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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae . A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S . cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S . cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum . Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae . The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S . cerevisiae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR)

An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 10 1 to 10 4 viruses per cell, and H1N1 ranging from 10 1 to 10 3 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Genomic Dissection of Anthracnose ( Colletotrichum sublineolum ) Resistance Response in Sorghum Differential Line SC112-14

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum , is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F 2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

Genetics & Heredity↗
DOE OSTI2023

Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Groundwater and Intruder Radionuclide Screening

Solid Waste Management (SWM) operates the E-Area Low-Level Waste Facility (ELLWF) where low level on-site and off-site solid waste streams are buried. The facility has been in operation since late 1994 and is currently projected to remain in operation until 2065. This facility can accommodate a broad range of waste forms resulting from the six different types of disposal unit options (i.e., varying degrees of engineered barriers → trenches to concrete vaults). This facility is currently operating under a Performance Assessment (PA) issued back in 2008, along with several subsequent supporting Special Analyses (SA). The Savannah River National Laboratory (SRNL) developed the prior PAs and SAs and has been tasked to update the facility’s PA. For operating the E-Area facility, a Waste Inventory Tracking System (e.g., WITS) is actively employed by waste generators where every radionuclide entering the facility (to be buried in one of its many disposal units) must be either directly or indirectly accounted for. Since there is a large number of radionuclides in existence (>3,000), the International Commission on Radiological Protection (ICRP-107) has provided guidance on the subset of radionuclides requiring further assessment in landfills such as the E-Area LLWF. The ICRP-107 publication provides critical radiological information on 1,252 radionuclides of 97 elements. This database is the critical starting point for developing a consistent inventory limit system. The explicit measurement and tracking of all radionuclides are not necessary when process knowledge, burial history, and radiological aspects are factored into conservative groundwater and intruder screening processes. Across the DOE complex these screening processes have been historically performed using the methodology suggested by the National Council on Radiation Protection and Measurements (NCRP) as presented in their original report (NCRP 1984) and then refined in a later report (NCRP 1996). In the recommended screening models employed within this report the traditional NCRP models are updated to better handle progeny and better reflect the known characteristics of E-Area. This improved screening process is referred to as the “NCRP-like” method. Various upgrades to the traditional NCRP methodology have been used by others (e.g., NRC funded effort by Kennedy and Strenge 1992). The more detailed models by Kennedy and Strenge (1992) were considered in this effort and are compared to the results from the more traditional NCRP-like models. The groundwater and inadvertent intruder screening analyses presented in this report start with this 1,252 radionuclide list and reduces it down to more manageable lists that are applicable to the various disposal unit types contained within E-Area. In order to reduce this starting list, some level of exposure risk must be considered acceptable. Historically, a dose (or concentration level) has been compared with a screening criterion set to 1% of a performance measure (e.g., a beta-gamma dose not to exceed the 4 mrem/yr beta-gamma performance measure x 0.01 = 0.04 mrem/yr). Thus, if a radionuclide produced a bounding or screening-level dose (or concentrations) less than the screening criterion, it could be safely removed from further consideration. Several tiers of screening and bounding level analyses have been considered in this report.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Groundwater and Intruder Radionuclide Screening

Solid Waste Management (SWM) operates the E-Area Low-Level Waste Facility (ELLWF) where low level on-site and off-site solid waste streams are buried. The facility has been in operation since late 1994 and is currently projected to remain in operation until 2065. This facility can accommodate a broad range of waste forms resulting from the six different types of disposal unit options (i.e., varying degrees of engineered barriers → trenches to concrete vaults). This facility is currently operating under a Performance Assessment (PA) issued back in 2008, along with several subsequent supporting Special Analyses (SA). The Savannah River National Laboratory (SRNL) developed the prior PAs and SAs and has been tasked to update the facility’s PA. For operating the E-Area facility, a Waste Inventory Tracking System (e.g., WITS) is actively employed by waste generators where every radionuclide entering the facility (to be buried in one of its many disposal units1) must be either directly or indirectly accounted for. Since there is a large number of radionuclides in existence (>3,000), the International Commission on Radiological Protection (ICRP-107) has provided guidance on the subset of radionuclides requiring further assessment in landfills such as the E-Area LLWF. The ICRP-107 publication provides critical radiological information on 1,252 radionuclides of 97 elements. This database is the critical starting point for developing a consistent inventory limit system. The explicit measurement and tracking of all 1,252 ICRP-107 radionuclides can be reduced when process knowledge, burial history, and radiological aspects are factored into conservative groundwater and intruder screening processes. Across the DOE complex these screening processes have been historically performed using the methodology suggested by the National Council on Radiation Protection and Measurements (NCRP) as presented in their original report (NCRP 1984) and then refined in a later report (NCRP 1996). In the recommended screening models employed within this report the traditional NCRP models are updated to better handle progeny and better reflect the known characteristics of E-Area. This improved screening process is referred to as the “NCRP-like” method. Various upgrades to the traditional NCRP methodology have been used by others (e.g., NRC funded effort by Kennedy and Strenge 1992). The more detailed models by Kennedy and Strenge (1992) were considered in this effort and are compared to the results from the more traditional NCRP-like models. The groundwater and inadvertent intruder screening analyses presented in this report start with this 1,252 radionuclide list and reduces it down to more manageable lists that are applicable to the various disposal unit types contained within E-Area. In order to reduce this starting list, some level of exposure risk must be considered acceptable. Historically, a dose (or concentration level) has been compared with a screening criterion set to 1% of a performance measure (e.g., a betagamma dose not to exceed the 4 mrem/yr beta-gamma performance measure x 0.01 = 0.04 mrem/yr). Thus, if a radionuclide produced a bounding or screening-level dose (or concentrations) less than the screening criterion, it could be safely removed from further consideration. Several tiers of screening and bounding level analyses have been considered in this report.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Unraveling the Genetics of Two Key Biomass Traits that Differentiate Upland and Lowland Tetraploid Switchgrass Ecotypes, Colonization by Mycorrhizal Fungi and Frost Tolerance

The overall objectives of the proposal were to dissect the genetics of the ability of switchgrass to interact with arbuscular mycorrhizal fungi (AMF) and to tolerate subzero temperatures, and to investigate the effect of AMF colonization on freezing tolerance and biomass production. In order to achieve this, we generated genetic maps in an F2 mapping population derived from a cross between the lowland genotype AP13 and the upland genotype VS16. In addition to providing a framework for identification of quantitative trait loci (QTL), the genetic maps were used to validate and improve the switchgrass genome assembly. We mapped phenotypic quantitative trait loci (QTL) for AMF colonization and cold tolerance in the F 2 population. We demonstrated that identification of QTL for AMF colonization was achieved only if AMF genus-specific colonization levels were used as phenotypes. No QTL were obtained when the overall level of AMF colonization was used as a trait. We conducted RNASeq on a subset of the F2 progeny following cold acclimation, and developed statistical methods to conduct expression QTL (eQTL) analyses in a polyploid organism. A preliminary analysis of the results identified eQTL for a range of genes that were differentially regulated in the lowland AP13 compared to the upland VS16 under cold acclimation. Once sequencing of the transcriptomes of a temporal replicate of the mapping population that was cold-acclimated using the same conditions has been completed, a final eQTL analysis will be conducted.

09 BIOMASS FUELS↗
DOE OSTI2022

A summary of air sampler filter performance data: Bladewerx Speclon 5(TM) and Millipore FMLW047 5um

Bladewerx™ LLC (Rio Rancho, NM) manufactures instrumentation, neutron shielding and activation foils for the radiation protection industry. Specializing in portable alpha/beta air monitors and sample counters, Bladewerx is the source of Speclon 5™ PTFE filter media that they recommend for high-resolution alpha spectroscopy. Los Alamos National Laboratory (LANL) utilizes Speclon™ filter material in CAM (Continuous Air Monitor) samplers for workplace air monitoring. Millipore FMLW (5μm) filters are also used at Los Alamos, and a comparison of the two filter types has been requested. For filter face air velocities from 0.066 m/s to 1.5 m/s, the aerosol collection efficiency (for 0.3 μm particle diameters) and the filter pressure drops were measured. The FWHM (full width half maximum) of alpha spectroscopy peaks was also determined, using naturally occurring radon progeny at an alpha energy of 6 MeV.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2022

On the Definition of the Prompt Neutron Lifetime

There are myriad definitions for the mean neutron lifetime, neutron generation time, and other related quantities to characterize a neutron and its progeny’s propagation through an assembly. In this document, we consider lifetime definitions that are associated with eigenvalue forms of the neutron transport equation. Specifically, we focus on the two most widely used eigenvalues: the $\kappa$ eigenvalue and the $\alpha$ eigenvalue. These eigenvalues are used more often than other eigenvalues due to the physical phenomenon they capture. The $\kappa$ eigenvalue allows for the ability to determine if the system can sustain a chain reaction, while the $\alpha$ eigenvalue captures the asymptotic time dependent behavior of the system. An advantage of using these eigenvalues resides in the biorthogonality of the solutions with their adjoint counterpart. This feature allows us to simplify the expressions and to obtain appropriately weighted definitions that highlight important physics and regions of an assembly.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A new TEVA-DGA chromatography procedure to separate Pu, Am, and Np from bulk U materials

Trace actinides present within uranium (U) material are diagnostic signatures of U processing history. For example, the emplacement of U material within the high neutron-flux environment of a nuclear reactor can cause neutron capture of U to form 241-plutonium ( 241 Pu). Plutonium-241 then decays to progeny isotopes 241-americium ( 241 Am) and 237-neptunium ( 237 Np); therefore, the presence and relative abundances of these trace actinides is indicative of the material’s production history and intended employment (Mayer et al., 2013). During a pre-detonation nuclear forensics investigation, measurement of trace actinide 241 Pu, 241 Am, and 237 Np concentrations by an analytical laboratory may be requested. However, chemically purifying these elements from bulk U is a challenging and involved procedure requiring several sequential chromatography columns across 4+ days. To expedite Pu-Am-Np separation from bulk U material, and to improve the yield recovery of these elements, this DHS Postdoc Fellowship has worked to create a new chromatography separation chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
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

New NBL Pu Isotopic Standards C137A and C136A as Working Reference Materials for Radiochronometry in Nuclear Forensics

Lawrence Livermore National Laboratory (LLNL) and the NBL Program Office (NBL PO) are collaborating on production of purified sub-units of the former NBS 936, 937 and 938 plutonium isotopic reference materials, which will be certified for plutonium isotopic composition and sold as certified reference materials (CRMs) C136A, C137A, and C138A, respectively. These reference materials are used throughout the United States and international community as standards for isotopic measurement method calibration and quality control and were first produced over 50 years ago. To reduce quantities of in-grown daughter products and potentially enable their use as Pu radiochronometry reference materials, the materials undergo a two-stage anion exchange purification to significantly reduce the quantities of U, Am, and Np in the source material. The purified Pu is aliquoted into ~1 mg units in the nitrate form, which will facilitate easier shipping and use compared to the 0.25 g parent units. The production process has been completed for the high- and medium- burnup isotopic standards C137A and C136A and will soon be performed for the weapons-grade Pu standard C138A. This report describes the measurement of trace actinide progeny of the Pu isotopes ( 234 U, 235 U, 236U, 241 Am and 237 Np) in purified C137A and 136A isotopic standards to provide informational values and assess the possibility of their use as working reference materials for radiochronometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An LSTM Deep Learning Network for ¿Background Radiation Prediction

Determination of appropriate background radiation is important in any measurement application. Environmental radiation monitors and monitors used to assess dose to individuals outside of controlled areas are particularly susceptible to changes in readings due to fluctuations in the environmental conditions. These fluctuations (e.g. radon progeny concentrations) lead to changes in the detector response in the actual radiation environment, and they need to be taken into account when extracting the net operational doses. Work has been ongoing to apply advances in Deep Learning and Artificial Intelligence to account for changes in detector responses based on environmental parameters; in particular, a Long-Short Term Memory (LSTM) Deep Learning architecture has been utilized to incorporate time-series data into a prediction model. In this work, we present the current status of the project to predict radiation measurements based on meteorological conditions and air packet trajectories extracted using the National Oceanic and Atmospheric Administration's (NOAA) Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT4) model.

Degtiarenko, Pavel↗
DOE OSTI2022

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↗
DOE OSTI2023

Genetics and Genomics of Pathogen Resistance in Switchgrass (Final Report)

This project was funded by DOE under Grant no. DE-SC0016108. Originally approved for the 2016-2019 period, two no-cost extensions were solicited and approved, which prolonged the lifespan through July 2021. This final report informs on the results obtained so far from the research implemented. The research hinged on integrating genomics (genomic selection, RNAseq, virus-plant interactions) with classical genetics (conventional breeding) to incorporate durable resistance to fungal (rust) and viral (mosaic) diseases in switchgrass (Panicum virgatum) populations being bred for bioenergy. Higher biomass yield, higher quality (low lignin content), and durable disease resistance are key features to make lignocellulosic switchgrass feedstocks economically competitive and sustainable. Genomic selection is being applied on three generations of a switchgrass population derived from crossing two ecotypes (Kanlow as lowland female and Summer as upland male) with differential performance in terms of biomass yield and quality, disease resistance, and winter survivability. Target populations were screened for rust and mosaic in field and/or lab and phenotyped for biomass yield and quality traits. Genetic analyses were applied across generations to capture the joint inheritance of the targeted traits and predict breeding values for parents and progeny with greater accuracy. Parental and a panel of different switchgrass populations were genotyped with the DArTseq technology to develop SNP (0, 1, 2) and in-silico (presence/absence) DArT markers. Rust inoculations techniques were developed and applied successfully on switchgrass. The original populations (Kanlow and Summer) were sequenced with RNAseq to capture the gene expression profiles across sequential time-points and appraise the basis of greater resistance in the Kanlow vs the Summer ecotype. Constructs of PMV and sPMV mosaic virus were assembled and tested first on proso millet to find the best protocol to use later on switchgrass. Results from the preliminary analyses indicate that 1) ample additive genetic variation is available for selection and improving this inter-ecotypic population for yield, quality, and disease traits, 2) significant gains are to be expected with the genetic correlations being favorable between yield and lignin content and between yield and disease ratings, 3) substantial differences exist in the genetic regions controlling rust resistance in the two ecotypes, 4) co-infection with PMV isolates from Nebraska and its satellite from Kansas elicit severe mosaic symptoms, and 5) two different genetic systems are responsible for imparting resistance to rust and virus in switchgrass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The Gene Fitness Atlas: A Roadmap for Predicting Evolution

We developed a novel, high-throughput microfluidic device design containing “interaction zones” where progeny cell lines compete against each other allowing for accurate analysis of bacterial cell fitness. The goal of the project was to use the device for two applications: 1) gene knockout screening and 2) antibiotic resistance screening. The microfluidic platform was fabricated using photolithography and soft lithography in polydimethylsiloxane (PDMS). E.coli Keio mutants and fluorescent wildtype parent were chosen for the study. Cells were grown overnight and their loading into the devices and seeding in mother machines was optimized. For mutant screening, the least fit mutant and wildtype parent were cultured individually and then added to the microfluidic device. The mother machines which were seeded with mutant and wildtype were imaged through time lapse microscopy and the growth of cells was observed. For antibiotic screening, wildtype E.coli cells which were grown overnight were added to the device and washed with media containing the antibiotic ampicillin. The growth pattern in presence and absence of ampicillin was observed through time lapse microscopy. It was observed that over a period of four hours, both the mutant and the wildtype divided in the mother machine and pushed daughter cells out into the interaction zone. In case of the antibiotic screening experiment, the fluorescent wildtype divided both in the absence and presence of sublethal concentration of ampicillin. This study is a proof of concept demonstration of high- throughput single cell analysis of cells using a novel microfluidics device.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of Production Strains of Chlamydomonas Using Breeding Technologies

Chlamydomonas is a well-studied strain with excellent breeding capability. It can produce recombinant proteins in the raceway in the greenhouse. Increasing the pH of the culture resulted in a very stable cultivation process and cultures did not crash. This strain was not tolerant of high UV levels at KAF. This is can be probably easily overcome by breeding with a light tolerant strain. Overall Chlamydomonas is a very promising strain for production of recombinant proteins not only in the lab but also outdoors. It has excellent breeding capability and its progeny expressed the introduced protein for a long tiem. Chlamydomonas sp. produced lipids but overall lipid yield was low with highest lipid content of 15%. Chlamydomonas is a genus with a great potential for production of various specific proteins. It can be potentially cultivated outdoors and should be further investigated for production of specific molecules.

09 BIOMASS FUELS↗
DOE OSTI2025

New NDA Methods for Thorium Fuel Cycle Safeguards (Final Report)

This project developed portable Neutron Resonance Transmission Analysis (pNRTA) as a new non-destructive assay (NDA) method for thorium fuel cycles safeguards and other applications where multiple isotopes must be measured when present together. pNRTA leverages epithermal neutron resonances to assay multiple safeguards-relevant isotopes (e.g., 233 U and 235 U) when they are present together in a sample. Existing techniques are challenged by this task, driving the need for new active interrogation methods. With selected detectors, pNRTA works in high gamma-ray backgrounds from fission and activation products and 232 U progeny expected in thorium fuel cycle samples. This project leveraged a pNRTA system developed at Pacific Northwest National Laboratory (PNNL) and collaboration with the Massachusetts Institute of Technology (MIT). The system uses a commercially available deuterium-tritium (DT) neutron generator at short standoff (2 m). Key achievements in this project included: first-of-a-kind pNRTA quantitative measurements of 233 U oxide samples, an assessment of neutron detector technologies suitable for pNRTA in high gamma-ray background environments, experimentally demonstrating quantitative assay of samples containing 233 U and 235 U, and modeling studies showing the applicability of pNRTA to a wide range of material forms. Further, a custom algorithm was developed at MIT, which provided mean bias of 9% and relative standard deviation of 36% in assaying 233 U, 235 U, 238 U, and 232 Th content in eight measured samples. These outcomes form a solid technical basis for pNRTA as a new promising capability for international safeguards verification that is portable, non-destructive, quantitative, and isotopic specific.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗