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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Assessment of habitat‐specific competition for oral rabies vaccine baits between raccoons and opossums

Abstract Throughout the eastern United States, the National Rabies Management Program (NRMP) distributes oral rabies vaccine (ORV) baits to manage rabies virus circulation in raccoon ( Procyon lotor ) populations. The consumption of vaccine baits by non‐target species including Virginia opossums ( Didelphis virginiana ) may reduce the effectiveness of ORV programs, but competition for baits remains poorly quantified in many areas of the southeastern United States. We distributed placebo ORV baits injected with a biomarker across 4 land cover types (bottomland hardwood, upland pine, riparian, isolated wetland) on the Savannah River Site in South Carolina, USA, 2017–2019. We then trapped and collected whiskers from 247 raccoons and 78 opossums to assess biomarker presence using fluorescent microscopy. Our data revealed greater bait uptake probability by raccoons (estimated x̅ = 0.30, 95% CI = 0.19–0.44) compared to opossums (estimated x̅ = 0.11, 95% CI = 0.05–0.23) across all cover types surveyed. Probability of bait consumption was not affected by cover type or the abundance of raccoons or opossums. Among raccoons, males were more likely to consume baits than females (estimated x̅ = 0.28, 95% CI = 0.17–0.44 for males and 0.14, 95% CI = 0.05–0.31 for females) and probability of consumption increased by 0.08 with each additional day trapped during the 10‐day trapping session. Uptake rates for raccoons were relatively low compared to other studies and not influenced by competition with opossums. These low consumption rates indicate that additional research addressing the roles of baiting season, bait density, and resource selection will be important to maximize ORV bait uptake by target species in these southeastern landscapes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales

Viruses are the most ubiquitous biological entities on Earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of unambiguous host-virus linkages-an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages via spacers in CRISPR-Cas arrays and subsequently reveal complex long-term host-virus dynamics. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days, resulting in 78 metagenomes from temporal sampling of six wells in the Denver-Julesburg Basin (Colorado, USA). At the community level, there was strong evidence for CRISPR-Cas defense systems being used through time and likely in response to viral interactions. Within our host genomes, represented by 202 unique MAGs, we also saw that CRISPR-Cas systems were widely encoded. Together, spacers from host CRISPR loci facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs spanning 25 phyla. We observed less redundancy in host-viral linkages and fewer spacers associated with hosts from the older, more established wells, possibly reflecting enrichment of more beneficial spacers through time. Leveraging temporal patterns of host-virus linkages across differing well ages, we report how host-virus co-existence dynamics develop and converge through time, possibly reflecting selection for viruses that can evade host CRISPR-Cas systems. Together, our findings shed light on the complexities of host-virus interactions as well as long-term dynamics of CRISPR-Cas defense among diverse microbial populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Arbuscular mycorrhizal trees cause a higher carbon to nitrogen ratio of soil organic matter decomposition via rhizosphere priming than ectomycorrhizal trees

Tree roots and their associated microbes can significantly influence soil organic matter (SOM) decomposition, i.e., the rhizosphere priming effect. This effect is expected to be greater in trees associated with arbuscular mycorrhizal (AM) fungi, which produce higher extracellular enzymes especially surrounding hyphae, than in trees associated with ectomycorrhizal (ECM) fungi. In this work, we selected five tree species associated with AM (Juglans mandshurica Maxim. and Cunninghamia lanceolata (Lamb.) Hook.) or ECM (Picea koraiensis Nakai, Quercus mongolica Fischer ex Turcz. and Larix kaempferi (Lamb.) Carriere). We grew tree seedlings inside of cores lined with different mesh sizes to investigate how roots, hyphae and exudates influence soil carbon (C) and nitrogen (N) mineralization via the rhizosphere priming effect, using a 13 C natural abundance approach and a 15 N pool dilution method, concurrently. We found that tree seedlings significantly accelerated soil C decomposition by on average 78%, i.e., positive priming, compared to unplanted control pots. AM-associated trees induced 2.1 times greater soil C decomposition than ECM-associated trees across all mesh sizes. In contrast, gross N mineralization did not differ between tree-mycorrhizal associations. Compared to ECM counterparts, AM-associated trees had higher C- and lower N-degrading enzyme activities. Consequently, AM-associated trees induced a significantly higher C:N ratio of SOM decomposition than their ECM counterparts, which could be associated with the differences in soil enzyme activities for C and N degradation. Further, for both AM- and ECM-associated trees, we found no significant influences of mesh size on soil C decomposition, suggesting that the rhizosphere priming effect of mycorrhizal symbiosis was predominantly driven by root exudates. We conclude that SOM decomposition caused by AM-associated trees may have a higher C:N ratio than that by ECM-associated trees mainly due to differences in microbial enzyme investment. Our findings imply that tree-mycorrhizal associations are capable of modulating soil biogeochemical cycling via the rhizosphere priming effect.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Tapping into the physiological responses to mistletoe infection during heat and drought stress

Mistletoes are important co-contributors to tree mortality globally, particularly during droughts. In Australia, mistletoe distributions are expanding in temperate woodlands, while their hosts have experienced unprecedented heat and drought stress in recent years. We investigated whether the excessive water use of mistletoes increased the probability of xylem emboli in a mature woodland during the recent record drought that was compounded by multiple heatwaves. Additionally, we continuously recorded transpiration ($T_{SLA}$) of infected and uninfected branches from two eucalypt species over two summers, monitored stem and leaf water potentials ($\Psi $) and used hydraulic vulnerability curves to estimate percent loss in conductivity (PLC) for each species. Variations in weather (vapor pressure deficit, photosynthetically active radiation, soil water content), host species and % mistletoe foliage explained 78% of hourly $T_{SLA}$. While mistletoe acted as an uncontrollable sink for water in the host even during typical summer days, daily $T_{SLA}$ increased up to 4-fold in infected branches on hot days, highlighting the previously overlooked importance of temperature stress in amplifying water loss in mistletoes. The increased water use of mistletoes resulted in significantly decreased host $\Psi _{\rm{leaf}}$ and $\Psi _{\rm{trunk}}$. It further translated to an estimated increase of up to 11% PLC for infected hosts, confirming greater hydraulic dysfunction of infected trees that place them at higher risk of hydraulic failure. However, uninfected branches of Eucalyptus fibrosa F.Muell. had much tighter controls on water loss than uninfected branches of Eucalyptus moluccana Roxb., which shifted the risk of hydraulic failure towards an increased risk of carbon starvation for E. fibrosa. The contrasting mechanistic responses to heat and drought stress between both co-occurring species demonstrates the complexity of host–parasite interactions and highlights the challenge in predicting species-specific responses to biotic agents in a warmer and drier climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The ABCflux database: Arctic–boreal CO 2 flux observations and ancillary information aggregated to monthly time steps across terrestrial ecosystems

Past efforts to synthesize and quantify the magnitude and change in carbon dioxide (CO 2 ) fluxes in terrestrial ecosystems across the rapidly warming Arctic–boreal zone (ABZ) have provided valuable information but were limited in their geographical and temporal coverage. Furthermore, these efforts have been based on data aggregated over varying time periods, often with only minimal site ancillary data, thus limiting their potential to be used in large-scale carbon budget assessments. To bridge these gaps, we developed a standardized monthly database of Arctic–boreal CO 2 fluxes (ABCflux) that aggregates in situ measurements of terrestrial net ecosystem CO 2 exchange and its derived partitioned component fluxes: gross primary productivity and ecosystem respiration. The data span from 1989 to 2020 with over 70 supporting variables that describe key site conditions (e.g., vegetation and disturbance type), micrometeorological and environmental measurements (e.g., air and soil temperatures), and flux measurement techniques. Here, we describe these variables, the spatial and temporal distribution of observations, the main strengths and limitations of the database, and the potential research opportunities it enables. In total, ABCflux includes 244 sites and 6309 monthly observations; 136 sites and 2217 monthly observations represent tundra, and 108 sites and 4092 observations represent the boreal biome. The database includes fluxes estimated with chamber (19 % of the monthly observations), snow diffusion (3 %) and eddy covariance (78 %) techniques. The largest number of observations were collected during the climatological summer (June–August; 32 %), and fewer observations were available for autumn (September–October; 25 %), winter (December–February; 18 %), and spring (March–May; 25 %). ABCflux can be used in a wide array of empirical, remote sensing and modeling studies to improve understanding of the regional and temporal variability in CO 2 fluxes and to better estimate the terrestrial ABZ CO 2 budget.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rational approach to drug discovery for human schistosomiasis

Human schistosomiasis is a debilitating, life-threatening disease affecting more than 229 million people in as many as 78 countries. There is only one drug of choice effective against all three major species of Schistosoma, praziquantel (PZQ). However, as with many monotherapies, evidence for resistance is emerging in the field and can be selected for in the laboratory. Previously used therapies include oxamniquine (OXA), but shortcomings such as drug resistance and affordability resulted in discontinuation. Employing a genetic, biochemical and molecular approach, a sulfotransferase (SULT-OR) was identified as responsible for OXA drug resistance. By crystallizing SmSULT- OR with OXA, the mode of action of OXA was determined. This information allowed a rational approach to novel drug design. Our team approach with schistosome biologists, medicinal chemists, structural biologists and geneticists has enabled us to develop and test novel drug derivatives of OXA to treat this disease. Using an iterative process for drug development, we have successfully identified derivatives that are effective against all three species of the parasite. One derivative CIDD-0149830 kills 100% of all three human schistosome species within 5 days. The goal is to generate a second therapeutic with a different mode of action that can be used in conjunction with praziquantel to overcome the ever-growing threat of resistance and improve efficacy. The ability and need to design, screen, and develop future, affordable therapeutics to treat human schistosomiasis is critical for successful control program outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Treatment of cholinergic‐induced status epilepticus with polytherapy targeting GABA and glutamate receptors

Abstract Despite new antiseizure medications, the development of cholinergic‐induced refractory status epilepticus (RSE) continues to be a therapeutic challenge as pharmacoresistance to benzodiazepines and other antiseizure medications quickly develops. Studies conducted by Epilepsia . 2005;46:142 demonstrated that the initiation and maintenance of cholinergic‐induced RSE are associated with trafficking and inactivation of gamma‐aminobutyric acid A receptors (GABA A R) thought to contribute to the development of benzodiazepine pharmacoresistance. In addition, Dr. Wasterlain's laboratory reported that increased N‐methyl‐ d ‐aspartate receptors (NMDAR) and alpha‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptors (AMPAR) contribute to enhanced glutamatergic excitation ( Neurobiol Dis . 2013;54:225; Epilepsia . 2013;54:78). Thus, Dr. Wasterlain postulated that targeting both maladaptive responses of reduced inhibition and increased excitation that is associated with cholinergic‐induced RSE should improve therapeutic outcome. We currently review studies in several animal models of cholinergic‐induced RSE that demonstrate that benzodiazepine monotherapy has reduced efficacy when treatment is delayed and that polytherapy with drugs that include a benzodiazepine (eg midazolam and diazepam) to counter loss of inhibition, concurrent with an NMDA antagonist (eg ketamine) to reduce excitation provide improved efficacy. Improved efficacy with polytherapy against cholinergic‐induced seizure is demonstrated by reduction in (1) seizure severity, (2) epileptogenesis, and (3) neurodegeneration compared with monotherapy. Animal models reviewed include pilocarpine‐induced seizure in rats, organophosphorus nerve agent (OPNA)‐induced seizure in rats, and OPNA‐induced seizure in two mouse models: (1) carboxylesterase knockout (Es1 −/− ) mice which, similarly to humans, lack plasma carboxylesterase and (2) human acetylcholinesterase knock‐in carboxylesterase knockout (KIKO) mice. We also review studies showing that supplementing midazolam and ketamine with a third antiseizure medication (valproate or phenobarbital) that targets a nonbenzodiazepine site rapidly terminates RSE and provides further protection against cholinergic‐induced SE. Finally, we review studies on the benefits of simultaneous compared with sequential drug treatments and the clinical implications that lead us to predict improved efficacy of early combination drug therapies. The data generated from seminal rodent studies of efficacious treatment of cholinergic‐induced RSE conducted under Dr. Wasterlain's guidance suggest that future clinical trials should treat the inadequate inhibition and temper the excess excitation that characterize RSE and that early combination therapies may provide improved outcome over benzodiazepine monotherapy.

59 BASIC BIOLOGICAL SCIENCES↗