the upper chromosphere, transition, and possibly corona. The proposed mechanism depends upon assumptions about the fate of spicules after they disappear from view in the visual spectrum where observations are limited to spectral lines formed at chromospheric temperatures. The present investigation is concerned with an analysis of meaurements of the spatial and temporal variations of EUV emission near the solar limb. The obtained results place empirical constraints on the fate of spicules after they disappear from view in the visible spectrum and thereby place constraints on their role in the transport of mass and energy between the chromosphere and corona.

Withbroe, G. L.↗

NASA NTRS1988

Airborne Oceanographic Lidar (AOL) flight mission participation

From February 1986 to the present, the AOL participated in six interagency flight missions. (1) Shelf Edge Exchange Processes (SEEP II) (Department of Energy). The SEEP experiments are designed to assess the assimilative capacity of the Continental Shelf to absorb the energy by-products introduced into the near-shore ocean environment from coastal communities and marine activities such as energy production plants and offshore oil operations. (2) BIOWATT II (Office of Naval Research). The major objective of this study was to provide a better understanding of the relationships between ocean physics, biology, bioluminescence, and optics in oligotrophic portions of the Atlantic Ocean. (3) Fall Experiment (FLEX) (Department of Energy). The FLEX studies were designed to determine the fate of low salinity water in the coastal boundary zone that is advected south towards the Florida coast during autumn. (4) Greenland Sea and Icelandic Marine Biological Experiments (NASA). The investigations were designed to evaluate the distribution of surface layer chlorophyll in the Greeland Sea and in the coastal waters in the vicinity of Iceland. (5) Submerged Oceanic Scattering Layer Experiment (Naval Ocean Systems Center). This flight experiment demonstrated for the first time the feasibility of detecting and metrically measuring the depth to submerged layers of particulate matter in the shelf break region and in the inner coastal zone. (6) Microbial Exchanges and Coupling in Coastal Atlantic Systems (National Science Foundation). This investigation was designed to study the transportation and fate of particulates in coastal waters and in particular the Chesapeake Bay/coastal Atlantic Ocean. Shortly after the conduct of the flight experiments, airborne laser-induced chlorophyll a and phycoerythrin fluorescence data, as well as sea surface temperature and airborne expendable bathythermograph water column temperature profiles are supplied to cooperating institutions.

Hoge, F. E.↗

NASA NTRS1997

Impact Cratering Calculations

Understanding the physical processes of impact cratering on planetary surfaces and atmospheres as well as collisions of finite-size self-gravitating objects is vitally important to planetary science. The observation has often been made that craters are the most ubiquitous landform on the solid planets and the satellites. The density of craters is used to date surfaces on planets and satellites. For large ringed basin craters (e.g. Chicxulub), the issue of identification of exactly what 'diameter' transient crater is associated with this structure is exemplified by the arguments of Sharpton et al. (1993) versus those of Hildebrand et al. (1995). The size of a transient crater, such as the K/T extinction crater at Yucatan, Mexico, which is thought to be the source of SO,-induced sulfuric acid aerosol that globally acidified surface waters as the result of massive vaporization of CASO, in the target rock, is addressed by our present project. The impact process excavates samples of planetary interiors. The degree to which this occurs (e.g. how deeply does excavation occur for a given crater diameter) has been of interest, both with regard to exposing mantle rocks in crater floors, as well as launching samples into space which become part of the terrestrial meteorite collection (e.g. lunar meteorites, SNC's from Mars). Only in the case of the Earth can we test calculations in the laboratory and field. Previous calculations predict, independent of diameter, that the depth of excavation, normalized by crater diameter, is d(sub ex)/D = 0.085 (O'Keefe and Ahrens, 1993). For Comet Shoemaker-Levy 9 (SL9) fragments impacting Jupiter, predicted excavation depths of different gas-rich layers in the atmosphere, were much larger. The trajectory and fate of highly shocked material from a large impact on the Earth, such as the K/T bolide is of interest. Melosh et al. (1990) proposed that the condensed material from the impact upon reentering the Earth's atmosphere induced. radiative heating, and producing global firestorms. The observed reentry splash of the SL-9 impact-induced plumes that reimpact Jupiter (Boslough et al., 1994) supported Melosh's K/T model. The fate of early primitive planetary atmospheres during the latter stages of planetary accretion, resulting from impactors in the 100 to 103 km diameter require modeling, e.g. Newman et al. (1997). Ahrens (1990; 1993) and Chen and Ahrens (1997) found that upon delivery of most of the impact energy to the solid planet, very large ground motions arise, which couple sufficient kinetic energy to the atmosphere to cause substantial atmospheric escape. The trade-off of this model with that of Cameron (1997) who suggests that atmospheric blow-off occurs as a result of the massive impact-induced heating of the atmosphere and Pepin (1997) who uses this heating event to model differential hydrodynamic loss of lighter atmospheric gases, requires further research.

Ahrens, Thomas J.↗

NASA NTRS2001

Deuterostome evolution: early development in the enteropneust hemichordate, Ptychodera flava

Molecular and morphological comparisons indicate that the Echinodermata and Hemichordata represent closely related sister-phyla within the Deuterostomia. Much less is known about the development of the hemichordates compared to other deuterostomes. For the first time, cell lineage analyses have been carried out for an indirect-developing representative of the enteropneust hemichordates, Ptychodera flava. Single blastomeres were iontophoretically labeled with Dil at the 2- through 16-cell stages, and their fates followed through development to the tornaria larval stage. The early cleavage pattern of P. flava is similar to that of the direct-developing hemichordate, Saccoglossus kowalevskii, as well as that displayed by indirect-developing echinoids. The 16-celled embryo contains eight animal "mesomeres," four slightly larger "macromeres," and four somewhat smaller vegetal "micromeres." The first cleavage plane was not found to bear one specific relationship relative to the larval dorsoventral axis. Although individual blastomeres generate discrete clones of cells, the appearance and exact locations of these clones are variable with respect to the embryonic dorsoventral and bilateral axes. The eight animal mesomeres generate anterior (animal) ectoderm of the larva, which includes the apical organ; however, contributions to the apical organ were found to be variable as only a subset of the animal blastomeres end up contributing to its formation and this varies from embryo to embryo. The macromeres generate posterior larval ectoderm, and the vegetal micromeres form all the internal, endomesodermal tissues. These blastomere contributions are similar to those found during development of the only other hemichordate studied, the direct-developing enteropneust, S. kowalevskii. Finally, isolated blastomeres prepared at either the two- or the four-cell stage are capable of forming normal-appearing, miniature tornaria larvae. These findings indicate that the fates of these cells and embryonic dorsoventral axial properties are not committed at these early stages of development. Comparisons with the developmental programs of other deuterostome phyla allow one to speculate on the conservation of some key developmental events/mechanisms and propose basal character states shared by the ancestor of echinoderms and hemichordates.

NASA Discipline Evolutionary Biology↗

NASA NTRS1994

Hycrest crested wheatgrass accelerates the degradation of pentachlorophenol in soil

We investigated the effects of vegetation on the fate of pentachlorophenol (PCP) in soil using a novel high-flow sealed test system. Pentachlorophenol has been widely used as a wood preservative, and this highly toxic biocide contaminates soil and ground water at many sites. Although plants are known to accelerate the rates of degradation of certain soil contaminants, this approach has not been thoroughly investigated for PCP. The fate of [14C]PCP, added to soil at a concentration of 100 mg/kg, was compared in three unplanted and three planted systems. The plant used was Hycrest, a perennial, drought-tolerant cultivar of crested wheatgrass [Agropyron desertorum (Fischer ex Link) Schultes]. The flow-through test system allowed us to maintain a budget for 14C-label as well as monitor mineralization (breakdown to 14CO2) and volatilization of the test compound in a 155-d trial. In the unplanted systems, an average of 88% of the total radiolabel remained in the soil and leachate and only 6% was mineralized. In the planted system, 33% of the radiolabel remained in the soil plus leachate, 22% was mineralized, and 36% was associated with plant tissue (21% with the root fraction and 15% with shoots). Mineralization rates were 23.1 mg PCP mineralized kg-1 soil in 20 wk in the planted system, and for the unplanted system 6.6 mg PCP kg-1 soil for the same time period. Similar amounts of volatile organic material were generated in the two systems (1.5%). Results indicated that establishing crested wheatgrass on PCP-contaminated surface soils may accelerate the removal of the contaminant.

Non-NASA Center↗

NASA NTRS2000

Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks

Development of characteristic tissue patterns requires that individual cells be switched locally between different phenotypes or "fates;" while one cell may proliferate, its neighbors may differentiate or die. Recent studies have revealed that local switching between these different gene programs is controlled through interplay between soluble growth factors, insoluble extracellular matrix molecules, and mechanical forces which produce cell shape distortion. Although the precise molecular basis remains unknown, shape-dependent control of cell growth and function appears to be mediated by tension-dependent changes in the actin cytoskeleton. However, the question remains: how can a generalized physical stimulus, such as cell distortion, activate the same set of genes and signaling proteins that are triggered by molecules which bind to specific cell surface receptors. In this article, we use computer simulations based on dynamic Boolean networks to show that the different cell fates that a particular cell can exhibit may represent a preprogrammed set of common end programs or "attractors" which self-organize within the cell's regulatory networks. In this type of dynamic network model of information processing, generalized stimuli (e.g., mechanical forces) and specific molecular cues elicit signals which follow different trajectories, but eventually converge onto one of a small set of common end programs (growth, quiescence, differentiation, apoptosis, etc.). In other words, if cells use this type of information processing system, then control of cell function would involve selection of preexisting (latent) behavioral modes of the cell, rather than instruction by specific binding molecules. Importantly, the results of the computer simulation closely mimic experimental data obtained with living endothelial cells. The major implication of this finding is that current methods used for analysis of cell function that rely on characterization of linear signaling pathways or clusters of genes with common activity profiles may overlook the most critical features of cellular information processing which normally determine how signal specificity is established and maintained in living cells. Copyright 2000 Academic Press.

Review↗

NASA NTRS2006

An Energy Balance Model to Predict Chemical Partitioning in a Photosynthetic Microbial Mat

Studies of biosignature formation in photosynthetic microbial mat communities offer potentially useful insights with regards to both solar and extrasolar astrobiology. Biosignature formation in such systems results from the chemical transformation of photosynthetically fixed carbon by accessory microorganisms. This fixed carbon represents a source not only of reducing power, but also energy, to these organisms, so that chemical and energy budgets should be coupled. We tested this hypothesis by applying an energy balance model to predict the fate of photosynthetic productivity under dark, anoxic conditions. Fermentation of photosynthetically fixed carbon is taken to be the only source of energy available to cyanobacteria in the absence of light and oxygen, and nitrogen fixation is the principal energy demand. The alternate fate for fixed carbon is to build cyanobacterial biomass with Redfield C:N ratio. The model predicts that, under completely nitrogen-limited conditions, growth is optimized when 78% of fixed carbon stores are directed into fermentative energy generation, with the remainder allocated to growth. These predictions were compared to measurements made on microbial mats that are known to be both nitrogen-limited and populated by actively nitrogen-fixing cyanobacteria. In these mats, under dark, anoxic conditions, 82% of fixed carbon stores were diverted into fermentation. The close agreement between these independent approaches suggests that energy balance models may provide a quantitative means of predicting chemical partitioning within such systems - an important step towards understanding how biological productivity is ultimately partitioned into biosignature compounds.

Hoehler, Tori M.↗