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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Application of Multi-Criteria Decision Analysis Techniques for Informing Select Agent Designation and Decision Making

The Centers for Disease Control and Prevention (CDC) Select Agent Program establishes a list of biological agents and toxins that potentially threaten public health and safety, the procedures governing the possession, utilization, and transfer of those agents, and training requirements for entities working with them. Every 2 years the Program reviews the select agent list, utilizing subject matter expert (SME) assessments to rank the agents. In this study, we explore the applicability of multi-criteria decision analysis (MCDA) techniques and logic tree analysis to support the CDC Select Agent Program biennial review process, applying the approach broadly to include non-select agents to evaluate its generality. We conducted a literature search for over 70 pathogens against 15 criteria for assessing public health and bioterrorism risk and documented the findings for archiving. The most prominent data gaps were found for aerosol stability and human infectious dose by inhalation and ingestion routes. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for accuracy, particularly for pathogens with very few known cases, or where proxy data (e.g., from animal models or similar organisms) were used to address data gaps. Analysis of results obtained from a two-dimensional plot of weighted scores for difficulty of attack (i.e., exposure and production criteria) vs. consequences of an attack (i.e., consequence and mitigation criteria) provided greater fidelity for understanding agent placement compared to a 1-to-n ranking and was used to define a region in the upper right-hand quadrant for identifying pathogens for consideration as select agents. A sensitivity analysis varied the numerical weights attributed to various properties of the pathogens to identify potential quantitative (x and y) thresholds for classifying select agents. The results indicate while there is some clustering of agent scores to suggest thresholds, there are still pathogens that score close to any threshold, suggesting that thresholding “by eye” may not be sufficient. The sensitivity analysis indicates quantitative thresholds are plausible, and there is good agreement of the analytical results with select agent designations. A second analytical approach that applied the data using a logic tree format to rule out pathogens for consideration as select agents arrived at similar conclusions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

High-Performance Hemofiltration via Molecular Sieving and Ultra-Low Friction in Carbon Nanotube Capillary Membranes

Conventional dialyzer membranes typically comprise of unevenly distributed polydisperse, tortuous, rough pores, embedded in relatively thick ≈20–50 µm polymer layers wherein separation occurs via size exclusion as well as differences in diffusivity of the permeating species. However, transport in such polymeric pores is increasingly hindered as the molecule size approaches the pore dimension, resulting in significant retention of undesirable middle molecules (≥15–60 kDa) and uremic toxins. Enhanced removal of middle molecules is usually accompanied by high albumin loss (≈66 kDa) causing hypoalbuminemia. Here, the scalable bottom-up fabrication of wafer-scale carbon nanotube (CNT) membranes with highly aligned, low-friction, straight-channels/capillaries and narrow pore-diameter distributions (≈0.5–4.5 nm) is demonstrated, to overcome persistent challenges in hemofiltration/hemodialysis. Using fluorescein isothiocyanate (FITC)-Ficoll 70 and albumin in phosphate buffered saline (PBS) as well as in bovine blood plasma, it is shown that CNT membranes can allow for significantly higher hydraulic permeability (more than an order of magnitude when normalized to pore area) than commercial high-flux hemofiltration/hemodialysis membranes (HF 400), as well as greatly enhance removal of middle molecules while maintaining comparable albumin retention. These findings are rationalized via an N-pore transport model that highlights the critical role of molecular flexing and deformation during size-selective transport within nanoscale confinements of the CNTs. In conclusion, the unique transport characteristics of CNTs coupled with size-exclusion and wafer-scale fabrication offer transformative advances for hemofiltration, and the obtained insight into molecular transport can aid advancements in several other bio-systems/applications beyond hemofiltration/hemodialysis.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Comprehensive review of combustion ion chromatography for the analysis of total, adsorbable, and extractable organic fluorine

Poly‐ and perfluoroalkyl substances (PFAS) are a class of persistent organic pollutants whose high stability and appreciable water solubility have led to near‐global contamination. PFAS are bioaccumulative toxins that have been linked to a myriad of disorders and have been detected nearly universally in human blood. Liquid chromatography‐tandem mass spectrometry is the most frequent method used for quantitation, though this typically only measures a few dozen of the >14 000 known PFAS and has been shown to account for a small portion of the total organic fluorine present. Sum parameter methods such as total, extractable, and adsorbable organic fluorine have emerged as alternative measurements for PFAS determination. Combustion ion chromatography has become the preferred method for organofluorine measurement where the sorbent or extract containing PFAS is combusted and the emitted hydrofluoric acid (HF) is a measure of the cumulative organofluorine present. Herein we critically review the types of organofluorine measurement, their separation from the sample matrix, and key parameters of the analytical instrument that affect sensitivity, reproducibility, and recovery with regards to PFAS analysis.

Chemistry↗
DOE OSTI2020

Physical drivers facilitating a toxigenic cyanobacterial bloom in a major Great Lakes tributary

The Maumee River is the primary source for nutrients fueling seasonal Microcystis -dominated blooms in western Lake Erie's open waters though such blooms in the river are infrequent. The river also serves as source water for multiple public water systems and a large food services facility in northwest Ohio. On 20 September 2017, an unprecedented bloom was reported in the Maumee River estuary within the Toledo metropolitan area, which triggered a recreational water advisory. Here we (1) explore physical drivers likely contributing to the bloom's occurrence, and (2) describe the toxin concentration and bacterioplankton taxonomic composition. A historical analysis using 10-years of seasonal river discharge, water level, and local wind data identified two instances when high-retention conditions occurred over ≥ 10 d in the Maumee River estuary: in 2016 and during the 2017 bloom. Observation by remote sensing imagery supported the advection of cyanobacterial cells into the estuary from the lake during 2017 and the lack of an estuary bloom in 2016 due to a weak cyanobacterial bloom in the lake. A rapid-response survey during the 2017 bloom determined levels of the cyanotoxins, specifically microcystins, in excess of recreational contact limits at sites within the lower 20 km of the river while amplicon sequencing found these sites were dominated by Microcystis . These results highlight the need to broaden our understanding of physical drivers of cyanobacterial blooms within the interface between riverine and lacustrine systems, particularly as such blooms are expected to become more prominent in response to a changing climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Dredged sediments contain potentially beneficial microorganisms for agriculture and little harmful cyanobacteria

Soils worldwide are degrading, raising concerns about our ability to feed the growing global population. Soil amendments that can alleviate degradation are gaining attention. The application of sediments dredged from waterways to agricultural fields has increasing promise as a means for improving degraded soils. However, herbaceous plant species may have difficulty establishing on dredged material because of low nutrient availability, inhibitory levels of toxins, unsuitable moisture conditions and lack of microorganisms capable of ameliorating these characteristics. To counteract these issues, we sought to understand if the use of a cover crop would increase the abundance, diversity and function of beneficial soil microorganisms compared to harmful microorganisms in dredged sediments. We collected soil samples from two 100% dredged sediment plots, one where winter cereal rye (Secale cereal) was grown as a winter cover crop and one left fallow over the winter, followed by traditional corn (Zea mays) planting. We sampled both plots three times during the growing season: before cover crop application, following cover crop application but before corn planting and following final corn harvest. We then used high-throughput sequencing to identify the bacterial and fungal communities present in the samples. Our data show that cover crop application did not alter the microbial community in these plots. However, sampling time decreased species diversity and altered the composition of both fungal and bacterial communities recovered from these plots. Across both plots, microorganisms associated with carbon cycling were more abundant than those associated with harmful effects, including microcystin-producing cyanobacteria, which were an extremely small portion of the overall community. Our work suggests that dredged sediments have the potential to improve soil function through the addition of microorganisms associated with nutrient cycling, but a cover crop is not necessary to incur these benefits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Scavenging dynamics on Guam and implications for invasive species management

Deployment of mouse carcasses laced with acetaminophen has become a common management tool to control invasive brown tree snakes (Boiga irregularis; BTS) on Guam. Additionally, anticoagulant rodenticides may be used to control invasive rats (Rattus spp.) if their populations increase due to predator release in the wake of BTS eradication. However, there has been little research examining how scavengers on Guam could be incidentally exposed to toxicants by scavenging carcasses of animals that die from these population control strategies. Furthermore, there is a limited understanding of how the proliferation of invasive species on Guam has influenced the composition of the scavenger community. We investigated these topics by examining scavenger consumption of mouse, rat, and BTS carcasses on Guam in both a coastal and upland site during the wet (May–Aug 2016) and dry season (Jan–Apr 2017). We documented carcass consumption by 9 species, which scavenged 48% of carcasses. Interactions between season, habitat, and carcass type influenced probability of scavenging, and appeared to be driven by consumption by the two main scavenger species, BTS and cane toads (Rhinella marina), both of which are invasive on Guam. Baiting programs should consider the potential for toxin exposure to land crabs (Coenobita spp., Birgus latro), native species that scavenged at every combination of carcass type, habitat, and season. Altogether, 60% of scavenging events were attributed to species considered pests that are recent introductions to Guam. Invasive species on Guam are the primary scavengers of small vertebrate carrion, suggesting a substantial role in trophic dynamics that extends beyond predation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Comprehensive Scientific Survey of Excipients Used in Currently Marketed, Therapeutic Biological Drug Products

The steady development of biotechnology-derived therapeutic biologics over the last few decades has generated drugs that are now standard medical treatments for a range of indications. While the development of protein products has surged in recent years, the formulation and delivery of these complex molecules have relied on drug-specific studies and, in some instances, data from non-proteinaceous drug products. The commonalities, trends, and gaps in excipient technologies used to support the development of therapeutic proteins largely remain unexplored due to the drug-specific nature of many formulations. Using a comprehensive and relational database approach, we aimed to provide a scientific survey of all approved or licensed biotechnology-derived drug products with the goal of providing evidence-based information on common attributes and trending features in protein product excipients. We examined 665 formulations, and 395 unique formulations based on having unique excipients within them, that supported 211 therapeutic proteins as of June 2020. We report the prevalence of each excipient class and excipient chemical used in eight different drug types including monoclonal antibodies, antibody conjugates, cytokines and growth factors, enzymes, polypeptide hormones, pulmonary surfactants, recombinant fusion proteins, and toxins. We also report the prevalence by excipient type among all therapeutic proteins, in the context of each drug’s recommended pH range, concentration ranges for excipients, and route of administration. The results of our analyses indicate certain excipients common to monoclonal antibodies, cytokines, and polypeptide hormones. We also report on excipients unique to protein drug products, such as amino acids, solubilizers, and lyoprotectants. Overall, our report summarizes the current landscape of excipients used in marketed biotechnology-derived therapeutic biologic products.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

The phage nucleus synergizes with an anti-defense protein to resist bacterial immunity

Chimallivirus bacteriophages enclose their replicating genomes in a protein-based compartment termed the phage nucleus. While the phage nucleus segregates phage DNA from host immune proteins, it is not known if additional factors are required to protect against DNA-targeting host defenses. Here, we identify a chimallivirus-encoded DarG2-like antitoxin that localizes to the phage nucleus and provides protection against phage-targeting DarTG2 toxin-antitoxin systems. This protein, which we term AdfM (anti-darT factor macro), contains a macrodomain and removes DarT2-mediated ADP-ribose modifications from DNA. In the absence of AdfM, DarT2 modifies phage DNA and restricts chimallivirus replication despite being largely excluded from the phage nucleus. Increasing the nuclear concentration of DarT2 while decreasing the nuclear concentration of AdfM reduces phage replication. These results show that the phage nucleus is insufficient to completely protect the chimallivirus genome from host defenses; rather, it is one component of a multilayered counter-defense strategy.

CRISPR↗
DOE OSTI2022

Morphological and crystallographic controls in the replacement of calcite and aragonite by cerussite and otavite

Mineral replacement reactions are essential solid-fluid interactions in natural and industrial processes including metasomatism, diagenesis, and metamorphism, and sequestration of metal toxins from polluted water. In this paper, we explore the morphological evolution of aragonite and calcite (polymorphs of CaCO 3 ) during their replacement by cerussite (PbCO 3 , an isomorph of aragonite) and otavite (CdCO 3 , an isomorph of calcite) in acidic aqueous solutions (with initial pH 3 to 4). Observations using scanning electron and synchrotron-based transmission X-ray microscopies reveal the formation of pseudomorphic shells (~5 to 10 µm thick) of cerussite and otavite when Pb 2+ is reacted with either calcite or aragonite and when Cd 2+ is reacted with aragonite. The formation of pore space at the substrate-precipitate interface and within the precipitate is found to be key in promoting chemical exchange between the dissolving phase and the solution. In contrast, minimal reactivity is observed when Cd 2+ is reacted with calcite. These results demonstrate that the lack of substrate-precipitate epitaxy (either because of inconsistent symmetries or due to large lattice constant mismatch) is a critical factor that enables replacement of primary CaCO 3 minerals by Pb- or Cd-bearing secondary minerals while the presence of epitaxial relationships inhibit those reactions. When calcite and aragonite coexist, the replacement of aragonite by cerussite and otavite occurs preferentially over calcite. We postulate that the relative reactivity of calcite and aragonite to Pb 2+ and Cd 2+ can be determined by interplay between morphological and crystallographic properties of CaCO 3 materials as well as solution chemistry. Our results demonstrate that coupled dissolution-precipitation processes of carbonate minerals play an important role in controlling mobility and bioavailability of lead and cadmium in environments where acidic metal-contaminated water interacts with carbonate-rich rocks and soils.

58 GEOSCIENCES↗
DOE OSTI2025

Manganese in drinking-water reservoirs: a multi-disciplinary review of current issues, biogeochemical controls, and oxygenation-based management

Decreased water quality and increased treatment costs due to excess manganese (Mn) in drinking-water supplies are critical issues globally. To combat on-going and emerging taste and odour issues with Mn and other contaminants (e.g., algal toxins), many utilities are using engineered oxygenation or aeration (EOA) systems to improve water quality in lakes and reservoirs. Resultant shifts in key biogeochemical and physical processes are still poorly understood, often leading to inefficiently managed systems. Paired with knowledge gaps regarding environmental drivers of Mn and the complexity of Mn redox kinetics, Mn problems persist. This review presents the state of current research in areas critical to optimisation of EOA mitigation of Mn, with focus on i) Mn biogeochemical cycling within drinking-water reservoirs; ii) influences of local catchment geology, hydrology, and land use on Mn dynamics; and iii) Mn management using different EOA approaches. The importance of considering the combined implications of these factors for successful Mn management in reservoirs is highlighted by an evaluation of relevant field-based studies; a wide range in EOA performance is observed, from a 97 % decrease in soluble Mn up to a ∼400 % increase in total Mn. Despite the breadth of studies that consider Mn in water-supply systems, there are still several areas of research which warrant further investigation, including: the influence of natural sources and anthropogenic activities on Mn within a given catchment, Mn speciation and transport in stratified and destratified lakes and reservoirs, and optimal site-specific EOA strategies for Mn mitigation.

Aeration↗
DOE OSTI2021

A geospatial environmental and techno-economic framework for sustainable phosphorus management at livestock facilities

Nutrient pollution of waterbodies is a major worldwide water quality problem. Excessive use and discharge of nutrients can lead to eutrophication and algal blooms in fresh and marine waters, resulting in environmental problems associated with hypoxia, public health issues related to the release of toxins and freshwater scarcity. A promising option to address this problem is the recovery of nutrient releases prior to being discharged into the environment. Driven by the sustainable materials management concept, the COW2NUTRIENT (Cattle Organic Waste to NUTRIent and ENergy Technologies) framework is developed for the techno-economic evaluation and selection of nutrient recovery systems at livestock facilities. Furthermore, environmental vulnerability to nutrient pollution determined through a geographic information system (GIS)-based model and techno-economic information of different state-of-the-art nutrient management technologies are combined in a multi-criteria decision analysis (MCDA) model, resulting in the selection and economic analysis of the most suitable process for each studied livestock facility. This framework has been employed for studying the implementation of sustainable phosphorus management systems at 2,217 livestock facilities in the Great Lakes area, resulting in capital expenses of 2.5 billion USD if only phosphorus recovery technologies are installed, and up to 5.2 billion USD if nutrient management is combined with biogas and power production. However, considering potential economic incentives for the recovery of phosphorus, net revenues up to 230 million USD per year can be achieved. Therefore, the framework presented reveals the potential of implementing nutrient management systems at regional scale for the abatement of phosphorus releases from livestock facilities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13 C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Inhibition of polyamine biosynthesis preserves β cell function in type 1 diabetes

In preclinical models, α-difluoromethylornithine (DFMO), an ornithine decarboxylase (ODC) inhibitor, delays the onset of type 1 diabetes (T1D) by reducing β cell stress. However, the mechanism of DFMO action and its human tolerability remain unclear. In this study, we show that mice with β cell ODC deletion are protected against toxin-induced diabetes, suggesting a cell-autonomous role of ODC during β cell stress. In a randomized controlled trial (ClinicalTrials.gov: NCT02384889) involving 41 recent-onset T1D subjects (3:1 drug:placebo) over a 3-month treatment period with a 3-month follow-up, DFMO (125–1,000 mg/m 2 ) is shown to meet its primary outcome of safety and tolerability. DFMO dose-dependently reduces urinary putrescine levels and, at higher doses, preserves C-peptide area under the curve without apparent immunomodulation. Transcriptomics and proteomics of DFMO-treated human islets exposed to cytokine stress reveal alterations in mRNA translation, nascent protein transport, and protein secretion. These findings suggest that DFMO may preserve β cell function in T1D through islet cell-autonomous effects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Dirks, Alden C↗
DOE OSTI2023

Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. Here we report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of “unknown unknown” trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Organophosphorus Binding Thermodynamics in Metal–Organic Frameworks: Interplay between Oxidation State, Lewis Acidity, and Node Structure

Organophosphorus compounds, including nerve agents and pesticides, represent a class of toxic chemicals causing harm to troops, civilians, and the environment. Metal–organic frameworks (MOFs) have emerged as a class of highly porous, crystalline, tunable materials adept at both capturing and catalytically neutralizing these harmful toxins. In particular, MOFs whose nodes display strong Lewis acidic character can hydrolyze such chemicals nearly instantaneously. However, without the help of a basic buffer to regenerate the active site, the benign organophosphorus product strongly binds to the node and prevents catalyst turnover. Here, we investigate a series of MOFs whose nodes contain metals of varying Lewis acidities and employ isothermal titration calorimetry (ITC) to directly measure the heat from the binding of an organophosphorus probe molecule, allowing the construction of a full thermodynamic binding profile (ΔH, ΔS, ΔG, K a ). We couple this with potentiometric titrations and solid state 31 P magic angle spinning (MAS) NMR to gain a clearer picture of how node identity, structure, and Lewis acidity interplay to impact binding strength and favorability. Furthermore, this study is the first to integrate these three complementary techniques to investigate binding interactions in MOFs, further showcasing the viability of ITC for probing MOF systems, which is still relatively underexplored.

Lewis acidity↗