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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comparative and pangenomic analysis of the genus Streptomyces

Abstract Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Redox active plant phenolic, acetosyringone, for electrogenetic signaling

Abstract Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H 2 O 2 ) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a “pro-signaling molecule” that can be activated by its oxidation—in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O 2 to form H 2 O 2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed “pro-signal” dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rubisco activity and activation state dictate photorespiratory plasticity in Betula papyrifera acclimated to future climate conditions

Plant metabolism faces a challenge of investing enough enzymatic capacity to a pathway without overinvestment. As it takes energy and resources to build, operate, and maintain enzymes, there are benefits and drawbacks to accurately matching capacity to the pathway influx. The relationship between functional capacity and physiological load could be explained through symmorphosis, which would quantitatively match enzymatic capacity to pathway influx. Alternatively, plants could maintain excess enzymatic capacity to manage unpredictable pathway influx. In this study, we use photorespiration as a case study to investigate these two hypotheses in Betula papyrifera. This involves altering photorespiratory influx by manipulating the growth environment, via changes in CO 2 concentration and temperature, to determine how photorespiratory capacity acclimates to environmental treatments. Surprisingly, the results from these measurements indicate that there is no plasticity in photorespiratory capacity in B. papyrifera, and that a fixed capacity is maintained under each growth condition. The fixed capacity is likely due to the existence of reserve capacity in the pathway that manages unpredictable photorespiratory influx in dynamic environments. Additionally, we found that B. papyrifera had a constant net carbon assimilation under each growth condition due to an adjustment of functional rubisco activity driven by changes in activation state. These results provide insight into the acclimation ability and limitations of B. papyrifera to future climate scenarios currently predicted in the next century.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Corn grown on dredged sediments alters rat behavior in the elevated plus maze via the gut mycobiome

The use of marginal lands for growing food has increased worldwide. Many of these lands are supplemented with soil amendments to enhance their productivity, but they may also introduce contaminants depending on their origin. The use of sediments dredged from commercial waterways as a soil amendment has increased in recent years. However, there is significant concern regarding their potential to negatively affect public health by transferring contaminants, like metals, to the food supply. This study examined the behavior, microbiome and physiology of rats fed corn grown on dredged sediments with rats fed commercial feed corn and related those metrics to kernel metal content. Metal content did not differ between kernels grown on dredged sediments and feed corn for most metals except iron which was greater in commercial feed corn. Although there is some variability by animal response, animals fed corn grown on dredged sediments had a gut microbial community that generally promoted anxiety-like behavior while animals fed feed corn had a gut microbial community that promoted a more typical response. These findings suggest the effect of corn grown on dredged sediments on public health is complex and highlights the need for further investigation.

Rua, Megan [Wright State University, Dayton, OH]↗
DOE OSTI2021

Strain-insensitive intrinsically stretchable transistors and circuits

An all-elastomer strain engineering approach, which uses patterned elastomer layers with tunable stiffnesses, can be used to create intrinsically stretchable transistor arrays with a device density of 340 transistors cm -2 and strain insensitivity of less than 5% performance variation when stretched to 100% strain. Intrinsically stretchable electronics can form intimate interfaces with the human body, creating devices that could be used to monitor physiological signals without constraining movement. However, mechanical strain invariably leads to the degradation of the electronic properties of the devices. Here we show that strain-insensitive intrinsically stretchable transistor arrays can be created using an all-elastomer strain engineering approach, in which the patterned elastomer layers with tunable stiffnesses are incorporated into the transistor structure. By varying the cross-linking density of the elastomers, areas of increased local stiffness are introduced, reducing strain on the active regions of the devices. This approach can be readily incorporated into existing fabrication processes, and we use it to create arrays with a device density of 340 transistors cm -2 and a strain insensitivity of less than 5% performance variation when stretched to 100% strain. We also show that it can be used to fabricate strain-insensitive circuit elements, including NOR gates, ring oscillators and high-gain amplifiers for the stable monitoring of electrophysiological signals.

42 ENGINEERING↗
DOE OSTI2021

Albumin in patients with liver disease shows an altered conformation

Abstract Human serum albumin (HSA) constitutes the primary transporter of fatty acids, bilirubin, and other plasma compounds. The binding, transport, and release of its cargos strongly depend on albumin conformation, which is affected by bound ligands induced by physiological and pathological conditions. HSA is both highly oxidized and heavily loaded with fatty acids and bilirubin in chronic liver disease. By employing small-angle X-ray scattering we show that HSA from the plasma of chronic liver disease patients undergoes a distinct opening compared to healthy donors. The extent of HSA opening correlates with clinically relevant variables, such as the model of end-stage liver disease score, bilirubin, and fatty acid levels. Although the mild oxidation of HSA in vitro does not alter overall structure, the alteration of patients’ HSA correlates with its redox state. This study connects clinical data with structural visualization of albumin dynamicity in solution and underlines the functional importance of albumin’s inherent flexibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state

Abstract AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH ( Tm FtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length Tm FtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Influence of sulfide on diazotrophic growth of the methanogen Methanococcus maripaludis and its implications for the origin of nitrogenase

Abstract Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth’s history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants

Abstract Using a fluorescence complementation assay, Delivered Complementation in Planta (DCIP), we demonstrate cell-penetrating peptide-mediated cytosolic delivery of peptides and recombinant proteins in Nicotiana benthamiana. We show that DCIP enables quantitative measurement of protein delivery efficiency and enables functional screening of cell-penetrating peptides for in-planta protein delivery. Finally, we demonstrate that DCIP detects cell-penetrating peptide-mediated delivery of recombinantly expressed proteins such as mCherry and Lifeact into intact leaves. We also demonstrate delivery of a recombinant plant transcription factor, WUSCHEL (AtWUS), into N. benthamiana. RT-qPCR analysis of AtWUS delivery in Arabidopsis seedlings also suggests delivered WUS can recapitulate transcriptional changes induced by overexpression of AtWUS. Taken together, our findings demonstrate that DCIP offers a new and powerful tool for interrogating cytosolic delivery of proteins in plants and highlights future avenues for engineering plant physiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A deep generative model enables automated structure elucidation of novel psychoactive substances

Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, in this study, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51% and a top-10 accuracy of 86%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analysed by mass spectrometry.

Cheminformatics↗
DOE OSTI2020

Distinct response of gross primary productivity in five terrestrial biomes to precipitation variability

Abstract Climate change will impact precipitation variability, potentially accelerating climate-terrestrial carbon feedbacks. However, the response of ecosystems to precipitation variability is difficult to constrain due to myriad physiological and abiotic variables that limit terrestrial productivity. Based on a combination of satellite imagery and a global network of daily precipitation data, we present here a statistical framework to isolate the impact of precipitation variability on the gross primary productivity of five biomes that collectively account for 50% of global land area. The productivity of mesic grasslands and forests decreases by ~28% and ~7% (respectively) in response to more irregular rain within the year, while the sensitivity is halved in response to higher year-to-year variability. Xeric grasslands are similarly impacted by intra-annual rainfall variance, but they show an increase in productivity with higher interannual rainfall variability. Conversely, the productivity of boreal forests increases under higher variability on both timescales. We conclude that projected changes in precipitation variability will have a measurable global impact on the terrestrial carbon sink.

Ritter, François↗
DOE OSTI2022

Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities

Abstract The trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.

Gilbert, Naomi E. (ORCID:0000000256915547)↗
DOE OSTI2023

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Host cell and viral protease targets of human SERPINs identified by in silico docking

Serine protease inhibitors (SERPINs) are involved in various physiological processes and diseases, such as inflammation, cancer metastasis, and neurodegeneration. Their role in viral infections is poorly understood, as their expression patterns during infection and the range of proteases they target have yet to be fully characterized. Here, we show widespread expression of human SERPINs in response to respiratory virus infections, both in bronchioalveolar lavages from COVID-19 patients and in polarized human airway epithelial cultures. Using in silico docking of 10 SERPINs to 48 host proteases, we confirm known targets and predict new interactions. Protease activity assays validated selected interactions, confirming the newly predicted host targets for PAI-1 (SERPINE1) and PAI-2 (SERPINB2). PAI-1 inhibits cathepsin L, essential for SARS-CoV-2 maturation, and suppresses multi-cycle replication of both ancestral SARS-CoV-2 WA-1 and its variant Omicron BA.1. In addition, we identify PAI-2 as an antiviral SERPIN that reduces infectivity of human adenovirus 5 by directly inhibiting the adenoviral protease. Our study leverages in silico docking using full-length 3D protein structures to uncover new SERPIN targets, offering a range of candidate targets for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sample preparation with sucrose cryoprotection dramatically alters Zn distribution in the rodent hippocampus, as revealed by elemental mapping

Transition metal ions (Fe, Mn, Cu, Zn) are essential for healthy brain function, but altered concentration, distribution, or chemical form of the metal ions has been implicated in numerous brain pathologies. Currently, it is not possible to image the cellular or sub-cellular distribution of metal ions in vivo and therefore, studying brain-metal homeostasis largely relies on ex vivo in situ elemental mapping. Sample preparation methods that accurately preserve the in vivo elemental distribution are essential if one wishes to translate the knowledge of elemental distributions measured ex vivo toward increased understanding of chemical and physiological pathways of brain disease. Furthermore, the choice of sample preparation is particularly important for metal ions that exist in a labile or mobile form, for which the in vivo distribution could be easily distorted by inappropriate sample preparation. One of the most widely studied brain structures, the hippocampus, contains a large pool of labile and mobile Zn. Herein, we describe how sucrose cryoprotection, the gold standard method of preparing tissues for immuno-histochemistry or immuno-fluorescence, which is also often used as a sample preparation method for elemental mapping studies, drastically alters hippocampal Zn distribution. Based on the results of this study, in combination with a comparison against the strong body of published literature that has used either rapid plunge freezing of brain tissue, or sucrose cryo-protection, we strongly urge investigators in the future to cease using sucrose cryoprotection as a method of sample preparation for elemental mapping, especially if Zn is an analyte of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Techniques to characterize dynamics in biomaterials microenvironments: XPCS and microrheology of alginate/PEO–PPO–PEO hydrogels

Many recent studies have highlighted the timescale for stress relaxation of biomaterials on the microscale as an important factor in regulating a number of cell-material interactions, including cell spreading, proliferation, and differentiation. Relevant timescales on the order of 0.1–100 s have been suggested by several studies. While such timescales are accessible through conventional mechanical rheology, several biomaterials have heterogeneous structures, and stress relaxation mechanisms of the bulk material may not correspond to that experienced in the cellular microenvironment. Here we employ X-ray photon correlation spectroscopy (XPCS) to explore the temperature-dependent dynamics, relaxation time, and microrheology of multicomponent hydrogels comprising of commercial poly(ethylene oxide)–poly(propylene oxide)–poly(ethylene oxide) (PEO–PPO–PEO) triblock copolymer F127 and alginate. Previous studies on this system have shown thermoreversible behavior in the bulk oscillatory shear rheology. At physiological temperatures, bulk rheology of these samples shows behavior characteristic of a soft solid, with G' > G" and no crossover between G' and G" over the measurable frequency range, indicating a relaxation time >125 s. By contrast, XPCS-based microrheology shows viscoelastic behavior at low frequencies, and XPCS-derived correlation functions show relaxation times ranging from 10–45 s on smaller length scales. Finally, we are able to use XPCS to effectively probe the viscoelasticity and relaxation behavior within the material microenvironments.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Influence of NaCl on shape deformation of polymersomes

Polymersomes frequently appear in the literature as promising candidates for a wide range of applications from targeted drug delivery to nanoreactors. From a cell mimetic point of view, it is important to understand the size and shape changes of the vesicles in the physiological environment since that can influence the drug delivery mechanism. In this work we studied the structural features of polymersomes consisting of poly(ethylene glycol)–poly(dimethylsiloxane)–poly(ethylene glycol) at the nanoscopic length scale in the presence of NaCl, which is a very common molecule in the biotic aqueous environment. Here, we used dynamic light scattering (DLS), cryo-TEM, small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS). We observed transformation of polymersomes from spherical to elongated vesicles at low salt concentration and into multivesicular structures at high salt concentration. Model fitting analysis of SANS data indicated a reduction of vesicle radius up to 47% and from the SAXS data we observed an increase in membrane thickness up to 8% and an increase of the PDMS hydrophobic segment up to 11% indicating stretching of the membrane due to osmotic imbalance. Also, from the increase in the interlamellar repeat distance up to 98% under high salt concentrations, we concluded that the shape and structural changes observed in the polymersomes are a combined result of osmotic pressure change and ion–membrane interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Go with the flow: modeling unique biological flows in engineered in vitro platforms

Interest in recapitulating in vivo phenomena in vitro using organ-on-a-chip technology has grown rapidly and with it, attention to the types of fluid flow experienced in the body has followed suit. These platforms offer distinct advantages over in vivo models with regards to human relevance, cost, and control of inputs (e.g., controlled manipulation of biomechanical cues from fluid perfusion). Given the critical role biophysical forces play in several tissues and organs, it is therefore imperative that engineered in vitro platforms capture the complex, unique flow profiles experienced in the body that are intimately tied with organ function. In this review, we outline the complex and unique flow regimes experienced by three different organ systems: blood vasculature, lymphatic vasculature, and the intestinal system. Here, we highlight current state-of-the-art platforms that strive to replicate physiological flows within engineered tissues while introducing potential limitations in current approaches.

42 ENGINEERING↗