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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Installation of the Dark Energy Spectroscopic Instrument at the Mayall 4-meter telescope

The Dark Energy Spectroscopic Instrument (DESI) is a Stage IV ground-based dark energy experiment that will measure the expansion history of the Universe using the Baryon Acoustic Oscillation technique. The spectra of 35 million galaxies and quasars over 14000 square degrees will be measured during the life of the experiment. We describe the installation of the major elements of the instrument at the Mayall 4m telescope, completed in late 2019. The previous prime focus corrector, spider vanes, and upper rings were removed from the Mayall’s Serrurier truss and replaced with the newlyconstructed DESI ring, vanes, cage, hexapod, and optical corrector. The new corrector was optically aligned with the primary mirror using a laser tracker system. The DESI focal plane system was integrated to the corrector, with each of its ten 500-fiber-positioner petal segments installed using custom installation hardware and the laser tracker. Ten DESI spectrographs with 30 cryostats were installed in a newly assembled clean room in the Large Coude Room. The ten cables carrying 5000 optical fibers from the positioners in the focal plane were routed down the telescope through cable wraps at the declination and hour angle axes, and their integral slitheads were integrated with the ten spectrographs. The fiber view camera assembly was installed to the Mayall’s primary mirror cell. Servers for the instrument control system replaced existing computer equipment. The fully integrated instrument has been commissioned and is ready to start its operations phase.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Dates and rates of loess deposition and soil formation on the Snake River Plain, Idaho, USA

Loess-paleosol sequences in eolian deposits on the Snake River Plain, Idaho, western United States, preserve records of late Pleistocene to Holocene glacial-interglacial cycles. Here, we examine climate-driven changes in the timing and rate of loess accretion, soil formation, and pedogenic carbonate accumulation in the eastern and central Snake River Plain. High rates of loess deposition often correspond with dry, cold, and windy conditions and/or high sediment supply, while soil formation indicates landscape stability. Optically stimulated luminescence dating of four loess-soil sequences provides a record of the timing of loess deposition, and radiocarbon dating ( 14 C) of soil inorganic carbon provides ages for soil formation and pedogenic carbonate precipitation. On the central Snake River Plain, marine isotope stage (MIS) 3 is marked by loess deposition between ca. 50 ka and 33 ka, and pedogenic carbonate accumulation between ca. 42 ka calibrated years before present (cal. B.P.) and 31 ka cal. B.P. During MIS 2, loess deposition between ca. 21 ka and 15 ka is contemporaneous with pedogenic carbonate precipitation. MIS 2 is characterized by diffuse pedogenic carbonate formation and rapid loess accumulation. Both the eastern and central Snake River Plain study sites experienced high rates of loess deposition during MIS 2; however, the eastern Snake River Plain had almost three times faster rates of loess accumulation (0.56−0.63 m/k.y. from ca. 25 ka to 17 ka) as compared to the central Snake River Plain (0.18−0.26 m/k.y. from ca. 21 ka to 15 ka). During MIS 1, loess deposition on the central Snake River Plain ca. 11 ka was coincident with pedogenic carbonate formation ca. 10 ka cal. B.P. MIS 3 and MIS 1 are characterized by A horizons and well-developed Bk horizons, indicating soil stability and lower rates of loess accumulation during these intervals. Finally, this study highlights the role of late Quaternary−scale climatic variability on rates and amounts of soil inorganic carbon storage.

Geosciences↗
DOE OSTI2022

The Evolving Chronology of Moon Formation

Defining the age of the Moon has proven to be an elusive task because it requires reliably dating lunar samples using radiometric isotopic systems that record fractionation of parent and daughter elements during events that are petrologically associated with planet formation. Crystallization of the magma ocean is the only event that unambiguously meets this criterion because it probably occurred within tens of millions of years of Moon formation. There are three dateable crystallization products of the magma ocean: mafic mantle cumulates, felsic crustal cumulates, and late-stage crystallization products known as urKREEP (uniform residuum K, rare earth elements, and P). Although ages for these materials in the literature span 200 million years, there is a preponderance of reliable ages around 4.35 billion years recorded in all three lunar rock types. This age is also observed in many secondary crustal rocks, indicating that they were produced contemporaneously (within uncertainty of the ages), possibly during crystallization and overturn of the magma ocean. •The duration of planet formation is key information in understanding the mechanisms by which the terrestrial planets formed. •Ages of the oldest lunar rocks range widely, reflecting either the duration of Moon formation or disturbed ages caused by impact metamorphism. •Ages determined for compositionally distinct crust and mantle materials produced by lunar magma ocean differentiation cluster near 4.35 Gyr. •The repeated occurrence of 4.35 Gyr ages implies that Moon formation occurred late in Solar System history, likely by giant impact into Earth.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Fracture, Dissolution, and Cementation Events in Ordovician Carbonate Reservoirs, Tarim Basin, NW China

Ordovician carbonate rocks of the Yijianfang Formation in the Tabei Uplift, Tarim Basin, contain deeply buried (>6000 m), highly productive oil and gas reservoirs associated with large cavities (>10 m). Previous workers inferred that large cavities are paleocaves (paleokarst) formed near the surface and subsequently buried. Alternately, caves may have formed by dissolution at depth along faults. Using 227 samples from 16 cores, we document textures and cement compositions bearing on cavity histories with petrographic, high-resolution scanning electron microscopy (SEM), isotopic, and fluid inclusion microthermometric observations. Results show that dissolution occurred at depth and was caused by (1) acidic fluids derived from Middle-Late Silurian and/or Devonian-Permian hydrocarbon generation and maturation, (2) high-temperature fluids, of which some were associated with Late Permian igneous activity, and (3) Mg-rich fluids that accompanied Jurassic-Cretaceous deformation and the formation of partially open fractures and stylobreccias (fault breccias). The relative paragenetic sequence of the structure-related diagenesis suggests seven stages of fracturing, dissolution, and cementation. Mottle fabrics in the Yijianfang Formation contain argillaceous carbonate-rich silt and are bioturbation features formed within the marine environment. Those mottled fabrics differ from clearly karstic features in the overlying Lianglitage Formation, which formed by near-surface dissolution and subsequent infilling of cavities by allochthonous sediment. Mottle fabrics are crosscut by compacted fractures filled with phreatic-vadose marine cements and followed by subsequent generations of cement-filled fractures and vugs indicating that some fractures and vugs became cement filled prior to later dissolution events. Calcite cements in fractures and vugs show progressively depleted values of δ18O documenting cement precipitation within the shallow (~220 m), intermediate (~625 m), and deep (~2000 m) diagenetic environments. Deep (mesogenetic) dissolution associated with fractures is therefore the principal source of the high porosity-permeability in the reservoir, consistent with other pieces of evidence for cavities localized near faults.

58 GEOSCIENCES↗
DOE OSTI2022

MRI-Based Radiotherapy Planning to Reduce Rectal Dose in Excess of Tolerance

Background and Purpose. Chronic rectal toxicity significantly decreases the quality of life for men who receive radiotherapy for prostate cancer. The most significant predictor of rectal toxicity is rectal dose-volume exceeding tolerance. To minimize the volume of rectum in the high dose field, it is essential to accurately define the prostate-rectum interface. This can be challenging to do by computed tomography (CT) imaging alone. The current study was undertaken to formally demonstrate in a clinical trial setting that image-guided intensity-modulated radiation therapy (IG-IMRT) planning using magnetic resonance imaging (MRI) can reduce the volume of rectum exceeding 70 Gy, a validated metric that predicts the risk of late rectal toxicity. Materials and Methods. This prospective single-arm study enrolled 15 men treated with IG-IMRT for localized prostate cancer. All participants received a dedicated 3 Tesla MRI examination of the prostate in addition to a pelvic CT examination for treatment planning. Two volumetric modulated arc therapy (VMAT) plans with a prescription dose of 79.2 Gy were designed using identical constraints based on CT- and MRI-defined consensus volumes. The volume of rectum exposed to 70 Gy or more was compared using the Wilcoxon paired signed rank test. Results. For CT-based treatment plans, the median volume of rectum receiving 70 Gy or more was 9.3 cubic centimeters (cc) (IQR 7.0 to 10.2) compared with 4.9 cc (IQR 4.1 to 7.8) for MRI-based plans. This resulted in a median volume reduction of 2.1 cc (IQR 0.5 to 5.3, P < .001). Conclusions. Using MRI to plan prostate IG-IMRT to a dose of 79.2 Gy reduces the volume of rectum receiving radiation dose in excess of tolerance (70 Gy or more) and should be considered in men who are at high risk for late rectal toxicity and are not good candidates for other rectal sparing techniques such as hydrogel spacer. This trial is registered with NCT02470910.

Schmidt, Daniel R.↗
DOE OSTI2025

Pathogenic SIV infection is associated with acceleration of epigenetic age in rhesus macaques

HIV infection accelerates biological aging, but the contribution of the host’s age to this process is unknown. We investigated the influence of SIV infection in macaques (SIVmac) on the risk of comorbidities and aging in young and old rhesus macaques (RMs) by assessing pathogenesis markers, DNA methylation–based epigenetic age (EA), and EA acceleration (EAA) in blood and tissues. Initially, upon SIV infection, the young RMs showed greater resilience to CD4 + T cell depletion, better control of T cell activation, hypercoagulation, and excessive inflammation, yet this resilience was progressively lost in the advanced stages of infection. During the late stages of infection, the young RMs, but not the aged ones, showed an increase in EA in PBMCs; also, EAA in the cerebellum and heart of young RMs was higher compared with old RMs. SIV infection was more pathogenic in aged animals in early stages, leading to a more rapid disease progression; however, accelerated aging mostly affected young animals, so that the levels of multiple key pathogenesis markers in the young RMs converged toward those specific to aged ones in the late stages of infection. We conclude that SIV infection–driven age acceleration is tissue specific, and that host age influences the susceptibility of different tissues to enhanced aging.

Research & Experimental Medicine↗
DOE OSTI2020

Sea Level Rise in the CESM Large Ensemble: The Role of Individual Climate Forcings and Consequences for the Coming Decades

The emergence of a spatial pattern in the externally forced response (FR) of dynamic sea level (DSL) during the altimeter era has recently been demonstrated using climate models but our understanding of its initial emergence, drivers, and implications for the future is poor. Here the anthropogenic forcings of the DSL pattern are explored using the Community Earth System Model Large Ensemble (CESM-LE) and Single-Forcing Large Ensemble, a newly available set of simulations where values of individual forcing agents remain fixed at 1920 levels, allowing for an estimation of their effects. Statistically significant contributions to the DSL FR are identified for greenhouse gases (GHGs) and industrial aerosols (AERs), with particularly strong contributions resulting from AERs in the mid-twentieth century and GHGs in the late twentieth and twenty-first century. Secondary, but important, contributions are identified for biomass burning aerosols in the equatorial Atlantic Ocean in the mid-twentieth century, and for stratospheric ozone in the Southern Ocean during the late twentieth century. Key to understanding regional DSL patterns are ocean heat content and salinity anomalies, which are driven by surface heat and freshwater fluxes, ocean dynamics, and the spatial structure of seawater thermal expansivity. Finally, potential implications for the interpretation of DSL during the satellite era and the longer records from tide gauges are suggested as a topic for future research.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

East Asian Rainbands and Associated Circulation over the Tibetan Plateau Region

Abstract Rainbands that migrate northward from spring to summer are persistent features of the East Asian summer monsoon. This study employs a machine learning algorithm to identify individual East Asian rainbands from May to August in the 6-hourly ERA-Interim reanalysis product and captures rainband events during these months for the period 1979–2018. The median duration of rainband events at any location in East Asia is 12 h, and the centroids of these rainbands move northward continuously from approximately 28°N in late May to approximately 33°N in July, instead of making jumps between quasi-stationary periods. Whereas the length and overall area of the rainbands grow monotonically from May to June, the intensity of the rainfall within the rainband dips slightly in early June before it peaks in late June. We find that extratropical northerly winds on all pressure levels over East China are the most important anomalous flow accompanying the rainband events. The anomalous northerlies augment climatological background northerlies in bringing low moist static energy air and thus generate the front associated with the rainband. Persistent lower-tropospheric southerly winds bring in moisture that feeds the rainband and are enhanced a few days prior to rainband events, but they are not directly tied to the actual rainband formation. The background northerlies could originate as part of the Rossby waves resulting from the jet stream interaction with the Tibetan Plateau. The ageostrophic circulation in the jet entrance region peaks in May and weakens in June and July and does not prove to be critical to the formation of the rainbands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Land–Atmosphere Coupling at the U.S. Southern Great Plains: A Comparison on Local Convective Regimes between ARM Observations, Reanalysis, and Climate Model Simulations

Using the 9-yr warm-season observations at the Atmospheric Radiation Measurement Southern Great Plains site, in this work we assess the land–atmosphere (LA) coupling in the North American Regional Reanalysis (NARR) and two climate models: hindcasts with the Community Atmosphere Model version 5.1 by Cloud-Associated Parameterizations Testbed (CAM5-CAPT) and nudged runs with the Energy Exascale Earth System Model Atmosphere Model version 1 Regionally Refined Model (EAMv1-RRM). We focus on three local convective regimes and diagnose model behaviors using the local coupling metrics. NARR agrees well with observations except a slightly warmer and drier surface with higher downwelling shortwave radiation and lower evaporative fraction. On clear-sky days, it shows warmer and drier early-morning conditions in both models with significant underestimates in surface evaporation by EAMv1-RRM. On the majority of the ARM-observed shallow cumulus days, there is no or little low-level clouds in either model. When captured in models, the simulated shallow cumulus shows much less cloud fraction and lower cloud bases than observed. On the days with late-afternoon deep convection, models tend to present a stable early-morning lower atmosphere more frequently than the observations, suggesting that the deep convection is triggered more often by elevated instabilities. Generally, CAM5-CAPT can reproduce the local LA coupling processes to some extent due to the constrained early-morning conditions and large-scale winds. EAMv1-RRM exhibits large precipitation deficits and warm and dry biases toward mid-to-late summers, which may be an amplification through a positive LA feedback among initial atmosphere and land states, convection triggering and large-scale circulations.

58 GEOSCIENCES↗
DOE OSTI2021

Performance of direct injected propane and gasoline in a high stroke-to-bore ratio SI engine: Pathways to diesel efficiency parity with ultra low soot

This work explores pathways to achieve diesel-like, high-efficiency combustion with stoichiometric 3-way catalyst compatible combustion in a single-cylinder spark ignition (SI) research engine. A unique high stroke-to-bore engine design (1.5:1) with cooled exhaust gas recirculation (EGR) and high compression ratio ( r c ) was used to improve engine efficiency by up to 30% compared with a production turbocharged gasoline direct injection spark ignition engine. Engine experiments were conducted with both 91 RON E10 gasoline and liquified petroleum gas (LPG) (i.e. autogas) and were compared to legacy gasoline data on the production engine. Geometric compression ratio ( r c ) of 13.3:1 was used for both fuels with additional experiments at 16.8:1 for LPG only. Measurements of exhaust soot particle size and number concentrations were made with both fuels. Significant reduction in soot particles across the whole particle size range were achieved with LPG due to the elimination of in-cylinder liquid films. The effects of EGR, late intake valve closing (IVC) and fuel characteristics were investigated through their effects on efficiency, combustion stability and soot production. Results of 47% gross thermal efficiency, and 45% net thermal efficiency at stoichiometric engine operation, at up to 17 bar IMEP and 2000 r/min with 16.8:1 r c were achieved with LPG. Estimated brake efficiency values were compared to a contemporary medium duty diesel engine illustrating the benefits of the chosen path for achieving diesel efficiency parity.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Cycle-to-cycle variability in spark-assisted compression ignition engines near optimal mean combustion phasing

Stoichiometric spark-assisted compression ignition (SACI) combustion with exhaust gas recirculation (EGR) dilution has demonstrated higher part-load thermal efficiencies compared to spark-ignited engines, while maintaining ultra-low tailpipe emissions. However, SACI is often characterized by high cyclic variability in heat release or torque output, which poses a challenge to its implementation in light-duty vehicles. This paper presents an experimental investigation of cyclic variability in stoichiometric SACI combustion under EGR-dilute conditions, while maintaining mean combustion phasing (θ 50 ) near optimal timing for thermal efficiency. The present work focuses on SACI conditions where the flame-based heat release fraction is between approximately 10% and 40% of the overall heat release, and therefore contributes significantly to the combustion process. For the SACI conditions examined, the variability in θ 50 was driven by variability in autoignition timing, which in turn correlated with the start of measurable heat release (θ 02 ). High variability in θ 50 caused unstable work output due to very late combustion with poor or no end-gas autoignition. The use of a high ignition energy dual-coil offset ignition system had negligible impact in reducing θ 50 variability. Analysis of experimental data from close to 1000 operating conditions showed that the magnitude of θ 50 variability correlates with the flame-based heat release fraction ([Formula: see text]), for a large range of intake pressures, spark timings and exhaust gas recirculation levels. For the SACI conditions examined, combustion phasing variability was largely determined by flame-based combustion and particularly the initial flame formation (θ IGN-02 ), and minimally by the end-gas autoignition heat release. The analysis also demonstrated that θ 50 variability is amplified as the contribution of the flame to the overall heat release increases.

Engineering↗
DOE OSTI2023

Parametric evaluation of ducted fuel injection in an optically accessible mixing-controlled compression-ignition engine with two- and four-duct assemblies

Ducted fuel injection (DFI) is a strategy to improve fuel/charge-gas mixing in direct-injection compression-ignition engines. DFI involves injecting fuel along the axis of a small tube in the combustion chamber, which promotes the formation of locally leaner mixtures in the autoignition zone relative to conventional diesel combustion. Previous work has demonstrated that DFI is effective at curtailing engine-out soot emissions across a wide range of operating conditions. This study extends previous investigations, presenting engine-out emissions and efficiency trends between ducted two-orifice and ducted four-orifice injector tip configurations. For each configuration, parameters investigated include injection pressure, injection duration, intake manifold pressure, intake manifold temperature, start of combustion timing, and intake-oxygen mole fraction. For both configurations and across all parameters, DFI reduced engine-out soot emissions compared to conventional diesel combustion, with little effect on other emissions and engine efficiency. Emissions trends for both configurations were qualitatively the same across the parameters investigated. The four-duct configuration had higher thermal efficiency and indicated-specific engine-out nitrogen oxide emissions but lower indicated-specific engine-out hydrocarbon and carbon monoxide emissions than the two-duct assembly. Both configurations achieved indicated-specific engine-out emissions for both soot and nitrogen oxides that comply with current on- and off-road heavy-duty regulations in the United States without exhaust-gas aftertreatment at an intake-oxygen mole fraction of 12%. High-speed in-cylinder imaging of natural soot luminosity shows that some conditions include a second soot-production phase late in the cycle. The probability of these late-cycle events is sensitive to both the number of ducted sprays and the operating conditions.

Yraguen, Boni Frances↗
DOE OSTI2023

Modeling the impact of the fuel injection strategy on the combustion and performance characteristics of a heavy-duty GCI engine

Gasoline compression ignition (GCI) is a promising strategy to achieve high thermal efficiency and low emissions with limited modifications to the conventional diesel engine hardware. It is a partially premixed concept, which derives its superiority from higher volatility and longer ignition delay of gasoline-like fuels combined with higher compression ratio typical of diesel engines. Here, the present study investigates the combustion process in a GCI engine operating with different injection strategies using computational fluid dynamics (CFD). Simulations are carried out on a single cylinder of a multi cylinder heavy-duty compression ignition engine, which operates at a compression ratio of 17:1 and an engine speed of 1038 rev/min. Two different injection strategies viz., late injection (LI), and early pilot injection (EP) are investigated to understand their impact on combustion and performance of the engine. Renormalized group (RNG) k-ε model is used to describe in-cylinder turbulence and KH RT model is used to simulate the fuel spray breakup. The developed CFD methodology is validated against relevant experimental data under a wide range of operating conditions for each injection strategy. The developed CFD methodology was found to capture the engine combustion behavior quite well. Based on the validated CFD model, the differences in the progress of combustion event for the two injection strategies is highlighted. It was found that a larger pilot fuel mass fraction results in a steeper rise in the initial heat release rate which in turn influences the transition to mixing controlled combustion. In line with the experimental data, the study showed that the late pilot injection strategy with three injection pulses, results in higher performance compared to the other conditions.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

Mapping ammonia-diesel combustion on a single-cylinder 107 mm bore diesel engine retrofitted for ammonia port-fuel injection

Ammonia is garnering significant interest from the international maritime sector as an alternative fuel. It is attractive as a hydrogen carrier and as a fuel because it has a higher volumetric energy density compared with gaseous or liquid hydrogen, making it easier to store and transport without requiring high pressures or cryogenic storage. Ammonia has significant toxicity concerns, but safe handling procedures have already been established because it is one of the most widely produced chemicals worldwide for use as a fertilizer. Barriers to consuming NH 3 as a fuel in engines include (1) less favorable ignition energy and flame speed compared with conventional fuels; (2) emissions challenges, including potentially high NH 3 , NO X , and N 2 O emissions; and (3) fuel delivery and handling challenges. Although NH 3 has been used to fuel compression-ignition marine engines in limited demonstration projects, technical barriers still exist. The use of NH 3 as a fuel in smaller-bore, high-speed auxiliary engines for large vessels and for smaller inland and coastal marine applications remains unaddressed. This work investigates a late-injection diesel pilot ignition dual-fuel NH 3 strategy using a single-cylinder, high-speed Cummins four-stroke diesel engine platform with a 107 mm bore and 1.1 L displacement per cylinder. The engine was modified for port fuel injection of heated gaseous anhydrous NH 3 . The diesel fuel injection system and the combustion geometry were unmodified to represent a retrofit application, which would minimize additional hardware to maximize diesel fuel displacement with NH 3 . Furthermore, the results show the applicability of a late injection diesel pilot strategy to overcome the challenging fuel properties of NH 3 over the engine operating envelope. Mapping results focusing on emissions are presented, and comparisons are made to a conventional diesel combustion baseline.

Ship engines↗
DOE OSTI2023

Long-term ultrasonic monitoring of concrete affected by alkali-silica reaction

This article presents continuous monitoring results of alkali-silica reaction (ASR) development in concrete specimens for over 400 days using ultrasonic testing and expansion measurements. Eight concrete specimens with nonreactive aggregate (Control), reactive coarse aggregate, and reactive fine aggregates were cast with two reinforced confinement conditions. The specimens were conditioned in an environmental chamber with high temperature and humidity (38°C and 90% relative humidity) to accelerate the ASR development. A multichannel ultrasonic monitoring system was developed to collect ultrasonic signals automatically, and the expansions in three directions were measured periodically. Results showed that the relative velocity change could detect the ASR initiation in all reactive specimens and show a correlation with expansion in the early stage. However, these correlations are inconsistent for different ASR specimens, and the velocity change becomes less sensitive to ASR damage in the late stage (after 300 days). Irrecoverable velocity drop was observed during every chamber shutdown period, especially in specimens with higher levels of ASR damage. This phenomenon suggests that the nonlinear ultrasonic response caused by the ambient temperature variation may indicate the ASR damage.

Engineering↗
DOE OSTI2021

De novo transcriptome in roots of switchgrass ( Panicum virgatum L. ) reveals gene expression dynamic and act network under alkaline salt stress

Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

Background: Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93–1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding.Results: A total of 34 progeny lines from SW93–1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate.Conclusion: In our study, we identify 100’s of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

When to vaccinate for seasonal influenza: check the peak forecast

Background Seasonal influenza infects 5-20% of people every year in the United States, resulting in hospitalizations, deaths, and adverse economic impacts. To mitigate these impacts, influenza vaccines are developed and distributed annually; however, growing evidence suggests that vaccine effectiveness (VE) wanes over the course of a flu season. Delaying influenza vaccination for older adults has attracted attention as a potential public health strategy. However, given the uncertainties in seasonal peak, vaccine effectiveness, and waning rates, postponing vaccination could also lead to increased morbidity, motivating an evaluation of a range of potential scenarios. The aim of this study was to investigate favorable age group-specific vaccination schedules that could lead to the greatest disease burden reduction. Methods We systematically investigated a broad range of vaccination start times for five age groups under six combinations of initial effectiveness and waning rates, based on influenza cases and vaccine uptake data from 10 influenza seasons. We defined the most favorable vaccination schedule as the one that resulted in the greatest reduction in disease burden. Results In scenarios with fast waning, all age groups benefit from delaying vaccination regardless of initial VE and peak timing. In scenarios with slower waning, results are mixed. For the ≥65 group, high initial VE and slow waning suggests that in early-peaking seasons, early vaccination most effectively reduces disease burden, while in late-peaking seasons delaying vaccination is most effective. For the ≥65 group in medium and low initial VE, and slow waning scenarios, delaying vaccination appears to prevent the greatest number of cases, regardless of whether the season peaks early or late. Conclusion The most favorable vaccination schedule is sensitive to changes in initial VE, waning rate, and peak timing. Given estimates of these quantities from statistical and immunological models and observations, our methods can inform vaccination recommendations in order to most effectively reduce the annual disease burden caused by seasonal influenza. Specifically, accurate peak timing forecasts for the upcoming season have the potential to guide decisions on when to vaccinate.

59 BASIC BIOLOGICAL SCIENCES↗