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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2025

Important Human Actions for Advanced Reactors: Implications for Human Factors

As advanced reactor platforms continue to develop and gain traction in the energy sector there is a need for risk-informed, scalable regulations that match that progress. This is a core component of the U.S. Nuclear Regulatory Commission’s proposed Part 53 Rule Making; the Accelerating Deployment of Versatile, Advanced Nuclear for Clean Energy (ADVANCE) Act; and other efforts that seek to update nuclear power regulations. This paper covers one key aspect of that regulatory evolution: Important Human Actions (IHA). In this paper, we discuss how the understanding and definitions of IHAs have changed and what that means for human factors engagement through the process of developing these technologies. Instead of a narrow focus on control actions that led to an increase in core damage risk, the new focus is on IHAs is “wherever they occur.” What this means is that having a highly automated or passive safety system does not eliminate IHAs. Rather, it shifts the focus point to all the actions that enable these systems. Everything from maintenance, to design, to training can be considered an IHA and that dramatically shifts the efforts and level of engagement necessary for human factors to enable these technologies. We discuss the notions of risk-informed human factors that underpin these efforts, give several examples, and briefly describe the risk assessment methodologies that will be needed. In the past, IHAs were identified and then became a focus point of human factors engineering (HFE) activities to ensure a robust evaluation of the task was completed. The future is less clear. HFE for nuclear energy will need to evolve and become more integrated in technology development than ever before.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Storage Field Development Plan: One Earth Energy

This Storage Field Development plan presents the Storage Complex characterization results, construction, monitoring, and operational plans, and costs associated with the proposed One Earth Sequestration Carbon Capture and Storage (OES-CCS) site in McLean County, Illinois, near Gibson City. The proposed storage complex, known as the Mt. Simon Storage Complex, comprises the Cambrian Mt. Simon Sandstone reservoir and the primary seal, the Cambrian Eau Claire Formation. The lowermost Underground Source of Drinking Water (USDW) identified for the site is the Ordovician St. Peter Sandstone. Geologic characterization of the Mt. Simon Storage Complex at the OES-CCS site was performed by the Illinois Storage Corridor CarbonSAFE Phase III project, which also prepared and submitted three UIC Class VI applications to construct three injection wells; the permit applications were submitted and are in the federal EPA review process. A characterization well, OEE #1, was drilled to collect site-specific data. These data were analyzed and used to develop the UIC Class VI applications. The OEE #1 well will be converted to an in-zone monitoring (IZM) well for the injection phase. The proposed buildout for the OES-CCS site includes (1) three injection wells (OES #1, OES #2, and OES #3), (2) two IZM wells, (3) two above confining zone (ACZ) monitoring wells, one of which will be used to monitor the lowermost USDW, (4) capture and compression facilities, and (5) transportation facilities, i.e., pipelines. A pre-operational testing program was proposed in the Class VI permit application and will be employed at the site pending approval. Additional pre-injection (baseline), syn-injection, and post-injection monitoring and site care procedures will be followed by OES to ensure that injection activities are protective of human health and the environment. Injection is scheduled to begin in 2025, distributed across the three injection wells in accordance with the permit operating conditions. One Earth Sequestration intends to inject up to 90 million tonnes of CO 2 over a period of approximately 20 years. Injection will begin at approximately 0.5 million tonnes of CO 2 annually and ramp up to a maximum of 4.5 million tonnes annually. Daily injection rates are expected to range from 1,400 to 1,500 tonnes per day initially and reach a maximum of approximately 4,225 tonnes per day, depending on site geology and injectivity at each injection well location, and CO 2 availability. The costs associated with the OES-CCS project include pre-operational costs (e. g. additional seismic data acquisition and well drilling), capture and transportation facility and equipment costs, predicted field operating expenditures (OpEx), and decommissioning and post-injection site care (PISC) costs. The risks associated with project activities, such as site construction, injection operations, and verification of secure storage were evaluated, and mitigation strategies proposed to alleviate those risks.

09 BIOMASS FUELS↗
DOE OSTI2025

Speeding-up fuzzing through directional seeds

Abstract Fuzzing is an automated process for discovering inputs in a program that may trigger unexpected behavior. Today, fuzzing has become a standard practice for the discovery of bugs and security vulnerabilities. However, the main issue with such practices is that the exploration of the input space of programs can often be prohibitively expensive. Therefore, several alternative fuzzing strategies have been introduced during the last few years. Some fuzzing techniques rely on human expertise to provide a plausible set of initial input examples, namely, seeds. However, the process of handcrafting seeds for fuzzing purposes often becomes strenuous for humans as it requires a deeper understanding of the Program-Under-Test (PUT). Also, the use of known inputs to programs often does not trigger vulnerable program behavior or may not reach potentially vulnerable code locations. To address those issues, we propose a seed generation framework that enables Human-In-The-Loop (HITL) directed fuzzing where the human assumes a more active role in the creation of seeds that can penetrate and assess desired locations of the PUT. Our proposed framework uses Symbolic Execution (SE) to generate seeds that exercise paths to target program locations. Moreover, our framework enables the visualization of the explored execution paths in the binary of the PUT for the generated seeds. We evaluated our approach on a set of 12 carefully designed C programs with diverse characteristics that mimic real-world programs. The experimental results show the effectiveness of the proposed approach in improving the performance of standard fuzzing tools such as the American Fuzzy Lop ("Image missing" <#comment/> ). Specifically, our solution can generate seeds that substantially enhance the performance of the fuzzer, achieving speedups ranging from $$1.46\times $$ 1.46 × to $$68.53\times $$ 68.53 × for branch conditions, $$1.39\times $$ 1.39 × to $$254.62\times $$ 254.62 × for branch depths, $$14,879.59\times $$ 14 , 879.59 × to $$30,295.88\times $$ 30 , 295.88 × for branch widths over traditional seeds. Additionally, the speedup increases with the number of target function ranging from $$12,260\times $$ 12 , 260 × to $$22,856.07\times $$ 22 , 856.07 × over traditional seeds while only requiring less than 15 seconds on average for the seed generation step.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

UrbanPop: A spatial microsimulation framework for exploring demographic influences on human dynamics

Ensuring the social equity of planning measures in social systems requires an understanding of human dynamics, particularly how individual relationships, activities, and interactions intersect with individual needs. Spatial microsimulation models (SMSMs) support planning for human security goals by representing human dynamics through realistic, georeferenced synthetic populations, that a) provide a complete representation of social systems while b) also protecting individual privacy. In this paper, we present UrbanPop, an open and reproducible SMSM framework for analysis of human dynamics with high spatial, temporal, and demographic resolution. UrbanPop creates synthetic populations of demographically detailed worker and student agents, positioning them first at probable nighttime locations (home), then moving them to probable daytime locations (work/school). Summary aggregations of these populations match the granular detail available at the census block group level in the American Community Survey Summary File (SF), providing realistic approximations of the actual population. UrbanPop users can select particular demographic traits important in their application, resulting in a highly tailored agent population. We first lay out UrbanPop's baseline methodology, including population synthesis, activity modeling, and diagnostics, then demonstrate these capabilities by developing case studies of shifting population distributions and high-risk populations in Knox County, TN during the global COVID-19 pandemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗
DOE OSTI2025

Electric spiking activity in epithelial cells

Epithelial cells (human keratinocyte cells and the canine MDCK cell line), traditionally viewed as electrically non-self-excitable and involved primarily in physiological functions such as barrier presentation, absorption, secretion, and protection, are shown here to exhibit traveling extracellular electric charge when they recover from spatially focused, laser-induced wounding of confluent monolayers cultured on a multielectrode array chip. Voltage spikes measured on these electrodes display depolarization, repolarization, and hyperpolarization phases with amplitudes similar to the action potentials of neurons but with the markedly slower duration of 1 to 2 s. Some propagate distances up to hundreds of μm from the wound with a mean speed of around 10 mm s −1 . Generation and transmission of bioelectric signals are significantly influenced by the perturbation of mechanosensitive cationic ion channels. These direct measurements confirm bioelectric signaling that previous work has hypothesized to regulate epithelial cell development and may have relevance to the frequency parameter selection of bioelectric devices.

Science & Technology - Other Topics↗
DOE OSTI2020

Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation

The many variants of human Ca2+/calmodulin-dependent protein kinase II (CaMKII) differ in the lengths and sequences of disordered linkers connecting the kinase domains to the oligomeric hubs of the holoenzyme. CaMKII activity depends on the balance between activating and inhibitory autophosphorylation (on Thr 286 and Thr 305/306, respectively, in the human α isoform). Variation in the linkers could alter transphosphorylation rates within a holoenzyme and the balance of autophosphorylation outcomes. We show, using mammalian cell expression and a single-molecule assay, that the balance of autophosphorylation is flipped between CaMKII variants with longer and shorter linkers. For the principal isoforms in the brain, CaMKII-α, with a ~30 residue linker, readily acquires activating autophosphorylation, while CaMKII-β, with a ~200 residue linker, is biased towards inhibitory autophosphorylation. Our results show how the responsiveness of CaMKII holoenzymes to calcium signals can be tuned by varying the relative levels of isoforms with long and short linkers.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2026

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗
DOE OSTI2023

Characterization of a monoclonal antibody specific to California serogroup orthobunyaviruses and development as a chimeric immunoglobulin M-positive control in human diagnostics

ABSTRACT California serogroup viruses (CSGVs) of medical importance in the United States include La Crosse virus, Jamestown Canyon virus (JCV), California encephalitis virus, and snowshoe hare virus. Current diagnosis of CSGVs relies heavily on serologic techniques for detecting immunoglobulin M (IgM), an indication of a recent CSGV infection. However, human-positive control sera reactive to viruses in the serogroup are scarce because detection of recent infections is rare. Here, we describe the development of new murine monoclonal antibodies (MAbs) reactive to CSGVs and the engineering of a human-murine chimeric antibody by combining the variable regions of the broadly CSGV cross-reactive murine MAb, 3-3B6/2-3B2 and the constant region of the human IgM. MAb 3-3B6/2-3B2 recognizes a tertiary epitope on the Gn/Gc heterodimer, and epitopes important in JCV neutralization were mapped to the Gc glycoprotein. This engineered human IgM constitutively expressed in a HEK-293 stable cell line can replace human-positive control sera in diagnostic serological techniques such as IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA). Compared to the parent murine MAbs, the human-chimeric IgM antibody had identical serological activity to CSGVs in ELISA and demonstrated equivalent reactivity compared to human immune sera in the MAC-ELISA. Importance Orthobunyaviruses in the California serogroup cause severe neurological disease in children and adults. While these viruses are known to circulate widely in North America, their occurrence is rare. Serological testing for CSGVs is hindered by the limited availability and volumes of human-positive specimens needed as controls in serologic assays. Here, we described the development of a murine monoclonal antibody cross-reactive to CSGVs engineered to contain the variable regions of the murine antibody on the backbone of human IgM. The chimeric IgM produced from the stably expressing HEK293 cell line was evaluated for use as a surrogate human-positive control in a serologic diagnostic test.

Microbiology↗
DOE OSTI2025

Underground Test Area Activity Waste Management Plan; and Attachment 1 Fluid Management Plan for the Underground Test Area Activity

The U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office initiated the Underground Test Area Activity to characterize the risk posed to human health and the environment as a result of underground nuclear testing activities at the Nevada National Security Site. The UGTA Activity is now administered by the DOE Environmental Management Nevada Program. This document is a revision to NNSA/NSO (2009). The new document and revision number reflect EM Nevada Program as the current UGTA Activity administrator.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Neutral rhenium( i ) tricarbonyl complexes with sulfur-donor ligands: anti-proliferative activity and cellular localization

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anti-cancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO) 3 (SR)] complexes, where (NN) is 2,2'-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO) 3 (OH 2 )]+ complexes; however, one of the complexes, fac-[Re(CO) 3 (phen)(SC(Ph)CH 2 C(O)OMe)] (3b), was active (IC 50 ~ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac-[Re(CO) 3 (phen)(OH 2 )]+, this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO) 3 (SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λ ex = 405 nm, λ em = 470–570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Neutral rhenium(i) tricarbonyl complexes with sulfur-donor ligands: anti-proliferative activity and cellular localization

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anticancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO) 3 (SR)] complexes, where (NN) is 2,2'-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO) 3 (OH 2 )] + complexes; however, one of the complexes, fac-[Re(CO) 3 (phen)(SC(Ph)CH 2 C(O)OMe))] (3b), was active (IC 50 ~ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac- [Re(CO) 3 (phen)(OH 2 )] + , this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO) 3 (SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λ ex = 405 nm, λ em = 470-570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A human antibody epitope map of the malaria vaccine antigen Pfs25

Pfs25 is a leading antigen for a malaria transmission-blocking vaccine and shows moderate transmission-blocking activity and induction of rapidly decreasing antibody titers in clinical trials. A comprehensive definition of all transmission-reducing epitopes of Pfs25 will inform structure-guided design to enhance Pfs25-based vaccines, leading to potent transmission-blocking activity. Here, we compiled a detailed human antibody epitope map comprising epitope binning data and structures of multiple human monoclonal antibodies, including three new crystal structures of Pfs25 in complex with transmission-reducing antibodies from Malian volunteers immunized with Pfs25 conjugated to EPA and adjuvanted with AS01. These structures revealed additional epitopes in Pfs25 capable of reducing transmission and expanded this characterization to malaria-exposed humans. This work informs immunogen design to focus the antibody response to transmission-reducing epitopes of Pfs25, enabling development of more potent transmission-blocking vaccines for malaria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Prediction of Specificity of α-Conotoxins to Subtypes of Human Nicotinic Acetylcholine Receptors with Semi-supervised Machine Learning

Conotoxins are a family of highly toxic neurotoxins composed of cysteine-rich peptides produced by marine cone snails. The most lethal cone snail species to humans is Conus geographus, with fatality rates of up to ∼65% from a single sting, which is caused mostly by the activity of α-conotoxins against human nicotinic acetylcholine receptors (nAChRs). While sequence-based machine learning (ML) classifiers have been trained to identify targets of conotoxins binding voltage-gated ion channels, no ML model has been built to predict the subtype-specific nAChR targets of α-conotoxins. Here, we trained an ML model in a semi-supervised manner to predict the specificity of α-conotoxin binding toward different human nAChR subtypes to overcome the challenge of limited data in subtype-specific nAChR targets of α-conotoxins and the issue that one α-conotoxin can bind multiple nAChR subtypes with high selectivity. We considered additional features of sequences of α-conotoxins in training our ML model, including the secondary structure propensities and electrostatic properties, which resulted in better prediction capability for the ML model. Notably, we identify that most α-conotoxins bind to α3β2, α1γδ, and α7 subtypes of human nAChRs. Our findings from this study provide a framework for predicting targets of various kinds of toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Simple Analysis of Primary and Secondary Bile Salt Hydrolysis in Mouse and Human Gut Microbiome Samples by Using Fluorogenic Substrates

Animals produce bile to maximize absorption of lipophilic nutrients in the gut. The physical properties of bile are largely dictated by amphipathic bile salt molecules, which also act as signaling molecules that bind host receptors and modulate physiological processes. Upon excretion of bile salts into the gut, the gut microbiome can create metabolites that have modified signaling capabilities. The category and magnitude of bile salt metabolism can affect the host either positively or negatively. A key modification is bile salt hydrolysis, which is a prerequisite step for all additional microbial modification. Here, we have synthesized five different fluorogenic bile salts that report on hydrolysis activity using a simple, continuous assay. We profile activity in both murine and human fecal samples. Our data demonstrate that most gut microbiomes have the highest capacity for hydrolysis of host-produced bile salts, but some microbially modified bile salts also display significant turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Forecasting influenza activity using machine-learned mobility map

Human mobility is a primary driver of infectious disease spread. However, existing data is limited in availability, coverage, granularity, and timeliness. Data-driven forecasts of disease dynamics are crucial for decision-making by health officials and private citizens alike. In this work, we focus on a machine-learned anonymized mobility map (hereon referred to as AMM) aggregated over hundreds of millions of smartphones and evaluate its utility in forecasting epidemics. We factor AMM into a metapopulation model to retrospectively forecast influenza in the USA and Australia. We show that the AMM model performs on-par with those based on commuter surveys, which are sparsely available and expensive. We also compare it with gravity and radiation based models of mobility, and find that the radiation model’s performance is quite similar to AMM and commuter flows. Additionally, we demonstrate our model’s ability to predict disease spread even across state boundaries. Our work contributes towards developing timely infectious disease forecasting at a global scale using human mobility datasets expanding their applications in the area of infectious disease epidemiology.

60 APPLIED LIFE SCIENCES↗