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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Survival, healing, and swim performance of juvenile migratory sea lamprey ( Petromyzon marinus ) implanted with a new acoustic microtransmitter designed for small eel-like fishes

Background: Little is known about the transformer stage of the parasitic lampreys, a brief but critical period that encompasses juvenile out-migration from rivers to lakes or oceans to begin parasitic feeding. Information about this life stage could have significant conservation implications for both imperiled and invasive lampreys. We investigated tag retention, survival, wound healing, and swim performance of newly transformed sea lamprey (Petromyzon marinus) implanted with a new micro-acoustic transmitter, the eel–lamprey acoustic transmitter (ELAT), in a controlled laboratory environment. Results: The 61-day survival of our tagged subjects was 71%, within the range reported in similar studies of juvenile lampreys. However, survival was significantly lower in the tagged animals (vs control), with no effect statistically attributable to measures of animal length, mass, condition, or population of origin (Great Lakes vs. Atlantic drainage). Mortality in tagged fish was concentrated in the first four days post-surgery, suggesting injury from the surgical process. An unusually long recovery time from anesthesia may have contributed to the increased mortality. In a simple burst swim assay, tagged animals swam significantly slower (– 22.5%) than untagged animals, but were not significantly different in endurance swim tests. A composite wound healing score at day four was a significant predictor of maximum burst swim speed at day 20, and wound condition was related to animal mass, but not length, at the time of tagging. Conclusions: Impairments to survival and swim performance of juvenile sea lamprey implanted with the ELAT transmitter were within currently reported ranges for telemetry studies with small, difficult to observe fishes. Our results could be improved with more refined anesthesia and surgical techniques. The ability to track migratory movements of imperiled and pest populations of parasitic lampreys will improve our ability to estimate vital rates that underlie recruitment to the adult population (growth, survival) and to investigate the environmental factors that regulate the timing and rates of movement, in wild populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The role of memory in non-genetic inheritance and its impact on cancer treatment resistance

Intra-tumour heterogeneity is a leading cause of treatment failure and disease progression in cancer. While genetic mutations have long been accepted as a primary mechanism of generating this heterogeneity, the role of phenotypic plasticity is becoming increasingly apparent as a driver of intra-tumour heterogeneity. Consequently, understanding the role of this plasticity in treatment resistance and failure is a key component of improving cancer therapy. We develop a mathematical model of stochastic phenotype switching that tracks the evolution of drug-sensitive and drug-tolerant subpopulations to clarify the role of phenotype switching on population growth rates and tumour persistence. By including cytotoxic therapy in the model, we show that, depending on the strategy of the drug-tolerant subpopulation, stochastic phenotype switching can lead to either transient or permanent drug resistance. We study the role of phenotypic heterogeneity in a drug-resistant, genetically homogeneous population of non-small cell lung cancer cells to derive a rational treatment schedule that drives population extinction and avoids competitive release of the drug-tolerant sub-population. This model-informed therapeutic schedule results in increased treatment efficacy when compared against periodic therapy, and, most importantly, sustained tumour decay without the development of resistance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Automated pipeline framework for processing of large-scale building energy time series data

Commercial buildings account for one third of the total electricity consumption in the United States and a significant amount of this energy is wasted. Therefore, there is a need for “virtual” energy audits, to identify energy inefficiencies and their associated savings opportunities using methods that can be non-intrusive and automated for application to large populations of buildings. Here we demonstrate virtual energy audits applied to large populations of buildings’ time-series smart-meter data using a systematic approach and a fully automated Building Energy Analytics (BEA) Pipeline that unifies, cleans, stores and analyzes building energy datasets in a non-relational data warehouse for efficient insights and results. This BEA pipeline is based on a custom compute job scheduler for a high performance computing cluster to enable parallel processing of Slurm jobs. Within the analytics pipeline, we introduced a data qualification tool that enhances data quality by fixing common errors, while also detecting abnormalities in a building’s daily operation using hierarchical clustering. We analyze the HVAC scheduling of a population of 816 buildings, using this analytics pipeline, as part of a cross-sectional study. With our approach, this sample of 816 buildings is improved in data quality and is efficiently analyzed in 34 minutes, which is 85 times faster than the time taken by a sequential processing. The analytical results for the HVAC operational hours of these buildings show that among 10 building use types, food sales buildings with 17.75 hours of daily HVAC cooling operation are decent targets for HVAC savings. Overall, this analytics pipeline enables the identification of statistically significant results from population based studies of large numbers of building energy time-series datasets with robust results. These types of BEA studies can explore numerous factors impacting building energy efficiency and virtual building energy audits. This approach enables a new generation of data-driven buildings energy analysis at scale.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cumulative effects of piscivorous colonial waterbirds on juvenile salmonids: A multi predator-prey species evaluation

We investigated the cumulative effects of predation by piscivorous colonial waterbirds on the survival of multiple salmonid ( Oncorhynchus spp.) populations listed under the U.S. Endangered Species Act (ESA) and determined what proportion of all sources of fish mortality (1 –survival) were due to birds in the Columbia River basin, USA. Anadromous juvenile salmonids (smolts) were exposed to predation by Caspian terns ( Hydroprogne caspia ), double-crested cormorants ( Nannopterum auritum ), California gulls ( Larus californicus ), and ring-billed gulls ( L . delawarensis ), birds known to consume both live and dead fish. Avian consumption and survival probabilities (proportion of available fish consumed or alive) were estimated for steelhead trout ( O . mykiss ), yearling Chinook salmon ( O . tshawytscha ), sub-yearling Chinook salmon, and sockeye salmon ( O . nerka ) during out-migration from the lower Snake River to the Pacific Ocean during an 11-year study period (2008–2018). Results indicated that probabilities of avian consumption varied greatly across salmonid populations, bird species, colony location, river reach, and year. Cumulative consumption probabilities (consumption by birds from all colonies combined) were consistently the highest for steelhead, with annual estimates ranging from 0.22 (95% credible interval = 0.20–0.26) to 0.51 (0.43–0.60) of available smolts. The cumulative effects of avian consumption were significantly lower for yearling and sub-yearling Chinook salmon, with consumption probabilities ranging annually from 0.04 (0.02–0.07) to 0.10 (0.07–0.15) and from 0.06 (0.3–0.09) to 0.15 (0.10–0.23), respectively. Avian consumption probabilities for sockeye salmon smolts was generally higher than for Chinook salmon smolts, but lower than for steelhead smolts, ranging annually from 0.08 (0.03–0.22) to 0.25 (0.14–0.44). Although annual consumption probabilities for birds from certain colonies were more than 0.20 of available smolts, probabilities from other colonies were less than 0.01 of available smolts, indicating that not all colonies of birds posed a substantial risk to smolt mortality. Consumption probabilities were lowest for small colonies and for colonies located a considerable distance from the Snake and Columbia rivers. Total mortality attributed to avian consumption was relatively small for Chinook salmon (less than 10%) but was the single greatest source of mortality for steelhead (greater than 50%) in all years evaluated. Results suggest that the potential benefits to salmonid populations of managing birds to reduce smolt mortality would vary widely depending on the salmonid population, the species of bird, and the size and location of the breeding colony.

Evans, Allen F.↗
DOE OSTI2020

Background Data and Statistics on Low-Income Energy Use and Burden for the Weatherization Assistance Program: Update for Fiscal Year 2020

This report provides updated estimates of the energy consumptions, energy expenditures, and energy burdens of the population eligible to be served through the US Department of Energy (DOE) Weatherization Assistance Program (WAP) and by proxy, those clients actually served by the program. WAP continues to serve a population with an energy burden that is much greater than the rest of the county. The mean energy burden for the WAP-eligible population across the United States for FY 2020 is estimated to be 13.9% compared to 3.0% for households living above the 200% poverty threshold. The mean energy burden for households living below the 100% federal poverty line was estimated to be 30.9%. These energy burdens for the WAP-eligible population have remained steady at this high level over the last decade.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Scat Detection Dog Surveys for the San Joaquin Kit Fox on the Lawrence Livermore National Laboratory's Experimental Test Site (Site 300) and the Corral Hollow Ecological Reserve: 2020 Deployment

The San Joaquin kit fox (Vulpes macrotis mutica) historically occupied an extensive range in the San Joaquin Valley, California; however, their populations and habitat have since been significantly reduced by human impacts (United States Fish and Wildlife Service [USFWS] 1998). More than 95% of the potential habitat for kit foxes on the San Joaquin Valley floor has been converted to irrigated agriculture, urbanized, or industrialized lands. The San Joaquin kit fox was listed as endangered by the USFWS in 1967 and as threatened by the State of California in 1971. Records from local surveys, research projects, and incidental sightings indicate the present distribution of kit foxes extends from 1) southern Kern County north to Contra Costa, Alameda, and San Joaquin counties on the west side of the valley and to Stanislaus County on the east side; 2) into some of the larger, uncultivated valley-floor land parcels in Kern, Tulare, Kings, Fresno, Madera, and Merced counties; and 3) westward within 5 counties in the interior coastal range (USFWS 1998). Kit foxes have been denoted to occur in 3 geographically distinct core and several satellite populations in a heavily fragmented landscape, with the largest extant populations concentrated in the southern part of the range and smaller populations and isolated sightings in the central and northern portions (USFWS 1998, 2010).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

2018 Report on Rare Plant Monitoring and Restoration at the Lawrence Livermore National Laboratory’s Experimental Test Site (Site 300)

This document meets the reporting requirements of LLNL’s California Endangered Species Act Scientific, Educational, or Management Permit (No. 2081 (a)-15-005-RP) for 2018. Section A describes monitoring and field activities conducted by LLNL biologists at the Site 300 native and experimental populations and the Carnegie Canyon native population of the federally-endangered plant, Amsinckia grandiflora (the large-flowered fiddleneck), between January 2018 and December 2018. In addition, monitoring and field activities conducted by LLNL biologists at the Site 300 native populations of the rare plants Eschscholzia rhombipetala (the diamond-petaled California poppy) and Blepharizonia plumosa (the big tarplant) between January 2018 and December 2018 are described in Sections B and C, respectively. Both plants have a California Rare Plant Rank (CRPR) of 1B, which includes species that are rare or endangered throughout their range. California macrophylla (the round-leaved filaree), formerly had a CRPR of 1B, but was downgraded to CBR (Considered But Rejected) in December 2017, as the species was “too common statewide: counties that contain small, localized populations under severe threat should track C. macrophylla as a species of local concern” (California Native Plant Society, 2018). As C. macrophylla is widespread at Site 300 (Carlsen and Paterson, 2018), 2018 will be the final year of monitoring C. macrophylla at Site 300, the results of which are described in Section D. Monitoring of the Navarretia nigelliformis ssp. radians (adobe navarretia), a CRPR 1B species, is planned, and results will be included in future reports.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Small field campaign: aerosol – ice formation closure pilot study. Final Report

Prediction of atmospheric ice formation from aerosol particles by heterogeneous nucleation represents one of the grand challenges in atmospheric science. Our insufficient predictive understanding of primary ice formation is the reason that climate models typically do not include heterogeneous ice nucleation with subsequent effects on climate uncertainty. Mixed-phase clouds, where supercooled water droplets and ice crystals coexist play globally an important role regulating climate. This is especially the case for the Arctic region that experiences the greatest warming due to climate change compared to other regions in the world. Immersion freezing initiated by ice-nucleating particles (INPs) in supercooled water droplets is recognized as the dominant primary ice formation pathway in mixed-phase cloud regimes. For this reason, it is crucial to evaluate our capability to predict immersion freezing for a given ambient aerosol population. The goal of this project is conducting a field-based pilot study at the U.S. DOE Atmospheric Radiation Measurement (ARM) user facility at Southern Great Plains (SGP) to evaluate our capability to predict the number concentration of aerosol particles that serve as INPs in the immersion freezing mode. Successful prediction of INP number concentrations is also termed “closure”. This field-observational approach represents a first-of-its kind attempt of an aerosol–ice formation closure study (AEROICESTUDY). Very few closure studies related to INPs have been conducted, and to our knowledge, none using robust size-resolved ambient aerosol composition measurements as a starting point. Achievement of aerosol–ice formation closure relies on our ability to characterize the ambient aerosol population with respect to particles size and composition and to determine INP number concentrations for specified freezing temperatures. This requires numerous online and offline instrumentation resulting in this pilot field campaign being a multi-institutional and community-collaborative effort. We chose the ARM SGP megasite for this first aerosol-ice formation closure pilot study due to its significant measurement capabilities available to obtain detailed physical characterization of the local aerosol population including size distribution, mass loading, and chemical composition of non-refractory aerosol particles. The overall objective of this project is to identify ice nucleation parameterizations that produce the most robust predictions of INP numbers and thus are best suited to be included in cloud and climate models. This objective includes the following goals for this field and laboratory-based project: i) What are the crucial aerosol physicochemical property measurements needed to accurately guide ice nucleation representations in models and long-term INP measurements? ii) What level of parameter details needs to be known to achieve aerosol–ice formation closure? iii) What are the leading causes for climate model bias in INP predictions? We found that the advances in our understanding of immersion freezing garnered over the last 20 years allowed us to yield partial and full closures of atmospheric immersion freezing from ambient aerosol particles. When the aerosol population is physicochemically complex and parameterizations for representative INP types are not yet available, we still struggle to accurately predict INP number concentrations. This project clearly demonstrates that with more laboratory and field measurements that are accompanied by particle composition analysis, the necessary datasets to achieve aerosol–ice formation closure for various locations will emerge, thus providing a robust foundation for guiding the representation of INPs in cloud and climate models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Exploring Impacts to COVID-19 Herd Immunity Thresholds Under Demographic Heterogeneity that Lowers Vaccine Effectiveness

The COVID-19 pandemic has caused severe health, economic, and societal impacts across the globe. Although highly efficacious vaccines were developed at an unprecedented rate, the heterogeneity in vaccinated populations has reduced the ability to achieve herd immunity. Specifically, as of Spring 2022, the 0–4 year-old population is still unable to be vaccinated and vaccination rates across 5-11 year olds are low. Additionally, vaccine hesitancy for older populations has further stalled efforts to reach herd immunity thresholds. This heterogeneous vaccine landscape increases the challenge of anticipating disease spread in a population. We developed an age-structured Susceptible-InfectiousRecovered-type mathematical model to investigate the impacts of unvaccinated subpopulations on herd immunity. The model considers two types of undervaccination - age-related and behaviorrelated - by incorporating four age groups based on available FDA-approved vaccines. The model accounts for two different types of vaccines, mRNA (e.g., Pfizer, Moderna) and vector (e.g., Johnson and Johnson), as well as their effectiveness. Our goal is to analyze different scenarios to quantify which subpopulations and vaccine characteristics (e.g., rate or efficacy) most impact infection levels in the United States, using the state of New Mexico as an example.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An Assessment of Non-Powered Dam Hydropower Development Opportunities in the United States

Retrofitting non-powered dams (NPDs) to add hydropower offers multiple benefits over traditional, new hydropower development. Since much of the civil works infrastructure already exists, many retrofits require minimal new construction and can leverage existing water conveyances and discharge for generation. Although NPDs vary considerably in terms of their defining characteristics, identifying similarities helps support targeted investment and find opportunities to develop solutions for common challenges. With the publication of NPD-related data in 2022 (Hansen et al. 2022b), the US Department of Energy and relevant stakeholders are equipped with key information across roughly 89,000 US NPDs. These data represent the best-available information to date and extend beyond previous assessments of potential power capacity by describing design, operational, socioeconomic, environmental aspects of NPDs (Hadjerioua et al. 2012). To capitalize on these efforts to improve breadth and depth of NPD data access, this study uses a data-driven approach to assess NPD hydropower development opportunities in the United States. To help describe project feasibility drivers for NPDs, recent NPD retrofits were reviewed to examine variability with respect to a variety of characteristics. Based on the assessment of recent retrofits and data availability, several attributes were selected to characterize the remaining NPD population: (1) owner type, (2) 30% exceedance flow (a common design flow that describes the flow that is exceeded by 30% of the flow in the record), (3) hydraulic head, and (4) maximum reservoir storage. These four characteristics were used as inputs to a statistical clustering analysis (a common technique for grouping individuals of a population based on similarities or how closely associated individuals are to one another) of a set of 2,709 NPDs with at least 100 kW potential capacity and recently retrofit dams with available data. With the large dataset of NPDs, the clusters help describe how the population breaks down into different types (i.e., how many types of dams there are and what portion of the population belongs to each cluster).

13 HYDRO ENERGY↗
DOE OSTI2023

Vertical Aerosol Profiling during SAIL (VAPS) Field Campaign Report

To more fully address the science goals of the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility’s Surface Atmosphere Integrated Field Laboratory (SAIL) campaign, particularly the key science question of “How strongly do aerosols affect the surface energy and water balance by altering clouds, precipitation, and surface albedo, and how do these impacts vary seasonally?”, our campaign added instrumentation to planned tethered balloon system (TBS) flights in May and July of 2022. A key aspect of aerosol-cloud interactions is understanding cloud condensation nuclei (CCN) and ice nucleating particle (INP) populations, and how they vary seasonally and spatially. Because the interactions between aerosols and clouds is the target of this work, vertical distributions are particularly important to evaluate. Measurements of aerosol at ground level, below-cloud, and in-cloud will allow a better understanding of the airmasses that are feeding cloud-active particles into low- and mid-level clouds. Measurements of INP and aerosol populations often differ between the ground and aloft, with relationships that likely depend on regional and seasonal. Because of this, collocated measurements of aerosol, CCN, and INP, across different seasons, are crucial to reducing uncertainties in relationships between ground-level and cloud-base aerosol populations. Our campaign added online measurements of CCN using a compact CCN counter and offline filter collections for measurement of INP populations to the SAIL campaign TBS flights in May and July of 2022. The CCN instrument, the CloudPuck, flew and successfully collected data for a total of eight flights across both campaign periods. The IcePuck flew for most flights during the same period. Both instruments have continued to be used for other campaign requests in the SAIL domain. Analysis of this data was proposed through a concurrent DOE Atmospheric System Research (ASR) project submission, which was not funded in 2022. A similar proposal, which would involve analysis of the samples and data collected from this campaign, has been resubmitted in 2023 but a funding decision has not yet been made. If the proposal is again declined, we will seek other resources to ensure that this data can be analyzed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Estimating IDP Origins Using ACLED Political Violence Events: Validation with Lebanon IDP Flow Data

A key input in modeling population distribution and flows following conflict events is the inclusion of Internally Displaced Person (IDP) flows between administrative units within a country. These flows are critical for capturing population movement and redistribution driven by current events, particularly conflict. In some cases, IDP destination data are available while origin data is incomplete or unavailable. This creates a gap in understanding where displacement is occurring, limiting the ability to model population redistribution accurately. Without origin data, it is not possible to reallocate population flows or accurately represent where displacement is occurring within the country. This report evaluates whether Armed Conflict Location Event Data (ACLED) political violence event data can be used to estimate IDP origin distributions when direct origin data are unavailable. The approach is validated using historical IDP flow data from Lebanon, where both origins and destinations are observed. Results show that ACLED event distributions strongly correspond to observed IDP-origin patterns, particularly when using cumulative 60-day event windows. The method is most reliable for identifying major origin districts and approximating proportional origin shares. However, it is not intended to reconstruct exact individual displacement flows, but rather to provide a probabilistic spatial allocation of displacement origins.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Likeness: a toolkit for connecting the social fabric of place to human dynamics

The ability to produce richly-attributed synthetic populations is key for understanding human dynamics, responding to emergencies, and preparing for future events, all while protecting individual privacy. The Likeness toolkit accomplishes these goals with a suite of Python packages: pymedm/pymedm\_legacy, livelike, and actlike. This production process is initialized in pymedm (or pymedm\_legacy) that utilizes census microdata records as the foundation on which disaggregated spatial allocation matrices are built. The next step, performed by livelike, is the generation of a fully autonomous agent population attributed with hundreds of demographic census variables. The agent population synthesized in livelike is then attributed with residential coordinates in actlike based on block assignment and, finally, allocated to an optimal daytime activity location via the street network. We present a case study in Knox County, Tennessee, synthesizing 30 populations of public K–12 school students \& teachers and allocating them to schools. Validation of our results shows they are highly promising by replicating reported school enrollment and teacher capacity with a high degree of fidelity.

Tuccillo, Joe↗
DOE OSTI2022

Giant kelp genetic monitoring before and after disturbance reveals stable genetic diversity in Southern California

Given the impacts of climate change and other anthropogenic stressors on marine systems, there is a need to accurately predict how species respond to changing environments and disturbance regimes. The use of genetic tools to monitor temporal trends in populations gives ecologists the ability to estimate changes in genetic diversity and effective population size that may be undetectable by traditional census methods. Although multiple studies have used temporal genetic analysis, they usually involve commercially important species, and rarely sample before and after disturbance. In this study, we run a temporal analysis of giant kelp, Macrocystis pyrifera , genetic diversity over the scope of 10 years (2008-2018) using the same microsatellite marker panel to assess the genetic consequences of disturbance in several populations of giant kelp ( Macrocystis pyrifera ) in the Southern California Bight. The study is a rare pre- and post-disturbance microsatellite analysis that included declines to giant kelp caused by the 2015/16 El Nino Southern Oscillation event. We used canopy biomass estimated by remote sensing (Landsat) to quantify the extent of disturbance to kelp beds, and sea surface temperature data to understand how kelp was pushed towards its temperature limits during this period. Despite prolonged periods with decreased canopy at several sites, no changes in genetic structure and allelic richness were observed. We argue that giant kelp in the region is best described as a “patchy population” system where true extinctions are rare. We discuss how deep refugia of subsurface sporophytes and cryptic microscopic life stages could have kept genetic diversity through disturbance. Given the increasing effects of climate change and uncertainty in modeling impacts of species with cryptic life history stages, we suggest further investigation to reveal the role such stages play in species resilience. Genetic monitoring studies of sites selected by remote census demographic and climate surveys should be continued in the future given the predicted impacts of climate change.

Klingbeil, III, William H.↗
DOE OSTI2020

Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection

Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2024

Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold’s Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold’s Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Toward Complete Characterization: Prospects for Directly Imaging Transiting Exoplanets

High-contrast direct imaging of exoplanets can provide many important observables, including measurements of the orbit, spectra that probe the lower layers of the atmosphere, and phase variations of the planet, but cannot directly measure planet radius or mass. Our future understanding of directly imaged exoplanets will therefore rely on extrapolated models of planetary atmospheres and bulk composition, which need robust calibration. We estimate the population of extrasolar planets that could serve as calibrators for these models. Critically, this population of “standard planets” must be accessible to both direct imaging and the transit method, allowing for radius measurement. We show that the search volume of a direct imaging mission eventually overcomes the transit probability falloff with semimajor axis, so that as long as cold planets are not exceedingly rare, the population of transiting planets and directly imageable planets overlaps. Using current extrapolations of Kepler occurrence rates, we estimate that ∼8 standard planets could be characterized shortward of 800 nm with an ambitious future direct imaging mission like LUVOIR-A and several dozen could be detected at the V band. We show the design space that would expand the sample size and discuss the extent to which ground- and space-based surveys could detect this small but crucial population of planets.

79 ASTRONOMY AND ASTROPHYSICS↗