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At least 163 records · Page 9

Bovine adapted transmissible mink encephalopathy is similar to L-BSE after passage through sheep with the VRQ/VRQ genotype but not VRQ/ARQ

Background: Transmissible mink encephalopathy (TME) is a fatal neurologic disease of farmed mink. Evidence indicates that TME and L-BSE are similar and may be linked in some outbreaks of TME. We previously transmitted bovine adapted TME (bTME) to sheep. The present study compared ovine passaged bTME (o-bTME) to C-BSE and L-BSE in transgenic mice expressing wild type bovine prion protein (TgBovXV). To directly compare the transmission efficiency of all prion strains in this study, we considered the attack rates and mean incubation periods. Additional methods for strain comparison were utilized including lesion profiles, fibril stability, and western blotting. Results: Sheep donor genotype elicited variable disease phenotypes in bovinized mice. Inoculum derived from a sheep with the VRQ/VRQ genotype (o-bTME VV ) resulted in an attack rate, incubation period, western blot profile, and neuropathology most similar to bTME and L-BSE. Conversely, donor material from a sheep with the VRQ/ARQ genotype (o-bTME AV ) elicited a phenotype distinct from o-bTME VV , bTME and L-BSE. The TSE with the highest transmission efficiency in bovinized mice was L-BSE. The tendency to efficiently transmit to TgBovXV mice decreased in the order bTME, C-BSE, o-bTME VV , and o-bTME AV . The transmission efficiency of L-BSE was approximately 1.3 times higher than o-bTMEVV and 3.2 times higher than o-bTME AV . Conclusions: Our findings provide insight on how sheep host genotype modulates strain genesis and influences interspecies transmission characteristics. Given that the transmission efficiencies of L-BSE and bTME are higher than C-BSE, coupled with previous reports of L-BSE transmission to mice expressing the human prion protein, continued monitoring for atypical BSE is advisable in order to prevent occurrences of interspecies transmission that may affect humans or other species.

59 BASIC BIOLOGICAL SCIENCES↗

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Abstract Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales ). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ).

59 BASIC BIOLOGICAL SCIENCES↗

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling

Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N 2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A ( Candidatus Atelocyanobacterium thalassa ). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N 2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya

Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003–2010. Nine isolates were identified as S . Typhimurium sequence type 313 while the other two were S . Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S . Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.

59 BASIC BIOLOGICAL SCIENCES↗

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population “arms” that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗

The underappreciated lone pair in halide perovskites underpins their unusual properties

The presence of 6s 2 (5s 2 ) lone-pair electrons on the B-site Pb (Sn) in all-inorganic and hybrid halide ABX 3 perovskites distinguishes these materials from the familiar tetrahedral semiconductors traditionally employed in optoelectronics and is key to many of their appealing properties. These electrons are stereochemically active, albeit often in a hidden fashion, resulting in unusual and highly anharmonic lattice dynamics that are linked to many of the special optoelectronic properties displayed by this material class. This article describes the connections between this atypical electronic configuration and the electronic structure and lattice dynamics of these compounds. We illustrate how the lone pair leads to favorable bandwidths and band alignments, mobile holes, large ionic dielectric response, large positive thermal expansion, and even possibly defect-tolerant electronic transport. Taken together, the evidence suggests that other high-performing semiconductors may be found among compounds with lone-pair-bearing cations in high symmetry environments and a high degree of connectivity between atoms.

36 MATERIALS SCIENCE↗

CEBAF Injector Model for KL Beam Conditions

The Jefferson Lab KL experiment will run at the Continuous Electron Beam Accelerator Facility with a much lower bunch repetition rate (7.80 or 15.59 MHz) than nominally used (249.5 or 499 MHz). While the proposed average current of 2.5 - 5.0 muA is relatively low compared to the maximum CEBAF current of approximately 180 muA, the corresponding bunch charge is atypically high for CEBAF injector operation. In this work, we investigated the evolution and transmission of low-rep-rate, high-bunch-charge (0.32 to 0.64 pC) beams through the CEBAF injector. Using the commercial software General Particle Tracer, we have simulated and analyzed the beam characteristics for both values of bunch charge. We performed these simulations with the existing injector using a 130 kV gun voltage. We have calculated and measured the transmission as a function of the photocathode laser spot size and pulse length. We report on the findings of these simulations and optimum parameters for operating the experiment.

Pokharel, Sunil↗

Modeling for the phased injector upgrade for 12 GeV CEBAF

The upcoming Jefferson Lab K-Long experiment at Hall D will require unique beam conditions with a much lower bunch repetition rate and atypically high bunch charge. To optimize the Continuous Electron Beam Accelerator Facility (CEBAF) injector for this experiment, we performed Multi-Objective Genetic Optimization (MGO) using General Particle Tracer (GPT) to determine the magnetic elements and RF settings necessary for the K-long bunch charge (0.64 pC) at 200 kV. We also investigated the transmission and beam characteristics of low to high charge per bunch electron beams through the injector for simultaneous operations of all four CEBAF Halls and characterized the transmission as a function of the photocathode laser spot size and pulse length. Our findings provide valuable insights into optimizing the CEBAF injector for the Jefferson Lab K-Long experiment, as well as for other experiments with similar beam conditions

Kazimi, R.↗

Loss Factors for Small Distributed Wind Turbines Based on Field Data in the United States

While wind energy production loss due to unavailability, environmental impacts, curtailment, and other causes has been studied and characterized at the utility-scale wind farm level, observation-based characterization of project loss is lacking for distributed wind energy, particularly for projects involving small wind turbines. Contemporary tools and research that support pre-construction distributed wind energy characterization present a wide range of default loss factors to convert gross energy estimates to net: 7-18%. We hypothesize that we can use generation observations from operational distributed wind projects to develop more accurate representations of loss. Using a density-based filtering technique on distributed wind power generation timeseries, we determine periods of typical performance and use them with regression algorithms in a measure-correlate-predict fashion to simulate what the generation would have been during periods of atypical or unreported performance. From there, the actual versus predicted generation leads to the establishment of observation-informed loss factors (median = 17%) for small, single turbine installation distributed wind projects.

17 WIND ENERGY↗

statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities

The Colorado River Basin (CRB) is experiencing an unprecedented water shortage crisis brought upon by a combination of factors arising from interactions across the region’s coupled human and natural systems. Allocation of water to the seven states that rely on the Colorado River was settled in the Colorado River Compact of 1922 during a period now known to be characterized by atypically high flows (Christensen et al., 2004). Since then, aridification due to anthropogenic-driven warming has steadily reduced the overall water supply available in the basin, with a 10% decrease in the river’s flow occurring over just the past two decades (Bass et al., 2023). The river is further strained by increasing demands associated with a growing population and diverse multi-sectoral demands. Navigating these challenges also requires accounting for the complex prior appropriation water rights system governing water allocation across the region’s diverse users.

54 ENVIRONMENTAL SCIENCES↗

Initial Evaluation of Fuel-Reactor Concepts for Advanced LEU Fuel Development

The National Nuclear Security Administration (NNSA) Office of Defense Nuclear Nonproliferation R&D has commenced a project to evaluate and develop low-enriched uranium (LEU) fuel systems, materials, and fabrication technologies that could be used for compact, advanced LEU (aLEU) fuel, power-producing, high-burnup reactor applications. Potential applications are intended to be off-grid power sources for ship-borne systems and transportable systems to fixed locations, e.g., to a remote base or to a seawater desalination service location. Reactors with these qualities and fuel enrichments between 5 and 20% are atypical. The aLEU Fuel for Nonproliferation Applications Project addresses this technology gap.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Transition Core Planning and Safety Analyses in Support of LEU Fuel Conversion of the University of Missouri Research Reactor (MURR)

The University of Missouri Research Reactor (MURR®) is one of six U.S. High Performance Research Reactors (USHPRR), including one critical facility, that is working with the National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M3) Reactor Conversion Program to convert from highly enriched uranium (HEU) to low-enriched uranium (LEU) fuel. The M3 Reactor Conversion USHPRR Project objectives include the development of LEU fuel element designs that will ensure safe reactor operations and to maintain the existing experimental performance of each facility. The work is being conducted through many inter-related activities being completed by four Project Pillars: Fuel Qualification (FQ), Fuel Fabrication (FF), Reactor Conversion (RC), and Cross Cutting (CC). A new type of LEU fuel based on an alloy of uranium-10 wt% molybdenum (U-10Mo) is expected to allow the conversion of those USHPRR, like MURR, requiring higher density fuels. The very-high-density LEU U-10Mo monolithic fuel is currently undergoing irradiation testing and post-irradiation examination under a planned and documented fuel qualification effort. The FQ Pillar will document fuel property and fuel performance data and qualify the fuel for use in these reactors. The FF Pillar is fabricating fuel for ongoing and future irradiation tests, as well as conducting fabrication demonstrations to validate or update preliminary fabrication assumptions. The FF Pillar is also working to develop and install commercial manufacturing capacity with the U-10Mo monolithic fuel to produce prototypic fuel. Working with the RC Pillar at Argonne, MURR has progressed through a preliminary fuel element design using preliminary data for the proposed monolithic alloy of U-10Mo. Analyses were completed in previous work that found for typical equilibrium operations with the preliminary LEU fuel element design, in conjunction with a power uprate to 12 MW and appropriate changes to the MURR Limiting safety system settings (LSSS), MURR will have adequate margins to safety for steady-state operations and postulated transient accidents and will have experimental performance in key locations that meets or exceeds current operations with HEU fuel. The purpose of this work is to develop a sequence of transition cycles that will enable MURR to transition from operation with the reactor core loaded with fresh LEU fuel elements only to typical equilibrium operations with mixed-burnup cores following conversion while meeting operational requirements on safety and experimental performance. It is expected that the use of fresh LEU fuel at conversion and subsequent low burnup of the LEU fuel elements that will initially be available for use following conversion will result in critical control blade positions that will substantially change the axial power distribution in the core and the neutron flux available in key experimental locations relative to equilibrium LEU operations. Given the constraints of MURR safety margins, operational practices, and production and research, a novel method has been developed to identify a transition sequence that minimizes the time MURR operates atypically compared to the current prototypic cycles using HEU fuel. The proposed transition sequence moves quickly to the same sort of equilibrium cycles for the LEU fuel that have already been evaluated in documented preliminary safety analyses. Although shifting the neutron flux peak to the lower half of the core during initial cycles with LEU at 12 MW reduces the experiment performance in some key locations relative to current HEU operations at 10 MW, all LEU cores provide an average performance that meets or exceeds that of HEU. An LEU cycle is reached that meets or exceeds the level of experimental performance predicted for current HEU and equilibrium LEU operations in more than 450 key locations identified by a reactor specialist at MURR by the 23rd cycle following conversion and that afterwards will enable MURR to consistently meet its experimental performance requirements. The proposed transition sequence only requires the fabrication of 34 fresh LEU elements in the first year of operation and does not exceed the anticipated availability of fresh elements that can be produced by the fuel fabricator. By the third year after conversion, 22 fresh LEU elements will be required each year, which is the same as expected for equilibrium LEU operations and the same as current operations with HEU fuel. The proposed transition sequence thus combines a relatively short time period before equilibrium burnup is achieved, a temporary increase of fuel elements needed annually relative to typical operations that are within the production capabilities of the fuel fabricator, and demonstrates comparable experimental performance of the LEU cores relative to current HEU operations. Further measures may be taken to reduce any initial experimental performance penalty even further, where possible, by repositioning certain experiments to leverage the increased performance in the lower axial experimental positions in the initial cycles following conversion or leaving the experiments in the irradiation facilities longer in order to achieve the required neutron fluence. This analysis may require refinement depending on the experimental facilities in use at the time of conversion. Nonetheless, the results presented here, including the experimental performance, core burnup, and critical control blade positions throughout the transition cycles, show that the proposed transition cycle fuel management patterns are consistent with what is expected and desired for MURR operation with LEU U-10Mo fuel. Detailed core power distributions from the neutronics models were also used to evaluate safety margins during steady-state operations for the selected transition cycles and the equilibrium LEU core. It is shown that there are adequate safety margins for both steady-state operations and postulated accident scenarios. For the steady-state operations with the preliminary LEU fuel element design the analysis predicts at least 2.49 MW margin to the onset of flow instability at the LSSS power of 15 MW. Considering the LSSS power is 125% of full license power, the margin to OFI is sufficient. In addition, the critical heat flux ratio at LSSS power is well above the requirement of CHFR > 2.0 from NUREG-1537 for all considered cases. For postulated transient accidents, the minimum margin to the fuel temperature safety limit is at least 109 °C. In summary, the proposed sequence of core loadings for MURR operations following conversion to LEU fuel and a power uprate to 12 MW provides sufficient safety margins for both steady-state operations and postulated transient accidents during a proposed sequence of transition cycles to equilibrium operations. Analysis has shown that there are some local experimental performance penalties during the initial cycles. Although there are local shifts in the experimental performance, on average all LEU cores at 12 MW have equal or higher performance than HEU at 10 MW. Temporary adjustments are being planned that will produce suitable experimental performance during these cycles. The results indicate that for the equilibrium LEU core the experimental performance exceeds that of current HEU operations in all key locations while also demonstrating sufficient safety margins.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Tritiated Sulfur Hexafluoride Disposition Strategies

Tritium (T 2 ) is a radioactive isotope of hydrogen that is produced in nuclear fission reactions and is often used in nuclear fusion reactions and accelerator-based applications for medical isotope production. As a hydrogen isotope, tritium can readily bind to hydroxyl radicals (OH), forming tritiated water (HTO or T 2 0), and to carbon atoms. Tritium decays to helium-3 ( 3 He) via beta-decay with max decay energy of 18.6 keV. While it is not an external radiation hazard, it can be an internal radiation hazard if tritium is inhaled, ingested, or absorbed through the skin. In applications where tritium is handled, tritium confinement is performed using different barriers to minimize releases to the environment. For gaseous (elemental), liquid (oxide), and metal (hydride) tritium, process piping and components provide the primary confinement function. Secondary tritium confinement is typically provided by inert (i.e. non-flammable gases such as nitrogen, argon, or helium) gloveboxes which are connected to a tritium stripper system. Primary tritium confinement barriers typically produce low volumes of high tritium concentrations of tritiated methane from carbon in steels or organic materials along with tritiated water/tritium oxide (e.g. HTO) and tritiated ammonia from reactions with oxygen and nitrogen. Tritium escaping primary confinement into secondary confinement atmospheres (e.g. gloveboxes) produce higher volumes of lower activity contamination than found in process piping. Tritium contamination also occurs by leaks or tritium permeation/diffusion through confinement materials. Tritium from inside primary confinement barriers will diffuse or leak out of the primary confinement barrier and usually into the air, if the system is inside an air hood or ventilated hot cell, or into the secondary confinement (e.g. glovebox) atmosphere which is either exhausted or stripped based on the function of the secondary confinement (glovebox) system. Accelerator based processes for medical isotope production represent an atypical tritium contamination challenge. In medical isotope production, deuterium supply gas is ionized and accelerated to a tritium gas target to produce neutrons that are then used to produce the medical isotopes through additional nuclear fission reactions. To create large voltage differentials for accelerator operations, an electrical insulation medium is needed to prevent or rapidly quench electric discharges. A common electrical insulation medium utilized in accelerator applications is sulfur hexafluoride (SF 6 ) gas. SF 6 has a high dielectric strength and allows for the construction of smaller accelerator systems compared to other electrical insulation mediums such as air or dry nitrogen. Due to tritium permeation/diffusion through accelerator process and confinement materials, there is the possibility that tritium can contaminate the electrical insulation medium of the accelerator. Tritium contaminated SF 6 creates a material without any obvious processes for managing the contamination, reuse, or disposal of the used SF 6 . This document will discuss possible management strategies for tritium contaminated SF 6 for accelerator-based processes for Molybdenum-99 (Mo-99) production.

07 ISOTOPE AND RADIATION SOURCES↗

Drones for Decommissioning

The U.S. Nuclear Regulatory Commission has responsibility for regulating the safe decommissioning of facilities and sites to meet the License Termination Rule in 10 Code of Federal Regulations (CFR) Part 20, Standards for Protection Against Radiation, Subpart E “Radiological Criteria for License Termination.” Decommissioning is performed in accordance with 10 CFR Part 50, Domestic Licensing of Production and Utilization Facilities, as part of license termination (§50.82) and release of the facility or site for unrestricted use (§50.83). The guidance currently demonstrates the minimum requirements and necessary conditions for conducting radiological surveys by a person carrying a radiation detector(s). The Pacific Northwest National Laboratory (PNNL) evaluated the use of an unoccupied aerial vehicle (UAV) to conduct radiological surveys that could be used in decommissioning to potentially reduce time, cost, and worker safety compared to current survey methods. The objective of this project was to evaluate the performance and limitations of a UAV to support a decommissioning radiological survey and compare it to a radiological survey conducted by a human. The primary research questions of interest evaluated were: 1. Did observed UAV paths differ from human paths and, if so, how much? 2. Did survey path deviation affect survey results and, if so, how? 3. Were radiological measurements from human and UAV surveys significantly different? To answer these research questions, an experimental field was set up at PNNL’s 3440 test track, and it included radiological sources commonly surveyed during decommissioning: cobalt-60 (Co-60), cesium-137 (Cs-137), and americium-241 (Am-241). Nine check sources (three each of Am-241, Cs-137, and Co-60) with activities ranging from 3.54 µCi to 39.34 µCi were set over a path that also included an area for measuring background radiation. An Aurelia X6 UAV coupled with a GPS and lidar unit was used to conduct the radiological surveys. UAV and human surveys were conducted using two different NaI(Tl) scintillation radiation detectors (2 in. × 2 in. Ludlum, Inc. and 2 in. × 0.04 in. Alpha Spectra, Inc.) at a travel velocity of approximately 0.2 m/s at a low (15–40 cm median altitude) or high (87–105 cm median altitude) survey altitude. Since the survey velocity and altitude parameters were atypical for normal UAV operations, testing was done prior to conducting the radiological surveys to establish airworthiness, evaluate the navigation system, and establish flight control. Human and UAV surveys were paired according to the detector type and altitude regime to compare the survey data. The results of this proof-of-concept research determined that the UAV and human surveys followed similar survey paths and detected the radiological sources with no significant statistical difference (in 33 out of 36 surveys). However, further research is needed prior to deploying UAVs for decommissioning surveys.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Evaluating the 3D PBL scheme for wind energy applications in the complex terrain of Altamont Pass, CA

In this study, the 3D PBL scheme, developed and tested during previous WETO projects, was used to simulate daily speedup flows in the Altamont Pass Wind Resource Area of California. These flows were observed as part of the WFIP2 companion experiment HilFlowS, which examined potential power output from taller turbines in the Altamont region. The regularity of the observed speedup events during the summer months, combined with the importance of terrain-induced wind acceleration, makes them a useful case study for evaluating mesoscale forecast models, which often underperform in regions of complex terrain. Compared to a traditional one-dimensional PBL scheme, the 3D PBL scheme shows evidence of improved wind speed predictions, including an ability to capture atypical wind speed profiles and reduce model overestimates of wind speed across the turbine rotor region. Such improvements will be necessary for wind farm siting and power forecasting, especially as taller turbines are deployed in complex terrain.

17 WIND ENERGY↗

Defining Lipidomic Responses to Coronavirus Infection

Highly pathogenic human coronavirus infection can cause a severe atypical, rapid onset pneumonia with a mortality rate of up to 10% for severe acute respiratory syndrome coronavirus 1 (SARS-CoV 1), 35% for Middle East respiratory syndrome coronavirus (MERS-CoV), or 1% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2 causative agent of COVID 19). While medical countermeasures successfully controlled the worldwide SARS-CoV epidemic, the MERS-CoV epidemic is still ongoing and continues to be a concern for travelers in the Middle East and the multi-year SARS-CoV 2 pandemic underscore the importance of defining biomarkers that are diagnostic and/or predictive of severe disease outcomes for respiratory viruses. Systems biology approaches provide global snapshots of infection induced changes in host cells/tissues and provide extremely rich datasets for understanding host pathogen interactions. Metabolites, especially lipids, are critical for viral replication but less is understood about infection induced changes to lipids due to limits in lipid species detection and identification. To characterize how individual lipid species and proteins with lipid associated functions contribute to highly pathogenic human coronavirus replication and disease severity, existing datasets were probed to determine cell type specific lipid responses to MERS-CoV infection and verification studies were performed to determine if modification of the host lipid signature (by inhibiting enzymatic functions that produce specific lipid species) can perturb CoV replication in human lung cells. MERS-CoV infects human lung epithelial, endothelial and fibroblast cells. All three cell types were infected with MERS-CoV and samples collected to analyze lipids, proteins, metabolites, and transcripts from 12 to 48 hours post infection. Time matched mock-infected cells were collected in parallel for each cell type. Following sample and statistical analysis, functional enrichment and bioinformatic analysis was performed to identify differentially expressed lipids and proteins. Two lipid species were found to be significantly upregulated following MERS-CoV infection, ceramides, and triacylglycerol both of which are indicative of cells undergoing apoptotic cell death. In contrast, sphingomyelins (lipid molecules that can serve as a precursor for one pathway for ceramide synthesis) had significantly decreased expression in MERS-CoV infected cells. An inhibitor of acid sphingomyelinase (that converts sphingomyelin to ceramides and phosphorylcholine) reduced MERS-CoV replication suggesting that production of ceramides is key for successful viral replication and transmission. Acyl-CoA-synthetase 3 (ACSL3), the only protein whose function is lipid associated and had increased differential expression in our dataset, regulates the synthesis of triacylglycerol (increased expression). Inhibitors that directly block ACSL3 (Triacsin C) but not steps later in the triacylglycerol synthesis pathway (Etomoxir) inhibit MERS-CoV replication suggesting that triacylglycerol production and/or ACSL3 activity is also key for viral replication. ACSL3 expression is also upregulated in lung cancer cells and is predicted to promote continued cell viability which would also enhance viral replication. The differentially expressed lipid and lipid-associated protein species identified in our studies suggest that MERS-CoV infection is activating cellular death pathways to limit the number of cells that become infected but also stimulating the production of lipid-associated enzymes that can prolong host cell viability and the amount of time progeny virions can be produced and released. As the inhibitors that worked against MERS-CoV infection were also efficacious against SARS-CoV 2 infection, countermeasures that target these host pathways may provide novel ways to block highly pathogenic human coronavirus infection and/or prevent severe disease outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

Multiplexed Probing for Functional Capacity Measurements in Complex and Limited-Size Samples

A new strategy using glass as a solid support for functionalization with chemical probes has been recently developed with successful results. The next step in glass functionalization is to pair chemical probes with fluorescent glass microspheres. This approach gives us a way to directly quantify probe-bound protein using Fluorescence-Activated Cell Sorting (FACS). FACS has already shown to be amendable to glass microspheres, demonstrating changes in probe-bound protein concentration. Suitable probing conditions for gram-positive and negative microbes, complex microbial communities from myriad ecosystems, and eukaryotic cells/tissues have traditionally suffered from set-backs, such as limited protein per sample and conditions atypical for probing. To remedy this, we propose to: (1) Demonstrate probe functionalization specific to glass microspheres by paired fluorophore and use those activity probes successfully with proteomics. Probes that are currently available (CYP5, GSH/GST, Glycoside Hydrolase) can be easily prepared onto glass surfaces. Probe-bound microspheres can be tested in ratios, first with known amounts of purified protein and then complex microbiome lysates. (2) Our validated microspheres are then used to determine quantitative amounts of protein through FACS sorting. Complimenting these results by proteomics, prepared microspheres are then optimized and condensed into a user-friendly kit. Once successfully commercialized, this multiplexed assay can be used with little to no technical expertise, making this available to various industries users.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Validation Analysis of Medium-Scale Methanol Pool Fire Simulated in SIERRA/Fuego [Slides]

Analysis of methanol pool fire conducted as part of validation study for SIERRA/Fuego. Results showed trends & errors consistent with related studies. Area validation metric provides way to quantify model form uncertainty. AVM shows that more work could be done to understand how model form uncertainty varies with mesh resolution. There is a possible atypical use of MAVM on time-series data. AVM shows mismatch between predicted flame height and experimental value less sensitive to variations in mixture fraction than temperature. Mismatch about experimental value also more symmetric for mixture fraction. Our analysis showed that mixture fraction is preferable for this application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗