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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD

Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A global lipid map defines a network essential for Zika virus replication

Zika virus (ZIKV), an emerging mosquito-borne pathogen of global concern, remodels intra-cellular lipid membranes to form replication factories. How ZIKV regulates lipid networks to allow infection, and consequences for disease is poorly understood. Here, we performed comprehensive lipidomics to create a lipid network map during ZIKV infection. We found that ZIKV significantly alters host lipid composition with striking changes seen within sub-classes of sphingolipids. We also demonstrated that ectopic expression of NS4B, one of the non-structural proteins of ZIKV with known roles in ZIKV replication resulted in similar changes on cellular lipidome. Ceramide, a key bioactive molecule with functions in signaling and apoptosis, redistributes to ZIKV replication factories. Increase of ceramide through knockout of sphingomyelin synthase or via sphingomyelinase-catalyzed degradation of sphingomyelin to ceramide sensitizes cells to ZIKV infection. Remarkably, we observed an enrichment of pro-apoptotic ceramide sub-species in infected cells, providing a link between ZIKV biogenesis and apoptosis. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MAL TIR ) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88 TIR ). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88 TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MAL TIR . We demonstrate via mutagenesis that the MyD88 TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88 TIR . Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana . Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo design of miniprotein antagonists of cytokine storm inducers

Cytokine release syndrome (CRS), commonly known as cytokine storm, is an acute systemic inflammatory response that is a significant global health threat. Interleukin-6 (IL-6) and interleukin-1 (IL-1) are key pro-inflammatory cytokines involved in CRS and are hence critical therapeutic targets. Current antagonists, such as tocilizumab and anakinra, target IL-6R/IL-1R but have limitations due to their long half-life and systemic anti-inflammatory effects, making them less suitable for acute or localized treatments. Here we present the de novo design of small protein antagonists that prevent IL-1 and IL-6 from interacting with their receptors to activate signaling. The designed proteins bind to the IL-6R, GP130 (an IL-6 co-receptor), and IL-1R1 receptor subunits with binding affinities in the picomolar to low-nanomolar range. X-ray crystallography studies reveal that the structures of these antagonists closely match their computational design models. In a human cardiac organoid disease model, the IL-1R antagonists demonstrated protective effects against inflammation and cardiac damage induced by IL-1β. These minibinders show promise for administration via subcutaneous injection or intranasal/inhaled routes to mitigate acute cytokine storm effects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

Abstract PROTAC® (proteolysis-targeting chimera) molecules induce proximity between an E3 ligase and protein-of-interest (POI) to target the POI for ubiquitin-mediated degradation. Cooperative E3-PROTAC-POI complexes have potential to achieve neo-substrate selectivity beyond that established by POI binding to the ligand alone. Here, we extend the collection of ubiquitin ligases employable for cooperative ternary complex formation to include the C-degron E3 KLHDC2. Ligands were identified that engage the C-degron binding site in KLHDC2, subjected to structure-based improvement, and linked to JQ1 for BET-family neo-substrate recruitment. Consideration of the exit vector emanating from the ligand engaged in KLHDC2’s U-shaped degron-binding pocket enabled generation of SJ46421, which drives formation of a remarkably cooperative, paralog-selective ternary complex with BRD3 BD2 . Meanwhile, screening pro-drug variants enabled surmounting cell permeability limitations imposed by acidic moieties resembling the KLHDC2-binding C-degron. Selectivity for BRD3 compared to other BET-family members is further manifested in ubiquitylation in vitro, and prodrug version SJ46420-mediated degradation in cells. Selectivity is also achieved for the ubiquitin ligase, overcoming E3 auto-inhibition to engage KLHDC2, but not the related KLHDC1, KLHDC3, or KLHDC10 E3s. In sum, our study establishes neo-substrate-specific targeted protein degradation via KLHDC2, and provides a framework for developing selective PROTAC protein degraders employing C-degron E3 ligases.

Science & Technology - Other Topics↗
DOE OSTI2022

The impact of bilateral injuries on the pathophysiology and functional outcomes of volumetric muscle loss

Volumetric muscle loss (VML)—defined as the irrecoverable loss of skeletal muscle tissue with associated persistent functional deficits—is among the most common and highly debilitating combat-related extremity injuries. This is particularly true in cases of severe polytrauma wherein multiple extremities may be involved as a result of high energy wounding mechanisms. As such, significant investment and effort has been made toward developing a clinically viable intervention capable of restoring the form and function of the affected musculature. While these investigations conducted to date have varied with respect to the species, breed, and sex of the chosen pre-clinical in-vivo model system, the majority of these studies have been performed in unilateral injury models, an aspect which may not fully exemplify the clinical representation of the multiply injured patient. Furthermore, while various components of the basal pathophysiology of VML (e.g., fibrosis and inflammation) have been investigated, relatively little effort has focused on how the pathophysiology and efficacy of pro-regenerative technologies is altered when there are multiple VML injuries. Thus, the purpose of this study was two-fold: (1) to investigate if/how the pathophysiology of unilateral VML injuries differs from bilateral VML injuries and (2) to interrogate the effect of bilateral VML injuries on the efficacy of a well-characterized regenerative therapy, minced muscle autograft (MMG). In contrast to our hypothesis, we show that bilateral VML injuries exhibit a similar systemic inflammatory response and improved muscle functional recovery, compared to unilateral injured animals. Furthermore, MMG treatment was found to only be effective at promoting an increase in functional outcomes in unilateral VML injuries. The findings presented herein add to the growing knowledge base of the pathophysiology of VML, and, importantly, reiterate the importance of comprehensively characterizing preclinical models which are utilized for early-stage screening of putative therapies as they can directly influence the translational research pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination

SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The cardiac molecular setting of metabolic syndrome in pigs reveals disease susceptibility and suggests mechanisms that exacerbate COVID-19 outcomes in patients

Abstract Although metabolic syndrome (MetS) is linked to an elevated risk of cardiovascular disease (CVD), the cardiac-specific risk mechanism is unknown. Obesity, hypertension, and diabetes (all MetS components) are the most common form of CVD and represent risk factors for worse COVID-19 outcomes compared to their non MetS peers. Here, we use obese Yorkshire pigs as a highly relevant animal model of human MetS, where pigs develop the hallmarks of human MetS and reproducibly mimics the myocardial pathophysiology in patients. Myocardium-specific mass spectroscopy-derived metabolomics, proteomics, and transcriptomics enabled the identity and quality of proteins and metabolites to be investigated in the myocardium to greater depth. Myocardium-specific deregulation of pro-inflammatory markers, propensity for arterial thrombosis, and platelet aggregation was revealed by computational analysis of differentially enriched pathways between MetS and control animals. While key components of the complement pathway and the immune response to viruses are under expressed, key N6-methyladenosin RNA methylation enzymes are largely overexpressed in MetS. Blood tests do not capture the entirety of metabolic changes that the myocardium undergoes, making this analysis of greater value than blood component analysis alone. Our findings create data associations to further characterize the MetS myocardium and disease vulnerability, emphasize the need for a multimodal therapeutic approach, and suggests a mechanism for observed worse outcomes in MetS patients with COVID-19 comorbidity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Activity, structure, and diversity of Type II proline-rich antimicrobial peptides from insects

Abstract Apidaecin 1b (Api), the first characterized Type II Proline-rich antimicrobial peptide (PrAMP), is encoded in the honey bee genome. It inhibits bacterial growth by binding in the nascent peptide exit tunnel of the ribosome after the release of the completed protein and trapping the release factors. By genome mining, we have identified 71 PrAMPs encoded in insect genomes as pre-pro-polyproteins. Having chemically synthesized and tested the activity of 26 peptides, we demonstrate that despite significant sequence variation in the N-terminal sequence, the majority of the PrAMPs that retain the conserved C-terminal sequence of Api are able to trap the ribosome at the stop codons and induce stop codon readthrough—all hallmarks of Type II PrAMP mode of action. Some of the characterized PrAMPs exhibit superior antibacterial activity in comparison with Api. The newly solved crystallographic structures of the ribosome complexed with Api and with the more active peptide Fva1 from the stingless bee demonstrate the universal placement of the PrAMPs’ C-terminal pharmacophore in the post-release ribosome despite variations in their N-terminal sequence.

Huang, Weiping (ORCID:0000000273063550)↗
DOE OSTI2020

Tuning electrochemical and transport processes to achieve extreme performance and efficiency in solid oxide cells

Solid oxide cells (SOCs) have important applications as fuel cells and electrolyzers. The application for storage of renewable electricity is also becoming increasingly relevant; however, it is difficult to meet stringent area-specific resistance (ASR) and long-term stability targets needed to achieve required efficiency and cost. Here we show a new SOC that utilizes a very thin Gd-doped ceria (GDC)/yttria-stabilized zirconia (YSZ) bi-layer electrolyte, Ni–YSZ cell support with enhanced porosity, and electrode surface modification using PrO x and GDC nanocatalysts to achieve unprecedented low ASR values < 0.1 Ω cm 2 , fuel cell power density ~3 W cm –2 , and electrolysis current density ~4 A cm –2 at 800 °C. Besides this exceptionally high performance, fuel cell and electrolysis life tests suggest very promising stability in fuel cell and steam electrolysis modes. Furthermore, electrochemical impedance spectroscopy analysis done using a novel impedance subtraction method shows how rate-limiting electrode processes are impacted by the new SOC materials and design.

25 ENERGY STORAGE↗
DOE OSTI2022

Precision surface modification of solid oxide fuel cells via layer-by-layer surface sol–gel deposition

While solid oxide fuel cells (SOFCs) are a promising technology for a clean and sustainable future, their commercialization is hindered by limited durability and performance. Here, we report our findings on the application of a layer-by-layer surface sol–gel (SSG) coating of catalysts to dramatically enhance the electro-catalytic activity and durability of SOFC cathodes. The SSG process is capable of penetrating and preserving complex backbone microstructures of porous electrodes, creating highly conformal coatings of controlled morphology, while tailoring the composition of the surface to improve catalytic properties and durability. For example, the application of an SSG coating of PrO x to a La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3–δ (LSCF) cathode has reduced the polarization resistance from 1.136 to 0.117 Ω cm 2 at 600 °C and the degradation rate from 1.13 × 10 –3 to 2.67 × 10 –4 Ω cm 2 h –1 at 650 °C. In addition, a continuous improvement in electrode performance is demonstrated as the thickness of the coating is increased, corresponding to the linear addition of catalyst. Furthermore, this first application of the SSG technique to SOFC systems opens the door for the controlled surface modification of porous components in electrochemical systems.

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

Atomic layer deposition for surface area determination of solid oxide electrodes

Surface area measurements are important for characterizing porous solids, but commonly used methods such as Brunauer–Emmett–Teller (BET) gas adsorption and computed nanotomography are lacking for certain applications such as the development of solid oxide fuel cell electrodes, which often have absolute surface areas <1 m 2 and contain nanoscale features. Presented is a novel method for the surface area determination of samples with total measurable areas of 1–1000 cm 2 with a standard deviation ± 1 cm 2 , utilizing the atomic layer deposition (ALD) of Al 2 O 3 over microstructurally complex internal porosity. The volume of alumina is then quantified using plasma spectroscopy and converted to an area using the known ALD layer thickness. Under the modest ALD reactor soak times used (8.5 s), the precursor penetration depth is found to be ~50 μm, exceeding the requirement for uniformly coating SOFC functional layers. A model system, (La 0.8 Sr 0.2 ) 0.98 MnO 3–δ /Ce 0.9 Gd 0.1 O 1.95 (LSM/GDC) scaffolds of ~2.7 m 2 g –1 , was measured using the technique and compared against the BET method, and comparable results were obtained but with 1000 times less material needed. The technique is demonstrated for measurements in two example areas of active SOFC research: exsolved (Ni, Fe) nanoparticles on an Sr(Ti, Fe, Ni)O 3–δ electrode and PrO x catalyst nanoparticles infiltrated onto LSM/GDC scaffolds. Finally, the technique may be broadly useful wherever the accurate surface area determination of small absolute quantities of porous ceramic structures on the order of 0.1–50 m 2 g –1 is sought.

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

Cytosine monohydrate under mechanical stress

We report nanoindentation performed with a conospherical tip on the (100) face of cytosine monohydrate (CM) revealed a highly anisotropic response over a range of loads. Post-indent atomic force microscopy images identified an asymmetric deformation response owing to the pro-chiral structure of the surface. Activation of low rugosity slip planes induces movement of π-stacks rather than their displacement along the 1-dimensional hydrogen bonded ribbon direction. Anisotropy arises because slip can only propagate to one side of the indent, as the tip itself imparts a barrier to slip on the preferred plane thereby forcing the activation of secondary slip systems and pileup. The anisotropic deformation is of interest in relation to previous work which proposed a ribbon–rotation model to account for the topotactic conversion between CM and the product of its dehydration. The asymmetry in the nanomechanical properties exhibited by CM provides further support for the rotational model put forth and also serves to underscore the inherent relationship between a hydrate's mechanical properties and its solid state dehydration mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Fast and fault-tolerant model predictive control of MMCs under selective harmonic elimination

Selective harmonic elimination (SHE) is a suitable pulse-width modulation (PWM) tech-nique for some applications of modular multilevel converters (MMC) with lower numberof semiconductor submodules (SM). However, SHE can make it difficult to control circu-lating currents in the MMC. Moreover, the MMC is vulnerable to SM switch failures thatreduce its output power magnitude and quality. This paper proposes a fault-tolerant modelpredictive control strategy for MMCs operating with SHE (FT SHE-MPC). The effects ofswitch failure on phase voltage waveforms are studied first. Then, a method is proposedto design the FT SHE waveform to preserve its harmonic performance. Next, the pro-posed FT SHE-MPC is designed to increase the capacitor voltages during an SM failure tomaintain the fundamental component of the faulty phase voltage and control the circulat-ing currents, maintaining balance among line voltages and the output power of the MMC.Additionally, the proposed method offers as much as 60% faster FT transition time and asmuch as 36% lower capacitor voltage ripple. The advantages of the proposed method areverified through offline and real-time simulation studies on a three-phase nine-level MMCin PSCAD/EMTDC software and RTDS.

42 ENGINEERING↗