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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 OSTI2025

Feed status and skin injury modulate immunopathology, global gene expression, and survival in channel catfish during virulent Aeromonas hydrophila infection

Introduction VirulentAeromonas hydrophilais a major pathogen in channel catfish (Ictalurus punctatus), that causes motileAeromonassepticemia and significant economic losses. We investigated the effect of feeding status and skin integrity on the host immune response, disease survival, and gastrointestinal pathology following a vAh challenge. Methods Using a bath immersion model, channel catfish were divided into four treatment groups: fin clipped and fed (FCF), fin clipped but not fed (FCN), not fin clipped but fed (NCF), and not fin clipped nor fed (NCN) alongside non-challenged control groups The FCF and NCF groups were fed 2 h prior to the challenge, but the FCN and NCN groups were not. Survival analysis, histopathological assessment, and RNA sequencing were conducted across groups at different time intervals throughout the vAh challenge. Results Survival rates were lowest in the FCF and FCN groups (30% and 23% survival, respectively), suggesting that both feeding and skin damage contributed to disease severity. Histopathological analyses revealed more severe intestinal and gastric lesions in fed groups, characterized by epithelial necrosis, hemorrhage, and edema. Transcriptomic analysis among the groups identified significant differentially expressed genes associated with inflammation, apoptosis, and metabolic stress, with notable upregulation of interleukin 1-beta (il-1β), and complement C3 (c3). Gene ontology enrichment highlighted distinct immune activation patterns between fed and unfed groups, with enhanced pathogen recognition and pro-inflammatory responses in unfed fish. Discussion These findings suggest feeding prior to infection may exacerbate disease pathology, potentially by creating a physiological state conducive to facilitate pathogen proliferation and dampened early immune responses, whereas short-term fasting appears to promote early immune activation. This study provides novel insights into the complex interplay between feed status, physical injury, and immune response to vAh infection.

Immunology↗
DOE OSTI2024

Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers

The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.

carbohydrate-binding protein↗
DOE OSTI2024

A ligand discovery toolbox for the WWE domain family of human E3 ligases

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15 N-NMR-based binding affinity assays and 19 F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso -ADP-ribose ( iso -ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Bridging the gap: linking Torulaspora delbrueckii genotypes to fermentation phenotypes and wine aroma

Abstract Climate change and consumer preferences are driving innovation in winemaking, with a growing interest in non-Saccharomyces species. Among these, Torulaspora delbrueckii (Td) has gained recognition for its ability to reduce volatile acidity and enhance aromatic complexity in wine. However, knowledge regarding its phenotypic and genomic diversity impacting alcoholic fermentation remains limited. Aiming to elucidate the metabolic differences between Td and Saccharomyces cerevisiae (Sc) and the Td intraspecies diversity, we conducted a comprehensive metabolic characterization of 15 Td strains. This analysis delved beyond standard fermentation parameters (kinetics and major metabolites production) to explore non-conventional aromas and establish genotype-phenotype links. Our findings confirmed that most Td strains produce less acetic acid and more succinate and glycerol than Sc. The overall aromatic profiles of Td strains differed from Sc, exhibiting higher levels of monoterpenes and higher alcohols, while producing less acetate esters, fatty acids, their corresponding ethyl esters, and lactones. Moreover, we identified the absence of genes responsible for specific aroma profiles, such as decreased ethyl esters production, as well as the absence of cell wall genes, which might negatively affect Td performance when compared to Sc. This work highlights the significant diversity within Td and underscores potential links between its genotype and phenotype.

Silva-Sousa, Flávia (ORCID:0000000307383190)↗
DOE OSTI2025

Coreii - Scout

COREII Scout employs React, Vite, TypeScript, Tailwind, and Daisy UI for its graphical user interface (GUI), offering both dark and light modes. The code is modular, with components and reusable wrappers to enhance efficiency. The primary goal of COREII Scout is to aid analysts in collecting and analyzing various sources related to cyber attacks, utilizing models to automate the report writing process. It uses Named Entity Recognition (NER), a type of Natural Language Processing (NLP), to extract key entities from each source. Analysts review and classify these entities using the COREII Attack Chain Estimator (ACE), adding their comments. Ultimately, a Large Language Model (LLM) generates a detailed report with user guidance. This setup ensures a streamlined and effective approach to cyber attack analysis and reporting.

Pluth, Adam [Idaho National Laboratory (INL), Idah↗
DOE OSTI2026

Scalability Analysis of Quantum Models for Stress and Emotion Detection

Stress and emotion detection from high-dimensional physiological signals is a challenging task, particularly when aiming for accurate classification across diverse behavioral states. Quantum machine learning (QML) is promising for modeling such high-dimensional data, but scalability is limited by qubit resources and the exponential cost of classical statevector simulation. This work studies the scalability of quantum support vector machines (QSVMs) for binary stress detection and three-class emotion recognition (Negative/Neutral/Positive) under varying qubit counts and angle-encoding strategies. We also present a comparison study with one-feature-per-qubit (1:1) and two-features-per-qubit (2:1) mappings. Experiments are executed on HPC infrastructure using NVIDIA CUDA-Q to evaluate performance, variance, and class-dependent separability at higher-qubit setups. Results show that larger Hilbert spaces can improve peak accuracy but may increase instability. At the same time, dense 2:1 encoding yields more consistent stress detection performance. For emotion recognition, scaling improves discrimination for classes like Negative and Positive more than Neutral. We find that effective QML scaling is task-dependent and benefits more from encoding design than simply increasing qubit count.

Onim, Md. Saif Hassan [University of Tennessee, Kn↗
DOE OSTI2026

Transformative Impacts of Laser-Induced Breakdown Spectroscopy on Environmental and Biological Research at Oak Ridge National Laboratory

This manuscript will present an advancement of transformative research that has been conducted at Oak Ridge National Laboratory (ORNL) over a 25-year period (2000–2025) on a variety of environmental and biological matrices. These investigations derived a fundamental understanding of how elemental detection and analysis of these matrices led to the knowledge and discovery of natural processes in plants and the environment. Each project led to the initiation of a new research area which unearthed awesome and novel breakthroughs. Highlights are listed below: 1. The preliminary research at ORNL centered on the detection of aerosols utilizing Laser-induced Breakdown Spectroscopy (LIBS) technology. The Clean Air Act Amendment (CAAA) of 1990 highlighted the importance of identifying hazardous air pollutants (HAPs) due to their impact on environmental and human health, thereby underscoring the need to detect various toxic elements. Research in aerosol chemistry aimed to identify these harmful elements released by factories during periods of increased emissions in their manufacturing processes. LIBS emerged as the most effective method for real-time, in situ measurements of metal species in both gaseous and aerosol phases. 2. An understanding of the presence of total carbon in soils gives perspective on how to develop carbon sequestration strategies. The recognition that carbon sinks can evolve back to carbon sources to emit back to the atmosphere was an important consideration. Also, the concentration of carbon in soil indicates the health of land areas for growing crops successfully. 3. The direct detection of most of the elements in a wood sample in a single emission spectrum, without sample preparation, encouraged the research to use the LIBS technique for preservative treated wood coupled with use of multivariate statistical methodology. Additionally, it encouraged the researchers to try to differentiate natural woods from different parts of the country, and it was successfully demonstrated that LIBS coupled with MVA analysis could differentiate wood of different species from each other and of similar species grown in different environments based on their elemental spectra. This was a breakthrough since it revealed a systematic approach to connect elemental scarcity and abundance to either drought or typical rainfall conditions for the hardwood trees grown in specific areas. 4. Furthermore, the research progressed to reveal physiological and developmental processes contributing to biomass production such that the variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles, as well as tracking the transfer of toxic elements from soils to living organisms. 5. Recently another breakthrough viz., ionomics initiated the correlation of elements to specific genes, uncovering the function that the element performed in the plant. More recently, this has been extended from plants to fungi as well as fungi growing in symbiotic relations with plants.

09 BIOMASS FUELS↗
DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cybersecurity Workforce Training for SMR Integration into Distribution Grids: A Competency Framework and Containerized Hands-On Lab for the SMR/DER/Microgrid Boundary

Small modular reactors (SMRs) and microreactors are entering the U.S. distribution grid as synchronous generation on feeders designed for loads and inverter-based distributed energy resources (DERs). No existing cybersecurity training program addresses this intersection of nuclear operations, DER management, and operational technology security. As subcontractor to Iowa State University on the CyDERMS Center, Argonne analyzed the relevant standards and training landscape, translated the resulting gaps into a twelve-objective competency framework across distribution-operator and graduate-analyst role tracks, and built a containerized training lab using a ∼400-bus composite grid model behind a realistically simulated Modbus TCP SCADA stack. The analysis isolates the balance-of-plant / energy-management-system (BOP/EMS) boundary as the critical jurisdictional seam where, as of March 2026, neither NRC nor NERC CIP cleanly claims cybersecurity responsibility for distribution-connected SMRs. The framework maps each objective across NIST CSF 2.0, ISA/IEC 62443, NIST NICE Task–Knowledge–Skill statements, and NRC RG 5.71 awareness-and-training controls. The training lab implements operator-recognition assessment scenarios spanning grid-side disturbances and telemetry-layer anomalies.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

A Computational Review of Privacy-Preserving Mechanisms for the Smart Grid

Smart grid technologies have rapidly become one of the largest and most comprehensive sources of data for the modern utility. For the most part, data streams are seen as an essential tool that enable utilities to carry their day-to-day business operations, but they also create the need for efficient and secure data management strategies. In the context of the smart grid, ensuring data privacy is becoming an increasing concern due to a combination of factors that range from shifts in operational paradigms and rapid technology evolution to changes in legislation. Furthermore, researchers have highlighted the risks associated with improperly protected energy records. For example, energy consumption data from homes could be used to infer the behaviors and habits of home occupants through activity recognition or user profiling (Fan, 2017), which may lead to unfair service pricing, targeted advertising, or other personal security violations. Similarly, Electric Vehicles’ (EVs) charging metadata could be used to reveal private information about the owner such as their payment methods, preferred charging stations, and other locational and timing information that could be used to reconstruct the vehicle owner’s behaviors. The privacy of user data, even when used for statistical analysis or machine learning training processes, also needs to be carefully considered, as an individual’s private traits may still be vulnerable if their inclusion/exclusion greatly impacts the result or could be linked to a public dataset through cross-reference. The breach of user privacy also has severe impacts for organizations that store, transmit, or work on the data in the form of diminishing the public’s trust in them while potentially incurring legal consequences (e.g., fines and suspensions under the European Union General Data Protection Regulation, Health Insurance Portability and Accountability Act, etc.). Because of these risks, several privacy-preserving mechanisms are available to help organizations comply with privacy legislations and prevent the unauthorized and malicious use of user data. In light of these concerns, this report focuses on performing a computational review of privacy-preserving mechanisms that have received a significant amount of interest in literature. It specifically focuses on 1) homomorphic encryption, 2) zero-knowledge proofs, 3) differential privacy, and 4) federated learning. It is worth noting that although many of the methods presented in this document rely on cryptographic primitives, their intent is not to provide perfect secrecy, but rather to enable users to maintain privacy, and thus they shall not be compared or equated to other constructs that are aimed to address cybersecurity constructs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Amino acid substrate specificities and tissue expression profiles of the nine CYP79A encoding genes in Sorghum bicolor

Cytochrome P450s of the CYP79 family catalyze two N-hydroxylation reactions, converting a selected number of amino acids into the corresponding oximes. The sorghum genome (Sorghum bicolor) harbours nine CYP79A encoding genes, and here sequence comparisons of the CYP79As along with their substrate recognition sites (SRSs) are provided. The substrate specificity of previously uncharacterized CYP79As was investigated by transient expression in Nicotiana benthamiana and subsequent transformation of the oximes formed into the corresponding stable oxime glucosides catalyzed by endogenous UDPG-glucosyltransferases (UGTs). CYP79A61 uses phenylalanine as a substrate, whereas CYP79A91, CYP79A93, and CYP79A95 use valine and isoleucine as substrates, with CYP79A93 showing the ability also to use phenylalanine. CYP79A94 uses isoleucine as a substrate. Analysis of 249 sorghum transcriptomes from two different sorghum cultivars showed the expression levels and tissue-specific expression of the CYP79As. CYP79A1 is the committed gene in dhurrin formation and was the highest expressed gene in most tissues/organs. CYP79A61 was primarily expressed in fully developed leaf blades and leaf sheaths. CYP79A91 and CYP79A92 were expressed mainly in roots >200 cm below ground, while CYP79A93 and CYP79A94 were most highly expressed in the leaf collar and leaf sheath, respectively. Here, the possible signalling effects of the oximes and their metabolites produced in different sorghum tissues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2025

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme

Abstract We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction–modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs—a multi-helical “knob” and a long antiparallel double-helical “paddle”—are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an ‘open’ to ‘closed’ configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme’s bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.

Shen, Betty W.↗
DOE OSTI2024

Studying CPU and memory utilization of applications on Fujitsu A64FX and Nvidia Grace Superchip

ARM-based manycore CPU architectures are well-positioned to provide the rising memory throughput requirements of modern data intensive scientific applications in High Performance Computing (HPC). The Fujitsu A64FX CPU platform is based on the ARM v8.2A architecture, and is the processor of the flagship Japanese supercomputer - "Fugaku", which was previously ranked as the #1 supercomputer in the world according to the Top500 list. The Nvidia Grace superchip features 144 Neoverse V2 cores based on the ARMv9 architecture with 4x128b SVE2, providing exceptional computational power. The chip supports up to 480GB of memory, making it ideal for AI, machine learning, and scientific computing workloads. In this paper, we conduct a thorough performance exploration of a variety of parallel bandwidth-sensitive benchmarks and applications compiled with the native Fujitsu compiler on a Fugaku A64FX compute node and ARM (LLVM) Compiler on an NVIDIA Grace superchip compute node, engaging all the computational cores per cluster using OpenMP multithreading (assuming the cores can drive the available bandwidth). Our ultimate goals are to study the resource utilization of scientific applications and benchmarks on A64FX and Grace superchip, considering graph application scenarios ( GAP Benchmark suite) and eleven appli- cation proxies from the Rodinia heterogeneous benchmark suite (considering domains such as Data Mining, Bioinformatics, Fluid Dynamics, Pattern Recognition, etc.). Through exhaustive performance monitoring, we quantify the resource utilization of diverse OpenMP-based HPC applications on both the Fujitsu A64FX and the Nvidia Grace Superchip platforms.

benchmarking, Performance Analysis, High performan↗
DOE OSTI2025

Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid–Amino Acid Bond Pair Concept

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Improving the User Interface of the DeepLynx Data Warehouse

DeepLynx is an open-source ontology-based data warehouse created by INL to support the creation and life cycle of digital engineering projects, with a particular emphasis on digital twins [1]. Digital twins are systems that represent physical assets and process in a real-time digital environment [1]. Most well-known commercial data warehouses use Graphical User Interfaces (GUIs) for users to interact with their systems [3]. Limited publications have addressed the design of these interfaces and understanding of their target users. The current users and development team acknowledge the need to improve the current UI, not just for aesthetics but to improve functionality and workflow of DeepLynx. Traditional data warehouse users are developers, data scientists and business analysts [2]. DeepLynx users have a vast range of experience using data warehouses, and diverse roles, including engineers, scientists and management positions. Because there is a broader audience of target users for DeepLynx than a typical data warehouse, it is essential that DeepLynx has a useable and intuitive user interface. To achieve this the team performed human-computer interaction methods, including a Heuristic Evaluation of current UI using Neilsen’s Usability Heuristic, create personas based on current users by designing a user survey, data analysis and develop of personas. Followed by a redesign of the UI following using Neilsen’s Usability Heuristic and Norman’s Principles of Interactive Design in industry standard software Figma. Lastly a Heuristic Evaluation of new UI design, using Neilsen’s Usability Heuristic and User testing of redesign UI and have a group of users complete a Thinking Aloud Test of the new UI. Preliminary results of the Heuristic Evaluation of current UI arise issue with Consistency and Standards, Visibility of System Status, Match System and Real World and Recognition Rather than Recall. These issues were addressed in the proposed redesign by applying Neilsen’s Usability Heuristic and Norman’s Principles of Interactive Design. Next steps include formalized list of lessons learned and design implications for future publications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Pyrrole‐Imine Macrocycle: Self‐Organizing Cross‐Reactive Anion Receptor and Sensor

Self-organizing macrocyclic receptor-sensors for phosphorus oxyanions, phosphates, and phosphonates comprising imine moieties were prepared by condensation of dipyrrolylmethane dicarbaldehyde with diethylene triamine. The incorporation of flexible ethylene moieties endows the macrocycle with unprecedented flexibility and ability to accommodate numerous phosphorus oxyanions from orthophosphate to large anions such as ATP or phosphonate glyphosate. The anion binding was elucidated by NMR titrations, low-temperature NMR, and NOESY NMR. The incorporation of dansyl fluorophore enables sensing of anions using the fluorescence signal, whereas the changes in fluorescence intensity, width of the fluorescence band, and position of the maxima are analyte-specific and useful in recognition and identification of eleven different P-oxyanions in water. The affinity (K assoc ) for Na + salts was H 2 PO 4 − ≈ Methylphosphonate > H 2 P 2 O 7 2− > Phenylphosphonate- > Glyphosate 2− > AMP 2− > ADP 2− > ATP 2− . Interestingly, phosphonates, including methylphosphonate and glyphosate anions, were also found to display a strong affinity (K assoc ∼10 6 M −1 ) while halides, nitrate, carbonates, or hydrogen sulfate did not show a significant affinity. The determined fluorescence spectral parameters were used to classify the 12 analytes (11 anions and water) using Linear Discriminant Analysis (LDA). Quantification was performed using LDA and Support Vector Machine (SVM), and the phosphonate concentrations in unknown samples were determined with an error of 3.5% or lower.

anions↗
DOE OSTI2024

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire

The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.

Microbiology↗