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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Engineering Anti-Microbial Peptide Production in Fungi and Bioprocess Development (CRADA 502)

Crop Protection, specifically controlling agricultural diseases and pests, is essential for crop production at every agricultural scale. Biologics hold enormous potential in this equation to decrease use of more toxic pesticides. Currently, the widespread use of biologics in crop protection is severely hampered by the lack of available tools for their mass production. To ensure biologics are regulated under EPA Biopesticide regulations, the following must be true: The biopesticide is a naturally occurring substance or structurally similar and functionally identical to a naturally occurring substance with a history of exposure to humans and the environment demonstrating minimal toxicity. Since this pertains to the marketed product it is also essential that fermentation hosts have a history of exposure and safe use by humans This research focuses on developing a novel platform for the production and delivery of the cghSAMP peptide using the filamentous fungus Aspergillus niger. A. niger is a well-established industrial microorganism, widely recognized for its strong protein secretion capabilities, high-yield production of enzymes, and classification as a generally recognized as safe (GRAS) organism. By genetically modifying A. niger to express the cghSAMP peptide transgene, we aim to leverage the fungus's robust fermentation system to produce a high volume of the antimicrobial agent. This engineered system represents a potential breakthrough in sustainable disease management, offering an environmentally friendly method for localized application or large-scale production of a biopesticide designed to mitigate the effects of citrus greening disease. The main objectives of this project were: 1. Developing a high-yield and cost-efficient bioprocess to produce an AMP in a current ABF host or readily onboarded hosts. 2. Scale up the process in stirred tank reactors and produce at least 100 grams of AMP at 1- 5g/L

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Partitioning of Seven Different Classes of Antibiotics into LPS Monolayers Supports Three Different Permeation Mechanisms through the Outer Bacterial Membrane

The outer membrane (OM) of Gram-negative (G-) bacteria presents a barrier for x classes of antibacterial agents. Lipopolysaccharide (LPS), present in the outer leaflet of the OM, is stabilized by divalent cations and is considered to be the major impediment for antibacterial agent permeation. However, the actual affinities of major antibiotic classes toward LPS have not yet been determined. In the present work, we use Langmuir monolayers formed from E. coli Re and Rd types of LPS to record pressure-area isotherms in the presence of antimicrobial agents. Our observations suggest three general types of interactions. Firstly, some antimicrobials demonstrated no measurable interactions with LPS. This lack of interaction in the case of cefsulodin, a third-generation cephalosporin antibiotic, correlates with its low efficacy against G- bacteria. Ampicillin and ciprofloxacin also show no interactions with LPS, but in contrast to cefsulodin, both exhibit good efficacy against G- bacteria, indicating permeation through common porins. Secondly, we observe substantial intercalation of the more hydrophobic antibiotics novobiocin, rifampicin, azithromycin, and telithromycin into relaxed LPS monolayers. These largely re-partition back to the subphase with monolayer compression. We find that the hydrophobic area, charge, and dipole all show correlations with both the mole fraction of antibiotic retained in the monolayer at the monolayer-bilayer equivalence pressure and the efficacies of these antibiotics against G- bacteria. Thirdly, amine-rich gentamicin and the cationic antimicrobial peptides polymyxin B and colistin show no hydrophobic insertion but are instead strongly driven into the polar LPS layer by electrostatic interactions in a pressure-independent manner. Their intercalation stably increases the area per molecule (by up to 20%), which indicates massive formation of defects in the LPS layer. These defects support a self-promoted permeation mechanism of these antibiotics through the OM, which explains the high efficacy and specificity of these antimicrobials against G- bacteria.

lateral pressure↗
DOE OSTI2022

Acid-Base Equilibrium and Dielectric Environment Regulate Charge in Supramolecular Nanofibers

Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these supramolecular nanofibers because the ionization state of the peptides are not fixed but liable to change due to the acid-base equilibrium that is coupled to the structural organization of the peptide amphiphile molecules. Here, we have developed a theoretical model to describe and predict the amount of charge found on self-assembled peptide amphiphiles as a function of pH and ion concentration. In particular, we computed the amount of charge of peptide amphiphiles nanofibers with the sequence C 16 − V 2 A 2 E 2 . In our theoretical formulation, we consider charge regulation of the carboxylic acid groups, which involves the acid-base chemical equilibrium of the glutamic acid residues and the possibility of ion condensation. The charge regulation is coupled with the local dielectric environment by allowing for a varying dielectric constant that also includes a position-dependent electrostatic solvation energy for the charged species. We find that the charges on the glutamic acid residues of the peptide amphiphile nanofiber are much lower than the same functional group in aqueous solution. There is a strong coupling between the charging via the acid-base equilibrium and the local dielectric environment. Our model predicts a much lower degree of deprotonation for a position-dependent relative dielectric constant compared to a constant dielectric background. Furthermore, the shape and size of the electrostatic potential as well as the counterion distribution are quantitatively and qualitatively different. These results indicate that an accurate model of peptide amphiphile self-assembly must take into account charge regulation of acidic groups through acid–base equilibria and ion condensation, as well as coupling to the local dielectric environment.

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

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Hyaloscypha finlandica Metabolome Repository

This repository provides the curated data tables, manuscript figure and table exports, dependency records, and workflow scripts supporting an integrated comparative genomics and untargeted LC-MS/MS metabolomics analysis of Hyaloscypha finlandica strain PMI 746, a root-associated dark septate endophyte of poplar. The repository includes genome-mining summaries from antiSMASH, FunBGCeX, BGC-Prophet, and BiG-SCAPE; processed metabolomics inputs; metabolite annotation evidence; statistical outputs; and publication-facing figures and tables. Raw LC-MS/MS spectra, full genome/protein downloads, and large generated tool outputs are referenced through public archive/accession records and are not stored in Git.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effects of HLA single chain trimer design on peptide presentation and stability

MHC class I “single-chain trimer” molecules, coupling MHC heavy chain, β 2 -microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection

In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The RIT1 C-terminus associates with lipid bilayers via charge complementarity

RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. For this study, we used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Room temperature slot-die coated perovskite layer modified with sulfonyl-γ-AApeptide for high performance perovskite solar devices

Perovskite solar cells (PSCs) exhibited remarkable progress for small aperture area cells, however, the performance of its counterpart, large aperture area cells, lags due to non-uniform and defective perovskite layers. Here, we fabricate reproducible large area homogeneous perovskite films at room temperature and without controlling humidity (up to 40 % RH) with a slot die coater on a c-TiO 2 layer deposited using a large area chemical bath. A new artificial peptide – sulfonyl-γ-AApeptide (F-GLU-S) was employed to modify the slot-die coated perovskite surface, grain boundaries and electronic defects. The multi-functional F-GLU-S with carbonyl, carboxyl, sulfonyl, benzene, and chloro groups was capable of strongly interacting with the perovskite layer and repairing the uncoordinated Pb 2+ ions and halide vacancies. As a result, both the electron and hole densities of defects were significantly suppressed; consequently, the non-radiative recombination was effectively suppressed for the modified device which can be explicitly seen in the device performance where both V oc and FF of the modified device improved considerably. Therefore, F-GLU-S modified slot-die coated MAPbI 3 – based devices demonstrated outstanding performance of 21.44 % PCE with a V oc of 1.13 V, J sc of 24.64 cm –2 , and FF 76.99 %. Furthermore, F-GLU-S passivation impeded the infiltration of moisture and oxygen due to its hydrophobic nature and defect repair potential. As a result, the modified device retained above 92 % of its original PCE after 720 h in air (room temperature and 40–60 % RH).

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

Elucidating regulatory processes of intense physical activity by multi-omics analysis

Abstract Background Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. Methods To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student’s t -test followed by pathway analysis and comparison between the different omics modalities. Results Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. Conclusion This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-Scale Approach

Soil microbial communities affect the formation of micro-scale mineral-associated organic matter (MAOM) where complex processes, including adhesion, aggregate formation, microbial mineral weathering and soil organic matter stabilization occur in a narrow zone of large biogeochemical gradients. Here we designed a field study to examine carbon stabilization mechanisms by using in-growth mesh bags containing biotite that were placed in a ponderosa pine root zone for 6 months and compared to the surrounding bulk soil. We sought to determine the composition of the microbial community in the mesh bags compared to the surrounding soils, analyze the direct interactions between microbes and biotite, and finally identify the nature of the newly formed MAOM within the mesh-bags. Our results revealed that minerals in the mesh bags were colonized by a microbial community that produced organic matter in situ. The 16S rRNA gene sequencing and ITS2 region characterization showed phylogenetic similarity between the mesh bag and bulk soil archaea/bacteria and fungi microbiomes, with significant differences in alpha- and beta-diversity and species abundances. Organic matter pools in the mesh bags, analyzed by Fourier transform ion cyclotron resonance mass spectrometry, contained protein- (peptides) and lipid-like compounds while the bulk soil OM was comprised of lignin-like and carboxyl-rich alicyclic molecules. These results support that the newly formed biotite associated organic compounds have a microbial signature in the mesh bags. High-resolution electron microscopy documented strongly adhered organic compounds to biotite surfaces, formation of microaggregates, elemental uptake at the microbe (organic matter)-mineral interface, and distortion of biotite layers. Overall, this study shows the direct and indirect involvement of soil microbial communities from the root zone of ponderosa pine in the formation of MAOM, soil organic carbon stabilization, microaggregation, and mineral weathering at micro- and nano-scales.

58 GEOSCIENCES↗
DOE OSTI2024

Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.

Xing, Yanhong↗
DOE OSTI2023

Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube

The effect of the protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was assessed by using molecular dynamics (MD) simulations. Anionic (GLU–), neutral zwitterionic (GLU0), and cationic (GLU+) forms of glutamic acid were selected as three different protonation states for an analysis of energetics and diffusivity for acid transport across a cyclic decapeptide nanotube. Based on the solubility-diffusion model, permeability coefficients for the three protonation states of the acid were calculated and compared with experimental results for CPN-mediated glutamate transport through CPNs. Potential of mean force (PMF) calculations reveal that, due to the cation-selective nature of the lumen of CPNs, GLU–, so-called glutamate, shows significantly high free energy barriers, while GLU+ displays deep energy wells and GLU0 has mild free energy barriers and wells inside the CPN. The considerable energy barriers for GLU– inside CPNs are mainly attributed to unfavorable interactions with DMPC bilayers and CPNs and are reduced by favorable interactions with channel water molecules through attractive electrostatic interactions and hydrogen bonding. Unlike the distinct PMF curves, position-dependent diffusion coefficient profiles exhibit comparable frictional behaviors regardless of the charge status of three protonation states due to similar confined environments imposed by the lumen of the CPN. The calculated permeability coefficients for the three protonation states clearly demonstrate that glutamic acid has a strong protonation state dependence for its transport through CPNs, as determined by the energetics rather than the diffusivity of the protonation state. In addition, the permeability coefficients also imply that GLU– is unlikely to pass through a CPN due to the high energy barriers inside the CPN, which is in disagreement with experimental measurements, where a considerable amount of glutamate permeating through the CPN was detected. To resolve the discrepancy between this work and the experimental observations, several possibilities are proposed, including a large concentration gradient of glutamate between the inside and outside of lipid vesicles and bilayers in the experiments, the glutamate activity difference between our MD simulations and experiments, an overestimation of energy barriers due to the artifacts imposed in MD simulations, and/or finally a transformation of the protonation state from GLU– to GLU0 to reduce the energy barriers. Altogether, our study demonstrates that the protonation state of glutamic acid has a strong effect on the transport of the acid and suggests a possible protonation state change for glutamate permeating through CPNs.

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

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

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

Comparative genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments

Abstract Background Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level. Results A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade (‘polar group’ hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas . Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions. Conclusions The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Black Liquor Valorization by Using Marine Protist Thraustochytrium striatum and the Preliminary Metabolic Mechanism Study

Black liquor that contains various phenolic compounds from lignin solubilization has been the main byproduct of alkaline pretreatment of lignocellulosic biomass in the biorefinery. In this study, black liquor from alkaline pretreatment of corn stover was used as a sole carbon source for the cultivation of a marine protist, Thraustochytrium striatum. It was found that this strain can grow on black liquor and accumulate valuable products (e.g., fatty acids and carotenoids) simultaneously. Under optimal conditions (pH = 7 and NH 4 Cl = 2 g/L), the cell mass concentration reached 5.2 g/L with total aromatics decreased from 8.18 to 3.09 g/L within 7 day incubation. Fed-batch cultivation was adopted to increase the contents of total fatty acids and carotenoids to 13% and 0.24 mg/g dry cell mass, respectively. Although various compounds such as sugars and organic acids were detected in black liquor and consumed during microbial fermentation as carbon sources, lignin-derived compounds were identified as the major substrates for T. striatum fermentation. Of total aromatics consumed, monomers including p-coumaric acid, ferulic acid, vanillin, and syringaldehyde were observed to be consumed and converted while polymeric fragments were also depolymerized and degraded. Under optimal conditions, around 50% of the total aromatics was consumed. The dynamic changes of compounds in black liquor indicated that diverse metabolic processes were involved in black liquor degradation and utilization by T. striatum. A strong adaptation of T. striatum to a wide range of pH (3–9) was also observed during black liquor fermentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗