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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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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses

Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ebolaviruses. Current cocktails contain antibodies that cross-react with the secreted soluble glycoprotein (sGP) that absorbs virus-neutralizing antibodies. By sorting memory B cells from EBOV infection survivors, we isolated two broadly reactive anti-GP monoclonal antibodies, 1C3 and 1C11, that potently neutralize, protect rodents from disease, and lack sGP cross-reactivity. Both antibodies recognize quaternary epitopes in trimeric ebolavirus GP. 1C11 bridges adjacent protomers via the fusion loop. 1C3 has a tripartite epitope in the center of the trimer apex. One 1C3 antigen-binding fragment anchors simultaneously to the three receptor-binding sites in the GP trimer, and separate 1C3 paratope regions interact differently with identical residues on the three protomers. A cocktail of both antibodies completely protected nonhuman primates from EBOV and SUDV infections, indicating their potential clinical value.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch

Cyclic dinucleotides are second messengers that target the adaptor STING and stimulate the innate immune response in mammals. Besides protein receptors, there are bacterial riboswitches that selectively recognize cyclic dinucleotides. We recently discovered a natural riboswitch that targets 3',3'-cGAMP, which is distinguished from the endogenous mammalian signal 2',3'-cGAMP by its backbone connectivity. Here, we report on structures of the aptamer domain of the 3',3'-cGAMP riboswitch from Geobacter in the 3',3'-cGAMP and c-di-GMP bound states. The riboswitch adopts a tuning forklike architecture with a junctional ligand-binding pocket and different orientations of the arms are correlated with the identity of the bound cyclic dinucleotide. Subsequent biochemical experiments revealed that specificity of ligand recognition can be affected by point mutations outside of the binding pocket, which has implications for both the assignment and reengineering of riboswitches in this structural class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quality-Control Mechanism for Telomerase RNA Folding in the Cell

Long non-coding RNAs can often fold into different conformations. Telomerase RNA, an essential component of the telomerase ribonucleoprotein (RNP) enzyme, must fold into a defined structure to fulfill its function with the protein catalytic subunit (TERT) and other accessory factors. However, the mechanism by which the correct folding of telomerase RNA is warranted in a cell is still unknown. Here we show that La-related protein Pof8 specifically recognizes the conserved pseudoknot region of telomerase RNA and instructs the binding of the Lsm2-8 complex to its mature 3' end, thus selectively protecting the correctly folded RNA from exonucleolytic degradation. In the absence of Pof8, TERT assembles with misfolded RNA and produces little telomerase activity. Therefore, Pof8 plays a key role in telomerase RNA folding quality control, ensuring that TERT only assembles with functional telomerase RNA to form active telomerase. Our finding reveals a mechanism for non-coding RNA folding quality control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

CD63-mediated cloaking of VEGF in small extracellular vesicles contributes to anti-VEGF therapy resistance

Despite wide use of anti-vascular endothelial growth factor (VEGF) therapy for many solid 30 cancers, most of them become resistant to this therapy and develop into progressive disease. 31 Therefore, new biomarkers and strategies for blocking adaptive resistance of cancer to anti-VEGF therapy are needed. As described herein, we found that cancer-derived small extracellular vesicles (EVs) package increasing quantities of VEGF and other factors in response to anti-VEGF therapy. Notably, small EV-VEGF (eVEGF) is not recognized by bevacizumab and can be transferred to endothelial cells and trigger intracrine signaling and promote angiogenesis. Also, serum eVEGF was present at higher levels in ovarian cancer mouse models with adaptive resistance to bevacizumab than in models sensitive to it. Ovarian cancer cell-derived eVEGF increased tumor growth despite treatment with bevacizumab. Notably, the eVEGF level was elevated in patient serum after bevacizumab-containing therapy. Proteomic data of small EVs from mouse models suggested that several novel biomarkers are promising for drug response prediction. Collectively, these data demonstrated a new mechanism whereby eVEGF evades recognition by therapeutic antibodies and promotes tumor angiogenesis and progression. These findings have clinical implications for biomarkers and new therapeutic strategies for ovarian cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies

Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display

The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.

SARS-CoV-2↗
DOE OSTI2020

Engineered Cementitious Composites (ECC) with limestone calcined clay cement (LC 3 )

Recent research have recognized that coupled use of calcined clay, limestone and cement clinker in concrete is viable to reduce environmental footprints at manufacture and to enhance material durability. In this study, a novel application of the limestone calcined clay cement (LC 3 ) is demonstrated by substituting the Ordinary Portland Cement (OPC) in Engineered Cementitious Composites (ECC). The composite mechanical properties including σ-δ and σ-ε relationships and residual crack widths were evaluated to 28 days under uniaxial tension. Matrix chemistry was characterized using thermogravimetric analysis and X-ray diffraction, while the pore structure of matrices and composites was analyzed using mercury intrusion porosimetry. The LC 3 -based ECC showed more rapid early strength development but lower 28-day strength (~32 MPa) due to a 20% higher water-to-solid ratio for attaining adequate workability and fiber dispersion. Nevertheless, the tensile strain capacity of LC 3 -based ECC achieved over 6% with an average residual crack width less than 50 μm. Additionally, the composite pore structure exhibited a decreasing volume fraction of large pores and voids (>100 nm) after substituting LC 3 for OPC. Here, the use of LC 3 marginally decreased the embodied material energy and cost, but led to about 32% and 28% reductions in CO 2 emissions compared to traditional OPC-based ECC and concrete, respectively. As a preliminary study, LC 3 -based ECC shows promise as a greener ductile concrete compared with OPC-based ECC.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Multifunctional application of nanoscratch technique to characterize cementitious materials

This study aims to further explore the multifunctional applicability of nanoscratch technique to cementitious materials for comprehensive characterization. Based on the investigation of deformation, applied force, and fracture toughness of hardened cement paste during scratching, the methods of phase identification, fracture toughness of individual phase, and the interfacial transition zone (ITZ) thickness quantification were proposed and discussed. After redefining the vertical loading rate of scratching, the slope of the square scratching depth vs. scratching length is recognized as a reliable parameter to distinguish the individual phases for the first time. A fracture toughness-based method is proposed to quantify the thickness of ITZ between clinker and hydrates. Meanwhile, the applicability of phase identification by the scratch method is discussed for different transverse scratching speeds and the vertical loading rates. The findings will benefit the investigation and mechanism understanding of cementitious materials at the microscale by utilizing nanoscratch technique.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Effects of anionic and nonionic surfactants on the dispersion and stability of nanoSiO2 in aqueous and cement pore solutions

It has been well recognized that the benefits and effectiveness of nanoparticles in cement-based materials could not be maximized if these are not well dispersed. To address this issue, in this study, different anionic (SDS and PCE) and nonionic surfactants (Tweens and Tritons) were used to disperse nanosilica (NS) in aqueous solution and cement pore solution. The results show that the dispersibility of NS in cement pore solution was improved, and the compressive strength of the cement-NS pastes increased linearly with critical micelle concentration (CMC) of nonionic surfactants. Among all surfactants studied, Triton X-405 led the paste to the highest increase in strength (33% at 1-day and 41% at 3-days) since it had the highest CMC. TEM and EDS analysis evidenced that this strength increase might be attributed to the nucleation of outer product CSH gel and its densification with calcite nanocrystals, attributed to Triton X-405 addition.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Specific molecular design of polycarboxylate polymers exhibiting optimal compatibility with clay contaminants in concrete

Highlights: • Allyl ether-based PCEs with short side chain length and low side chain density presented superior clay resistance. • PCEs with medium side chain density exhibited best clay robustness when compared at the absolute dosed quantities. • The proportion of PCE being intercalated into the layered structure of clay was quantified. It is widely recognized that the dispersing ability of polycarboxylate superplasticizers (PCEs) could be hindered due to the presence of clay contaminants in concrete. In this study, a series of allyl ether-based polycarboxylate superplasticizers possessing short polyethylene glycol side chains was successfully synthesized and probed for their clay tolerance. The resulting PCE polymers were characterized via Size Exclusion Chromatography (SEC) to obtain their molecular properties. Thereafter, their dispersing ability was probed in the absence and presence of sodium bentonite. Allyl ether-based polycarboxylate (APEG) polymers possessing short side chains were found to exhibit enhanced clay resistance as compared to that of conventional MPEG PCEs holding long pendant chains. The mode of interaction between APEG PCEs and bentonite was investigated via sorption and XRD measurements. The data revealed that APEG PCEs possessing a lower side chain density intercalate less into the interlayer space of bentonite than those exhibiting higher side chain density.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Water transport properties of virtual fractal porous media: Implications for the unsaturated transport properties of cement-based materials

Cement-based materials are more and more recognized as fractal materials. From a practical point of view, fractality means that the pore size distribution can be described using fractal scaling law (i.e. power functions). Here, the simplest scaling law making use of a single fractal dimension was used to generate simple and virtual fractal porous media (based on bundles of parallel cylindrical pores). The capillary curve and permeability (relative and intrinsic) of the virtual porous media were then estimated through theoretical and numerical approaches. The results show that: (1) although bereft of any physical basis, van Genuchten equation bears some fractal information; (2) although highly flexible, van Genuchten equation fails to perfectly fit the capillary curves and can thus generate error in inverse analysis (for intrinsic permeability evaluation) and (3) there seems to be a relation between the intrinsic permeability and van Genuchten pressure parameter.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled. Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. Furthermore, we seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Amantadine interactions with phase separated lipid membranes

Amantadine, a small amphilphic organic compound that consists of an adamantane backbone and an amino group, was first recognized as an antiviral in 1963 and received approval for prophylaxis against the type A influenza virus in 1976. Since then, it has also been used to treat Parkinson’s disease-related dyskinesia and is being considered as a treatment for corona viruses. Since amantadine usually targets membrane-bound proteins, its interactions with the membrane are also thought to be important. Biological membranes are now widely understood to be laterally heterogeneous and certain proteins are known to preferentially co-localize within specific lipid domains. Does amantadine, therefore, preferentially localize in certain lipid composition domains? To address this question, here, we studied amantadine’s interactions with phase separating membranes composed of cholesterol, DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine), POPC (1-palmitoyl-2-oleoyl-glycero-3-phosphocholine), and DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), as well as single-phase DPhPC (1,2-diphytanoyl-sn-glycero-3-phos-phocholine) membranes. From Langmuir trough and differential scanning calorimetry (DSC) measurements, we determined, respectively, that amantadine preferentially binds to disordered lipids, such as POPC, and lowers the phase transition temperature of POPC/DSPC/cholesterol mixtures, implying that amantadine increases membrane disorder. Further, using droplet interface bilayers (DIBs), we observed that amantadine disrupts DPhPC membranes, consistent with its disordering properties. Finally, we carried out molecular dynamics (MD) simulations on POPC/DSPC/cholesterol membranes with varying amounts of amantadine. Consistent with experiment, MD simulations showed that amantadine prefers to associate with disordered POPC-rich domains, domain boundaries, and lipid glycerol backbones. Since different proteins co-localize with different lipid domains, our results have possible implications as to which classes of proteins may be better targets for amantadine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Breaking the trade-off between selectivity and adsorption capacity for gas separation

It is generally recognized that porous solids (sorbents) with high selectivity and high adsorption capacity offer potential for energy-efficient gas separations. Unfortunately, there is generally a trade-off between capacity and selectivity, which represents a roadblock to the utility of sorbents in key industrial processes. For example, acetylene (C 2 H 2 ), an important fuel and chemical intermediate, is produced with CO 2 as an impurity, and the similar physicochemical properties of C 2 H 2 and CO 2 mean that most sorbents are poorly selective. Hybrid ultramicroporous materials (HUMs) are candidates for gas separations as they exhibit benchmark selectivity for several key gas pairs. Unfortunately, existing HUMs are handicapped by low capacity. Here, we report a new HUM, SIFSIX-21-Ni, that addresses the trade-off between selectivity and capacity that has plagued sorbents, as its high uptake and high selectivity renders it the new benchmark for C 2 H 2 /CO 2 separation performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An encoder–decoder LSTM-based EMPC framework applied to a building HVAC system

Numerous studies have demonstrated the benefit of economic model predictive control (EMPC) applied to building heating, ventilation, and air conditioning (HVAC) systems. However, the construction and training of predictive models for building HVAC systems are widely recognized as a key technological barrier preventing large-scale adoption of EMPC for buildings. In this work, an encoder–decoder long short-term memory-based EMPC framework is developed. The key advantage of the approach is that a model may be automatically generated from a list of inputs and outputs. From the definition of inputs and outputs, the constructed model may be trained and automatically embedded into the EMPC framework for real-time estimation and control. The overall end-to-end EMPC framework from model training to on-line estimation and control are described. To this end, the encoder–decoder model provides a natural framework for state estimation (encoder), which is required to provide an initial condition for the predictive model of EMPC (decoder). Closed-loop simulations using EnergyPlus are performed to demonstrate the approach. The simulated closed-loop system consists of a building zone from a multi-zone building, which is served by an air handling unit-variable air volume HVAC system. For the HVAC example considered, the trained encoder–decoder model can predict the indoor air temperature and HVAC sensible cooling rate of a building zone over a two-day horizon with high accuracy. Overall, we find that considering a time-of-use electric rate structure, the EMPC, which manipulates the zone temperature setpoint, can reduce the HVAC power consumption cost relative to keeping the zone temperature setpoint at its maximum value (i.e., minimum energy approach).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2019

Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies

The fusion peptide (FP) of HIV-1 envelope glycoprotein (Env) is essential for mediating viral entry. Detection of broadly neutralizing antibodies (bnAbs) that interact with the FP has revealed it as a site of vulnerability. We delineate X-ray and cryo-electron microscopy (cryo-EM) structures of bnAb ACS202, from an HIV-infected elite neutralizer, with an FP and with a soluble Env trimer (AMC011 SOSIP.v4.2) derived from the same patient. We show that ACS202 CDRH3 forms a “β strand” interaction with the exposed hydrophobic FP and recognizes a continuous region of gp120, including a conserved N-linked glycan at N88. A cryo-EM structure of another previously identified bnAb VRC34.01 with AMC011 SOSIP.v4.2 shows that it also penetrates through glycans to target the FP. We further demonstrate that the FP can twist and present different conformations for recognition by bnAbs, which enables approach to Env from diverse angles. The variable recognition of FP by bnAbs thus provides insights for vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghum

Screening for drought tolerance is critical to ensure high biomass production of bioenergy sorghum in arid or semi-arid environments. The bottleneck in drought tolerance selection is the challenge of accurately predicting biomass for a large number of genotypes. Although biomass prediction by low-altitude remote sensing has been widely investigated on various crops, the performance of the predictions are not consistent, especially when applied in a breeding context with hundreds of genotypes. In some cases, biomass prediction of a large group of genotypes benefited from multimodal remote sensing data; while in other cases, the benefits were not obvious. In this study, we evaluated the performance of single and multimodal data (thermal, RGB, and multispectral) derived from an unmanned aerial vehicle (UAV) for biomass prediction for drought tolerance assessments within a context of bioenergy sorghum breeding. The biomass of 360 sorghum genotypes grown under well-watered and water-stressed regimes was predicted with a series of UAV-derived canopy features, including canopy structure, spectral reflectance, and thermal radiation features. Biomass predictions using canopy features derived from the multimodal data showed comparable performance with the best results obtained with the single modal data with coefficients of determination (R 2 ) ranging from 0.40 to 0.53 under water-stressed environment and 0.11 to 0.35 under well-watered environment. The significance in biomass prediction was highest with multispectral followed by RGB and lowest with the thermal sensor. Finally, two well-recognized yield-based drought tolerance indices were calculated from ground truth biomass data and UAV predicted biomass, respectively. Results showed that the geometric mean productivity index outperformed the yield stability index in terms of the potential for reliable predictions by the remotely sensed data. Collectively, this study demonstrated a promising strategy for the use of different UAV-based imaging sensors to quantify yield-based drought tolerance.

09 BIOMASS FUELS↗