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At least 595 records · Page 33

Crystal structure of an Okazaki fragment at 2-A resolution

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Non-NASA Center↗

Genotoxic Effects of Low- and High-LET Radiation on Human Epithelial Cells Grown in 2-D Versus 3-D Culture

Risk estimation for radiation-induced cancer relies heavily on human epidemiology data obtained from terrestrial irradiation incidents from sources such as medical and occupational exposures as well as from the atomic bomb survivors. No such data exists for exposures to the types and doses of high-LET radiation that will be encountered during space travel; therefore, risk assessment for space radiation requires the use of data derived from cell culture and animal models. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. This work compares the genotoxic effects of radiation on normal human epithelial cells grown in standard 2-D monolayer culture compared to 3-D organotypic co-culture conditions. These 3-D organotypic models mimic the morphological features, differentiation markers, and growth characteristics of fully-differentiated normal human tissue and are reproducible using defined components. Cultures were irradiated with 2 Gy low-LET gamma rays or varying doses of high-LET particle radiation and genotoxic damage was measured using a modified cytokinesis block micronucleus assay. Our results revealed a 2-fold increase in residual damage in 2 Gy gamma irradiated cells grown under organotypic culture conditions compared to monolayer culture. Irradiation with high-LET particle radiation gave similar results, while background levels of damage were comparable under both scenarios. These observations may be related to the phenomenon of "multicellular resistance" where cancer cells grown as 3-D spheroids or in vivo exhibit an increased resistance to killing by chemotherapeutic agents compared to the same cells grown in 2-D culture. A variety of factors are likely involved in mediating this process, including increased cell-cell communication, microenvironment influences, and changes in cell cycle kinetics that may promote survival of damaged cells in 3-D culture that would otherwise die or be rendered reproductively inactive in 2-D culture.

Patel, Z. S.↗

Accelerated Creep Testing of High Strength Aramid Webbing

A series of preliminary accelerated creep tests were performed on four variants of 12K and 24K lbf rated Vectran webbing to help develop an accelerated creep test methodology and analysis capability for high strength aramid webbings. The variants included pristine, aged, folded and stitched samples. This class of webbings is used in the restraint layer of habitable, inflatable space structures, for which the lifetime properties are currently not well characterized. The Stepped Isothermal Method was used to accelerate the creep life of the webbings and a novel stereo photogrammetry system was used to measure the full-field strains. A custom MATLAB code is described, and used to reduce the strain data to produce master creep curves for the test samples. Initial results show good correlation between replicates; however, it is clear that a larger number of samples are needed to build confidence in the consistency of the results. It is noted that local fiber breaks affect the creep response in a similar manner to increasing the load, thus raising the creep rate and reducing the time to creep failure. The stitched webbings produced the highest variance between replicates, due to the combination of higher local stresses and thread-on-fiber damage. Large variability in the strength of the webbings is also shown to have an impact on the range of predicted creep life.

Jones, Thomas C.↗

Validation of 3-D Ice Accretion Measurement Methodology for Experimental Aerodynamic Simulation

Determining the adverse aerodynamic effects due to ice accretion often relies on dry-air wind-tunnel testing of artificial, or simulated, ice shapes. Recent developments in ice accretion documentation methods have yielded a laser-scanning capability that can measure highly three-dimensional features of ice accreted in icing wind tunnels. The objective of this paper was to evaluate the aerodynamic accuracy of ice-accretion simulations generated from laser-scan data. Ice-accretion tests were conducted in the NASA Icing Research Tunnel using an 18-inch chord, 2-D straight wing with NACA 23012 airfoil section. For six ice accretion cases, a 3-D laser scan was performed to document the ice geometry prior to the molding process. Aerodynamic performance testing was conducted at the University of Illinois low-speed wind tunnel at a Reynolds number of 1.8 x 10(exp 6) and a Mach number of 0.18 with an 18-inch chord NACA 23012 airfoil model that was designed to accommodate the artificial ice shapes. The ice-accretion molds were used to fabricate one set of artificial ice shapes from polyurethane castings. The laser-scan data were used to fabricate another set of artificial ice shapes using rapid prototype manufacturing such as stereolithography. The iced-airfoil results with both sets of artificial ice shapes were compared to evaluate the aerodynamic simulation accuracy of the laser-scan data. For four of the six ice-accretion cases, there was excellent agreement in the iced-airfoil aerodynamic performance between the casting and laser-scan based simulations. For example, typical differences in iced-airfoil maximum lift coefficient were less than 3% with corresponding differences in stall angle of approximately one degree or less. The aerodynamic simulation accuracy reported in this paper has demonstrated the combined accuracy of the laser-scan and rapid-prototype manufacturing approach to simulating ice accretion for a NACA 23012 airfoil. For several of the ice-accretion cases tested, the aerodynamics is known to depend upon the small, three dimensional features of the ice. These data show that the laser-scan and rapid-prototype manufacturing approach is capable of replicating these ice features within the reported accuracies of the laser-scan measurement and rapid-prototyping method; thus providing a new capability for high-fidelity ice-accretion documentation and artificial ice-shape fabrication for icing research.

Scale Models↗

Validation of 3-D Ice Accretion Measurement Methodology for Experimental Aerodynamic Simulation

Determining the adverse aerodynamic effects due to ice accretion often relies on dry-air wind-tunnel testing of artificial, or simulated, ice shapes. Recent developments in ice-accretion documentation methods have yielded a laser-scanning capability that can measure highly three-dimensional (3-D) features of ice accreted in icing wind tunnels. The objective of this paper was to evaluate the aerodynamic accuracy of ice-accretion simulations generated from laser-scan data. Ice-accretion tests were conducted in the NASA Icing Research Tunnel using an 18-in. chord, two-dimensional (2-D) straight wing with NACA 23012 airfoil section. For six ice-accretion cases, a 3-D laser scan was performed to document the ice geometry prior to the molding process. Aerodynamic performance testing was conducted at the University of Illinois low-speed wind tunnel at a Reynolds number of 1.8 × 10(exp 6) and a Mach number of 0.18 with an 18-in. chord NACA 23012 airfoil model that was designed to accommodate the artificial ice shapes. The ice-accretion molds were used to fabricate one set of artificial ice shapes from polyurethane castings. The laser-scan data were used to fabricate another set of artificial ice shapes using rapid prototype manufacturing such as stereolithography. The iced-airfoil results with both sets of artificial ice shapes were compared to evaluate the aerodynamic simulation accuracy of the laser-scan data. For five of the six ice-accretion cases, there was excellent agreement in the iced-airfoil aerodynamic performance between the casting and laser-scan based simulations. For example, typical differences in iced-airfoil maximum lift coefficient were less than 3 percent with corresponding differences in stall angle of approximately 1 deg or less. The aerodynamic simulation accuracy reported in this paper has demonstrated the combined accuracy of the laser-scan and rapid-prototype manufacturing approach to simulating ice accretion for a NACA 23012 airfoil. For several of the ice-accretion cases tested, the aerodynamics is known to depend upon the small, three-dimensional features of the ice. These data show that the laser-scan and rapid-prototype manufacturing approach is capable of replicating these ice features within the reported accuracies of the laser-scan measurement and rapid-prototyping method; thus providing a new capability for high-fidelity ice-accretion documentation and artificial ice-shape fabrication for icing research.

Aircraft Icing↗

AstroAmpSeq: Microbial Bioinformatics Education with NASA GeneLab’s Amplicon Pipeline

The prevalence and importance of large sequencing datasets in microbiology has led to a movement to share microbial ecology experimental data through open-access databases. This is particularly true of experiments that are difficult to replicate, such as those conducted in the spaceflight environment and shared via NASA GeneLab. It is now possible and indeed valuable for students to access and re-analyze these shared datasets for educational and research purposes. To provide students with experience utilizing microbial bioinformatics tools, GeneLab for Colleges and Universities (GL4U) has designed AstroAmpSeq, a week-long, virtually implemented project-based learning (PBL) minicourse to instruct undergraduate students on 16S amplicon sequencing. AstroAmpSeq was created to be accessible to students without prior bioinformatics or microbial ecology experience. During the minicourse students work in teams to process, analyze, and visualize a subsample of GeneLab dataset GLDS-280 using GeneLab’s standard amplicon processing pipeline, which is based in R. Students develop a hypothesis related to the dataset then generate and analyze figures to evaluate their hypothesis. Formative assessment of student learning is determined via pre- and post-evaluations, peer feedback, and self-reflection. Project and presentation rubrics serve as a summative assessment of student learning. GL4U AstroAmpSeq not only meets American Society for Microbiology Curriculum Guidelines, but also incites student interest in research by an inquiry-based approach and can be made part of a larger semester-long curriculum. GL4U AstroAmpSeq raises awareness of space microbiology and bioinformatics as a field and career path among undergraduates. Further, by using a GeneLab dataset and nesting microbiology techniques into the real-world application of space biology, AstroAmpSeq enforces deeper and longer-lasting student learning.

microbiology↗

Utilization of GIS technology to support development of flow and contaminant fate and transport models at US DOE sites - 15457

U.S. Department of Energy (DOE) sites have accumulated years of data and millions of spatial and temporal records related to the hydrological cycle, contaminant transport, and parameters of remediation technologies. In addition, numerical models which use field monitoring data to help understand flow and transport produce gigabytes of computed spatial and temporal data for each computation node. There is a need therefore for an advanced spatial data structure that can be used to address the management, processing, and analysis of spatial and temporal numerical modeling data derived from multiple sources. This can be accomplished using a geo-database. The development of an ArcSDE geo-database facilitates the centralized storage, backup, accessibility, organization, and management of model configuration and computed simulation data, putting it into a structured, coherent, and logical computer-supported system. GIS data processing and automation would enable faster and hence more complex analyses of field test data. The Applied Research Center (ARC) at Florida International University (FIU) has provided analysis of flow and transport for several watersheds at DOE's Oak Ridge Reservation (ORR), including East Fork Poplar Creek (EFPC), Upper EFPC in the Y-12 National Security Complex area (Y-12 NSC) and White Oak Creek (WOC). Integrated surface and subsurface flow, fate and transport models were developed to provide analysis of contaminant patterns within each watershed. In addition, digital monitoring data available from the Oak Ridge Environmental Information System (OREIS) related to mercury (Hg) contamination and remediation within these watersheds was used for calibration and verification of the model. Experimental studies were also carried out which provided kinetic and equilibrium data about important parameters related to Hg transport, speciation and methylation/demethylation kinetics within the watershed. Geographic Information Systems (GIS) technology was employed to support the modeling work through storage and geo-processing of spatial and temporal data required by the models and to produce hydrogeological maps for visualization. An ArcGIS geo-database was developed for centralized storage and management of experimental and computed model data and its capabilities were extended over the years using tools such as ModelBuilder combined with Python scripting to automate repetitive tasks, perform statistical analyses and generate maps and reports. The hydrologic geo-database model developed possesses a structure that enables linkage with scalable hydrologic modeling tools/applications to model hydrologic systems, and in this case, enables the testing of the potential impacts of various remediation scenarios on the ORR watersheds. The ArcSDE geo-database can also be used to automate and simplify the process of calling stored GIS and time series data. This geo-database can serve as a tool for contaminant flow and transport analyses which require large amounts of high-quality spatial and temporal data in order to ensure reliability and validity of modeling results. The existing geo-database structure developed for the hydrological modeling at ORR was designed to be replicable for application at other DOE sites. An investigation of downloadable free/open source GIS software along with required security protocols to facilitate online querying of the database was also conducted to determine methods by which project-derived data can be more easily shared with other project stakeholders such as DOE personnel and site contractors. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗

Phase II Nevada Water Resources Data, Modeling, and Visualization (DMV) Center (Final Report)

Water is unquestionably a critical resource throughout the United States. In the semi-arid west -- an area stressed by increase in human population and sprawl of the built environment -- water is the most important limiting resource. Crucially, science must understand factors that affect availability and distribution of water. To sustain growing consumptive demand, science needs to translate understanding into reliable and robust predictions of availability under weather conditions that could be average but might be extreme. These predictions are needed to support current and long-term planning. Similar to the role of weather forecast and climate prediction, water prediction over short and long temporal scales can contribute to resource strategy, governmental policy and municipal infrastructure decisions, which are arguably tied to the natural variability and unnatural change to climate. Change in seasonal and annual temperature, precipitation, snowmelt, and runoff affect the distribution of water over large temporal and spatial scales, which impact the risk of flooding and the groundwater recharge. Anthropogenic influences and impacts increase the complexity and urgency of the challenge. The goal of this project has been to develop a decision support framework of data acquisition, digital modeling, and 3D visualization. This integrated framework consists of tools for compiling, discovering and projecting our understanding of processes that control the availability and distribution of water. The framework is intended to support the analysis of the complex interactions between processes that affect water supply, from controlled availability to either scarcity or deluge. The developed framework enables DRI to promote excellence in water resource management, particularly within the Lake Tahoe basin. In principle, this framework could be replicated for other watersheds throughout the United States. Phase II of this project builds upon the research conducted during Phase I, in which the hydrologic framework was investigated and the development initiated. Phase II concentrates on practical implementation of the earlier work but emphasizes applications to the hydrology of the Lake Tahoe basin. Phase 1 efforts have been refined and extended by creating a toolset for geographic information systems (GIS) that is usable for disparate types of geospatial and geo-referenced data. The toolset is intended to serve multiple users for a variety of applications. The web portal for internet access to hydrologic and remotely sensed product data, prototyped in Phase I, has been significantly enhanced. The portal provides high performance access to LANDSAT-derived data using techniques developed during the course of the project. The portal is interactive, and supports the geo-referenced display of hydrologic information derived from remotely sensed data, such as various vegetative indices used to calculate water consumption. The platform can serve both internal and external constituencies using inter-operating infrastructure that spans both sides of the DRI firewall. The platform is intended grow its supported data assets and to serve as a template for replication to other geographic areas. An unanticipated development during the project was the use of ArcGIS software on a new computer system, called the IBM PureSytems, and the parallel use of the systems for faster, more efficient image processing. Additional data, independent of the portal, was collected within the Sagehen basin and provides detailed information regarding the processes that control hydrologic responses within mountain watersheds. The newly collected data include elevation, evapotranspiration, energy balance and remotely sensed snow-pack data. A Lake Tahoe basin hydrologic model has been developed, in part to help predict the hydrologic impacts of climate change. The model couples both the surface and subsurface hydrology, with the two components having been independently calibrated. Results from the coupled simulations involving both surface water and groundwater processes show that it is possible to fairly accurately simulate lake effects and water budget variables over a wide range of dry and wet cycles in the historical record. The Lake Tahoe basin is representative of the hydrology, topography and climate throughout the Sierra Nevada Range, and the entire model development is prototypical of the efforts required to replicate the decision support framework to other locales. The Lake Tahoe model in particular, could allow water managers to evaluate more accurately components of the water budget (ET, runoff, groundwater, etc) and to answer important questions regarding water resources in northern Nevada. This report discusses the geographic scale and the hydrologic complexity of the calibrated model developed as part of this project, as well as simulation results for historical and future climate projects To enable human-driven data exploration and discovery, de novo software for a globalized rendering module that extends the capability of our evolving custom visualization engine from Phase I (called SMEngine) has been developed. The new rendering component, called Horizon, supports terrain rendering capable of displaying and interrogating both remotely sensed and modeled data. The development of Horizon necessitated adaptation of the visualization engine to allow extensible integration of components such as the global rendering module and support for associated features. The resulting software is general in its GIS capability, but a specific Lake Tahoe visualization application suitable for immersive decision support in the DRIVE6 virtual reality facility has been developed. During the development, various features to enhance the value of the visualization experience were explored, including the use of hyperspectral image overlays. An over-arching goal of the visualization aspect of the project has been to develop and demonstrate the CAVE (CAVE Automatic Virtual Environment) as a practical tool for hydrologic research.

54 ENVIRONMENTAL SCIENCES↗

Enhancing Streamflow Reanalysis Across the Conterminous US Leveraging Multiple Gridded Precipitation Data Sets

Streamflow observations, essential for various water resource applications, are often unavailable at critical locations in need. Although different models have been proposed to enhance streamflow predictability at ungauged locations, the challenge extends beyond model fidelity. Differences in meteorologic forcing data sets, precipitation in particular, can significantly affect the accuracy of hydrologic predictions. This challenge intensifies across regions characterized by diverse hydro-climatological and geographical conditions, such as in the conterminous US (CONUS) where a single precipitation product struggles to consistently replicate observed hydrographs, particularly peak flow dynamics. To enhance streamflow predictions, we utilize a VIC-RAPID hydrologic modeling framework driven by multiple commonly used meteorological forcing data sets, such as Daymet, PRISM, ST4, AORC, and their hybrids and create multiple sets of 40-year (1980–2019) hourly, daily, and monthly streamflow reanalysis, Dayflow Version 2, for 2.7 million river reaches across the CONUS. Most forcings lead to skillful streamflow performance, except for ST4 in the mountainous west, where severe radar blockage adversely affects the accuracy. The evaluation using over 6,000 hourly stream gauges shows that hourly AORC and ST4 lead to improved annual peak flow performance over Daymet—driven streamflow (Dayflow V1), particularly in smaller basins, highlighting the value of high temporal resolution forcings in hydrologic predictions. Compared with other benchmark data sets like National Water Model V3.0, AORC-driven VIC-RAPID exhibits improved regional streamflow performance, with comparable peak flow representation. We envision that multi-forcing streamflow reanalysis data can inform regions in need of forcing data enhancement, diagnose hydrologic model performance, and benefit diverse water resource applications.

54 ENVIRONMENTAL SCIENCES↗

Dry in-pile fracture test (DRIFT) for separate-effects validation of ceramic fuel fracture models

Fracture is an important component of nuclear fuel behavior, and significant efforts have been invested into developing fuel performance models that are capable of accurately representing fracture. Usable data on the process of fracture propagation in nuclear fuel under realistic service conditions are very limited. To address this need, a series of separate-effects experiments were developed and performed at Idaho National Laboratory's Transient Reactor Test (TREAT) facility. These experiments employ a heat sink to radially remove heat from the fuel in a manner that approximates the effect of coolant in an operating light-water reactor (LWR). The test holder for these experiments is known as the Dry In-pile Fracture Test (DRIFT). A series of experiments employing DRIFT and TREAT were performed to provide data on the extent and nature of fracture in fresh fuel at various points during a ramp to full power. Novel aspects of these experiments include the way they employ a heat sink to replicate steady-state LWR conditions, as well as the use of fiber optic sensors for in-reactor thermal instrumentation. Details on the development of this experiment, experimental conditions, and resulting data (including in situ thermal measurements and post-irradiation imaging of fracture) are provided in this work. LWR-equivalent powers ranging from 10 to 25 kW/m were tested using this apparatus. Cracking was visible at all power levels, with increasing cracking extent as the power level increased, although there was little difference in the cracking between the two highest-power tests, which had LWR-equivalent powers of 20 and 25 kW/m.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Emission spectra of selected SSME elements and materials

Stennis Space Center (SSC) is pursuing the advancement of experimental techniques and theoretical developments in the field of plume spectroscopy for application to rocket development testing programs and engine health monitoring. Exhaust plume spectral data for the Space Shuttle Main Engine (SSME) are routinely acquired. The usefulness of this data depends upon qualitative and quantitative interpretation of spectral features and their correlation with the engine performance. A knowledge of the emission spectral characteristics of effluent materials in the exhaust plume is essential. A study of SSME critical components and their materials identified 30 elements and 53 materials whose engine exhaust plume spectral might be required. The most important were evaluated using SSC's Diagnostic Testbed Facility Thruster (DTFT), a 1200-lbf, liquid oxygen/gaseous hydrogen rocket engine which very nearly replicates the temperature and pressure conditions of the SSME exhaust plume in the first Mach diamond. This report presents the spectral data for the 10 most important elements and 27 most important materials which are strongly to moderately emitting in the DTFT exhaust plume. The covered spectral range is 300 to 426 nm and the spectral resolution is 0.25 nm. Spectral line identification information is provided and line interference effects are considered.

Tejwani, Gopal D.↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Level 2 Sensor Data v2-1

This is the version v2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Please see v2-1 TEMPEST L2 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. The TEMPEST flood events occurred on the following dates. They lasted for ~10 hours each day and delivered ~80,000 gallons to each plot; many data streams are available at 1 or 5 minute frequency during these periods. * Tests: Aug 25 (fresh plot) and Sep 9 (salt plot), 2021 * TEMPEST 1: June 22, 2022 * TEMPEST 2: June 6-7, 2023 * TEMPEST 3: June 11-13, 2024

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗

Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories

The rotavirus (RV) genome is replicated and packaged into virus progeny in cytoplasmic inclusions called viroplasms, which require interactions between RV nonstructural proteins NSP2 and NSP5. How viroplasms form remains unknown. We previously found two forms of NSP2 in RV-infected cells: a cytoplasmically dispersed dNSP2, which interacts with hypophosphorylated NSP5; and a viroplasm-specific vNSP2, which interacts with hyperphosphorylated NSP5. Other studies report that CK1α, a ubiquitous cellular kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons that are unclear. Here we show that silencing CK1α in cells before RV infection resulted in ( i ) >90% decrease in RV replication, ( ii ) disrupted vNSP2 and NSP5 interaction, ( iii ) dispersion of vNSP2 throughout the cytoplasm, and ( iv ) reduced vNSP2 protein levels. Together, these data indicate that CK1α directly affects NSP2. Accordingly, an in vitro kinase assay showed that CK1α phosphorylates serine 313 of NSP2 and triggers NSP2 octamers to form a lattice structure as demonstrated by crystallographic analysis. Additionally, a dual-specificity autokinase activity for NSP2 was identified and confirmed by mass spectrometry. Together, our studies show that phosphorylation of NSP2 involving CK1α controls viroplasm assembly. Considering that CK1α plays a role in the replication of other RNA viruses, similar phosphorylation-dependent mechanisms may exist for other virus pathogens that require cytoplasmic virus factories for replication.

59 BASIC BIOLOGICAL SCIENCES↗

3+2+X: What Is the Most Useful Depolarization Input for Inverting Lidar Measurements of Non-Spherical Particles to Microphysical Properties?

The typical multiwavelength aerosol lidar data set for inversion of optical to microphysical parameters is composed of three backscatter coefficients (β ) at 355, 532, and 1064 nm and two extinction coefficients (α ) at 355 and 532 nm. This data combination is referred to as 3β +2α or 3+2 data set. This set of data is sufficient for retrieving some important microphysical particle parameters if the particles have spherical shape. Here, we investigate the effect of including the particle linear depolarization ratio (δ) as a third input parameter to the inversion of lidar data. The inversion algorithm is generally not used if measurements show values of δ that exceed 0.10 at 532 nm, i.e. in the presence of non-spherical particles such as desert dust, volcanic ash, and under special circumstances biomass-burning smoke.We use experimental data collected with instruments that are capable of measuring δ at all three lidar wavelengths with an inversion routine that uses the theory of light scattering by randomly oriented spheroids to replicate scattering properties of non-spherical particles. This is the first systematic test of the effect of using all theoretically possible combinations of δ taken at 355, 532, and 1064 nm as input in the lidar data inversion. We find that depolarization information at least at one wavelength already provides useful information in the in version of optical data that describe light-scattering by nonspherical particles. However, any choice of δ(λ) will give lower values of the single-scattering albedo than the traditional 3+2 data set. We find that input data sets that include 355 give a non-spherical fraction that closely resembles the dust ratio we obtain from using β(532) and δ(532) in a methodology applied in aerosol-type separation. The use of 355 in data sets of two or three reduces the fraction of non-spherical particles that is retrieved when using δ(532) and δ(1064). Use of the latter two without accounting for 355 generally leads to high fractions of non-spherical particles that we consider not trustworthy. The use of three δ(λ) instead of two δ(λ) including the constraint that one of these is measured at 355 nm does not provide any advantage over using 3+2+δ(355). Because of the technical challenges involved with accurately measuring δ(1064) we conclude that — depending on measurement capability — the future standard input for inversion using spheroid kernels might be 3+2+δ(355) or 3+2+δ(355)+δ(532).

Tesche, M.↗

Climate data, analysis and models for the study of natural variability and anthropogenic change

Gridded Temperature Under prior/current support, we completed and published (Jones et al., 2012) the fourth major update to our global land dataset of near-surface air temperatures, CRUTEM4. This is one of the most widely used records of the climate system, having been updated, maintained and further developed with DoE support since the 1980s. We have continued to update the CRUTEM4 (Jones et al., 2012) database that is combined with marine data to produce HadCRUT4 (Morice et al., 2012). The emphasis in our use of station temperature data is to access as many land series that have been homogenized by National Meteorological Services (NMSs, including NCDC/NOAA, Asheville, NC). Unlike the three US groups monitoring surface temperatures in a similar way, we do not infill areas that have no or missing data. We can only infill such regions in CRUTEM4 by accessing more station temperature series. During early 2014, we have begun the extensive task of updating as many of these series as possible using data provided by some NMSs and also through a number of research projects and programs around the world. All the station data used in CRUTEM4 have been available since 2009, but in Osborn and Jones (2014) we have made this more usable using a Google Earth interface (http://www.cru.uea.ac.uk/cru/data/crutem/ge/ ). We have recently completed the update of our infilled land multi-variable dataset (CRU TS 3.10, Harris et al., 2014). This additionally produces complete land fields (except for the Antarctic) for temperature, precipitation, diurnal temperature range, vapour pressure and sunshine/cloud. Using this dataset we have calculated sc-PDSI (self-calibrating Palmer Drought Severity Index) data and compared with other PDSI datasets (Trenberth et al., 2014). Also using CRU TS 3.10 and Reanalysis datasets, we showed no overall increase in global temperature variability despite changing regional patterns (Huntingford et al., 2013). Harris et al. (2014) is an update of an earlier dataset (Mitchell and Jones, 2005) which also had earlier DoE support. The earlier dataset has been cited over 1700 times according to ResearcherID on 31/July/2014 and the recent paper has already been cited 22 times. Analyses of Temperature Data Using the ERA-Interim estimate of the absolute surface air temperature of the Earth (instead of in the more normal form of anomalies) we compared the result against estimates we produced in 1999 with earlier DoE support. The two estimates are surprisingly close (differing by a couple of tenths of a degree Celsius), with the average temperature of the world (for 1981-2010) being very close to 14°C (Jones and Harpham, 2013). We have assessed ERA-Interim against station temperatures from manned and automatic weather station measurements across the Antarctic (Jones and Lister, 2014). Agreement is generally excellent across the Antarctic Peninsula and the sparsely sampled western parts of Antarctica. Differences tend to occur over eastern Antarctica where ERA-Interim is biased warm (up to 6°C) in the interior of the continent and biased cool (up to 6°C) for some of the coastal locations. Opportunities presented themselves during 2012 for collaborative work with a couple of Chinese groups. Three papers develop new temperature series for China as a whole and also for the eastern third of China (Wang et al., 2014, Cao et al., 2013 and Zhao et al., 2014). A dataset of ~400 daily Chinese temperature stations has been added to the CRU datasets. The latter paper finds that urban effects are generally about 10% of the long-term warming trend across eastern China. A fourth paper (Wang et al., 2013) illustrates issues with comparisons between reanalyses and surface temperatures across China, a method that has been widely used by some to suggest urban heating effects are much larger in the region. ERA-Interim can be used but NCEP/NCAR comparisons are very dependent on the period analysed. Earlier a new temperature dataset of homogenized records was developed for China (Li et al., 2009). Urbanization has also been addressed for London (Jones and Lister, 2009) where two rural sites have not warmed more than a city centre site since 1900. Additionally, in Ethymiadis and Jones (2010) we show that land air temperatures agree with marine data around coastal areas, further illustrating that urbanization is not a major component of large-scale surface air temperature change. Early instrumental data (before the development of modern thermometer screens) have always been suspected of being biased warm in summer, due to possible direct exposure to the sun. Two studies (Böhm et al., 2010 and Brunet et al., 2010) show this for the Greater Alpine Region (GAR) and for mainland Spain respectively. The issue is important before about 1870 in the GAR and before about 1900 in Spain. After correction for the problems, summer temperature estimates before these dates are cooler by about 0.4°C. In Jones and Wigley (2010), we discussed the importance of the biases in global temperature estimation. Exposure and to a lesser extent urbanization are the most important biases for the land areas, but both are dwarfed by the necessary adjustments for bucket SST measurements before about 1950. Individual station homogeneity is only important at the local scale. This was additionally illustrated by Hawkins and Jones (2013) where we replicated the temperature record developed by Guy Stewart Callendar in papers in 1938 and 1961. Analyses of Daily Climate Data Work here indicates that ERA-Interim (at least in Europe, Cornes and Jones, 2013, discussed in more detail in this proposal) can be used to monitor extremes (using the ETCCDI software – see Zhang et al., 2011). Additionally, also as a result of Chinese collaboration, a new method of daily temperature homogenization has been developed (Li et al., 2014). In Cornes and Jones (2011) we assessed storm activity in the northeast Atlantic region using daily gridded data. Even though the grid resolution is coarse (5° by 5° lat/long) the changes in storm activity are similar to those developed from the pressure triangle approach with station data. Analyses of humidity and pressure data In Simmons et al. (2010) we showed a reduction in relative humidity over low-latitude and mid-latitude land areas for the 10 years to 2008, based on monthly anomalies of surface air temperature and humidity from ECMWF reanalyses (ERA-40 and ERA-Interim) and our earlier land-only dataset (CRUTEM3) and synoptic humidity observations (HadCRUH). Updates of this station-based humidity dataset (now called HadISDH) extend the record, showing continued reductions (Willett et al., 2013). Analyses of Proxy Temperature Data In Vinther et al. (2010), relationships between the seasonal stable isotope data from Greenland Ice Cores and Greenland and Icelandic instrumental temperatures were investigated for the past 150-200 years. The winter season stable isotope data are found to be influenced by the North Atlantic Oscillation (NAO) and very closely related to SW Greenland temperatures. The summer season stable isotope data display higher correlations with Icelandic summer temperatures and North Atlantic SST conditions than with local SW Greenland temperatures. In Jones et al. (2014) we use these winter isotope reconstructions to show the expected inverse correlation (due to the NAO) with winter-season documentary reconstructions from the Netherlands and Sweden over the last 800 years. Finally, in this section Jones et al. (2013) shows the agreement between tree-ring width measurements from Northern Sweden and Finland and an assessment of the link to explosive volcanic eruptions. An instrumental record for the region in the early 19th century indicates that the summer of 1816 was only slightly below normal, explaining why this year has normal growth for both ring width and density. GCM/RCM/Reanalysis Evaluation In this section we have intercompared daily temperature extremes across Europe in Cornes and Jones (2013) using station data, E-OBS and ERA-Interim. We have additionally considered the impact of the urban issue on the global scale using the results of the Compo et al. (2011) Reanalyses, 20CR. These only make use of SST and station pressure data. Across the world’s land areas, they indicate similar warming since 1900 to that which has occurred (Compo et al., 2013), again illustrating that urbanization is not the cause of the long-term warming. Changes in HadCRUH global land surface specific humidity and CRUTEM3 surface temperatures from 1973 to 1999 were compared to the CMIP3 archive of climate model simulations with 20th Century forcings (Willett et al., 2010). The models reproduce the magnitude of observed interannual variance over all large regions. Observed and modelled trends and temperature-humidity relationships are comparable with the exception of the extra-tropical Southern Hemisphere where observations exhibit no trend but models exhibit moistening.

54 ENVIRONMENTAL SCIENCES↗

Numerical analysis of experimental studies of methane hydrate formation in a sandy porous medium

Here we analyse numerically an earlier experimental study that involved the formation of methane hydrates by the excess water method in a small reactor filled with a sandy porous medium, and seek to address questions about the type of the hydration reaction and the phase heterogeneity in the resulting hydrate-bearing sand. Using a fine discretization describing the reactor assembly, the experimental process is faithfully replicated numerically. The multi-stage process of hydrate formation is subdivided in 7 steps. The experimental data from the continuously-monitored pressure and temperature during each step are used for comparison against the numerical predictions, the identification of the dominant processes and the determination of the associated parameters through a history-matching process that minimizes deviations between observations and simulation results. The results of this first-ever study on this subject demonstrate unequivocally that the hydration reaction is a kinetic (as opposed to an equilibrium) process, and that the spatial distributions of the various phases (aqueous, gas and hydrate) at the end of the formation process are strongly heterogeneous. This has serious implications in simulation studies of hydrate dissociation that assume uniform initial phase saturation distributions. Finally, the history-matching process indicates that (a) the system behaviour is sensitive to some flow parameters (porosity and irreducible water saturation) only during the first water injection, (b) it is insensitive to the sand intrinsic permeability during all steps of the study, and (c) thermal processes dominate after the first water injection, yielding estimates of the thermal properties of the sand and of time-variable key parameters of the kinetic reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity

Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.

59 BASIC BIOLOGICAL SCIENCES↗